10 from __future__
import print_function, division, absolute_import
15 from sys
import version_info
as _swig_python_version_info
16 if _swig_python_version_info >= (2, 7, 0):
17 def swig_import_helper():
19 pkg = __name__.rpartition(
'.')[0]
20 mname =
'.'.join((pkg,
'_IMP_multifit')).lstrip(
'.')
22 return importlib.import_module(mname)
24 return importlib.import_module(
'_IMP_multifit')
25 _IMP_multifit = swig_import_helper()
26 del swig_import_helper
27 elif _swig_python_version_info >= (2, 6, 0):
28 def swig_import_helper():
29 from os.path
import dirname
33 fp, pathname, description = imp.find_module(
'_IMP_multifit', [dirname(__file__)])
39 _mod = imp.load_module(
'_IMP_multifit', fp, pathname, description)
43 _IMP_multifit = swig_import_helper()
44 del swig_import_helper
47 del _swig_python_version_info
49 _swig_property = property
54 import builtins
as __builtin__
58 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
59 if (name ==
"thisown"):
60 return self.this.own(value)
62 if type(value).__name__ ==
'SwigPyObject':
63 self.__dict__[name] = value
65 method = class_type.__swig_setmethods__.get(name,
None)
67 return method(self, value)
69 object.__setattr__(self, name, value)
71 raise AttributeError(
"You cannot add attributes to %s" % self)
74 def _swig_setattr(self, class_type, name, value):
75 return _swig_setattr_nondynamic(self, class_type, name, value, 0)
78 def _swig_getattr(self, class_type, name):
79 if (name ==
"thisown"):
80 return self.this.own()
81 method = class_type.__swig_getmethods__.get(name,
None)
84 raise AttributeError(
"'%s' object has no attribute '%s'" % (class_type.__name__, name))
89 strthis =
"proxy of " + self.this.__repr__()
90 except __builtin__.Exception:
92 return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
95 def _swig_setattr_nondynamic_method(set):
96 def set_attr(self, name, value):
97 if (name ==
"thisown"):
98 return self.this.own(value)
99 if hasattr(self, name)
or (name ==
"this"):
100 set(self, name, value)
102 raise AttributeError(
"You cannot add attributes to %s" % self)
108 weakref_proxy = weakref.proxy
109 except __builtin__.Exception:
110 weakref_proxy =
lambda x: x
113 class IMP_MULTIFIT_SwigPyIterator(object):
114 """Proxy of C++ swig::IMP_MULTIFIT_SwigPyIterator class."""
116 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
118 def __init__(self, *args, **kwargs):
119 raise AttributeError(
"No constructor defined - class is abstract")
120 __repr__ = _swig_repr
121 __swig_destroy__ = _IMP_multifit.delete_IMP_MULTIFIT_SwigPyIterator
122 __del__ =
lambda self:
None
125 """value(IMP_MULTIFIT_SwigPyIterator self) -> PyObject *"""
126 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_value(self)
131 incr(IMP_MULTIFIT_SwigPyIterator self, size_t n=1) -> IMP_MULTIFIT_SwigPyIterator
132 incr(IMP_MULTIFIT_SwigPyIterator self) -> IMP_MULTIFIT_SwigPyIterator
134 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_incr(self, n)
139 decr(IMP_MULTIFIT_SwigPyIterator self, size_t n=1) -> IMP_MULTIFIT_SwigPyIterator
140 decr(IMP_MULTIFIT_SwigPyIterator self) -> IMP_MULTIFIT_SwigPyIterator
142 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_decr(self, n)
145 def distance(self, x):
146 """distance(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> ptrdiff_t"""
147 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_distance(self, x)
151 """equal(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> bool"""
152 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_equal(self, x)
156 """copy(IMP_MULTIFIT_SwigPyIterator self) -> IMP_MULTIFIT_SwigPyIterator"""
157 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_copy(self)
161 """next(IMP_MULTIFIT_SwigPyIterator self) -> PyObject *"""
162 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_next(self)
166 """__next__(IMP_MULTIFIT_SwigPyIterator self) -> PyObject *"""
167 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___next__(self)
171 """previous(IMP_MULTIFIT_SwigPyIterator self) -> PyObject *"""
172 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_previous(self)
175 def advance(self, n):
176 """advance(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator"""
177 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_advance(self, n)
181 """__eq__(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> bool"""
182 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___eq__(self, x)
186 """__ne__(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> bool"""
187 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___ne__(self, x)
190 def __iadd__(self, n):
191 """__iadd__(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator"""
192 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___iadd__(self, n)
195 def __isub__(self, n):
196 """__isub__(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator"""
197 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___isub__(self, n)
200 def __add__(self, n):
201 """__add__(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator"""
202 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___add__(self, n)
205 def __sub__(self, *args):
207 __sub__(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator
208 __sub__(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> ptrdiff_t
210 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___sub__(self, *args)
214 IMP_MULTIFIT_SwigPyIterator_swigregister = _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_swigregister
215 IMP_MULTIFIT_SwigPyIterator_swigregister(IMP_MULTIFIT_SwigPyIterator)
223 IMP_DEBUG = _IMP_multifit.IMP_DEBUG
224 IMP_RELEASE = _IMP_multifit.IMP_RELEASE
225 IMP_SILENT = _IMP_multifit.IMP_SILENT
226 IMP_PROGRESS = _IMP_multifit.IMP_PROGRESS
227 IMP_TERSE = _IMP_multifit.IMP_TERSE
228 IMP_VERBOSE = _IMP_multifit.IMP_VERBOSE
229 IMP_MEMORY = _IMP_multifit.IMP_MEMORY
230 IMP_NONE = _IMP_multifit.IMP_NONE
231 IMP_USAGE = _IMP_multifit.IMP_USAGE
232 IMP_INTERNAL = _IMP_multifit.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_multifit.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_multifit.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_multifit.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_multifit.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_multifit.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_NUMPY = _IMP_multifit.IMP_KERNEL_HAS_NUMPY
239 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_multifit.IMP_KERNEL_HAS_GPERFTOOLS
240 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_multifit.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
241 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_multifit.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
242 IMPKERNEL_SHOW_WARNINGS = _IMP_multifit.IMPKERNEL_SHOW_WARNINGS
245 class _DirectorObjects(object):
246 """@internal Simple class to keep references to director objects
247 to prevent premature deletion."""
250 def register(self, obj):
251 """Take a reference to a director object; will only work for
252 refcounted C++ classes"""
253 if hasattr(obj,
'get_ref_count'):
254 self._objects.append(obj)
256 """Only drop our reference and allow cleanup by Python if no other
257 Python references exist (we hold 3 references: one in self._objects,
258 one in x, and one in the argument list for getrefcount) *and* no
259 other C++ references exist (the Python object always holds one)"""
260 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
261 or x.get_ref_count() > 1]
265 def get_object_count(self):
266 """Get number of director objects (useful for testing only)"""
267 return len(self._objects)
268 _director_objects = _DirectorObjects()
270 class _ostream(object):
271 """Proxy of C++ std::ostream class."""
273 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
275 def __init__(self, *args, **kwargs):
276 raise AttributeError(
"No constructor defined")
277 __repr__ = _swig_repr
279 def write(self, osa_buf):
280 """write(_ostream self, char const * osa_buf)"""
281 return _IMP_multifit._ostream_write(self, osa_buf)
283 _ostream_swigregister = _IMP_multifit._ostream_swigregister
284 _ostream_swigregister(_ostream)
286 IMP_COMPILER_HAS_OVERRIDE = _IMP_multifit.IMP_COMPILER_HAS_OVERRIDE
287 IMP_COMPILER_HAS_FINAL = _IMP_multifit.IMP_COMPILER_HAS_FINAL
288 IMP_HAS_NOEXCEPT = _IMP_multifit.IMP_HAS_NOEXCEPT
289 IMP_C_OPEN_BINARY = _IMP_multifit.IMP_C_OPEN_BINARY
291 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CGAL_HAS_BOOST_FILESYSTEM
292 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
293 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CGAL_HAS_BOOST_RANDOM
294 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CGAL_HAS_BOOST_SYSTEM
295 IMP_CGAL_HAS_NUMPY = _IMP_multifit.IMP_CGAL_HAS_NUMPY
296 IMPCGAL_SHOW_WARNINGS = _IMP_multifit.IMPCGAL_SHOW_WARNINGS
298 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_multifit.IMP_ALGEBRA_HAS_IMP_CGAL
299 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
300 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
301 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_RANDOM
302 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_SYSTEM
303 IMP_ALGEBRA_HAS_CGAL = _IMP_multifit.IMP_ALGEBRA_HAS_CGAL
304 IMP_ALGEBRA_HAS_NUMPY = _IMP_multifit.IMP_ALGEBRA_HAS_NUMPY
305 IMP_ALGEBRA_HAS_ANN = _IMP_multifit.IMP_ALGEBRA_HAS_ANN
306 IMPALGEBRA_SHOW_WARNINGS = _IMP_multifit.IMPALGEBRA_SHOW_WARNINGS
308 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_multifit.IMP_DISPLAY_HAS_IMP_CGAL
309 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
310 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
311 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_RANDOM
312 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_SYSTEM
313 IMP_DISPLAY_HAS_CGAL = _IMP_multifit.IMP_DISPLAY_HAS_CGAL
314 IMP_DISPLAY_HAS_NUMPY = _IMP_multifit.IMP_DISPLAY_HAS_NUMPY
315 IMPDISPLAY_SHOW_WARNINGS = _IMP_multifit.IMPDISPLAY_SHOW_WARNINGS
317 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
318 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
319 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
320 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
321 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
322 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_CGAL
323 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_HDF5
324 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_NUMPY
325 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_multifit.IMPSCOREFUNCTOR_SHOW_WARNINGS
327 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_multifit.IMP_STATISTICS_HAS_IMP_CGAL
328 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
329 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
330 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_RANDOM
331 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_SYSTEM
332 IMP_STATISTICS_HAS_CGAL = _IMP_multifit.IMP_STATISTICS_HAS_CGAL
333 IMP_STATISTICS_HAS_NUMPY = _IMP_multifit.IMP_STATISTICS_HAS_NUMPY
334 IMPSTATISTICS_SHOW_WARNINGS = _IMP_multifit.IMPSTATISTICS_SHOW_WARNINGS
336 IMP_CORE_HAS_IMP_CGAL = _IMP_multifit.IMP_CORE_HAS_IMP_CGAL
337 IMP_CORE_HAS_IMP_KERNEL = _IMP_multifit.IMP_CORE_HAS_IMP_KERNEL
338 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CORE_HAS_BOOST_FILESYSTEM
339 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
340 IMP_CORE_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CORE_HAS_BOOST_RANDOM
341 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CORE_HAS_BOOST_SYSTEM
342 IMP_CORE_HAS_CGAL = _IMP_multifit.IMP_CORE_HAS_CGAL
343 IMP_CORE_HAS_HDF5 = _IMP_multifit.IMP_CORE_HAS_HDF5
344 IMP_CORE_HAS_NUMPY = _IMP_multifit.IMP_CORE_HAS_NUMPY
345 IMPCORE_SHOW_WARNINGS = _IMP_multifit.IMPCORE_SHOW_WARNINGS
347 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_multifit.IMP_CONTAINER_HAS_IMP_ALGEBRA
348 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_multifit.IMP_CONTAINER_HAS_IMP_CGAL
349 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_multifit.IMP_CONTAINER_HAS_IMP_DISPLAY
350 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_multifit.IMP_CONTAINER_HAS_IMP_KERNEL
351 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
352 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
353 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
354 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_RANDOM
355 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_SYSTEM
356 IMP_CONTAINER_HAS_CGAL = _IMP_multifit.IMP_CONTAINER_HAS_CGAL
357 IMP_CONTAINER_HAS_HDF5 = _IMP_multifit.IMP_CONTAINER_HAS_HDF5
358 IMP_CONTAINER_HAS_NUMPY = _IMP_multifit.IMP_CONTAINER_HAS_NUMPY
359 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_multifit.IMP_CONTAINER_HAS_PYTHON_IHM
360 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_multifit.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
361 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_multifit.IMP_CONTAINER_HAS_ROBIN_MAP
362 IMPCONTAINER_SHOW_WARNINGS = _IMP_multifit.IMPCONTAINER_SHOW_WARNINGS
364 IMP_ATOM_HAS_IMP_CGAL = _IMP_multifit.IMP_ATOM_HAS_IMP_CGAL
365 IMP_ATOM_HAS_IMP_KERNEL = _IMP_multifit.IMP_ATOM_HAS_IMP_KERNEL
366 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
367 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
368 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_multifit.IMP_ATOM_HAS_BOOST_RANDOM
369 IMP_ATOM_HAS_BOOST_REGEX = _IMP_multifit.IMP_ATOM_HAS_BOOST_REGEX
370 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_ATOM_HAS_BOOST_SYSTEM
371 IMP_ATOM_HAS_CGAL = _IMP_multifit.IMP_ATOM_HAS_CGAL
372 IMP_ATOM_HAS_HDF5 = _IMP_multifit.IMP_ATOM_HAS_HDF5
373 IMP_ATOM_HAS_NUMPY = _IMP_multifit.IMP_ATOM_HAS_NUMPY
374 IMP_ATOM_HAS_PYTHON_IHM = _IMP_multifit.IMP_ATOM_HAS_PYTHON_IHM
375 IMPATOM_SHOW_WARNINGS = _IMP_multifit.IMPATOM_SHOW_WARNINGS
376 IMP_ATOM_TYPE_INDEX = _IMP_multifit.IMP_ATOM_TYPE_INDEX
377 IMP_RESIDUE_TYPE_INDEX = _IMP_multifit.IMP_RESIDUE_TYPE_INDEX
378 IMP_HIERARCHY_TYPE_INDEX = _IMP_multifit.IMP_HIERARCHY_TYPE_INDEX
379 IMP_CHAIN_TYPE_INDEX = _IMP_multifit.IMP_CHAIN_TYPE_INDEX
381 IMP_EM_HAS_IMP_CGAL = _IMP_multifit.IMP_EM_HAS_IMP_CGAL
382 IMP_EM_HAS_IMP_CONTAINER = _IMP_multifit.IMP_EM_HAS_IMP_CONTAINER
383 IMP_EM_HAS_IMP_DISPLAY = _IMP_multifit.IMP_EM_HAS_IMP_DISPLAY
384 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_EM_HAS_IMP_SCORE_FUNCTOR
385 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_EM_HAS_BOOST_FILESYSTEM
386 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
387 IMP_EM_HAS_BOOST_RANDOM = _IMP_multifit.IMP_EM_HAS_BOOST_RANDOM
388 IMP_EM_HAS_BOOST_REGEX = _IMP_multifit.IMP_EM_HAS_BOOST_REGEX
389 IMP_EM_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_EM_HAS_BOOST_SYSTEM
390 IMP_EM_HAS_CGAL = _IMP_multifit.IMP_EM_HAS_CGAL
391 IMP_EM_HAS_HDF5 = _IMP_multifit.IMP_EM_HAS_HDF5
392 IMP_EM_HAS_NUMPY = _IMP_multifit.IMP_EM_HAS_NUMPY
393 IMP_EM_HAS_PYTHON_IHM = _IMP_multifit.IMP_EM_HAS_PYTHON_IHM
394 IMPEM_SHOW_WARNINGS = _IMP_multifit.IMPEM_SHOW_WARNINGS
396 IMP_SAXS_HAS_IMP_CGAL = _IMP_multifit.IMP_SAXS_HAS_IMP_CGAL
397 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_multifit.IMP_SAXS_HAS_IMP_CONTAINER
398 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_multifit.IMP_SAXS_HAS_IMP_DISPLAY
399 IMP_SAXS_HAS_IMP_KERNEL = _IMP_multifit.IMP_SAXS_HAS_IMP_KERNEL
400 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
401 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_SAXS_HAS_BOOST_FILESYSTEM
402 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
403 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_multifit.IMP_SAXS_HAS_BOOST_RANDOM
404 IMP_SAXS_HAS_BOOST_REGEX = _IMP_multifit.IMP_SAXS_HAS_BOOST_REGEX
405 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_SAXS_HAS_BOOST_SYSTEM
406 IMP_SAXS_HAS_CGAL = _IMP_multifit.IMP_SAXS_HAS_CGAL
407 IMP_SAXS_HAS_HDF5 = _IMP_multifit.IMP_SAXS_HAS_HDF5
408 IMP_SAXS_HAS_NUMPY = _IMP_multifit.IMP_SAXS_HAS_NUMPY
409 IMP_SAXS_HAS_PYTHON_IHM = _IMP_multifit.IMP_SAXS_HAS_PYTHON_IHM
410 IMPSAXS_SHOW_WARNINGS = _IMP_multifit.IMPSAXS_SHOW_WARNINGS
412 IMP_ISD_HAS_IMP_CGAL = _IMP_multifit.IMP_ISD_HAS_IMP_CGAL
413 IMP_ISD_HAS_IMP_DISPLAY = _IMP_multifit.IMP_ISD_HAS_IMP_DISPLAY
414 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
415 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_ISD_HAS_BOOST_FILESYSTEM
416 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
417 IMP_ISD_HAS_BOOST_RANDOM = _IMP_multifit.IMP_ISD_HAS_BOOST_RANDOM
418 IMP_ISD_HAS_BOOST_REGEX = _IMP_multifit.IMP_ISD_HAS_BOOST_REGEX
419 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_ISD_HAS_BOOST_SYSTEM
420 IMP_ISD_HAS_CGAL = _IMP_multifit.IMP_ISD_HAS_CGAL
421 IMP_ISD_HAS_HDF5 = _IMP_multifit.IMP_ISD_HAS_HDF5
422 IMP_ISD_HAS_NUMPY = _IMP_multifit.IMP_ISD_HAS_NUMPY
423 IMP_ISD_HAS_PYTHON_IHM = _IMP_multifit.IMP_ISD_HAS_PYTHON_IHM
424 IMPISD_SHOW_WARNINGS = _IMP_multifit.IMPISD_SHOW_WARNINGS
426 IMP_RMF_HAS_IMP_CGAL = _IMP_multifit.IMP_RMF_HAS_IMP_CGAL
427 IMP_RMF_HAS_IMP_EM = _IMP_multifit.IMP_RMF_HAS_IMP_EM
428 IMP_RMF_HAS_IMP_SAXS = _IMP_multifit.IMP_RMF_HAS_IMP_SAXS
429 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
430 IMP_RMF_HAS_IMP_STATISTICS = _IMP_multifit.IMP_RMF_HAS_IMP_STATISTICS
431 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_RMF_HAS_BOOST_FILESYSTEM
432 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
433 IMP_RMF_HAS_BOOST_RANDOM = _IMP_multifit.IMP_RMF_HAS_BOOST_RANDOM
434 IMP_RMF_HAS_BOOST_REGEX = _IMP_multifit.IMP_RMF_HAS_BOOST_REGEX
435 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_RMF_HAS_BOOST_SYSTEM
436 IMP_RMF_HAS_CGAL = _IMP_multifit.IMP_RMF_HAS_CGAL
437 IMP_RMF_HAS_HDF5 = _IMP_multifit.IMP_RMF_HAS_HDF5
438 IMP_RMF_HAS_NUMPY = _IMP_multifit.IMP_RMF_HAS_NUMPY
439 IMP_RMF_HAS_PYTHON_IHM = _IMP_multifit.IMP_RMF_HAS_PYTHON_IHM
440 IMPRMF_SHOW_WARNINGS = _IMP_multifit.IMPRMF_SHOW_WARNINGS
443 IMP_DOMINO_HAS_IMP_ATOM = _IMP_multifit.IMP_DOMINO_HAS_IMP_ATOM
444 IMP_DOMINO_HAS_IMP_CGAL = _IMP_multifit.IMP_DOMINO_HAS_IMP_CGAL
445 IMP_DOMINO_HAS_IMP_EM = _IMP_multifit.IMP_DOMINO_HAS_IMP_EM
446 IMP_DOMINO_HAS_IMP_ISD = _IMP_multifit.IMP_DOMINO_HAS_IMP_ISD
447 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_multifit.IMP_DOMINO_HAS_IMP_KERNEL
448 IMP_DOMINO_HAS_IMP_RMF = _IMP_multifit.IMP_DOMINO_HAS_IMP_RMF
449 IMP_DOMINO_HAS_IMP_SAXS = _IMP_multifit.IMP_DOMINO_HAS_IMP_SAXS
450 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
451 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_FILESYSTEM
452 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
453 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_RANDOM
454 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_multifit.IMP_DOMINO_HAS_BOOST_REGEX
455 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_SYSTEM
456 IMP_DOMINO_HAS_CGAL = _IMP_multifit.IMP_DOMINO_HAS_CGAL
457 IMP_DOMINO_HAS_HDF5 = _IMP_multifit.IMP_DOMINO_HAS_HDF5
458 IMP_DOMINO_HAS_NUMPY = _IMP_multifit.IMP_DOMINO_HAS_NUMPY
459 IMP_DOMINO_HAS_RMF = _IMP_multifit.IMP_DOMINO_HAS_RMF
460 IMP_DOMINO_HAS_PYTHON_IHM = _IMP_multifit.IMP_DOMINO_HAS_PYTHON_IHM
461 IMPDOMINO_SHOW_WARNINGS = _IMP_multifit.IMPDOMINO_SHOW_WARNINGS
464 IMP_MULTIFIT_HAS_IMP_CGAL = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_CGAL
465 IMP_MULTIFIT_HAS_IMP_CONTAINER = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_CONTAINER
466 IMP_MULTIFIT_HAS_IMP_DISPLAY = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_DISPLAY
467 IMP_MULTIFIT_HAS_IMP_ISD = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_ISD
468 IMP_MULTIFIT_HAS_IMP_KERNEL = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_KERNEL
469 IMP_MULTIFIT_HAS_IMP_RMF = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_RMF
470 IMP_MULTIFIT_HAS_IMP_SAXS = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_SAXS
471 IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR
472 IMP_MULTIFIT_HAS_BOOST_GRAPH = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_GRAPH
473 IMP_MULTIFIT_HAS_BOOST_RANDOM = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_RANDOM
474 IMP_MULTIFIT_HAS_BOOST_REGEX = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_REGEX
475 IMP_MULTIFIT_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_SYSTEM
476 IMP_MULTIFIT_HAS_CGAL = _IMP_multifit.IMP_MULTIFIT_HAS_CGAL
477 IMP_MULTIFIT_HAS_HDF5 = _IMP_multifit.IMP_MULTIFIT_HAS_HDF5
478 IMP_MULTIFIT_HAS_NUMPY = _IMP_multifit.IMP_MULTIFIT_HAS_NUMPY
479 IMP_MULTIFIT_HAS_RMF = _IMP_multifit.IMP_MULTIFIT_HAS_RMF
480 IMP_MULTIFIT_HAS_PYTHON_IHM = _IMP_multifit.IMP_MULTIFIT_HAS_PYTHON_IHM
481 IMPMULTIFIT_SHOW_WARNINGS = _IMP_multifit.IMPMULTIFIT_SHOW_WARNINGS
483 _object_types.append(
"RadiusOfGyrationRestraint")
486 def _object_cast_to_RadiusOfGyrationRestraint(o):
487 """_object_cast_to_RadiusOfGyrationRestraint(Object o) -> RadiusOfGyrationRestraint"""
488 return _IMP_multifit._object_cast_to_RadiusOfGyrationRestraint(o)
490 _object_types.append(
"ComponentHeader")
493 def _object_cast_to_ComponentHeader(o):
494 """_object_cast_to_ComponentHeader(Object o) -> ComponentHeader"""
495 return _IMP_multifit._object_cast_to_ComponentHeader(o)
497 _object_types.append(
"AssemblyHeader")
500 def _object_cast_to_AssemblyHeader(o):
501 """_object_cast_to_AssemblyHeader(Object o) -> AssemblyHeader"""
502 return _IMP_multifit._object_cast_to_AssemblyHeader(o)
504 _object_types.append(
"SettingsData")
507 def _object_cast_to_SettingsData(o):
508 """_object_cast_to_SettingsData(Object o) -> SettingsData"""
509 return _IMP_multifit._object_cast_to_SettingsData(o)
511 _object_types.append(
"WeightedExcludedVolumeRestraint")
514 def _object_cast_to_WeightedExcludedVolumeRestraint(o):
515 """_object_cast_to_WeightedExcludedVolumeRestraint(Object o) -> WeightedExcludedVolumeRestraint"""
516 return _IMP_multifit._object_cast_to_WeightedExcludedVolumeRestraint(o)
518 _object_types.append(
"ComplementarityRestraint")
521 def _object_cast_to_ComplementarityRestraint(o):
522 """_object_cast_to_ComplementarityRestraint(Object o) -> ComplementarityRestraint"""
523 return _IMP_multifit._object_cast_to_ComplementarityRestraint(o)
525 ProteinRecordDataList=list
526 _plural_types.append(
"ProteinRecordDataList")
527 _value_types.append(
"ProteinRecordData")
530 FittingSolutionRecords=list
531 _plural_types.append(
"FittingSolutionRecords")
532 _value_types.append(
"FittingSolutionRecord")
536 _plural_types.append(
"AnchorsDataList")
537 _value_types.append(
"AnchorsData")
540 DominoParamsList=list
541 _plural_types.append(
"DominoParamsList")
542 _value_types.append(
"DominoParams")
545 ComplementarityParamsList=list
546 _plural_types.append(
"ComplementarityParamsList")
547 _value_types.append(
"ComplementarityParams")
551 _plural_types.append(
"XlinkParamsList")
552 _value_types.append(
"XlinkParams")
555 ConnectivityParamsList=list
556 _plural_types.append(
"ConnectivityParamsList")
557 _value_types.append(
"ConnectivityParams")
560 FragmentsParamsList=list
561 _plural_types.append(
"FragmentsParamsList")
562 _value_types.append(
"FragmentsParams")
566 _plural_types.append(
"RogParamsList")
567 _value_types.append(
"RogParams")
571 _plural_types.append(
"EVParamsList")
572 _value_types.append(
"EVParams")
575 FiltersParamsList=list
576 _plural_types.append(
"FiltersParamsList")
577 _value_types.append(
"FiltersParams")
580 AlignmentParamsList=list
581 _plural_types.append(
"AlignmentParamsList")
582 _value_types.append(
"AlignmentParams")
585 FittingParamsList=list
586 _plural_types.append(
"FittingParamsList")
587 _value_types.append(
"FittingParams")
590 ProteinsAnchorsSamplingSpaces=list
591 _plural_types.append(
"ProteinsAnchorsSamplingSpaces")
592 _value_types.append(
"ProteinsAnchorsSamplingSpace")
595 _object_types.append(
"ProteomicsData")
598 def _object_cast_to_ProteomicsData(o):
599 """_object_cast_to_ProteomicsData(Object o) -> ProteomicsData"""
600 return _IMP_multifit._object_cast_to_ProteomicsData(o)
602 _object_types.append(
"FFTFitting")
605 def _object_cast_to_FFTFitting(o):
606 """_object_cast_to_FFTFitting(Object o) -> FFTFitting"""
607 return _IMP_multifit._object_cast_to_FFTFitting(o)
609 _object_types.append(
"FFTFittingOutput")
612 def _object_cast_to_FFTFittingOutput(o):
613 """_object_cast_to_FFTFittingOutput(Object o) -> FFTFittingOutput"""
614 return _IMP_multifit._object_cast_to_FFTFittingOutput(o)
616 _object_types.append(
"ProbabilisticAnchorGraph")
619 def _object_cast_to_ProbabilisticAnchorGraph(o):
620 """_object_cast_to_ProbabilisticAnchorGraph(Object o) -> ProbabilisticAnchorGraph"""
621 return _IMP_multifit._object_cast_to_ProbabilisticAnchorGraph(o)
623 _object_types.append(
"Ensemble")
626 def _object_cast_to_Ensemble(o):
627 """_object_cast_to_Ensemble(Object o) -> Ensemble"""
628 return _IMP_multifit._object_cast_to_Ensemble(o)
630 _object_types.append(
"ProteomicsEMAlignmentAtomic")
633 def _object_cast_to_ProteomicsEMAlignmentAtomic(o):
634 """_object_cast_to_ProteomicsEMAlignmentAtomic(Object o) -> ProteomicsEMAlignmentAtomic"""
635 return _IMP_multifit._object_cast_to_ProteomicsEMAlignmentAtomic(o)
637 _object_types.append(
"RigidLeavesRefiner")
640 def _object_cast_to_RigidLeavesRefiner(o):
641 """_object_cast_to_RigidLeavesRefiner(Object o) -> RigidLeavesRefiner"""
642 return _IMP_multifit._object_cast_to_RigidLeavesRefiner(o)
646 add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key, FloatKey radius_key, FloatKey weight_key)
647 add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key, FloatKey radius_key)
648 add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key)
649 add_surface_index(Hierarchy mhd, IMP::Float apix)
651 return _IMP_multifit.add_surface_index(*args)
655 create_weighted_excluded_volume_restraint(RigidBody rb1, RigidBody rb2, FloatKey shell_key) -> Restraint
656 create_weighted_excluded_volume_restraint(RigidBody rb1, RigidBody rb2) -> Restraint
658 return _IMP_multifit.create_weighted_excluded_volume_restraint(*args)
659 class FittingSolutionRecord(object):
660 """Proxy of C++ IMP::multifit::FittingSolutionRecord class."""
662 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
665 """__init__(IMP::multifit::FittingSolutionRecord self) -> FittingSolutionRecord"""
666 this = _IMP_multifit.new_FittingSolutionRecord()
668 self.this.append(this)
669 except __builtin__.Exception:
673 """get_index(FittingSolutionRecord self) -> unsigned int"""
674 return _IMP_multifit.FittingSolutionRecord_get_index(self)
677 def set_index(self, new_ind):
678 """set_index(FittingSolutionRecord self, unsigned int new_ind)"""
679 return _IMP_multifit.FittingSolutionRecord_set_index(self, new_ind)
682 def get_solution_filename(self):
683 """get_solution_filename(FittingSolutionRecord self) -> std::string"""
684 return _IMP_multifit.FittingSolutionRecord_get_solution_filename(self)
687 def set_solution_filename(self, sol_fn):
688 """set_solution_filename(FittingSolutionRecord self, std::string sol_fn)"""
689 return _IMP_multifit.FittingSolutionRecord_set_solution_filename(self, sol_fn)
692 def get_fit_transformation(self):
693 """get_fit_transformation(FittingSolutionRecord self) -> Transformation3D"""
694 return _IMP_multifit.FittingSolutionRecord_get_fit_transformation(self)
697 def set_fit_transformation(self, t):
698 """set_fit_transformation(FittingSolutionRecord self, Transformation3D t)"""
699 return _IMP_multifit.FittingSolutionRecord_set_fit_transformation(self, t)
702 def get_match_size(self):
703 """get_match_size(FittingSolutionRecord self) -> unsigned int"""
704 return _IMP_multifit.FittingSolutionRecord_get_match_size(self)
707 def set_match_size(self, match_size):
708 """set_match_size(FittingSolutionRecord self, unsigned int match_size)"""
709 return _IMP_multifit.FittingSolutionRecord_set_match_size(self, match_size)
712 def get_match_average_distance(self):
713 """get_match_average_distance(FittingSolutionRecord self) -> IMP::Float"""
714 return _IMP_multifit.FittingSolutionRecord_get_match_average_distance(self)
717 def set_match_average_distance(self, match_avg_dist):
718 """set_match_average_distance(FittingSolutionRecord self, IMP::Float match_avg_dist)"""
719 return _IMP_multifit.FittingSolutionRecord_set_match_average_distance(self, match_avg_dist)
722 def get_fitting_score(self):
723 """get_fitting_score(FittingSolutionRecord self) -> IMP::Float"""
724 return _IMP_multifit.FittingSolutionRecord_get_fitting_score(self)
727 def set_fitting_score(self, fit_score):
728 """set_fitting_score(FittingSolutionRecord self, IMP::Float fit_score)"""
729 return _IMP_multifit.FittingSolutionRecord_set_fitting_score(self, fit_score)
732 def get_rmsd_to_reference(self):
733 """get_rmsd_to_reference(FittingSolutionRecord self) -> IMP::Float"""
734 return _IMP_multifit.FittingSolutionRecord_get_rmsd_to_reference(self)
737 def set_rmsd_to_reference(self, rmsd_to_ref):
738 """set_rmsd_to_reference(FittingSolutionRecord self, IMP::Float rmsd_to_ref)"""
739 return _IMP_multifit.FittingSolutionRecord_set_rmsd_to_reference(self, rmsd_to_ref)
742 def get_dock_transformation(self):
743 """get_dock_transformation(FittingSolutionRecord self) -> Transformation3D"""
744 return _IMP_multifit.FittingSolutionRecord_get_dock_transformation(self)
747 def set_dock_transformation(self, t):
748 """set_dock_transformation(FittingSolutionRecord self, Transformation3D t)"""
749 return _IMP_multifit.FittingSolutionRecord_set_dock_transformation(self, t)
752 def get_envelope_penetration_score(self):
753 """get_envelope_penetration_score(FittingSolutionRecord self) -> IMP::Float"""
754 return _IMP_multifit.FittingSolutionRecord_get_envelope_penetration_score(self)
757 def set_envelope_penetration_score(self, s):
758 """set_envelope_penetration_score(FittingSolutionRecord self, IMP::Float s)"""
759 return _IMP_multifit.FittingSolutionRecord_set_envelope_penetration_score(self, s)
762 def show(self, *args):
764 show(FittingSolutionRecord self, _ostream out)
765 show(FittingSolutionRecord self)
767 return _IMP_multifit.FittingSolutionRecord_show(self, *args)
770 def get_record_header():
771 """get_record_header() -> std::string"""
772 return _IMP_multifit.FittingSolutionRecord_get_record_header()
774 get_record_header = staticmethod(get_record_header)
777 """__str__(FittingSolutionRecord self) -> std::string"""
778 return _IMP_multifit.FittingSolutionRecord___str__(self)
782 """__repr__(FittingSolutionRecord self) -> std::string"""
783 return _IMP_multifit.FittingSolutionRecord___repr__(self)
785 __swig_destroy__ = _IMP_multifit.delete_FittingSolutionRecord
786 __del__ =
lambda self:
None
787 FittingSolutionRecord_swigregister = _IMP_multifit.FittingSolutionRecord_swigregister
788 FittingSolutionRecord_swigregister(FittingSolutionRecord)
790 def FittingSolutionRecord_get_record_header():
791 """FittingSolutionRecord_get_record_header() -> std::string"""
792 return _IMP_multifit.FittingSolutionRecord_get_record_header()
797 pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold, FloatKey wei_key, PrincipalComponentAnalysis3D dens_pca_input) -> FittingSolutions
798 pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold, FloatKey wei_key) -> FittingSolutions
799 pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold) -> FittingSolutions
800 pca_based_rigid_fitting(IMP::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold, FloatKey wei_key, PrincipalComponentAnalysis3D dens_pca_input) -> FittingSolutions
801 pca_based_rigid_fitting(IMP::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold, FloatKey wei_key) -> FittingSolutions
802 pca_based_rigid_fitting(IMP::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold) -> FittingSolutions
804 return _IMP_multifit.pca_based_rigid_fitting(*args)
806 def write_markers(pca, out):
807 """write_markers(PrincipalComponentAnalysis3D pca, _ostream out)"""
808 return _IMP_multifit.write_markers(pca, out)
810 """Proxy of C++ IMP::multifit::ComponentHeader class."""
812 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
815 """__init__(IMP::multifit::ComponentHeader self) -> ComponentHeader"""
816 this = _IMP_multifit.new_ComponentHeader()
818 self.this.append(this)
819 except __builtin__.Exception:
822 def set_name(self, name):
823 """set_name(ComponentHeader self, std::string const & name)"""
824 return _IMP_multifit.ComponentHeader_set_name(self, name)
828 """get_name(ComponentHeader self) -> std::string"""
829 return _IMP_multifit.ComponentHeader_get_name(self)
832 def get_filename(self):
833 """get_filename(ComponentHeader self) -> std::string"""
834 return _IMP_multifit.ComponentHeader_get_filename(self)
837 def set_filename(self, filename):
838 """set_filename(ComponentHeader self, std::string const & filename)"""
839 return _IMP_multifit.ComponentHeader_set_filename(self, filename)
842 def get_surface_fn(self):
843 """get_surface_fn(ComponentHeader self) -> std::string"""
844 return _IMP_multifit.ComponentHeader_get_surface_fn(self)
847 def set_surface_fn(self, fn):
848 """set_surface_fn(ComponentHeader self, std::string const & fn)"""
849 return _IMP_multifit.ComponentHeader_set_surface_fn(self, fn)
852 def set_txt_ap_fn(self, pdb_ap_fn):
853 """set_txt_ap_fn(ComponentHeader self, std::string const & pdb_ap_fn)"""
854 return _IMP_multifit.ComponentHeader_set_txt_ap_fn(self, pdb_ap_fn)
857 def get_txt_ap_fn(self):
858 """get_txt_ap_fn(ComponentHeader self) -> std::string"""
859 return _IMP_multifit.ComponentHeader_get_txt_ap_fn(self)
862 def set_txt_fine_ap_fn(self, pdb_ap_fn):
863 """set_txt_fine_ap_fn(ComponentHeader self, std::string const & pdb_ap_fn)"""
864 return _IMP_multifit.ComponentHeader_set_txt_fine_ap_fn(self, pdb_ap_fn)
867 def get_txt_fine_ap_fn(self):
868 """get_txt_fine_ap_fn(ComponentHeader self) -> std::string"""
869 return _IMP_multifit.ComponentHeader_get_txt_fine_ap_fn(self)
872 def set_num_ap(self, num_ap):
873 """set_num_ap(ComponentHeader self, int num_ap)"""
874 return _IMP_multifit.ComponentHeader_set_num_ap(self, num_ap)
877 def get_num_ap(self):
878 """get_num_ap(ComponentHeader self) -> int"""
879 return _IMP_multifit.ComponentHeader_get_num_ap(self)
882 def set_num_fine_ap(self, num_ap):
883 """set_num_fine_ap(ComponentHeader self, int num_ap)"""
884 return _IMP_multifit.ComponentHeader_set_num_fine_ap(self, num_ap)
887 def get_num_fine_ap(self):
888 """get_num_fine_ap(ComponentHeader self) -> int"""
889 return _IMP_multifit.ComponentHeader_get_num_fine_ap(self)
892 def set_transformations_fn(self, transformations_fn):
893 """set_transformations_fn(ComponentHeader self, std::string transformations_fn)"""
894 return _IMP_multifit.ComponentHeader_set_transformations_fn(self, transformations_fn)
897 def get_transformations_fn(self):
898 """get_transformations_fn(ComponentHeader self) -> std::string"""
899 return _IMP_multifit.ComponentHeader_get_transformations_fn(self)
902 def set_reference_fn(self, ref_fn):
903 """set_reference_fn(ComponentHeader self, std::string const & ref_fn)"""
904 return _IMP_multifit.ComponentHeader_set_reference_fn(self, ref_fn)
907 def get_reference_fn(self):
908 """get_reference_fn(ComponentHeader self) -> std::string"""
909 return _IMP_multifit.ComponentHeader_get_reference_fn(self)
912 def get_version_info(self):
913 """get_version_info(ComponentHeader self) -> VersionInfo"""
914 return _IMP_multifit.ComponentHeader_get_version_info(self)
918 """__str__(ComponentHeader self) -> std::string"""
919 return _IMP_multifit.ComponentHeader___str__(self)
923 """__repr__(ComponentHeader self) -> std::string"""
924 return _IMP_multifit.ComponentHeader___repr__(self)
929 return _object_cast_to_ComponentHeader(o)
931 ComponentHeader_swigregister = _IMP_multifit.ComponentHeader_swigregister
932 ComponentHeader_swigregister(ComponentHeader)
935 """Proxy of C++ IMP::multifit::AssemblyHeader class."""
937 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
940 """__init__(IMP::multifit::AssemblyHeader self) -> AssemblyHeader"""
941 this = _IMP_multifit.new_AssemblyHeader()
943 self.this.append(this)
944 except __builtin__.Exception:
947 def set_dens_fn(self, dens_fn):
948 """set_dens_fn(AssemblyHeader self, std::string const & dens_fn)"""
949 return _IMP_multifit.AssemblyHeader_set_dens_fn(self, dens_fn)
952 def get_dens_fn(self):
953 """get_dens_fn(AssemblyHeader self) -> std::string"""
954 return _IMP_multifit.AssemblyHeader_get_dens_fn(self)
957 def set_resolution(self, res):
958 """set_resolution(AssemblyHeader self, float res)"""
959 return _IMP_multifit.AssemblyHeader_set_resolution(self, res)
963 """get_resolution(AssemblyHeader self) -> float"""
964 return _IMP_multifit.AssemblyHeader_get_resolution(self)
967 def get_spacing(self):
968 """get_spacing(AssemblyHeader self) -> float"""
969 return _IMP_multifit.AssemblyHeader_get_spacing(self)
972 def set_spacing(self, spacing):
973 """set_spacing(AssemblyHeader self, float spacing)"""
974 return _IMP_multifit.AssemblyHeader_set_spacing(self, spacing)
977 def set_threshold(self, t):
978 """set_threshold(AssemblyHeader self, float t)"""
979 return _IMP_multifit.AssemblyHeader_set_threshold(self, t)
982 def get_threshold(self):
983 """get_threshold(AssemblyHeader self) -> float"""
984 return _IMP_multifit.AssemblyHeader_get_threshold(self)
987 def get_origin(self):
988 """get_origin(AssemblyHeader self) -> Vector3D"""
989 return _IMP_multifit.AssemblyHeader_get_origin(self)
992 def set_origin(self, origin):
993 """set_origin(AssemblyHeader self, Vector3D origin)"""
994 return _IMP_multifit.AssemblyHeader_set_origin(self, origin)
997 def get_coarse_ap_fn(self):
998 """get_coarse_ap_fn(AssemblyHeader self) -> std::string"""
999 return _IMP_multifit.AssemblyHeader_get_coarse_ap_fn(self)
1002 def set_coarse_ap_fn(self, new_fn):
1003 """set_coarse_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
1004 return _IMP_multifit.AssemblyHeader_set_coarse_ap_fn(self, new_fn)
1007 def get_coarse_over_sampled_ap_fn(self):
1008 """get_coarse_over_sampled_ap_fn(AssemblyHeader self) -> std::string"""
1009 return _IMP_multifit.AssemblyHeader_get_coarse_over_sampled_ap_fn(self)
1012 def set_coarse_over_sampled_ap_fn(self, new_fn):
1013 """set_coarse_over_sampled_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
1014 return _IMP_multifit.AssemblyHeader_set_coarse_over_sampled_ap_fn(self, new_fn)
1017 def get_fine_ap_fn(self):
1018 """get_fine_ap_fn(AssemblyHeader self) -> std::string"""
1019 return _IMP_multifit.AssemblyHeader_get_fine_ap_fn(self)
1022 def set_fine_ap_fn(self, new_fn):
1023 """set_fine_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
1024 return _IMP_multifit.AssemblyHeader_set_fine_ap_fn(self, new_fn)
1027 def get_fine_over_sampled_ap_fn(self):
1028 """get_fine_over_sampled_ap_fn(AssemblyHeader self) -> std::string"""
1029 return _IMP_multifit.AssemblyHeader_get_fine_over_sampled_ap_fn(self)
1032 def set_fine_over_sampled_ap_fn(self, new_fn):
1033 """set_fine_over_sampled_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
1034 return _IMP_multifit.AssemblyHeader_set_fine_over_sampled_ap_fn(self, new_fn)
1037 def get_version_info(self):
1038 """get_version_info(AssemblyHeader self) -> VersionInfo"""
1039 return _IMP_multifit.AssemblyHeader_get_version_info(self)
1043 """__str__(AssemblyHeader self) -> std::string"""
1044 return _IMP_multifit.AssemblyHeader___str__(self)
1048 """__repr__(AssemblyHeader self) -> std::string"""
1049 return _IMP_multifit.AssemblyHeader___repr__(self)
1054 return _object_cast_to_AssemblyHeader(o)
1056 AssemblyHeader_swigregister = _IMP_multifit.AssemblyHeader_swigregister
1057 AssemblyHeader_swigregister(AssemblyHeader)
1060 """Proxy of C++ IMP::multifit::SettingsData class."""
1062 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1065 """__init__(IMP::multifit::SettingsData self) -> SettingsData"""
1066 this = _IMP_multifit.new_SettingsData()
1068 self.this.append(this)
1069 except __builtin__.Exception:
1072 def show_component_header_line(*args):
1074 show_component_header_line(_ostream out)
1075 show_component_header_line()
1077 return _IMP_multifit.SettingsData_show_component_header_line(*args)
1079 show_component_header_line = staticmethod(show_component_header_line)
1081 def get_component_header_line():
1082 """get_component_header_line() -> std::string"""
1083 return _IMP_multifit.SettingsData_get_component_header_line()
1085 get_component_header_line = staticmethod(get_component_header_line)
1087 def show_density_header_line(*args):
1089 show_density_header_line(_ostream out)
1090 show_density_header_line()
1092 return _IMP_multifit.SettingsData_show_density_header_line(*args)
1094 show_density_header_line = staticmethod(show_density_header_line)
1096 def get_density_header_line():
1097 """get_density_header_line() -> std::string"""
1098 return _IMP_multifit.SettingsData_get_density_header_line()
1100 get_density_header_line = staticmethod(get_density_header_line)
1102 def set_assembly_filename(self, fn):
1103 """set_assembly_filename(SettingsData self, std::string const & fn)"""
1104 return _IMP_multifit.SettingsData_set_assembly_filename(self, fn)
1107 def get_assembly_filename(self):
1108 """get_assembly_filename(SettingsData self) -> char const *"""
1109 return _IMP_multifit.SettingsData_get_assembly_filename(self)
1112 def set_assembly_header(self, h):
1113 """set_assembly_header(SettingsData self, AssemblyHeader h)"""
1114 return _IMP_multifit.SettingsData_set_assembly_header(self, h)
1117 def get_assembly_header(self):
1118 """get_assembly_header(SettingsData self) -> AssemblyHeader"""
1119 return _IMP_multifit.SettingsData_get_assembly_header(self)
1122 def set_data_path(self, fn):
1123 """set_data_path(SettingsData self, std::string const & fn)"""
1124 return _IMP_multifit.SettingsData_set_data_path(self, fn)
1128 """get_data_path(SettingsData self) -> std::string"""
1129 return _IMP_multifit.SettingsData_get_data_path(self)
1132 def get_version_info(self):
1133 """get_version_info(SettingsData self) -> VersionInfo"""
1134 return _IMP_multifit.SettingsData_get_version_info(self)
1137 def remove_component_header(self, d):
1138 """remove_component_header(SettingsData self, ComponentHeader d)"""
1139 return _IMP_multifit.SettingsData_remove_component_header(self, d)
1142 def remove_component_headers(self, d):
1143 """remove_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & d)"""
1144 return _IMP_multifit.SettingsData_remove_component_headers(self, d)
1147 def set_component_headers(self, ps):
1148 """set_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & ps)"""
1149 return _IMP_multifit.SettingsData_set_component_headers(self, ps)
1152 def set_component_headers_order(self, objs):
1153 """set_component_headers_order(SettingsData self, IMP::multifit::ComponentHeaders const & objs)"""
1154 return _IMP_multifit.SettingsData_set_component_headers_order(self, objs)
1157 def add_component_header(self, obj):
1158 """add_component_header(SettingsData self, ComponentHeader obj) -> unsigned int"""
1159 return _IMP_multifit.SettingsData_add_component_header(self, obj)
1162 def add_component_headers(self, objs):
1163 """add_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & objs)"""
1164 return _IMP_multifit.SettingsData_add_component_headers(self, objs)
1167 def clear_component_headers(self):
1168 """clear_component_headers(SettingsData self)"""
1169 return _IMP_multifit.SettingsData_clear_component_headers(self)
1172 def get_number_of_component_headers(self):
1173 """get_number_of_component_headers(SettingsData self) -> unsigned int"""
1174 return _IMP_multifit.SettingsData_get_number_of_component_headers(self)
1177 def get_has_component_headers(self):
1178 """get_has_component_headers(SettingsData self) -> bool"""
1179 return _IMP_multifit.SettingsData_get_has_component_headers(self)
1182 def get_component_header(self, i):
1183 """get_component_header(SettingsData self, unsigned int i) -> ComponentHeader"""
1184 return _IMP_multifit.SettingsData_get_component_header(self, i)
1187 def get_component_headers(self):
1188 """get_component_headers(SettingsData self) -> IMP::multifit::ComponentHeaders"""
1189 return _IMP_multifit.SettingsData_get_component_headers(self)
1192 def reserve_component_headers(self, sz):
1193 """reserve_component_headers(SettingsData self, unsigned int sz)"""
1194 return _IMP_multifit.SettingsData_reserve_component_headers(self, sz)
1198 """__str__(SettingsData self) -> std::string"""
1199 return _IMP_multifit.SettingsData___str__(self)
1203 """__repr__(SettingsData self) -> std::string"""
1204 return _IMP_multifit.SettingsData___repr__(self)
1209 return _object_cast_to_SettingsData(o)
1211 SettingsData_swigregister = _IMP_multifit.SettingsData_swigregister
1212 SettingsData_swigregister(SettingsData)
1214 def SettingsData_show_component_header_line(*args):
1216 show_component_header_line(_ostream out)
1217 SettingsData_show_component_header_line()
1219 return _IMP_multifit.SettingsData_show_component_header_line(*args)
1221 def SettingsData_get_component_header_line():
1222 """SettingsData_get_component_header_line() -> std::string"""
1223 return _IMP_multifit.SettingsData_get_component_header_line()
1225 def SettingsData_show_density_header_line(*args):
1227 show_density_header_line(_ostream out)
1228 SettingsData_show_density_header_line()
1230 return _IMP_multifit.SettingsData_show_density_header_line(*args)
1232 def SettingsData_get_density_header_line():
1233 """SettingsData_get_density_header_line() -> std::string"""
1234 return _IMP_multifit.SettingsData_get_density_header_line()
1237 def read_settings(filename):
1238 """read_settings(char const * filename) -> SettingsData"""
1239 return _IMP_multifit.read_settings(filename)
1241 def write_settings(filename, sd):
1242 """write_settings(char const * filename, SettingsData sd)"""
1243 return _IMP_multifit.write_settings(filename, sd)
1245 """Proxy of C++ IMP::multifit::WeightedExcludedVolumeRestraint class."""
1247 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1251 __init__(IMP::multifit::WeightedExcludedVolumeRestraint self, IMP::core::RigidBodies rbs, Refiner refiner, FloatKey weight_key) -> WeightedExcludedVolumeRestraint
1252 __init__(IMP::multifit::WeightedExcludedVolumeRestraint self, IMP::core::RigidBodies rbs, Refiner refiner) -> WeightedExcludedVolumeRestraint
1254 this = _IMP_multifit.new_WeightedExcludedVolumeRestraint(*args)
1256 self.this.append(this)
1257 except __builtin__.Exception:
1260 def do_get_inputs(self):
1261 """do_get_inputs(WeightedExcludedVolumeRestraint self) -> IMP::ModelObjectsTemp"""
1262 return _IMP_multifit.WeightedExcludedVolumeRestraint_do_get_inputs(self)
1265 def get_version_info(self):
1266 """get_version_info(WeightedExcludedVolumeRestraint self) -> VersionInfo"""
1267 return _IMP_multifit.WeightedExcludedVolumeRestraint_get_version_info(self)
1271 """__str__(WeightedExcludedVolumeRestraint self) -> std::string"""
1272 return _IMP_multifit.WeightedExcludedVolumeRestraint___str__(self)
1276 """__repr__(WeightedExcludedVolumeRestraint self) -> std::string"""
1277 return _IMP_multifit.WeightedExcludedVolumeRestraint___repr__(self)
1282 return _object_cast_to_WeightedExcludedVolumeRestraint(o)
1284 WeightedExcludedVolumeRestraint_swigregister = _IMP_multifit.WeightedExcludedVolumeRestraint_swigregister
1285 WeightedExcludedVolumeRestraint_swigregister(WeightedExcludedVolumeRestraint)
1288 """Proxy of C++ IMP::multifit::FFTFittingOutput class."""
1290 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1293 """__init__(IMP::multifit::FFTFittingOutput self) -> FFTFittingOutput"""
1294 this = _IMP_multifit.new_FFTFittingOutput()
1296 self.this.append(this)
1297 except __builtin__.Exception:
1300 def get_version_info(self):
1301 """get_version_info(FFTFittingOutput self) -> VersionInfo"""
1302 return _IMP_multifit.FFTFittingOutput_get_version_info(self)
1304 best_fits_ = _swig_property(_IMP_multifit.FFTFittingOutput_best_fits__get, _IMP_multifit.FFTFittingOutput_best_fits__set)
1305 best_trans_per_rot_ = _swig_property(_IMP_multifit.FFTFittingOutput_best_trans_per_rot__get, _IMP_multifit.FFTFittingOutput_best_trans_per_rot__set)
1308 """__str__(FFTFittingOutput self) -> std::string"""
1309 return _IMP_multifit.FFTFittingOutput___str__(self)
1313 """__repr__(FFTFittingOutput self) -> std::string"""
1314 return _IMP_multifit.FFTFittingOutput___repr__(self)
1319 return _object_cast_to_FFTFittingOutput(o)
1321 FFTFittingOutput_swigregister = _IMP_multifit.FFTFittingOutput_swigregister
1322 FFTFittingOutput_swigregister(FFTFittingOutput)
1325 """Proxy of C++ IMP::multifit::FFTFitting class."""
1327 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1329 def get_version_info(self):
1330 """get_version_info(FFTFitting self) -> VersionInfo"""
1331 return _IMP_multifit.FFTFitting_get_version_info(self)
1335 """__init__(IMP::multifit::FFTFitting self) -> FFTFitting"""
1336 this = _IMP_multifit.new_FFTFitting()
1338 self.this.append(this)
1339 except __builtin__.Exception:
1342 def do_global_fitting(self, *args):
1344 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
1345 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
1346 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
1347 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
1349 return _IMP_multifit.FFTFitting_do_global_fitting(self, *args)
1352 def do_local_fitting(self, *args):
1354 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
1355 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
1357 return _IMP_multifit.FFTFitting_do_local_fitting(self, *args)
1361 """__str__(FFTFitting self) -> std::string"""
1362 return _IMP_multifit.FFTFitting___str__(self)
1366 """__repr__(FFTFitting self) -> std::string"""
1367 return _IMP_multifit.FFTFitting___repr__(self)
1372 return _object_cast_to_FFTFitting(o)
1374 FFTFitting_swigregister = _IMP_multifit.FFTFitting_swigregister
1375 FFTFitting_swigregister(FFTFitting)
1379 """fft_based_rigid_fitting(Hierarchy mol2fit, DensityMap dmap, double density_threshold, double angle_sampling_interval_rad) -> IMP::multifit::FittingSolutionRecords"""
1380 return _IMP_multifit.fft_based_rigid_fitting(mol2fit, dmap, density_threshold, angle_sampling_interval_rad)
1383 """remove_background(DensityMap dmap, float threshold, float edge_threshold) -> DensityMap"""
1384 return _IMP_multifit.remove_background(dmap, threshold, edge_threshold)
1387 """get_connected_components(DensityMap dmap, float threshold, float edge_threshold) -> IMP::IntsList"""
1388 return _IMP_multifit.get_connected_components(dmap, threshold, edge_threshold)
1390 def get_segmentation(dmap, apix, density_threshold, num_means, pdb_filename, cmm_filename, seg_filename, txt_filename):
1391 """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)"""
1392 return _IMP_multifit.get_segmentation(dmap, apix, density_threshold, num_means, pdb_filename, cmm_filename, seg_filename, txt_filename)
1394 """Proxy of C++ IMP::multifit::ComplementarityRestraint class."""
1396 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1400 __init__(IMP::multifit::ComplementarityRestraint self, IMP::ParticlesTemp const & a, IMP::ParticlesTemp const & b, std::string name) -> ComplementarityRestraint
1401 __init__(IMP::multifit::ComplementarityRestraint self, IMP::ParticlesTemp const & a, IMP::ParticlesTemp const & b) -> ComplementarityRestraint
1403 this = _IMP_multifit.new_ComplementarityRestraint(*args)
1405 self.this.append(this)
1406 except __builtin__.Exception:
1409 def set_maximum_penetration_score(self, s):
1410 """set_maximum_penetration_score(ComplementarityRestraint self, double s)"""
1411 return _IMP_multifit.ComplementarityRestraint_set_maximum_penetration_score(self, s)
1414 def set_maximum_penetration(self, d):
1415 """set_maximum_penetration(ComplementarityRestraint self, double d)"""
1416 return _IMP_multifit.ComplementarityRestraint_set_maximum_penetration(self, d)
1419 def set_maximum_separation(self, s):
1420 """set_maximum_separation(ComplementarityRestraint self, double s)"""
1421 return _IMP_multifit.ComplementarityRestraint_set_maximum_separation(self, s)
1424 def set_complementarity_thickness(self, th):
1425 """set_complementarity_thickness(ComplementarityRestraint self, double th)"""
1426 return _IMP_multifit.ComplementarityRestraint_set_complementarity_thickness(self, th)
1429 def set_complementarity_value(self, th):
1430 """set_complementarity_value(ComplementarityRestraint self, double th)"""
1431 return _IMP_multifit.ComplementarityRestraint_set_complementarity_value(self, th)
1434 def set_interior_layer_thickness(self, th):
1435 """set_interior_layer_thickness(ComplementarityRestraint self, double th)"""
1436 return _IMP_multifit.ComplementarityRestraint_set_interior_layer_thickness(self, th)
1439 def set_penetration_coefficient(self, pc):
1440 """set_penetration_coefficient(ComplementarityRestraint self, double pc)"""
1441 return _IMP_multifit.ComplementarityRestraint_set_penetration_coefficient(self, pc)
1444 def set_complementarity_coefficient(self, cc):
1445 """set_complementarity_coefficient(ComplementarityRestraint self, double cc)"""
1446 return _IMP_multifit.ComplementarityRestraint_set_complementarity_coefficient(self, cc)
1449 def set_boundary_coefficient(self, bc):
1450 """set_boundary_coefficient(ComplementarityRestraint self, double bc)"""
1451 return _IMP_multifit.ComplementarityRestraint_set_boundary_coefficient(self, bc)
1454 def get_voxel_size(self):
1455 """get_voxel_size(ComplementarityRestraint self) -> float"""
1456 return _IMP_multifit.ComplementarityRestraint_get_voxel_size(self)
1459 def do_get_inputs(self):
1460 """do_get_inputs(ComplementarityRestraint self) -> IMP::ModelObjectsTemp"""
1461 return _IMP_multifit.ComplementarityRestraint_do_get_inputs(self)
1464 def get_version_info(self):
1465 """get_version_info(ComplementarityRestraint self) -> VersionInfo"""
1466 return _IMP_multifit.ComplementarityRestraint_get_version_info(self)
1470 """__str__(ComplementarityRestraint self) -> std::string"""
1471 return _IMP_multifit.ComplementarityRestraint___str__(self)
1475 """__repr__(ComplementarityRestraint self) -> std::string"""
1476 return _IMP_multifit.ComplementarityRestraint___repr__(self)
1481 return _object_cast_to_ComplementarityRestraint(o)
1483 ComplementarityRestraint_swigregister = _IMP_multifit.ComplementarityRestraint_swigregister
1484 ComplementarityRestraint_swigregister(ComplementarityRestraint)
1488 """read_fitting_solutions(char const * fitting_fn) -> IMP::multifit::FittingSolutionRecords"""
1489 return _IMP_multifit.read_fitting_solutions(fitting_fn)
1493 write_fitting_solutions(char const * fitting_fn, IMP::multifit::FittingSolutionRecords const & fit_sols, int num_sols=-1)
1494 write_fitting_solutions(char const * fitting_fn, IMP::multifit::FittingSolutionRecords const & fit_sols)
1496 return _IMP_multifit.write_fitting_solutions(fitting_fn, fit_sols, num_sols)
1498 def convert_em_to_multifit_format(em_fits):
1499 """convert_em_to_multifit_format(FittingSolutions em_fits) -> IMP::multifit::FittingSolutionRecords"""
1500 return _IMP_multifit.convert_em_to_multifit_format(em_fits)
1502 def convert_multifit_to_em_format(multifit_fits):
1503 """convert_multifit_to_em_format(IMP::multifit::FittingSolutionRecords const & multifit_fits) -> FittingSolutions"""
1504 return _IMP_multifit.convert_multifit_to_em_format(multifit_fits)
1506 def convert_transformations_to_multifit_format(trans):
1507 """convert_transformations_to_multifit_format(IMP::algebra::Transformation3Ds const & trans) -> IMP::multifit::FittingSolutionRecords"""
1508 return _IMP_multifit.convert_transformations_to_multifit_format(trans)
1510 def convert_multifit_format_to_transformations(recs):
1511 """convert_multifit_format_to_transformations(IMP::multifit::FittingSolutionRecords const & recs) -> IMP::algebra::Transformation3Ds"""
1512 return _IMP_multifit.convert_multifit_format_to_transformations(recs)
1515 """get_close_to_point(IMP::multifit::FittingSolutionRecords const & fit_sols, Hierarchy mh, Particle ap, IMP::Float dist) -> IMP::multifit::FittingSolutionRecords"""
1516 return _IMP_multifit.get_close_to_point(fit_sols, mh, ap, dist)
1518 """Proxy of C++ IMP::multifit::ProbabilisticAnchorGraph class."""
1520 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1522 def __init__(self, anchor_positions):
1523 """__init__(IMP::multifit::ProbabilisticAnchorGraph self, IMP::algebra::Vector3Ds anchor_positions) -> ProbabilisticAnchorGraph"""
1524 this = _IMP_multifit.new_ProbabilisticAnchorGraph(anchor_positions)
1526 self.this.append(this)
1527 except __builtin__.Exception:
1530 def add_edge(self, i, j):
1531 """add_edge(ProbabilisticAnchorGraph self, int i, int j)"""
1532 return _IMP_multifit.ProbabilisticAnchorGraph_add_edge(self, i, j)
1535 def set_particle_probabilities_on_anchors(self, p, sols):
1536 """set_particle_probabilities_on_anchors(ProbabilisticAnchorGraph self, Particle p, IMP::multifit::FittingSolutionRecords sols)"""
1537 return _IMP_multifit.ProbabilisticAnchorGraph_set_particle_probabilities_on_anchors(self, p, sols)
1540 def show(self, *args):
1542 show(ProbabilisticAnchorGraph self, _ostream out)
1543 show(ProbabilisticAnchorGraph self)
1545 return _IMP_multifit.ProbabilisticAnchorGraph_show(self, *args)
1548 def get_number_of_anchors(self):
1549 """get_number_of_anchors(ProbabilisticAnchorGraph self) -> unsigned int"""
1550 return _IMP_multifit.ProbabilisticAnchorGraph_get_number_of_anchors(self)
1553 def get_number_of_edges(self):
1554 """get_number_of_edges(ProbabilisticAnchorGraph self) -> unsigned int"""
1555 return _IMP_multifit.ProbabilisticAnchorGraph_get_number_of_edges(self)
1558 def get_edge_list(self):
1559 """get_edge_list(ProbabilisticAnchorGraph self) -> IMP::IntRanges"""
1560 return _IMP_multifit.ProbabilisticAnchorGraph_get_edge_list(self)
1563 def get_anchors(self):
1564 """get_anchors(ProbabilisticAnchorGraph self) -> IMP::algebra::Vector3Ds"""
1565 return _IMP_multifit.ProbabilisticAnchorGraph_get_anchors(self)
1568 def get_particle_anchors(self, p, min_prob=0):
1570 get_particle_anchors(ProbabilisticAnchorGraph self, Particle p, float min_prob=0) -> IMP::algebra::Vector3Ds
1571 get_particle_anchors(ProbabilisticAnchorGraph self, Particle p) -> IMP::algebra::Vector3Ds
1573 return _IMP_multifit.ProbabilisticAnchorGraph_get_particle_anchors(self, p, min_prob)
1576 def get_are_probabilities_for_particle_set(self, p):
1577 """get_are_probabilities_for_particle_set(ProbabilisticAnchorGraph self, Particle p) -> bool"""
1578 return _IMP_multifit.ProbabilisticAnchorGraph_get_are_probabilities_for_particle_set(self, p)
1581 def get_particle_probabilities(self, p):
1582 """get_particle_probabilities(ProbabilisticAnchorGraph self, Particle p) -> IMP::Floats"""
1583 return _IMP_multifit.ProbabilisticAnchorGraph_get_particle_probabilities(self, p)
1586 def get_version_info(self):
1587 """get_version_info(ProbabilisticAnchorGraph self) -> VersionInfo"""
1588 return _IMP_multifit.ProbabilisticAnchorGraph_get_version_info(self)
1592 """__str__(ProbabilisticAnchorGraph self) -> std::string"""
1593 return _IMP_multifit.ProbabilisticAnchorGraph___str__(self)
1597 """__repr__(ProbabilisticAnchorGraph self) -> std::string"""
1598 return _IMP_multifit.ProbabilisticAnchorGraph___repr__(self)
1603 return _object_cast_to_ProbabilisticAnchorGraph(o)
1605 ProbabilisticAnchorGraph_swigregister = _IMP_multifit.ProbabilisticAnchorGraph_swigregister
1606 ProbabilisticAnchorGraph_swigregister(ProbabilisticAnchorGraph)
1608 class ProteinRecordData(object):
1609 """Proxy of C++ IMP::multifit::ProteinRecordData class."""
1611 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1613 def reset_all(self):
1614 """reset_all(ProteinRecordData self)"""
1615 return _IMP_multifit.ProteinRecordData_reset_all(self)
1620 __init__(IMP::multifit::ProteinRecordData self) -> ProteinRecordData
1621 __init__(IMP::multifit::ProteinRecordData self, std::string const & name) -> ProteinRecordData
1622 __init__(IMP::multifit::ProteinRecordData self, std::string const & name, std::string const fn) -> ProteinRecordData
1623 __init__(IMP::multifit::ProteinRecordData self, std::string const & name, int start_res, int end_res, std::string const fn) -> ProteinRecordData
1624 __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
1626 this = _IMP_multifit.new_ProteinRecordData(*args)
1628 self.this.append(this)
1629 except __builtin__.Exception:
1632 def show(self, *args):
1634 show(ProteinRecordData self, _ostream out)
1635 show(ProteinRecordData self)
1637 return _IMP_multifit.ProteinRecordData_show(self, *args)
1639 name_ = _swig_property(_IMP_multifit.ProteinRecordData_name__get, _IMP_multifit.ProteinRecordData_name__set)
1640 start_res_ = _swig_property(_IMP_multifit.ProteinRecordData_start_res__get, _IMP_multifit.ProteinRecordData_start_res__set)
1641 end_res_ = _swig_property(_IMP_multifit.ProteinRecordData_end_res__get, _IMP_multifit.ProteinRecordData_end_res__set)
1642 filename_ = _swig_property(_IMP_multifit.ProteinRecordData_filename__get, _IMP_multifit.ProteinRecordData_filename__set)
1643 surface_filename_ = _swig_property(_IMP_multifit.ProteinRecordData_surface_filename__get, _IMP_multifit.ProteinRecordData_surface_filename__set)
1644 ref_filename_ = _swig_property(_IMP_multifit.ProteinRecordData_ref_filename__get, _IMP_multifit.ProteinRecordData_ref_filename__set)
1647 """__str__(ProteinRecordData self) -> std::string"""
1648 return _IMP_multifit.ProteinRecordData___str__(self)
1652 """__repr__(ProteinRecordData self) -> std::string"""
1653 return _IMP_multifit.ProteinRecordData___repr__(self)
1655 __swig_destroy__ = _IMP_multifit.delete_ProteinRecordData
1656 __del__ =
lambda self:
None
1657 ProteinRecordData_swigregister = _IMP_multifit.ProteinRecordData_swigregister
1658 ProteinRecordData_swigregister(ProteinRecordData)
1661 """Proxy of C++ IMP::multifit::ProteomicsData class."""
1663 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1666 """__init__(IMP::multifit::ProteomicsData self) -> ProteomicsData"""
1667 this = _IMP_multifit.new_ProteomicsData()
1669 self.this.append(this)
1670 except __builtin__.Exception:
1673 def add_protein(self, *args):
1675 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
1676 add_protein(ProteomicsData self, ProteinRecordData rec) -> int
1678 return _IMP_multifit.ProteomicsData_add_protein(self, *args)
1681 def find(self, name):
1682 """find(ProteomicsData self, std::string const & name) -> int"""
1683 return _IMP_multifit.ProteomicsData_find(self, name)
1686 def add_interaction(self, ii, used_for_filter, linker_len):
1687 """add_interaction(ProteomicsData self, IMP::Ints const & ii, bool used_for_filter, float linker_len)"""
1688 return _IMP_multifit.ProteomicsData_add_interaction(self, ii, used_for_filter, linker_len)
1691 def add_cross_link_interaction(self, prot1, res1, prot2, res2, used_in_filter, linker_len):
1692 """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)"""
1693 return _IMP_multifit.ProteomicsData_add_cross_link_interaction(self, prot1, res1, prot2, res2, used_in_filter, linker_len)
1696 def add_ev_pair(self, prot1, prot2):
1697 """add_ev_pair(ProteomicsData self, IMP::Int prot1, IMP::Int prot2)"""
1698 return _IMP_multifit.ProteomicsData_add_ev_pair(self, prot1, prot2)
1701 def get_number_of_proteins(self):
1702 """get_number_of_proteins(ProteomicsData self) -> int"""
1703 return _IMP_multifit.ProteomicsData_get_number_of_proteins(self)
1706 def get_number_of_interactions(self):
1707 """get_number_of_interactions(ProteomicsData self) -> int"""
1708 return _IMP_multifit.ProteomicsData_get_number_of_interactions(self)
1711 def get_interaction(self, interaction_ind):
1712 """get_interaction(ProteomicsData self, int interaction_ind) -> IMP::Ints"""
1713 return _IMP_multifit.ProteomicsData_get_interaction(self, interaction_ind)
1716 def get_interaction_part_of_filter(self, interaction_ind):
1717 """get_interaction_part_of_filter(ProteomicsData self, int interaction_ind) -> bool"""
1718 return _IMP_multifit.ProteomicsData_get_interaction_part_of_filter(self, interaction_ind)
1721 def get_interaction_linker_length(self, interaction_ind):
1722 """get_interaction_linker_length(ProteomicsData self, int interaction_ind) -> int"""
1723 return _IMP_multifit.ProteomicsData_get_interaction_linker_length(self, interaction_ind)
1726 def get_number_of_cross_links(self):
1727 """get_number_of_cross_links(ProteomicsData self) -> int"""
1728 return _IMP_multifit.ProteomicsData_get_number_of_cross_links(self)
1731 def get_cross_link(self, xlink_ind):
1732 """get_cross_link(ProteomicsData self, int xlink_ind) -> std::pair< IMP::IntPair,IMP::IntPair >"""
1733 return _IMP_multifit.ProteomicsData_get_cross_link(self, xlink_ind)
1736 def get_cross_link_part_of_filter(self, xlink_ind):
1737 """get_cross_link_part_of_filter(ProteomicsData self, int xlink_ind) -> bool"""
1738 return _IMP_multifit.ProteomicsData_get_cross_link_part_of_filter(self, xlink_ind)
1741 def get_cross_link_length(self, xlink_ind):
1742 """get_cross_link_length(ProteomicsData self, int xlink_ind) -> float"""
1743 return _IMP_multifit.ProteomicsData_get_cross_link_length(self, xlink_ind)
1746 def get_number_of_ev_pairs(self):
1747 """get_number_of_ev_pairs(ProteomicsData self) -> int"""
1748 return _IMP_multifit.ProteomicsData_get_number_of_ev_pairs(self)
1751 def get_ev_pair(self, ev_ind):
1752 """get_ev_pair(ProteomicsData self, int ev_ind) -> IMP::IntPair"""
1753 return _IMP_multifit.ProteomicsData_get_ev_pair(self, ev_ind)
1756 def get_protein_name(self, protein_ind):
1757 """get_protein_name(ProteomicsData self, int protein_ind) -> std::string"""
1758 return _IMP_multifit.ProteomicsData_get_protein_name(self, protein_ind)
1761 def get_end_res(self, protein_ind):
1762 """get_end_res(ProteomicsData self, int protein_ind) -> int"""
1763 return _IMP_multifit.ProteomicsData_get_end_res(self, protein_ind)
1766 def get_start_res(self, protein_ind):
1767 """get_start_res(ProteomicsData self, int protein_ind) -> int"""
1768 return _IMP_multifit.ProteomicsData_get_start_res(self, protein_ind)
1771 def get_protein_filename(self, protein_ind):
1772 """get_protein_filename(ProteomicsData self, int protein_ind) -> std::string"""
1773 return _IMP_multifit.ProteomicsData_get_protein_filename(self, protein_ind)
1776 def get_reference_filename(self, protein_ind):
1777 """get_reference_filename(ProteomicsData self, int protein_ind) -> std::string"""
1778 return _IMP_multifit.ProteomicsData_get_reference_filename(self, protein_ind)
1781 def get_surface_filename(self, protein_ind):
1782 """get_surface_filename(ProteomicsData self, int protein_ind) -> std::string"""
1783 return _IMP_multifit.ProteomicsData_get_surface_filename(self, protein_ind)
1786 def get_protein_data(self, protein_ind):
1787 """get_protein_data(ProteomicsData self, int protein_ind) -> ProteinRecordData"""
1788 return _IMP_multifit.ProteomicsData_get_protein_data(self, protein_ind)
1791 def get_version_info(self):
1792 """get_version_info(ProteomicsData self) -> VersionInfo"""
1793 return _IMP_multifit.ProteomicsData_get_version_info(self)
1796 def get_num_allowed_violated_interactions(self):
1797 """get_num_allowed_violated_interactions(ProteomicsData self) -> int"""
1798 return _IMP_multifit.ProteomicsData_get_num_allowed_violated_interactions(self)
1801 def set_num_allowed_violated_interactions(self, n):
1802 """set_num_allowed_violated_interactions(ProteomicsData self, int n)"""
1803 return _IMP_multifit.ProteomicsData_set_num_allowed_violated_interactions(self, n)
1806 def get_num_allowed_violated_cross_links(self):
1807 """get_num_allowed_violated_cross_links(ProteomicsData self) -> int"""
1808 return _IMP_multifit.ProteomicsData_get_num_allowed_violated_cross_links(self)
1811 def set_num_allowed_violated_cross_links(self, n):
1812 """set_num_allowed_violated_cross_links(ProteomicsData self, int n)"""
1813 return _IMP_multifit.ProteomicsData_set_num_allowed_violated_cross_links(self, n)
1816 def get_num_allowed_violated_ev(self):
1817 """get_num_allowed_violated_ev(ProteomicsData self) -> int"""
1818 return _IMP_multifit.ProteomicsData_get_num_allowed_violated_ev(self)
1821 def set_num_allowed_violated_ev(self, n):
1822 """set_num_allowed_violated_ev(ProteomicsData self, int n)"""
1823 return _IMP_multifit.ProteomicsData_set_num_allowed_violated_ev(self, n)
1827 """__str__(ProteomicsData self) -> std::string"""
1828 return _IMP_multifit.ProteomicsData___str__(self)
1832 """__repr__(ProteomicsData self) -> std::string"""
1833 return _IMP_multifit.ProteomicsData___repr__(self)
1838 return _object_cast_to_ProteomicsData(o)
1840 ProteomicsData_swigregister = _IMP_multifit.ProteomicsData_swigregister
1841 ProteomicsData_swigregister(ProteomicsData)
1845 """read_proteomics_data(char const * proteomics_fn) -> ProteomicsData"""
1846 return _IMP_multifit.read_proteomics_data(proteomics_fn)
1848 def get_partial_proteomics_data(pd, prot_names):
1849 """get_partial_proteomics_data(ProteomicsData pd, IMP::Strings const & prot_names) -> ProteomicsData"""
1850 return _IMP_multifit.get_partial_proteomics_data(pd, prot_names)
1851 class AnchorsData(object):
1852 """Proxy of C++ IMP::multifit::AnchorsData class."""
1854 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1858 __init__(IMP::multifit::AnchorsData self) -> AnchorsData
1859 __init__(IMP::multifit::AnchorsData self, IMP::algebra::Vector3Ds points, IMP::IntPairs edges) -> AnchorsData
1861 this = _IMP_multifit.new_AnchorsData(*args)
1863 self.this.append(this)
1864 except __builtin__.Exception:
1867 def remove_edges_for_node(self, node_ind):
1868 """remove_edges_for_node(AnchorsData self, int node_ind)"""
1869 return _IMP_multifit.AnchorsData_remove_edges_for_node(self, node_ind)
1872 def get_number_of_points(self):
1873 """get_number_of_points(AnchorsData self) -> int"""
1874 return _IMP_multifit.AnchorsData_get_number_of_points(self)
1877 def get_number_of_edges(self):
1878 """get_number_of_edges(AnchorsData self) -> int"""
1879 return _IMP_multifit.AnchorsData_get_number_of_edges(self)
1882 def get_is_point_considered(self, node_ind):
1883 """get_is_point_considered(AnchorsData self, int node_ind) -> bool"""
1884 return _IMP_multifit.AnchorsData_get_is_point_considered(self, node_ind)
1887 def show(self, *args):
1889 show(AnchorsData self, _ostream out)
1890 show(AnchorsData self)
1892 return _IMP_multifit.AnchorsData_show(self, *args)
1895 def get_secondary_structure_is_set(self):
1896 """get_secondary_structure_is_set(AnchorsData self) -> bool"""
1897 return _IMP_multifit.AnchorsData_get_secondary_structure_is_set(self)
1900 def setup_secondary_structure(self, mdl):
1901 """setup_secondary_structure(AnchorsData self, Model mdl)"""
1902 return _IMP_multifit.AnchorsData_setup_secondary_structure(self, mdl)
1905 def set_secondary_structure_probabilities(self, *args):
1907 set_secondary_structure_probabilities(AnchorsData self, IMP::Particles const & ssres_ps, IMP::Ints const & indices)
1908 set_secondary_structure_probabilities(AnchorsData self, IMP::Particles const & ssres_ps)
1910 return _IMP_multifit.AnchorsData_set_secondary_structure_probabilities(self, *args)
1913 def get_secondary_structure_particles(self):
1914 """get_secondary_structure_particles(AnchorsData self) -> IMP::Particles"""
1915 return _IMP_multifit.AnchorsData_get_secondary_structure_particles(self)
1917 points_ = _swig_property(_IMP_multifit.AnchorsData_points__get, _IMP_multifit.AnchorsData_points__set)
1918 consider_point_ = _swig_property(_IMP_multifit.AnchorsData_consider_point__get, _IMP_multifit.AnchorsData_consider_point__set)
1919 edges_ = _swig_property(_IMP_multifit.AnchorsData_edges__get, _IMP_multifit.AnchorsData_edges__set)
1922 """__str__(AnchorsData self) -> std::string"""
1923 return _IMP_multifit.AnchorsData___str__(self)
1927 """__repr__(AnchorsData self) -> std::string"""
1928 return _IMP_multifit.AnchorsData___repr__(self)
1930 __swig_destroy__ = _IMP_multifit.delete_AnchorsData
1931 __del__ =
lambda self:
None
1932 AnchorsData_swigregister = _IMP_multifit.AnchorsData_swigregister
1933 AnchorsData_swigregister(AnchorsData)
1936 def read_anchors_data(txt_filename):
1937 """read_anchors_data(char const * txt_filename) -> AnchorsData"""
1938 return _IMP_multifit.read_anchors_data(txt_filename)
1940 def write_txt(txt_filename, ad):
1941 """write_txt(std::string const & txt_filename, AnchorsData ad)"""
1942 return _IMP_multifit.write_txt(txt_filename, ad)
1944 def write_cmm(cmm_filename, marker_set_name, dpa):
1945 """write_cmm(std::string const & cmm_filename, std::string const & marker_set_name, AnchorsData dpa)"""
1946 return _IMP_multifit.write_cmm(cmm_filename, marker_set_name, dpa)
1949 """create_coarse_molecule_from_density(DensityMap dmap, float dens_threshold, int num_beads, Model mdl, float bead_radius) -> Hierarchy"""
1950 return _IMP_multifit.create_coarse_molecule_from_density(dmap, dens_threshold, num_beads, mdl, bead_radius)
1952 def create_hit_map(rb, rb_ref, sols, damp):
1953 """create_hit_map(RigidBody rb, Refiner rb_ref, IMP::multifit::FittingSolutionRecords const & sols, DensityMap damp) -> DensityMap"""
1954 return _IMP_multifit.create_hit_map(rb, rb_ref, sols, damp)
1957 """get_points_close_to_molecule(Hierarchy mh, IMP::algebra::Vector3Ds const points, IMP::Float max_dist) -> IMP::algebra::Vector3Ds"""
1958 return _IMP_multifit.get_points_close_to_molecule(mh, points, max_dist)
1960 def get_points_far_from_molecule(mh, points, max_dist):
1961 """get_points_far_from_molecule(Hierarchy mh, IMP::algebra::Vector3Ds const points, IMP::Float max_dist) -> IMP::algebra::Vector3Ds"""
1962 return _IMP_multifit.get_points_far_from_molecule(mh, points, max_dist)
1964 """Proxy of C++ IMP::multifit::RadiusOfGyrationRestraint class."""
1966 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1968 def __init__(self, ps, num_residues, scale=1.):
1970 __init__(IMP::multifit::RadiusOfGyrationRestraint self, IMP::Particles ps, int num_residues, IMP::Float scale=1.) -> RadiusOfGyrationRestraint
1971 __init__(IMP::multifit::RadiusOfGyrationRestraint self, IMP::Particles ps, int num_residues) -> RadiusOfGyrationRestraint
1973 this = _IMP_multifit.new_RadiusOfGyrationRestraint(ps, num_residues, scale)
1975 self.this.append(this)
1976 except __builtin__.Exception:
1979 def do_get_inputs(self):
1980 """do_get_inputs(RadiusOfGyrationRestraint self) -> IMP::ModelObjectsTemp"""
1981 return _IMP_multifit.RadiusOfGyrationRestraint_do_get_inputs(self)
1984 def get_version_info(self):
1985 """get_version_info(RadiusOfGyrationRestraint self) -> VersionInfo"""
1986 return _IMP_multifit.RadiusOfGyrationRestraint_get_version_info(self)
1989 def set_radius_of_gyration(self, r):
1990 """set_radius_of_gyration(RadiusOfGyrationRestraint self, IMP::Float r)"""
1991 return _IMP_multifit.RadiusOfGyrationRestraint_set_radius_of_gyration(self, r)
1995 """get_radius_of_gyration(RadiusOfGyrationRestraint self) -> IMP::Float"""
1996 return _IMP_multifit.RadiusOfGyrationRestraint_get_radius_of_gyration(self)
2000 """__str__(RadiusOfGyrationRestraint self) -> std::string"""
2001 return _IMP_multifit.RadiusOfGyrationRestraint___str__(self)
2005 """__repr__(RadiusOfGyrationRestraint self) -> std::string"""
2006 return _IMP_multifit.RadiusOfGyrationRestraint___repr__(self)
2011 return _object_cast_to_RadiusOfGyrationRestraint(o)
2013 RadiusOfGyrationRestraint_swigregister = _IMP_multifit.RadiusOfGyrationRestraint_swigregister
2014 RadiusOfGyrationRestraint_swigregister(RadiusOfGyrationRestraint)
2017 def get_approximated_radius_of_gyration(len):
2018 """get_approximated_radius_of_gyration(int len) -> float"""
2019 return _IMP_multifit.get_approximated_radius_of_gyration(len)
2021 def get_actual_radius_of_gyration(ps):
2022 """get_actual_radius_of_gyration(IMP::ParticlesTemp ps) -> float"""
2023 return _IMP_multifit.get_actual_radius_of_gyration(ps)
2025 def get_approximated_radius(len):
2026 """get_approximated_radius(int len) -> float"""
2027 return _IMP_multifit.get_approximated_radius(len)
2028 class ProteinsAnchorsSamplingSpace(object):
2029 """Proxy of C++ IMP::multifit::ProteinsAnchorsSamplingSpace class."""
2031 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2035 __init__(IMP::multifit::ProteinsAnchorsSamplingSpace self, ProteomicsData prots=None) -> ProteinsAnchorsSamplingSpace
2036 __init__(IMP::multifit::ProteinsAnchorsSamplingSpace self) -> ProteinsAnchorsSamplingSpace
2038 this = _IMP_multifit.new_ProteinsAnchorsSamplingSpace(prots)
2040 self.this.append(this)
2041 except __builtin__.Exception:
2044 def set_anchors(self, data):
2045 """set_anchors(ProteinsAnchorsSamplingSpace self, AnchorsData data)"""
2046 return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_anchors(self, data)
2049 def get_anchors(self):
2050 """get_anchors(ProteinsAnchorsSamplingSpace self) -> AnchorsData"""
2051 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_anchors(self)
2054 def get_anchors_filename(self):
2055 """get_anchors_filename(ProteinsAnchorsSamplingSpace self) -> std::string"""
2056 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_anchors_filename(self)
2059 def set_anchors_filename(self, fn):
2060 """set_anchors_filename(ProteinsAnchorsSamplingSpace self, std::string const & fn)"""
2061 return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_anchors_filename(self, fn)
2064 def get_proteomics_data(self):
2065 """get_proteomics_data(ProteinsAnchorsSamplingSpace self) -> ProteomicsData"""
2066 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_proteomics_data(self)
2069 def add_protein(self, rec):
2070 """add_protein(ProteinsAnchorsSamplingSpace self, ProteinRecordData rec)"""
2071 return _IMP_multifit.ProteinsAnchorsSamplingSpace_add_protein(self, rec)
2074 def get_paths_for_protein(self, prot_name):
2075 """get_paths_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name) -> IMP::IntsList"""
2076 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_paths_for_protein(self, prot_name)
2079 def set_paths_filename_for_protein(self, prot_name, paths_filename):
2080 """set_paths_filename_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name, std::string const & paths_filename)"""
2081 return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_paths_filename_for_protein(self, prot_name, paths_filename)
2084 def get_paths_filename_for_protein(self, prot_name):
2085 """get_paths_filename_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name) -> std::string"""
2086 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_paths_filename_for_protein(self, prot_name)
2089 def set_paths_for_protein(self, prot_name, paths):
2090 """set_paths_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name, IMP::IntsList paths)"""
2091 return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_paths_for_protein(self, prot_name, paths)
2094 def show(self, *args):
2096 show(ProteinsAnchorsSamplingSpace self, _ostream s)
2097 show(ProteinsAnchorsSamplingSpace self)
2099 return _IMP_multifit.ProteinsAnchorsSamplingSpace_show(self, *args)
2103 """__str__(ProteinsAnchorsSamplingSpace self) -> std::string"""
2104 return _IMP_multifit.ProteinsAnchorsSamplingSpace___str__(self)
2108 """__repr__(ProteinsAnchorsSamplingSpace self) -> std::string"""
2109 return _IMP_multifit.ProteinsAnchorsSamplingSpace___repr__(self)
2111 __swig_destroy__ = _IMP_multifit.delete_ProteinsAnchorsSamplingSpace
2112 __del__ =
lambda self:
None
2113 ProteinsAnchorsSamplingSpace_swigregister = _IMP_multifit.ProteinsAnchorsSamplingSpace_swigregister
2114 ProteinsAnchorsSamplingSpace_swigregister(ProteinsAnchorsSamplingSpace)
2117 def read_protein_anchors_mapping(*args):
2119 read_protein_anchors_mapping(ProteomicsData prots, std::string const & anchors_prot_map_fn, int max_paths) -> ProteinsAnchorsSamplingSpace
2120 read_protein_anchors_mapping(ProteomicsData prots, std::string const & anchors_prot_map_fn) -> ProteinsAnchorsSamplingSpace
2122 return _IMP_multifit.read_protein_anchors_mapping(*args)
2124 def write_protein_anchors_mapping(*args):
2126 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)
2127 write_protein_anchors_mapping(std::string const & anchors_prot_map_fn, ProteinsAnchorsSamplingSpace pa, IMP::Strings const & prot_names)
2129 return _IMP_multifit.write_protein_anchors_mapping(*args)
2132 """get_part_of_sampling_space(ProteinsAnchorsSamplingSpace prots_ss, IMP::Strings const & prot_names) -> ProteinsAnchorsSamplingSpace"""
2133 return _IMP_multifit.get_part_of_sampling_space(prots_ss, prot_names)
2136 """get_partial_assembly_setting_data(SettingsData prots_sd, IMP::Strings const & prot_names) -> SettingsData"""
2137 return _IMP_multifit.get_partial_assembly_setting_data(prots_sd, prot_names)
2141 read_paths(char const * txt_filename, int max_paths) -> IMP::IntsList
2142 read_paths(char const * txt_filename) -> IMP::IntsList
2144 return _IMP_multifit.read_paths(*args)
2146 def write_paths(paths, txt_filename):
2147 """write_paths(IMP::IntsList const & paths, std::string const & txt_filename)"""
2148 return _IMP_multifit.write_paths(paths, txt_filename)
2150 def molecule2anchors(mh, k):
2151 """molecule2anchors(Hierarchy mh, int k) -> AnchorsData"""
2152 return _IMP_multifit.molecule2anchors(mh, k)
2154 def get_anchors_for_density(dmap, number_of_means, density_threshold, pdb_filename, cmm_filename, seg_filename, txt_filename):
2155 """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)"""
2156 return _IMP_multifit.get_anchors_for_density(dmap, number_of_means, density_threshold, pdb_filename, cmm_filename, seg_filename, txt_filename)
2160 get_anchor_indices_matching_secondary_structure(AnchorsData ad, IMP::atom::SecondaryStructureResidues const & ssrs, IMP::Float max_rmsd=0.7) -> IMP::IntsList
2161 get_anchor_indices_matching_secondary_structure(AnchorsData ad, IMP::atom::SecondaryStructureResidues const & ssrs) -> IMP::IntsList
2163 return _IMP_multifit.get_anchor_indices_matching_secondary_structure(ad, ssrs, max_rmsd)
2164 class DominoParams(object):
2165 """Proxy of C++ IMP::multifit::DominoParams class."""
2167 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2170 """__init__(IMP::multifit::DominoParams self) -> DominoParams"""
2171 this = _IMP_multifit.new_DominoParams()
2173 self.this.append(this)
2174 except __builtin__.Exception:
2178 """add(DominoParams self, boost::property_tree::ptree const & pt)"""
2179 return _IMP_multifit.DominoParams_add(self, pt)
2182 def show(self, *args):
2184 show(DominoParams self, _ostream s)
2185 show(DominoParams self)
2187 return _IMP_multifit.DominoParams_show(self, *args)
2189 max_value_threshold_ = _swig_property(_IMP_multifit.DominoParams_max_value_threshold__get, _IMP_multifit.DominoParams_max_value_threshold__set)
2190 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)
2191 max_anchor_penetration_ = _swig_property(_IMP_multifit.DominoParams_max_anchor_penetration__get, _IMP_multifit.DominoParams_max_anchor_penetration__set)
2192 heap_size_ = _swig_property(_IMP_multifit.DominoParams_heap_size__get, _IMP_multifit.DominoParams_heap_size__set)
2193 cache_size_ = _swig_property(_IMP_multifit.DominoParams_cache_size__get, _IMP_multifit.DominoParams_cache_size__set)
2196 """__str__(DominoParams self) -> std::string"""
2197 return _IMP_multifit.DominoParams___str__(self)
2201 """__repr__(DominoParams self) -> std::string"""
2202 return _IMP_multifit.DominoParams___repr__(self)
2204 __swig_destroy__ = _IMP_multifit.delete_DominoParams
2205 __del__ =
lambda self:
None
2206 DominoParams_swigregister = _IMP_multifit.DominoParams_swigregister
2207 DominoParams_swigregister(DominoParams)
2209 class XlinkParams(object):
2210 """Proxy of C++ IMP::multifit::XlinkParams class."""
2212 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2215 """__init__(IMP::multifit::XlinkParams self) -> XlinkParams"""
2216 this = _IMP_multifit.new_XlinkParams()
2218 self.this.append(this)
2219 except __builtin__.Exception:
2223 """add(XlinkParams self, boost::property_tree::ptree const & pt)"""
2224 return _IMP_multifit.XlinkParams_add(self, pt)
2227 def show(self, *args):
2229 show(XlinkParams self, _ostream s)
2230 show(XlinkParams self)
2232 return _IMP_multifit.XlinkParams_show(self, *args)
2234 upper_bound_ = _swig_property(_IMP_multifit.XlinkParams_upper_bound__get, _IMP_multifit.XlinkParams_upper_bound__set)
2235 k_ = _swig_property(_IMP_multifit.XlinkParams_k__get, _IMP_multifit.XlinkParams_k__set)
2236 max_xlink_val_ = _swig_property(_IMP_multifit.XlinkParams_max_xlink_val__get, _IMP_multifit.XlinkParams_max_xlink_val__set)
2237 treat_between_residues_ = _swig_property(_IMP_multifit.XlinkParams_treat_between_residues__get, _IMP_multifit.XlinkParams_treat_between_residues__set)
2240 """__str__(XlinkParams self) -> std::string"""
2241 return _IMP_multifit.XlinkParams___str__(self)
2245 """__repr__(XlinkParams self) -> std::string"""
2246 return _IMP_multifit.XlinkParams___repr__(self)
2248 __swig_destroy__ = _IMP_multifit.delete_XlinkParams
2249 __del__ =
lambda self:
None
2250 XlinkParams_swigregister = _IMP_multifit.XlinkParams_swigregister
2251 XlinkParams_swigregister(XlinkParams)
2253 class ConnectivityParams(object):
2254 """Proxy of C++ IMP::multifit::ConnectivityParams class."""
2256 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2259 """__init__(IMP::multifit::ConnectivityParams self) -> ConnectivityParams"""
2260 this = _IMP_multifit.new_ConnectivityParams()
2262 self.this.append(this)
2263 except __builtin__.Exception:
2267 """add(ConnectivityParams self, boost::property_tree::ptree const & pt)"""
2268 return _IMP_multifit.ConnectivityParams_add(self, pt)
2271 def show(self, *args):
2273 show(ConnectivityParams self, _ostream s)
2274 show(ConnectivityParams self)
2276 return _IMP_multifit.ConnectivityParams_show(self, *args)
2278 upper_bound_ = _swig_property(_IMP_multifit.ConnectivityParams_upper_bound__get, _IMP_multifit.ConnectivityParams_upper_bound__set)
2279 k_ = _swig_property(_IMP_multifit.ConnectivityParams_k__get, _IMP_multifit.ConnectivityParams_k__set)
2280 max_conn_rest_val_ = _swig_property(_IMP_multifit.ConnectivityParams_max_conn_rest_val__get, _IMP_multifit.ConnectivityParams_max_conn_rest_val__set)
2283 """__str__(ConnectivityParams self) -> std::string"""
2284 return _IMP_multifit.ConnectivityParams___str__(self)
2288 """__repr__(ConnectivityParams self) -> std::string"""
2289 return _IMP_multifit.ConnectivityParams___repr__(self)
2291 __swig_destroy__ = _IMP_multifit.delete_ConnectivityParams
2292 __del__ =
lambda self:
None
2293 ConnectivityParams_swigregister = _IMP_multifit.ConnectivityParams_swigregister
2294 ConnectivityParams_swigregister(ConnectivityParams)
2296 class FragmentsParams(object):
2297 """Proxy of C++ IMP::multifit::FragmentsParams class."""
2299 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2302 """__init__(IMP::multifit::FragmentsParams self) -> FragmentsParams"""
2303 this = _IMP_multifit.new_FragmentsParams()
2305 self.this.append(this)
2306 except __builtin__.Exception:
2310 """add(FragmentsParams self, boost::property_tree::ptree const & pt)"""
2311 return _IMP_multifit.FragmentsParams_add(self, pt)
2314 def show(self, *args):
2316 show(FragmentsParams self, _ostream s)
2317 show(FragmentsParams self)
2319 return _IMP_multifit.FragmentsParams_show(self, *args)
2321 frag_len_ = _swig_property(_IMP_multifit.FragmentsParams_frag_len__get, _IMP_multifit.FragmentsParams_frag_len__set)
2322 bead_radius_scale_ = _swig_property(_IMP_multifit.FragmentsParams_bead_radius_scale__get, _IMP_multifit.FragmentsParams_bead_radius_scale__set)
2323 load_atomic_ = _swig_property(_IMP_multifit.FragmentsParams_load_atomic__get, _IMP_multifit.FragmentsParams_load_atomic__set)
2324 subunit_rigid_ = _swig_property(_IMP_multifit.FragmentsParams_subunit_rigid__get, _IMP_multifit.FragmentsParams_subunit_rigid__set)
2327 """__str__(FragmentsParams self) -> std::string"""
2328 return _IMP_multifit.FragmentsParams___str__(self)
2332 """__repr__(FragmentsParams self) -> std::string"""
2333 return _IMP_multifit.FragmentsParams___repr__(self)
2335 __swig_destroy__ = _IMP_multifit.delete_FragmentsParams
2336 __del__ =
lambda self:
None
2337 FragmentsParams_swigregister = _IMP_multifit.FragmentsParams_swigregister
2338 FragmentsParams_swigregister(FragmentsParams)
2340 class RogParams(object):
2341 """Proxy of C++ IMP::multifit::RogParams class."""
2343 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2346 """__init__(IMP::multifit::RogParams self) -> RogParams"""
2347 this = _IMP_multifit.new_RogParams()
2349 self.this.append(this)
2350 except __builtin__.Exception:
2354 """add(RogParams self, boost::property_tree::ptree const & pt)"""
2355 return _IMP_multifit.RogParams_add(self, pt)
2358 def get_max_score(self):
2359 """get_max_score(RogParams self) -> float"""
2360 return _IMP_multifit.RogParams_get_max_score(self)
2363 def get_scale(self):
2364 """get_scale(RogParams self) -> float"""
2365 return _IMP_multifit.RogParams_get_scale(self)
2368 def show(self, *args):
2370 show(RogParams self, _ostream s)
2371 show(RogParams self)
2373 return _IMP_multifit.RogParams_show(self, *args)
2377 """__str__(RogParams self) -> std::string"""
2378 return _IMP_multifit.RogParams___str__(self)
2382 """__repr__(RogParams self) -> std::string"""
2383 return _IMP_multifit.RogParams___repr__(self)
2385 __swig_destroy__ = _IMP_multifit.delete_RogParams
2386 __del__ =
lambda self:
None
2387 RogParams_swigregister = _IMP_multifit.RogParams_swigregister
2388 RogParams_swigregister(RogParams)
2390 class EVParams(object):
2391 """Proxy of C++ IMP::multifit::EVParams class."""
2393 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2396 """__init__(IMP::multifit::EVParams self) -> EVParams"""
2397 this = _IMP_multifit.new_EVParams()
2399 self.this.append(this)
2400 except __builtin__.Exception:
2404 """add(EVParams self, boost::property_tree::ptree const & pt)"""
2405 return _IMP_multifit.EVParams_add(self, pt)
2408 def show(self, *args):
2410 show(EVParams self, _ostream s)
2413 return _IMP_multifit.EVParams_show(self, *args)
2415 pair_distance_ = _swig_property(_IMP_multifit.EVParams_pair_distance__get, _IMP_multifit.EVParams_pair_distance__set)
2416 pair_slack_ = _swig_property(_IMP_multifit.EVParams_pair_slack__get, _IMP_multifit.EVParams_pair_slack__set)
2417 hlb_mean_ = _swig_property(_IMP_multifit.EVParams_hlb_mean__get, _IMP_multifit.EVParams_hlb_mean__set)
2418 hlb_k_ = _swig_property(_IMP_multifit.EVParams_hlb_k__get, _IMP_multifit.EVParams_hlb_k__set)
2419 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)
2420 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)
2421 scoring_mode_ = _swig_property(_IMP_multifit.EVParams_scoring_mode__get, _IMP_multifit.EVParams_scoring_mode__set)
2424 """__str__(EVParams self) -> std::string"""
2425 return _IMP_multifit.EVParams___str__(self)
2429 """__repr__(EVParams self) -> std::string"""
2430 return _IMP_multifit.EVParams___repr__(self)
2432 __swig_destroy__ = _IMP_multifit.delete_EVParams
2433 __del__ =
lambda self:
None
2434 EVParams_swigregister = _IMP_multifit.EVParams_swigregister
2435 EVParams_swigregister(EVParams)
2437 class FiltersParams(object):
2438 """Proxy of C++ IMP::multifit::FiltersParams class."""
2440 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2443 """__init__(IMP::multifit::FiltersParams self) -> FiltersParams"""
2444 this = _IMP_multifit.new_FiltersParams()
2446 self.this.append(this)
2447 except __builtin__.Exception:
2451 """add(FiltersParams self, boost::property_tree::ptree const & pt)"""
2452 return _IMP_multifit.FiltersParams_add(self, pt)
2455 def show(self, *args):
2457 show(FiltersParams self, _ostream s)
2458 show(FiltersParams self)
2460 return _IMP_multifit.FiltersParams_show(self, *args)
2462 max_num_violated_xlink_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_xlink__get, _IMP_multifit.FiltersParams_max_num_violated_xlink__set)
2463 max_num_violated_conn_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_conn__get, _IMP_multifit.FiltersParams_max_num_violated_conn__set)
2464 max_num_violated_ev_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_ev__get, _IMP_multifit.FiltersParams_max_num_violated_ev__set)
2467 """__str__(FiltersParams self) -> std::string"""
2468 return _IMP_multifit.FiltersParams___str__(self)
2472 """__repr__(FiltersParams self) -> std::string"""
2473 return _IMP_multifit.FiltersParams___repr__(self)
2475 __swig_destroy__ = _IMP_multifit.delete_FiltersParams
2476 __del__ =
lambda self:
None
2477 FiltersParams_swigregister = _IMP_multifit.FiltersParams_swigregister
2478 FiltersParams_swigregister(FiltersParams)
2480 class FittingParams(object):
2481 """Proxy of C++ IMP::multifit::FittingParams class."""
2483 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2486 """__init__(IMP::multifit::FittingParams self) -> FittingParams"""
2487 this = _IMP_multifit.new_FittingParams()
2489 self.this.append(this)
2490 except __builtin__.Exception:
2494 """add(FittingParams self, boost::property_tree::ptree const & pt)"""
2495 return _IMP_multifit.FittingParams_add(self, pt)
2498 def show(self, *args):
2500 show(FittingParams self, _ostream s)
2501 show(FittingParams self)
2503 return _IMP_multifit.FittingParams_show(self, *args)
2505 pca_max_angle_diff_ = _swig_property(_IMP_multifit.FittingParams_pca_max_angle_diff__get, _IMP_multifit.FittingParams_pca_max_angle_diff__set)
2506 pca_max_size_diff_ = _swig_property(_IMP_multifit.FittingParams_pca_max_size_diff__get, _IMP_multifit.FittingParams_pca_max_size_diff__set)
2507 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)
2508 max_asmb_fit_score_ = _swig_property(_IMP_multifit.FittingParams_max_asmb_fit_score__get, _IMP_multifit.FittingParams_max_asmb_fit_score__set)
2511 """__str__(FittingParams self) -> std::string"""
2512 return _IMP_multifit.FittingParams___str__(self)
2516 """__repr__(FittingParams self) -> std::string"""
2517 return _IMP_multifit.FittingParams___repr__(self)
2519 __swig_destroy__ = _IMP_multifit.delete_FittingParams
2520 __del__ =
lambda self:
None
2521 FittingParams_swigregister = _IMP_multifit.FittingParams_swigregister
2522 FittingParams_swigregister(FittingParams)
2524 class ComplementarityParams(object):
2525 """Proxy of C++ IMP::multifit::ComplementarityParams class."""
2527 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2530 """__init__(IMP::multifit::ComplementarityParams self) -> ComplementarityParams"""
2531 this = _IMP_multifit.new_ComplementarityParams()
2533 self.this.append(this)
2534 except __builtin__.Exception:
2538 """add(ComplementarityParams self, boost::property_tree::ptree const & pt)"""
2539 return _IMP_multifit.ComplementarityParams_add(self, pt)
2542 def show(self, *args):
2544 show(ComplementarityParams self, _ostream s)
2545 show(ComplementarityParams self)
2547 return _IMP_multifit.ComplementarityParams_show(self, *args)
2549 max_score_ = _swig_property(_IMP_multifit.ComplementarityParams_max_score__get, _IMP_multifit.ComplementarityParams_max_score__set)
2550 max_penetration_ = _swig_property(_IMP_multifit.ComplementarityParams_max_penetration__get, _IMP_multifit.ComplementarityParams_max_penetration__set)
2551 interior_layer_thickness_ = _swig_property(_IMP_multifit.ComplementarityParams_interior_layer_thickness__get, _IMP_multifit.ComplementarityParams_interior_layer_thickness__set)
2552 boundary_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_boundary_coef__get, _IMP_multifit.ComplementarityParams_boundary_coef__set)
2553 comp_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_comp_coef__get, _IMP_multifit.ComplementarityParams_comp_coef__set)
2554 penetration_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_penetration_coef__get, _IMP_multifit.ComplementarityParams_penetration_coef__set)
2557 """__str__(ComplementarityParams self) -> std::string"""
2558 return _IMP_multifit.ComplementarityParams___str__(self)
2562 """__repr__(ComplementarityParams self) -> std::string"""
2563 return _IMP_multifit.ComplementarityParams___repr__(self)
2565 __swig_destroy__ = _IMP_multifit.delete_ComplementarityParams
2566 __del__ =
lambda self:
None
2567 ComplementarityParams_swigregister = _IMP_multifit.ComplementarityParams_swigregister
2568 ComplementarityParams_swigregister(ComplementarityParams)
2570 class AlignmentParams(object):
2571 """Proxy of C++ IMP::multifit::AlignmentParams class."""
2573 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2575 def __init__(self, param_filename):
2576 """__init__(IMP::multifit::AlignmentParams self, char const * param_filename) -> AlignmentParams"""
2577 this = _IMP_multifit.new_AlignmentParams(param_filename)
2579 self.this.append(this)
2580 except __builtin__.Exception:
2583 def get_domino_params(self):
2584 """get_domino_params(AlignmentParams self) -> DominoParams"""
2585 return _IMP_multifit.AlignmentParams_get_domino_params(self)
2588 def get_fitting_params(self):
2589 """get_fitting_params(AlignmentParams self) -> FittingParams"""
2590 return _IMP_multifit.AlignmentParams_get_fitting_params(self)
2593 def get_complementarity_params(self):
2594 """get_complementarity_params(AlignmentParams self) -> ComplementarityParams"""
2595 return _IMP_multifit.AlignmentParams_get_complementarity_params(self)
2598 def get_xlink_params(self):
2599 """get_xlink_params(AlignmentParams self) -> XlinkParams"""
2600 return _IMP_multifit.AlignmentParams_get_xlink_params(self)
2603 def get_connectivity_params(self):
2604 """get_connectivity_params(AlignmentParams self) -> ConnectivityParams"""
2605 return _IMP_multifit.AlignmentParams_get_connectivity_params(self)
2608 def get_rog_params(self):
2609 """get_rog_params(AlignmentParams self) -> RogParams"""
2610 return _IMP_multifit.AlignmentParams_get_rog_params(self)
2613 def get_fragments_params(self):
2614 """get_fragments_params(AlignmentParams self) -> FragmentsParams"""
2615 return _IMP_multifit.AlignmentParams_get_fragments_params(self)
2618 def get_filters_params(self):
2619 """get_filters_params(AlignmentParams self) -> FiltersParams"""
2620 return _IMP_multifit.AlignmentParams_get_filters_params(self)
2623 def get_ev_params(self):
2624 """get_ev_params(AlignmentParams self) -> EVParams"""
2625 return _IMP_multifit.AlignmentParams_get_ev_params(self)
2628 def show(self, *args):
2630 show(AlignmentParams self, _ostream s)
2631 show(AlignmentParams self)
2633 return _IMP_multifit.AlignmentParams_show(self, *args)
2637 """__str__(AlignmentParams self) -> std::string"""
2638 return _IMP_multifit.AlignmentParams___str__(self)
2642 """__repr__(AlignmentParams self) -> std::string"""
2643 return _IMP_multifit.AlignmentParams___repr__(self)
2645 __swig_destroy__ = _IMP_multifit.delete_AlignmentParams
2646 __del__ =
lambda self:
None
2647 AlignmentParams_swigregister = _IMP_multifit.AlignmentParams_swigregister
2648 AlignmentParams_swigregister(AlignmentParams)
2650 class ProteomicsEMAlignmentAtomic(
IMP.Object):
2651 """Proxy of C++ IMP::multifit::ProteomicsEMAlignmentAtomic class."""
2653 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2655 def __init__(self, mapping_data, asmb_data, align_param):
2656 """__init__(IMP::multifit::ProteomicsEMAlignmentAtomic self, ProteinsAnchorsSamplingSpace mapping_data, SettingsData asmb_data, AlignmentParams align_param) -> ProteomicsEMAlignmentAtomic"""
2657 this = _IMP_multifit.new_ProteomicsEMAlignmentAtomic(mapping_data, asmb_data, align_param)
2659 self.this.append(this)
2660 except __builtin__.Exception:
2664 """align(ProteomicsEMAlignmentAtomic self)"""
2665 return _IMP_multifit.ProteomicsEMAlignmentAtomic_align(self)
2668 def add_all_restraints(self):
2669 """add_all_restraints(ProteomicsEMAlignmentAtomic self)"""
2670 return _IMP_multifit.ProteomicsEMAlignmentAtomic_add_all_restraints(self)
2673 def get_restraint_set(self):
2674 """get_restraint_set(ProteomicsEMAlignmentAtomic self) -> RestraintSet"""
2675 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_restraint_set(self)
2678 def add_states_and_filters(self):
2679 """add_states_and_filters(ProteomicsEMAlignmentAtomic self)"""
2680 return _IMP_multifit.ProteomicsEMAlignmentAtomic_add_states_and_filters(self)
2683 def show_domino_merge_tree(self):
2684 """show_domino_merge_tree(ProteomicsEMAlignmentAtomic self)"""
2685 return _IMP_multifit.ProteomicsEMAlignmentAtomic_show_domino_merge_tree(self)
2688 def get_combinations(self, uniques=False):
2690 get_combinations(ProteomicsEMAlignmentAtomic self, bool uniques=False) -> IMP::domino::Assignments
2691 get_combinations(ProteomicsEMAlignmentAtomic self) -> IMP::domino::Assignments
2693 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_combinations(self, uniques)
2696 def set_density_map(self, dmap, threshold):
2697 """set_density_map(ProteomicsEMAlignmentAtomic self, DensityMap dmap, float threshold)"""
2698 return _IMP_multifit.ProteomicsEMAlignmentAtomic_set_density_map(self, dmap, threshold)
2701 def get_molecules(self):
2702 """get_molecules(ProteomicsEMAlignmentAtomic self) -> IMP::atom::Hierarchies"""
2703 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_molecules(self)
2706 def get_rigid_bodies(self):
2707 """get_rigid_bodies(ProteomicsEMAlignmentAtomic self) -> IMP::core::RigidBodies"""
2708 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_rigid_bodies(self)
2711 def load_combination_of_states(self, state4particles):
2712 """load_combination_of_states(ProteomicsEMAlignmentAtomic self, IMP::Ints const & state4particles)"""
2713 return _IMP_multifit.ProteomicsEMAlignmentAtomic_load_combination_of_states(self, state4particles)
2716 def show_scores_header(self, *args):
2718 show_scores_header(ProteomicsEMAlignmentAtomic self, _ostream ous)
2719 show_scores_header(ProteomicsEMAlignmentAtomic self)
2721 return _IMP_multifit.ProteomicsEMAlignmentAtomic_show_scores_header(self, *args)
2724 def get_model(self):
2725 """get_model(ProteomicsEMAlignmentAtomic self) -> Model"""
2726 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_model(self)
2729 def set_fast_scoring(self, state):
2730 """set_fast_scoring(ProteomicsEMAlignmentAtomic self, bool state)"""
2731 return _IMP_multifit.ProteomicsEMAlignmentAtomic_set_fast_scoring(self, state)
2734 def get_version_info(self):
2735 """get_version_info(ProteomicsEMAlignmentAtomic self) -> VersionInfo"""
2736 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_version_info(self)
2740 """__str__(ProteomicsEMAlignmentAtomic self) -> std::string"""
2741 return _IMP_multifit.ProteomicsEMAlignmentAtomic___str__(self)
2745 """__repr__(ProteomicsEMAlignmentAtomic self) -> std::string"""
2746 return _IMP_multifit.ProteomicsEMAlignmentAtomic___repr__(self)
2751 return _object_cast_to_ProteomicsEMAlignmentAtomic(o)
2753 ProteomicsEMAlignmentAtomic_swigregister = _IMP_multifit.ProteomicsEMAlignmentAtomic_swigregister
2754 ProteomicsEMAlignmentAtomic_swigregister(ProteomicsEMAlignmentAtomic)
2758 """write_connolly_surface(IMP::atom::Atoms atoms, TextOutput fn, float density, float probe_radius)"""
2759 return _IMP_multifit.write_connolly_surface(atoms, fn, density, probe_radius)
2761 """Proxy of C++ IMP::multifit::Ensemble class."""
2763 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2765 def load_combination(self, fit_comb):
2766 """load_combination(Ensemble self, IMP::Ints fit_comb)"""
2767 return _IMP_multifit.Ensemble_load_combination(self, fit_comb)
2770 def unload_combination(self, fit_comb):
2771 """unload_combination(Ensemble self, IMP::Ints fit_comb)"""
2772 return _IMP_multifit.Ensemble_unload_combination(self, fit_comb)
2775 def add_component_and_fits(self, mh, fits):
2776 """add_component_and_fits(Ensemble self, Hierarchy mh, IMP::multifit::FittingSolutionRecords const & fits)"""
2777 return _IMP_multifit.Ensemble_add_component_and_fits(self, mh, fits)
2780 def get_molecules(self):
2781 """get_molecules(Ensemble self) -> IMP::atom::Hierarchies"""
2782 return _IMP_multifit.Ensemble_get_molecules(self)
2785 def get_rigid_bodies(self):
2786 """get_rigid_bodies(Ensemble self) -> IMP::core::RigidBodies"""
2787 return _IMP_multifit.Ensemble_get_rigid_bodies(self)
2791 """get_rmsd(Ensemble self, IMP::core::XYZs const & second_xyz) -> float"""
2792 return _IMP_multifit.Ensemble_get_rmsd(self, second_xyz)
2795 def __init__(self, sd, mapping_data):
2796 """__init__(IMP::multifit::Ensemble self, SettingsData sd, ProteinsAnchorsSamplingSpace mapping_data) -> Ensemble"""
2797 this = _IMP_multifit.new_Ensemble(sd, mapping_data)
2799 self.this.append(this)
2800 except __builtin__.Exception:
2803 def score_by_restraints(self, rs, combinations):
2804 """score_by_restraints(Ensemble self, IMP::Restraints rs, IMP::IntsList const & combinations) -> std::vector< IMP::Floats,std::allocator< IMP::Floats > >"""
2805 return _IMP_multifit.Ensemble_score_by_restraints(self, rs, combinations)
2808 def get_version_info(self):
2809 """get_version_info(Ensemble self) -> VersionInfo"""
2810 return _IMP_multifit.Ensemble_get_version_info(self)
2814 """__str__(Ensemble self) -> std::string"""
2815 return _IMP_multifit.Ensemble___str__(self)
2819 """__repr__(Ensemble self) -> std::string"""
2820 return _IMP_multifit.Ensemble___repr__(self)
2825 return _object_cast_to_Ensemble(o)
2827 Ensemble_swigregister = _IMP_multifit.Ensemble_swigregister
2828 Ensemble_swigregister(Ensemble)
2831 def load_ensemble(sd, mdl, mapping_data):
2832 """load_ensemble(SettingsData sd, Model mdl, ProteinsAnchorsSamplingSpace mapping_data) -> Ensemble"""
2833 return _IMP_multifit.load_ensemble(sd, mdl, mapping_data)
2835 """Proxy of C++ IMP::multifit::RigidLeavesRefiner class."""
2837 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2841 __init__(IMP::multifit::RigidLeavesRefiner self, std::string name) -> RigidLeavesRefiner
2842 __init__(IMP::multifit::RigidLeavesRefiner self) -> RigidLeavesRefiner
2844 this = _IMP_multifit.new_RigidLeavesRefiner(*args)
2846 self.this.append(this)
2847 except __builtin__.Exception:
2850 def do_get_inputs(self, m, pis):
2851 """do_get_inputs(RigidLeavesRefiner self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2852 return _IMP_multifit.RigidLeavesRefiner_do_get_inputs(self, m, pis)
2855 def get_version_info(self):
2856 """get_version_info(RigidLeavesRefiner self) -> VersionInfo"""
2857 return _IMP_multifit.RigidLeavesRefiner_get_version_info(self)
2861 """__str__(RigidLeavesRefiner self) -> std::string"""
2862 return _IMP_multifit.RigidLeavesRefiner___str__(self)
2866 """__repr__(RigidLeavesRefiner self) -> std::string"""
2867 return _IMP_multifit.RigidLeavesRefiner___repr__(self)
2872 return _object_cast_to_RigidLeavesRefiner(o)
2874 RigidLeavesRefiner_swigregister = _IMP_multifit.RigidLeavesRefiner_swigregister
2875 RigidLeavesRefiner_swigregister(RigidLeavesRefiner)
2878 _all_commands = [
"param",
"anchors",
"fit_fft",
"cluster",
"add_fit_rmsd",
2879 "indexes",
"proteomics",
"align",
"models",
"transforms",
2880 "score",
"merge_tree",
"reference",
"refine_fft",
"segment"]
2884 """get_module_version() -> std::string const"""
2885 return _IMP_multifit.get_module_version()
2888 """get_example_path(std::string fname) -> std::string"""
2889 return _IMP_multifit.get_example_path(fname)
2892 """get_data_path(std::string fname) -> std::string"""
2893 return _IMP_multifit.get_data_path(fname)
2895 from .
import _version_check
IntsList get_anchor_indices_matching_secondary_structure(const AnchorsData &ad, const atom::SecondaryStructureResidues &ssrs, Float max_rmsd=0.7)
Get lists of anchors that match a sequence of secondary structures.
FittingSolutionRecords get_close_to_point(const FittingSolutionRecords &fit_sols, atom::Hierarchy mh, IMP::Particle *ap, Float dist)
prune solutions by distance to an anchor point
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
IntsList get_connected_components(em::DensityMap *dmap, float threshold, float edge_threshold)
Return connected components based on density values.
Various classes to hold sets of particles.
Make CGAL functionality available to IMP.
em::DensityMap * remove_background(em::DensityMap *dmap, float threshold, float edge_threshold)
Returns a map containing all density without the background.
ProteinsAnchorsSamplingSpace get_part_of_sampling_space(const ProteinsAnchorsSamplingSpace &prots_ss, const Strings &prot_names)
Get the sampling space of few of the proteins.
std::string get_module_version()
Return the version of this module, as a string.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
multifit::SettingsData * get_partial_assembly_setting_data(multifit::SettingsData *prots_sd, const Strings &prot_names)
Get the assembly data for a few of the proteins.
Composable functors to implement scores via compile-time composition.
em::FittingSolutions pca_based_rigid_fitting(core::RigidBody rb, Refiner *rb_refiner, em::DensityMap *em_map, Float threshold, FloatKey wei_key=atom::Mass::get_mass_key(), algebra::PrincipalComponentAnalysis dens_pca_input=algebra::PrincipalComponentAnalysis())
Compute fitting scores for a given set of rigid transformations.
Code to compute statistical measures.
void add_surface_index(core::Hierarchy mhd, Float apix, FloatKey shell_key=FloatKey("surf_ind"), FloatKey radius_key=core::XYZR::get_radius_key(), FloatKey weight_key=atom::Mass::get_mass_key())
Add shell index to leaves.
Ints get_index(const ParticlesTemp &particles, const Subset &subset, const Subsets &excluded)
Common base class for heavy weight IMP objects.
void get_anchors_for_density(em::DensityMap *dmap, int number_of_means, float density_threshold, std::string pdb_filename, std::string cmm_filename, std::string seg_filename, std::string txt_filename)
Generate anchors in several formats for a given density map.
double get_rmsd(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
double get_radius_of_gyration(const Vector3Ds &ps)
Return the radius of gyration of a set of points.
Basic utilities for handling cryo-electron microscopy 3D density maps.
void write_fitting_solutions(const char *fitting_fn, const FittingSolutionRecords &fit_sols, int num_sols=-1)
Write fitting solutions to a file.
ProteomicsData * read_proteomics_data(const char *proteomics_fn)
Proteomics reader.
IMP::Restraint * create_weighted_excluded_volume_restraint(core::RigidBody rb1, core::RigidBody rb2, FloatKey shell_key=FloatKey("surf_ind"))
Create a weighted excluded volume restraint between two rigid bodies.
algebra::Vector3Ds get_points_close_to_molecule(const atom::Hierarchy &mh, const algebra::Vector3Ds points, Float max_dist)
void get_segmentation(em::DensityMap *dmap, double apix, double density_threshold, int num_means, const std::string pdb_filename, const std::string cmm_filename, const std::string seg_filename, const std::string txt_filename)
Segment a density map using the anchor graph.
void write_connolly_surface(atom::Atoms atoms, TextOutput fn, float density, float probe_radius)
Write the Connolly surface for a set of atoms to a file.
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
multifit::FittingSolutionRecords fft_based_rigid_fitting(atom::Hierarchy mol2fit, em::DensityMap *dmap, double density_threshold, double angle_sampling_interval_rad)
FFT fit of a molecule in the density.
Basic functionality that is expected to be used by a wide variety of IMP users.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
IntsList read_paths(const char *txt_filename, int max_paths=INT_MAX)
Read paths.
FittingSolutionRecords read_fitting_solutions(const char *fitting_fn)
Fitting solutions reader.
Abstract class to implement hierarchical methods.
double get_resolution(Model *m, ParticleIndex pi)
Estimate the resolution of the hierarchy as used by Representation.
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for the RMF file format for storing hierarchical molecular data and markup.
Divide-and-conquer inferential optimization in discrete space.
Support for small angle X-ray scattering (SAXS) data.
Inferential scoring building on methods developed as part of the Inferential Structure Determination ...
A restraint is a term in an IMP ScoringFunction.
atom::Hierarchy create_coarse_molecule_from_density(em::DensityMap *dmap, float dens_threshold, int num_beads, Model *mdl, float bead_radius)
Coarsen a density map based on voxels clustering.