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
289 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CGAL_HAS_BOOST_FILESYSTEM
290 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
291 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CGAL_HAS_BOOST_RANDOM
292 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CGAL_HAS_BOOST_SYSTEM
293 IMPCGAL_SHOW_WARNINGS = _IMP_multifit.IMPCGAL_SHOW_WARNINGS
295 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_multifit.IMP_ALGEBRA_HAS_IMP_CGAL
296 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
297 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
298 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_RANDOM
299 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_SYSTEM
300 IMP_ALGEBRA_HAS_CGAL = _IMP_multifit.IMP_ALGEBRA_HAS_CGAL
301 IMP_ALGEBRA_HAS_ANN = _IMP_multifit.IMP_ALGEBRA_HAS_ANN
302 IMPALGEBRA_SHOW_WARNINGS = _IMP_multifit.IMPALGEBRA_SHOW_WARNINGS
304 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_multifit.IMP_DISPLAY_HAS_IMP_CGAL
305 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
306 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
307 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_RANDOM
308 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_SYSTEM
309 IMP_DISPLAY_HAS_CGAL = _IMP_multifit.IMP_DISPLAY_HAS_CGAL
310 IMPDISPLAY_SHOW_WARNINGS = _IMP_multifit.IMPDISPLAY_SHOW_WARNINGS
312 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
313 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
314 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
315 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
316 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
317 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_CGAL
318 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_HDF5
319 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_multifit.IMPSCOREFUNCTOR_SHOW_WARNINGS
321 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_multifit.IMP_STATISTICS_HAS_IMP_CGAL
322 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
323 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
324 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_RANDOM
325 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_SYSTEM
326 IMP_STATISTICS_HAS_CGAL = _IMP_multifit.IMP_STATISTICS_HAS_CGAL
327 IMPSTATISTICS_SHOW_WARNINGS = _IMP_multifit.IMPSTATISTICS_SHOW_WARNINGS
329 IMP_CORE_HAS_IMP_CGAL = _IMP_multifit.IMP_CORE_HAS_IMP_CGAL
330 IMP_CORE_HAS_IMP_KERNEL = _IMP_multifit.IMP_CORE_HAS_IMP_KERNEL
331 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CORE_HAS_BOOST_FILESYSTEM
332 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
333 IMP_CORE_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CORE_HAS_BOOST_RANDOM
334 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CORE_HAS_BOOST_SYSTEM
335 IMP_CORE_HAS_CGAL = _IMP_multifit.IMP_CORE_HAS_CGAL
336 IMP_CORE_HAS_HDF5 = _IMP_multifit.IMP_CORE_HAS_HDF5
337 IMPCORE_SHOW_WARNINGS = _IMP_multifit.IMPCORE_SHOW_WARNINGS
339 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_multifit.IMP_CONTAINER_HAS_IMP_ALGEBRA
340 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_multifit.IMP_CONTAINER_HAS_IMP_CGAL
341 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_multifit.IMP_CONTAINER_HAS_IMP_DISPLAY
342 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_multifit.IMP_CONTAINER_HAS_IMP_KERNEL
343 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
344 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
345 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
346 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_RANDOM
347 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_SYSTEM
348 IMP_CONTAINER_HAS_CGAL = _IMP_multifit.IMP_CONTAINER_HAS_CGAL
349 IMP_CONTAINER_HAS_HDF5 = _IMP_multifit.IMP_CONTAINER_HAS_HDF5
350 IMPCONTAINER_SHOW_WARNINGS = _IMP_multifit.IMPCONTAINER_SHOW_WARNINGS
352 IMP_ATOM_HAS_IMP_CGAL = _IMP_multifit.IMP_ATOM_HAS_IMP_CGAL
353 IMP_ATOM_HAS_IMP_KERNEL = _IMP_multifit.IMP_ATOM_HAS_IMP_KERNEL
354 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
355 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
356 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_multifit.IMP_ATOM_HAS_BOOST_RANDOM
357 IMP_ATOM_HAS_BOOST_REGEX = _IMP_multifit.IMP_ATOM_HAS_BOOST_REGEX
358 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_ATOM_HAS_BOOST_SYSTEM
359 IMP_ATOM_HAS_CGAL = _IMP_multifit.IMP_ATOM_HAS_CGAL
360 IMP_ATOM_HAS_HDF5 = _IMP_multifit.IMP_ATOM_HAS_HDF5
361 IMPATOM_SHOW_WARNINGS = _IMP_multifit.IMPATOM_SHOW_WARNINGS
362 IMP_ATOM_TYPE_INDEX = _IMP_multifit.IMP_ATOM_TYPE_INDEX
363 IMP_RESIDUE_TYPE_INDEX = _IMP_multifit.IMP_RESIDUE_TYPE_INDEX
364 IMP_HIERARCHY_TYPE_INDEX = _IMP_multifit.IMP_HIERARCHY_TYPE_INDEX
366 IMP_EM_HAS_IMP_CGAL = _IMP_multifit.IMP_EM_HAS_IMP_CGAL
367 IMP_EM_HAS_IMP_CONTAINER = _IMP_multifit.IMP_EM_HAS_IMP_CONTAINER
368 IMP_EM_HAS_IMP_DISPLAY = _IMP_multifit.IMP_EM_HAS_IMP_DISPLAY
369 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_EM_HAS_IMP_SCORE_FUNCTOR
370 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_EM_HAS_BOOST_FILESYSTEM
371 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
372 IMP_EM_HAS_BOOST_RANDOM = _IMP_multifit.IMP_EM_HAS_BOOST_RANDOM
373 IMP_EM_HAS_BOOST_REGEX = _IMP_multifit.IMP_EM_HAS_BOOST_REGEX
374 IMP_EM_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_EM_HAS_BOOST_SYSTEM
375 IMP_EM_HAS_CGAL = _IMP_multifit.IMP_EM_HAS_CGAL
376 IMP_EM_HAS_HDF5 = _IMP_multifit.IMP_EM_HAS_HDF5
377 IMPEM_SHOW_WARNINGS = _IMP_multifit.IMPEM_SHOW_WARNINGS
379 IMP_RMF_HAS_IMP_CGAL = _IMP_multifit.IMP_RMF_HAS_IMP_CGAL
380 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
381 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_RMF_HAS_BOOST_FILESYSTEM
382 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
383 IMP_RMF_HAS_BOOST_RANDOM = _IMP_multifit.IMP_RMF_HAS_BOOST_RANDOM
384 IMP_RMF_HAS_BOOST_REGEX = _IMP_multifit.IMP_RMF_HAS_BOOST_REGEX
385 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_RMF_HAS_BOOST_SYSTEM
386 IMP_RMF_HAS_CGAL = _IMP_multifit.IMP_RMF_HAS_CGAL
387 IMP_RMF_HAS_HDF5 = _IMP_multifit.IMP_RMF_HAS_HDF5
388 IMPRMF_SHOW_WARNINGS = _IMP_multifit.IMPRMF_SHOW_WARNINGS
391 IMP_DOMINO_HAS_IMP_ATOM = _IMP_multifit.IMP_DOMINO_HAS_IMP_ATOM
392 IMP_DOMINO_HAS_IMP_CGAL = _IMP_multifit.IMP_DOMINO_HAS_IMP_CGAL
393 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_multifit.IMP_DOMINO_HAS_IMP_KERNEL
394 IMP_DOMINO_HAS_IMP_RMF = _IMP_multifit.IMP_DOMINO_HAS_IMP_RMF
395 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
396 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_FILESYSTEM
397 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
398 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_RANDOM
399 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_multifit.IMP_DOMINO_HAS_BOOST_REGEX
400 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_SYSTEM
401 IMP_DOMINO_HAS_CGAL = _IMP_multifit.IMP_DOMINO_HAS_CGAL
402 IMP_DOMINO_HAS_HDF5 = _IMP_multifit.IMP_DOMINO_HAS_HDF5
403 IMP_DOMINO_HAS_RMF = _IMP_multifit.IMP_DOMINO_HAS_RMF
404 IMPDOMINO_SHOW_WARNINGS = _IMP_multifit.IMPDOMINO_SHOW_WARNINGS
407 IMP_MULTIFIT_HAS_IMP_CGAL = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_CGAL
408 IMP_MULTIFIT_HAS_IMP_CONTAINER = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_CONTAINER
409 IMP_MULTIFIT_HAS_IMP_DISPLAY = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_DISPLAY
410 IMP_MULTIFIT_HAS_IMP_KERNEL = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_KERNEL
411 IMP_MULTIFIT_HAS_IMP_RMF = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_RMF
412 IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR
413 IMP_MULTIFIT_HAS_BOOST_GRAPH = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_GRAPH
414 IMP_MULTIFIT_HAS_BOOST_RANDOM = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_RANDOM
415 IMP_MULTIFIT_HAS_BOOST_REGEX = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_REGEX
416 IMP_MULTIFIT_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_SYSTEM
417 IMP_MULTIFIT_HAS_CGAL = _IMP_multifit.IMP_MULTIFIT_HAS_CGAL
418 IMP_MULTIFIT_HAS_HDF5 = _IMP_multifit.IMP_MULTIFIT_HAS_HDF5
419 IMP_MULTIFIT_HAS_RMF = _IMP_multifit.IMP_MULTIFIT_HAS_RMF
420 IMPMULTIFIT_SHOW_WARNINGS = _IMP_multifit.IMPMULTIFIT_SHOW_WARNINGS
422 _object_types.append(
"RadiusOfGyrationRestraint")
425 def _object_cast_to_RadiusOfGyrationRestraint(o):
426 """_object_cast_to_RadiusOfGyrationRestraint(Object o) -> RadiusOfGyrationRestraint"""
427 return _IMP_multifit._object_cast_to_RadiusOfGyrationRestraint(o)
429 _object_types.append(
"ComponentHeader")
432 def _object_cast_to_ComponentHeader(o):
433 """_object_cast_to_ComponentHeader(Object o) -> ComponentHeader"""
434 return _IMP_multifit._object_cast_to_ComponentHeader(o)
436 _object_types.append(
"AssemblyHeader")
439 def _object_cast_to_AssemblyHeader(o):
440 """_object_cast_to_AssemblyHeader(Object o) -> AssemblyHeader"""
441 return _IMP_multifit._object_cast_to_AssemblyHeader(o)
443 _object_types.append(
"SettingsData")
446 def _object_cast_to_SettingsData(o):
447 """_object_cast_to_SettingsData(Object o) -> SettingsData"""
448 return _IMP_multifit._object_cast_to_SettingsData(o)
450 _object_types.append(
"WeightedExcludedVolumeRestraint")
453 def _object_cast_to_WeightedExcludedVolumeRestraint(o):
454 """_object_cast_to_WeightedExcludedVolumeRestraint(Object o) -> WeightedExcludedVolumeRestraint"""
455 return _IMP_multifit._object_cast_to_WeightedExcludedVolumeRestraint(o)
457 _object_types.append(
"ComplementarityRestraint")
460 def _object_cast_to_ComplementarityRestraint(o):
461 """_object_cast_to_ComplementarityRestraint(Object o) -> ComplementarityRestraint"""
462 return _IMP_multifit._object_cast_to_ComplementarityRestraint(o)
464 ProteinRecordDataList=list
465 _plural_types.append(
"ProteinRecordDataList")
466 _value_types.append(
"ProteinRecordData")
469 FittingSolutionRecords=list
470 _plural_types.append(
"FittingSolutionRecords")
471 _value_types.append(
"FittingSolutionRecord")
475 _plural_types.append(
"AnchorsDataList")
476 _value_types.append(
"AnchorsData")
479 DominoParamsList=list
480 _plural_types.append(
"DominoParamsList")
481 _value_types.append(
"DominoParams")
484 ComplementarityParamsList=list
485 _plural_types.append(
"ComplementarityParamsList")
486 _value_types.append(
"ComplementarityParams")
490 _plural_types.append(
"XlinkParamsList")
491 _value_types.append(
"XlinkParams")
494 ConnectivityParamsList=list
495 _plural_types.append(
"ConnectivityParamsList")
496 _value_types.append(
"ConnectivityParams")
499 FragmentsParamsList=list
500 _plural_types.append(
"FragmentsParamsList")
501 _value_types.append(
"FragmentsParams")
505 _plural_types.append(
"RogParamsList")
506 _value_types.append(
"RogParams")
510 _plural_types.append(
"EVParamsList")
511 _value_types.append(
"EVParams")
514 FiltersParamsList=list
515 _plural_types.append(
"FiltersParamsList")
516 _value_types.append(
"FiltersParams")
519 AlignmentParamsList=list
520 _plural_types.append(
"AlignmentParamsList")
521 _value_types.append(
"AlignmentParams")
524 FittingParamsList=list
525 _plural_types.append(
"FittingParamsList")
526 _value_types.append(
"FittingParams")
529 ProteinsAnchorsSamplingSpaces=list
530 _plural_types.append(
"ProteinsAnchorsSamplingSpaces")
531 _value_types.append(
"ProteinsAnchorsSamplingSpace")
534 _object_types.append(
"ProteomicsData")
537 def _object_cast_to_ProteomicsData(o):
538 """_object_cast_to_ProteomicsData(Object o) -> ProteomicsData"""
539 return _IMP_multifit._object_cast_to_ProteomicsData(o)
541 _object_types.append(
"FFTFitting")
544 def _object_cast_to_FFTFitting(o):
545 """_object_cast_to_FFTFitting(Object o) -> FFTFitting"""
546 return _IMP_multifit._object_cast_to_FFTFitting(o)
548 _object_types.append(
"FFTFittingOutput")
551 def _object_cast_to_FFTFittingOutput(o):
552 """_object_cast_to_FFTFittingOutput(Object o) -> FFTFittingOutput"""
553 return _IMP_multifit._object_cast_to_FFTFittingOutput(o)
555 _object_types.append(
"ProbabilisticAnchorGraph")
558 def _object_cast_to_ProbabilisticAnchorGraph(o):
559 """_object_cast_to_ProbabilisticAnchorGraph(Object o) -> ProbabilisticAnchorGraph"""
560 return _IMP_multifit._object_cast_to_ProbabilisticAnchorGraph(o)
562 _object_types.append(
"Ensemble")
565 def _object_cast_to_Ensemble(o):
566 """_object_cast_to_Ensemble(Object o) -> Ensemble"""
567 return _IMP_multifit._object_cast_to_Ensemble(o)
569 _object_types.append(
"ProteomicsEMAlignmentAtomic")
572 def _object_cast_to_ProteomicsEMAlignmentAtomic(o):
573 """_object_cast_to_ProteomicsEMAlignmentAtomic(Object o) -> ProteomicsEMAlignmentAtomic"""
574 return _IMP_multifit._object_cast_to_ProteomicsEMAlignmentAtomic(o)
576 _object_types.append(
"RigidLeavesRefiner")
579 def _object_cast_to_RigidLeavesRefiner(o):
580 """_object_cast_to_RigidLeavesRefiner(Object o) -> RigidLeavesRefiner"""
581 return _IMP_multifit._object_cast_to_RigidLeavesRefiner(o)
585 add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key, FloatKey radius_key, FloatKey weight_key)
586 add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key, FloatKey radius_key)
587 add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key)
588 add_surface_index(Hierarchy mhd, IMP::Float apix)
590 return _IMP_multifit.add_surface_index(*args)
594 create_weighted_excluded_volume_restraint(RigidBody rb1, RigidBody rb2, FloatKey shell_key) -> Restraint
595 create_weighted_excluded_volume_restraint(RigidBody rb1, RigidBody rb2) -> Restraint
597 return _IMP_multifit.create_weighted_excluded_volume_restraint(*args)
598 class FittingSolutionRecord(object):
599 """Proxy of C++ IMP::multifit::FittingSolutionRecord class."""
601 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
604 """__init__(IMP::multifit::FittingSolutionRecord self) -> FittingSolutionRecord"""
605 this = _IMP_multifit.new_FittingSolutionRecord()
607 self.this.append(this)
608 except __builtin__.Exception:
612 """get_index(FittingSolutionRecord self) -> unsigned int"""
613 return _IMP_multifit.FittingSolutionRecord_get_index(self)
616 def set_index(self, new_ind):
617 """set_index(FittingSolutionRecord self, unsigned int new_ind)"""
618 return _IMP_multifit.FittingSolutionRecord_set_index(self, new_ind)
621 def get_solution_filename(self):
622 """get_solution_filename(FittingSolutionRecord self) -> std::string"""
623 return _IMP_multifit.FittingSolutionRecord_get_solution_filename(self)
626 def set_solution_filename(self, sol_fn):
627 """set_solution_filename(FittingSolutionRecord self, std::string sol_fn)"""
628 return _IMP_multifit.FittingSolutionRecord_set_solution_filename(self, sol_fn)
631 def get_fit_transformation(self):
632 """get_fit_transformation(FittingSolutionRecord self) -> Transformation3D"""
633 return _IMP_multifit.FittingSolutionRecord_get_fit_transformation(self)
636 def set_fit_transformation(self, t):
637 """set_fit_transformation(FittingSolutionRecord self, Transformation3D t)"""
638 return _IMP_multifit.FittingSolutionRecord_set_fit_transformation(self, t)
641 def get_match_size(self):
642 """get_match_size(FittingSolutionRecord self) -> unsigned int"""
643 return _IMP_multifit.FittingSolutionRecord_get_match_size(self)
646 def set_match_size(self, match_size):
647 """set_match_size(FittingSolutionRecord self, unsigned int match_size)"""
648 return _IMP_multifit.FittingSolutionRecord_set_match_size(self, match_size)
651 def get_match_average_distance(self):
652 """get_match_average_distance(FittingSolutionRecord self) -> IMP::Float"""
653 return _IMP_multifit.FittingSolutionRecord_get_match_average_distance(self)
656 def set_match_average_distance(self, match_avg_dist):
657 """set_match_average_distance(FittingSolutionRecord self, IMP::Float match_avg_dist)"""
658 return _IMP_multifit.FittingSolutionRecord_set_match_average_distance(self, match_avg_dist)
661 def get_fitting_score(self):
662 """get_fitting_score(FittingSolutionRecord self) -> IMP::Float"""
663 return _IMP_multifit.FittingSolutionRecord_get_fitting_score(self)
666 def set_fitting_score(self, fit_score):
667 """set_fitting_score(FittingSolutionRecord self, IMP::Float fit_score)"""
668 return _IMP_multifit.FittingSolutionRecord_set_fitting_score(self, fit_score)
671 def get_rmsd_to_reference(self):
672 """get_rmsd_to_reference(FittingSolutionRecord self) -> IMP::Float"""
673 return _IMP_multifit.FittingSolutionRecord_get_rmsd_to_reference(self)
676 def set_rmsd_to_reference(self, rmsd_to_ref):
677 """set_rmsd_to_reference(FittingSolutionRecord self, IMP::Float rmsd_to_ref)"""
678 return _IMP_multifit.FittingSolutionRecord_set_rmsd_to_reference(self, rmsd_to_ref)
681 def get_dock_transformation(self):
682 """get_dock_transformation(FittingSolutionRecord self) -> Transformation3D"""
683 return _IMP_multifit.FittingSolutionRecord_get_dock_transformation(self)
686 def set_dock_transformation(self, t):
687 """set_dock_transformation(FittingSolutionRecord self, Transformation3D t)"""
688 return _IMP_multifit.FittingSolutionRecord_set_dock_transformation(self, t)
691 def get_envelope_penetration_score(self):
692 """get_envelope_penetration_score(FittingSolutionRecord self) -> IMP::Float"""
693 return _IMP_multifit.FittingSolutionRecord_get_envelope_penetration_score(self)
696 def set_envelope_penetration_score(self, s):
697 """set_envelope_penetration_score(FittingSolutionRecord self, IMP::Float s)"""
698 return _IMP_multifit.FittingSolutionRecord_set_envelope_penetration_score(self, s)
701 def show(self, *args):
703 show(FittingSolutionRecord self, _ostream out)
704 show(FittingSolutionRecord self)
706 return _IMP_multifit.FittingSolutionRecord_show(self, *args)
709 def get_record_header():
710 """get_record_header() -> std::string"""
711 return _IMP_multifit.FittingSolutionRecord_get_record_header()
713 get_record_header = staticmethod(get_record_header)
716 """__str__(FittingSolutionRecord self) -> std::string"""
717 return _IMP_multifit.FittingSolutionRecord___str__(self)
721 """__repr__(FittingSolutionRecord self) -> std::string"""
722 return _IMP_multifit.FittingSolutionRecord___repr__(self)
724 __swig_destroy__ = _IMP_multifit.delete_FittingSolutionRecord
725 __del__ =
lambda self:
None
726 FittingSolutionRecord_swigregister = _IMP_multifit.FittingSolutionRecord_swigregister
727 FittingSolutionRecord_swigregister(FittingSolutionRecord)
729 def FittingSolutionRecord_get_record_header():
730 """FittingSolutionRecord_get_record_header() -> std::string"""
731 return _IMP_multifit.FittingSolutionRecord_get_record_header()
736 pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold, FloatKey wei_key, PrincipalComponentAnalysis3D dens_pca_input) -> FittingSolutions
737 pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold, FloatKey wei_key) -> FittingSolutions
738 pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold) -> FittingSolutions
739 pca_based_rigid_fitting(IMP::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold, FloatKey wei_key, PrincipalComponentAnalysis3D dens_pca_input) -> FittingSolutions
740 pca_based_rigid_fitting(IMP::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold, FloatKey wei_key) -> FittingSolutions
741 pca_based_rigid_fitting(IMP::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold) -> FittingSolutions
743 return _IMP_multifit.pca_based_rigid_fitting(*args)
745 def write_markers(pca, out):
746 """write_markers(PrincipalComponentAnalysis3D pca, _ostream out)"""
747 return _IMP_multifit.write_markers(pca, out)
749 """Proxy of C++ IMP::multifit::ComponentHeader class."""
751 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
754 """__init__(IMP::multifit::ComponentHeader self) -> ComponentHeader"""
755 this = _IMP_multifit.new_ComponentHeader()
757 self.this.append(this)
758 except __builtin__.Exception:
761 def set_name(self, name):
762 """set_name(ComponentHeader self, std::string const & name)"""
763 return _IMP_multifit.ComponentHeader_set_name(self, name)
767 """get_name(ComponentHeader self) -> std::string"""
768 return _IMP_multifit.ComponentHeader_get_name(self)
771 def get_filename(self):
772 """get_filename(ComponentHeader self) -> std::string"""
773 return _IMP_multifit.ComponentHeader_get_filename(self)
776 def set_filename(self, filename):
777 """set_filename(ComponentHeader self, std::string const & filename)"""
778 return _IMP_multifit.ComponentHeader_set_filename(self, filename)
781 def get_surface_fn(self):
782 """get_surface_fn(ComponentHeader self) -> std::string"""
783 return _IMP_multifit.ComponentHeader_get_surface_fn(self)
786 def set_surface_fn(self, fn):
787 """set_surface_fn(ComponentHeader self, std::string const & fn)"""
788 return _IMP_multifit.ComponentHeader_set_surface_fn(self, fn)
791 def set_txt_ap_fn(self, pdb_ap_fn):
792 """set_txt_ap_fn(ComponentHeader self, std::string const & pdb_ap_fn)"""
793 return _IMP_multifit.ComponentHeader_set_txt_ap_fn(self, pdb_ap_fn)
796 def get_txt_ap_fn(self):
797 """get_txt_ap_fn(ComponentHeader self) -> std::string"""
798 return _IMP_multifit.ComponentHeader_get_txt_ap_fn(self)
801 def set_txt_fine_ap_fn(self, pdb_ap_fn):
802 """set_txt_fine_ap_fn(ComponentHeader self, std::string const & pdb_ap_fn)"""
803 return _IMP_multifit.ComponentHeader_set_txt_fine_ap_fn(self, pdb_ap_fn)
806 def get_txt_fine_ap_fn(self):
807 """get_txt_fine_ap_fn(ComponentHeader self) -> std::string"""
808 return _IMP_multifit.ComponentHeader_get_txt_fine_ap_fn(self)
811 def set_num_ap(self, num_ap):
812 """set_num_ap(ComponentHeader self, int num_ap)"""
813 return _IMP_multifit.ComponentHeader_set_num_ap(self, num_ap)
816 def get_num_ap(self):
817 """get_num_ap(ComponentHeader self) -> int"""
818 return _IMP_multifit.ComponentHeader_get_num_ap(self)
821 def set_num_fine_ap(self, num_ap):
822 """set_num_fine_ap(ComponentHeader self, int num_ap)"""
823 return _IMP_multifit.ComponentHeader_set_num_fine_ap(self, num_ap)
826 def get_num_fine_ap(self):
827 """get_num_fine_ap(ComponentHeader self) -> int"""
828 return _IMP_multifit.ComponentHeader_get_num_fine_ap(self)
831 def set_transformations_fn(self, transformations_fn):
832 """set_transformations_fn(ComponentHeader self, std::string transformations_fn)"""
833 return _IMP_multifit.ComponentHeader_set_transformations_fn(self, transformations_fn)
836 def get_transformations_fn(self):
837 """get_transformations_fn(ComponentHeader self) -> std::string"""
838 return _IMP_multifit.ComponentHeader_get_transformations_fn(self)
841 def set_reference_fn(self, ref_fn):
842 """set_reference_fn(ComponentHeader self, std::string const & ref_fn)"""
843 return _IMP_multifit.ComponentHeader_set_reference_fn(self, ref_fn)
846 def get_reference_fn(self):
847 """get_reference_fn(ComponentHeader self) -> std::string"""
848 return _IMP_multifit.ComponentHeader_get_reference_fn(self)
851 def get_version_info(self):
852 """get_version_info(ComponentHeader self) -> VersionInfo"""
853 return _IMP_multifit.ComponentHeader_get_version_info(self)
857 """__str__(ComponentHeader self) -> std::string"""
858 return _IMP_multifit.ComponentHeader___str__(self)
862 """__repr__(ComponentHeader self) -> std::string"""
863 return _IMP_multifit.ComponentHeader___repr__(self)
868 return _object_cast_to_ComponentHeader(o)
870 ComponentHeader_swigregister = _IMP_multifit.ComponentHeader_swigregister
871 ComponentHeader_swigregister(ComponentHeader)
874 """Proxy of C++ IMP::multifit::AssemblyHeader class."""
876 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
879 """__init__(IMP::multifit::AssemblyHeader self) -> AssemblyHeader"""
880 this = _IMP_multifit.new_AssemblyHeader()
882 self.this.append(this)
883 except __builtin__.Exception:
886 def set_dens_fn(self, dens_fn):
887 """set_dens_fn(AssemblyHeader self, std::string const & dens_fn)"""
888 return _IMP_multifit.AssemblyHeader_set_dens_fn(self, dens_fn)
891 def get_dens_fn(self):
892 """get_dens_fn(AssemblyHeader self) -> std::string"""
893 return _IMP_multifit.AssemblyHeader_get_dens_fn(self)
896 def set_resolution(self, res):
897 """set_resolution(AssemblyHeader self, float res)"""
898 return _IMP_multifit.AssemblyHeader_set_resolution(self, res)
902 """get_resolution(AssemblyHeader self) -> float"""
903 return _IMP_multifit.AssemblyHeader_get_resolution(self)
906 def get_spacing(self):
907 """get_spacing(AssemblyHeader self) -> float"""
908 return _IMP_multifit.AssemblyHeader_get_spacing(self)
911 def set_spacing(self, spacing):
912 """set_spacing(AssemblyHeader self, float spacing)"""
913 return _IMP_multifit.AssemblyHeader_set_spacing(self, spacing)
916 def set_threshold(self, t):
917 """set_threshold(AssemblyHeader self, float t)"""
918 return _IMP_multifit.AssemblyHeader_set_threshold(self, t)
921 def get_threshold(self):
922 """get_threshold(AssemblyHeader self) -> float"""
923 return _IMP_multifit.AssemblyHeader_get_threshold(self)
926 def get_origin(self):
927 """get_origin(AssemblyHeader self) -> Vector3D"""
928 return _IMP_multifit.AssemblyHeader_get_origin(self)
931 def set_origin(self, origin):
932 """set_origin(AssemblyHeader self, Vector3D origin)"""
933 return _IMP_multifit.AssemblyHeader_set_origin(self, origin)
936 def get_coarse_ap_fn(self):
937 """get_coarse_ap_fn(AssemblyHeader self) -> std::string"""
938 return _IMP_multifit.AssemblyHeader_get_coarse_ap_fn(self)
941 def set_coarse_ap_fn(self, new_fn):
942 """set_coarse_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
943 return _IMP_multifit.AssemblyHeader_set_coarse_ap_fn(self, new_fn)
946 def get_coarse_over_sampled_ap_fn(self):
947 """get_coarse_over_sampled_ap_fn(AssemblyHeader self) -> std::string"""
948 return _IMP_multifit.AssemblyHeader_get_coarse_over_sampled_ap_fn(self)
951 def set_coarse_over_sampled_ap_fn(self, new_fn):
952 """set_coarse_over_sampled_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
953 return _IMP_multifit.AssemblyHeader_set_coarse_over_sampled_ap_fn(self, new_fn)
956 def get_fine_ap_fn(self):
957 """get_fine_ap_fn(AssemblyHeader self) -> std::string"""
958 return _IMP_multifit.AssemblyHeader_get_fine_ap_fn(self)
961 def set_fine_ap_fn(self, new_fn):
962 """set_fine_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
963 return _IMP_multifit.AssemblyHeader_set_fine_ap_fn(self, new_fn)
966 def get_fine_over_sampled_ap_fn(self):
967 """get_fine_over_sampled_ap_fn(AssemblyHeader self) -> std::string"""
968 return _IMP_multifit.AssemblyHeader_get_fine_over_sampled_ap_fn(self)
971 def set_fine_over_sampled_ap_fn(self, new_fn):
972 """set_fine_over_sampled_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
973 return _IMP_multifit.AssemblyHeader_set_fine_over_sampled_ap_fn(self, new_fn)
976 def get_version_info(self):
977 """get_version_info(AssemblyHeader self) -> VersionInfo"""
978 return _IMP_multifit.AssemblyHeader_get_version_info(self)
982 """__str__(AssemblyHeader self) -> std::string"""
983 return _IMP_multifit.AssemblyHeader___str__(self)
987 """__repr__(AssemblyHeader self) -> std::string"""
988 return _IMP_multifit.AssemblyHeader___repr__(self)
993 return _object_cast_to_AssemblyHeader(o)
995 AssemblyHeader_swigregister = _IMP_multifit.AssemblyHeader_swigregister
996 AssemblyHeader_swigregister(AssemblyHeader)
999 """Proxy of C++ IMP::multifit::SettingsData class."""
1001 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1004 """__init__(IMP::multifit::SettingsData self) -> SettingsData"""
1005 this = _IMP_multifit.new_SettingsData()
1007 self.this.append(this)
1008 except __builtin__.Exception:
1011 def show_component_header_line(*args):
1013 show_component_header_line(_ostream out)
1014 show_component_header_line()
1016 return _IMP_multifit.SettingsData_show_component_header_line(*args)
1018 show_component_header_line = staticmethod(show_component_header_line)
1020 def get_component_header_line():
1021 """get_component_header_line() -> std::string"""
1022 return _IMP_multifit.SettingsData_get_component_header_line()
1024 get_component_header_line = staticmethod(get_component_header_line)
1026 def show_density_header_line(*args):
1028 show_density_header_line(_ostream out)
1029 show_density_header_line()
1031 return _IMP_multifit.SettingsData_show_density_header_line(*args)
1033 show_density_header_line = staticmethod(show_density_header_line)
1035 def get_density_header_line():
1036 """get_density_header_line() -> std::string"""
1037 return _IMP_multifit.SettingsData_get_density_header_line()
1039 get_density_header_line = staticmethod(get_density_header_line)
1041 def set_assembly_filename(self, fn):
1042 """set_assembly_filename(SettingsData self, std::string const & fn)"""
1043 return _IMP_multifit.SettingsData_set_assembly_filename(self, fn)
1046 def get_assembly_filename(self):
1047 """get_assembly_filename(SettingsData self) -> char const *"""
1048 return _IMP_multifit.SettingsData_get_assembly_filename(self)
1051 def set_assembly_header(self, h):
1052 """set_assembly_header(SettingsData self, AssemblyHeader h)"""
1053 return _IMP_multifit.SettingsData_set_assembly_header(self, h)
1056 def get_assembly_header(self):
1057 """get_assembly_header(SettingsData self) -> AssemblyHeader"""
1058 return _IMP_multifit.SettingsData_get_assembly_header(self)
1061 def set_data_path(self, fn):
1062 """set_data_path(SettingsData self, std::string const & fn)"""
1063 return _IMP_multifit.SettingsData_set_data_path(self, fn)
1067 """get_data_path(SettingsData self) -> std::string"""
1068 return _IMP_multifit.SettingsData_get_data_path(self)
1071 def get_version_info(self):
1072 """get_version_info(SettingsData self) -> VersionInfo"""
1073 return _IMP_multifit.SettingsData_get_version_info(self)
1076 def remove_component_header(self, d):
1077 """remove_component_header(SettingsData self, ComponentHeader d)"""
1078 return _IMP_multifit.SettingsData_remove_component_header(self, d)
1081 def remove_component_headers(self, d):
1082 """remove_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & d)"""
1083 return _IMP_multifit.SettingsData_remove_component_headers(self, d)
1086 def set_component_headers(self, ps):
1087 """set_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & ps)"""
1088 return _IMP_multifit.SettingsData_set_component_headers(self, ps)
1091 def set_component_headers_order(self, objs):
1092 """set_component_headers_order(SettingsData self, IMP::multifit::ComponentHeaders const & objs)"""
1093 return _IMP_multifit.SettingsData_set_component_headers_order(self, objs)
1096 def add_component_header(self, obj):
1097 """add_component_header(SettingsData self, ComponentHeader obj) -> unsigned int"""
1098 return _IMP_multifit.SettingsData_add_component_header(self, obj)
1101 def add_component_headers(self, objs):
1102 """add_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & objs)"""
1103 return _IMP_multifit.SettingsData_add_component_headers(self, objs)
1106 def clear_component_headers(self):
1107 """clear_component_headers(SettingsData self)"""
1108 return _IMP_multifit.SettingsData_clear_component_headers(self)
1111 def get_number_of_component_headers(self):
1112 """get_number_of_component_headers(SettingsData self) -> unsigned int"""
1113 return _IMP_multifit.SettingsData_get_number_of_component_headers(self)
1116 def get_has_component_headers(self):
1117 """get_has_component_headers(SettingsData self) -> bool"""
1118 return _IMP_multifit.SettingsData_get_has_component_headers(self)
1121 def get_component_header(self, i):
1122 """get_component_header(SettingsData self, unsigned int i) -> ComponentHeader"""
1123 return _IMP_multifit.SettingsData_get_component_header(self, i)
1126 def get_component_headers(self):
1127 """get_component_headers(SettingsData self) -> IMP::multifit::ComponentHeaders"""
1128 return _IMP_multifit.SettingsData_get_component_headers(self)
1131 def reserve_component_headers(self, sz):
1132 """reserve_component_headers(SettingsData self, unsigned int sz)"""
1133 return _IMP_multifit.SettingsData_reserve_component_headers(self, sz)
1137 """__str__(SettingsData self) -> std::string"""
1138 return _IMP_multifit.SettingsData___str__(self)
1142 """__repr__(SettingsData self) -> std::string"""
1143 return _IMP_multifit.SettingsData___repr__(self)
1148 return _object_cast_to_SettingsData(o)
1150 SettingsData_swigregister = _IMP_multifit.SettingsData_swigregister
1151 SettingsData_swigregister(SettingsData)
1153 def SettingsData_show_component_header_line(*args):
1155 show_component_header_line(_ostream out)
1156 SettingsData_show_component_header_line()
1158 return _IMP_multifit.SettingsData_show_component_header_line(*args)
1160 def SettingsData_get_component_header_line():
1161 """SettingsData_get_component_header_line() -> std::string"""
1162 return _IMP_multifit.SettingsData_get_component_header_line()
1164 def SettingsData_show_density_header_line(*args):
1166 show_density_header_line(_ostream out)
1167 SettingsData_show_density_header_line()
1169 return _IMP_multifit.SettingsData_show_density_header_line(*args)
1171 def SettingsData_get_density_header_line():
1172 """SettingsData_get_density_header_line() -> std::string"""
1173 return _IMP_multifit.SettingsData_get_density_header_line()
1176 def read_settings(filename):
1177 """read_settings(char const * filename) -> SettingsData"""
1178 return _IMP_multifit.read_settings(filename)
1180 def write_settings(filename, sd):
1181 """write_settings(char const * filename, SettingsData sd)"""
1182 return _IMP_multifit.write_settings(filename, sd)
1184 """Proxy of C++ IMP::multifit::WeightedExcludedVolumeRestraint class."""
1186 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1190 __init__(IMP::multifit::WeightedExcludedVolumeRestraint self, IMP::core::RigidBodies rbs, Refiner refiner, FloatKey weight_key) -> WeightedExcludedVolumeRestraint
1191 __init__(IMP::multifit::WeightedExcludedVolumeRestraint self, IMP::core::RigidBodies rbs, Refiner refiner) -> WeightedExcludedVolumeRestraint
1193 this = _IMP_multifit.new_WeightedExcludedVolumeRestraint(*args)
1195 self.this.append(this)
1196 except __builtin__.Exception:
1199 def do_get_inputs(self):
1200 """do_get_inputs(WeightedExcludedVolumeRestraint self) -> IMP::ModelObjectsTemp"""
1201 return _IMP_multifit.WeightedExcludedVolumeRestraint_do_get_inputs(self)
1204 def get_version_info(self):
1205 """get_version_info(WeightedExcludedVolumeRestraint self) -> VersionInfo"""
1206 return _IMP_multifit.WeightedExcludedVolumeRestraint_get_version_info(self)
1210 """__str__(WeightedExcludedVolumeRestraint self) -> std::string"""
1211 return _IMP_multifit.WeightedExcludedVolumeRestraint___str__(self)
1215 """__repr__(WeightedExcludedVolumeRestraint self) -> std::string"""
1216 return _IMP_multifit.WeightedExcludedVolumeRestraint___repr__(self)
1221 return _object_cast_to_WeightedExcludedVolumeRestraint(o)
1223 WeightedExcludedVolumeRestraint_swigregister = _IMP_multifit.WeightedExcludedVolumeRestraint_swigregister
1224 WeightedExcludedVolumeRestraint_swigregister(WeightedExcludedVolumeRestraint)
1227 """Proxy of C++ IMP::multifit::FFTFittingOutput class."""
1229 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1232 """__init__(IMP::multifit::FFTFittingOutput self) -> FFTFittingOutput"""
1233 this = _IMP_multifit.new_FFTFittingOutput()
1235 self.this.append(this)
1236 except __builtin__.Exception:
1239 def get_version_info(self):
1240 """get_version_info(FFTFittingOutput self) -> VersionInfo"""
1241 return _IMP_multifit.FFTFittingOutput_get_version_info(self)
1243 best_fits_ = _swig_property(_IMP_multifit.FFTFittingOutput_best_fits__get, _IMP_multifit.FFTFittingOutput_best_fits__set)
1244 best_trans_per_rot_ = _swig_property(_IMP_multifit.FFTFittingOutput_best_trans_per_rot__get, _IMP_multifit.FFTFittingOutput_best_trans_per_rot__set)
1247 """__str__(FFTFittingOutput self) -> std::string"""
1248 return _IMP_multifit.FFTFittingOutput___str__(self)
1252 """__repr__(FFTFittingOutput self) -> std::string"""
1253 return _IMP_multifit.FFTFittingOutput___repr__(self)
1258 return _object_cast_to_FFTFittingOutput(o)
1260 FFTFittingOutput_swigregister = _IMP_multifit.FFTFittingOutput_swigregister
1261 FFTFittingOutput_swigregister(FFTFittingOutput)
1264 """Proxy of C++ IMP::multifit::FFTFitting class."""
1266 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1268 def get_version_info(self):
1269 """get_version_info(FFTFitting self) -> VersionInfo"""
1270 return _IMP_multifit.FFTFitting_get_version_info(self)
1274 """__init__(IMP::multifit::FFTFitting self) -> FFTFitting"""
1275 this = _IMP_multifit.new_FFTFitting()
1277 self.this.append(this)
1278 except __builtin__.Exception:
1281 def do_global_fitting(self, *args):
1283 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
1284 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
1285 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
1286 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
1288 return _IMP_multifit.FFTFitting_do_global_fitting(self, *args)
1291 def do_local_fitting(self, *args):
1293 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
1294 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
1296 return _IMP_multifit.FFTFitting_do_local_fitting(self, *args)
1300 """__str__(FFTFitting self) -> std::string"""
1301 return _IMP_multifit.FFTFitting___str__(self)
1305 """__repr__(FFTFitting self) -> std::string"""
1306 return _IMP_multifit.FFTFitting___repr__(self)
1311 return _object_cast_to_FFTFitting(o)
1313 FFTFitting_swigregister = _IMP_multifit.FFTFitting_swigregister
1314 FFTFitting_swigregister(FFTFitting)
1318 """fft_based_rigid_fitting(Hierarchy mol2fit, DensityMap dmap, double density_threshold, double angle_sampling_interval_rad) -> IMP::multifit::FittingSolutionRecords"""
1319 return _IMP_multifit.fft_based_rigid_fitting(mol2fit, dmap, density_threshold, angle_sampling_interval_rad)
1322 """remove_background(DensityMap dmap, float threshold, float edge_threshold) -> DensityMap"""
1323 return _IMP_multifit.remove_background(dmap, threshold, edge_threshold)
1326 """get_connected_components(DensityMap dmap, float threshold, float edge_threshold) -> IMP::IntsList"""
1327 return _IMP_multifit.get_connected_components(dmap, threshold, edge_threshold)
1329 def get_segmentation(dmap, apix, density_threshold, num_means, pdb_filename, cmm_filename, seg_filename, txt_filename):
1330 """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)"""
1331 return _IMP_multifit.get_segmentation(dmap, apix, density_threshold, num_means, pdb_filename, cmm_filename, seg_filename, txt_filename)
1333 """Proxy of C++ IMP::multifit::ComplementarityRestraint class."""
1335 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1339 __init__(IMP::multifit::ComplementarityRestraint self, IMP::ParticlesTemp const & a, IMP::ParticlesTemp const & b, std::string name) -> ComplementarityRestraint
1340 __init__(IMP::multifit::ComplementarityRestraint self, IMP::ParticlesTemp const & a, IMP::ParticlesTemp const & b) -> ComplementarityRestraint
1342 this = _IMP_multifit.new_ComplementarityRestraint(*args)
1344 self.this.append(this)
1345 except __builtin__.Exception:
1348 def set_maximum_penetration_score(self, s):
1349 """set_maximum_penetration_score(ComplementarityRestraint self, double s)"""
1350 return _IMP_multifit.ComplementarityRestraint_set_maximum_penetration_score(self, s)
1353 def set_maximum_penetration(self, d):
1354 """set_maximum_penetration(ComplementarityRestraint self, double d)"""
1355 return _IMP_multifit.ComplementarityRestraint_set_maximum_penetration(self, d)
1358 def set_maximum_separation(self, s):
1359 """set_maximum_separation(ComplementarityRestraint self, double s)"""
1360 return _IMP_multifit.ComplementarityRestraint_set_maximum_separation(self, s)
1363 def set_complementarity_thickness(self, th):
1364 """set_complementarity_thickness(ComplementarityRestraint self, double th)"""
1365 return _IMP_multifit.ComplementarityRestraint_set_complementarity_thickness(self, th)
1368 def set_complementarity_value(self, th):
1369 """set_complementarity_value(ComplementarityRestraint self, double th)"""
1370 return _IMP_multifit.ComplementarityRestraint_set_complementarity_value(self, th)
1373 def set_interior_layer_thickness(self, th):
1374 """set_interior_layer_thickness(ComplementarityRestraint self, double th)"""
1375 return _IMP_multifit.ComplementarityRestraint_set_interior_layer_thickness(self, th)
1378 def set_penetration_coefficient(self, pc):
1379 """set_penetration_coefficient(ComplementarityRestraint self, double pc)"""
1380 return _IMP_multifit.ComplementarityRestraint_set_penetration_coefficient(self, pc)
1383 def set_complementarity_coefficient(self, cc):
1384 """set_complementarity_coefficient(ComplementarityRestraint self, double cc)"""
1385 return _IMP_multifit.ComplementarityRestraint_set_complementarity_coefficient(self, cc)
1388 def set_boundary_coefficient(self, bc):
1389 """set_boundary_coefficient(ComplementarityRestraint self, double bc)"""
1390 return _IMP_multifit.ComplementarityRestraint_set_boundary_coefficient(self, bc)
1393 def get_voxel_size(self):
1394 """get_voxel_size(ComplementarityRestraint self) -> float"""
1395 return _IMP_multifit.ComplementarityRestraint_get_voxel_size(self)
1398 def do_get_inputs(self):
1399 """do_get_inputs(ComplementarityRestraint self) -> IMP::ModelObjectsTemp"""
1400 return _IMP_multifit.ComplementarityRestraint_do_get_inputs(self)
1403 def get_version_info(self):
1404 """get_version_info(ComplementarityRestraint self) -> VersionInfo"""
1405 return _IMP_multifit.ComplementarityRestraint_get_version_info(self)
1409 """__str__(ComplementarityRestraint self) -> std::string"""
1410 return _IMP_multifit.ComplementarityRestraint___str__(self)
1414 """__repr__(ComplementarityRestraint self) -> std::string"""
1415 return _IMP_multifit.ComplementarityRestraint___repr__(self)
1420 return _object_cast_to_ComplementarityRestraint(o)
1422 ComplementarityRestraint_swigregister = _IMP_multifit.ComplementarityRestraint_swigregister
1423 ComplementarityRestraint_swigregister(ComplementarityRestraint)
1427 """read_fitting_solutions(char const * fitting_fn) -> IMP::multifit::FittingSolutionRecords"""
1428 return _IMP_multifit.read_fitting_solutions(fitting_fn)
1432 write_fitting_solutions(char const * fitting_fn, IMP::multifit::FittingSolutionRecords const & fit_sols, int num_sols=-1)
1433 write_fitting_solutions(char const * fitting_fn, IMP::multifit::FittingSolutionRecords const & fit_sols)
1435 return _IMP_multifit.write_fitting_solutions(fitting_fn, fit_sols, num_sols)
1437 def convert_em_to_multifit_format(em_fits):
1438 """convert_em_to_multifit_format(FittingSolutions em_fits) -> IMP::multifit::FittingSolutionRecords"""
1439 return _IMP_multifit.convert_em_to_multifit_format(em_fits)
1441 def convert_multifit_to_em_format(multifit_fits):
1442 """convert_multifit_to_em_format(IMP::multifit::FittingSolutionRecords const & multifit_fits) -> FittingSolutions"""
1443 return _IMP_multifit.convert_multifit_to_em_format(multifit_fits)
1445 def convert_transformations_to_multifit_format(trans):
1446 """convert_transformations_to_multifit_format(IMP::algebra::Transformation3Ds const & trans) -> IMP::multifit::FittingSolutionRecords"""
1447 return _IMP_multifit.convert_transformations_to_multifit_format(trans)
1449 def convert_multifit_format_to_transformations(recs):
1450 """convert_multifit_format_to_transformations(IMP::multifit::FittingSolutionRecords const & recs) -> IMP::algebra::Transformation3Ds"""
1451 return _IMP_multifit.convert_multifit_format_to_transformations(recs)
1454 """get_close_to_point(IMP::multifit::FittingSolutionRecords const & fit_sols, Hierarchy mh, Particle ap, IMP::Float dist) -> IMP::multifit::FittingSolutionRecords"""
1455 return _IMP_multifit.get_close_to_point(fit_sols, mh, ap, dist)
1457 """Proxy of C++ IMP::multifit::ProbabilisticAnchorGraph class."""
1459 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1461 def __init__(self, anchor_positions):
1462 """__init__(IMP::multifit::ProbabilisticAnchorGraph self, IMP::algebra::Vector3Ds anchor_positions) -> ProbabilisticAnchorGraph"""
1463 this = _IMP_multifit.new_ProbabilisticAnchorGraph(anchor_positions)
1465 self.this.append(this)
1466 except __builtin__.Exception:
1469 def add_edge(self, i, j):
1470 """add_edge(ProbabilisticAnchorGraph self, int i, int j)"""
1471 return _IMP_multifit.ProbabilisticAnchorGraph_add_edge(self, i, j)
1474 def set_particle_probabilities_on_anchors(self, p, sols):
1475 """set_particle_probabilities_on_anchors(ProbabilisticAnchorGraph self, Particle p, IMP::multifit::FittingSolutionRecords sols)"""
1476 return _IMP_multifit.ProbabilisticAnchorGraph_set_particle_probabilities_on_anchors(self, p, sols)
1479 def show(self, *args):
1481 show(ProbabilisticAnchorGraph self, _ostream out)
1482 show(ProbabilisticAnchorGraph self)
1484 return _IMP_multifit.ProbabilisticAnchorGraph_show(self, *args)
1487 def get_number_of_anchors(self):
1488 """get_number_of_anchors(ProbabilisticAnchorGraph self) -> unsigned int"""
1489 return _IMP_multifit.ProbabilisticAnchorGraph_get_number_of_anchors(self)
1492 def get_number_of_edges(self):
1493 """get_number_of_edges(ProbabilisticAnchorGraph self) -> unsigned int"""
1494 return _IMP_multifit.ProbabilisticAnchorGraph_get_number_of_edges(self)
1497 def get_edge_list(self):
1498 """get_edge_list(ProbabilisticAnchorGraph self) -> IMP::IntRanges"""
1499 return _IMP_multifit.ProbabilisticAnchorGraph_get_edge_list(self)
1502 def get_anchors(self):
1503 """get_anchors(ProbabilisticAnchorGraph self) -> IMP::algebra::Vector3Ds"""
1504 return _IMP_multifit.ProbabilisticAnchorGraph_get_anchors(self)
1507 def get_particle_anchors(self, p, min_prob=0):
1509 get_particle_anchors(ProbabilisticAnchorGraph self, Particle p, float min_prob=0) -> IMP::algebra::Vector3Ds
1510 get_particle_anchors(ProbabilisticAnchorGraph self, Particle p) -> IMP::algebra::Vector3Ds
1512 return _IMP_multifit.ProbabilisticAnchorGraph_get_particle_anchors(self, p, min_prob)
1515 def get_are_probabilities_for_particle_set(self, p):
1516 """get_are_probabilities_for_particle_set(ProbabilisticAnchorGraph self, Particle p) -> bool"""
1517 return _IMP_multifit.ProbabilisticAnchorGraph_get_are_probabilities_for_particle_set(self, p)
1520 def get_particle_probabilities(self, p):
1521 """get_particle_probabilities(ProbabilisticAnchorGraph self, Particle p) -> IMP::Floats"""
1522 return _IMP_multifit.ProbabilisticAnchorGraph_get_particle_probabilities(self, p)
1525 def get_version_info(self):
1526 """get_version_info(ProbabilisticAnchorGraph self) -> VersionInfo"""
1527 return _IMP_multifit.ProbabilisticAnchorGraph_get_version_info(self)
1531 """__str__(ProbabilisticAnchorGraph self) -> std::string"""
1532 return _IMP_multifit.ProbabilisticAnchorGraph___str__(self)
1536 """__repr__(ProbabilisticAnchorGraph self) -> std::string"""
1537 return _IMP_multifit.ProbabilisticAnchorGraph___repr__(self)
1542 return _object_cast_to_ProbabilisticAnchorGraph(o)
1544 ProbabilisticAnchorGraph_swigregister = _IMP_multifit.ProbabilisticAnchorGraph_swigregister
1545 ProbabilisticAnchorGraph_swigregister(ProbabilisticAnchorGraph)
1547 class ProteinRecordData(object):
1548 """Proxy of C++ IMP::multifit::ProteinRecordData class."""
1550 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1552 def reset_all(self):
1553 """reset_all(ProteinRecordData self)"""
1554 return _IMP_multifit.ProteinRecordData_reset_all(self)
1559 __init__(IMP::multifit::ProteinRecordData self) -> ProteinRecordData
1560 __init__(IMP::multifit::ProteinRecordData self, std::string const & name) -> ProteinRecordData
1561 __init__(IMP::multifit::ProteinRecordData self, std::string const & name, std::string const fn) -> ProteinRecordData
1562 __init__(IMP::multifit::ProteinRecordData self, std::string const & name, int start_res, int end_res, std::string const fn) -> ProteinRecordData
1563 __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
1565 this = _IMP_multifit.new_ProteinRecordData(*args)
1567 self.this.append(this)
1568 except __builtin__.Exception:
1571 def show(self, *args):
1573 show(ProteinRecordData self, _ostream out)
1574 show(ProteinRecordData self)
1576 return _IMP_multifit.ProteinRecordData_show(self, *args)
1578 name_ = _swig_property(_IMP_multifit.ProteinRecordData_name__get, _IMP_multifit.ProteinRecordData_name__set)
1579 start_res_ = _swig_property(_IMP_multifit.ProteinRecordData_start_res__get, _IMP_multifit.ProteinRecordData_start_res__set)
1580 end_res_ = _swig_property(_IMP_multifit.ProteinRecordData_end_res__get, _IMP_multifit.ProteinRecordData_end_res__set)
1581 filename_ = _swig_property(_IMP_multifit.ProteinRecordData_filename__get, _IMP_multifit.ProteinRecordData_filename__set)
1582 surface_filename_ = _swig_property(_IMP_multifit.ProteinRecordData_surface_filename__get, _IMP_multifit.ProteinRecordData_surface_filename__set)
1583 ref_filename_ = _swig_property(_IMP_multifit.ProteinRecordData_ref_filename__get, _IMP_multifit.ProteinRecordData_ref_filename__set)
1586 """__str__(ProteinRecordData self) -> std::string"""
1587 return _IMP_multifit.ProteinRecordData___str__(self)
1591 """__repr__(ProteinRecordData self) -> std::string"""
1592 return _IMP_multifit.ProteinRecordData___repr__(self)
1594 __swig_destroy__ = _IMP_multifit.delete_ProteinRecordData
1595 __del__ =
lambda self:
None
1596 ProteinRecordData_swigregister = _IMP_multifit.ProteinRecordData_swigregister
1597 ProteinRecordData_swigregister(ProteinRecordData)
1600 """Proxy of C++ IMP::multifit::ProteomicsData class."""
1602 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1605 """__init__(IMP::multifit::ProteomicsData self) -> ProteomicsData"""
1606 this = _IMP_multifit.new_ProteomicsData()
1608 self.this.append(this)
1609 except __builtin__.Exception:
1612 def add_protein(self, *args):
1614 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
1615 add_protein(ProteomicsData self, ProteinRecordData rec) -> int
1617 return _IMP_multifit.ProteomicsData_add_protein(self, *args)
1620 def find(self, name):
1621 """find(ProteomicsData self, std::string const & name) -> int"""
1622 return _IMP_multifit.ProteomicsData_find(self, name)
1625 def add_interaction(self, ii, used_for_filter, linker_len):
1626 """add_interaction(ProteomicsData self, IMP::Ints const & ii, bool used_for_filter, float linker_len)"""
1627 return _IMP_multifit.ProteomicsData_add_interaction(self, ii, used_for_filter, linker_len)
1630 def add_cross_link_interaction(self, prot1, res1, prot2, res2, used_in_filter, linker_len):
1631 """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)"""
1632 return _IMP_multifit.ProteomicsData_add_cross_link_interaction(self, prot1, res1, prot2, res2, used_in_filter, linker_len)
1635 def add_ev_pair(self, prot1, prot2):
1636 """add_ev_pair(ProteomicsData self, IMP::Int prot1, IMP::Int prot2)"""
1637 return _IMP_multifit.ProteomicsData_add_ev_pair(self, prot1, prot2)
1640 def get_number_of_proteins(self):
1641 """get_number_of_proteins(ProteomicsData self) -> int"""
1642 return _IMP_multifit.ProteomicsData_get_number_of_proteins(self)
1645 def get_number_of_interactions(self):
1646 """get_number_of_interactions(ProteomicsData self) -> int"""
1647 return _IMP_multifit.ProteomicsData_get_number_of_interactions(self)
1650 def get_interaction(self, interaction_ind):
1651 """get_interaction(ProteomicsData self, int interaction_ind) -> IMP::Ints"""
1652 return _IMP_multifit.ProteomicsData_get_interaction(self, interaction_ind)
1655 def get_interaction_part_of_filter(self, interaction_ind):
1656 """get_interaction_part_of_filter(ProteomicsData self, int interaction_ind) -> bool"""
1657 return _IMP_multifit.ProteomicsData_get_interaction_part_of_filter(self, interaction_ind)
1660 def get_interaction_linker_length(self, interaction_ind):
1661 """get_interaction_linker_length(ProteomicsData self, int interaction_ind) -> int"""
1662 return _IMP_multifit.ProteomicsData_get_interaction_linker_length(self, interaction_ind)
1665 def get_number_of_cross_links(self):
1666 """get_number_of_cross_links(ProteomicsData self) -> int"""
1667 return _IMP_multifit.ProteomicsData_get_number_of_cross_links(self)
1670 def get_cross_link(self, xlink_ind):
1671 """get_cross_link(ProteomicsData self, int xlink_ind) -> std::pair< IMP::IntPair,IMP::IntPair >"""
1672 return _IMP_multifit.ProteomicsData_get_cross_link(self, xlink_ind)
1675 def get_cross_link_part_of_filter(self, xlink_ind):
1676 """get_cross_link_part_of_filter(ProteomicsData self, int xlink_ind) -> bool"""
1677 return _IMP_multifit.ProteomicsData_get_cross_link_part_of_filter(self, xlink_ind)
1680 def get_cross_link_length(self, xlink_ind):
1681 """get_cross_link_length(ProteomicsData self, int xlink_ind) -> float"""
1682 return _IMP_multifit.ProteomicsData_get_cross_link_length(self, xlink_ind)
1685 def get_number_of_ev_pairs(self):
1686 """get_number_of_ev_pairs(ProteomicsData self) -> int"""
1687 return _IMP_multifit.ProteomicsData_get_number_of_ev_pairs(self)
1690 def get_ev_pair(self, ev_ind):
1691 """get_ev_pair(ProteomicsData self, int ev_ind) -> IMP::IntPair"""
1692 return _IMP_multifit.ProteomicsData_get_ev_pair(self, ev_ind)
1695 def get_protein_name(self, protein_ind):
1696 """get_protein_name(ProteomicsData self, int protein_ind) -> std::string"""
1697 return _IMP_multifit.ProteomicsData_get_protein_name(self, protein_ind)
1700 def get_end_res(self, protein_ind):
1701 """get_end_res(ProteomicsData self, int protein_ind) -> int"""
1702 return _IMP_multifit.ProteomicsData_get_end_res(self, protein_ind)
1705 def get_start_res(self, protein_ind):
1706 """get_start_res(ProteomicsData self, int protein_ind) -> int"""
1707 return _IMP_multifit.ProteomicsData_get_start_res(self, protein_ind)
1710 def get_protein_filename(self, protein_ind):
1711 """get_protein_filename(ProteomicsData self, int protein_ind) -> std::string"""
1712 return _IMP_multifit.ProteomicsData_get_protein_filename(self, protein_ind)
1715 def get_reference_filename(self, protein_ind):
1716 """get_reference_filename(ProteomicsData self, int protein_ind) -> std::string"""
1717 return _IMP_multifit.ProteomicsData_get_reference_filename(self, protein_ind)
1720 def get_surface_filename(self, protein_ind):
1721 """get_surface_filename(ProteomicsData self, int protein_ind) -> std::string"""
1722 return _IMP_multifit.ProteomicsData_get_surface_filename(self, protein_ind)
1725 def get_protein_data(self, protein_ind):
1726 """get_protein_data(ProteomicsData self, int protein_ind) -> ProteinRecordData"""
1727 return _IMP_multifit.ProteomicsData_get_protein_data(self, protein_ind)
1730 def get_version_info(self):
1731 """get_version_info(ProteomicsData self) -> VersionInfo"""
1732 return _IMP_multifit.ProteomicsData_get_version_info(self)
1735 def get_num_allowed_violated_interactions(self):
1736 """get_num_allowed_violated_interactions(ProteomicsData self) -> int"""
1737 return _IMP_multifit.ProteomicsData_get_num_allowed_violated_interactions(self)
1740 def set_num_allowed_violated_interactions(self, n):
1741 """set_num_allowed_violated_interactions(ProteomicsData self, int n)"""
1742 return _IMP_multifit.ProteomicsData_set_num_allowed_violated_interactions(self, n)
1745 def get_num_allowed_violated_cross_links(self):
1746 """get_num_allowed_violated_cross_links(ProteomicsData self) -> int"""
1747 return _IMP_multifit.ProteomicsData_get_num_allowed_violated_cross_links(self)
1750 def set_num_allowed_violated_cross_links(self, n):
1751 """set_num_allowed_violated_cross_links(ProteomicsData self, int n)"""
1752 return _IMP_multifit.ProteomicsData_set_num_allowed_violated_cross_links(self, n)
1755 def get_num_allowed_violated_ev(self):
1756 """get_num_allowed_violated_ev(ProteomicsData self) -> int"""
1757 return _IMP_multifit.ProteomicsData_get_num_allowed_violated_ev(self)
1760 def set_num_allowed_violated_ev(self, n):
1761 """set_num_allowed_violated_ev(ProteomicsData self, int n)"""
1762 return _IMP_multifit.ProteomicsData_set_num_allowed_violated_ev(self, n)
1766 """__str__(ProteomicsData self) -> std::string"""
1767 return _IMP_multifit.ProteomicsData___str__(self)
1771 """__repr__(ProteomicsData self) -> std::string"""
1772 return _IMP_multifit.ProteomicsData___repr__(self)
1777 return _object_cast_to_ProteomicsData(o)
1779 ProteomicsData_swigregister = _IMP_multifit.ProteomicsData_swigregister
1780 ProteomicsData_swigregister(ProteomicsData)
1784 """read_proteomics_data(char const * proteomics_fn) -> ProteomicsData"""
1785 return _IMP_multifit.read_proteomics_data(proteomics_fn)
1787 def get_partial_proteomics_data(pd, prot_names):
1788 """get_partial_proteomics_data(ProteomicsData pd, IMP::Strings const & prot_names) -> ProteomicsData"""
1789 return _IMP_multifit.get_partial_proteomics_data(pd, prot_names)
1790 class AnchorsData(object):
1791 """Proxy of C++ IMP::multifit::AnchorsData class."""
1793 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1797 __init__(IMP::multifit::AnchorsData self) -> AnchorsData
1798 __init__(IMP::multifit::AnchorsData self, IMP::algebra::Vector3Ds points, IMP::IntPairs edges) -> AnchorsData
1800 this = _IMP_multifit.new_AnchorsData(*args)
1802 self.this.append(this)
1803 except __builtin__.Exception:
1806 def remove_edges_for_node(self, node_ind):
1807 """remove_edges_for_node(AnchorsData self, int node_ind)"""
1808 return _IMP_multifit.AnchorsData_remove_edges_for_node(self, node_ind)
1811 def get_number_of_points(self):
1812 """get_number_of_points(AnchorsData self) -> int"""
1813 return _IMP_multifit.AnchorsData_get_number_of_points(self)
1816 def get_number_of_edges(self):
1817 """get_number_of_edges(AnchorsData self) -> int"""
1818 return _IMP_multifit.AnchorsData_get_number_of_edges(self)
1821 def get_is_point_considered(self, node_ind):
1822 """get_is_point_considered(AnchorsData self, int node_ind) -> bool"""
1823 return _IMP_multifit.AnchorsData_get_is_point_considered(self, node_ind)
1826 def show(self, *args):
1828 show(AnchorsData self, _ostream out)
1829 show(AnchorsData self)
1831 return _IMP_multifit.AnchorsData_show(self, *args)
1834 def get_secondary_structure_is_set(self):
1835 """get_secondary_structure_is_set(AnchorsData self) -> bool"""
1836 return _IMP_multifit.AnchorsData_get_secondary_structure_is_set(self)
1839 def setup_secondary_structure(self, mdl):
1840 """setup_secondary_structure(AnchorsData self, Model mdl)"""
1841 return _IMP_multifit.AnchorsData_setup_secondary_structure(self, mdl)
1844 def set_secondary_structure_probabilities(self, *args):
1846 set_secondary_structure_probabilities(AnchorsData self, IMP::Particles const & ssres_ps, IMP::Ints const & indices)
1847 set_secondary_structure_probabilities(AnchorsData self, IMP::Particles const & ssres_ps)
1849 return _IMP_multifit.AnchorsData_set_secondary_structure_probabilities(self, *args)
1852 def get_secondary_structure_particles(self):
1853 """get_secondary_structure_particles(AnchorsData self) -> IMP::Particles"""
1854 return _IMP_multifit.AnchorsData_get_secondary_structure_particles(self)
1856 points_ = _swig_property(_IMP_multifit.AnchorsData_points__get, _IMP_multifit.AnchorsData_points__set)
1857 consider_point_ = _swig_property(_IMP_multifit.AnchorsData_consider_point__get, _IMP_multifit.AnchorsData_consider_point__set)
1858 edges_ = _swig_property(_IMP_multifit.AnchorsData_edges__get, _IMP_multifit.AnchorsData_edges__set)
1861 """__str__(AnchorsData self) -> std::string"""
1862 return _IMP_multifit.AnchorsData___str__(self)
1866 """__repr__(AnchorsData self) -> std::string"""
1867 return _IMP_multifit.AnchorsData___repr__(self)
1869 __swig_destroy__ = _IMP_multifit.delete_AnchorsData
1870 __del__ =
lambda self:
None
1871 AnchorsData_swigregister = _IMP_multifit.AnchorsData_swigregister
1872 AnchorsData_swigregister(AnchorsData)
1875 def read_anchors_data(txt_filename):
1876 """read_anchors_data(char const * txt_filename) -> AnchorsData"""
1877 return _IMP_multifit.read_anchors_data(txt_filename)
1879 def write_txt(txt_filename, ad):
1880 """write_txt(std::string const & txt_filename, AnchorsData ad)"""
1881 return _IMP_multifit.write_txt(txt_filename, ad)
1883 def write_cmm(cmm_filename, marker_set_name, dpa):
1884 """write_cmm(std::string const & cmm_filename, std::string const & marker_set_name, AnchorsData dpa)"""
1885 return _IMP_multifit.write_cmm(cmm_filename, marker_set_name, dpa)
1888 """create_coarse_molecule_from_density(DensityMap dmap, float dens_threshold, int num_beads, Model mdl, float bead_radius) -> Hierarchy"""
1889 return _IMP_multifit.create_coarse_molecule_from_density(dmap, dens_threshold, num_beads, mdl, bead_radius)
1891 def create_hit_map(rb, rb_ref, sols, damp):
1892 """create_hit_map(RigidBody rb, Refiner rb_ref, IMP::multifit::FittingSolutionRecords const & sols, DensityMap damp) -> DensityMap"""
1893 return _IMP_multifit.create_hit_map(rb, rb_ref, sols, damp)
1896 """get_points_close_to_molecule(Hierarchy mh, IMP::algebra::Vector3Ds const points, IMP::Float max_dist) -> IMP::algebra::Vector3Ds"""
1897 return _IMP_multifit.get_points_close_to_molecule(mh, points, max_dist)
1899 def get_points_far_from_molecule(mh, points, max_dist):
1900 """get_points_far_from_molecule(Hierarchy mh, IMP::algebra::Vector3Ds const points, IMP::Float max_dist) -> IMP::algebra::Vector3Ds"""
1901 return _IMP_multifit.get_points_far_from_molecule(mh, points, max_dist)
1903 """Proxy of C++ IMP::multifit::RadiusOfGyrationRestraint class."""
1905 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1907 def __init__(self, ps, num_residues, scale=1.):
1909 __init__(IMP::multifit::RadiusOfGyrationRestraint self, IMP::Particles ps, int num_residues, IMP::Float scale=1.) -> RadiusOfGyrationRestraint
1910 __init__(IMP::multifit::RadiusOfGyrationRestraint self, IMP::Particles ps, int num_residues) -> RadiusOfGyrationRestraint
1912 this = _IMP_multifit.new_RadiusOfGyrationRestraint(ps, num_residues, scale)
1914 self.this.append(this)
1915 except __builtin__.Exception:
1918 def do_get_inputs(self):
1919 """do_get_inputs(RadiusOfGyrationRestraint self) -> IMP::ModelObjectsTemp"""
1920 return _IMP_multifit.RadiusOfGyrationRestraint_do_get_inputs(self)
1923 def get_version_info(self):
1924 """get_version_info(RadiusOfGyrationRestraint self) -> VersionInfo"""
1925 return _IMP_multifit.RadiusOfGyrationRestraint_get_version_info(self)
1928 def set_radius_of_gyration(self, r):
1929 """set_radius_of_gyration(RadiusOfGyrationRestraint self, IMP::Float r)"""
1930 return _IMP_multifit.RadiusOfGyrationRestraint_set_radius_of_gyration(self, r)
1934 """get_radius_of_gyration(RadiusOfGyrationRestraint self) -> IMP::Float"""
1935 return _IMP_multifit.RadiusOfGyrationRestraint_get_radius_of_gyration(self)
1939 """__str__(RadiusOfGyrationRestraint self) -> std::string"""
1940 return _IMP_multifit.RadiusOfGyrationRestraint___str__(self)
1944 """__repr__(RadiusOfGyrationRestraint self) -> std::string"""
1945 return _IMP_multifit.RadiusOfGyrationRestraint___repr__(self)
1950 return _object_cast_to_RadiusOfGyrationRestraint(o)
1952 RadiusOfGyrationRestraint_swigregister = _IMP_multifit.RadiusOfGyrationRestraint_swigregister
1953 RadiusOfGyrationRestraint_swigregister(RadiusOfGyrationRestraint)
1956 def get_approximated_radius_of_gyration(len):
1957 """get_approximated_radius_of_gyration(int len) -> float"""
1958 return _IMP_multifit.get_approximated_radius_of_gyration(len)
1960 def get_actual_radius_of_gyration(ps):
1961 """get_actual_radius_of_gyration(IMP::ParticlesTemp ps) -> float"""
1962 return _IMP_multifit.get_actual_radius_of_gyration(ps)
1964 def get_approximated_radius(len):
1965 """get_approximated_radius(int len) -> float"""
1966 return _IMP_multifit.get_approximated_radius(len)
1967 class ProteinsAnchorsSamplingSpace(object):
1968 """Proxy of C++ IMP::multifit::ProteinsAnchorsSamplingSpace class."""
1970 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1974 __init__(IMP::multifit::ProteinsAnchorsSamplingSpace self, ProteomicsData prots=None) -> ProteinsAnchorsSamplingSpace
1975 __init__(IMP::multifit::ProteinsAnchorsSamplingSpace self) -> ProteinsAnchorsSamplingSpace
1977 this = _IMP_multifit.new_ProteinsAnchorsSamplingSpace(prots)
1979 self.this.append(this)
1980 except __builtin__.Exception:
1983 def set_anchors(self, data):
1984 """set_anchors(ProteinsAnchorsSamplingSpace self, AnchorsData data)"""
1985 return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_anchors(self, data)
1988 def get_anchors(self):
1989 """get_anchors(ProteinsAnchorsSamplingSpace self) -> AnchorsData"""
1990 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_anchors(self)
1993 def get_anchors_filename(self):
1994 """get_anchors_filename(ProteinsAnchorsSamplingSpace self) -> std::string"""
1995 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_anchors_filename(self)
1998 def set_anchors_filename(self, fn):
1999 """set_anchors_filename(ProteinsAnchorsSamplingSpace self, std::string const & fn)"""
2000 return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_anchors_filename(self, fn)
2003 def get_proteomics_data(self):
2004 """get_proteomics_data(ProteinsAnchorsSamplingSpace self) -> ProteomicsData"""
2005 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_proteomics_data(self)
2008 def add_protein(self, rec):
2009 """add_protein(ProteinsAnchorsSamplingSpace self, ProteinRecordData rec)"""
2010 return _IMP_multifit.ProteinsAnchorsSamplingSpace_add_protein(self, rec)
2013 def get_paths_for_protein(self, prot_name):
2014 """get_paths_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name) -> IMP::IntsList"""
2015 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_paths_for_protein(self, prot_name)
2018 def set_paths_filename_for_protein(self, prot_name, paths_filename):
2019 """set_paths_filename_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name, std::string const & paths_filename)"""
2020 return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_paths_filename_for_protein(self, prot_name, paths_filename)
2023 def get_paths_filename_for_protein(self, prot_name):
2024 """get_paths_filename_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name) -> std::string"""
2025 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_paths_filename_for_protein(self, prot_name)
2028 def set_paths_for_protein(self, prot_name, paths):
2029 """set_paths_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name, IMP::IntsList paths)"""
2030 return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_paths_for_protein(self, prot_name, paths)
2033 def show(self, *args):
2035 show(ProteinsAnchorsSamplingSpace self, _ostream s)
2036 show(ProteinsAnchorsSamplingSpace self)
2038 return _IMP_multifit.ProteinsAnchorsSamplingSpace_show(self, *args)
2042 """__str__(ProteinsAnchorsSamplingSpace self) -> std::string"""
2043 return _IMP_multifit.ProteinsAnchorsSamplingSpace___str__(self)
2047 """__repr__(ProteinsAnchorsSamplingSpace self) -> std::string"""
2048 return _IMP_multifit.ProteinsAnchorsSamplingSpace___repr__(self)
2050 __swig_destroy__ = _IMP_multifit.delete_ProteinsAnchorsSamplingSpace
2051 __del__ =
lambda self:
None
2052 ProteinsAnchorsSamplingSpace_swigregister = _IMP_multifit.ProteinsAnchorsSamplingSpace_swigregister
2053 ProteinsAnchorsSamplingSpace_swigregister(ProteinsAnchorsSamplingSpace)
2056 def read_protein_anchors_mapping(*args):
2058 read_protein_anchors_mapping(ProteomicsData prots, std::string const & anchors_prot_map_fn, int max_paths) -> ProteinsAnchorsSamplingSpace
2059 read_protein_anchors_mapping(ProteomicsData prots, std::string const & anchors_prot_map_fn) -> ProteinsAnchorsSamplingSpace
2061 return _IMP_multifit.read_protein_anchors_mapping(*args)
2063 def write_protein_anchors_mapping(*args):
2065 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)
2066 write_protein_anchors_mapping(std::string const & anchors_prot_map_fn, ProteinsAnchorsSamplingSpace pa, IMP::Strings const & prot_names)
2068 return _IMP_multifit.write_protein_anchors_mapping(*args)
2071 """get_part_of_sampling_space(ProteinsAnchorsSamplingSpace prots_ss, IMP::Strings const & prot_names) -> ProteinsAnchorsSamplingSpace"""
2072 return _IMP_multifit.get_part_of_sampling_space(prots_ss, prot_names)
2075 """get_partial_assembly_setting_data(SettingsData prots_sd, IMP::Strings const & prot_names) -> SettingsData"""
2076 return _IMP_multifit.get_partial_assembly_setting_data(prots_sd, prot_names)
2080 read_paths(char const * txt_filename, int max_paths) -> IMP::IntsList
2081 read_paths(char const * txt_filename) -> IMP::IntsList
2083 return _IMP_multifit.read_paths(*args)
2085 def write_paths(paths, txt_filename):
2086 """write_paths(IMP::IntsList const & paths, std::string const & txt_filename)"""
2087 return _IMP_multifit.write_paths(paths, txt_filename)
2089 def molecule2anchors(mh, k):
2090 """molecule2anchors(Hierarchy mh, int k) -> AnchorsData"""
2091 return _IMP_multifit.molecule2anchors(mh, k)
2093 def get_anchors_for_density(dmap, number_of_means, density_threshold, pdb_filename, cmm_filename, seg_filename, txt_filename):
2094 """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)"""
2095 return _IMP_multifit.get_anchors_for_density(dmap, number_of_means, density_threshold, pdb_filename, cmm_filename, seg_filename, txt_filename)
2099 get_anchor_indices_matching_secondary_structure(AnchorsData ad, IMP::atom::SecondaryStructureResidues const & ssrs, IMP::Float max_rmsd=0.7) -> IMP::IntsList
2100 get_anchor_indices_matching_secondary_structure(AnchorsData ad, IMP::atom::SecondaryStructureResidues const & ssrs) -> IMP::IntsList
2102 return _IMP_multifit.get_anchor_indices_matching_secondary_structure(ad, ssrs, max_rmsd)
2103 class DominoParams(object):
2104 """Proxy of C++ IMP::multifit::DominoParams class."""
2106 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2109 """__init__(IMP::multifit::DominoParams self) -> DominoParams"""
2110 this = _IMP_multifit.new_DominoParams()
2112 self.this.append(this)
2113 except __builtin__.Exception:
2117 """add(DominoParams self, boost::property_tree::ptree const & pt)"""
2118 return _IMP_multifit.DominoParams_add(self, pt)
2121 def show(self, *args):
2123 show(DominoParams self, _ostream s)
2124 show(DominoParams self)
2126 return _IMP_multifit.DominoParams_show(self, *args)
2128 max_value_threshold_ = _swig_property(_IMP_multifit.DominoParams_max_value_threshold__get, _IMP_multifit.DominoParams_max_value_threshold__set)
2129 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)
2130 max_anchor_penetration_ = _swig_property(_IMP_multifit.DominoParams_max_anchor_penetration__get, _IMP_multifit.DominoParams_max_anchor_penetration__set)
2131 heap_size_ = _swig_property(_IMP_multifit.DominoParams_heap_size__get, _IMP_multifit.DominoParams_heap_size__set)
2132 cache_size_ = _swig_property(_IMP_multifit.DominoParams_cache_size__get, _IMP_multifit.DominoParams_cache_size__set)
2135 """__str__(DominoParams self) -> std::string"""
2136 return _IMP_multifit.DominoParams___str__(self)
2140 """__repr__(DominoParams self) -> std::string"""
2141 return _IMP_multifit.DominoParams___repr__(self)
2143 __swig_destroy__ = _IMP_multifit.delete_DominoParams
2144 __del__ =
lambda self:
None
2145 DominoParams_swigregister = _IMP_multifit.DominoParams_swigregister
2146 DominoParams_swigregister(DominoParams)
2148 class XlinkParams(object):
2149 """Proxy of C++ IMP::multifit::XlinkParams class."""
2151 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2154 """__init__(IMP::multifit::XlinkParams self) -> XlinkParams"""
2155 this = _IMP_multifit.new_XlinkParams()
2157 self.this.append(this)
2158 except __builtin__.Exception:
2162 """add(XlinkParams self, boost::property_tree::ptree const & pt)"""
2163 return _IMP_multifit.XlinkParams_add(self, pt)
2166 def show(self, *args):
2168 show(XlinkParams self, _ostream s)
2169 show(XlinkParams self)
2171 return _IMP_multifit.XlinkParams_show(self, *args)
2173 upper_bound_ = _swig_property(_IMP_multifit.XlinkParams_upper_bound__get, _IMP_multifit.XlinkParams_upper_bound__set)
2174 k_ = _swig_property(_IMP_multifit.XlinkParams_k__get, _IMP_multifit.XlinkParams_k__set)
2175 max_xlink_val_ = _swig_property(_IMP_multifit.XlinkParams_max_xlink_val__get, _IMP_multifit.XlinkParams_max_xlink_val__set)
2176 treat_between_residues_ = _swig_property(_IMP_multifit.XlinkParams_treat_between_residues__get, _IMP_multifit.XlinkParams_treat_between_residues__set)
2179 """__str__(XlinkParams self) -> std::string"""
2180 return _IMP_multifit.XlinkParams___str__(self)
2184 """__repr__(XlinkParams self) -> std::string"""
2185 return _IMP_multifit.XlinkParams___repr__(self)
2187 __swig_destroy__ = _IMP_multifit.delete_XlinkParams
2188 __del__ =
lambda self:
None
2189 XlinkParams_swigregister = _IMP_multifit.XlinkParams_swigregister
2190 XlinkParams_swigregister(XlinkParams)
2192 class ConnectivityParams(object):
2193 """Proxy of C++ IMP::multifit::ConnectivityParams class."""
2195 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2198 """__init__(IMP::multifit::ConnectivityParams self) -> ConnectivityParams"""
2199 this = _IMP_multifit.new_ConnectivityParams()
2201 self.this.append(this)
2202 except __builtin__.Exception:
2206 """add(ConnectivityParams self, boost::property_tree::ptree const & pt)"""
2207 return _IMP_multifit.ConnectivityParams_add(self, pt)
2210 def show(self, *args):
2212 show(ConnectivityParams self, _ostream s)
2213 show(ConnectivityParams self)
2215 return _IMP_multifit.ConnectivityParams_show(self, *args)
2217 upper_bound_ = _swig_property(_IMP_multifit.ConnectivityParams_upper_bound__get, _IMP_multifit.ConnectivityParams_upper_bound__set)
2218 k_ = _swig_property(_IMP_multifit.ConnectivityParams_k__get, _IMP_multifit.ConnectivityParams_k__set)
2219 max_conn_rest_val_ = _swig_property(_IMP_multifit.ConnectivityParams_max_conn_rest_val__get, _IMP_multifit.ConnectivityParams_max_conn_rest_val__set)
2222 """__str__(ConnectivityParams self) -> std::string"""
2223 return _IMP_multifit.ConnectivityParams___str__(self)
2227 """__repr__(ConnectivityParams self) -> std::string"""
2228 return _IMP_multifit.ConnectivityParams___repr__(self)
2230 __swig_destroy__ = _IMP_multifit.delete_ConnectivityParams
2231 __del__ =
lambda self:
None
2232 ConnectivityParams_swigregister = _IMP_multifit.ConnectivityParams_swigregister
2233 ConnectivityParams_swigregister(ConnectivityParams)
2235 class FragmentsParams(object):
2236 """Proxy of C++ IMP::multifit::FragmentsParams class."""
2238 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2241 """__init__(IMP::multifit::FragmentsParams self) -> FragmentsParams"""
2242 this = _IMP_multifit.new_FragmentsParams()
2244 self.this.append(this)
2245 except __builtin__.Exception:
2249 """add(FragmentsParams self, boost::property_tree::ptree const & pt)"""
2250 return _IMP_multifit.FragmentsParams_add(self, pt)
2253 def show(self, *args):
2255 show(FragmentsParams self, _ostream s)
2256 show(FragmentsParams self)
2258 return _IMP_multifit.FragmentsParams_show(self, *args)
2260 frag_len_ = _swig_property(_IMP_multifit.FragmentsParams_frag_len__get, _IMP_multifit.FragmentsParams_frag_len__set)
2261 bead_radius_scale_ = _swig_property(_IMP_multifit.FragmentsParams_bead_radius_scale__get, _IMP_multifit.FragmentsParams_bead_radius_scale__set)
2262 load_atomic_ = _swig_property(_IMP_multifit.FragmentsParams_load_atomic__get, _IMP_multifit.FragmentsParams_load_atomic__set)
2263 subunit_rigid_ = _swig_property(_IMP_multifit.FragmentsParams_subunit_rigid__get, _IMP_multifit.FragmentsParams_subunit_rigid__set)
2266 """__str__(FragmentsParams self) -> std::string"""
2267 return _IMP_multifit.FragmentsParams___str__(self)
2271 """__repr__(FragmentsParams self) -> std::string"""
2272 return _IMP_multifit.FragmentsParams___repr__(self)
2274 __swig_destroy__ = _IMP_multifit.delete_FragmentsParams
2275 __del__ =
lambda self:
None
2276 FragmentsParams_swigregister = _IMP_multifit.FragmentsParams_swigregister
2277 FragmentsParams_swigregister(FragmentsParams)
2279 class RogParams(object):
2280 """Proxy of C++ IMP::multifit::RogParams class."""
2282 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2285 """__init__(IMP::multifit::RogParams self) -> RogParams"""
2286 this = _IMP_multifit.new_RogParams()
2288 self.this.append(this)
2289 except __builtin__.Exception:
2293 """add(RogParams self, boost::property_tree::ptree const & pt)"""
2294 return _IMP_multifit.RogParams_add(self, pt)
2297 def get_max_score(self):
2298 """get_max_score(RogParams self) -> float"""
2299 return _IMP_multifit.RogParams_get_max_score(self)
2302 def get_scale(self):
2303 """get_scale(RogParams self) -> float"""
2304 return _IMP_multifit.RogParams_get_scale(self)
2307 def show(self, *args):
2309 show(RogParams self, _ostream s)
2310 show(RogParams self)
2312 return _IMP_multifit.RogParams_show(self, *args)
2316 """__str__(RogParams self) -> std::string"""
2317 return _IMP_multifit.RogParams___str__(self)
2321 """__repr__(RogParams self) -> std::string"""
2322 return _IMP_multifit.RogParams___repr__(self)
2324 __swig_destroy__ = _IMP_multifit.delete_RogParams
2325 __del__ =
lambda self:
None
2326 RogParams_swigregister = _IMP_multifit.RogParams_swigregister
2327 RogParams_swigregister(RogParams)
2329 class EVParams(object):
2330 """Proxy of C++ IMP::multifit::EVParams class."""
2332 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2335 """__init__(IMP::multifit::EVParams self) -> EVParams"""
2336 this = _IMP_multifit.new_EVParams()
2338 self.this.append(this)
2339 except __builtin__.Exception:
2343 """add(EVParams self, boost::property_tree::ptree const & pt)"""
2344 return _IMP_multifit.EVParams_add(self, pt)
2347 def show(self, *args):
2349 show(EVParams self, _ostream s)
2352 return _IMP_multifit.EVParams_show(self, *args)
2354 pair_distance_ = _swig_property(_IMP_multifit.EVParams_pair_distance__get, _IMP_multifit.EVParams_pair_distance__set)
2355 pair_slack_ = _swig_property(_IMP_multifit.EVParams_pair_slack__get, _IMP_multifit.EVParams_pair_slack__set)
2356 hlb_mean_ = _swig_property(_IMP_multifit.EVParams_hlb_mean__get, _IMP_multifit.EVParams_hlb_mean__set)
2357 hlb_k_ = _swig_property(_IMP_multifit.EVParams_hlb_k__get, _IMP_multifit.EVParams_hlb_k__set)
2358 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)
2359 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)
2360 scoring_mode_ = _swig_property(_IMP_multifit.EVParams_scoring_mode__get, _IMP_multifit.EVParams_scoring_mode__set)
2363 """__str__(EVParams self) -> std::string"""
2364 return _IMP_multifit.EVParams___str__(self)
2368 """__repr__(EVParams self) -> std::string"""
2369 return _IMP_multifit.EVParams___repr__(self)
2371 __swig_destroy__ = _IMP_multifit.delete_EVParams
2372 __del__ =
lambda self:
None
2373 EVParams_swigregister = _IMP_multifit.EVParams_swigregister
2374 EVParams_swigregister(EVParams)
2376 class FiltersParams(object):
2377 """Proxy of C++ IMP::multifit::FiltersParams class."""
2379 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2382 """__init__(IMP::multifit::FiltersParams self) -> FiltersParams"""
2383 this = _IMP_multifit.new_FiltersParams()
2385 self.this.append(this)
2386 except __builtin__.Exception:
2390 """add(FiltersParams self, boost::property_tree::ptree const & pt)"""
2391 return _IMP_multifit.FiltersParams_add(self, pt)
2394 def show(self, *args):
2396 show(FiltersParams self, _ostream s)
2397 show(FiltersParams self)
2399 return _IMP_multifit.FiltersParams_show(self, *args)
2401 max_num_violated_xlink_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_xlink__get, _IMP_multifit.FiltersParams_max_num_violated_xlink__set)
2402 max_num_violated_conn_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_conn__get, _IMP_multifit.FiltersParams_max_num_violated_conn__set)
2403 max_num_violated_ev_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_ev__get, _IMP_multifit.FiltersParams_max_num_violated_ev__set)
2406 """__str__(FiltersParams self) -> std::string"""
2407 return _IMP_multifit.FiltersParams___str__(self)
2411 """__repr__(FiltersParams self) -> std::string"""
2412 return _IMP_multifit.FiltersParams___repr__(self)
2414 __swig_destroy__ = _IMP_multifit.delete_FiltersParams
2415 __del__ =
lambda self:
None
2416 FiltersParams_swigregister = _IMP_multifit.FiltersParams_swigregister
2417 FiltersParams_swigregister(FiltersParams)
2419 class FittingParams(object):
2420 """Proxy of C++ IMP::multifit::FittingParams class."""
2422 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2425 """__init__(IMP::multifit::FittingParams self) -> FittingParams"""
2426 this = _IMP_multifit.new_FittingParams()
2428 self.this.append(this)
2429 except __builtin__.Exception:
2433 """add(FittingParams self, boost::property_tree::ptree const & pt)"""
2434 return _IMP_multifit.FittingParams_add(self, pt)
2437 def show(self, *args):
2439 show(FittingParams self, _ostream s)
2440 show(FittingParams self)
2442 return _IMP_multifit.FittingParams_show(self, *args)
2444 pca_max_angle_diff_ = _swig_property(_IMP_multifit.FittingParams_pca_max_angle_diff__get, _IMP_multifit.FittingParams_pca_max_angle_diff__set)
2445 pca_max_size_diff_ = _swig_property(_IMP_multifit.FittingParams_pca_max_size_diff__get, _IMP_multifit.FittingParams_pca_max_size_diff__set)
2446 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)
2447 max_asmb_fit_score_ = _swig_property(_IMP_multifit.FittingParams_max_asmb_fit_score__get, _IMP_multifit.FittingParams_max_asmb_fit_score__set)
2450 """__str__(FittingParams self) -> std::string"""
2451 return _IMP_multifit.FittingParams___str__(self)
2455 """__repr__(FittingParams self) -> std::string"""
2456 return _IMP_multifit.FittingParams___repr__(self)
2458 __swig_destroy__ = _IMP_multifit.delete_FittingParams
2459 __del__ =
lambda self:
None
2460 FittingParams_swigregister = _IMP_multifit.FittingParams_swigregister
2461 FittingParams_swigregister(FittingParams)
2463 class ComplementarityParams(object):
2464 """Proxy of C++ IMP::multifit::ComplementarityParams class."""
2466 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2469 """__init__(IMP::multifit::ComplementarityParams self) -> ComplementarityParams"""
2470 this = _IMP_multifit.new_ComplementarityParams()
2472 self.this.append(this)
2473 except __builtin__.Exception:
2477 """add(ComplementarityParams self, boost::property_tree::ptree const & pt)"""
2478 return _IMP_multifit.ComplementarityParams_add(self, pt)
2481 def show(self, *args):
2483 show(ComplementarityParams self, _ostream s)
2484 show(ComplementarityParams self)
2486 return _IMP_multifit.ComplementarityParams_show(self, *args)
2488 max_score_ = _swig_property(_IMP_multifit.ComplementarityParams_max_score__get, _IMP_multifit.ComplementarityParams_max_score__set)
2489 max_penetration_ = _swig_property(_IMP_multifit.ComplementarityParams_max_penetration__get, _IMP_multifit.ComplementarityParams_max_penetration__set)
2490 interior_layer_thickness_ = _swig_property(_IMP_multifit.ComplementarityParams_interior_layer_thickness__get, _IMP_multifit.ComplementarityParams_interior_layer_thickness__set)
2491 boundary_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_boundary_coef__get, _IMP_multifit.ComplementarityParams_boundary_coef__set)
2492 comp_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_comp_coef__get, _IMP_multifit.ComplementarityParams_comp_coef__set)
2493 penetration_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_penetration_coef__get, _IMP_multifit.ComplementarityParams_penetration_coef__set)
2496 """__str__(ComplementarityParams self) -> std::string"""
2497 return _IMP_multifit.ComplementarityParams___str__(self)
2501 """__repr__(ComplementarityParams self) -> std::string"""
2502 return _IMP_multifit.ComplementarityParams___repr__(self)
2504 __swig_destroy__ = _IMP_multifit.delete_ComplementarityParams
2505 __del__ =
lambda self:
None
2506 ComplementarityParams_swigregister = _IMP_multifit.ComplementarityParams_swigregister
2507 ComplementarityParams_swigregister(ComplementarityParams)
2509 class AlignmentParams(object):
2510 """Proxy of C++ IMP::multifit::AlignmentParams class."""
2512 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2514 def __init__(self, param_filename):
2515 """__init__(IMP::multifit::AlignmentParams self, char const * param_filename) -> AlignmentParams"""
2516 this = _IMP_multifit.new_AlignmentParams(param_filename)
2518 self.this.append(this)
2519 except __builtin__.Exception:
2522 def get_domino_params(self):
2523 """get_domino_params(AlignmentParams self) -> DominoParams"""
2524 return _IMP_multifit.AlignmentParams_get_domino_params(self)
2527 def get_fitting_params(self):
2528 """get_fitting_params(AlignmentParams self) -> FittingParams"""
2529 return _IMP_multifit.AlignmentParams_get_fitting_params(self)
2532 def get_complementarity_params(self):
2533 """get_complementarity_params(AlignmentParams self) -> ComplementarityParams"""
2534 return _IMP_multifit.AlignmentParams_get_complementarity_params(self)
2537 def get_xlink_params(self):
2538 """get_xlink_params(AlignmentParams self) -> XlinkParams"""
2539 return _IMP_multifit.AlignmentParams_get_xlink_params(self)
2542 def get_connectivity_params(self):
2543 """get_connectivity_params(AlignmentParams self) -> ConnectivityParams"""
2544 return _IMP_multifit.AlignmentParams_get_connectivity_params(self)
2547 def get_rog_params(self):
2548 """get_rog_params(AlignmentParams self) -> RogParams"""
2549 return _IMP_multifit.AlignmentParams_get_rog_params(self)
2552 def get_fragments_params(self):
2553 """get_fragments_params(AlignmentParams self) -> FragmentsParams"""
2554 return _IMP_multifit.AlignmentParams_get_fragments_params(self)
2557 def get_filters_params(self):
2558 """get_filters_params(AlignmentParams self) -> FiltersParams"""
2559 return _IMP_multifit.AlignmentParams_get_filters_params(self)
2562 def get_ev_params(self):
2563 """get_ev_params(AlignmentParams self) -> EVParams"""
2564 return _IMP_multifit.AlignmentParams_get_ev_params(self)
2567 def show(self, *args):
2569 show(AlignmentParams self, _ostream s)
2570 show(AlignmentParams self)
2572 return _IMP_multifit.AlignmentParams_show(self, *args)
2576 """__str__(AlignmentParams self) -> std::string"""
2577 return _IMP_multifit.AlignmentParams___str__(self)
2581 """__repr__(AlignmentParams self) -> std::string"""
2582 return _IMP_multifit.AlignmentParams___repr__(self)
2584 __swig_destroy__ = _IMP_multifit.delete_AlignmentParams
2585 __del__ =
lambda self:
None
2586 AlignmentParams_swigregister = _IMP_multifit.AlignmentParams_swigregister
2587 AlignmentParams_swigregister(AlignmentParams)
2589 class ProteomicsEMAlignmentAtomic(
IMP.Object):
2590 """Proxy of C++ IMP::multifit::ProteomicsEMAlignmentAtomic class."""
2592 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2594 def __init__(self, mapping_data, asmb_data, align_param):
2595 """__init__(IMP::multifit::ProteomicsEMAlignmentAtomic self, ProteinsAnchorsSamplingSpace mapping_data, SettingsData asmb_data, AlignmentParams align_param) -> ProteomicsEMAlignmentAtomic"""
2596 this = _IMP_multifit.new_ProteomicsEMAlignmentAtomic(mapping_data, asmb_data, align_param)
2598 self.this.append(this)
2599 except __builtin__.Exception:
2603 """align(ProteomicsEMAlignmentAtomic self)"""
2604 return _IMP_multifit.ProteomicsEMAlignmentAtomic_align(self)
2607 def add_all_restraints(self):
2608 """add_all_restraints(ProteomicsEMAlignmentAtomic self)"""
2609 return _IMP_multifit.ProteomicsEMAlignmentAtomic_add_all_restraints(self)
2612 def get_restraint_set(self):
2613 """get_restraint_set(ProteomicsEMAlignmentAtomic self) -> RestraintSet"""
2614 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_restraint_set(self)
2617 def add_states_and_filters(self):
2618 """add_states_and_filters(ProteomicsEMAlignmentAtomic self)"""
2619 return _IMP_multifit.ProteomicsEMAlignmentAtomic_add_states_and_filters(self)
2622 def show_domino_merge_tree(self):
2623 """show_domino_merge_tree(ProteomicsEMAlignmentAtomic self)"""
2624 return _IMP_multifit.ProteomicsEMAlignmentAtomic_show_domino_merge_tree(self)
2627 def get_combinations(self, uniques=False):
2629 get_combinations(ProteomicsEMAlignmentAtomic self, bool uniques=False) -> IMP::domino::Assignments
2630 get_combinations(ProteomicsEMAlignmentAtomic self) -> IMP::domino::Assignments
2632 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_combinations(self, uniques)
2635 def set_density_map(self, dmap, threshold):
2636 """set_density_map(ProteomicsEMAlignmentAtomic self, DensityMap dmap, float threshold)"""
2637 return _IMP_multifit.ProteomicsEMAlignmentAtomic_set_density_map(self, dmap, threshold)
2640 def get_molecules(self):
2641 """get_molecules(ProteomicsEMAlignmentAtomic self) -> IMP::atom::Hierarchies"""
2642 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_molecules(self)
2645 def get_rigid_bodies(self):
2646 """get_rigid_bodies(ProteomicsEMAlignmentAtomic self) -> IMP::core::RigidBodies"""
2647 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_rigid_bodies(self)
2650 def load_combination_of_states(self, state4particles):
2651 """load_combination_of_states(ProteomicsEMAlignmentAtomic self, IMP::Ints const & state4particles)"""
2652 return _IMP_multifit.ProteomicsEMAlignmentAtomic_load_combination_of_states(self, state4particles)
2655 def show_scores_header(self, *args):
2657 show_scores_header(ProteomicsEMAlignmentAtomic self, _ostream ous)
2658 show_scores_header(ProteomicsEMAlignmentAtomic self)
2660 return _IMP_multifit.ProteomicsEMAlignmentAtomic_show_scores_header(self, *args)
2663 def get_model(self):
2664 """get_model(ProteomicsEMAlignmentAtomic self) -> Model"""
2665 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_model(self)
2668 def set_fast_scoring(self, state):
2669 """set_fast_scoring(ProteomicsEMAlignmentAtomic self, bool state)"""
2670 return _IMP_multifit.ProteomicsEMAlignmentAtomic_set_fast_scoring(self, state)
2673 def get_version_info(self):
2674 """get_version_info(ProteomicsEMAlignmentAtomic self) -> VersionInfo"""
2675 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_version_info(self)
2679 """__str__(ProteomicsEMAlignmentAtomic self) -> std::string"""
2680 return _IMP_multifit.ProteomicsEMAlignmentAtomic___str__(self)
2684 """__repr__(ProteomicsEMAlignmentAtomic self) -> std::string"""
2685 return _IMP_multifit.ProteomicsEMAlignmentAtomic___repr__(self)
2690 return _object_cast_to_ProteomicsEMAlignmentAtomic(o)
2692 ProteomicsEMAlignmentAtomic_swigregister = _IMP_multifit.ProteomicsEMAlignmentAtomic_swigregister
2693 ProteomicsEMAlignmentAtomic_swigregister(ProteomicsEMAlignmentAtomic)
2697 """write_connolly_surface(IMP::atom::Atoms atoms, TextOutput fn, float density, float probe_radius)"""
2698 return _IMP_multifit.write_connolly_surface(atoms, fn, density, probe_radius)
2700 """Proxy of C++ IMP::multifit::Ensemble class."""
2702 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2704 def load_combination(self, fit_comb):
2705 """load_combination(Ensemble self, IMP::Ints fit_comb)"""
2706 return _IMP_multifit.Ensemble_load_combination(self, fit_comb)
2709 def unload_combination(self, fit_comb):
2710 """unload_combination(Ensemble self, IMP::Ints fit_comb)"""
2711 return _IMP_multifit.Ensemble_unload_combination(self, fit_comb)
2714 def add_component_and_fits(self, mh, fits):
2715 """add_component_and_fits(Ensemble self, Hierarchy mh, IMP::multifit::FittingSolutionRecords const & fits)"""
2716 return _IMP_multifit.Ensemble_add_component_and_fits(self, mh, fits)
2719 def get_molecules(self):
2720 """get_molecules(Ensemble self) -> IMP::atom::Hierarchies"""
2721 return _IMP_multifit.Ensemble_get_molecules(self)
2724 def get_rigid_bodies(self):
2725 """get_rigid_bodies(Ensemble self) -> IMP::core::RigidBodies"""
2726 return _IMP_multifit.Ensemble_get_rigid_bodies(self)
2730 """get_rmsd(Ensemble self, IMP::core::XYZs const & second_xyz) -> float"""
2731 return _IMP_multifit.Ensemble_get_rmsd(self, second_xyz)
2734 def __init__(self, sd, mapping_data):
2735 """__init__(IMP::multifit::Ensemble self, SettingsData sd, ProteinsAnchorsSamplingSpace mapping_data) -> Ensemble"""
2736 this = _IMP_multifit.new_Ensemble(sd, mapping_data)
2738 self.this.append(this)
2739 except __builtin__.Exception:
2742 def score_by_restraints(self, rs, combinations):
2743 """score_by_restraints(Ensemble self, IMP::Restraints rs, IMP::IntsList const & combinations) -> std::vector< IMP::Floats,std::allocator< IMP::Floats > >"""
2744 return _IMP_multifit.Ensemble_score_by_restraints(self, rs, combinations)
2747 def get_version_info(self):
2748 """get_version_info(Ensemble self) -> VersionInfo"""
2749 return _IMP_multifit.Ensemble_get_version_info(self)
2753 """__str__(Ensemble self) -> std::string"""
2754 return _IMP_multifit.Ensemble___str__(self)
2758 """__repr__(Ensemble self) -> std::string"""
2759 return _IMP_multifit.Ensemble___repr__(self)
2764 return _object_cast_to_Ensemble(o)
2766 Ensemble_swigregister = _IMP_multifit.Ensemble_swigregister
2767 Ensemble_swigregister(Ensemble)
2770 def load_ensemble(sd, mdl, mapping_data):
2771 """load_ensemble(SettingsData sd, Model mdl, ProteinsAnchorsSamplingSpace mapping_data) -> Ensemble"""
2772 return _IMP_multifit.load_ensemble(sd, mdl, mapping_data)
2774 """Proxy of C++ IMP::multifit::RigidLeavesRefiner class."""
2776 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2780 __init__(IMP::multifit::RigidLeavesRefiner self, std::string name) -> RigidLeavesRefiner
2781 __init__(IMP::multifit::RigidLeavesRefiner self) -> RigidLeavesRefiner
2783 this = _IMP_multifit.new_RigidLeavesRefiner(*args)
2785 self.this.append(this)
2786 except __builtin__.Exception:
2789 def do_get_inputs(self, m, pis):
2790 """do_get_inputs(RigidLeavesRefiner self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2791 return _IMP_multifit.RigidLeavesRefiner_do_get_inputs(self, m, pis)
2794 def get_version_info(self):
2795 """get_version_info(RigidLeavesRefiner self) -> VersionInfo"""
2796 return _IMP_multifit.RigidLeavesRefiner_get_version_info(self)
2800 """__str__(RigidLeavesRefiner self) -> std::string"""
2801 return _IMP_multifit.RigidLeavesRefiner___str__(self)
2805 """__repr__(RigidLeavesRefiner self) -> std::string"""
2806 return _IMP_multifit.RigidLeavesRefiner___repr__(self)
2811 return _object_cast_to_RigidLeavesRefiner(o)
2813 RigidLeavesRefiner_swigregister = _IMP_multifit.RigidLeavesRefiner_swigregister
2814 RigidLeavesRefiner_swigregister(RigidLeavesRefiner)
2817 _all_commands = [
"param",
"anchors",
"fit_fft",
"cluster",
"add_fit_rmsd",
2818 "indexes",
"proteomics",
"align",
"models",
"transforms",
2819 "score",
"merge_tree",
"reference",
"refine_fft",
"segment"]
2822 def get_module_version():
2823 """get_module_version() -> std::string const"""
2824 return _IMP_multifit.get_module_version()
2827 """get_example_path(std::string fname) -> std::string"""
2828 return _IMP_multifit.get_example_path(fname)
2831 """get_data_path(std::string fname) -> std::string"""
2832 return _IMP_multifit.get_data_path(fname)
2834 from .
import _version_check
2835 _version_check.check_version(get_module_version())
2836 __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.