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_cnmultifit')).lstrip(
'.')
22 return importlib.import_module(mname)
24 return importlib.import_module(
'_IMP_cnmultifit')
25 _IMP_cnmultifit = 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_cnmultifit', [dirname(__file__)])
35 import _IMP_cnmultifit
36 return _IMP_cnmultifit
39 _mod = imp.load_module(
'_IMP_cnmultifit', fp, pathname, description)
43 _IMP_cnmultifit = swig_import_helper()
44 del swig_import_helper
46 import _IMP_cnmultifit
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_CNMULTIFIT_SwigPyIterator(object):
114 """Proxy of C++ swig::IMP_CNMULTIFIT_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_cnmultifit.delete_IMP_CNMULTIFIT_SwigPyIterator
122 __del__ =
lambda self:
None
125 """value(IMP_CNMULTIFIT_SwigPyIterator self) -> PyObject *"""
126 return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_value(self)
131 incr(IMP_CNMULTIFIT_SwigPyIterator self, size_t n=1) -> IMP_CNMULTIFIT_SwigPyIterator
132 incr(IMP_CNMULTIFIT_SwigPyIterator self) -> IMP_CNMULTIFIT_SwigPyIterator
134 return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_incr(self, n)
139 decr(IMP_CNMULTIFIT_SwigPyIterator self, size_t n=1) -> IMP_CNMULTIFIT_SwigPyIterator
140 decr(IMP_CNMULTIFIT_SwigPyIterator self) -> IMP_CNMULTIFIT_SwigPyIterator
142 return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_decr(self, n)
145 def distance(self, x):
146 """distance(IMP_CNMULTIFIT_SwigPyIterator self, IMP_CNMULTIFIT_SwigPyIterator x) -> ptrdiff_t"""
147 return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_distance(self, x)
151 """equal(IMP_CNMULTIFIT_SwigPyIterator self, IMP_CNMULTIFIT_SwigPyIterator x) -> bool"""
152 return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_equal(self, x)
156 """copy(IMP_CNMULTIFIT_SwigPyIterator self) -> IMP_CNMULTIFIT_SwigPyIterator"""
157 return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_copy(self)
161 """next(IMP_CNMULTIFIT_SwigPyIterator self) -> PyObject *"""
162 return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_next(self)
166 """__next__(IMP_CNMULTIFIT_SwigPyIterator self) -> PyObject *"""
167 return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___next__(self)
171 """previous(IMP_CNMULTIFIT_SwigPyIterator self) -> PyObject *"""
172 return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_previous(self)
175 def advance(self, n):
176 """advance(IMP_CNMULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_CNMULTIFIT_SwigPyIterator"""
177 return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_advance(self, n)
181 """__eq__(IMP_CNMULTIFIT_SwigPyIterator self, IMP_CNMULTIFIT_SwigPyIterator x) -> bool"""
182 return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___eq__(self, x)
186 """__ne__(IMP_CNMULTIFIT_SwigPyIterator self, IMP_CNMULTIFIT_SwigPyIterator x) -> bool"""
187 return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___ne__(self, x)
190 def __iadd__(self, n):
191 """__iadd__(IMP_CNMULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_CNMULTIFIT_SwigPyIterator"""
192 return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___iadd__(self, n)
195 def __isub__(self, n):
196 """__isub__(IMP_CNMULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_CNMULTIFIT_SwigPyIterator"""
197 return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___isub__(self, n)
200 def __add__(self, n):
201 """__add__(IMP_CNMULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_CNMULTIFIT_SwigPyIterator"""
202 return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___add__(self, n)
205 def __sub__(self, *args):
207 __sub__(IMP_CNMULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_CNMULTIFIT_SwigPyIterator
208 __sub__(IMP_CNMULTIFIT_SwigPyIterator self, IMP_CNMULTIFIT_SwigPyIterator x) -> ptrdiff_t
210 return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___sub__(self, *args)
214 IMP_CNMULTIFIT_SwigPyIterator_swigregister = _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_swigregister
215 IMP_CNMULTIFIT_SwigPyIterator_swigregister(IMP_CNMULTIFIT_SwigPyIterator)
223 IMP_DEBUG = _IMP_cnmultifit.IMP_DEBUG
224 IMP_RELEASE = _IMP_cnmultifit.IMP_RELEASE
225 IMP_SILENT = _IMP_cnmultifit.IMP_SILENT
226 IMP_PROGRESS = _IMP_cnmultifit.IMP_PROGRESS
227 IMP_TERSE = _IMP_cnmultifit.IMP_TERSE
228 IMP_VERBOSE = _IMP_cnmultifit.IMP_VERBOSE
229 IMP_MEMORY = _IMP_cnmultifit.IMP_MEMORY
230 IMP_NONE = _IMP_cnmultifit.IMP_NONE
231 IMP_USAGE = _IMP_cnmultifit.IMP_USAGE
232 IMP_INTERNAL = _IMP_cnmultifit.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_cnmultifit.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_cnmultifit.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_cnmultifit.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_cnmultifit.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_cnmultifit.IMP_KERNEL_HAS_GPERFTOOLS
239 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_cnmultifit.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
240 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_cnmultifit.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
241 IMPKERNEL_SHOW_WARNINGS = _IMP_cnmultifit.IMPKERNEL_SHOW_WARNINGS
244 class _DirectorObjects(object):
245 """@internal Simple class to keep references to director objects
246 to prevent premature deletion."""
249 def register(self, obj):
250 """Take a reference to a director object; will only work for
251 refcounted C++ classes"""
252 if hasattr(obj,
'get_ref_count'):
253 self._objects.append(obj)
255 """Only drop our reference and allow cleanup by Python if no other
256 Python references exist (we hold 3 references: one in self._objects,
257 one in x, and one in the argument list for getrefcount) *and* no
258 other C++ references exist (the Python object always holds one)"""
259 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
260 or x.get_ref_count() > 1]
264 def get_object_count(self):
265 """Get number of director objects (useful for testing only)"""
266 return len(self._objects)
267 _director_objects = _DirectorObjects()
269 class _ostream(object):
270 """Proxy of C++ std::ostream class."""
272 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
274 def __init__(self, *args, **kwargs):
275 raise AttributeError(
"No constructor defined")
276 __repr__ = _swig_repr
278 def write(self, osa_buf):
279 """write(_ostream self, char const * osa_buf)"""
280 return _IMP_cnmultifit._ostream_write(self, osa_buf)
282 _ostream_swigregister = _IMP_cnmultifit._ostream_swigregister
283 _ostream_swigregister(_ostream)
285 IMP_COMPILER_HAS_OVERRIDE = _IMP_cnmultifit.IMP_COMPILER_HAS_OVERRIDE
286 IMP_COMPILER_HAS_FINAL = _IMP_cnmultifit.IMP_COMPILER_HAS_FINAL
287 IMP_HAS_NOEXCEPT = _IMP_cnmultifit.IMP_HAS_NOEXCEPT
289 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_CGAL_HAS_BOOST_FILESYSTEM
290 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
291 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_CGAL_HAS_BOOST_RANDOM
292 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_CGAL_HAS_BOOST_SYSTEM
293 IMPCGAL_SHOW_WARNINGS = _IMP_cnmultifit.IMPCGAL_SHOW_WARNINGS
295 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_ALGEBRA_HAS_IMP_CGAL
296 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
297 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
298 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_ALGEBRA_HAS_BOOST_RANDOM
299 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_ALGEBRA_HAS_BOOST_SYSTEM
300 IMP_ALGEBRA_HAS_CGAL = _IMP_cnmultifit.IMP_ALGEBRA_HAS_CGAL
301 IMP_ALGEBRA_HAS_ANN = _IMP_cnmultifit.IMP_ALGEBRA_HAS_ANN
302 IMPALGEBRA_SHOW_WARNINGS = _IMP_cnmultifit.IMPALGEBRA_SHOW_WARNINGS
304 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_DISPLAY_HAS_IMP_CGAL
305 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
306 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
307 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_DISPLAY_HAS_BOOST_RANDOM
308 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_DISPLAY_HAS_BOOST_SYSTEM
309 IMP_DISPLAY_HAS_CGAL = _IMP_cnmultifit.IMP_DISPLAY_HAS_CGAL
310 IMPDISPLAY_SHOW_WARNINGS = _IMP_cnmultifit.IMPDISPLAY_SHOW_WARNINGS
312 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
313 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
314 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
315 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
316 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
317 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_CGAL
318 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_HDF5
319 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_cnmultifit.IMPSCOREFUNCTOR_SHOW_WARNINGS
321 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_STATISTICS_HAS_IMP_CGAL
322 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
323 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
324 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_STATISTICS_HAS_BOOST_RANDOM
325 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_STATISTICS_HAS_BOOST_SYSTEM
326 IMP_STATISTICS_HAS_CGAL = _IMP_cnmultifit.IMP_STATISTICS_HAS_CGAL
327 IMPSTATISTICS_SHOW_WARNINGS = _IMP_cnmultifit.IMPSTATISTICS_SHOW_WARNINGS
329 IMP_CORE_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_CORE_HAS_IMP_CGAL
330 IMP_CORE_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_CORE_HAS_IMP_KERNEL
331 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_CORE_HAS_BOOST_FILESYSTEM
332 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
333 IMP_CORE_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_CORE_HAS_BOOST_RANDOM
334 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_CORE_HAS_BOOST_SYSTEM
335 IMP_CORE_HAS_CGAL = _IMP_cnmultifit.IMP_CORE_HAS_CGAL
336 IMP_CORE_HAS_HDF5 = _IMP_cnmultifit.IMP_CORE_HAS_HDF5
337 IMPCORE_SHOW_WARNINGS = _IMP_cnmultifit.IMPCORE_SHOW_WARNINGS
339 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_ALGEBRA
340 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_CGAL
341 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_DISPLAY
342 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_KERNEL
343 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
344 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
345 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
346 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_CONTAINER_HAS_BOOST_RANDOM
347 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_CONTAINER_HAS_BOOST_SYSTEM
348 IMP_CONTAINER_HAS_CGAL = _IMP_cnmultifit.IMP_CONTAINER_HAS_CGAL
349 IMP_CONTAINER_HAS_HDF5 = _IMP_cnmultifit.IMP_CONTAINER_HAS_HDF5
350 IMPCONTAINER_SHOW_WARNINGS = _IMP_cnmultifit.IMPCONTAINER_SHOW_WARNINGS
352 IMP_ATOM_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_ATOM_HAS_IMP_CGAL
353 IMP_ATOM_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_ATOM_HAS_IMP_KERNEL
354 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
355 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
356 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_ATOM_HAS_BOOST_RANDOM
357 IMP_ATOM_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_ATOM_HAS_BOOST_REGEX
358 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_ATOM_HAS_BOOST_SYSTEM
359 IMP_ATOM_HAS_CGAL = _IMP_cnmultifit.IMP_ATOM_HAS_CGAL
360 IMP_ATOM_HAS_HDF5 = _IMP_cnmultifit.IMP_ATOM_HAS_HDF5
361 IMPATOM_SHOW_WARNINGS = _IMP_cnmultifit.IMPATOM_SHOW_WARNINGS
362 IMP_ATOM_TYPE_INDEX = _IMP_cnmultifit.IMP_ATOM_TYPE_INDEX
363 IMP_RESIDUE_TYPE_INDEX = _IMP_cnmultifit.IMP_RESIDUE_TYPE_INDEX
364 IMP_HIERARCHY_TYPE_INDEX = _IMP_cnmultifit.IMP_HIERARCHY_TYPE_INDEX
366 IMP_EM_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_EM_HAS_IMP_CGAL
367 IMP_EM_HAS_IMP_CONTAINER = _IMP_cnmultifit.IMP_EM_HAS_IMP_CONTAINER
368 IMP_EM_HAS_IMP_DISPLAY = _IMP_cnmultifit.IMP_EM_HAS_IMP_DISPLAY
369 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_EM_HAS_IMP_SCORE_FUNCTOR
370 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_EM_HAS_BOOST_FILESYSTEM
371 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
372 IMP_EM_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_EM_HAS_BOOST_RANDOM
373 IMP_EM_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_EM_HAS_BOOST_REGEX
374 IMP_EM_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_EM_HAS_BOOST_SYSTEM
375 IMP_EM_HAS_CGAL = _IMP_cnmultifit.IMP_EM_HAS_CGAL
376 IMP_EM_HAS_HDF5 = _IMP_cnmultifit.IMP_EM_HAS_HDF5
377 IMPEM_SHOW_WARNINGS = _IMP_cnmultifit.IMPEM_SHOW_WARNINGS
379 IMP_RMF_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_RMF_HAS_IMP_CGAL
380 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
381 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_FILESYSTEM
382 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
383 IMP_RMF_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_RANDOM
384 IMP_RMF_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_REGEX
385 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_SYSTEM
386 IMP_RMF_HAS_CGAL = _IMP_cnmultifit.IMP_RMF_HAS_CGAL
387 IMP_RMF_HAS_HDF5 = _IMP_cnmultifit.IMP_RMF_HAS_HDF5
388 IMPRMF_SHOW_WARNINGS = _IMP_cnmultifit.IMPRMF_SHOW_WARNINGS
391 IMP_DOMINO_HAS_IMP_ATOM = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_ATOM
392 IMP_DOMINO_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_CGAL
393 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_KERNEL
394 IMP_DOMINO_HAS_IMP_RMF = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_RMF
395 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
396 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_FILESYSTEM
397 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
398 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_RANDOM
399 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_REGEX
400 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_SYSTEM
401 IMP_DOMINO_HAS_CGAL = _IMP_cnmultifit.IMP_DOMINO_HAS_CGAL
402 IMP_DOMINO_HAS_HDF5 = _IMP_cnmultifit.IMP_DOMINO_HAS_HDF5
403 IMP_DOMINO_HAS_RMF = _IMP_cnmultifit.IMP_DOMINO_HAS_RMF
404 IMPDOMINO_SHOW_WARNINGS = _IMP_cnmultifit.IMPDOMINO_SHOW_WARNINGS
407 IMP_MULTIFIT_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_CGAL
408 IMP_MULTIFIT_HAS_IMP_CONTAINER = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_CONTAINER
409 IMP_MULTIFIT_HAS_IMP_DISPLAY = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_DISPLAY
410 IMP_MULTIFIT_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_KERNEL
411 IMP_MULTIFIT_HAS_IMP_RMF = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_RMF
412 IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR
413 IMP_MULTIFIT_HAS_BOOST_GRAPH = _IMP_cnmultifit.IMP_MULTIFIT_HAS_BOOST_GRAPH
414 IMP_MULTIFIT_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_MULTIFIT_HAS_BOOST_RANDOM
415 IMP_MULTIFIT_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_MULTIFIT_HAS_BOOST_REGEX
416 IMP_MULTIFIT_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_MULTIFIT_HAS_BOOST_SYSTEM
417 IMP_MULTIFIT_HAS_CGAL = _IMP_cnmultifit.IMP_MULTIFIT_HAS_CGAL
418 IMP_MULTIFIT_HAS_HDF5 = _IMP_cnmultifit.IMP_MULTIFIT_HAS_HDF5
419 IMP_MULTIFIT_HAS_RMF = _IMP_cnmultifit.IMP_MULTIFIT_HAS_RMF
420 IMPMULTIFIT_SHOW_WARNINGS = _IMP_cnmultifit.IMPMULTIFIT_SHOW_WARNINGS
422 IMP_CNMULTIFIT_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_CGAL
423 IMP_CNMULTIFIT_HAS_IMP_CONTAINER = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_CONTAINER
424 IMP_CNMULTIFIT_HAS_IMP_DISPLAY = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_DISPLAY
425 IMP_CNMULTIFIT_HAS_IMP_DOMINO = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_DOMINO
426 IMP_CNMULTIFIT_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_KERNEL
427 IMP_CNMULTIFIT_HAS_IMP_RMF = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_RMF
428 IMP_CNMULTIFIT_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_SCORE_FUNCTOR
429 IMP_CNMULTIFIT_HAS_BOOST_GRAPH = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_BOOST_GRAPH
430 IMP_CNMULTIFIT_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_BOOST_RANDOM
431 IMP_CNMULTIFIT_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_BOOST_REGEX
432 IMP_CNMULTIFIT_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_BOOST_SYSTEM
433 IMP_CNMULTIFIT_HAS_CGAL = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_CGAL
434 IMP_CNMULTIFIT_HAS_FFTW3 = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_FFTW3
435 IMP_CNMULTIFIT_HAS_HDF5 = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_HDF5
436 IMP_CNMULTIFIT_HAS_RMF = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_RMF
437 IMPCNMULTIFIT_SHOW_WARNINGS = _IMP_cnmultifit.IMPCNMULTIFIT_SHOW_WARNINGS
440 _plural_types.append(
"AlignSymmetrics")
441 _value_types.append(
"AlignSymmetric")
444 CnSymmAxisDetectors=list
445 _plural_types.append(
"CnSymmAxisDetectors")
446 _value_types.append(
"CnSymmAxisDetector")
449 MolCnSymmAxisDetectors=list
450 _plural_types.append(
"MolCnSymmAxisDetectors")
451 _value_types.append(
"MolCnSymmAxisDetector")
453 class CnSymmAxisDetector(object):
454 """Proxy of C++ IMP::cnmultifit::CnSymmAxisDetector class."""
456 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
458 def __init__(self, *args):
460 __init__(IMP::cnmultifit::CnSymmAxisDetector self, int symm_deg, DensityMap dmap, float density_threshold, float top_p=0.8) -> CnSymmAxisDetector
461 __init__(IMP::cnmultifit::CnSymmAxisDetector self, int symm_deg, DensityMap dmap, float density_threshold) -> CnSymmAxisDetector
462 __init__(IMP::cnmultifit::CnSymmAxisDetector self, int symm_deg, IMP::atom::Hierarchies const & mhs) -> CnSymmAxisDetector
464 this = _IMP_cnmultifit.new_CnSymmAxisDetector(*args)
466 self.this.append(this)
467 except __builtin__.Exception:
471 """get_pca(CnSymmAxisDetector self) -> PrincipalComponentAnalysis3D"""
472 return _IMP_cnmultifit.CnSymmAxisDetector_get_pca(self)
475 def calc_symm_score(self, symm_axis_ind):
476 """calc_symm_score(CnSymmAxisDetector self, int symm_axis_ind) -> float"""
477 return _IMP_cnmultifit.CnSymmAxisDetector_calc_symm_score(self, symm_axis_ind)
480 def get_symmetry_axis(self):
481 """get_symmetry_axis(CnSymmAxisDetector self) -> Vector3D"""
482 return _IMP_cnmultifit.CnSymmAxisDetector_get_symmetry_axis(self)
485 def get_symmetry_axis_index(self):
486 """get_symmetry_axis_index(CnSymmAxisDetector self) -> int"""
487 return _IMP_cnmultifit.CnSymmAxisDetector_get_symmetry_axis_index(self)
490 def get_non_symmetry_axis_length(self):
491 """get_non_symmetry_axis_length(CnSymmAxisDetector self) -> int"""
492 return _IMP_cnmultifit.CnSymmAxisDetector_get_non_symmetry_axis_length(self)
495 def show(self, *args):
497 show(CnSymmAxisDetector self, _ostream out)
498 show(CnSymmAxisDetector self)
500 return _IMP_cnmultifit.CnSymmAxisDetector_show(self, *args)
504 """__str__(CnSymmAxisDetector self) -> std::string"""
505 return _IMP_cnmultifit.CnSymmAxisDetector___str__(self)
509 """__repr__(CnSymmAxisDetector self) -> std::string"""
510 return _IMP_cnmultifit.CnSymmAxisDetector___repr__(self)
512 __swig_destroy__ = _IMP_cnmultifit.delete_CnSymmAxisDetector
513 __del__ =
lambda self:
None
514 CnSymmAxisDetector_swigregister = _IMP_cnmultifit.CnSymmAxisDetector_swigregister
515 CnSymmAxisDetector_swigregister(CnSymmAxisDetector)
517 class MolCnSymmAxisDetector(object):
518 """Proxy of C++ IMP::cnmultifit::MolCnSymmAxisDetector class."""
520 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
522 def __init__(self, symm_deg, mhs):
523 """__init__(IMP::cnmultifit::MolCnSymmAxisDetector self, int symm_deg, IMP::atom::Hierarchies const & mhs) -> MolCnSymmAxisDetector"""
524 this = _IMP_cnmultifit.new_MolCnSymmAxisDetector(symm_deg, mhs)
526 self.this.append(this)
527 except __builtin__.Exception:
531 """get_pca(MolCnSymmAxisDetector self) -> PrincipalComponentAnalysis3D"""
532 return _IMP_cnmultifit.MolCnSymmAxisDetector_get_pca(self)
535 def get_symmetry_axis(self):
536 """get_symmetry_axis(MolCnSymmAxisDetector self) -> Vector3D"""
537 return _IMP_cnmultifit.MolCnSymmAxisDetector_get_symmetry_axis(self)
540 def get_symmetry_axis_index(self):
541 """get_symmetry_axis_index(MolCnSymmAxisDetector self) -> int"""
542 return _IMP_cnmultifit.MolCnSymmAxisDetector_get_symmetry_axis_index(self)
545 def show(self, *args):
547 show(MolCnSymmAxisDetector self, _ostream out)
548 show(MolCnSymmAxisDetector self)
550 return _IMP_cnmultifit.MolCnSymmAxisDetector_show(self, *args)
553 def calc_symm_score(self, symm_axis_ind):
554 """calc_symm_score(MolCnSymmAxisDetector self, int symm_axis_ind) -> float"""
555 return _IMP_cnmultifit.MolCnSymmAxisDetector_calc_symm_score(self, symm_axis_ind)
559 """__str__(MolCnSymmAxisDetector self) -> std::string"""
560 return _IMP_cnmultifit.MolCnSymmAxisDetector___str__(self)
564 """__repr__(MolCnSymmAxisDetector self) -> std::string"""
565 return _IMP_cnmultifit.MolCnSymmAxisDetector___repr__(self)
567 __swig_destroy__ = _IMP_cnmultifit.delete_MolCnSymmAxisDetector
568 __del__ =
lambda self:
None
569 MolCnSymmAxisDetector_swigregister = _IMP_cnmultifit.MolCnSymmAxisDetector_swigregister
570 MolCnSymmAxisDetector_swigregister(MolCnSymmAxisDetector)
572 class AlignSymmetric(object):
573 """Proxy of C++ IMP::cnmultifit::AlignSymmetric class."""
575 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
577 def __init__(self, dmap, threshold, cn_symm_deg):
578 """__init__(IMP::cnmultifit::AlignSymmetric self, DensityMap dmap, float threshold, int cn_symm_deg) -> AlignSymmetric"""
579 this = _IMP_cnmultifit.new_AlignSymmetric(dmap, threshold, cn_symm_deg)
581 self.this.append(this)
582 except __builtin__.Exception:
585 def get_sorted_principal_values(self):
586 """get_sorted_principal_values(AlignSymmetric self) -> IMP::Floats"""
587 return _IMP_cnmultifit.AlignSymmetric_get_sorted_principal_values(self)
590 def score_alignment(self, mhs, max_allowed_diff):
591 """score_alignment(AlignSymmetric self, IMP::atom::Hierarchies mhs, float max_allowed_diff) -> int"""
592 return _IMP_cnmultifit.AlignSymmetric_score_alignment(self, mhs, max_allowed_diff)
595 def get_symm_axis_alignments_from_model_to_density(self, mhs, sample_translation, fine_rotation_sampling=True):
597 get_symm_axis_alignments_from_model_to_density(AlignSymmetric self, IMP::atom::Hierarchies mhs, bool sample_translation, bool fine_rotation_sampling=True) -> IMP::algebra::Transformation3Ds
598 get_symm_axis_alignments_from_model_to_density(AlignSymmetric self, IMP::atom::Hierarchies mhs, bool sample_translation) -> IMP::algebra::Transformation3Ds
600 return _IMP_cnmultifit.AlignSymmetric_get_symm_axis_alignments_from_model_to_density(self, mhs, sample_translation, fine_rotation_sampling)
603 def show(self, *args):
605 show(AlignSymmetric self, _ostream out)
606 show(AlignSymmetric self)
608 return _IMP_cnmultifit.AlignSymmetric_show(self, *args)
612 """__str__(AlignSymmetric self) -> std::string"""
613 return _IMP_cnmultifit.AlignSymmetric___str__(self)
617 """__repr__(AlignSymmetric self) -> std::string"""
618 return _IMP_cnmultifit.AlignSymmetric___repr__(self)
620 __swig_destroy__ = _IMP_cnmultifit.delete_AlignSymmetric
621 __del__ =
lambda self:
None
622 AlignSymmetric_swigregister = _IMP_cnmultifit.AlignSymmetric_swigregister
623 AlignSymmetric_swigregister(AlignSymmetric)
626 def generate_cn_transformations(mhs, symm_deg):
627 """generate_cn_transformations(IMP::atom::Hierarchies mhs, int symm_deg) -> IMP::algebra::Transformation3Ds"""
628 return _IMP_cnmultifit.generate_cn_transformations(mhs, symm_deg)
630 def generate_translations_along_symm_axis(mhs, symm_deg):
631 """generate_translations_along_symm_axis(IMP::atom::Hierarchies mhs, int symm_deg) -> IMP::algebra::Transformation3Ds"""
632 return _IMP_cnmultifit.generate_translations_along_symm_axis(mhs, symm_deg)
634 def symmetry_local_fitting(mhs, cn_symm_deg, dn_symm_deg, dmap, num_of_trans_to_consider):
635 """symmetry_local_fitting(IMP::atom::Hierarchies mhs, int cn_symm_deg, int dn_symm_deg, DensityMap dmap, int num_of_trans_to_consider) -> FittingSolutions"""
636 return _IMP_cnmultifit.symmetry_local_fitting(mhs, cn_symm_deg, dn_symm_deg, dmap, num_of_trans_to_consider)
638 def build_cn_dens_assembly(subunit_dens, asmb_dens_header, monomer_t, symm_deg):
639 """build_cn_dens_assembly(DensityMap subunit_dens, DensityHeader asmb_dens_header, Transformation3D monomer_t, int symm_deg) -> DensityMap"""
640 return _IMP_cnmultifit.build_cn_dens_assembly(subunit_dens, asmb_dens_header, monomer_t, symm_deg)
642 def transform_cn_assembly(mhs, monomer_t):
643 """transform_cn_assembly(IMP::atom::Hierarchies mhs, Transformation3D monomer_t)"""
644 return _IMP_cnmultifit.transform_cn_assembly(mhs, monomer_t)
648 fit_cn_assembly(IMP::atom::Hierarchies mhs, int dn_symm_deg, DensityMap dmap, float threshold, AlignSymmetric aligner, bool sample_translation=False, bool fine_rotational_sampling=True) -> FittingSolutions
649 fit_cn_assembly(IMP::atom::Hierarchies mhs, int dn_symm_deg, DensityMap dmap, float threshold, AlignSymmetric aligner, bool sample_translation=False) -> FittingSolutions
650 fit_cn_assembly(IMP::atom::Hierarchies mhs, int dn_symm_deg, DensityMap dmap, float threshold, AlignSymmetric aligner) -> FittingSolutions
651 fit_cn_assembly(DensityMap asmb_map, MolCnSymmAxisDetector symm_mol, DensityMap dmap, CnSymmAxisDetector symm_map, int symm_deg, float threshold) -> FittingSolutions
653 return _IMP_cnmultifit.fit_cn_assembly(*args)
655 def pca_matching(pca1, pca2, resolution):
656 """pca_matching(PrincipalComponentAnalysis3D pca1, PrincipalComponentAnalysis3D pca2, float resolution) -> bool"""
657 return _IMP_cnmultifit.pca_matching(pca1, pca2, resolution)
660 """cn_symm_score(IMP::atom::Hierarchies mhs, Vector3D center, Vector3D direction, int symm_deg) -> float"""
661 return _IMP_cnmultifit.cn_symm_score(mhs, center, direction, symm_deg)
663 def prune_by_pca(param_fn, sols, dn=1):
665 prune_by_pca(std::string const & param_fn, IMP::multifit::FittingSolutionRecords const & sols, int dn=1) -> IMP::multifit::FittingSolutionRecords
666 prune_by_pca(std::string const & param_fn, IMP::multifit::FittingSolutionRecords const & sols) -> IMP::multifit::FittingSolutionRecords
668 return _IMP_cnmultifit.prune_by_pca(param_fn, sols, dn)
670 def calc_transformation_around_axis(a, b, angle_rad):
671 """calc_transformation_around_axis(Vector3D a, Vector3D b, float angle_rad) -> Transformation3D"""
672 return _IMP_cnmultifit.calc_transformation_around_axis(a, b, angle_rad)
675 """get_cn_rmsd(IMP::atom::Hierarchies mh1, IMP::atom::Hierarchies mh2) -> float"""
676 return _IMP_cnmultifit.get_cn_rmsd(mh1, mh2)
680 do_all_fitting(std::string const param_filename, std::string const chimera_filename)
681 do_all_fitting(std::string const param_filename)
683 return _IMP_cnmultifit.do_all_fitting(*args)
685 def get_rmsd_for_models(param_filename, trans_filename, ref_filename, start_model=0, end_model=-1):
687 get_rmsd_for_models(std::string const param_filename, std::string const trans_filename, std::string const ref_filename, int start_model=0, int end_model=-1) -> IMP::Floats
688 get_rmsd_for_models(std::string const param_filename, std::string const trans_filename, std::string const ref_filename, int start_model=0) -> IMP::Floats
689 get_rmsd_for_models(std::string const param_filename, std::string const trans_filename, std::string const ref_filename) -> IMP::Floats
691 return _IMP_cnmultifit.get_rmsd_for_models(param_filename, trans_filename, ref_filename, start_model, end_model)
693 _all_commands = [
"build",
"rmsd",
"surface",
694 "param",
"chimera_models"]
697 def get_module_version():
698 """get_module_version() -> std::string const"""
699 return _IMP_cnmultifit.get_module_version()
702 """get_example_path(std::string fname) -> std::string"""
703 return _IMP_cnmultifit.get_example_path(fname)
706 """get_data_path(std::string fname) -> std::string"""
707 return _IMP_cnmultifit.get_data_path(fname)
709 from .
import _version_check
710 _version_check.check_version(get_module_version())
711 __version__ = get_module_version()
Various classes to hold sets of particles.
void do_all_fitting(const std::string param_filename, const std::string chimera_filename="")
High level interface to build cyclic symmetric complexes.
Make CGAL functionality available to IMP.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
Composable functors to implement scores via compile-time composition.
Code to compute statistical measures.
float cn_symm_score(atom::Hierarchies mhs, const algebra::Vector3D ¢er, const algebra::Vector3D &direction, int symm_deg)
scores an input vector as a symmetry axis
Fitting atomic structures into a cryo-electron microscopy density map.
Basic utilities for handling cryo-electron microscopy 3D density maps.
float get_cn_rmsd(atom::Hierarchies mh1, atom::Hierarchies mh2)
Find correspondence between the two rings and calculate rmsd.
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
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...
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
em::FittingSolutions fit_cn_assembly(atom::Hierarchies mhs, int dn_symm_deg, em::DensityMap *dmap, float threshold, const AlignSymmetric &aligner, bool sample_translation=false, bool fine_rotational_sampling=true)
Fit a symmetric model to its density.
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.