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_em')).lstrip(
'.')
22 return importlib.import_module(mname)
24 return importlib.import_module(
'_IMP_em')
25 _IMP_em = 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_em', [dirname(__file__)])
39 _mod = imp.load_module(
'_IMP_em', fp, pathname, description)
43 _IMP_em = 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_EM_SwigPyIterator(object):
114 """Proxy of C++ swig::IMP_EM_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_em.delete_IMP_EM_SwigPyIterator
122 __del__ =
lambda self:
None
125 """value(IMP_EM_SwigPyIterator self) -> PyObject *"""
126 return _IMP_em.IMP_EM_SwigPyIterator_value(self)
131 incr(IMP_EM_SwigPyIterator self, size_t n=1) -> IMP_EM_SwigPyIterator
132 incr(IMP_EM_SwigPyIterator self) -> IMP_EM_SwigPyIterator
134 return _IMP_em.IMP_EM_SwigPyIterator_incr(self, n)
139 decr(IMP_EM_SwigPyIterator self, size_t n=1) -> IMP_EM_SwigPyIterator
140 decr(IMP_EM_SwigPyIterator self) -> IMP_EM_SwigPyIterator
142 return _IMP_em.IMP_EM_SwigPyIterator_decr(self, n)
145 def distance(self, x):
146 """distance(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> ptrdiff_t"""
147 return _IMP_em.IMP_EM_SwigPyIterator_distance(self, x)
151 """equal(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> bool"""
152 return _IMP_em.IMP_EM_SwigPyIterator_equal(self, x)
156 """copy(IMP_EM_SwigPyIterator self) -> IMP_EM_SwigPyIterator"""
157 return _IMP_em.IMP_EM_SwigPyIterator_copy(self)
161 """next(IMP_EM_SwigPyIterator self) -> PyObject *"""
162 return _IMP_em.IMP_EM_SwigPyIterator_next(self)
166 """__next__(IMP_EM_SwigPyIterator self) -> PyObject *"""
167 return _IMP_em.IMP_EM_SwigPyIterator___next__(self)
171 """previous(IMP_EM_SwigPyIterator self) -> PyObject *"""
172 return _IMP_em.IMP_EM_SwigPyIterator_previous(self)
175 def advance(self, n):
176 """advance(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator"""
177 return _IMP_em.IMP_EM_SwigPyIterator_advance(self, n)
181 """__eq__(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> bool"""
182 return _IMP_em.IMP_EM_SwigPyIterator___eq__(self, x)
186 """__ne__(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> bool"""
187 return _IMP_em.IMP_EM_SwigPyIterator___ne__(self, x)
190 def __iadd__(self, n):
191 """__iadd__(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator"""
192 return _IMP_em.IMP_EM_SwigPyIterator___iadd__(self, n)
195 def __isub__(self, n):
196 """__isub__(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator"""
197 return _IMP_em.IMP_EM_SwigPyIterator___isub__(self, n)
200 def __add__(self, n):
201 """__add__(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator"""
202 return _IMP_em.IMP_EM_SwigPyIterator___add__(self, n)
205 def __sub__(self, *args):
207 __sub__(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator
208 __sub__(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> ptrdiff_t
210 return _IMP_em.IMP_EM_SwigPyIterator___sub__(self, *args)
214 IMP_EM_SwigPyIterator_swigregister = _IMP_em.IMP_EM_SwigPyIterator_swigregister
215 IMP_EM_SwigPyIterator_swigregister(IMP_EM_SwigPyIterator)
223 IMP_DEBUG = _IMP_em.IMP_DEBUG
224 IMP_RELEASE = _IMP_em.IMP_RELEASE
225 IMP_SILENT = _IMP_em.IMP_SILENT
226 IMP_PROGRESS = _IMP_em.IMP_PROGRESS
227 IMP_TERSE = _IMP_em.IMP_TERSE
228 IMP_VERBOSE = _IMP_em.IMP_VERBOSE
229 IMP_MEMORY = _IMP_em.IMP_MEMORY
230 IMP_NONE = _IMP_em.IMP_NONE
231 IMP_USAGE = _IMP_em.IMP_USAGE
232 IMP_INTERNAL = _IMP_em.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_em.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_em.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_em.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_em.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_em.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_em.IMP_KERNEL_HAS_GPERFTOOLS
239 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
240 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
241 IMPKERNEL_SHOW_WARNINGS = _IMP_em.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_em._ostream_write(self, osa_buf)
282 _ostream_swigregister = _IMP_em._ostream_swigregister
283 _ostream_swigregister(_ostream)
285 IMP_COMPILER_HAS_OVERRIDE = _IMP_em.IMP_COMPILER_HAS_OVERRIDE
286 IMP_COMPILER_HAS_FINAL = _IMP_em.IMP_COMPILER_HAS_FINAL
287 IMP_HAS_NOEXCEPT = _IMP_em.IMP_HAS_NOEXCEPT
289 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CGAL_HAS_BOOST_FILESYSTEM
290 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
291 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_em.IMP_CGAL_HAS_BOOST_RANDOM
292 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_em.IMP_CGAL_HAS_BOOST_SYSTEM
293 IMPCGAL_SHOW_WARNINGS = _IMP_em.IMPCGAL_SHOW_WARNINGS
295 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_em.IMP_ALGEBRA_HAS_IMP_CGAL
296 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
297 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
298 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_RANDOM
299 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_SYSTEM
300 IMP_ALGEBRA_HAS_CGAL = _IMP_em.IMP_ALGEBRA_HAS_CGAL
301 IMP_ALGEBRA_HAS_ANN = _IMP_em.IMP_ALGEBRA_HAS_ANN
302 IMPALGEBRA_SHOW_WARNINGS = _IMP_em.IMPALGEBRA_SHOW_WARNINGS
304 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_em.IMP_DISPLAY_HAS_IMP_CGAL
305 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
306 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
307 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_em.IMP_DISPLAY_HAS_BOOST_RANDOM
308 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_em.IMP_DISPLAY_HAS_BOOST_SYSTEM
309 IMP_DISPLAY_HAS_CGAL = _IMP_em.IMP_DISPLAY_HAS_CGAL
310 IMPDISPLAY_SHOW_WARNINGS = _IMP_em.IMPDISPLAY_SHOW_WARNINGS
312 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_em.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
313 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
314 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
315 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
316 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
317 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_em.IMP_SCORE_FUNCTOR_HAS_CGAL
318 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_em.IMP_SCORE_FUNCTOR_HAS_HDF5
319 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_em.IMPSCOREFUNCTOR_SHOW_WARNINGS
321 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_em.IMP_STATISTICS_HAS_IMP_CGAL
322 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
323 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
324 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_em.IMP_STATISTICS_HAS_BOOST_RANDOM
325 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_SYSTEM
326 IMP_STATISTICS_HAS_CGAL = _IMP_em.IMP_STATISTICS_HAS_CGAL
327 IMPSTATISTICS_SHOW_WARNINGS = _IMP_em.IMPSTATISTICS_SHOW_WARNINGS
329 IMP_CORE_HAS_IMP_CGAL = _IMP_em.IMP_CORE_HAS_IMP_CGAL
330 IMP_CORE_HAS_IMP_KERNEL = _IMP_em.IMP_CORE_HAS_IMP_KERNEL
331 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_FILESYSTEM
332 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
333 IMP_CORE_HAS_BOOST_RANDOM = _IMP_em.IMP_CORE_HAS_BOOST_RANDOM
334 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_SYSTEM
335 IMP_CORE_HAS_CGAL = _IMP_em.IMP_CORE_HAS_CGAL
336 IMP_CORE_HAS_HDF5 = _IMP_em.IMP_CORE_HAS_HDF5
337 IMPCORE_SHOW_WARNINGS = _IMP_em.IMPCORE_SHOW_WARNINGS
339 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_em.IMP_CONTAINER_HAS_IMP_ALGEBRA
340 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_em.IMP_CONTAINER_HAS_IMP_CGAL
341 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_em.IMP_CONTAINER_HAS_IMP_DISPLAY
342 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_em.IMP_CONTAINER_HAS_IMP_KERNEL
343 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
344 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
345 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
346 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_em.IMP_CONTAINER_HAS_BOOST_RANDOM
347 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_SYSTEM
348 IMP_CONTAINER_HAS_CGAL = _IMP_em.IMP_CONTAINER_HAS_CGAL
349 IMP_CONTAINER_HAS_HDF5 = _IMP_em.IMP_CONTAINER_HAS_HDF5
350 IMPCONTAINER_SHOW_WARNINGS = _IMP_em.IMPCONTAINER_SHOW_WARNINGS
352 IMP_ATOM_HAS_IMP_CGAL = _IMP_em.IMP_ATOM_HAS_IMP_CGAL
353 IMP_ATOM_HAS_IMP_KERNEL = _IMP_em.IMP_ATOM_HAS_IMP_KERNEL
354 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
355 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
356 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_em.IMP_ATOM_HAS_BOOST_RANDOM
357 IMP_ATOM_HAS_BOOST_REGEX = _IMP_em.IMP_ATOM_HAS_BOOST_REGEX
358 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_em.IMP_ATOM_HAS_BOOST_SYSTEM
359 IMP_ATOM_HAS_CGAL = _IMP_em.IMP_ATOM_HAS_CGAL
360 IMP_ATOM_HAS_HDF5 = _IMP_em.IMP_ATOM_HAS_HDF5
361 IMPATOM_SHOW_WARNINGS = _IMP_em.IMPATOM_SHOW_WARNINGS
362 IMP_ATOM_TYPE_INDEX = _IMP_em.IMP_ATOM_TYPE_INDEX
363 IMP_RESIDUE_TYPE_INDEX = _IMP_em.IMP_RESIDUE_TYPE_INDEX
364 IMP_HIERARCHY_TYPE_INDEX = _IMP_em.IMP_HIERARCHY_TYPE_INDEX
366 IMP_EM_HAS_IMP_CGAL = _IMP_em.IMP_EM_HAS_IMP_CGAL
367 IMP_EM_HAS_IMP_CONTAINER = _IMP_em.IMP_EM_HAS_IMP_CONTAINER
368 IMP_EM_HAS_IMP_DISPLAY = _IMP_em.IMP_EM_HAS_IMP_DISPLAY
369 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_EM_HAS_IMP_SCORE_FUNCTOR
370 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_EM_HAS_BOOST_FILESYSTEM
371 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
372 IMP_EM_HAS_BOOST_RANDOM = _IMP_em.IMP_EM_HAS_BOOST_RANDOM
373 IMP_EM_HAS_BOOST_REGEX = _IMP_em.IMP_EM_HAS_BOOST_REGEX
374 IMP_EM_HAS_BOOST_SYSTEM = _IMP_em.IMP_EM_HAS_BOOST_SYSTEM
375 IMP_EM_HAS_CGAL = _IMP_em.IMP_EM_HAS_CGAL
376 IMP_EM_HAS_HDF5 = _IMP_em.IMP_EM_HAS_HDF5
377 IMPEM_SHOW_WARNINGS = _IMP_em.IMPEM_SHOW_WARNINGS
379 _object_types.append(
"DensityMap")
382 def _object_cast_to_DensityMap(o):
383 """_object_cast_to_DensityMap(Object o) -> DensityMap"""
384 return _IMP_em._object_cast_to_DensityMap(o)
386 _object_types.append(
"SampledDensityMap")
389 def _object_cast_to_SampledDensityMap(o):
390 """_object_cast_to_SampledDensityMap(Object o) -> SampledDensityMap"""
391 return _IMP_em._object_cast_to_SampledDensityMap(o)
393 _object_types.append(
"SurfaceShellDensityMap")
396 def _object_cast_to_SurfaceShellDensityMap(o):
397 """_object_cast_to_SurfaceShellDensityMap(Object o) -> SurfaceShellDensityMap"""
398 return _IMP_em._object_cast_to_SurfaceShellDensityMap(o)
400 _object_types.append(
"FitRestraint")
403 def _object_cast_to_FitRestraint(o):
404 """_object_cast_to_FitRestraint(Object o) -> FitRestraint"""
405 return _IMP_em._object_cast_to_FitRestraint(o)
407 _object_types.append(
"PCAFitRestraint")
410 def _object_cast_to_PCAFitRestraint(o):
411 """_object_cast_to_PCAFitRestraint(Object o) -> PCAFitRestraint"""
412 return _IMP_em._object_cast_to_PCAFitRestraint(o)
414 _object_types.append(
"EnvelopePenetrationRestraint")
417 def _object_cast_to_EnvelopePenetrationRestraint(o):
418 """_object_cast_to_EnvelopePenetrationRestraint(Object o) -> EnvelopePenetrationRestraint"""
419 return _IMP_em._object_cast_to_EnvelopePenetrationRestraint(o)
421 _object_types.append(
"EnvelopeFitRestraint")
424 def _object_cast_to_EnvelopeFitRestraint(o):
425 """_object_cast_to_EnvelopeFitRestraint(Object o) -> EnvelopeFitRestraint"""
426 return _IMP_em._object_cast_to_EnvelopeFitRestraint(o)
428 KernelParametersList=list
429 _plural_types.append(
"KernelParametersList")
430 _value_types.append(
"KernelParameters")
433 _object_types.append(
"HighDensityEmbedding")
436 def _object_cast_to_HighDensityEmbedding(o):
437 """_object_cast_to_HighDensityEmbedding(Object o) -> HighDensityEmbedding"""
438 return _IMP_em._object_cast_to_HighDensityEmbedding(o)
440 _object_types.append(
"MapReaderWriter")
443 def _object_cast_to_MapReaderWriter(o):
444 """_object_cast_to_MapReaderWriter(Object o) -> MapReaderWriter"""
445 return _IMP_em._object_cast_to_MapReaderWriter(o)
447 _object_types.append(
"MRCReaderWriter")
450 def _object_cast_to_MRCReaderWriter(o):
451 """_object_cast_to_MRCReaderWriter(Object o) -> MRCReaderWriter"""
452 return _IMP_em._object_cast_to_MRCReaderWriter(o)
454 _object_types.append(
"SpiderMapReaderWriter")
457 def _object_cast_to_SpiderMapReaderWriter(o):
458 """_object_cast_to_SpiderMapReaderWriter(Object o) -> SpiderMapReaderWriter"""
459 return _IMP_em._object_cast_to_SpiderMapReaderWriter(o)
461 _object_types.append(
"EMReaderWriter")
464 def _object_cast_to_EMReaderWriter(o):
465 """_object_cast_to_EMReaderWriter(Object o) -> EMReaderWriter"""
466 return _IMP_em._object_cast_to_EMReaderWriter(o)
468 _object_types.append(
"XplorReaderWriter")
471 def _object_cast_to_XplorReaderWriter(o):
472 """_object_cast_to_XplorReaderWriter(Object o) -> XplorReaderWriter"""
473 return _IMP_em._object_cast_to_XplorReaderWriter(o)
475 _object_types.append(
"CoarseCC")
478 def _object_cast_to_CoarseCC(o):
479 """_object_cast_to_CoarseCC(Object o) -> CoarseCC"""
480 return _IMP_em._object_cast_to_CoarseCC(o)
482 _object_types.append(
"CoarseCCatIntervals")
485 def _object_cast_to_CoarseCCatIntervals(o):
486 """_object_cast_to_CoarseCCatIntervals(Object o) -> CoarseCCatIntervals"""
487 return _IMP_em._object_cast_to_CoarseCCatIntervals(o)
489 FittingSolutionsList=list
490 _plural_types.append(
"FittingSolutionsList")
491 _value_types.append(
"FittingSolutions")
494 """Proxy of C++ IMP::em::MapReaderWriter class."""
496 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
499 """__init__(IMP::em::MapReaderWriter self) -> MapReaderWriter"""
500 this = _IMP_em.new_MapReaderWriter()
502 self.this.append(this)
503 except __builtin__.Exception:
506 def get_version_info(self):
507 """get_version_info(MapReaderWriter self) -> VersionInfo"""
508 return _IMP_em.MapReaderWriter_get_version_info(self)
512 """__str__(MapReaderWriter self) -> std::string"""
513 return _IMP_em.MapReaderWriter___str__(self)
517 """__repr__(MapReaderWriter self) -> std::string"""
518 return _IMP_em.MapReaderWriter___repr__(self)
523 return _object_cast_to_MapReaderWriter(o)
525 MapReaderWriter_swigregister = _IMP_em.MapReaderWriter_swigregister
526 MapReaderWriter_swigregister(MapReaderWriter)
530 class DensityHeader(object):
531 """Proxy of C++ IMP::em::DensityHeader class."""
533 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
534 __repr__ = _swig_repr
537 """__init__(IMP::em::DensityHeader self) -> DensityHeader"""
538 this = _IMP_em.new_DensityHeader()
540 self.this.append(this)
541 except __builtin__.Exception:
544 def get_top(self, ind):
545 """get_top(DensityHeader self, int ind) -> IMP::em::emreal"""
546 return _IMP_em.DensityHeader_get_top(self, ind)
549 def compute_xyz_top(self, force=False):
551 compute_xyz_top(DensityHeader self, bool force=False)
552 compute_xyz_top(DensityHeader self)
554 return _IMP_em.DensityHeader_compute_xyz_top(self, force)
557 def update_map_dimensions(self, nnx, nny, nnz):
558 """update_map_dimensions(DensityHeader self, int nnx, int nny, int nnz)"""
559 return _IMP_em.DensityHeader_update_map_dimensions(self, nnx, nny, nnz)
562 def update_cell_dimensions(self):
563 """update_cell_dimensions(DensityHeader self)"""
564 return _IMP_em.DensityHeader_update_cell_dimensions(self)
567 def show(self, *args):
569 show(DensityHeader self, _ostream out)
570 show(DensityHeader self)
572 return _IMP_em.DensityHeader_show(self, *args)
574 MAP_FIELD_SIZE = _IMP_em.DensityHeader_MAP_FIELD_SIZE
575 USER_FIELD_SIZE = _IMP_em.DensityHeader_USER_FIELD_SIZE
576 COMMENT_FIELD_NUM_OF = _IMP_em.DensityHeader_COMMENT_FIELD_NUM_OF
577 COMMENT_FIELD_SINGLE_SIZE = _IMP_em.DensityHeader_COMMENT_FIELD_SINGLE_SIZE
578 nxstart = _swig_property(_IMP_em.DensityHeader_nxstart_get, _IMP_em.DensityHeader_nxstart_set)
579 nystart = _swig_property(_IMP_em.DensityHeader_nystart_get, _IMP_em.DensityHeader_nystart_set)
580 nzstart = _swig_property(_IMP_em.DensityHeader_nzstart_get, _IMP_em.DensityHeader_nzstart_set)
581 mx = _swig_property(_IMP_em.DensityHeader_mx_get, _IMP_em.DensityHeader_mx_set)
582 my = _swig_property(_IMP_em.DensityHeader_my_get, _IMP_em.DensityHeader_my_set)
583 mz = _swig_property(_IMP_em.DensityHeader_mz_get, _IMP_em.DensityHeader_mz_set)
584 xlen = _swig_property(_IMP_em.DensityHeader_xlen_get, _IMP_em.DensityHeader_xlen_set)
585 ylen = _swig_property(_IMP_em.DensityHeader_ylen_get, _IMP_em.DensityHeader_ylen_set)
586 zlen = _swig_property(_IMP_em.DensityHeader_zlen_get, _IMP_em.DensityHeader_zlen_set)
587 alpha = _swig_property(_IMP_em.DensityHeader_alpha_get, _IMP_em.DensityHeader_alpha_set)
588 beta = _swig_property(_IMP_em.DensityHeader_beta_get, _IMP_em.DensityHeader_beta_set)
589 gamma = _swig_property(_IMP_em.DensityHeader_gamma_get, _IMP_em.DensityHeader_gamma_set)
590 mapc = _swig_property(_IMP_em.DensityHeader_mapc_get, _IMP_em.DensityHeader_mapc_set)
591 mapr = _swig_property(_IMP_em.DensityHeader_mapr_get, _IMP_em.DensityHeader_mapr_set)
592 maps = _swig_property(_IMP_em.DensityHeader_maps_get, _IMP_em.DensityHeader_maps_set)
593 dmin = _swig_property(_IMP_em.DensityHeader_dmin_get, _IMP_em.DensityHeader_dmin_set)
594 dmax = _swig_property(_IMP_em.DensityHeader_dmax_get, _IMP_em.DensityHeader_dmax_set)
595 dmean = _swig_property(_IMP_em.DensityHeader_dmean_get, _IMP_em.DensityHeader_dmean_set)
596 ispg = _swig_property(_IMP_em.DensityHeader_ispg_get, _IMP_em.DensityHeader_ispg_set)
597 nsymbt = _swig_property(_IMP_em.DensityHeader_nsymbt_get, _IMP_em.DensityHeader_nsymbt_set)
598 user = _swig_property(_IMP_em.DensityHeader_user_get, _IMP_em.DensityHeader_user_set)
599 map = _swig_property(_IMP_em.DensityHeader_map_get, _IMP_em.DensityHeader_map_set)
600 machinestamp = _swig_property(_IMP_em.DensityHeader_machinestamp_get, _IMP_em.DensityHeader_machinestamp_set)
601 rms = _swig_property(_IMP_em.DensityHeader_rms_get, _IMP_em.DensityHeader_rms_set)
602 nlabl = _swig_property(_IMP_em.DensityHeader_nlabl_get, _IMP_em.DensityHeader_nlabl_set)
603 comments = _swig_property(_IMP_em.DensityHeader_comments_get, _IMP_em.DensityHeader_comments_set)
604 magic = _swig_property(_IMP_em.DensityHeader_magic_get, _IMP_em.DensityHeader_magic_set)
605 voltage = _swig_property(_IMP_em.DensityHeader_voltage_get, _IMP_em.DensityHeader_voltage_set)
606 Cs = _swig_property(_IMP_em.DensityHeader_Cs_get, _IMP_em.DensityHeader_Cs_set)
607 Aperture = _swig_property(_IMP_em.DensityHeader_Aperture_get, _IMP_em.DensityHeader_Aperture_set)
608 Magnification = _swig_property(_IMP_em.DensityHeader_Magnification_get, _IMP_em.DensityHeader_Magnification_set)
609 Postmagnification = _swig_property(_IMP_em.DensityHeader_Postmagnification_get, _IMP_em.DensityHeader_Postmagnification_set)
610 Exposuretime = _swig_property(_IMP_em.DensityHeader_Exposuretime_get, _IMP_em.DensityHeader_Exposuretime_set)
611 Microscope = _swig_property(_IMP_em.DensityHeader_Microscope_get, _IMP_em.DensityHeader_Microscope_set)
612 Pixelsize = _swig_property(_IMP_em.DensityHeader_Pixelsize_get, _IMP_em.DensityHeader_Pixelsize_set)
613 CCDArea = _swig_property(_IMP_em.DensityHeader_CCDArea_get, _IMP_em.DensityHeader_CCDArea_set)
614 Defocus = _swig_property(_IMP_em.DensityHeader_Defocus_get, _IMP_em.DensityHeader_Defocus_set)
615 Astigmatism = _swig_property(_IMP_em.DensityHeader_Astigmatism_get, _IMP_em.DensityHeader_Astigmatism_set)
616 AstigmatismAngle = _swig_property(_IMP_em.DensityHeader_AstigmatismAngle_get, _IMP_em.DensityHeader_AstigmatismAngle_set)
617 FocusIncrement = _swig_property(_IMP_em.DensityHeader_FocusIncrement_get, _IMP_em.DensityHeader_FocusIncrement_set)
618 CountsPerElectron = _swig_property(_IMP_em.DensityHeader_CountsPerElectron_get, _IMP_em.DensityHeader_CountsPerElectron_set)
619 Intensity = _swig_property(_IMP_em.DensityHeader_Intensity_get, _IMP_em.DensityHeader_Intensity_set)
620 EnergySlitwidth = _swig_property(_IMP_em.DensityHeader_EnergySlitwidth_get, _IMP_em.DensityHeader_EnergySlitwidth_set)
621 EnergyOffset = _swig_property(_IMP_em.DensityHeader_EnergyOffset_get, _IMP_em.DensityHeader_EnergyOffset_set)
622 Tiltangle = _swig_property(_IMP_em.DensityHeader_Tiltangle_get, _IMP_em.DensityHeader_Tiltangle_set)
623 Tiltaxis = _swig_property(_IMP_em.DensityHeader_Tiltaxis_get, _IMP_em.DensityHeader_Tiltaxis_set)
624 MarkerX = _swig_property(_IMP_em.DensityHeader_MarkerX_get, _IMP_em.DensityHeader_MarkerX_set)
625 MarkerY = _swig_property(_IMP_em.DensityHeader_MarkerY_get, _IMP_em.DensityHeader_MarkerY_set)
626 lswap = _swig_property(_IMP_em.DensityHeader_lswap_get, _IMP_em.DensityHeader_lswap_set)
629 """get_resolution(DensityHeader self) -> float"""
630 return _IMP_em.DensityHeader_get_resolution(self)
633 def get_has_resolution(self):
634 """get_has_resolution(DensityHeader self) -> bool"""
635 return _IMP_em.DensityHeader_get_has_resolution(self)
638 def set_resolution(self, resolution):
639 """set_resolution(DensityHeader self, float resolution)"""
640 return _IMP_em.DensityHeader_set_resolution(self, resolution)
643 def get_spacing(self):
644 """get_spacing(DensityHeader self) -> float"""
645 return _IMP_em.DensityHeader_get_spacing(self)
648 def get_xorigin(self):
649 """get_xorigin(DensityHeader self) -> float"""
650 return _IMP_em.DensityHeader_get_xorigin(self)
653 def get_yorigin(self):
654 """get_yorigin(DensityHeader self) -> float"""
655 return _IMP_em.DensityHeader_get_yorigin(self)
658 def get_zorigin(self):
659 """get_zorigin(DensityHeader self) -> float"""
660 return _IMP_em.DensityHeader_get_zorigin(self)
663 def get_origin(self, i):
664 """get_origin(DensityHeader self, int i) -> float"""
665 return _IMP_em.DensityHeader_get_origin(self, i)
668 def set_xorigin(self, x):
669 """set_xorigin(DensityHeader self, float x)"""
670 return _IMP_em.DensityHeader_set_xorigin(self, x)
673 def set_yorigin(self, y):
674 """set_yorigin(DensityHeader self, float y)"""
675 return _IMP_em.DensityHeader_set_yorigin(self, y)
678 def set_zorigin(self, z):
679 """set_zorigin(DensityHeader self, float z)"""
680 return _IMP_em.DensityHeader_set_zorigin(self, z)
683 def is_top_calculated(self):
684 """is_top_calculated(DensityHeader self) -> bool"""
685 return _IMP_em.DensityHeader_is_top_calculated(self)
687 Objectpixelsize_ = _swig_property(_IMP_em.DensityHeader_Objectpixelsize__get, _IMP_em.DensityHeader_Objectpixelsize__set)
690 """get_nx(DensityHeader self) -> int"""
691 return _IMP_em.DensityHeader_get_nx(self)
695 """get_ny(DensityHeader self) -> int"""
696 return _IMP_em.DensityHeader_get_ny(self)
700 """get_nz(DensityHeader self) -> int"""
701 return _IMP_em.DensityHeader_get_nz(self)
704 def get_number_of_voxels(self):
705 """get_number_of_voxels(DensityHeader self) -> int"""
706 return _IMP_em.DensityHeader_get_number_of_voxels(self)
709 def get_data_type(self):
710 """get_data_type(DensityHeader self) -> int"""
711 return _IMP_em.DensityHeader_get_data_type(self)
714 def set_data_type(self, data_type):
715 """set_data_type(DensityHeader self, int data_type)"""
716 return _IMP_em.DensityHeader_set_data_type(self, data_type)
718 __swig_destroy__ = _IMP_em.delete_DensityHeader
719 __del__ =
lambda self:
None
720 DensityHeader_swigregister = _IMP_em.DensityHeader_swigregister
721 DensityHeader_swigregister(DensityHeader)
725 """create_density_header(BoundingBox3D bb, float spacing) -> DensityHeader"""
726 return _IMP_em.create_density_header(bb, spacing)
730 read_map(std::string filename, MapReaderWriter reader) -> DensityMap
731 read_map(std::string filename) -> DensityMap
733 return _IMP_em.read_map(*args)
735 def write_map(*args):
737 write_map(DensityMap m, std::string filename, MapReaderWriter writer)
738 write_map(DensityMap m, std::string filename)
740 return _IMP_em.write_map(*args)
743 """approximate_molecular_mass(DensityMap m, IMP::Float threshold) -> IMP::Float"""
744 return _IMP_em.approximate_molecular_mass(m, threshold)
746 """Proxy of C++ IMP::em::DensityMap class."""
748 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
750 def __init__(self, *args):
752 __init__(IMP::em::DensityMap self, std::string name) -> DensityMap
753 __init__(IMP::em::DensityMap self) -> DensityMap
754 __init__(IMP::em::DensityMap self, DensityHeader header, std::string name) -> DensityMap
755 __init__(IMP::em::DensityMap self, DensityHeader header) -> DensityMap
757 this = _IMP_em.new_DensityMap(*args)
759 self.this.append(this)
760 except __builtin__.Exception:
763 def reset_data(self, value=0.0):
765 reset_data(DensityMap self, float value=0.0)
766 reset_data(DensityMap self)
768 return _IMP_em.DensityMap_reset_data(self, value)
772 """calcRMS(DensityMap self) -> IMP::em::emreal"""
773 return _IMP_em.DensityMap_calcRMS(self)
776 def std_normalize(self):
777 """std_normalize(DensityMap self)"""
778 return _IMP_em.DensityMap_std_normalize(self)
781 def is_normalized(self):
782 """is_normalized(DensityMap self) -> bool"""
783 return _IMP_em.DensityMap_is_normalized(self)
786 def get_location_in_dim_by_voxel(self, index, dim):
787 """get_location_in_dim_by_voxel(DensityMap self, long index, int dim) -> float"""
788 return _IMP_em.DensityMap_get_location_in_dim_by_voxel(self, index, dim)
791 def xyz_ind2voxel(self, x, y, z):
792 """xyz_ind2voxel(DensityMap self, int x, int y, int z) -> long"""
793 return _IMP_em.DensityMap_xyz_ind2voxel(self, x, y, z)
796 def get_voxel_by_location(self, *args):
798 get_voxel_by_location(DensityMap self, float x, float y, float z) -> long
799 get_voxel_by_location(DensityMap self, Vector3D v) -> long
801 return _IMP_em.DensityMap_get_voxel_by_location(self, *args)
804 def get_location_by_voxel(self, index):
805 """get_location_by_voxel(DensityMap self, long index) -> Vector3D"""
806 return _IMP_em.DensityMap_get_location_by_voxel(self, index)
809 def is_xyz_ind_part_of_volume(self, ix, iy, iz):
810 """is_xyz_ind_part_of_volume(DensityMap self, int ix, int iy, int iz) -> bool"""
811 return _IMP_em.DensityMap_is_xyz_ind_part_of_volume(self, ix, iy, iz)
814 def is_part_of_volume(self, *args):
816 is_part_of_volume(DensityMap self, float x, float y, float z) -> bool
817 is_part_of_volume(DensityMap self, Vector3D v) -> bool
819 return _IMP_em.DensityMap_is_part_of_volume(self, *args)
822 def get_value(self, *args):
824 get_value(DensityMap self, float x, float y, float z) -> IMP::em::emreal
825 get_value(DensityMap self, Vector3D point) -> IMP::em::emreal
826 get_value(DensityMap self, long index) -> IMP::em::emreal
828 return _IMP_em.DensityMap_get_value(self, *args)
831 def set_value(self, *args):
833 set_value(DensityMap self, long index, IMP::em::emreal value)
834 set_value(DensityMap self, float x, float y, float z, IMP::em::emreal value)
836 return _IMP_em.DensityMap_set_value(self, *args)
839 def set_origin(self, *args):
841 set_origin(DensityMap self, float x, float y, float z)
842 set_origin(DensityMap self, Vector3D v)
844 return _IMP_em.DensityMap_set_origin(self, *args)
847 def get_origin(self):
848 """get_origin(DensityMap self) -> Vector3D"""
849 return _IMP_em.DensityMap_get_origin(self)
853 """get_top(DensityMap self) -> Vector3D"""
854 return _IMP_em.DensityMap_get_top(self)
857 def get_header(self):
858 h = _IMP_em.DensityMap_get_header(self)
864 def get_header_writable(self):
865 h = _IMP_em.DensityMap_get_header_writable(self)
871 def same_origin(self, other):
872 """same_origin(DensityMap self, DensityMap other) -> bool"""
873 return _IMP_em.DensityMap_same_origin(self, other)
876 def same_dimensions(self, other):
877 """same_dimensions(DensityMap self, DensityMap other) -> bool"""
878 return _IMP_em.DensityMap_same_dimensions(self, other)
881 def same_voxel_size(self, other):
882 """same_voxel_size(DensityMap self, DensityMap other) -> bool"""
883 return _IMP_em.DensityMap_same_voxel_size(self, other)
888 get_centroid(DensityMap self, IMP::em::emreal threshold=0.0) -> Vector3D
889 get_centroid(DensityMap self) -> Vector3D
891 return _IMP_em.DensityMap_get_centroid(self, threshold)
894 def get_max_value(self):
895 """get_max_value(DensityMap self) -> IMP::em::emreal"""
896 return _IMP_em.DensityMap_get_max_value(self)
899 def get_min_value(self):
900 """get_min_value(DensityMap self) -> IMP::em::emreal"""
901 return _IMP_em.DensityMap_get_min_value(self)
904 def add(self, *args):
906 add(DensityMap self, DensityMap other)
907 add(DensityMap self, IMP::Float d)
909 return _IMP_em.DensityMap_add(self, *args)
912 def pick_max(self, other):
913 """pick_max(DensityMap self, DensityMap other)"""
914 return _IMP_em.DensityMap_pick_max(self, other)
917 def get_number_of_voxels(self):
918 """get_number_of_voxels(DensityMap self) -> long"""
919 return _IMP_em.DensityMap_get_number_of_voxels(self)
922 def set_void_map(self, nx, ny, nz):
923 """set_void_map(DensityMap self, int nx, int ny, int nz)"""
924 return _IMP_em.DensityMap_set_void_map(self, nx, ny, nz)
927 def pad(self, nx, ny, nz, val=0.0):
929 pad(DensityMap self, int nx, int ny, int nz, float val=0.0)
930 pad(DensityMap self, int nx, int ny, int nz)
932 return _IMP_em.DensityMap_pad(self, nx, ny, nz, val)
935 def pad_margin(self, mrg_x, mrg_y, mrg_z, val=0.0):
937 pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z, float val=0.0) -> DensityMap
938 pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z) -> DensityMap
940 return _IMP_em.DensityMap_pad_margin(self, mrg_x, mrg_y, mrg_z, val)
943 def get_cropped(self, *args):
945 get_cropped(DensityMap self, float threshold) -> DensityMap
946 get_cropped(DensityMap self, BoundingBox3D bb) -> DensityMap
948 return _IMP_em.DensityMap_get_cropped(self, *args)
951 def get_maximum_value_in_xy_plane(self, z_ind):
952 """get_maximum_value_in_xy_plane(DensityMap self, int z_ind) -> float"""
953 return _IMP_em.DensityMap_get_maximum_value_in_xy_plane(self, z_ind)
956 def get_maximum_value_in_xz_plane(self, y_ind):
957 """get_maximum_value_in_xz_plane(DensityMap self, int y_ind) -> float"""
958 return _IMP_em.DensityMap_get_maximum_value_in_xz_plane(self, y_ind)
961 def get_maximum_value_in_yz_plane(self, x_ind):
962 """get_maximum_value_in_yz_plane(DensityMap self, int x_ind) -> float"""
963 return _IMP_em.DensityMap_get_maximum_value_in_yz_plane(self, x_ind)
967 """multiply(DensityMap self, float factor)"""
968 return _IMP_em.DensityMap_multiply(self, factor)
971 def get_locations_string(self, t):
972 """get_locations_string(DensityMap self, float t) -> std::string"""
973 return _IMP_em.DensityMap_get_locations_string(self, t)
976 def update_voxel_size(self, new_apix):
977 """update_voxel_size(DensityMap self, float new_apix)"""
978 return _IMP_em.DensityMap_update_voxel_size(self, new_apix)
981 def get_spacing(self):
982 """get_spacing(DensityMap self) -> IMP::Float"""
983 return _IMP_em.DensityMap_get_spacing(self)
986 def calc_all_voxel2loc(self):
987 """calc_all_voxel2loc(DensityMap self)"""
988 return _IMP_em.DensityMap_calc_all_voxel2loc(self)
991 def copy_map(self, other):
992 """copy_map(DensityMap self, DensityMap other)"""
993 return _IMP_em.DensityMap_copy_map(self, other)
996 def get_version_info(self):
997 """get_version_info(DensityMap self) -> VersionInfo"""
998 return _IMP_em.DensityMap_get_version_info(self)
1001 def lower_voxel_shift(self, loc, kdist, orig, ndim):
1002 """lower_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
1003 return _IMP_em.DensityMap_lower_voxel_shift(self, loc, kdist, orig, ndim)
1006 def upper_voxel_shift(self, loc, kdist, orig, ndim):
1007 """upper_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
1008 return _IMP_em.DensityMap_upper_voxel_shift(self, loc, kdist, orig, ndim)
1011 def get_rms_calculated(self):
1012 """get_rms_calculated(DensityMap self) -> bool"""
1013 return _IMP_em.DensityMap_get_rms_calculated(self)
1016 def get_dim_index_by_location(self, *args):
1018 get_dim_index_by_location(DensityMap self, Vector3D v, int ind) -> int
1019 get_dim_index_by_location(DensityMap self, float loc_val, int ind) -> int
1021 return _IMP_em.DensityMap_get_dim_index_by_location(self, *args)
1025 """__str__(DensityMap self) -> std::string"""
1026 return _IMP_em.DensityMap___str__(self)
1030 """__repr__(DensityMap self) -> std::string"""
1031 return _IMP_em.DensityMap___repr__(self)
1036 return _object_cast_to_DensityMap(o)
1038 DensityMap_swigregister = _IMP_em.DensityMap_swigregister
1039 DensityMap_swigregister(DensityMap)
1044 get_bounding_box(DensityMap m, IMP::Float threshold) -> BoundingBox3D
1045 get_bounding_box(DensityMap m) -> BoundingBox3D
1047 return _IMP_em.get_bounding_box(*args)
1049 def get_density(m, v):
1050 """get_density(DensityMap m, Vector3D v) -> double"""
1051 return _IMP_em.get_density(m, v)
1053 def get_transformed(*args):
1055 get_transformed(DensityMap input, Transformation3D tr, double threshold) -> DensityMap
1056 get_transformed(DensityMap input, Transformation3D tr) -> DensityMap
1058 return _IMP_em.get_transformed(*args)
1060 def get_resampled(input, scaling):
1061 """get_resampled(DensityMap input, double scaling) -> DensityMap"""
1062 return _IMP_em.get_resampled(input, scaling)
1064 def get_transformed_into(source, tr, into, calc_rms=True):
1066 get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into, bool calc_rms=True)
1067 get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into)
1069 return _IMP_em.get_transformed_into(source, tr, into, calc_rms)
1071 def get_transformed_into2(source, tr, into):
1072 """get_transformed_into2(DensityMap source, Transformation3D tr, DensityMap into)"""
1073 return _IMP_em.get_transformed_into2(source, tr, into)
1075 def get_interiors_intersect(d1, d2):
1076 """get_interiors_intersect(DensityMap d1, DensityMap d2) -> bool"""
1077 return _IMP_em.get_interiors_intersect(d1, d2)
1081 get_segment(DensityMap map_to_segment, int nx_start, int nx_end, int ny_start, int ny_end, int nz_start, int nz_end) -> DensityMap
1082 get_segment(DensityMap map_to_segment, IMP::algebra::Vector3Ds vecs, float dist) -> DensityMap
1084 return _IMP_em.get_segment(*args)
1087 """get_segment_by_masking(DensityMap map_to_segment, DensityMap mask, float mas_threshold) -> DensityMap"""
1088 return _IMP_em.get_segment_by_masking(map_to_segment, mask, mas_threshold)
1090 def binarize(orig_map, threshold, reverse=False):
1092 binarize(DensityMap orig_map, float threshold, bool reverse=False) -> DensityMap
1093 binarize(DensityMap orig_map, float threshold) -> DensityMap
1095 return _IMP_em.binarize(orig_map, threshold, reverse)
1098 """get_threshold_map(DensityMap orig_map, float threshold) -> DensityMap"""
1099 return _IMP_em.get_threshold_map(orig_map, threshold)
1102 """multiply(DensityMap m1, DensityMap m2) -> DensityMap"""
1103 return _IMP_em.multiply(m1, m2)
1106 """convolute(DensityMap m1, DensityMap m2) -> double"""
1107 return _IMP_em.convolute(m1, m2)
1110 """get_sum(DensityMap m1) -> double"""
1111 return _IMP_em.get_sum(m1)
1114 """get_max_map(IMP::em::DensityMaps maps) -> DensityMap"""
1115 return _IMP_em.get_max_map(maps)
1118 """interpolate_map(DensityMap in_map, double new_spacing) -> DensityMap"""
1119 return _IMP_em.interpolate_map(in_map, new_spacing)
1122 """get_grid(DensityMap in_map) -> IMP::algebra::GridD< 3,IMP::algebra::DenseGridStorageD< 3,float >,float,IMP::algebra::DefaultEmbeddingD< 3 > >"""
1123 return _IMP_em.get_grid(in_map)
1127 create_density_map(DensityMap other) -> DensityMap
1128 create_density_map(BoundingBox3D bb, double spacing) -> DensityMap
1129 create_density_map(int nx, int ny, int nz, double spacing) -> DensityMap
1130 create_density_map(DenseFloatGrid3D grid) -> DensityMap
1131 create_density_map(DenseDoubleGrid3D grid) -> DensityMap
1133 return _IMP_em.create_density_map(*args)
1135 def get_binarized_interior(dmap):
1136 """get_binarized_interior(DensityMap dmap) -> DensityMap"""
1137 return _IMP_em.get_binarized_interior(dmap)
1139 def add_to_map(dm, pis):
1140 """add_to_map(DensityMap dm, IMP::Particles const & pis)"""
1141 return _IMP_em.add_to_map(dm, pis)
1142 class RadiusDependentDistanceMask(object):
1143 """Proxy of C++ IMP::em::RadiusDependentDistanceMask class."""
1145 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1146 __repr__ = _swig_repr
1148 def __init__(self, sampling_radius, header):
1149 """__init__(IMP::em::RadiusDependentDistanceMask self, float sampling_radius, DensityHeader header) -> RadiusDependentDistanceMask"""
1150 this = _IMP_em.new_RadiusDependentDistanceMask(sampling_radius, header)
1152 self.this.append(this)
1153 except __builtin__.Exception:
1156 def get_neighbor_shift(self):
1157 """get_neighbor_shift(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1158 return _IMP_em.RadiusDependentDistanceMask_get_neighbor_shift(self)
1161 def get_neighbor_dist(self):
1162 """get_neighbor_dist(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1163 return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist(self)
1166 def get_neighbor_dist_exp(self):
1167 """get_neighbor_dist_exp(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1168 return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist_exp(self)
1171 def show(self, out):
1172 """show(RadiusDependentDistanceMask self, _ostream out)"""
1173 return _IMP_em.RadiusDependentDistanceMask_show(self, out)
1175 __swig_destroy__ = _IMP_em.delete_RadiusDependentDistanceMask
1176 __del__ =
lambda self:
None
1177 RadiusDependentDistanceMask_swigregister = _IMP_em.RadiusDependentDistanceMask_swigregister
1178 RadiusDependentDistanceMask_swigregister(RadiusDependentDistanceMask)
1180 class DistanceMask(object):
1181 """Proxy of C++ IMP::em::DistanceMask class."""
1183 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1184 __repr__ = _swig_repr
1186 def __init__(self, *args):
1188 __init__(IMP::em::DistanceMask self) -> DistanceMask
1189 __init__(IMP::em::DistanceMask self, DensityHeader header) -> DistanceMask
1191 this = _IMP_em.new_DistanceMask(*args)
1193 self.this.append(this)
1194 except __builtin__.Exception:
1197 def show(self, out):
1198 """show(DistanceMask self, _ostream out)"""
1199 return _IMP_em.DistanceMask_show(self, out)
1202 def is_mask_set(self, radius, eps=0.001):
1204 is_mask_set(DistanceMask self, float radius, float eps=0.001) -> bool
1205 is_mask_set(DistanceMask self, float radius) -> bool
1207 return _IMP_em.DistanceMask_is_mask_set(self, radius, eps)
1209 __swig_destroy__ = _IMP_em.delete_DistanceMask
1210 __del__ =
lambda self:
None
1211 DistanceMask_swigregister = _IMP_em.DistanceMask_swigregister
1212 DistanceMask_swigregister(DistanceMask)
1214 class EMReaderWriter(MapReaderWriter):
1215 """Proxy of C++ IMP::em::EMReaderWriter class."""
1217 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1220 """__str__(EMReaderWriter self) -> std::string"""
1221 return _IMP_em.EMReaderWriter___str__(self)
1225 """__repr__(EMReaderWriter self) -> std::string"""
1226 return _IMP_em.EMReaderWriter___repr__(self)
1231 return _object_cast_to_EMReaderWriter(o)
1235 """__init__(IMP::em::EMReaderWriter self) -> EMReaderWriter"""
1236 this = _IMP_em.new_EMReaderWriter()
1238 self.this.append(this)
1239 except __builtin__.Exception:
1241 EMReaderWriter_swigregister = _IMP_em.EMReaderWriter_swigregister
1242 EMReaderWriter_swigregister(EMReaderWriter)
1244 class XplorReaderWriter(MapReaderWriter):
1245 """Proxy of C++ IMP::em::XplorReaderWriter class."""
1247 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1250 """__str__(XplorReaderWriter self) -> std::string"""
1251 return _IMP_em.XplorReaderWriter___str__(self)
1255 """__repr__(XplorReaderWriter self) -> std::string"""
1256 return _IMP_em.XplorReaderWriter___repr__(self)
1261 return _object_cast_to_XplorReaderWriter(o)
1265 """__init__(IMP::em::XplorReaderWriter self) -> XplorReaderWriter"""
1266 this = _IMP_em.new_XplorReaderWriter()
1268 self.this.append(this)
1269 except __builtin__.Exception:
1271 XplorReaderWriter_swigregister = _IMP_em.XplorReaderWriter_swigregister
1272 XplorReaderWriter_swigregister(XplorReaderWriter)
1274 class MRCReaderWriter(MapReaderWriter):
1275 """Proxy of C++ IMP::em::MRCReaderWriter class."""
1277 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1279 def __init__(self, *args):
1281 __init__(IMP::em::MRCReaderWriter self) -> MRCReaderWriter
1282 __init__(IMP::em::MRCReaderWriter self, std::string fn) -> MRCReaderWriter
1284 this = _IMP_em.new_MRCReaderWriter(*args)
1286 self.this.append(this)
1287 except __builtin__.Exception:
1291 """__str__(MRCReaderWriter self) -> std::string"""
1292 return _IMP_em.MRCReaderWriter___str__(self)
1296 """__repr__(MRCReaderWriter self) -> std::string"""
1297 return _IMP_em.MRCReaderWriter___repr__(self)
1302 return _object_cast_to_MRCReaderWriter(o)
1304 MRCReaderWriter_swigregister = _IMP_em.MRCReaderWriter_swigregister
1305 MRCReaderWriter_swigregister(MRCReaderWriter)
1307 class KernelParameters(object):
1308 """Proxy of C++ IMP::em::KernelParameters class."""
1310 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1312 def __init__(self, *args):
1314 __init__(IMP::em::KernelParameters self) -> KernelParameters
1315 __init__(IMP::em::KernelParameters self, float resolution) -> KernelParameters
1317 this = _IMP_em.new_KernelParameters(*args)
1319 self.this.append(this)
1320 except __builtin__.Exception:
1322 __swig_destroy__ = _IMP_em.delete_KernelParameters
1323 __del__ =
lambda self:
None
1326 """get_rsig(KernelParameters self) -> float"""
1327 return _IMP_em.KernelParameters_get_rsig(self)
1330 def get_rsigsq(self):
1331 """get_rsigsq(KernelParameters self) -> float"""
1332 return _IMP_em.KernelParameters_get_rsigsq(self)
1335 def get_inv_rsigsq(self):
1336 """get_inv_rsigsq(KernelParameters self) -> float"""
1337 return _IMP_em.KernelParameters_get_inv_rsigsq(self)
1340 def get_timessig(self):
1341 """get_timessig(KernelParameters self) -> float"""
1342 return _IMP_em.KernelParameters_get_timessig(self)
1345 def get_sq2pi3(self):
1346 """get_sq2pi3(KernelParameters self) -> float"""
1347 return _IMP_em.KernelParameters_get_sq2pi3(self)
1350 def get_rnormfac(self):
1351 """get_rnormfac(KernelParameters self) -> float"""
1352 return _IMP_em.KernelParameters_get_rnormfac(self)
1355 def get_rkdist(self):
1356 """get_rkdist(KernelParameters self) -> float"""
1357 return _IMP_em.KernelParameters_get_rkdist(self)
1360 def get_rkdistsq(self):
1361 """get_rkdistsq(KernelParameters self) -> float"""
1362 return _IMP_em.KernelParameters_get_rkdistsq(self)
1366 """get_lim(KernelParameters self) -> float"""
1367 return _IMP_em.KernelParameters_get_lim(self)
1370 def show(self, *args):
1372 show(KernelParameters self, _ostream out)
1373 show(KernelParameters self)
1375 return _IMP_em.KernelParameters_show(self, *args)
1379 """__str__(KernelParameters self) -> std::string"""
1380 return _IMP_em.KernelParameters___str__(self)
1384 """__repr__(KernelParameters self) -> std::string"""
1385 return _IMP_em.KernelParameters___repr__(self)
1387 KernelParameters_swigregister = _IMP_em.KernelParameters_swigregister
1388 KernelParameters_swigregister(KernelParameters)
1390 GAUSSIAN = _IMP_em.GAUSSIAN
1391 BINARIZED_SPHERE = _IMP_em.BINARIZED_SPHERE
1392 SPHERE = _IMP_em.SPHERE
1393 class SampledDensityMap(DensityMap):
1394 """Proxy of C++ IMP::em::SampledDensityMap class."""
1396 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1398 def __init__(self, *args):
1400 __init__(IMP::em::SampledDensityMap self, IMP::em::KernelType kt) -> SampledDensityMap
1401 __init__(IMP::em::SampledDensityMap self) -> SampledDensityMap
1402 __init__(IMP::em::SampledDensityMap self, DensityHeader header, IMP::em::KernelType kt) -> SampledDensityMap
1403 __init__(IMP::em::SampledDensityMap self, DensityHeader header) -> SampledDensityMap
1404 __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size, FloatKey mass_key, int sig_cutoff=3, IMP::em::KernelType kt) -> SampledDensityMap
1405 __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size, FloatKey mass_key, int sig_cutoff=3) -> SampledDensityMap
1406 __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size, FloatKey mass_key) -> SampledDensityMap
1407 __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size) -> SampledDensityMap
1409 this = _IMP_em.new_SampledDensityMap(*args)
1411 self.this.append(this)
1412 except __builtin__.Exception:
1416 """resample(SampledDensityMap self)"""
1417 return _IMP_em.SampledDensityMap_resample(self)
1420 def project(self, *args):
1422 project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin, Vector3D shift, FloatKey mass_key)
1423 project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin, Vector3D shift)
1424 project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin)
1426 return _IMP_em.SampledDensityMap_project(self, *args)
1429 def set_particles(self, *args):
1431 set_particles(SampledDensityMap self, IMP::ParticlesTemp const & ps, FloatKey mass_key)
1432 set_particles(SampledDensityMap self, IMP::ParticlesTemp const & ps)
1434 return _IMP_em.SampledDensityMap_set_particles(self, *args)
1437 def get_xyzr_particles(self):
1438 """get_xyzr_particles(SampledDensityMap self) -> IMP::core::XYZRs const &"""
1439 return _IMP_em.SampledDensityMap_get_xyzr_particles(self)
1442 def get_sampled_particles(self):
1443 """get_sampled_particles(SampledDensityMap self) -> IMP::Particles const &"""
1444 return _IMP_em.SampledDensityMap_get_sampled_particles(self)
1447 def get_weight_key(self):
1448 """get_weight_key(SampledDensityMap self) -> FloatKey"""
1449 return _IMP_em.SampledDensityMap_get_weight_key(self)
1452 def get_minimum_resampled_value(self):
1453 """get_minimum_resampled_value(SampledDensityMap self) -> float"""
1454 return _IMP_em.SampledDensityMap_get_minimum_resampled_value(self)
1457 def update_resolution(self, res):
1458 """update_resolution(SampledDensityMap self, IMP::Float res)"""
1459 return _IMP_em.SampledDensityMap_update_resolution(self, res)
1461 __swig_destroy__ = _IMP_em.delete_SampledDensityMap
1462 __del__ =
lambda self:
None
1465 """__str__(SampledDensityMap self) -> std::string"""
1466 return _IMP_em.SampledDensityMap___str__(self)
1470 """__repr__(SampledDensityMap self) -> std::string"""
1471 return _IMP_em.SampledDensityMap___repr__(self)
1476 return _object_cast_to_SampledDensityMap(o)
1478 SampledDensityMap_swigregister = _IMP_em.SampledDensityMap_swigregister
1479 SampledDensityMap_swigregister(SampledDensityMap)
1481 IMP_DEFAULT_NUM_SHELLS = _IMP_em.IMP_DEFAULT_NUM_SHELLS
1482 IMP_SIG_CUTOFF = _IMP_em.IMP_SIG_CUTOFF
1483 class SurfaceShellDensityMap(SampledDensityMap):
1484 """Proxy of C++ IMP::em::SurfaceShellDensityMap class."""
1486 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1488 def __init__(self, *args):
1490 __init__(IMP::em::SurfaceShellDensityMap self) -> SurfaceShellDensityMap
1491 __init__(IMP::em::SurfaceShellDensityMap self, DensityHeader header) -> SurfaceShellDensityMap
1492 __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key, int num_shells=5) -> SurfaceShellDensityMap
1493 __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key) -> SurfaceShellDensityMap
1494 __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size) -> SurfaceShellDensityMap
1496 this = _IMP_em.new_SurfaceShellDensityMap(*args)
1498 self.this.append(this)
1499 except __builtin__.Exception:
1503 """binarize(SurfaceShellDensityMap self, float scene_val)"""
1504 return _IMP_em.SurfaceShellDensityMap_binarize(self, scene_val)
1507 def has_background_neighbor(self, voxel_ind):
1508 """has_background_neighbor(SurfaceShellDensityMap self, long voxel_ind) -> bool"""
1509 return _IMP_em.SurfaceShellDensityMap_has_background_neighbor(self, voxel_ind)
1511 __swig_destroy__ = _IMP_em.delete_SurfaceShellDensityMap
1512 __del__ =
lambda self:
None
1515 """__str__(SurfaceShellDensityMap self) -> std::string"""
1516 return _IMP_em.SurfaceShellDensityMap___str__(self)
1520 """__repr__(SurfaceShellDensityMap self) -> std::string"""
1521 return _IMP_em.SurfaceShellDensityMap___repr__(self)
1526 return _object_cast_to_SurfaceShellDensityMap(o)
1528 SurfaceShellDensityMap_swigregister = _IMP_em.SurfaceShellDensityMap_swigregister
1529 SurfaceShellDensityMap_swigregister(SurfaceShellDensityMap)
1532 """Proxy of C++ IMP::em::CoarseCC class."""
1534 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1537 """__init__(IMP::em::CoarseCC self) -> CoarseCC"""
1538 this = _IMP_em.new_CoarseCC()
1540 self.this.append(this)
1541 except __builtin__.Exception:
1544 def calc_score(*args):
1546 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True, IMP::FloatPair norm_factors) -> float
1547 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True) -> float
1548 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1549 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1551 return _IMP_em.CoarseCC_calc_score(*args)
1553 calc_score = staticmethod(calc_score)
1555 def cross_correlation_coefficient(*args):
1557 cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False, IMP::FloatPair norm_factors) -> double
1558 cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1559 cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1561 return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1563 cross_correlation_coefficient = staticmethod(cross_correlation_coefficient)
1565 def local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold):
1566 """local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1567 return _IMP_em.CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold)
1569 local_cross_correlation_coefficient = staticmethod(local_cross_correlation_coefficient)
1571 def get_version_info(self):
1572 """get_version_info(CoarseCC self) -> VersionInfo"""
1573 return _IMP_em.CoarseCC_get_version_info(self)
1577 """__str__(CoarseCC self) -> std::string"""
1578 return _IMP_em.CoarseCC___str__(self)
1582 """__repr__(CoarseCC self) -> std::string"""
1583 return _IMP_em.CoarseCC___repr__(self)
1588 return _object_cast_to_CoarseCC(o)
1590 CoarseCC_swigregister = _IMP_em.CoarseCC_swigregister
1591 CoarseCC_swigregister(CoarseCC)
1593 def CoarseCC_calc_score(*args):
1595 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True, IMP::FloatPair norm_factors) -> float
1596 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True) -> float
1597 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1598 CoarseCC_calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1600 return _IMP_em.CoarseCC_calc_score(*args)
1602 def CoarseCC_cross_correlation_coefficient(*args):
1604 cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False, IMP::FloatPair norm_factors) -> double
1605 cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1606 CoarseCC_cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1608 return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1610 def CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold):
1611 """CoarseCC_local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1612 return _IMP_em.CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold)
1614 class CoarseConvolution(object):
1615 """Proxy of C++ IMP::em::CoarseConvolution class."""
1617 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1618 __repr__ = _swig_repr
1620 def convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac=True):
1622 convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1623 convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1625 return _IMP_em.CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac)
1627 convolution = staticmethod(convolution)
1630 """__init__(IMP::em::CoarseConvolution self) -> CoarseConvolution"""
1631 this = _IMP_em.new_CoarseConvolution()
1633 self.this.append(this)
1634 except __builtin__.Exception:
1636 __swig_destroy__ = _IMP_em.delete_CoarseConvolution
1637 __del__ =
lambda self:
None
1638 CoarseConvolution_swigregister = _IMP_em.CoarseConvolution_swigregister
1639 CoarseConvolution_swigregister(CoarseConvolution)
1641 def CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac=True):
1643 convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1644 CoarseConvolution_convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1646 return _IMP_em.CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac)
1648 class CoarseCCatIntervals(CoarseCC):
1649 """Proxy of C++ IMP::em::CoarseCCatIntervals class."""
1651 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1653 def __init__(self, *args):
1655 __init__(IMP::em::CoarseCCatIntervals self, int const & ncd) -> CoarseCCatIntervals
1656 __init__(IMP::em::CoarseCCatIntervals self) -> CoarseCCatIntervals
1658 this = _IMP_em.new_CoarseCCatIntervals(*args)
1660 self.this.append(this)
1661 except __builtin__.Exception:
1664 def evaluate(self, em_map, model_map, deriv, scalefac, lderiv, eval_interval):
1665 """evaluate(CoarseCCatIntervals self, DensityMap em_map, SampledDensityMap model_map, IMP::algebra::Vector3Ds const & deriv, float scalefac, bool lderiv, unsigned long eval_interval) -> std::pair< double,IMP::algebra::Vector3Ds >"""
1666 return _IMP_em.CoarseCCatIntervals_evaluate(self, em_map, model_map, deriv, scalefac, lderiv, eval_interval)
1670 """__str__(CoarseCCatIntervals self) -> std::string"""
1671 return _IMP_em.CoarseCCatIntervals___str__(self)
1675 """__repr__(CoarseCCatIntervals self) -> std::string"""
1676 return _IMP_em.CoarseCCatIntervals___repr__(self)
1681 return _object_cast_to_CoarseCCatIntervals(o)
1683 CoarseCCatIntervals_swigregister = _IMP_em.CoarseCCatIntervals_swigregister
1684 CoarseCCatIntervals_swigregister(CoarseCCatIntervals)
1687 """Proxy of C++ IMP::em::FitRestraint class."""
1689 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1691 def __init__(self, *args):
1693 __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key, float scale=1, bool use_rigid_bodies=True, IMP::em::KernelType kt) -> FitRestraint
1694 __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key, float scale=1, bool use_rigid_bodies=True) -> FitRestraint
1695 __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key, float scale=1) -> FitRestraint
1696 __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key) -> FitRestraint
1697 __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors) -> FitRestraint
1698 __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map) -> FitRestraint
1700 this = _IMP_em.new_FitRestraint(*args)
1702 self.this.append(this)
1703 except __builtin__.Exception:
1706 def get_model_dens_map(self):
1707 """get_model_dens_map(FitRestraint self) -> SampledDensityMap"""
1708 return _IMP_em.FitRestraint_get_model_dens_map(self)
1711 def set_scale_factor(self, scale):
1712 """set_scale_factor(FitRestraint self, float scale)"""
1713 return _IMP_em.FitRestraint_set_scale_factor(self, scale)
1716 def get_scale_factor(self):
1717 """get_scale_factor(FitRestraint self) -> float"""
1718 return _IMP_em.FitRestraint_get_scale_factor(self)
1721 def do_get_inputs(self):
1722 """do_get_inputs(FitRestraint self) -> IMP::ModelObjectsTemp"""
1723 return _IMP_em.FitRestraint_do_get_inputs(self)
1726 def get_version_info(self):
1727 """get_version_info(FitRestraint self) -> VersionInfo"""
1728 return _IMP_em.FitRestraint_get_version_info(self)
1732 """__str__(FitRestraint self) -> std::string"""
1733 return _IMP_em.FitRestraint___str__(self)
1737 """__repr__(FitRestraint self) -> std::string"""
1738 return _IMP_em.FitRestraint___repr__(self)
1743 return _object_cast_to_FitRestraint(o)
1747 """cast(Restraint r) -> FitRestraint"""
1748 return _IMP_em.FitRestraint_cast(r)
1750 cast = staticmethod(cast)
1751 FitRestraint_swigregister = _IMP_em.FitRestraint_swigregister
1752 FitRestraint_swigregister(FitRestraint)
1754 def FitRestraint_cast(r):
1755 """FitRestraint_cast(Restraint r) -> FitRestraint"""
1756 return _IMP_em.FitRestraint_cast(r)
1761 density2particles(DensityMap dmap, IMP::Float threshold, Model m, int step=1) -> IMP::Particles
1762 density2particles(DensityMap dmap, IMP::Float threshold, Model m) -> IMP::Particles
1764 return _IMP_em.density2particles(dmap, threshold, m, step)
1767 """density2vectors(DensityMap dmap, IMP::Float threshold) -> IMP::algebra::Vector3Ds"""
1768 return _IMP_em.density2vectors(dmap, threshold)
1772 particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3, FloatKey weight_key) -> SampledDensityMap
1773 particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
1774 particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
1776 return _IMP_em.particles2density(*args)
1780 particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3, FloatKey weight_key) -> SampledDensityMap
1781 particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
1782 particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
1784 return _IMP_em.particles2binarized_density(*args)
1788 particles2surface(IMP::ParticlesTemp const & ps, IMP::Float apix, FloatKey weight_key) -> SurfaceShellDensityMap
1789 particles2surface(IMP::ParticlesTemp const & ps, IMP::Float apix) -> SurfaceShellDensityMap
1791 return _IMP_em.particles2surface(*args)
1793 def calculate_intersection_score(d1, d2):
1794 """calculate_intersection_score(SurfaceShellDensityMap d1, SurfaceShellDensityMap d2) -> IMP::Float"""
1795 return _IMP_em.calculate_intersection_score(d1, d2)
1796 class SpiderHeader(object):
1797 """Proxy of C++ IMP::em::SpiderHeader class."""
1799 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1800 __repr__ = _swig_repr
1801 fNslice = _swig_property(_IMP_em.SpiderHeader_fNslice_get, _IMP_em.SpiderHeader_fNslice_set)
1802 fNrow = _swig_property(_IMP_em.SpiderHeader_fNrow_get, _IMP_em.SpiderHeader_fNrow_set)
1803 fNrec = _swig_property(_IMP_em.SpiderHeader_fNrec_get, _IMP_em.SpiderHeader_fNrec_set)
1804 fNlabel = _swig_property(_IMP_em.SpiderHeader_fNlabel_get, _IMP_em.SpiderHeader_fNlabel_set)
1805 fIform = _swig_property(_IMP_em.SpiderHeader_fIform_get, _IMP_em.SpiderHeader_fIform_set)
1806 fImami = _swig_property(_IMP_em.SpiderHeader_fImami_get, _IMP_em.SpiderHeader_fImami_set)
1807 fFmax = _swig_property(_IMP_em.SpiderHeader_fFmax_get, _IMP_em.SpiderHeader_fFmax_set)
1808 fFmin = _swig_property(_IMP_em.SpiderHeader_fFmin_get, _IMP_em.SpiderHeader_fFmin_set)
1809 fAv = _swig_property(_IMP_em.SpiderHeader_fAv_get, _IMP_em.SpiderHeader_fAv_set)
1810 fSig = _swig_property(_IMP_em.SpiderHeader_fSig_get, _IMP_em.SpiderHeader_fSig_set)
1811 fIhist = _swig_property(_IMP_em.SpiderHeader_fIhist_get, _IMP_em.SpiderHeader_fIhist_set)
1812 fNcol = _swig_property(_IMP_em.SpiderHeader_fNcol_get, _IMP_em.SpiderHeader_fNcol_set)
1813 fLabrec = _swig_property(_IMP_em.SpiderHeader_fLabrec_get, _IMP_em.SpiderHeader_fLabrec_set)
1814 fIangle = _swig_property(_IMP_em.SpiderHeader_fIangle_get, _IMP_em.SpiderHeader_fIangle_set)
1815 fPhi = _swig_property(_IMP_em.SpiderHeader_fPhi_get, _IMP_em.SpiderHeader_fPhi_set)
1816 fTheta = _swig_property(_IMP_em.SpiderHeader_fTheta_get, _IMP_em.SpiderHeader_fTheta_set)
1817 fPsi = _swig_property(_IMP_em.SpiderHeader_fPsi_get, _IMP_em.SpiderHeader_fPsi_set)
1818 fXoff = _swig_property(_IMP_em.SpiderHeader_fXoff_get, _IMP_em.SpiderHeader_fXoff_set)
1819 fYoff = _swig_property(_IMP_em.SpiderHeader_fYoff_get, _IMP_em.SpiderHeader_fYoff_set)
1820 fZoff = _swig_property(_IMP_em.SpiderHeader_fZoff_get, _IMP_em.SpiderHeader_fZoff_set)
1821 fScale = _swig_property(_IMP_em.SpiderHeader_fScale_get, _IMP_em.SpiderHeader_fScale_set)
1822 fLabbyt = _swig_property(_IMP_em.SpiderHeader_fLabbyt_get, _IMP_em.SpiderHeader_fLabbyt_set)
1823 fLenbyt = _swig_property(_IMP_em.SpiderHeader_fLenbyt_get, _IMP_em.SpiderHeader_fLenbyt_set)
1824 fNothing = _swig_property(_IMP_em.SpiderHeader_fNothing_get, _IMP_em.SpiderHeader_fNothing_set)
1825 fFlag = _swig_property(_IMP_em.SpiderHeader_fFlag_get, _IMP_em.SpiderHeader_fFlag_set)
1826 fPhi1 = _swig_property(_IMP_em.SpiderHeader_fPhi1_get, _IMP_em.SpiderHeader_fPhi1_set)
1827 fTheta1 = _swig_property(_IMP_em.SpiderHeader_fTheta1_get, _IMP_em.SpiderHeader_fTheta1_set)
1828 fPsi1 = _swig_property(_IMP_em.SpiderHeader_fPsi1_get, _IMP_em.SpiderHeader_fPsi1_set)
1829 fPhi2 = _swig_property(_IMP_em.SpiderHeader_fPhi2_get, _IMP_em.SpiderHeader_fPhi2_set)
1830 fTheta2 = _swig_property(_IMP_em.SpiderHeader_fTheta2_get, _IMP_em.SpiderHeader_fTheta2_set)
1831 fPsi2 = _swig_property(_IMP_em.SpiderHeader_fPsi2_get, _IMP_em.SpiderHeader_fPsi2_set)
1832 fGeo_matrix = _swig_property(_IMP_em.SpiderHeader_fGeo_matrix_get, _IMP_em.SpiderHeader_fGeo_matrix_set)
1833 fAngle1 = _swig_property(_IMP_em.SpiderHeader_fAngle1_get, _IMP_em.SpiderHeader_fAngle1_set)
1834 fr1 = _swig_property(_IMP_em.SpiderHeader_fr1_get, _IMP_em.SpiderHeader_fr1_set)
1835 fr2 = _swig_property(_IMP_em.SpiderHeader_fr2_get, _IMP_em.SpiderHeader_fr2_set)
1836 RTflag = _swig_property(_IMP_em.SpiderHeader_RTflag_get, _IMP_em.SpiderHeader_RTflag_set)
1837 Astart = _swig_property(_IMP_em.SpiderHeader_Astart_get, _IMP_em.SpiderHeader_Astart_set)
1838 Aend = _swig_property(_IMP_em.SpiderHeader_Aend_get, _IMP_em.SpiderHeader_Aend_set)
1839 Ainc = _swig_property(_IMP_em.SpiderHeader_Ainc_get, _IMP_em.SpiderHeader_Ainc_set)
1840 Rsigma = _swig_property(_IMP_em.SpiderHeader_Rsigma_get, _IMP_em.SpiderHeader_Rsigma_set)
1841 Tstart = _swig_property(_IMP_em.SpiderHeader_Tstart_get, _IMP_em.SpiderHeader_Tstart_set)
1842 Tend = _swig_property(_IMP_em.SpiderHeader_Tend_get, _IMP_em.SpiderHeader_Tend_set)
1843 Tinc = _swig_property(_IMP_em.SpiderHeader_Tinc_get, _IMP_em.SpiderHeader_Tinc_set)
1844 Weight = _swig_property(_IMP_em.SpiderHeader_Weight_get, _IMP_em.SpiderHeader_Weight_set)
1845 Flip = _swig_property(_IMP_em.SpiderHeader_Flip_get, _IMP_em.SpiderHeader_Flip_set)
1846 empty = _swig_property(_IMP_em.SpiderHeader_empty_get, _IMP_em.SpiderHeader_empty_set)
1847 szIDat = _swig_property(_IMP_em.SpiderHeader_szIDat_get, _IMP_em.SpiderHeader_szIDat_set)
1848 szITim = _swig_property(_IMP_em.SpiderHeader_szITim_get, _IMP_em.SpiderHeader_szITim_set)
1849 szITit = _swig_property(_IMP_em.SpiderHeader_szITit_get, _IMP_em.SpiderHeader_szITit_set)
1851 def show(self, out):
1852 """show(SpiderHeader self, _ostream out)"""
1853 return _IMP_em.SpiderHeader_show(self, out)
1857 """__init__(IMP::em::SpiderHeader self) -> SpiderHeader"""
1858 this = _IMP_em.new_SpiderHeader()
1860 self.this.append(this)
1861 except __builtin__.Exception:
1863 __swig_destroy__ = _IMP_em.delete_SpiderHeader
1864 __del__ =
lambda self:
None
1865 SpiderHeader_swigregister = _IMP_em.SpiderHeader_swigregister
1866 SpiderHeader_swigregister(SpiderHeader)
1868 class ImageHeader(object):
1869 """Proxy of C++ IMP::em::ImageHeader class."""
1871 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1872 __repr__ = _swig_repr
1873 IMG_BYTE = _IMP_em.ImageHeader_IMG_BYTE
1874 IMG_IMPEM = _IMP_em.ImageHeader_IMG_IMPEM
1875 IMG_INT = _IMP_em.ImageHeader_IMG_INT
1876 VOL_BYTE = _IMP_em.ImageHeader_VOL_BYTE
1877 VOL_IMPEM = _IMP_em.ImageHeader_VOL_IMPEM
1878 VOL_INT = _IMP_em.ImageHeader_VOL_INT
1879 IMG_FOURIER = _IMP_em.ImageHeader_IMG_FOURIER
1880 VOL_FOURIER = _IMP_em.ImageHeader_VOL_FOURIER
1882 def __init__(self, *args):
1884 __init__(IMP::em::ImageHeader self) -> ImageHeader
1885 __init__(IMP::em::ImageHeader self, IMP::em::ImageHeader::img_type im) -> ImageHeader
1886 __init__(IMP::em::ImageHeader self, float im) -> ImageHeader
1888 this = _IMP_em.new_ImageHeader(*args)
1890 self.this.append(this)
1891 except __builtin__.Exception:
1894 def get_image_type(self):
1895 """get_image_type(ImageHeader self) -> float"""
1896 return _IMP_em.ImageHeader_get_image_type(self)
1899 def set_image_type(self, *args):
1901 set_image_type(ImageHeader self, IMP::em::ImageHeader::img_type im)
1902 set_image_type(ImageHeader self, float im)
1904 return _IMP_em.ImageHeader_set_image_type(self, *args)
1907 def do_show(self, out):
1908 """do_show(ImageHeader self, _ostream out)"""
1909 return _IMP_em.ImageHeader_do_show(self, out)
1912 def show(self, *args):
1914 show(ImageHeader self, _ostream out)
1915 show(ImageHeader self)
1917 return _IMP_em.ImageHeader_show(self, *args)
1920 def print_hard(self, out):
1921 """print_hard(ImageHeader self, _ostream out)"""
1922 return _IMP_em.ImageHeader_print_hard(self, out)
1925 def show_projection_params(self, out):
1926 """show_projection_params(ImageHeader self, _ostream out)"""
1927 return _IMP_em.ImageHeader_show_projection_params(self, out)
1930 def read(self, *args):
1932 read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False, bool skip_extra_checkings=False) -> int
1933 read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False) -> int
1934 read(ImageHeader self, IMP::String const filename, bool skip_type_check=False) -> int
1935 read(ImageHeader self, IMP::String const filename) -> int
1936 read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False, bool skip_extra_checkings=False) -> bool
1937 read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False) -> bool
1938 read(ImageHeader self, std::ifstream & f, bool skip_type_check=False) -> bool
1939 read(ImageHeader self, std::ifstream & f) -> bool
1941 return _IMP_em.ImageHeader_read(self, *args)
1944 def write(self, *args):
1946 write(ImageHeader self, IMP::String const & filename, bool force_reversed=False)
1947 write(ImageHeader self, IMP::String const & filename)
1948 write(ImageHeader self, std::ofstream & f, bool force_reversed=False)
1949 write(ImageHeader self, std::ofstream & f)
1951 return _IMP_em.ImageHeader_write(self, *args)
1955 """clear(ImageHeader self)"""
1956 return _IMP_em.ImageHeader_clear(self)
1959 def set_header(self):
1960 """set_header(ImageHeader self)"""
1961 return _IMP_em.ImageHeader_set_header(self)
1964 def get_reversed(self):
1965 """get_reversed(ImageHeader self) -> bool"""
1966 return _IMP_em.ImageHeader_get_reversed(self)
1969 def set_reversed(self, value):
1970 """set_reversed(ImageHeader self, bool value)"""
1971 return _IMP_em.ImageHeader_set_reversed(self, value)
1974 def get_number_of_slices(self):
1975 """get_number_of_slices(ImageHeader self) -> unsigned int"""
1976 return _IMP_em.ImageHeader_get_number_of_slices(self)
1979 def set_number_of_slices(self, n):
1980 """set_number_of_slices(ImageHeader self, unsigned int n)"""
1981 return _IMP_em.ImageHeader_set_number_of_slices(self, n)
1984 def get_number_of_rows(self):
1985 """get_number_of_rows(ImageHeader self) -> unsigned int"""
1986 return _IMP_em.ImageHeader_get_number_of_rows(self)
1989 def set_number_of_rows(self, n):
1990 """set_number_of_rows(ImageHeader self, unsigned int n)"""
1991 return _IMP_em.ImageHeader_set_number_of_rows(self, n)
1994 def get_number_of_columns(self):
1995 """get_number_of_columns(ImageHeader self) -> unsigned int"""
1996 return _IMP_em.ImageHeader_get_number_of_columns(self)
1999 def set_number_of_columns(self, n):
2000 """set_number_of_columns(ImageHeader self, unsigned int n)"""
2001 return _IMP_em.ImageHeader_set_number_of_columns(self, n)
2004 def get_old_rot(self):
2005 """get_old_rot(ImageHeader self) -> float"""
2006 return _IMP_em.ImageHeader_get_old_rot(self)
2009 def set_old_rot(self, value):
2010 """set_old_rot(ImageHeader self, float value)"""
2011 return _IMP_em.ImageHeader_set_old_rot(self, value)
2014 def get_fAngle1(self):
2015 """get_fAngle1(ImageHeader self) -> float"""
2016 return _IMP_em.ImageHeader_get_fAngle1(self)
2019 def set_fAngle1(self, value):
2020 """set_fAngle1(ImageHeader self, float value)"""
2021 return _IMP_em.ImageHeader_set_fAngle1(self, value)
2024 def get_Scale(self):
2025 """get_Scale(ImageHeader self) -> float"""
2026 return _IMP_em.ImageHeader_get_Scale(self)
2029 def set_Scale(self, value):
2030 """set_Scale(ImageHeader self, float value)"""
2031 return _IMP_em.ImageHeader_set_Scale(self, value)
2035 """get_Flip(ImageHeader self) -> float"""
2036 return _IMP_em.ImageHeader_get_Flip(self)
2039 def set_Flip(self, value):
2040 """set_Flip(ImageHeader self, float value)"""
2041 return _IMP_em.ImageHeader_set_Flip(self, value)
2044 def get_Weight(self):
2045 """get_Weight(ImageHeader self) -> float"""
2046 return _IMP_em.ImageHeader_get_Weight(self)
2049 def set_Weight(self, value):
2050 """set_Weight(ImageHeader self, float value)"""
2051 return _IMP_em.ImageHeader_set_Weight(self, value)
2054 def get_fNrec(self):
2055 """get_fNrec(ImageHeader self) -> float"""
2056 return _IMP_em.ImageHeader_get_fNrec(self)
2059 def set_fNrec(self, value):
2060 """set_fNrec(ImageHeader self, float value)"""
2061 return _IMP_em.ImageHeader_set_fNrec(self, value)
2064 def get_fNlabel(self):
2065 """get_fNlabel(ImageHeader self) -> float"""
2066 return _IMP_em.ImageHeader_get_fNlabel(self)
2069 def set_fNlabel(self, value):
2070 """set_fNlabel(ImageHeader self, float value)"""
2071 return _IMP_em.ImageHeader_set_fNlabel(self, value)
2074 def get_fIform(self):
2075 """get_fIform(ImageHeader self) -> float"""
2076 return _IMP_em.ImageHeader_get_fIform(self)
2079 def set_fIform(self, value):
2080 """set_fIform(ImageHeader self, float value)"""
2081 return _IMP_em.ImageHeader_set_fIform(self, value)
2084 def get_fImami(self):
2085 """get_fImami(ImageHeader self) -> float"""
2086 return _IMP_em.ImageHeader_get_fImami(self)
2089 def set_fImami(self, value):
2090 """set_fImami(ImageHeader self, float value)"""
2091 return _IMP_em.ImageHeader_set_fImami(self, value)
2094 def get_fFmax(self):
2095 """get_fFmax(ImageHeader self) -> float"""
2096 return _IMP_em.ImageHeader_get_fFmax(self)
2099 def set_fFmax(self, value):
2100 """set_fFmax(ImageHeader self, float value)"""
2101 return _IMP_em.ImageHeader_set_fFmax(self, value)
2104 def get_fFmin(self):
2105 """get_fFmin(ImageHeader self) -> float"""
2106 return _IMP_em.ImageHeader_get_fFmin(self)
2109 def set_fFmin(self, value):
2110 """set_fFmin(ImageHeader self, float value)"""
2111 return _IMP_em.ImageHeader_set_fFmin(self, value)
2115 """get_fAv(ImageHeader self) -> float"""
2116 return _IMP_em.ImageHeader_get_fAv(self)
2119 def set_fAv(self, value):
2120 """set_fAv(ImageHeader self, float value)"""
2121 return _IMP_em.ImageHeader_set_fAv(self, value)
2125 """get_fSig(ImageHeader self) -> float"""
2126 return _IMP_em.ImageHeader_get_fSig(self)
2129 def set_fSig(self, value):
2130 """set_fSig(ImageHeader self, float value)"""
2131 return _IMP_em.ImageHeader_set_fSig(self, value)
2134 def get_fIhist(self):
2135 """get_fIhist(ImageHeader self) -> float"""
2136 return _IMP_em.ImageHeader_get_fIhist(self)
2139 def set_fIhist(self, value):
2140 """set_fIhist(ImageHeader self, float value)"""
2141 return _IMP_em.ImageHeader_set_fIhist(self, value)
2144 def get_fLabrec(self):
2145 """get_fLabrec(ImageHeader self) -> float"""
2146 return _IMP_em.ImageHeader_get_fLabrec(self)
2149 def set_fLabrec(self, value):
2150 """set_fLabrec(ImageHeader self, float value)"""
2151 return _IMP_em.ImageHeader_set_fLabrec(self, value)
2154 def get_fIangle(self):
2155 """get_fIangle(ImageHeader self) -> float"""
2156 return _IMP_em.ImageHeader_get_fIangle(self)
2159 def set_fIangle(self, value):
2160 """set_fIangle(ImageHeader self, float value)"""
2161 return _IMP_em.ImageHeader_set_fIangle(self, value)
2164 def get_origin(self):
2165 """get_origin(ImageHeader self) -> Vector3D"""
2166 return _IMP_em.ImageHeader_get_origin(self)
2169 def set_origin(self, *args):
2171 set_origin(ImageHeader self, Vector3D v)
2172 set_origin(ImageHeader self, Vector2D v)
2174 return _IMP_em.ImageHeader_set_origin(self, *args)
2177 def get_object_pixel_size(self):
2178 """get_object_pixel_size(ImageHeader self) -> float"""
2179 return _IMP_em.ImageHeader_get_object_pixel_size(self)
2182 def set_object_pixel_size(self, value):
2183 """set_object_pixel_size(ImageHeader self, float value)"""
2184 return _IMP_em.ImageHeader_set_object_pixel_size(self, value)
2187 def get_fLabbyt(self):
2188 """get_fLabbyt(ImageHeader self) -> float"""
2189 return _IMP_em.ImageHeader_get_fLabbyt(self)
2192 def set_fLabbyt(self, value):
2193 """set_fLabbyt(ImageHeader self, float value)"""
2194 return _IMP_em.ImageHeader_set_fLabbyt(self, value)
2197 def get_fLenbyt(self):
2198 """get_fLenbyt(ImageHeader self) -> float"""
2199 return _IMP_em.ImageHeader_get_fLenbyt(self)
2202 def set_fLenbyt(self, value):
2203 """set_fLenbyt(ImageHeader self, float value)"""
2204 return _IMP_em.ImageHeader_set_fLenbyt(self, value)
2207 def get_fGeo_matrix(self, i, j):
2208 """get_fGeo_matrix(ImageHeader self, unsigned int i, unsigned int j) -> double"""
2209 return _IMP_em.ImageHeader_get_fGeo_matrix(self, i, j)
2212 def get_fFlag(self):
2213 """get_fFlag(ImageHeader self) -> float"""
2214 return _IMP_em.ImageHeader_get_fFlag(self)
2217 def set_fFlag(self, value):
2218 """set_fFlag(ImageHeader self, float value)"""
2219 return _IMP_em.ImageHeader_set_fFlag(self, value)
2222 def get_euler_angles(self):
2223 """get_euler_angles(ImageHeader self) -> Vector3D"""
2224 return _IMP_em.ImageHeader_get_euler_angles(self)
2227 def get_euler_angles1(self):
2228 """get_euler_angles1(ImageHeader self) -> Vector3D"""
2229 return _IMP_em.ImageHeader_get_euler_angles1(self)
2232 def get_euler_angles2(self):
2233 """get_euler_angles2(ImageHeader self) -> Vector3D"""
2234 return _IMP_em.ImageHeader_get_euler_angles2(self)
2237 def set_euler_angles(self, euler):
2238 """set_euler_angles(ImageHeader self, Vector3D euler)"""
2239 return _IMP_em.ImageHeader_set_euler_angles(self, euler)
2242 def set_euler_angles1(self, euler):
2243 """set_euler_angles1(ImageHeader self, Vector3D euler)"""
2244 return _IMP_em.ImageHeader_set_euler_angles1(self, euler)
2247 def set_euler_angles2(self, euler):
2248 """set_euler_angles2(ImageHeader self, Vector3D euler)"""
2249 return _IMP_em.ImageHeader_set_euler_angles2(self, euler)
2252 def is_normalized(self):
2253 """is_normalized(ImageHeader self) -> bool"""
2254 return _IMP_em.ImageHeader_is_normalized(self)
2258 """set_date(ImageHeader self)"""
2259 return _IMP_em.ImageHeader_set_date(self)
2263 """set_time(ImageHeader self)"""
2264 return _IMP_em.ImageHeader_set_time(self)
2267 def set_title(self, newName):
2268 """set_title(ImageHeader self, IMP::String newName)"""
2269 return _IMP_em.ImageHeader_set_title(self, newName)
2271 __swig_destroy__ = _IMP_em.delete_ImageHeader
2272 __del__ =
lambda self:
None
2273 ImageHeader_swigregister = _IMP_em.ImageHeader_swigregister
2274 ImageHeader_swigregister(ImageHeader)
2276 class SpiderMapReaderWriter(MapReaderWriter):
2277 """Proxy of C++ IMP::em::SpiderMapReaderWriter class."""
2279 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2280 filename_ = _swig_property(_IMP_em.SpiderMapReaderWriter_filename__get, _IMP_em.SpiderMapReaderWriter_filename__set)
2281 skip_type_check_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_type_check__get, _IMP_em.SpiderMapReaderWriter_skip_type_check__set)
2282 force_reversed_ = _swig_property(_IMP_em.SpiderMapReaderWriter_force_reversed__get, _IMP_em.SpiderMapReaderWriter_force_reversed__set)
2283 skip_extra_checkings_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_extra_checkings__get, _IMP_em.SpiderMapReaderWriter_skip_extra_checkings__set)
2285 def __init__(self, *args):
2287 __init__(IMP::em::SpiderMapReaderWriter self) -> SpiderMapReaderWriter
2288 __init__(IMP::em::SpiderMapReaderWriter self, IMP::String filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings) -> SpiderMapReaderWriter
2290 this = _IMP_em.new_SpiderMapReaderWriter(*args)
2292 self.this.append(this)
2293 except __builtin__.Exception:
2297 """__str__(SpiderMapReaderWriter self) -> std::string"""
2298 return _IMP_em.SpiderMapReaderWriter___str__(self)
2302 """__repr__(SpiderMapReaderWriter self) -> std::string"""
2303 return _IMP_em.SpiderMapReaderWriter___repr__(self)
2308 return _object_cast_to_SpiderMapReaderWriter(o)
2310 SpiderMapReaderWriter_swigregister = _IMP_em.SpiderMapReaderWriter_swigregister
2311 SpiderMapReaderWriter_swigregister(SpiderMapReaderWriter)
2313 class FittingSolutions(object):
2314 """Proxy of C++ IMP::em::FittingSolutions class."""
2316 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2319 """__init__(IMP::em::FittingSolutions self) -> FittingSolutions"""
2320 this = _IMP_em.new_FittingSolutions()
2322 self.this.append(this)
2323 except __builtin__.Exception:
2326 def get_number_of_solutions(self):
2327 """get_number_of_solutions(FittingSolutions self) -> int"""
2328 return _IMP_em.FittingSolutions_get_number_of_solutions(self)
2331 def get_transformation(self, i):
2332 """get_transformation(FittingSolutions self, unsigned int i) -> Transformation3D"""
2333 return _IMP_em.FittingSolutions_get_transformation(self, i)
2336 def get_score(self, i):
2337 """get_score(FittingSolutions self, unsigned int i) -> IMP::Float"""
2338 return _IMP_em.FittingSolutions_get_score(self, i)
2341 def set_score(self, i, score):
2342 """set_score(FittingSolutions self, unsigned int i, IMP::Float score)"""
2343 return _IMP_em.FittingSolutions_set_score(self, i, score)
2346 def add_solution(self, t, score):
2347 """add_solution(FittingSolutions self, Transformation3D t, IMP::Float score)"""
2348 return _IMP_em.FittingSolutions_add_solution(self, t, score)
2351 def sort(self, reverse=False):
2353 sort(FittingSolutions self, bool reverse=False)
2354 sort(FittingSolutions self)
2356 return _IMP_em.FittingSolutions_sort(self, reverse)
2360 """multiply(FittingSolutions self, Transformation3D t)"""
2361 return _IMP_em.FittingSolutions_multiply(self, t)
2364 def get_transformations(self):
2365 """get_transformations(FittingSolutions self) -> IMP::algebra::Transformation3Ds"""
2366 return _IMP_em.FittingSolutions_get_transformations(self)
2369 def show(self, *args):
2371 show(FittingSolutions self, _ostream out)
2372 show(FittingSolutions self)
2374 return _IMP_em.FittingSolutions_show(self, *args)
2378 """__str__(FittingSolutions self) -> std::string"""
2379 return _IMP_em.FittingSolutions___str__(self)
2383 """__repr__(FittingSolutions self) -> std::string"""
2384 return _IMP_em.FittingSolutions___repr__(self)
2386 __swig_destroy__ = _IMP_em.delete_FittingSolutions
2387 __del__ =
lambda self:
None
2388 FittingSolutions_swigregister = _IMP_em.FittingSolutions_swigregister
2389 FittingSolutions_swigregister(FittingSolutions)
2392 def local_rigid_fitting_around_point(p, refiner, weight_key, dmap, anchor_centroid, display_log, number_of_optimization_runs=5, number_of_mc_steps=10, number_of_cg_steps=100, max_translation=2., max_rotation=.3, fast=False):
2394 local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2., IMP::Float max_rotation=.3, bool fast=False) -> FittingSolutions
2395 local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2., IMP::Float max_rotation=.3) -> FittingSolutions
2396 local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2.) -> FittingSolutions
2397 local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100) -> FittingSolutions
2398 local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10) -> FittingSolutions
2399 local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2400 local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log) -> FittingSolutions
2402 return _IMP_em.local_rigid_fitting_around_point(p, refiner, weight_key, dmap, anchor_centroid, display_log, number_of_optimization_runs, number_of_mc_steps, number_of_cg_steps, max_translation, max_rotation, fast)
2404 def local_rigid_fitting(p, refiner, weight_key, dmap, display_log, number_of_optimization_runs=5, number_of_mc_steps=10, number_of_cg_steps=100, max_translation=2., max_rotation=.3, fast=True):
2406 local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2., IMP::Float max_rotation=.3, bool fast=True) -> FittingSolutions
2407 local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2., IMP::Float max_rotation=.3) -> FittingSolutions
2408 local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2.) -> FittingSolutions
2409 local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100) -> FittingSolutions
2410 local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10) -> FittingSolutions
2411 local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2412 local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log) -> FittingSolutions
2414 return _IMP_em.local_rigid_fitting(p, refiner, weight_key, dmap, display_log, number_of_optimization_runs, number_of_mc_steps, number_of_cg_steps, max_translation, max_rotation, fast)
2416 def local_rigid_fitting_around_points(p, refiner, wei_key, dmap, anchor_centroids, display_log, number_of_optimization_runs=5, number_of_mc_steps=10, number_of_cg_steps=100, max_translation=2., max_rotation=.3):
2418 local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2., IMP::Float max_rotation=.3) -> FittingSolutions
2419 local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2.) -> FittingSolutions
2420 local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100) -> FittingSolutions
2421 local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10) -> FittingSolutions
2422 local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2423 local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids, IMP::OptimizerStates display_log) -> FittingSolutions
2425 return _IMP_em.local_rigid_fitting_around_points(p, refiner, wei_key, dmap, anchor_centroids, display_log, number_of_optimization_runs, number_of_mc_steps, number_of_cg_steps, max_translation, max_rotation)
2427 def local_rigid_fitting_grid_search(ps, wei_key, dmap, max_voxels_translation=2, translation_step=1, max_angle_in_radians=0.174, number_of_rotations=100):
2429 local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2, IMP::Int translation_step=1, IMP::Float max_angle_in_radians=0.174, IMP::Int number_of_rotations=100) -> FittingSolutions
2430 local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2, IMP::Int translation_step=1, IMP::Float max_angle_in_radians=0.174) -> FittingSolutions
2431 local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2, IMP::Int translation_step=1) -> FittingSolutions
2432 local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2) -> FittingSolutions
2433 local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap) -> FittingSolutions
2435 return _IMP_em.local_rigid_fitting_grid_search(ps, wei_key, dmap, max_voxels_translation, translation_step, max_angle_in_radians, number_of_rotations)
2439 compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations, bool fast_version=False, bool local_score=False, FloatKey wei_key) -> FittingSolutions
2440 compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations, bool fast_version=False, bool local_score=False) -> FittingSolutions
2441 compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations, bool fast_version=False) -> FittingSolutions
2442 compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2443 compute_fitting_scores(DensityMap em_map, RigidBody rb, Refiner refiner, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2445 return _IMP_em.compute_fitting_scores(*args)
2449 compute_fitting_score(IMP::ParticlesTemp const & ps, DensityMap em_map, FloatKey wei_key) -> IMP::Float
2450 compute_fitting_score(IMP::ParticlesTemp const & ps, DensityMap em_map) -> IMP::Float
2452 return _IMP_em.compute_fitting_score(*args)
2456 get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, Transformation3D t, float thr=0.0) -> long
2457 get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, Transformation3D t) -> long
2458 get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps) -> long
2460 return _IMP_em.get_number_of_particles_outside_of_the_density(*args)
2464 get_numbers_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, IMP::algebra::Transformation3Ds const & transformations, float thr=0.0) -> IMP::Ints
2465 get_numbers_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, IMP::algebra::Transformation3Ds const & transformations) -> IMP::Ints
2467 return _IMP_em.get_numbers_of_particles_outside_of_the_density(dmap, ps, transformations, thr)
2471 get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3., Transformation3D t, float thr=0.0) -> double
2472 get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3., Transformation3D t) -> double
2473 get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3.) -> double
2474 get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps) -> double
2476 return _IMP_em.get_percentage_of_voxels_covered_by_particles(*args)
2478 """Proxy of C++ IMP::em::HighDensityEmbedding class."""
2480 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2482 def __init__(self, dm, threshold):
2483 """__init__(IMP::em::HighDensityEmbedding self, DensityMap dm, double threshold) -> HighDensityEmbedding"""
2484 this = _IMP_em.new_HighDensityEmbedding(dm, threshold)
2486 self.this.append(this)
2487 except __builtin__.Exception:
2490 def get_version_info(self):
2491 """get_version_info(HighDensityEmbedding self) -> VersionInfo"""
2492 return _IMP_em.HighDensityEmbedding_get_version_info(self)
2496 """__str__(HighDensityEmbedding self) -> std::string"""
2497 return _IMP_em.HighDensityEmbedding___str__(self)
2501 """__repr__(HighDensityEmbedding self) -> std::string"""
2502 return _IMP_em.HighDensityEmbedding___repr__(self)
2507 return _object_cast_to_HighDensityEmbedding(o)
2509 HighDensityEmbedding_swigregister = _IMP_em.HighDensityEmbedding_swigregister
2510 HighDensityEmbedding_swigregister(HighDensityEmbedding)
2514 """mask_and_norm(DensityMap dmap, DensityMap mask) -> DensityMap"""
2515 return _IMP_em.mask_and_norm(dmap, mask)
2518 """get_volume_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float"""
2519 return _IMP_em.get_volume_at_threshold(m, threshold)
2523 get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold, IMP::atom::ProteinDensityReference ref) -> IMP::Float
2524 get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float
2526 return _IMP_em.get_molecular_mass_at_threshold(*args)
2529 """get_threshold_for_approximate_volume(DensityMap m, IMP::Float desired_volume) -> IMP::Float"""
2530 return _IMP_em.get_threshold_for_approximate_volume(m, desired_volume)
2534 get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass, IMP::atom::ProteinDensityReference ref) -> IMP::Float
2535 get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass) -> IMP::Float
2537 return _IMP_em.get_threshold_for_approximate_mass(*args)
2539 """Proxy of C++ IMP::em::EnvelopePenetrationRestraint class."""
2541 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2543 def __init__(self, ps, em_map, threshold):
2544 """__init__(IMP::em::EnvelopePenetrationRestraint self, IMP::Particles ps, DensityMap em_map, IMP::Float threshold) -> EnvelopePenetrationRestraint"""
2545 this = _IMP_em.new_EnvelopePenetrationRestraint(ps, em_map, threshold)
2547 self.this.append(this)
2548 except __builtin__.Exception:
2551 def do_get_inputs(self):
2552 """do_get_inputs(EnvelopePenetrationRestraint self) -> IMP::ModelObjectsTemp"""
2553 return _IMP_em.EnvelopePenetrationRestraint_do_get_inputs(self)
2556 def get_version_info(self):
2557 """get_version_info(EnvelopePenetrationRestraint self) -> VersionInfo"""
2558 return _IMP_em.EnvelopePenetrationRestraint_get_version_info(self)
2562 """__str__(EnvelopePenetrationRestraint self) -> std::string"""
2563 return _IMP_em.EnvelopePenetrationRestraint___str__(self)
2567 """__repr__(EnvelopePenetrationRestraint self) -> std::string"""
2568 return _IMP_em.EnvelopePenetrationRestraint___repr__(self)
2573 return _object_cast_to_EnvelopePenetrationRestraint(o)
2575 EnvelopePenetrationRestraint_swigregister = _IMP_em.EnvelopePenetrationRestraint_swigregister
2576 EnvelopePenetrationRestraint_swigregister(EnvelopePenetrationRestraint)
2579 """Proxy of C++ IMP::em::PCAFitRestraint class."""
2581 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2583 def __init__(self, *args):
2585 __init__(IMP::em::PCAFitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, float threahold, float max_pca_size_diff, float max_angle_diff, float max_centroid_diff, FloatKey weight_key) -> PCAFitRestraint
2586 __init__(IMP::em::PCAFitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, float threahold, float max_pca_size_diff, float max_angle_diff, float max_centroid_diff) -> PCAFitRestraint
2588 this = _IMP_em.new_PCAFitRestraint(*args)
2590 self.this.append(this)
2591 except __builtin__.Exception:
2594 def do_get_inputs(self):
2595 """do_get_inputs(PCAFitRestraint self) -> IMP::ModelObjectsTemp"""
2596 return _IMP_em.PCAFitRestraint_do_get_inputs(self)
2599 def get_version_info(self):
2600 """get_version_info(PCAFitRestraint self) -> VersionInfo"""
2601 return _IMP_em.PCAFitRestraint_get_version_info(self)
2605 """__str__(PCAFitRestraint self) -> std::string"""
2606 return _IMP_em.PCAFitRestraint___str__(self)
2610 """__repr__(PCAFitRestraint self) -> std::string"""
2611 return _IMP_em.PCAFitRestraint___repr__(self)
2616 return _object_cast_to_PCAFitRestraint(o)
2618 PCAFitRestraint_swigregister = _IMP_em.PCAFitRestraint_swigregister
2619 PCAFitRestraint_swigregister(PCAFitRestraint)
2622 """Proxy of C++ IMP::em::EnvelopeFitRestraint class."""
2624 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2626 def __init__(self, particles, em_map, density_threshold, penetration_threshold):
2627 """__init__(IMP::em::EnvelopeFitRestraint self, IMP::Particles particles, DensityMap em_map, double density_threshold, double penetration_threshold) -> EnvelopeFitRestraint"""
2628 this = _IMP_em.new_EnvelopeFitRestraint(particles, em_map, density_threshold, penetration_threshold)
2630 self.this.append(this)
2631 except __builtin__.Exception:
2634 def get_transformation(self):
2635 """get_transformation(EnvelopeFitRestraint self) -> Transformation3D"""
2636 return _IMP_em.EnvelopeFitRestraint_get_transformation(self)
2639 def apply_transformation(self):
2640 """apply_transformation(EnvelopeFitRestraint self)"""
2641 return _IMP_em.EnvelopeFitRestraint_apply_transformation(self)
2644 def do_get_inputs(self):
2645 """do_get_inputs(EnvelopeFitRestraint self) -> IMP::ModelObjectsTemp"""
2646 return _IMP_em.EnvelopeFitRestraint_do_get_inputs(self)
2649 def get_version_info(self):
2650 """get_version_info(EnvelopeFitRestraint self) -> VersionInfo"""
2651 return _IMP_em.EnvelopeFitRestraint_get_version_info(self)
2655 """__str__(EnvelopeFitRestraint self) -> std::string"""
2656 return _IMP_em.EnvelopeFitRestraint___str__(self)
2660 """__repr__(EnvelopeFitRestraint self) -> std::string"""
2661 return _IMP_em.EnvelopeFitRestraint___repr__(self)
2666 return _object_cast_to_EnvelopeFitRestraint(o)
2668 EnvelopeFitRestraint_swigregister = _IMP_em.EnvelopeFitRestraint_swigregister
2669 EnvelopeFitRestraint_swigregister(EnvelopeFitRestraint)
2675 """Write out principal components to a file in Chimera Marker format"""
2676 eigen_values = pca.get_principal_values()
2677 eigen_vecs = pca.get_principal_components()
2678 centroid = pca.get_centroid()
2680 fh.write(
"<marker_set>\n")
2681 fh.write(
"<!-- PCA with eigen values: (%g,%g,%g) and "
2682 "centroid (%g,%g,%g) -->\n"
2683 % (math.sqrt(eigen_values[0]),
2684 math.sqrt(eigen_values[1]),
2685 math.sqrt(eigen_values[2]),
2686 centroid[0], centroid[1], centroid[2]))
2691 val = math.sqrt(eigen_values[i])
2692 v1 = centroid - val * eigen_vecs[i]
2693 v2 = centroid + val * eigen_vecs[i]
2694 for markerid, v
in ((i*2+1, v1), (i*2+2, v2)):
2695 fh.write(
"<marker id=\"%d\" x=\"%g\" y=\"%g\" z=\"%g\" "
2697 % (markerid, v[0], v[1], v[2], radius))
2699 for i
in range(1, 7, 2):
2700 fh.write(
"<link id1= \"%d\" id2=\"%d\" radius=\"%g\"/>\n"
2702 fh.write(
"</marker_set>\n")
2705 def get_module_version():
2706 """get_module_version() -> std::string const"""
2707 return _IMP_em.get_module_version()
2710 """get_example_path(std::string fname) -> std::string"""
2711 return _IMP_em.get_example_path(fname)
2714 """get_data_path(std::string fname) -> std::string"""
2715 return _IMP_em.get_data_path(fname)
2717 from .
import _version_check
2718 _version_check.check_version(get_module_version())
2719 __version__ = get_module_version()
Float get_threshold_for_approximate_mass(DensityMap *m, Float desired_mass, atom::ProteinDensityReference ref=atom::HARPAZ)
Computes the threshold to consider in an EM map to get a desired mass.
DensityMap * interpolate_map(DensityMap *in_map, double new_spacing)
Return a new map with an updated spacing.
Particles density2particles(DensityMap *dmap, Float threshold, Model *m, int step=1)
Convert a density grid to a set of particles.
algebra::Vector3Ds density2vectors(DensityMap *dmap, Float threshold)
Convert a density grid to a set of vectors.
algebra::BoundingBoxD< 3 > get_bounding_box(const DensityMap *m, Float threshold)
Get the bounding box for a map.
Ints get_numbers_of_particles_outside_of_the_density(DensityMap *dmap, const Particles &ps, const IMP::algebra::Transformation3Ds &transformations, float thr=0.0)
Get numbers of particles (mult transforms) that are outside the density.
Various classes to hold sets of particles.
DensityMap * binarize(DensityMap *orig_map, float threshold, bool reverse=false)
Return a map with 0 for all voxels below the threshold and 1 for those above.
double get_sum(const DensityMap *m1)
Return the sum of all voxels.
SampledDensityMap * particles2binarized_density(const ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
Make CGAL functionality available to IMP.
DensityMap * mask_and_norm(em::DensityMap *dmap, em::DensityMap *mask)
Return a masked density, and normalize the output map within the mask region.
FittingSolutions compute_fitting_scores(const ParticlesTemp &ps, DensityMap *em_map, const algebra::Transformation3Ds &transformations, bool fast_version=false, bool local_score=false, const FloatKey &wei_key=atom::Mass::get_mass_key())
Compute fitting scores for a given set of rigid transformations.
DensityMap * get_threshold_map(const DensityMap *orig_map, float threshold)
Return a map with 0 for all voxels below the threshold.
DensityMap * get_segment_by_masking(DensityMap *map_to_segment, DensityMap *mask, float mas_threshold)
Get a segment of the map covered by another map.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
SampledDensityMap * particles2density(const ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
Resample a set of particles into a density grid.
Composable functors to implement scores via compile-time composition.
Code to compute statistical measures.
algebra::GridD< 3, algebra::DenseGridStorageD< 3, float >, float > get_grid(DensityMap *in_map)
Return a dense grid containing the voxels of the passed density map.
def write_pca_cmm
Write out principal components to a file in Chimera Marker format.
double convolute(const DensityMap *m1, const DensityMap *m2)
Return a convolution between density maps m1 and m2.
Common base class for heavy weight IMP objects.
DensityMap * multiply(const DensityMap *m1, const DensityMap *m2)
Return a density map for which voxel i contains the result of m1[i]*m2[i].
DensityHeader create_density_header(const algebra::BoundingBoxD< 3 > &bb, float spacing)
Create a header from a bounding box in 3D.
Float compute_fitting_score(const ParticlesTemp &ps, DensityMap *em_map, FloatKey wei_key=atom::Mass::get_mass_key())
Compute fitting scores for a given set of rigid transformations.
FittingSolutions local_rigid_fitting_around_point(Particle *p, Refiner *refiner, const FloatKey &weight_key, DensityMap *dmap, const algebra::Vector3D &anchor_centroid, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3, bool fast=false)
Local rigid fitting of a rigid body around a center point.
long get_number_of_particles_outside_of_the_density(DensityMap *dmap, const Particles &ps, const IMP::algebra::Transformation3D &t=IMP::algebra::get_identity_transformation_3d(), float thr=0.0)
Get the number of particles that are outside of the density.
DensityMap * get_max_map(DensityMaps maps)
Return a map where each voxel is the maximum value from the input maps.
DensityMap * create_density_map(const DensityMap *other)
Create a copy of another map.
Store data to be clustered for embedding based algorithms.
Float approximate_molecular_mass(DensityMap *m, Float threshold)
Estimate the molecular mass from a map.
double get_percentage_of_voxels_covered_by_particles(DensityMap *dmap, const Particles &ps, float smoothing_radius=3., const IMP::algebra::Transformation3D &t=IMP::algebra::get_identity_transformation_3d(), float thr=0.0)
Get the number of density voxels that are not covered by particles.
Vector3D get_centroid(const Vector3Ds &ps)
Return the centroid of a set of vectors.
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
FittingSolutions local_rigid_fitting(Particle *p, Refiner *refiner, const FloatKey &weight_key, DensityMap *dmap, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3, bool fast=true)
Local rigid fitting of a rigid body.
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...
SurfaceShellDensityMap * particles2surface(const ParticlesTemp &ps, Float apix, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
Resample a set of particles into a density grid.
FittingSolutions local_rigid_fitting_around_points(Particle *p, Refiner *refiner, const FloatKey &wei_key, DensityMap *dmap, const algebra::Vector3Ds &anchor_centroids, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3)
Local rigid fitting of a rigid body around a set of center points.
FittingSolutions local_rigid_fitting_grid_search(const ParticlesTemp &ps, const FloatKey &wei_key, DensityMap *dmap, Int max_voxels_translation=2, Int translation_step=1, Float max_angle_in_radians=0.174, Int number_of_rotations=100)
Local grid search rigid fitting.
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.
Float get_molecular_mass_at_threshold(DensityMap *m, Float threshold, atom::ProteinDensityReference ref=atom::HARPAZ)
Compute an approximate molecular mass.
DensityMap * get_segment(DensityMap *map_to_segment, int nx_start, int nx_end, int ny_start, int ny_end, int nz_start, int nz_end)
Get a segment of the map according to xyz indexes.
Float get_threshold_for_approximate_volume(DensityMap *m, Float desired_volume)
Computes the threshold consider in an EM map to get a desired volume.
Float get_volume_at_threshold(DensityMap *m, Float threshold)
Compute an approximate volume.
A restraint is a term in an IMP ScoringFunction.