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_GPERFTOOLS = _IMP_multifit.IMP_KERNEL_HAS_GPERFTOOLS
239 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_multifit.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
240 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_multifit.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
241 IMPKERNEL_SHOW_WARNINGS = _IMP_multifit.IMPKERNEL_SHOW_WARNINGS
244 class _DirectorObjects(object):
245 """@internal Simple class to keep references to director objects
246 to prevent premature deletion."""
249 def register(self, obj):
250 """Take a reference to a director object; will only work for
251 refcounted C++ classes"""
252 if hasattr(obj,
'get_ref_count'):
253 self._objects.append(obj)
255 """Only drop our reference and allow cleanup by Python if no other
256 Python references exist (we hold 3 references: one in self._objects,
257 one in x, and one in the argument list for getrefcount) *and* no
258 other C++ references exist (the Python object always holds one)"""
259 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
260 or x.get_ref_count() > 1]
264 def get_object_count(self):
265 """Get number of director objects (useful for testing only)"""
266 return len(self._objects)
267 _director_objects = _DirectorObjects()
269 class _ostream(object):
270 """Proxy of C++ std::ostream class."""
272 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
274 def __init__(self, *args, **kwargs):
275 raise AttributeError(
"No constructor defined")
276 __repr__ = _swig_repr
278 def write(self, osa_buf):
279 """write(_ostream self, char const * osa_buf)"""
280 return _IMP_multifit._ostream_write(self, osa_buf)
282 _ostream_swigregister = _IMP_multifit._ostream_swigregister
283 _ostream_swigregister(_ostream)
285 IMP_COMPILER_HAS_OVERRIDE = _IMP_multifit.IMP_COMPILER_HAS_OVERRIDE
286 IMP_COMPILER_HAS_FINAL = _IMP_multifit.IMP_COMPILER_HAS_FINAL
287 IMP_HAS_NOEXCEPT = _IMP_multifit.IMP_HAS_NOEXCEPT
288 IMP_C_OPEN_BINARY = _IMP_multifit.IMP_C_OPEN_BINARY
290 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CGAL_HAS_BOOST_FILESYSTEM
291 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
292 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CGAL_HAS_BOOST_RANDOM
293 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CGAL_HAS_BOOST_SYSTEM
294 IMPCGAL_SHOW_WARNINGS = _IMP_multifit.IMPCGAL_SHOW_WARNINGS
296 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_multifit.IMP_ALGEBRA_HAS_IMP_CGAL
297 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
298 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
299 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_RANDOM
300 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_SYSTEM
301 IMP_ALGEBRA_HAS_CGAL = _IMP_multifit.IMP_ALGEBRA_HAS_CGAL
302 IMP_ALGEBRA_HAS_ANN = _IMP_multifit.IMP_ALGEBRA_HAS_ANN
303 IMPALGEBRA_SHOW_WARNINGS = _IMP_multifit.IMPALGEBRA_SHOW_WARNINGS
305 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_multifit.IMP_DISPLAY_HAS_IMP_CGAL
306 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
307 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
308 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_RANDOM
309 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_SYSTEM
310 IMP_DISPLAY_HAS_CGAL = _IMP_multifit.IMP_DISPLAY_HAS_CGAL
311 IMPDISPLAY_SHOW_WARNINGS = _IMP_multifit.IMPDISPLAY_SHOW_WARNINGS
313 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
314 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
315 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
316 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
317 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
318 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_CGAL
319 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_HDF5
320 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_multifit.IMPSCOREFUNCTOR_SHOW_WARNINGS
322 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_multifit.IMP_STATISTICS_HAS_IMP_CGAL
323 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
324 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
325 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_RANDOM
326 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_SYSTEM
327 IMP_STATISTICS_HAS_CGAL = _IMP_multifit.IMP_STATISTICS_HAS_CGAL
328 IMPSTATISTICS_SHOW_WARNINGS = _IMP_multifit.IMPSTATISTICS_SHOW_WARNINGS
330 IMP_CORE_HAS_IMP_CGAL = _IMP_multifit.IMP_CORE_HAS_IMP_CGAL
331 IMP_CORE_HAS_IMP_KERNEL = _IMP_multifit.IMP_CORE_HAS_IMP_KERNEL
332 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CORE_HAS_BOOST_FILESYSTEM
333 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
334 IMP_CORE_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CORE_HAS_BOOST_RANDOM
335 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CORE_HAS_BOOST_SYSTEM
336 IMP_CORE_HAS_CGAL = _IMP_multifit.IMP_CORE_HAS_CGAL
337 IMP_CORE_HAS_HDF5 = _IMP_multifit.IMP_CORE_HAS_HDF5
338 IMPCORE_SHOW_WARNINGS = _IMP_multifit.IMPCORE_SHOW_WARNINGS
340 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_multifit.IMP_CONTAINER_HAS_IMP_ALGEBRA
341 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_multifit.IMP_CONTAINER_HAS_IMP_CGAL
342 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_multifit.IMP_CONTAINER_HAS_IMP_DISPLAY
343 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_multifit.IMP_CONTAINER_HAS_IMP_KERNEL
344 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
345 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
346 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
347 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_RANDOM
348 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_SYSTEM
349 IMP_CONTAINER_HAS_CGAL = _IMP_multifit.IMP_CONTAINER_HAS_CGAL
350 IMP_CONTAINER_HAS_HDF5 = _IMP_multifit.IMP_CONTAINER_HAS_HDF5
351 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_multifit.IMP_CONTAINER_HAS_PYTHON_IHM
352 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_multifit.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
353 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_multifit.IMP_CONTAINER_HAS_ROBIN_MAP
354 IMPCONTAINER_SHOW_WARNINGS = _IMP_multifit.IMPCONTAINER_SHOW_WARNINGS
356 IMP_ATOM_HAS_IMP_CGAL = _IMP_multifit.IMP_ATOM_HAS_IMP_CGAL
357 IMP_ATOM_HAS_IMP_KERNEL = _IMP_multifit.IMP_ATOM_HAS_IMP_KERNEL
358 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
359 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
360 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_multifit.IMP_ATOM_HAS_BOOST_RANDOM
361 IMP_ATOM_HAS_BOOST_REGEX = _IMP_multifit.IMP_ATOM_HAS_BOOST_REGEX
362 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_ATOM_HAS_BOOST_SYSTEM
363 IMP_ATOM_HAS_CGAL = _IMP_multifit.IMP_ATOM_HAS_CGAL
364 IMP_ATOM_HAS_HDF5 = _IMP_multifit.IMP_ATOM_HAS_HDF5
365 IMP_ATOM_HAS_PYTHON_IHM = _IMP_multifit.IMP_ATOM_HAS_PYTHON_IHM
366 IMPATOM_SHOW_WARNINGS = _IMP_multifit.IMPATOM_SHOW_WARNINGS
367 IMP_ATOM_TYPE_INDEX = _IMP_multifit.IMP_ATOM_TYPE_INDEX
368 IMP_RESIDUE_TYPE_INDEX = _IMP_multifit.IMP_RESIDUE_TYPE_INDEX
369 IMP_HIERARCHY_TYPE_INDEX = _IMP_multifit.IMP_HIERARCHY_TYPE_INDEX
370 IMP_CHAIN_TYPE_INDEX = _IMP_multifit.IMP_CHAIN_TYPE_INDEX
372 IMP_EM_HAS_IMP_CGAL = _IMP_multifit.IMP_EM_HAS_IMP_CGAL
373 IMP_EM_HAS_IMP_CONTAINER = _IMP_multifit.IMP_EM_HAS_IMP_CONTAINER
374 IMP_EM_HAS_IMP_DISPLAY = _IMP_multifit.IMP_EM_HAS_IMP_DISPLAY
375 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_EM_HAS_IMP_SCORE_FUNCTOR
376 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_EM_HAS_BOOST_FILESYSTEM
377 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
378 IMP_EM_HAS_BOOST_RANDOM = _IMP_multifit.IMP_EM_HAS_BOOST_RANDOM
379 IMP_EM_HAS_BOOST_REGEX = _IMP_multifit.IMP_EM_HAS_BOOST_REGEX
380 IMP_EM_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_EM_HAS_BOOST_SYSTEM
381 IMP_EM_HAS_CGAL = _IMP_multifit.IMP_EM_HAS_CGAL
382 IMP_EM_HAS_HDF5 = _IMP_multifit.IMP_EM_HAS_HDF5
383 IMP_EM_HAS_PYTHON_IHM = _IMP_multifit.IMP_EM_HAS_PYTHON_IHM
384 IMPEM_SHOW_WARNINGS = _IMP_multifit.IMPEM_SHOW_WARNINGS
386 IMP_RMF_HAS_IMP_CGAL = _IMP_multifit.IMP_RMF_HAS_IMP_CGAL
387 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
388 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_RMF_HAS_BOOST_FILESYSTEM
389 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
390 IMP_RMF_HAS_BOOST_RANDOM = _IMP_multifit.IMP_RMF_HAS_BOOST_RANDOM
391 IMP_RMF_HAS_BOOST_REGEX = _IMP_multifit.IMP_RMF_HAS_BOOST_REGEX
392 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_RMF_HAS_BOOST_SYSTEM
393 IMP_RMF_HAS_CGAL = _IMP_multifit.IMP_RMF_HAS_CGAL
394 IMP_RMF_HAS_HDF5 = _IMP_multifit.IMP_RMF_HAS_HDF5
395 IMP_RMF_HAS_PYTHON_IHM = _IMP_multifit.IMP_RMF_HAS_PYTHON_IHM
396 IMPRMF_SHOW_WARNINGS = _IMP_multifit.IMPRMF_SHOW_WARNINGS
399 IMP_DOMINO_HAS_IMP_ATOM = _IMP_multifit.IMP_DOMINO_HAS_IMP_ATOM
400 IMP_DOMINO_HAS_IMP_CGAL = _IMP_multifit.IMP_DOMINO_HAS_IMP_CGAL
401 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_multifit.IMP_DOMINO_HAS_IMP_KERNEL
402 IMP_DOMINO_HAS_IMP_RMF = _IMP_multifit.IMP_DOMINO_HAS_IMP_RMF
403 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
404 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_FILESYSTEM
405 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
406 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_RANDOM
407 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_multifit.IMP_DOMINO_HAS_BOOST_REGEX
408 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_SYSTEM
409 IMP_DOMINO_HAS_CGAL = _IMP_multifit.IMP_DOMINO_HAS_CGAL
410 IMP_DOMINO_HAS_HDF5 = _IMP_multifit.IMP_DOMINO_HAS_HDF5
411 IMP_DOMINO_HAS_RMF = _IMP_multifit.IMP_DOMINO_HAS_RMF
412 IMP_DOMINO_HAS_PYTHON_IHM = _IMP_multifit.IMP_DOMINO_HAS_PYTHON_IHM
413 IMPDOMINO_SHOW_WARNINGS = _IMP_multifit.IMPDOMINO_SHOW_WARNINGS
416 IMP_MULTIFIT_HAS_IMP_CGAL = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_CGAL
417 IMP_MULTIFIT_HAS_IMP_CONTAINER = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_CONTAINER
418 IMP_MULTIFIT_HAS_IMP_DISPLAY = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_DISPLAY
419 IMP_MULTIFIT_HAS_IMP_KERNEL = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_KERNEL
420 IMP_MULTIFIT_HAS_IMP_RMF = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_RMF
421 IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR
422 IMP_MULTIFIT_HAS_BOOST_GRAPH = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_GRAPH
423 IMP_MULTIFIT_HAS_BOOST_RANDOM = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_RANDOM
424 IMP_MULTIFIT_HAS_BOOST_REGEX = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_REGEX
425 IMP_MULTIFIT_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_SYSTEM
426 IMP_MULTIFIT_HAS_CGAL = _IMP_multifit.IMP_MULTIFIT_HAS_CGAL
427 IMP_MULTIFIT_HAS_HDF5 = _IMP_multifit.IMP_MULTIFIT_HAS_HDF5
428 IMP_MULTIFIT_HAS_RMF = _IMP_multifit.IMP_MULTIFIT_HAS_RMF
429 IMP_MULTIFIT_HAS_PYTHON_IHM = _IMP_multifit.IMP_MULTIFIT_HAS_PYTHON_IHM
430 IMPMULTIFIT_SHOW_WARNINGS = _IMP_multifit.IMPMULTIFIT_SHOW_WARNINGS
432 _object_types.append(
"RadiusOfGyrationRestraint")
435 def _object_cast_to_RadiusOfGyrationRestraint(o):
436 """_object_cast_to_RadiusOfGyrationRestraint(Object o) -> RadiusOfGyrationRestraint"""
437 return _IMP_multifit._object_cast_to_RadiusOfGyrationRestraint(o)
439 _object_types.append(
"ComponentHeader")
442 def _object_cast_to_ComponentHeader(o):
443 """_object_cast_to_ComponentHeader(Object o) -> ComponentHeader"""
444 return _IMP_multifit._object_cast_to_ComponentHeader(o)
446 _object_types.append(
"AssemblyHeader")
449 def _object_cast_to_AssemblyHeader(o):
450 """_object_cast_to_AssemblyHeader(Object o) -> AssemblyHeader"""
451 return _IMP_multifit._object_cast_to_AssemblyHeader(o)
453 _object_types.append(
"SettingsData")
456 def _object_cast_to_SettingsData(o):
457 """_object_cast_to_SettingsData(Object o) -> SettingsData"""
458 return _IMP_multifit._object_cast_to_SettingsData(o)
460 _object_types.append(
"WeightedExcludedVolumeRestraint")
463 def _object_cast_to_WeightedExcludedVolumeRestraint(o):
464 """_object_cast_to_WeightedExcludedVolumeRestraint(Object o) -> WeightedExcludedVolumeRestraint"""
465 return _IMP_multifit._object_cast_to_WeightedExcludedVolumeRestraint(o)
467 _object_types.append(
"ComplementarityRestraint")
470 def _object_cast_to_ComplementarityRestraint(o):
471 """_object_cast_to_ComplementarityRestraint(Object o) -> ComplementarityRestraint"""
472 return _IMP_multifit._object_cast_to_ComplementarityRestraint(o)
474 ProteinRecordDataList=list
475 _plural_types.append(
"ProteinRecordDataList")
476 _value_types.append(
"ProteinRecordData")
479 FittingSolutionRecords=list
480 _plural_types.append(
"FittingSolutionRecords")
481 _value_types.append(
"FittingSolutionRecord")
485 _plural_types.append(
"AnchorsDataList")
486 _value_types.append(
"AnchorsData")
489 DominoParamsList=list
490 _plural_types.append(
"DominoParamsList")
491 _value_types.append(
"DominoParams")
494 ComplementarityParamsList=list
495 _plural_types.append(
"ComplementarityParamsList")
496 _value_types.append(
"ComplementarityParams")
500 _plural_types.append(
"XlinkParamsList")
501 _value_types.append(
"XlinkParams")
504 ConnectivityParamsList=list
505 _plural_types.append(
"ConnectivityParamsList")
506 _value_types.append(
"ConnectivityParams")
509 FragmentsParamsList=list
510 _plural_types.append(
"FragmentsParamsList")
511 _value_types.append(
"FragmentsParams")
515 _plural_types.append(
"RogParamsList")
516 _value_types.append(
"RogParams")
520 _plural_types.append(
"EVParamsList")
521 _value_types.append(
"EVParams")
524 FiltersParamsList=list
525 _plural_types.append(
"FiltersParamsList")
526 _value_types.append(
"FiltersParams")
529 AlignmentParamsList=list
530 _plural_types.append(
"AlignmentParamsList")
531 _value_types.append(
"AlignmentParams")
534 FittingParamsList=list
535 _plural_types.append(
"FittingParamsList")
536 _value_types.append(
"FittingParams")
539 ProteinsAnchorsSamplingSpaces=list
540 _plural_types.append(
"ProteinsAnchorsSamplingSpaces")
541 _value_types.append(
"ProteinsAnchorsSamplingSpace")
544 _object_types.append(
"ProteomicsData")
547 def _object_cast_to_ProteomicsData(o):
548 """_object_cast_to_ProteomicsData(Object o) -> ProteomicsData"""
549 return _IMP_multifit._object_cast_to_ProteomicsData(o)
551 _object_types.append(
"FFTFitting")
554 def _object_cast_to_FFTFitting(o):
555 """_object_cast_to_FFTFitting(Object o) -> FFTFitting"""
556 return _IMP_multifit._object_cast_to_FFTFitting(o)
558 _object_types.append(
"FFTFittingOutput")
561 def _object_cast_to_FFTFittingOutput(o):
562 """_object_cast_to_FFTFittingOutput(Object o) -> FFTFittingOutput"""
563 return _IMP_multifit._object_cast_to_FFTFittingOutput(o)
565 _object_types.append(
"ProbabilisticAnchorGraph")
568 def _object_cast_to_ProbabilisticAnchorGraph(o):
569 """_object_cast_to_ProbabilisticAnchorGraph(Object o) -> ProbabilisticAnchorGraph"""
570 return _IMP_multifit._object_cast_to_ProbabilisticAnchorGraph(o)
572 _object_types.append(
"Ensemble")
575 def _object_cast_to_Ensemble(o):
576 """_object_cast_to_Ensemble(Object o) -> Ensemble"""
577 return _IMP_multifit._object_cast_to_Ensemble(o)
579 _object_types.append(
"ProteomicsEMAlignmentAtomic")
582 def _object_cast_to_ProteomicsEMAlignmentAtomic(o):
583 """_object_cast_to_ProteomicsEMAlignmentAtomic(Object o) -> ProteomicsEMAlignmentAtomic"""
584 return _IMP_multifit._object_cast_to_ProteomicsEMAlignmentAtomic(o)
586 _object_types.append(
"RigidLeavesRefiner")
589 def _object_cast_to_RigidLeavesRefiner(o):
590 """_object_cast_to_RigidLeavesRefiner(Object o) -> RigidLeavesRefiner"""
591 return _IMP_multifit._object_cast_to_RigidLeavesRefiner(o)
595 add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key, FloatKey radius_key, FloatKey weight_key)
596 add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key, FloatKey radius_key)
597 add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key)
598 add_surface_index(Hierarchy mhd, IMP::Float apix)
600 return _IMP_multifit.add_surface_index(*args)
604 create_weighted_excluded_volume_restraint(RigidBody rb1, RigidBody rb2, FloatKey shell_key) -> Restraint
605 create_weighted_excluded_volume_restraint(RigidBody rb1, RigidBody rb2) -> Restraint
607 return _IMP_multifit.create_weighted_excluded_volume_restraint(*args)
608 class FittingSolutionRecord(object):
609 """Proxy of C++ IMP::multifit::FittingSolutionRecord class."""
611 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
614 """__init__(IMP::multifit::FittingSolutionRecord self) -> FittingSolutionRecord"""
615 this = _IMP_multifit.new_FittingSolutionRecord()
617 self.this.append(this)
618 except __builtin__.Exception:
622 """get_index(FittingSolutionRecord self) -> unsigned int"""
623 return _IMP_multifit.FittingSolutionRecord_get_index(self)
626 def set_index(self, new_ind):
627 """set_index(FittingSolutionRecord self, unsigned int new_ind)"""
628 return _IMP_multifit.FittingSolutionRecord_set_index(self, new_ind)
631 def get_solution_filename(self):
632 """get_solution_filename(FittingSolutionRecord self) -> std::string"""
633 return _IMP_multifit.FittingSolutionRecord_get_solution_filename(self)
636 def set_solution_filename(self, sol_fn):
637 """set_solution_filename(FittingSolutionRecord self, std::string sol_fn)"""
638 return _IMP_multifit.FittingSolutionRecord_set_solution_filename(self, sol_fn)
641 def get_fit_transformation(self):
642 """get_fit_transformation(FittingSolutionRecord self) -> Transformation3D"""
643 return _IMP_multifit.FittingSolutionRecord_get_fit_transformation(self)
646 def set_fit_transformation(self, t):
647 """set_fit_transformation(FittingSolutionRecord self, Transformation3D t)"""
648 return _IMP_multifit.FittingSolutionRecord_set_fit_transformation(self, t)
651 def get_match_size(self):
652 """get_match_size(FittingSolutionRecord self) -> unsigned int"""
653 return _IMP_multifit.FittingSolutionRecord_get_match_size(self)
656 def set_match_size(self, match_size):
657 """set_match_size(FittingSolutionRecord self, unsigned int match_size)"""
658 return _IMP_multifit.FittingSolutionRecord_set_match_size(self, match_size)
661 def get_match_average_distance(self):
662 """get_match_average_distance(FittingSolutionRecord self) -> IMP::Float"""
663 return _IMP_multifit.FittingSolutionRecord_get_match_average_distance(self)
666 def set_match_average_distance(self, match_avg_dist):
667 """set_match_average_distance(FittingSolutionRecord self, IMP::Float match_avg_dist)"""
668 return _IMP_multifit.FittingSolutionRecord_set_match_average_distance(self, match_avg_dist)
671 def get_fitting_score(self):
672 """get_fitting_score(FittingSolutionRecord self) -> IMP::Float"""
673 return _IMP_multifit.FittingSolutionRecord_get_fitting_score(self)
676 def set_fitting_score(self, fit_score):
677 """set_fitting_score(FittingSolutionRecord self, IMP::Float fit_score)"""
678 return _IMP_multifit.FittingSolutionRecord_set_fitting_score(self, fit_score)
681 def get_rmsd_to_reference(self):
682 """get_rmsd_to_reference(FittingSolutionRecord self) -> IMP::Float"""
683 return _IMP_multifit.FittingSolutionRecord_get_rmsd_to_reference(self)
686 def set_rmsd_to_reference(self, rmsd_to_ref):
687 """set_rmsd_to_reference(FittingSolutionRecord self, IMP::Float rmsd_to_ref)"""
688 return _IMP_multifit.FittingSolutionRecord_set_rmsd_to_reference(self, rmsd_to_ref)
691 def get_dock_transformation(self):
692 """get_dock_transformation(FittingSolutionRecord self) -> Transformation3D"""
693 return _IMP_multifit.FittingSolutionRecord_get_dock_transformation(self)
696 def set_dock_transformation(self, t):
697 """set_dock_transformation(FittingSolutionRecord self, Transformation3D t)"""
698 return _IMP_multifit.FittingSolutionRecord_set_dock_transformation(self, t)
701 def get_envelope_penetration_score(self):
702 """get_envelope_penetration_score(FittingSolutionRecord self) -> IMP::Float"""
703 return _IMP_multifit.FittingSolutionRecord_get_envelope_penetration_score(self)
706 def set_envelope_penetration_score(self, s):
707 """set_envelope_penetration_score(FittingSolutionRecord self, IMP::Float s)"""
708 return _IMP_multifit.FittingSolutionRecord_set_envelope_penetration_score(self, s)
711 def show(self, *args):
713 show(FittingSolutionRecord self, _ostream out)
714 show(FittingSolutionRecord self)
716 return _IMP_multifit.FittingSolutionRecord_show(self, *args)
719 def get_record_header():
720 """get_record_header() -> std::string"""
721 return _IMP_multifit.FittingSolutionRecord_get_record_header()
723 get_record_header = staticmethod(get_record_header)
726 """__str__(FittingSolutionRecord self) -> std::string"""
727 return _IMP_multifit.FittingSolutionRecord___str__(self)
731 """__repr__(FittingSolutionRecord self) -> std::string"""
732 return _IMP_multifit.FittingSolutionRecord___repr__(self)
734 __swig_destroy__ = _IMP_multifit.delete_FittingSolutionRecord
735 __del__ =
lambda self:
None
736 FittingSolutionRecord_swigregister = _IMP_multifit.FittingSolutionRecord_swigregister
737 FittingSolutionRecord_swigregister(FittingSolutionRecord)
739 def FittingSolutionRecord_get_record_header():
740 """FittingSolutionRecord_get_record_header() -> std::string"""
741 return _IMP_multifit.FittingSolutionRecord_get_record_header()
746 pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold, FloatKey wei_key, PrincipalComponentAnalysis3D dens_pca_input) -> FittingSolutions
747 pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold, FloatKey wei_key) -> FittingSolutions
748 pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold) -> FittingSolutions
749 pca_based_rigid_fitting(IMP::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold, FloatKey wei_key, PrincipalComponentAnalysis3D dens_pca_input) -> FittingSolutions
750 pca_based_rigid_fitting(IMP::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold, FloatKey wei_key) -> FittingSolutions
751 pca_based_rigid_fitting(IMP::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold) -> FittingSolutions
753 return _IMP_multifit.pca_based_rigid_fitting(*args)
755 def write_markers(pca, out):
756 """write_markers(PrincipalComponentAnalysis3D pca, _ostream out)"""
757 return _IMP_multifit.write_markers(pca, out)
759 """Proxy of C++ IMP::multifit::ComponentHeader class."""
761 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
764 """__init__(IMP::multifit::ComponentHeader self) -> ComponentHeader"""
765 this = _IMP_multifit.new_ComponentHeader()
767 self.this.append(this)
768 except __builtin__.Exception:
771 def set_name(self, name):
772 """set_name(ComponentHeader self, std::string const & name)"""
773 return _IMP_multifit.ComponentHeader_set_name(self, name)
777 """get_name(ComponentHeader self) -> std::string"""
778 return _IMP_multifit.ComponentHeader_get_name(self)
781 def get_filename(self):
782 """get_filename(ComponentHeader self) -> std::string"""
783 return _IMP_multifit.ComponentHeader_get_filename(self)
786 def set_filename(self, filename):
787 """set_filename(ComponentHeader self, std::string const & filename)"""
788 return _IMP_multifit.ComponentHeader_set_filename(self, filename)
791 def get_surface_fn(self):
792 """get_surface_fn(ComponentHeader self) -> std::string"""
793 return _IMP_multifit.ComponentHeader_get_surface_fn(self)
796 def set_surface_fn(self, fn):
797 """set_surface_fn(ComponentHeader self, std::string const & fn)"""
798 return _IMP_multifit.ComponentHeader_set_surface_fn(self, fn)
801 def set_txt_ap_fn(self, pdb_ap_fn):
802 """set_txt_ap_fn(ComponentHeader self, std::string const & pdb_ap_fn)"""
803 return _IMP_multifit.ComponentHeader_set_txt_ap_fn(self, pdb_ap_fn)
806 def get_txt_ap_fn(self):
807 """get_txt_ap_fn(ComponentHeader self) -> std::string"""
808 return _IMP_multifit.ComponentHeader_get_txt_ap_fn(self)
811 def set_txt_fine_ap_fn(self, pdb_ap_fn):
812 """set_txt_fine_ap_fn(ComponentHeader self, std::string const & pdb_ap_fn)"""
813 return _IMP_multifit.ComponentHeader_set_txt_fine_ap_fn(self, pdb_ap_fn)
816 def get_txt_fine_ap_fn(self):
817 """get_txt_fine_ap_fn(ComponentHeader self) -> std::string"""
818 return _IMP_multifit.ComponentHeader_get_txt_fine_ap_fn(self)
821 def set_num_ap(self, num_ap):
822 """set_num_ap(ComponentHeader self, int num_ap)"""
823 return _IMP_multifit.ComponentHeader_set_num_ap(self, num_ap)
826 def get_num_ap(self):
827 """get_num_ap(ComponentHeader self) -> int"""
828 return _IMP_multifit.ComponentHeader_get_num_ap(self)
831 def set_num_fine_ap(self, num_ap):
832 """set_num_fine_ap(ComponentHeader self, int num_ap)"""
833 return _IMP_multifit.ComponentHeader_set_num_fine_ap(self, num_ap)
836 def get_num_fine_ap(self):
837 """get_num_fine_ap(ComponentHeader self) -> int"""
838 return _IMP_multifit.ComponentHeader_get_num_fine_ap(self)
841 def set_transformations_fn(self, transformations_fn):
842 """set_transformations_fn(ComponentHeader self, std::string transformations_fn)"""
843 return _IMP_multifit.ComponentHeader_set_transformations_fn(self, transformations_fn)
846 def get_transformations_fn(self):
847 """get_transformations_fn(ComponentHeader self) -> std::string"""
848 return _IMP_multifit.ComponentHeader_get_transformations_fn(self)
851 def set_reference_fn(self, ref_fn):
852 """set_reference_fn(ComponentHeader self, std::string const & ref_fn)"""
853 return _IMP_multifit.ComponentHeader_set_reference_fn(self, ref_fn)
856 def get_reference_fn(self):
857 """get_reference_fn(ComponentHeader self) -> std::string"""
858 return _IMP_multifit.ComponentHeader_get_reference_fn(self)
861 def get_version_info(self):
862 """get_version_info(ComponentHeader self) -> VersionInfo"""
863 return _IMP_multifit.ComponentHeader_get_version_info(self)
867 """__str__(ComponentHeader self) -> std::string"""
868 return _IMP_multifit.ComponentHeader___str__(self)
872 """__repr__(ComponentHeader self) -> std::string"""
873 return _IMP_multifit.ComponentHeader___repr__(self)
878 return _object_cast_to_ComponentHeader(o)
880 ComponentHeader_swigregister = _IMP_multifit.ComponentHeader_swigregister
881 ComponentHeader_swigregister(ComponentHeader)
884 """Proxy of C++ IMP::multifit::AssemblyHeader class."""
886 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
889 """__init__(IMP::multifit::AssemblyHeader self) -> AssemblyHeader"""
890 this = _IMP_multifit.new_AssemblyHeader()
892 self.this.append(this)
893 except __builtin__.Exception:
896 def set_dens_fn(self, dens_fn):
897 """set_dens_fn(AssemblyHeader self, std::string const & dens_fn)"""
898 return _IMP_multifit.AssemblyHeader_set_dens_fn(self, dens_fn)
901 def get_dens_fn(self):
902 """get_dens_fn(AssemblyHeader self) -> std::string"""
903 return _IMP_multifit.AssemblyHeader_get_dens_fn(self)
906 def set_resolution(self, res):
907 """set_resolution(AssemblyHeader self, float res)"""
908 return _IMP_multifit.AssemblyHeader_set_resolution(self, res)
912 """get_resolution(AssemblyHeader self) -> float"""
913 return _IMP_multifit.AssemblyHeader_get_resolution(self)
916 def get_spacing(self):
917 """get_spacing(AssemblyHeader self) -> float"""
918 return _IMP_multifit.AssemblyHeader_get_spacing(self)
921 def set_spacing(self, spacing):
922 """set_spacing(AssemblyHeader self, float spacing)"""
923 return _IMP_multifit.AssemblyHeader_set_spacing(self, spacing)
926 def set_threshold(self, t):
927 """set_threshold(AssemblyHeader self, float t)"""
928 return _IMP_multifit.AssemblyHeader_set_threshold(self, t)
931 def get_threshold(self):
932 """get_threshold(AssemblyHeader self) -> float"""
933 return _IMP_multifit.AssemblyHeader_get_threshold(self)
936 def get_origin(self):
937 """get_origin(AssemblyHeader self) -> Vector3D"""
938 return _IMP_multifit.AssemblyHeader_get_origin(self)
941 def set_origin(self, origin):
942 """set_origin(AssemblyHeader self, Vector3D origin)"""
943 return _IMP_multifit.AssemblyHeader_set_origin(self, origin)
946 def get_coarse_ap_fn(self):
947 """get_coarse_ap_fn(AssemblyHeader self) -> std::string"""
948 return _IMP_multifit.AssemblyHeader_get_coarse_ap_fn(self)
951 def set_coarse_ap_fn(self, new_fn):
952 """set_coarse_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
953 return _IMP_multifit.AssemblyHeader_set_coarse_ap_fn(self, new_fn)
956 def get_coarse_over_sampled_ap_fn(self):
957 """get_coarse_over_sampled_ap_fn(AssemblyHeader self) -> std::string"""
958 return _IMP_multifit.AssemblyHeader_get_coarse_over_sampled_ap_fn(self)
961 def set_coarse_over_sampled_ap_fn(self, new_fn):
962 """set_coarse_over_sampled_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
963 return _IMP_multifit.AssemblyHeader_set_coarse_over_sampled_ap_fn(self, new_fn)
966 def get_fine_ap_fn(self):
967 """get_fine_ap_fn(AssemblyHeader self) -> std::string"""
968 return _IMP_multifit.AssemblyHeader_get_fine_ap_fn(self)
971 def set_fine_ap_fn(self, new_fn):
972 """set_fine_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
973 return _IMP_multifit.AssemblyHeader_set_fine_ap_fn(self, new_fn)
976 def get_fine_over_sampled_ap_fn(self):
977 """get_fine_over_sampled_ap_fn(AssemblyHeader self) -> std::string"""
978 return _IMP_multifit.AssemblyHeader_get_fine_over_sampled_ap_fn(self)
981 def set_fine_over_sampled_ap_fn(self, new_fn):
982 """set_fine_over_sampled_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
983 return _IMP_multifit.AssemblyHeader_set_fine_over_sampled_ap_fn(self, new_fn)
986 def get_version_info(self):
987 """get_version_info(AssemblyHeader self) -> VersionInfo"""
988 return _IMP_multifit.AssemblyHeader_get_version_info(self)
992 """__str__(AssemblyHeader self) -> std::string"""
993 return _IMP_multifit.AssemblyHeader___str__(self)
997 """__repr__(AssemblyHeader self) -> std::string"""
998 return _IMP_multifit.AssemblyHeader___repr__(self)
1003 return _object_cast_to_AssemblyHeader(o)
1005 AssemblyHeader_swigregister = _IMP_multifit.AssemblyHeader_swigregister
1006 AssemblyHeader_swigregister(AssemblyHeader)
1009 """Proxy of C++ IMP::multifit::SettingsData class."""
1011 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1014 """__init__(IMP::multifit::SettingsData self) -> SettingsData"""
1015 this = _IMP_multifit.new_SettingsData()
1017 self.this.append(this)
1018 except __builtin__.Exception:
1021 def show_component_header_line(*args):
1023 show_component_header_line(_ostream out)
1024 show_component_header_line()
1026 return _IMP_multifit.SettingsData_show_component_header_line(*args)
1028 show_component_header_line = staticmethod(show_component_header_line)
1030 def get_component_header_line():
1031 """get_component_header_line() -> std::string"""
1032 return _IMP_multifit.SettingsData_get_component_header_line()
1034 get_component_header_line = staticmethod(get_component_header_line)
1036 def show_density_header_line(*args):
1038 show_density_header_line(_ostream out)
1039 show_density_header_line()
1041 return _IMP_multifit.SettingsData_show_density_header_line(*args)
1043 show_density_header_line = staticmethod(show_density_header_line)
1045 def get_density_header_line():
1046 """get_density_header_line() -> std::string"""
1047 return _IMP_multifit.SettingsData_get_density_header_line()
1049 get_density_header_line = staticmethod(get_density_header_line)
1051 def set_assembly_filename(self, fn):
1052 """set_assembly_filename(SettingsData self, std::string const & fn)"""
1053 return _IMP_multifit.SettingsData_set_assembly_filename(self, fn)
1056 def get_assembly_filename(self):
1057 """get_assembly_filename(SettingsData self) -> char const *"""
1058 return _IMP_multifit.SettingsData_get_assembly_filename(self)
1061 def set_assembly_header(self, h):
1062 """set_assembly_header(SettingsData self, AssemblyHeader h)"""
1063 return _IMP_multifit.SettingsData_set_assembly_header(self, h)
1066 def get_assembly_header(self):
1067 """get_assembly_header(SettingsData self) -> AssemblyHeader"""
1068 return _IMP_multifit.SettingsData_get_assembly_header(self)
1071 def set_data_path(self, fn):
1072 """set_data_path(SettingsData self, std::string const & fn)"""
1073 return _IMP_multifit.SettingsData_set_data_path(self, fn)
1077 """get_data_path(SettingsData self) -> std::string"""
1078 return _IMP_multifit.SettingsData_get_data_path(self)
1081 def get_version_info(self):
1082 """get_version_info(SettingsData self) -> VersionInfo"""
1083 return _IMP_multifit.SettingsData_get_version_info(self)
1086 def remove_component_header(self, d):
1087 """remove_component_header(SettingsData self, ComponentHeader d)"""
1088 return _IMP_multifit.SettingsData_remove_component_header(self, d)
1091 def remove_component_headers(self, d):
1092 """remove_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & d)"""
1093 return _IMP_multifit.SettingsData_remove_component_headers(self, d)
1096 def set_component_headers(self, ps):
1097 """set_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & ps)"""
1098 return _IMP_multifit.SettingsData_set_component_headers(self, ps)
1101 def set_component_headers_order(self, objs):
1102 """set_component_headers_order(SettingsData self, IMP::multifit::ComponentHeaders const & objs)"""
1103 return _IMP_multifit.SettingsData_set_component_headers_order(self, objs)
1106 def add_component_header(self, obj):
1107 """add_component_header(SettingsData self, ComponentHeader obj) -> unsigned int"""
1108 return _IMP_multifit.SettingsData_add_component_header(self, obj)
1111 def add_component_headers(self, objs):
1112 """add_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & objs)"""
1113 return _IMP_multifit.SettingsData_add_component_headers(self, objs)
1116 def clear_component_headers(self):
1117 """clear_component_headers(SettingsData self)"""
1118 return _IMP_multifit.SettingsData_clear_component_headers(self)
1121 def get_number_of_component_headers(self):
1122 """get_number_of_component_headers(SettingsData self) -> unsigned int"""
1123 return _IMP_multifit.SettingsData_get_number_of_component_headers(self)
1126 def get_has_component_headers(self):
1127 """get_has_component_headers(SettingsData self) -> bool"""
1128 return _IMP_multifit.SettingsData_get_has_component_headers(self)
1131 def get_component_header(self, i):
1132 """get_component_header(SettingsData self, unsigned int i) -> ComponentHeader"""
1133 return _IMP_multifit.SettingsData_get_component_header(self, i)
1136 def get_component_headers(self):
1137 """get_component_headers(SettingsData self) -> IMP::multifit::ComponentHeaders"""
1138 return _IMP_multifit.SettingsData_get_component_headers(self)
1141 def reserve_component_headers(self, sz):
1142 """reserve_component_headers(SettingsData self, unsigned int sz)"""
1143 return _IMP_multifit.SettingsData_reserve_component_headers(self, sz)
1147 """__str__(SettingsData self) -> std::string"""
1148 return _IMP_multifit.SettingsData___str__(self)
1152 """__repr__(SettingsData self) -> std::string"""
1153 return _IMP_multifit.SettingsData___repr__(self)
1158 return _object_cast_to_SettingsData(o)
1160 SettingsData_swigregister = _IMP_multifit.SettingsData_swigregister
1161 SettingsData_swigregister(SettingsData)
1163 def SettingsData_show_component_header_line(*args):
1165 show_component_header_line(_ostream out)
1166 SettingsData_show_component_header_line()
1168 return _IMP_multifit.SettingsData_show_component_header_line(*args)
1170 def SettingsData_get_component_header_line():
1171 """SettingsData_get_component_header_line() -> std::string"""
1172 return _IMP_multifit.SettingsData_get_component_header_line()
1174 def SettingsData_show_density_header_line(*args):
1176 show_density_header_line(_ostream out)
1177 SettingsData_show_density_header_line()
1179 return _IMP_multifit.SettingsData_show_density_header_line(*args)
1181 def SettingsData_get_density_header_line():
1182 """SettingsData_get_density_header_line() -> std::string"""
1183 return _IMP_multifit.SettingsData_get_density_header_line()
1186 def read_settings(filename):
1187 """read_settings(char const * filename) -> SettingsData"""
1188 return _IMP_multifit.read_settings(filename)
1190 def write_settings(filename, sd):
1191 """write_settings(char const * filename, SettingsData sd)"""
1192 return _IMP_multifit.write_settings(filename, sd)
1194 """Proxy of C++ IMP::multifit::WeightedExcludedVolumeRestraint class."""
1196 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1200 __init__(IMP::multifit::WeightedExcludedVolumeRestraint self, IMP::core::RigidBodies rbs, Refiner refiner, FloatKey weight_key) -> WeightedExcludedVolumeRestraint
1201 __init__(IMP::multifit::WeightedExcludedVolumeRestraint self, IMP::core::RigidBodies rbs, Refiner refiner) -> WeightedExcludedVolumeRestraint
1203 this = _IMP_multifit.new_WeightedExcludedVolumeRestraint(*args)
1205 self.this.append(this)
1206 except __builtin__.Exception:
1209 def do_get_inputs(self):
1210 """do_get_inputs(WeightedExcludedVolumeRestraint self) -> IMP::ModelObjectsTemp"""
1211 return _IMP_multifit.WeightedExcludedVolumeRestraint_do_get_inputs(self)
1214 def get_version_info(self):
1215 """get_version_info(WeightedExcludedVolumeRestraint self) -> VersionInfo"""
1216 return _IMP_multifit.WeightedExcludedVolumeRestraint_get_version_info(self)
1220 """__str__(WeightedExcludedVolumeRestraint self) -> std::string"""
1221 return _IMP_multifit.WeightedExcludedVolumeRestraint___str__(self)
1225 """__repr__(WeightedExcludedVolumeRestraint self) -> std::string"""
1226 return _IMP_multifit.WeightedExcludedVolumeRestraint___repr__(self)
1231 return _object_cast_to_WeightedExcludedVolumeRestraint(o)
1233 WeightedExcludedVolumeRestraint_swigregister = _IMP_multifit.WeightedExcludedVolumeRestraint_swigregister
1234 WeightedExcludedVolumeRestraint_swigregister(WeightedExcludedVolumeRestraint)
1237 """Proxy of C++ IMP::multifit::FFTFittingOutput class."""
1239 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1242 """__init__(IMP::multifit::FFTFittingOutput self) -> FFTFittingOutput"""
1243 this = _IMP_multifit.new_FFTFittingOutput()
1245 self.this.append(this)
1246 except __builtin__.Exception:
1249 def get_version_info(self):
1250 """get_version_info(FFTFittingOutput self) -> VersionInfo"""
1251 return _IMP_multifit.FFTFittingOutput_get_version_info(self)
1253 best_fits_ = _swig_property(_IMP_multifit.FFTFittingOutput_best_fits__get, _IMP_multifit.FFTFittingOutput_best_fits__set)
1254 best_trans_per_rot_ = _swig_property(_IMP_multifit.FFTFittingOutput_best_trans_per_rot__get, _IMP_multifit.FFTFittingOutput_best_trans_per_rot__set)
1257 """__str__(FFTFittingOutput self) -> std::string"""
1258 return _IMP_multifit.FFTFittingOutput___str__(self)
1262 """__repr__(FFTFittingOutput self) -> std::string"""
1263 return _IMP_multifit.FFTFittingOutput___repr__(self)
1268 return _object_cast_to_FFTFittingOutput(o)
1270 FFTFittingOutput_swigregister = _IMP_multifit.FFTFittingOutput_swigregister
1271 FFTFittingOutput_swigregister(FFTFittingOutput)
1274 """Proxy of C++ IMP::multifit::FFTFitting class."""
1276 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1278 def get_version_info(self):
1279 """get_version_info(FFTFitting self) -> VersionInfo"""
1280 return _IMP_multifit.FFTFitting_get_version_info(self)
1284 """__init__(IMP::multifit::FFTFitting self) -> FFTFitting"""
1285 this = _IMP_multifit.new_FFTFitting()
1287 self.this.append(this)
1288 except __builtin__.Exception:
1291 def do_global_fitting(self, *args):
1293 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
1294 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
1295 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
1296 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
1298 return _IMP_multifit.FFTFitting_do_global_fitting(self, *args)
1301 def do_local_fitting(self, *args):
1303 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
1304 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
1306 return _IMP_multifit.FFTFitting_do_local_fitting(self, *args)
1310 """__str__(FFTFitting self) -> std::string"""
1311 return _IMP_multifit.FFTFitting___str__(self)
1315 """__repr__(FFTFitting self) -> std::string"""
1316 return _IMP_multifit.FFTFitting___repr__(self)
1321 return _object_cast_to_FFTFitting(o)
1323 FFTFitting_swigregister = _IMP_multifit.FFTFitting_swigregister
1324 FFTFitting_swigregister(FFTFitting)
1328 """fft_based_rigid_fitting(Hierarchy mol2fit, DensityMap dmap, double density_threshold, double angle_sampling_interval_rad) -> IMP::multifit::FittingSolutionRecords"""
1329 return _IMP_multifit.fft_based_rigid_fitting(mol2fit, dmap, density_threshold, angle_sampling_interval_rad)
1332 """remove_background(DensityMap dmap, float threshold, float edge_threshold) -> DensityMap"""
1333 return _IMP_multifit.remove_background(dmap, threshold, edge_threshold)
1336 """get_connected_components(DensityMap dmap, float threshold, float edge_threshold) -> IMP::IntsList"""
1337 return _IMP_multifit.get_connected_components(dmap, threshold, edge_threshold)
1339 def get_segmentation(dmap, apix, density_threshold, num_means, pdb_filename, cmm_filename, seg_filename, txt_filename):
1340 """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)"""
1341 return _IMP_multifit.get_segmentation(dmap, apix, density_threshold, num_means, pdb_filename, cmm_filename, seg_filename, txt_filename)
1343 """Proxy of C++ IMP::multifit::ComplementarityRestraint class."""
1345 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1349 __init__(IMP::multifit::ComplementarityRestraint self, IMP::ParticlesTemp const & a, IMP::ParticlesTemp const & b, std::string name) -> ComplementarityRestraint
1350 __init__(IMP::multifit::ComplementarityRestraint self, IMP::ParticlesTemp const & a, IMP::ParticlesTemp const & b) -> ComplementarityRestraint
1352 this = _IMP_multifit.new_ComplementarityRestraint(*args)
1354 self.this.append(this)
1355 except __builtin__.Exception:
1358 def set_maximum_penetration_score(self, s):
1359 """set_maximum_penetration_score(ComplementarityRestraint self, double s)"""
1360 return _IMP_multifit.ComplementarityRestraint_set_maximum_penetration_score(self, s)
1363 def set_maximum_penetration(self, d):
1364 """set_maximum_penetration(ComplementarityRestraint self, double d)"""
1365 return _IMP_multifit.ComplementarityRestraint_set_maximum_penetration(self, d)
1368 def set_maximum_separation(self, s):
1369 """set_maximum_separation(ComplementarityRestraint self, double s)"""
1370 return _IMP_multifit.ComplementarityRestraint_set_maximum_separation(self, s)
1373 def set_complementarity_thickness(self, th):
1374 """set_complementarity_thickness(ComplementarityRestraint self, double th)"""
1375 return _IMP_multifit.ComplementarityRestraint_set_complementarity_thickness(self, th)
1378 def set_complementarity_value(self, th):
1379 """set_complementarity_value(ComplementarityRestraint self, double th)"""
1380 return _IMP_multifit.ComplementarityRestraint_set_complementarity_value(self, th)
1383 def set_interior_layer_thickness(self, th):
1384 """set_interior_layer_thickness(ComplementarityRestraint self, double th)"""
1385 return _IMP_multifit.ComplementarityRestraint_set_interior_layer_thickness(self, th)
1388 def set_penetration_coefficient(self, pc):
1389 """set_penetration_coefficient(ComplementarityRestraint self, double pc)"""
1390 return _IMP_multifit.ComplementarityRestraint_set_penetration_coefficient(self, pc)
1393 def set_complementarity_coefficient(self, cc):
1394 """set_complementarity_coefficient(ComplementarityRestraint self, double cc)"""
1395 return _IMP_multifit.ComplementarityRestraint_set_complementarity_coefficient(self, cc)
1398 def set_boundary_coefficient(self, bc):
1399 """set_boundary_coefficient(ComplementarityRestraint self, double bc)"""
1400 return _IMP_multifit.ComplementarityRestraint_set_boundary_coefficient(self, bc)
1403 def get_voxel_size(self):
1404 """get_voxel_size(ComplementarityRestraint self) -> float"""
1405 return _IMP_multifit.ComplementarityRestraint_get_voxel_size(self)
1408 def do_get_inputs(self):
1409 """do_get_inputs(ComplementarityRestraint self) -> IMP::ModelObjectsTemp"""
1410 return _IMP_multifit.ComplementarityRestraint_do_get_inputs(self)
1413 def get_version_info(self):
1414 """get_version_info(ComplementarityRestraint self) -> VersionInfo"""
1415 return _IMP_multifit.ComplementarityRestraint_get_version_info(self)
1419 """__str__(ComplementarityRestraint self) -> std::string"""
1420 return _IMP_multifit.ComplementarityRestraint___str__(self)
1424 """__repr__(ComplementarityRestraint self) -> std::string"""
1425 return _IMP_multifit.ComplementarityRestraint___repr__(self)
1430 return _object_cast_to_ComplementarityRestraint(o)
1432 ComplementarityRestraint_swigregister = _IMP_multifit.ComplementarityRestraint_swigregister
1433 ComplementarityRestraint_swigregister(ComplementarityRestraint)
1437 """read_fitting_solutions(char const * fitting_fn) -> IMP::multifit::FittingSolutionRecords"""
1438 return _IMP_multifit.read_fitting_solutions(fitting_fn)
1442 write_fitting_solutions(char const * fitting_fn, IMP::multifit::FittingSolutionRecords const & fit_sols, int num_sols=-1)
1443 write_fitting_solutions(char const * fitting_fn, IMP::multifit::FittingSolutionRecords const & fit_sols)
1445 return _IMP_multifit.write_fitting_solutions(fitting_fn, fit_sols, num_sols)
1447 def convert_em_to_multifit_format(em_fits):
1448 """convert_em_to_multifit_format(FittingSolutions em_fits) -> IMP::multifit::FittingSolutionRecords"""
1449 return _IMP_multifit.convert_em_to_multifit_format(em_fits)
1451 def convert_multifit_to_em_format(multifit_fits):
1452 """convert_multifit_to_em_format(IMP::multifit::FittingSolutionRecords const & multifit_fits) -> FittingSolutions"""
1453 return _IMP_multifit.convert_multifit_to_em_format(multifit_fits)
1455 def convert_transformations_to_multifit_format(trans):
1456 """convert_transformations_to_multifit_format(IMP::algebra::Transformation3Ds const & trans) -> IMP::multifit::FittingSolutionRecords"""
1457 return _IMP_multifit.convert_transformations_to_multifit_format(trans)
1459 def convert_multifit_format_to_transformations(recs):
1460 """convert_multifit_format_to_transformations(IMP::multifit::FittingSolutionRecords const & recs) -> IMP::algebra::Transformation3Ds"""
1461 return _IMP_multifit.convert_multifit_format_to_transformations(recs)
1464 """get_close_to_point(IMP::multifit::FittingSolutionRecords const & fit_sols, Hierarchy mh, Particle ap, IMP::Float dist) -> IMP::multifit::FittingSolutionRecords"""
1465 return _IMP_multifit.get_close_to_point(fit_sols, mh, ap, dist)
1467 """Proxy of C++ IMP::multifit::ProbabilisticAnchorGraph class."""
1469 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1471 def __init__(self, anchor_positions):
1472 """__init__(IMP::multifit::ProbabilisticAnchorGraph self, IMP::algebra::Vector3Ds anchor_positions) -> ProbabilisticAnchorGraph"""
1473 this = _IMP_multifit.new_ProbabilisticAnchorGraph(anchor_positions)
1475 self.this.append(this)
1476 except __builtin__.Exception:
1479 def add_edge(self, i, j):
1480 """add_edge(ProbabilisticAnchorGraph self, int i, int j)"""
1481 return _IMP_multifit.ProbabilisticAnchorGraph_add_edge(self, i, j)
1484 def set_particle_probabilities_on_anchors(self, p, sols):
1485 """set_particle_probabilities_on_anchors(ProbabilisticAnchorGraph self, Particle p, IMP::multifit::FittingSolutionRecords sols)"""
1486 return _IMP_multifit.ProbabilisticAnchorGraph_set_particle_probabilities_on_anchors(self, p, sols)
1489 def show(self, *args):
1491 show(ProbabilisticAnchorGraph self, _ostream out)
1492 show(ProbabilisticAnchorGraph self)
1494 return _IMP_multifit.ProbabilisticAnchorGraph_show(self, *args)
1497 def get_number_of_anchors(self):
1498 """get_number_of_anchors(ProbabilisticAnchorGraph self) -> unsigned int"""
1499 return _IMP_multifit.ProbabilisticAnchorGraph_get_number_of_anchors(self)
1502 def get_number_of_edges(self):
1503 """get_number_of_edges(ProbabilisticAnchorGraph self) -> unsigned int"""
1504 return _IMP_multifit.ProbabilisticAnchorGraph_get_number_of_edges(self)
1507 def get_edge_list(self):
1508 """get_edge_list(ProbabilisticAnchorGraph self) -> IMP::IntRanges"""
1509 return _IMP_multifit.ProbabilisticAnchorGraph_get_edge_list(self)
1512 def get_anchors(self):
1513 """get_anchors(ProbabilisticAnchorGraph self) -> IMP::algebra::Vector3Ds"""
1514 return _IMP_multifit.ProbabilisticAnchorGraph_get_anchors(self)
1517 def get_particle_anchors(self, p, min_prob=0):
1519 get_particle_anchors(ProbabilisticAnchorGraph self, Particle p, float min_prob=0) -> IMP::algebra::Vector3Ds
1520 get_particle_anchors(ProbabilisticAnchorGraph self, Particle p) -> IMP::algebra::Vector3Ds
1522 return _IMP_multifit.ProbabilisticAnchorGraph_get_particle_anchors(self, p, min_prob)
1525 def get_are_probabilities_for_particle_set(self, p):
1526 """get_are_probabilities_for_particle_set(ProbabilisticAnchorGraph self, Particle p) -> bool"""
1527 return _IMP_multifit.ProbabilisticAnchorGraph_get_are_probabilities_for_particle_set(self, p)
1530 def get_particle_probabilities(self, p):
1531 """get_particle_probabilities(ProbabilisticAnchorGraph self, Particle p) -> IMP::Floats"""
1532 return _IMP_multifit.ProbabilisticAnchorGraph_get_particle_probabilities(self, p)
1535 def get_version_info(self):
1536 """get_version_info(ProbabilisticAnchorGraph self) -> VersionInfo"""
1537 return _IMP_multifit.ProbabilisticAnchorGraph_get_version_info(self)
1541 """__str__(ProbabilisticAnchorGraph self) -> std::string"""
1542 return _IMP_multifit.ProbabilisticAnchorGraph___str__(self)
1546 """__repr__(ProbabilisticAnchorGraph self) -> std::string"""
1547 return _IMP_multifit.ProbabilisticAnchorGraph___repr__(self)
1552 return _object_cast_to_ProbabilisticAnchorGraph(o)
1554 ProbabilisticAnchorGraph_swigregister = _IMP_multifit.ProbabilisticAnchorGraph_swigregister
1555 ProbabilisticAnchorGraph_swigregister(ProbabilisticAnchorGraph)
1557 class ProteinRecordData(object):
1558 """Proxy of C++ IMP::multifit::ProteinRecordData class."""
1560 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1562 def reset_all(self):
1563 """reset_all(ProteinRecordData self)"""
1564 return _IMP_multifit.ProteinRecordData_reset_all(self)
1569 __init__(IMP::multifit::ProteinRecordData self) -> ProteinRecordData
1570 __init__(IMP::multifit::ProteinRecordData self, std::string const & name) -> ProteinRecordData
1571 __init__(IMP::multifit::ProteinRecordData self, std::string const & name, std::string const fn) -> ProteinRecordData
1572 __init__(IMP::multifit::ProteinRecordData self, std::string const & name, int start_res, int end_res, std::string const fn) -> ProteinRecordData
1573 __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
1575 this = _IMP_multifit.new_ProteinRecordData(*args)
1577 self.this.append(this)
1578 except __builtin__.Exception:
1581 def show(self, *args):
1583 show(ProteinRecordData self, _ostream out)
1584 show(ProteinRecordData self)
1586 return _IMP_multifit.ProteinRecordData_show(self, *args)
1588 name_ = _swig_property(_IMP_multifit.ProteinRecordData_name__get, _IMP_multifit.ProteinRecordData_name__set)
1589 start_res_ = _swig_property(_IMP_multifit.ProteinRecordData_start_res__get, _IMP_multifit.ProteinRecordData_start_res__set)
1590 end_res_ = _swig_property(_IMP_multifit.ProteinRecordData_end_res__get, _IMP_multifit.ProteinRecordData_end_res__set)
1591 filename_ = _swig_property(_IMP_multifit.ProteinRecordData_filename__get, _IMP_multifit.ProteinRecordData_filename__set)
1592 surface_filename_ = _swig_property(_IMP_multifit.ProteinRecordData_surface_filename__get, _IMP_multifit.ProteinRecordData_surface_filename__set)
1593 ref_filename_ = _swig_property(_IMP_multifit.ProteinRecordData_ref_filename__get, _IMP_multifit.ProteinRecordData_ref_filename__set)
1596 """__str__(ProteinRecordData self) -> std::string"""
1597 return _IMP_multifit.ProteinRecordData___str__(self)
1601 """__repr__(ProteinRecordData self) -> std::string"""
1602 return _IMP_multifit.ProteinRecordData___repr__(self)
1604 __swig_destroy__ = _IMP_multifit.delete_ProteinRecordData
1605 __del__ =
lambda self:
None
1606 ProteinRecordData_swigregister = _IMP_multifit.ProteinRecordData_swigregister
1607 ProteinRecordData_swigregister(ProteinRecordData)
1610 """Proxy of C++ IMP::multifit::ProteomicsData class."""
1612 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1615 """__init__(IMP::multifit::ProteomicsData self) -> ProteomicsData"""
1616 this = _IMP_multifit.new_ProteomicsData()
1618 self.this.append(this)
1619 except __builtin__.Exception:
1622 def add_protein(self, *args):
1624 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
1625 add_protein(ProteomicsData self, ProteinRecordData rec) -> int
1627 return _IMP_multifit.ProteomicsData_add_protein(self, *args)
1630 def find(self, name):
1631 """find(ProteomicsData self, std::string const & name) -> int"""
1632 return _IMP_multifit.ProteomicsData_find(self, name)
1635 def add_interaction(self, ii, used_for_filter, linker_len):
1636 """add_interaction(ProteomicsData self, IMP::Ints const & ii, bool used_for_filter, float linker_len)"""
1637 return _IMP_multifit.ProteomicsData_add_interaction(self, ii, used_for_filter, linker_len)
1640 def add_cross_link_interaction(self, prot1, res1, prot2, res2, used_in_filter, linker_len):
1641 """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)"""
1642 return _IMP_multifit.ProteomicsData_add_cross_link_interaction(self, prot1, res1, prot2, res2, used_in_filter, linker_len)
1645 def add_ev_pair(self, prot1, prot2):
1646 """add_ev_pair(ProteomicsData self, IMP::Int prot1, IMP::Int prot2)"""
1647 return _IMP_multifit.ProteomicsData_add_ev_pair(self, prot1, prot2)
1650 def get_number_of_proteins(self):
1651 """get_number_of_proteins(ProteomicsData self) -> int"""
1652 return _IMP_multifit.ProteomicsData_get_number_of_proteins(self)
1655 def get_number_of_interactions(self):
1656 """get_number_of_interactions(ProteomicsData self) -> int"""
1657 return _IMP_multifit.ProteomicsData_get_number_of_interactions(self)
1660 def get_interaction(self, interaction_ind):
1661 """get_interaction(ProteomicsData self, int interaction_ind) -> IMP::Ints"""
1662 return _IMP_multifit.ProteomicsData_get_interaction(self, interaction_ind)
1665 def get_interaction_part_of_filter(self, interaction_ind):
1666 """get_interaction_part_of_filter(ProteomicsData self, int interaction_ind) -> bool"""
1667 return _IMP_multifit.ProteomicsData_get_interaction_part_of_filter(self, interaction_ind)
1670 def get_interaction_linker_length(self, interaction_ind):
1671 """get_interaction_linker_length(ProteomicsData self, int interaction_ind) -> int"""
1672 return _IMP_multifit.ProteomicsData_get_interaction_linker_length(self, interaction_ind)
1675 def get_number_of_cross_links(self):
1676 """get_number_of_cross_links(ProteomicsData self) -> int"""
1677 return _IMP_multifit.ProteomicsData_get_number_of_cross_links(self)
1680 def get_cross_link(self, xlink_ind):
1681 """get_cross_link(ProteomicsData self, int xlink_ind) -> std::pair< IMP::IntPair,IMP::IntPair >"""
1682 return _IMP_multifit.ProteomicsData_get_cross_link(self, xlink_ind)
1685 def get_cross_link_part_of_filter(self, xlink_ind):
1686 """get_cross_link_part_of_filter(ProteomicsData self, int xlink_ind) -> bool"""
1687 return _IMP_multifit.ProteomicsData_get_cross_link_part_of_filter(self, xlink_ind)
1690 def get_cross_link_length(self, xlink_ind):
1691 """get_cross_link_length(ProteomicsData self, int xlink_ind) -> float"""
1692 return _IMP_multifit.ProteomicsData_get_cross_link_length(self, xlink_ind)
1695 def get_number_of_ev_pairs(self):
1696 """get_number_of_ev_pairs(ProteomicsData self) -> int"""
1697 return _IMP_multifit.ProteomicsData_get_number_of_ev_pairs(self)
1700 def get_ev_pair(self, ev_ind):
1701 """get_ev_pair(ProteomicsData self, int ev_ind) -> IMP::IntPair"""
1702 return _IMP_multifit.ProteomicsData_get_ev_pair(self, ev_ind)
1705 def get_protein_name(self, protein_ind):
1706 """get_protein_name(ProteomicsData self, int protein_ind) -> std::string"""
1707 return _IMP_multifit.ProteomicsData_get_protein_name(self, protein_ind)
1710 def get_end_res(self, protein_ind):
1711 """get_end_res(ProteomicsData self, int protein_ind) -> int"""
1712 return _IMP_multifit.ProteomicsData_get_end_res(self, protein_ind)
1715 def get_start_res(self, protein_ind):
1716 """get_start_res(ProteomicsData self, int protein_ind) -> int"""
1717 return _IMP_multifit.ProteomicsData_get_start_res(self, protein_ind)
1720 def get_protein_filename(self, protein_ind):
1721 """get_protein_filename(ProteomicsData self, int protein_ind) -> std::string"""
1722 return _IMP_multifit.ProteomicsData_get_protein_filename(self, protein_ind)
1725 def get_reference_filename(self, protein_ind):
1726 """get_reference_filename(ProteomicsData self, int protein_ind) -> std::string"""
1727 return _IMP_multifit.ProteomicsData_get_reference_filename(self, protein_ind)
1730 def get_surface_filename(self, protein_ind):
1731 """get_surface_filename(ProteomicsData self, int protein_ind) -> std::string"""
1732 return _IMP_multifit.ProteomicsData_get_surface_filename(self, protein_ind)
1735 def get_protein_data(self, protein_ind):
1736 """get_protein_data(ProteomicsData self, int protein_ind) -> ProteinRecordData"""
1737 return _IMP_multifit.ProteomicsData_get_protein_data(self, protein_ind)
1740 def get_version_info(self):
1741 """get_version_info(ProteomicsData self) -> VersionInfo"""
1742 return _IMP_multifit.ProteomicsData_get_version_info(self)
1745 def get_num_allowed_violated_interactions(self):
1746 """get_num_allowed_violated_interactions(ProteomicsData self) -> int"""
1747 return _IMP_multifit.ProteomicsData_get_num_allowed_violated_interactions(self)
1750 def set_num_allowed_violated_interactions(self, n):
1751 """set_num_allowed_violated_interactions(ProteomicsData self, int n)"""
1752 return _IMP_multifit.ProteomicsData_set_num_allowed_violated_interactions(self, n)
1755 def get_num_allowed_violated_cross_links(self):
1756 """get_num_allowed_violated_cross_links(ProteomicsData self) -> int"""
1757 return _IMP_multifit.ProteomicsData_get_num_allowed_violated_cross_links(self)
1760 def set_num_allowed_violated_cross_links(self, n):
1761 """set_num_allowed_violated_cross_links(ProteomicsData self, int n)"""
1762 return _IMP_multifit.ProteomicsData_set_num_allowed_violated_cross_links(self, n)
1765 def get_num_allowed_violated_ev(self):
1766 """get_num_allowed_violated_ev(ProteomicsData self) -> int"""
1767 return _IMP_multifit.ProteomicsData_get_num_allowed_violated_ev(self)
1770 def set_num_allowed_violated_ev(self, n):
1771 """set_num_allowed_violated_ev(ProteomicsData self, int n)"""
1772 return _IMP_multifit.ProteomicsData_set_num_allowed_violated_ev(self, n)
1776 """__str__(ProteomicsData self) -> std::string"""
1777 return _IMP_multifit.ProteomicsData___str__(self)
1781 """__repr__(ProteomicsData self) -> std::string"""
1782 return _IMP_multifit.ProteomicsData___repr__(self)
1787 return _object_cast_to_ProteomicsData(o)
1789 ProteomicsData_swigregister = _IMP_multifit.ProteomicsData_swigregister
1790 ProteomicsData_swigregister(ProteomicsData)
1794 """read_proteomics_data(char const * proteomics_fn) -> ProteomicsData"""
1795 return _IMP_multifit.read_proteomics_data(proteomics_fn)
1797 def get_partial_proteomics_data(pd, prot_names):
1798 """get_partial_proteomics_data(ProteomicsData pd, IMP::Strings const & prot_names) -> ProteomicsData"""
1799 return _IMP_multifit.get_partial_proteomics_data(pd, prot_names)
1800 class AnchorsData(object):
1801 """Proxy of C++ IMP::multifit::AnchorsData class."""
1803 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1807 __init__(IMP::multifit::AnchorsData self) -> AnchorsData
1808 __init__(IMP::multifit::AnchorsData self, IMP::algebra::Vector3Ds points, IMP::IntPairs edges) -> AnchorsData
1810 this = _IMP_multifit.new_AnchorsData(*args)
1812 self.this.append(this)
1813 except __builtin__.Exception:
1816 def remove_edges_for_node(self, node_ind):
1817 """remove_edges_for_node(AnchorsData self, int node_ind)"""
1818 return _IMP_multifit.AnchorsData_remove_edges_for_node(self, node_ind)
1821 def get_number_of_points(self):
1822 """get_number_of_points(AnchorsData self) -> int"""
1823 return _IMP_multifit.AnchorsData_get_number_of_points(self)
1826 def get_number_of_edges(self):
1827 """get_number_of_edges(AnchorsData self) -> int"""
1828 return _IMP_multifit.AnchorsData_get_number_of_edges(self)
1831 def get_is_point_considered(self, node_ind):
1832 """get_is_point_considered(AnchorsData self, int node_ind) -> bool"""
1833 return _IMP_multifit.AnchorsData_get_is_point_considered(self, node_ind)
1836 def show(self, *args):
1838 show(AnchorsData self, _ostream out)
1839 show(AnchorsData self)
1841 return _IMP_multifit.AnchorsData_show(self, *args)
1844 def get_secondary_structure_is_set(self):
1845 """get_secondary_structure_is_set(AnchorsData self) -> bool"""
1846 return _IMP_multifit.AnchorsData_get_secondary_structure_is_set(self)
1849 def setup_secondary_structure(self, mdl):
1850 """setup_secondary_structure(AnchorsData self, Model mdl)"""
1851 return _IMP_multifit.AnchorsData_setup_secondary_structure(self, mdl)
1854 def set_secondary_structure_probabilities(self, *args):
1856 set_secondary_structure_probabilities(AnchorsData self, IMP::Particles const & ssres_ps, IMP::Ints const & indices)
1857 set_secondary_structure_probabilities(AnchorsData self, IMP::Particles const & ssres_ps)
1859 return _IMP_multifit.AnchorsData_set_secondary_structure_probabilities(self, *args)
1862 def get_secondary_structure_particles(self):
1863 """get_secondary_structure_particles(AnchorsData self) -> IMP::Particles"""
1864 return _IMP_multifit.AnchorsData_get_secondary_structure_particles(self)
1866 points_ = _swig_property(_IMP_multifit.AnchorsData_points__get, _IMP_multifit.AnchorsData_points__set)
1867 consider_point_ = _swig_property(_IMP_multifit.AnchorsData_consider_point__get, _IMP_multifit.AnchorsData_consider_point__set)
1868 edges_ = _swig_property(_IMP_multifit.AnchorsData_edges__get, _IMP_multifit.AnchorsData_edges__set)
1871 """__str__(AnchorsData self) -> std::string"""
1872 return _IMP_multifit.AnchorsData___str__(self)
1876 """__repr__(AnchorsData self) -> std::string"""
1877 return _IMP_multifit.AnchorsData___repr__(self)
1879 __swig_destroy__ = _IMP_multifit.delete_AnchorsData
1880 __del__ =
lambda self:
None
1881 AnchorsData_swigregister = _IMP_multifit.AnchorsData_swigregister
1882 AnchorsData_swigregister(AnchorsData)
1885 def read_anchors_data(txt_filename):
1886 """read_anchors_data(char const * txt_filename) -> AnchorsData"""
1887 return _IMP_multifit.read_anchors_data(txt_filename)
1889 def write_txt(txt_filename, ad):
1890 """write_txt(std::string const & txt_filename, AnchorsData ad)"""
1891 return _IMP_multifit.write_txt(txt_filename, ad)
1893 def write_cmm(cmm_filename, marker_set_name, dpa):
1894 """write_cmm(std::string const & cmm_filename, std::string const & marker_set_name, AnchorsData dpa)"""
1895 return _IMP_multifit.write_cmm(cmm_filename, marker_set_name, dpa)
1898 """create_coarse_molecule_from_density(DensityMap dmap, float dens_threshold, int num_beads, Model mdl, float bead_radius) -> Hierarchy"""
1899 return _IMP_multifit.create_coarse_molecule_from_density(dmap, dens_threshold, num_beads, mdl, bead_radius)
1901 def create_hit_map(rb, rb_ref, sols, damp):
1902 """create_hit_map(RigidBody rb, Refiner rb_ref, IMP::multifit::FittingSolutionRecords const & sols, DensityMap damp) -> DensityMap"""
1903 return _IMP_multifit.create_hit_map(rb, rb_ref, sols, damp)
1906 """get_points_close_to_molecule(Hierarchy mh, IMP::algebra::Vector3Ds const points, IMP::Float max_dist) -> IMP::algebra::Vector3Ds"""
1907 return _IMP_multifit.get_points_close_to_molecule(mh, points, max_dist)
1909 def get_points_far_from_molecule(mh, points, max_dist):
1910 """get_points_far_from_molecule(Hierarchy mh, IMP::algebra::Vector3Ds const points, IMP::Float max_dist) -> IMP::algebra::Vector3Ds"""
1911 return _IMP_multifit.get_points_far_from_molecule(mh, points, max_dist)
1913 """Proxy of C++ IMP::multifit::RadiusOfGyrationRestraint class."""
1915 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1917 def __init__(self, ps, num_residues, scale=1.):
1919 __init__(IMP::multifit::RadiusOfGyrationRestraint self, IMP::Particles ps, int num_residues, IMP::Float scale=1.) -> RadiusOfGyrationRestraint
1920 __init__(IMP::multifit::RadiusOfGyrationRestraint self, IMP::Particles ps, int num_residues) -> RadiusOfGyrationRestraint
1922 this = _IMP_multifit.new_RadiusOfGyrationRestraint(ps, num_residues, scale)
1924 self.this.append(this)
1925 except __builtin__.Exception:
1928 def do_get_inputs(self):
1929 """do_get_inputs(RadiusOfGyrationRestraint self) -> IMP::ModelObjectsTemp"""
1930 return _IMP_multifit.RadiusOfGyrationRestraint_do_get_inputs(self)
1933 def get_version_info(self):
1934 """get_version_info(RadiusOfGyrationRestraint self) -> VersionInfo"""
1935 return _IMP_multifit.RadiusOfGyrationRestraint_get_version_info(self)
1938 def set_radius_of_gyration(self, r):
1939 """set_radius_of_gyration(RadiusOfGyrationRestraint self, IMP::Float r)"""
1940 return _IMP_multifit.RadiusOfGyrationRestraint_set_radius_of_gyration(self, r)
1944 """get_radius_of_gyration(RadiusOfGyrationRestraint self) -> IMP::Float"""
1945 return _IMP_multifit.RadiusOfGyrationRestraint_get_radius_of_gyration(self)
1949 """__str__(RadiusOfGyrationRestraint self) -> std::string"""
1950 return _IMP_multifit.RadiusOfGyrationRestraint___str__(self)
1954 """__repr__(RadiusOfGyrationRestraint self) -> std::string"""
1955 return _IMP_multifit.RadiusOfGyrationRestraint___repr__(self)
1960 return _object_cast_to_RadiusOfGyrationRestraint(o)
1962 RadiusOfGyrationRestraint_swigregister = _IMP_multifit.RadiusOfGyrationRestraint_swigregister
1963 RadiusOfGyrationRestraint_swigregister(RadiusOfGyrationRestraint)
1966 def get_approximated_radius_of_gyration(len):
1967 """get_approximated_radius_of_gyration(int len) -> float"""
1968 return _IMP_multifit.get_approximated_radius_of_gyration(len)
1970 def get_actual_radius_of_gyration(ps):
1971 """get_actual_radius_of_gyration(IMP::ParticlesTemp ps) -> float"""
1972 return _IMP_multifit.get_actual_radius_of_gyration(ps)
1974 def get_approximated_radius(len):
1975 """get_approximated_radius(int len) -> float"""
1976 return _IMP_multifit.get_approximated_radius(len)
1977 class ProteinsAnchorsSamplingSpace(object):
1978 """Proxy of C++ IMP::multifit::ProteinsAnchorsSamplingSpace class."""
1980 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1984 __init__(IMP::multifit::ProteinsAnchorsSamplingSpace self, ProteomicsData prots=None) -> ProteinsAnchorsSamplingSpace
1985 __init__(IMP::multifit::ProteinsAnchorsSamplingSpace self) -> ProteinsAnchorsSamplingSpace
1987 this = _IMP_multifit.new_ProteinsAnchorsSamplingSpace(prots)
1989 self.this.append(this)
1990 except __builtin__.Exception:
1993 def set_anchors(self, data):
1994 """set_anchors(ProteinsAnchorsSamplingSpace self, AnchorsData data)"""
1995 return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_anchors(self, data)
1998 def get_anchors(self):
1999 """get_anchors(ProteinsAnchorsSamplingSpace self) -> AnchorsData"""
2000 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_anchors(self)
2003 def get_anchors_filename(self):
2004 """get_anchors_filename(ProteinsAnchorsSamplingSpace self) -> std::string"""
2005 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_anchors_filename(self)
2008 def set_anchors_filename(self, fn):
2009 """set_anchors_filename(ProteinsAnchorsSamplingSpace self, std::string const & fn)"""
2010 return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_anchors_filename(self, fn)
2013 def get_proteomics_data(self):
2014 """get_proteomics_data(ProteinsAnchorsSamplingSpace self) -> ProteomicsData"""
2015 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_proteomics_data(self)
2018 def add_protein(self, rec):
2019 """add_protein(ProteinsAnchorsSamplingSpace self, ProteinRecordData rec)"""
2020 return _IMP_multifit.ProteinsAnchorsSamplingSpace_add_protein(self, rec)
2023 def get_paths_for_protein(self, prot_name):
2024 """get_paths_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name) -> IMP::IntsList"""
2025 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_paths_for_protein(self, prot_name)
2028 def set_paths_filename_for_protein(self, prot_name, paths_filename):
2029 """set_paths_filename_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name, std::string const & paths_filename)"""
2030 return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_paths_filename_for_protein(self, prot_name, paths_filename)
2033 def get_paths_filename_for_protein(self, prot_name):
2034 """get_paths_filename_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name) -> std::string"""
2035 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_paths_filename_for_protein(self, prot_name)
2038 def set_paths_for_protein(self, prot_name, paths):
2039 """set_paths_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name, IMP::IntsList paths)"""
2040 return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_paths_for_protein(self, prot_name, paths)
2043 def show(self, *args):
2045 show(ProteinsAnchorsSamplingSpace self, _ostream s)
2046 show(ProteinsAnchorsSamplingSpace self)
2048 return _IMP_multifit.ProteinsAnchorsSamplingSpace_show(self, *args)
2052 """__str__(ProteinsAnchorsSamplingSpace self) -> std::string"""
2053 return _IMP_multifit.ProteinsAnchorsSamplingSpace___str__(self)
2057 """__repr__(ProteinsAnchorsSamplingSpace self) -> std::string"""
2058 return _IMP_multifit.ProteinsAnchorsSamplingSpace___repr__(self)
2060 __swig_destroy__ = _IMP_multifit.delete_ProteinsAnchorsSamplingSpace
2061 __del__ =
lambda self:
None
2062 ProteinsAnchorsSamplingSpace_swigregister = _IMP_multifit.ProteinsAnchorsSamplingSpace_swigregister
2063 ProteinsAnchorsSamplingSpace_swigregister(ProteinsAnchorsSamplingSpace)
2066 def read_protein_anchors_mapping(*args):
2068 read_protein_anchors_mapping(ProteomicsData prots, std::string const & anchors_prot_map_fn, int max_paths) -> ProteinsAnchorsSamplingSpace
2069 read_protein_anchors_mapping(ProteomicsData prots, std::string const & anchors_prot_map_fn) -> ProteinsAnchorsSamplingSpace
2071 return _IMP_multifit.read_protein_anchors_mapping(*args)
2073 def write_protein_anchors_mapping(*args):
2075 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)
2076 write_protein_anchors_mapping(std::string const & anchors_prot_map_fn, ProteinsAnchorsSamplingSpace pa, IMP::Strings const & prot_names)
2078 return _IMP_multifit.write_protein_anchors_mapping(*args)
2081 """get_part_of_sampling_space(ProteinsAnchorsSamplingSpace prots_ss, IMP::Strings const & prot_names) -> ProteinsAnchorsSamplingSpace"""
2082 return _IMP_multifit.get_part_of_sampling_space(prots_ss, prot_names)
2085 """get_partial_assembly_setting_data(SettingsData prots_sd, IMP::Strings const & prot_names) -> SettingsData"""
2086 return _IMP_multifit.get_partial_assembly_setting_data(prots_sd, prot_names)
2090 read_paths(char const * txt_filename, int max_paths) -> IMP::IntsList
2091 read_paths(char const * txt_filename) -> IMP::IntsList
2093 return _IMP_multifit.read_paths(*args)
2095 def write_paths(paths, txt_filename):
2096 """write_paths(IMP::IntsList const & paths, std::string const & txt_filename)"""
2097 return _IMP_multifit.write_paths(paths, txt_filename)
2099 def molecule2anchors(mh, k):
2100 """molecule2anchors(Hierarchy mh, int k) -> AnchorsData"""
2101 return _IMP_multifit.molecule2anchors(mh, k)
2103 def get_anchors_for_density(dmap, number_of_means, density_threshold, pdb_filename, cmm_filename, seg_filename, txt_filename):
2104 """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)"""
2105 return _IMP_multifit.get_anchors_for_density(dmap, number_of_means, density_threshold, pdb_filename, cmm_filename, seg_filename, txt_filename)
2109 get_anchor_indices_matching_secondary_structure(AnchorsData ad, IMP::atom::SecondaryStructureResidues const & ssrs, IMP::Float max_rmsd=0.7) -> IMP::IntsList
2110 get_anchor_indices_matching_secondary_structure(AnchorsData ad, IMP::atom::SecondaryStructureResidues const & ssrs) -> IMP::IntsList
2112 return _IMP_multifit.get_anchor_indices_matching_secondary_structure(ad, ssrs, max_rmsd)
2113 class DominoParams(object):
2114 """Proxy of C++ IMP::multifit::DominoParams class."""
2116 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2119 """__init__(IMP::multifit::DominoParams self) -> DominoParams"""
2120 this = _IMP_multifit.new_DominoParams()
2122 self.this.append(this)
2123 except __builtin__.Exception:
2127 """add(DominoParams self, boost::property_tree::ptree const & pt)"""
2128 return _IMP_multifit.DominoParams_add(self, pt)
2131 def show(self, *args):
2133 show(DominoParams self, _ostream s)
2134 show(DominoParams self)
2136 return _IMP_multifit.DominoParams_show(self, *args)
2138 max_value_threshold_ = _swig_property(_IMP_multifit.DominoParams_max_value_threshold__get, _IMP_multifit.DominoParams_max_value_threshold__set)
2139 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)
2140 max_anchor_penetration_ = _swig_property(_IMP_multifit.DominoParams_max_anchor_penetration__get, _IMP_multifit.DominoParams_max_anchor_penetration__set)
2141 heap_size_ = _swig_property(_IMP_multifit.DominoParams_heap_size__get, _IMP_multifit.DominoParams_heap_size__set)
2142 cache_size_ = _swig_property(_IMP_multifit.DominoParams_cache_size__get, _IMP_multifit.DominoParams_cache_size__set)
2145 """__str__(DominoParams self) -> std::string"""
2146 return _IMP_multifit.DominoParams___str__(self)
2150 """__repr__(DominoParams self) -> std::string"""
2151 return _IMP_multifit.DominoParams___repr__(self)
2153 __swig_destroy__ = _IMP_multifit.delete_DominoParams
2154 __del__ =
lambda self:
None
2155 DominoParams_swigregister = _IMP_multifit.DominoParams_swigregister
2156 DominoParams_swigregister(DominoParams)
2158 class XlinkParams(object):
2159 """Proxy of C++ IMP::multifit::XlinkParams class."""
2161 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2164 """__init__(IMP::multifit::XlinkParams self) -> XlinkParams"""
2165 this = _IMP_multifit.new_XlinkParams()
2167 self.this.append(this)
2168 except __builtin__.Exception:
2172 """add(XlinkParams self, boost::property_tree::ptree const & pt)"""
2173 return _IMP_multifit.XlinkParams_add(self, pt)
2176 def show(self, *args):
2178 show(XlinkParams self, _ostream s)
2179 show(XlinkParams self)
2181 return _IMP_multifit.XlinkParams_show(self, *args)
2183 upper_bound_ = _swig_property(_IMP_multifit.XlinkParams_upper_bound__get, _IMP_multifit.XlinkParams_upper_bound__set)
2184 k_ = _swig_property(_IMP_multifit.XlinkParams_k__get, _IMP_multifit.XlinkParams_k__set)
2185 max_xlink_val_ = _swig_property(_IMP_multifit.XlinkParams_max_xlink_val__get, _IMP_multifit.XlinkParams_max_xlink_val__set)
2186 treat_between_residues_ = _swig_property(_IMP_multifit.XlinkParams_treat_between_residues__get, _IMP_multifit.XlinkParams_treat_between_residues__set)
2189 """__str__(XlinkParams self) -> std::string"""
2190 return _IMP_multifit.XlinkParams___str__(self)
2194 """__repr__(XlinkParams self) -> std::string"""
2195 return _IMP_multifit.XlinkParams___repr__(self)
2197 __swig_destroy__ = _IMP_multifit.delete_XlinkParams
2198 __del__ =
lambda self:
None
2199 XlinkParams_swigregister = _IMP_multifit.XlinkParams_swigregister
2200 XlinkParams_swigregister(XlinkParams)
2202 class ConnectivityParams(object):
2203 """Proxy of C++ IMP::multifit::ConnectivityParams class."""
2205 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2208 """__init__(IMP::multifit::ConnectivityParams self) -> ConnectivityParams"""
2209 this = _IMP_multifit.new_ConnectivityParams()
2211 self.this.append(this)
2212 except __builtin__.Exception:
2216 """add(ConnectivityParams self, boost::property_tree::ptree const & pt)"""
2217 return _IMP_multifit.ConnectivityParams_add(self, pt)
2220 def show(self, *args):
2222 show(ConnectivityParams self, _ostream s)
2223 show(ConnectivityParams self)
2225 return _IMP_multifit.ConnectivityParams_show(self, *args)
2227 upper_bound_ = _swig_property(_IMP_multifit.ConnectivityParams_upper_bound__get, _IMP_multifit.ConnectivityParams_upper_bound__set)
2228 k_ = _swig_property(_IMP_multifit.ConnectivityParams_k__get, _IMP_multifit.ConnectivityParams_k__set)
2229 max_conn_rest_val_ = _swig_property(_IMP_multifit.ConnectivityParams_max_conn_rest_val__get, _IMP_multifit.ConnectivityParams_max_conn_rest_val__set)
2232 """__str__(ConnectivityParams self) -> std::string"""
2233 return _IMP_multifit.ConnectivityParams___str__(self)
2237 """__repr__(ConnectivityParams self) -> std::string"""
2238 return _IMP_multifit.ConnectivityParams___repr__(self)
2240 __swig_destroy__ = _IMP_multifit.delete_ConnectivityParams
2241 __del__ =
lambda self:
None
2242 ConnectivityParams_swigregister = _IMP_multifit.ConnectivityParams_swigregister
2243 ConnectivityParams_swigregister(ConnectivityParams)
2245 class FragmentsParams(object):
2246 """Proxy of C++ IMP::multifit::FragmentsParams class."""
2248 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2251 """__init__(IMP::multifit::FragmentsParams self) -> FragmentsParams"""
2252 this = _IMP_multifit.new_FragmentsParams()
2254 self.this.append(this)
2255 except __builtin__.Exception:
2259 """add(FragmentsParams self, boost::property_tree::ptree const & pt)"""
2260 return _IMP_multifit.FragmentsParams_add(self, pt)
2263 def show(self, *args):
2265 show(FragmentsParams self, _ostream s)
2266 show(FragmentsParams self)
2268 return _IMP_multifit.FragmentsParams_show(self, *args)
2270 frag_len_ = _swig_property(_IMP_multifit.FragmentsParams_frag_len__get, _IMP_multifit.FragmentsParams_frag_len__set)
2271 bead_radius_scale_ = _swig_property(_IMP_multifit.FragmentsParams_bead_radius_scale__get, _IMP_multifit.FragmentsParams_bead_radius_scale__set)
2272 load_atomic_ = _swig_property(_IMP_multifit.FragmentsParams_load_atomic__get, _IMP_multifit.FragmentsParams_load_atomic__set)
2273 subunit_rigid_ = _swig_property(_IMP_multifit.FragmentsParams_subunit_rigid__get, _IMP_multifit.FragmentsParams_subunit_rigid__set)
2276 """__str__(FragmentsParams self) -> std::string"""
2277 return _IMP_multifit.FragmentsParams___str__(self)
2281 """__repr__(FragmentsParams self) -> std::string"""
2282 return _IMP_multifit.FragmentsParams___repr__(self)
2284 __swig_destroy__ = _IMP_multifit.delete_FragmentsParams
2285 __del__ =
lambda self:
None
2286 FragmentsParams_swigregister = _IMP_multifit.FragmentsParams_swigregister
2287 FragmentsParams_swigregister(FragmentsParams)
2289 class RogParams(object):
2290 """Proxy of C++ IMP::multifit::RogParams class."""
2292 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2295 """__init__(IMP::multifit::RogParams self) -> RogParams"""
2296 this = _IMP_multifit.new_RogParams()
2298 self.this.append(this)
2299 except __builtin__.Exception:
2303 """add(RogParams self, boost::property_tree::ptree const & pt)"""
2304 return _IMP_multifit.RogParams_add(self, pt)
2307 def get_max_score(self):
2308 """get_max_score(RogParams self) -> float"""
2309 return _IMP_multifit.RogParams_get_max_score(self)
2312 def get_scale(self):
2313 """get_scale(RogParams self) -> float"""
2314 return _IMP_multifit.RogParams_get_scale(self)
2317 def show(self, *args):
2319 show(RogParams self, _ostream s)
2320 show(RogParams self)
2322 return _IMP_multifit.RogParams_show(self, *args)
2326 """__str__(RogParams self) -> std::string"""
2327 return _IMP_multifit.RogParams___str__(self)
2331 """__repr__(RogParams self) -> std::string"""
2332 return _IMP_multifit.RogParams___repr__(self)
2334 __swig_destroy__ = _IMP_multifit.delete_RogParams
2335 __del__ =
lambda self:
None
2336 RogParams_swigregister = _IMP_multifit.RogParams_swigregister
2337 RogParams_swigregister(RogParams)
2339 class EVParams(object):
2340 """Proxy of C++ IMP::multifit::EVParams class."""
2342 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2345 """__init__(IMP::multifit::EVParams self) -> EVParams"""
2346 this = _IMP_multifit.new_EVParams()
2348 self.this.append(this)
2349 except __builtin__.Exception:
2353 """add(EVParams self, boost::property_tree::ptree const & pt)"""
2354 return _IMP_multifit.EVParams_add(self, pt)
2357 def show(self, *args):
2359 show(EVParams self, _ostream s)
2362 return _IMP_multifit.EVParams_show(self, *args)
2364 pair_distance_ = _swig_property(_IMP_multifit.EVParams_pair_distance__get, _IMP_multifit.EVParams_pair_distance__set)
2365 pair_slack_ = _swig_property(_IMP_multifit.EVParams_pair_slack__get, _IMP_multifit.EVParams_pair_slack__set)
2366 hlb_mean_ = _swig_property(_IMP_multifit.EVParams_hlb_mean__get, _IMP_multifit.EVParams_hlb_mean__set)
2367 hlb_k_ = _swig_property(_IMP_multifit.EVParams_hlb_k__get, _IMP_multifit.EVParams_hlb_k__set)
2368 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)
2369 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)
2370 scoring_mode_ = _swig_property(_IMP_multifit.EVParams_scoring_mode__get, _IMP_multifit.EVParams_scoring_mode__set)
2373 """__str__(EVParams self) -> std::string"""
2374 return _IMP_multifit.EVParams___str__(self)
2378 """__repr__(EVParams self) -> std::string"""
2379 return _IMP_multifit.EVParams___repr__(self)
2381 __swig_destroy__ = _IMP_multifit.delete_EVParams
2382 __del__ =
lambda self:
None
2383 EVParams_swigregister = _IMP_multifit.EVParams_swigregister
2384 EVParams_swigregister(EVParams)
2386 class FiltersParams(object):
2387 """Proxy of C++ IMP::multifit::FiltersParams class."""
2389 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2392 """__init__(IMP::multifit::FiltersParams self) -> FiltersParams"""
2393 this = _IMP_multifit.new_FiltersParams()
2395 self.this.append(this)
2396 except __builtin__.Exception:
2400 """add(FiltersParams self, boost::property_tree::ptree const & pt)"""
2401 return _IMP_multifit.FiltersParams_add(self, pt)
2404 def show(self, *args):
2406 show(FiltersParams self, _ostream s)
2407 show(FiltersParams self)
2409 return _IMP_multifit.FiltersParams_show(self, *args)
2411 max_num_violated_xlink_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_xlink__get, _IMP_multifit.FiltersParams_max_num_violated_xlink__set)
2412 max_num_violated_conn_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_conn__get, _IMP_multifit.FiltersParams_max_num_violated_conn__set)
2413 max_num_violated_ev_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_ev__get, _IMP_multifit.FiltersParams_max_num_violated_ev__set)
2416 """__str__(FiltersParams self) -> std::string"""
2417 return _IMP_multifit.FiltersParams___str__(self)
2421 """__repr__(FiltersParams self) -> std::string"""
2422 return _IMP_multifit.FiltersParams___repr__(self)
2424 __swig_destroy__ = _IMP_multifit.delete_FiltersParams
2425 __del__ =
lambda self:
None
2426 FiltersParams_swigregister = _IMP_multifit.FiltersParams_swigregister
2427 FiltersParams_swigregister(FiltersParams)
2429 class FittingParams(object):
2430 """Proxy of C++ IMP::multifit::FittingParams class."""
2432 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2435 """__init__(IMP::multifit::FittingParams self) -> FittingParams"""
2436 this = _IMP_multifit.new_FittingParams()
2438 self.this.append(this)
2439 except __builtin__.Exception:
2443 """add(FittingParams self, boost::property_tree::ptree const & pt)"""
2444 return _IMP_multifit.FittingParams_add(self, pt)
2447 def show(self, *args):
2449 show(FittingParams self, _ostream s)
2450 show(FittingParams self)
2452 return _IMP_multifit.FittingParams_show(self, *args)
2454 pca_max_angle_diff_ = _swig_property(_IMP_multifit.FittingParams_pca_max_angle_diff__get, _IMP_multifit.FittingParams_pca_max_angle_diff__set)
2455 pca_max_size_diff_ = _swig_property(_IMP_multifit.FittingParams_pca_max_size_diff__get, _IMP_multifit.FittingParams_pca_max_size_diff__set)
2456 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)
2457 max_asmb_fit_score_ = _swig_property(_IMP_multifit.FittingParams_max_asmb_fit_score__get, _IMP_multifit.FittingParams_max_asmb_fit_score__set)
2460 """__str__(FittingParams self) -> std::string"""
2461 return _IMP_multifit.FittingParams___str__(self)
2465 """__repr__(FittingParams self) -> std::string"""
2466 return _IMP_multifit.FittingParams___repr__(self)
2468 __swig_destroy__ = _IMP_multifit.delete_FittingParams
2469 __del__ =
lambda self:
None
2470 FittingParams_swigregister = _IMP_multifit.FittingParams_swigregister
2471 FittingParams_swigregister(FittingParams)
2473 class ComplementarityParams(object):
2474 """Proxy of C++ IMP::multifit::ComplementarityParams class."""
2476 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2479 """__init__(IMP::multifit::ComplementarityParams self) -> ComplementarityParams"""
2480 this = _IMP_multifit.new_ComplementarityParams()
2482 self.this.append(this)
2483 except __builtin__.Exception:
2487 """add(ComplementarityParams self, boost::property_tree::ptree const & pt)"""
2488 return _IMP_multifit.ComplementarityParams_add(self, pt)
2491 def show(self, *args):
2493 show(ComplementarityParams self, _ostream s)
2494 show(ComplementarityParams self)
2496 return _IMP_multifit.ComplementarityParams_show(self, *args)
2498 max_score_ = _swig_property(_IMP_multifit.ComplementarityParams_max_score__get, _IMP_multifit.ComplementarityParams_max_score__set)
2499 max_penetration_ = _swig_property(_IMP_multifit.ComplementarityParams_max_penetration__get, _IMP_multifit.ComplementarityParams_max_penetration__set)
2500 interior_layer_thickness_ = _swig_property(_IMP_multifit.ComplementarityParams_interior_layer_thickness__get, _IMP_multifit.ComplementarityParams_interior_layer_thickness__set)
2501 boundary_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_boundary_coef__get, _IMP_multifit.ComplementarityParams_boundary_coef__set)
2502 comp_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_comp_coef__get, _IMP_multifit.ComplementarityParams_comp_coef__set)
2503 penetration_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_penetration_coef__get, _IMP_multifit.ComplementarityParams_penetration_coef__set)
2506 """__str__(ComplementarityParams self) -> std::string"""
2507 return _IMP_multifit.ComplementarityParams___str__(self)
2511 """__repr__(ComplementarityParams self) -> std::string"""
2512 return _IMP_multifit.ComplementarityParams___repr__(self)
2514 __swig_destroy__ = _IMP_multifit.delete_ComplementarityParams
2515 __del__ =
lambda self:
None
2516 ComplementarityParams_swigregister = _IMP_multifit.ComplementarityParams_swigregister
2517 ComplementarityParams_swigregister(ComplementarityParams)
2519 class AlignmentParams(object):
2520 """Proxy of C++ IMP::multifit::AlignmentParams class."""
2522 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2524 def __init__(self, param_filename):
2525 """__init__(IMP::multifit::AlignmentParams self, char const * param_filename) -> AlignmentParams"""
2526 this = _IMP_multifit.new_AlignmentParams(param_filename)
2528 self.this.append(this)
2529 except __builtin__.Exception:
2532 def get_domino_params(self):
2533 """get_domino_params(AlignmentParams self) -> DominoParams"""
2534 return _IMP_multifit.AlignmentParams_get_domino_params(self)
2537 def get_fitting_params(self):
2538 """get_fitting_params(AlignmentParams self) -> FittingParams"""
2539 return _IMP_multifit.AlignmentParams_get_fitting_params(self)
2542 def get_complementarity_params(self):
2543 """get_complementarity_params(AlignmentParams self) -> ComplementarityParams"""
2544 return _IMP_multifit.AlignmentParams_get_complementarity_params(self)
2547 def get_xlink_params(self):
2548 """get_xlink_params(AlignmentParams self) -> XlinkParams"""
2549 return _IMP_multifit.AlignmentParams_get_xlink_params(self)
2552 def get_connectivity_params(self):
2553 """get_connectivity_params(AlignmentParams self) -> ConnectivityParams"""
2554 return _IMP_multifit.AlignmentParams_get_connectivity_params(self)
2557 def get_rog_params(self):
2558 """get_rog_params(AlignmentParams self) -> RogParams"""
2559 return _IMP_multifit.AlignmentParams_get_rog_params(self)
2562 def get_fragments_params(self):
2563 """get_fragments_params(AlignmentParams self) -> FragmentsParams"""
2564 return _IMP_multifit.AlignmentParams_get_fragments_params(self)
2567 def get_filters_params(self):
2568 """get_filters_params(AlignmentParams self) -> FiltersParams"""
2569 return _IMP_multifit.AlignmentParams_get_filters_params(self)
2572 def get_ev_params(self):
2573 """get_ev_params(AlignmentParams self) -> EVParams"""
2574 return _IMP_multifit.AlignmentParams_get_ev_params(self)
2577 def show(self, *args):
2579 show(AlignmentParams self, _ostream s)
2580 show(AlignmentParams self)
2582 return _IMP_multifit.AlignmentParams_show(self, *args)
2586 """__str__(AlignmentParams self) -> std::string"""
2587 return _IMP_multifit.AlignmentParams___str__(self)
2591 """__repr__(AlignmentParams self) -> std::string"""
2592 return _IMP_multifit.AlignmentParams___repr__(self)
2594 __swig_destroy__ = _IMP_multifit.delete_AlignmentParams
2595 __del__ =
lambda self:
None
2596 AlignmentParams_swigregister = _IMP_multifit.AlignmentParams_swigregister
2597 AlignmentParams_swigregister(AlignmentParams)
2599 class ProteomicsEMAlignmentAtomic(
IMP.Object):
2600 """Proxy of C++ IMP::multifit::ProteomicsEMAlignmentAtomic class."""
2602 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2604 def __init__(self, mapping_data, asmb_data, align_param):
2605 """__init__(IMP::multifit::ProteomicsEMAlignmentAtomic self, ProteinsAnchorsSamplingSpace mapping_data, SettingsData asmb_data, AlignmentParams align_param) -> ProteomicsEMAlignmentAtomic"""
2606 this = _IMP_multifit.new_ProteomicsEMAlignmentAtomic(mapping_data, asmb_data, align_param)
2608 self.this.append(this)
2609 except __builtin__.Exception:
2613 """align(ProteomicsEMAlignmentAtomic self)"""
2614 return _IMP_multifit.ProteomicsEMAlignmentAtomic_align(self)
2617 def add_all_restraints(self):
2618 """add_all_restraints(ProteomicsEMAlignmentAtomic self)"""
2619 return _IMP_multifit.ProteomicsEMAlignmentAtomic_add_all_restraints(self)
2622 def get_restraint_set(self):
2623 """get_restraint_set(ProteomicsEMAlignmentAtomic self) -> RestraintSet"""
2624 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_restraint_set(self)
2627 def add_states_and_filters(self):
2628 """add_states_and_filters(ProteomicsEMAlignmentAtomic self)"""
2629 return _IMP_multifit.ProteomicsEMAlignmentAtomic_add_states_and_filters(self)
2632 def show_domino_merge_tree(self):
2633 """show_domino_merge_tree(ProteomicsEMAlignmentAtomic self)"""
2634 return _IMP_multifit.ProteomicsEMAlignmentAtomic_show_domino_merge_tree(self)
2637 def get_combinations(self, uniques=False):
2639 get_combinations(ProteomicsEMAlignmentAtomic self, bool uniques=False) -> IMP::domino::Assignments
2640 get_combinations(ProteomicsEMAlignmentAtomic self) -> IMP::domino::Assignments
2642 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_combinations(self, uniques)
2645 def set_density_map(self, dmap, threshold):
2646 """set_density_map(ProteomicsEMAlignmentAtomic self, DensityMap dmap, float threshold)"""
2647 return _IMP_multifit.ProteomicsEMAlignmentAtomic_set_density_map(self, dmap, threshold)
2650 def get_molecules(self):
2651 """get_molecules(ProteomicsEMAlignmentAtomic self) -> IMP::atom::Hierarchies"""
2652 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_molecules(self)
2655 def get_rigid_bodies(self):
2656 """get_rigid_bodies(ProteomicsEMAlignmentAtomic self) -> IMP::core::RigidBodies"""
2657 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_rigid_bodies(self)
2660 def load_combination_of_states(self, state4particles):
2661 """load_combination_of_states(ProteomicsEMAlignmentAtomic self, IMP::Ints const & state4particles)"""
2662 return _IMP_multifit.ProteomicsEMAlignmentAtomic_load_combination_of_states(self, state4particles)
2665 def show_scores_header(self, *args):
2667 show_scores_header(ProteomicsEMAlignmentAtomic self, _ostream ous)
2668 show_scores_header(ProteomicsEMAlignmentAtomic self)
2670 return _IMP_multifit.ProteomicsEMAlignmentAtomic_show_scores_header(self, *args)
2673 def get_model(self):
2674 """get_model(ProteomicsEMAlignmentAtomic self) -> Model"""
2675 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_model(self)
2678 def set_fast_scoring(self, state):
2679 """set_fast_scoring(ProteomicsEMAlignmentAtomic self, bool state)"""
2680 return _IMP_multifit.ProteomicsEMAlignmentAtomic_set_fast_scoring(self, state)
2683 def get_version_info(self):
2684 """get_version_info(ProteomicsEMAlignmentAtomic self) -> VersionInfo"""
2685 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_version_info(self)
2689 """__str__(ProteomicsEMAlignmentAtomic self) -> std::string"""
2690 return _IMP_multifit.ProteomicsEMAlignmentAtomic___str__(self)
2694 """__repr__(ProteomicsEMAlignmentAtomic self) -> std::string"""
2695 return _IMP_multifit.ProteomicsEMAlignmentAtomic___repr__(self)
2700 return _object_cast_to_ProteomicsEMAlignmentAtomic(o)
2702 ProteomicsEMAlignmentAtomic_swigregister = _IMP_multifit.ProteomicsEMAlignmentAtomic_swigregister
2703 ProteomicsEMAlignmentAtomic_swigregister(ProteomicsEMAlignmentAtomic)
2707 """write_connolly_surface(IMP::atom::Atoms atoms, TextOutput fn, float density, float probe_radius)"""
2708 return _IMP_multifit.write_connolly_surface(atoms, fn, density, probe_radius)
2710 """Proxy of C++ IMP::multifit::Ensemble class."""
2712 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2714 def load_combination(self, fit_comb):
2715 """load_combination(Ensemble self, IMP::Ints fit_comb)"""
2716 return _IMP_multifit.Ensemble_load_combination(self, fit_comb)
2719 def unload_combination(self, fit_comb):
2720 """unload_combination(Ensemble self, IMP::Ints fit_comb)"""
2721 return _IMP_multifit.Ensemble_unload_combination(self, fit_comb)
2724 def add_component_and_fits(self, mh, fits):
2725 """add_component_and_fits(Ensemble self, Hierarchy mh, IMP::multifit::FittingSolutionRecords const & fits)"""
2726 return _IMP_multifit.Ensemble_add_component_and_fits(self, mh, fits)
2729 def get_molecules(self):
2730 """get_molecules(Ensemble self) -> IMP::atom::Hierarchies"""
2731 return _IMP_multifit.Ensemble_get_molecules(self)
2734 def get_rigid_bodies(self):
2735 """get_rigid_bodies(Ensemble self) -> IMP::core::RigidBodies"""
2736 return _IMP_multifit.Ensemble_get_rigid_bodies(self)
2740 """get_rmsd(Ensemble self, IMP::core::XYZs const & second_xyz) -> float"""
2741 return _IMP_multifit.Ensemble_get_rmsd(self, second_xyz)
2744 def __init__(self, sd, mapping_data):
2745 """__init__(IMP::multifit::Ensemble self, SettingsData sd, ProteinsAnchorsSamplingSpace mapping_data) -> Ensemble"""
2746 this = _IMP_multifit.new_Ensemble(sd, mapping_data)
2748 self.this.append(this)
2749 except __builtin__.Exception:
2752 def score_by_restraints(self, rs, combinations):
2753 """score_by_restraints(Ensemble self, IMP::Restraints rs, IMP::IntsList const & combinations) -> std::vector< IMP::Floats,std::allocator< IMP::Floats > >"""
2754 return _IMP_multifit.Ensemble_score_by_restraints(self, rs, combinations)
2757 def get_version_info(self):
2758 """get_version_info(Ensemble self) -> VersionInfo"""
2759 return _IMP_multifit.Ensemble_get_version_info(self)
2763 """__str__(Ensemble self) -> std::string"""
2764 return _IMP_multifit.Ensemble___str__(self)
2768 """__repr__(Ensemble self) -> std::string"""
2769 return _IMP_multifit.Ensemble___repr__(self)
2774 return _object_cast_to_Ensemble(o)
2776 Ensemble_swigregister = _IMP_multifit.Ensemble_swigregister
2777 Ensemble_swigregister(Ensemble)
2780 def load_ensemble(sd, mdl, mapping_data):
2781 """load_ensemble(SettingsData sd, Model mdl, ProteinsAnchorsSamplingSpace mapping_data) -> Ensemble"""
2782 return _IMP_multifit.load_ensemble(sd, mdl, mapping_data)
2784 """Proxy of C++ IMP::multifit::RigidLeavesRefiner class."""
2786 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2790 __init__(IMP::multifit::RigidLeavesRefiner self, std::string name) -> RigidLeavesRefiner
2791 __init__(IMP::multifit::RigidLeavesRefiner self) -> RigidLeavesRefiner
2793 this = _IMP_multifit.new_RigidLeavesRefiner(*args)
2795 self.this.append(this)
2796 except __builtin__.Exception:
2799 def do_get_inputs(self, m, pis):
2800 """do_get_inputs(RigidLeavesRefiner self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2801 return _IMP_multifit.RigidLeavesRefiner_do_get_inputs(self, m, pis)
2804 def get_version_info(self):
2805 """get_version_info(RigidLeavesRefiner self) -> VersionInfo"""
2806 return _IMP_multifit.RigidLeavesRefiner_get_version_info(self)
2810 """__str__(RigidLeavesRefiner self) -> std::string"""
2811 return _IMP_multifit.RigidLeavesRefiner___str__(self)
2815 """__repr__(RigidLeavesRefiner self) -> std::string"""
2816 return _IMP_multifit.RigidLeavesRefiner___repr__(self)
2821 return _object_cast_to_RigidLeavesRefiner(o)
2823 RigidLeavesRefiner_swigregister = _IMP_multifit.RigidLeavesRefiner_swigregister
2824 RigidLeavesRefiner_swigregister(RigidLeavesRefiner)
2827 _all_commands = [
"param",
"anchors",
"fit_fft",
"cluster",
"add_fit_rmsd",
2828 "indexes",
"proteomics",
"align",
"models",
"transforms",
2829 "score",
"merge_tree",
"reference",
"refine_fft",
"segment"]
2832 def get_module_version():
2833 """get_module_version() -> std::string const"""
2834 return _IMP_multifit.get_module_version()
2837 """get_example_path(std::string fname) -> std::string"""
2838 return _IMP_multifit.get_example_path(fname)
2841 """get_data_path(std::string fname) -> std::string"""
2842 return _IMP_multifit.get_data_path(fname)
2844 from .
import _version_check
2845 _version_check.check_version(get_module_version())
2846 __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.