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_NUMPY = _IMP_em.IMP_KERNEL_HAS_NUMPY
239 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_em.IMP_KERNEL_HAS_GPERFTOOLS
240 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
241 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
242 IMPKERNEL_SHOW_WARNINGS = _IMP_em.IMPKERNEL_SHOW_WARNINGS
245 class _DirectorObjects(object):
246 """@internal Simple class to keep references to director objects
247 to prevent premature deletion."""
250 def register(self, obj):
251 """Take a reference to a director object; will only work for
252 refcounted C++ classes"""
253 if hasattr(obj,
'get_ref_count'):
254 self._objects.append(obj)
256 """Only drop our reference and allow cleanup by Python if no other
257 Python references exist (we hold 3 references: one in self._objects,
258 one in x, and one in the argument list for getrefcount) *and* no
259 other C++ references exist (the Python object always holds one)"""
260 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
261 or x.get_ref_count() > 1]
265 def get_object_count(self):
266 """Get number of director objects (useful for testing only)"""
267 return len(self._objects)
268 _director_objects = _DirectorObjects()
270 class _ostream(object):
271 """Proxy of C++ std::ostream class."""
273 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
275 def __init__(self, *args, **kwargs):
276 raise AttributeError(
"No constructor defined")
277 __repr__ = _swig_repr
279 def write(self, osa_buf):
280 """write(_ostream self, char const * osa_buf)"""
281 return _IMP_em._ostream_write(self, osa_buf)
283 _ostream_swigregister = _IMP_em._ostream_swigregister
284 _ostream_swigregister(_ostream)
286 IMP_COMPILER_HAS_OVERRIDE = _IMP_em.IMP_COMPILER_HAS_OVERRIDE
287 IMP_COMPILER_HAS_FINAL = _IMP_em.IMP_COMPILER_HAS_FINAL
288 IMP_HAS_NOEXCEPT = _IMP_em.IMP_HAS_NOEXCEPT
289 IMP_C_OPEN_BINARY = _IMP_em.IMP_C_OPEN_BINARY
291 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CGAL_HAS_BOOST_FILESYSTEM
292 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
293 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_em.IMP_CGAL_HAS_BOOST_RANDOM
294 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_em.IMP_CGAL_HAS_BOOST_SYSTEM
295 IMP_CGAL_HAS_NUMPY = _IMP_em.IMP_CGAL_HAS_NUMPY
296 IMPCGAL_SHOW_WARNINGS = _IMP_em.IMPCGAL_SHOW_WARNINGS
298 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_em.IMP_ALGEBRA_HAS_IMP_CGAL
299 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
300 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
301 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_RANDOM
302 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_SYSTEM
303 IMP_ALGEBRA_HAS_CGAL = _IMP_em.IMP_ALGEBRA_HAS_CGAL
304 IMP_ALGEBRA_HAS_NUMPY = _IMP_em.IMP_ALGEBRA_HAS_NUMPY
305 IMP_ALGEBRA_HAS_ANN = _IMP_em.IMP_ALGEBRA_HAS_ANN
306 IMPALGEBRA_SHOW_WARNINGS = _IMP_em.IMPALGEBRA_SHOW_WARNINGS
308 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_em.IMP_DISPLAY_HAS_IMP_CGAL
309 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
310 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
311 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_em.IMP_DISPLAY_HAS_BOOST_RANDOM
312 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_em.IMP_DISPLAY_HAS_BOOST_SYSTEM
313 IMP_DISPLAY_HAS_CGAL = _IMP_em.IMP_DISPLAY_HAS_CGAL
314 IMP_DISPLAY_HAS_NUMPY = _IMP_em.IMP_DISPLAY_HAS_NUMPY
315 IMPDISPLAY_SHOW_WARNINGS = _IMP_em.IMPDISPLAY_SHOW_WARNINGS
317 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_em.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
318 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
319 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
320 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
321 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
322 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_em.IMP_SCORE_FUNCTOR_HAS_CGAL
323 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_em.IMP_SCORE_FUNCTOR_HAS_HDF5
324 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_em.IMP_SCORE_FUNCTOR_HAS_NUMPY
325 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_em.IMPSCOREFUNCTOR_SHOW_WARNINGS
327 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_em.IMP_STATISTICS_HAS_IMP_CGAL
328 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
329 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
330 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_em.IMP_STATISTICS_HAS_BOOST_RANDOM
331 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_SYSTEM
332 IMP_STATISTICS_HAS_CGAL = _IMP_em.IMP_STATISTICS_HAS_CGAL
333 IMP_STATISTICS_HAS_NUMPY = _IMP_em.IMP_STATISTICS_HAS_NUMPY
334 IMPSTATISTICS_SHOW_WARNINGS = _IMP_em.IMPSTATISTICS_SHOW_WARNINGS
336 IMP_CORE_HAS_IMP_CGAL = _IMP_em.IMP_CORE_HAS_IMP_CGAL
337 IMP_CORE_HAS_IMP_KERNEL = _IMP_em.IMP_CORE_HAS_IMP_KERNEL
338 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_FILESYSTEM
339 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
340 IMP_CORE_HAS_BOOST_RANDOM = _IMP_em.IMP_CORE_HAS_BOOST_RANDOM
341 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_SYSTEM
342 IMP_CORE_HAS_CGAL = _IMP_em.IMP_CORE_HAS_CGAL
343 IMP_CORE_HAS_HDF5 = _IMP_em.IMP_CORE_HAS_HDF5
344 IMP_CORE_HAS_NUMPY = _IMP_em.IMP_CORE_HAS_NUMPY
345 IMPCORE_SHOW_WARNINGS = _IMP_em.IMPCORE_SHOW_WARNINGS
347 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_em.IMP_CONTAINER_HAS_IMP_ALGEBRA
348 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_em.IMP_CONTAINER_HAS_IMP_CGAL
349 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_em.IMP_CONTAINER_HAS_IMP_DISPLAY
350 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_em.IMP_CONTAINER_HAS_IMP_KERNEL
351 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
352 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
353 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
354 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_em.IMP_CONTAINER_HAS_BOOST_RANDOM
355 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_SYSTEM
356 IMP_CONTAINER_HAS_CGAL = _IMP_em.IMP_CONTAINER_HAS_CGAL
357 IMP_CONTAINER_HAS_HDF5 = _IMP_em.IMP_CONTAINER_HAS_HDF5
358 IMP_CONTAINER_HAS_NUMPY = _IMP_em.IMP_CONTAINER_HAS_NUMPY
359 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_em.IMP_CONTAINER_HAS_PYTHON_IHM
360 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_em.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
361 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_em.IMP_CONTAINER_HAS_ROBIN_MAP
362 IMPCONTAINER_SHOW_WARNINGS = _IMP_em.IMPCONTAINER_SHOW_WARNINGS
364 IMP_ATOM_HAS_IMP_CGAL = _IMP_em.IMP_ATOM_HAS_IMP_CGAL
365 IMP_ATOM_HAS_IMP_KERNEL = _IMP_em.IMP_ATOM_HAS_IMP_KERNEL
366 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
367 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
368 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_em.IMP_ATOM_HAS_BOOST_RANDOM
369 IMP_ATOM_HAS_BOOST_REGEX = _IMP_em.IMP_ATOM_HAS_BOOST_REGEX
370 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_em.IMP_ATOM_HAS_BOOST_SYSTEM
371 IMP_ATOM_HAS_CGAL = _IMP_em.IMP_ATOM_HAS_CGAL
372 IMP_ATOM_HAS_HDF5 = _IMP_em.IMP_ATOM_HAS_HDF5
373 IMP_ATOM_HAS_NUMPY = _IMP_em.IMP_ATOM_HAS_NUMPY
374 IMP_ATOM_HAS_PYTHON_IHM = _IMP_em.IMP_ATOM_HAS_PYTHON_IHM
375 IMPATOM_SHOW_WARNINGS = _IMP_em.IMPATOM_SHOW_WARNINGS
376 IMP_ATOM_TYPE_INDEX = _IMP_em.IMP_ATOM_TYPE_INDEX
377 IMP_RESIDUE_TYPE_INDEX = _IMP_em.IMP_RESIDUE_TYPE_INDEX
378 IMP_HIERARCHY_TYPE_INDEX = _IMP_em.IMP_HIERARCHY_TYPE_INDEX
379 IMP_CHAIN_TYPE_INDEX = _IMP_em.IMP_CHAIN_TYPE_INDEX
381 IMP_EM_HAS_IMP_CGAL = _IMP_em.IMP_EM_HAS_IMP_CGAL
382 IMP_EM_HAS_IMP_CONTAINER = _IMP_em.IMP_EM_HAS_IMP_CONTAINER
383 IMP_EM_HAS_IMP_DISPLAY = _IMP_em.IMP_EM_HAS_IMP_DISPLAY
384 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_EM_HAS_IMP_SCORE_FUNCTOR
385 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_EM_HAS_BOOST_FILESYSTEM
386 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
387 IMP_EM_HAS_BOOST_RANDOM = _IMP_em.IMP_EM_HAS_BOOST_RANDOM
388 IMP_EM_HAS_BOOST_REGEX = _IMP_em.IMP_EM_HAS_BOOST_REGEX
389 IMP_EM_HAS_BOOST_SYSTEM = _IMP_em.IMP_EM_HAS_BOOST_SYSTEM
390 IMP_EM_HAS_CGAL = _IMP_em.IMP_EM_HAS_CGAL
391 IMP_EM_HAS_HDF5 = _IMP_em.IMP_EM_HAS_HDF5
392 IMP_EM_HAS_NUMPY = _IMP_em.IMP_EM_HAS_NUMPY
393 IMP_EM_HAS_PYTHON_IHM = _IMP_em.IMP_EM_HAS_PYTHON_IHM
394 IMPEM_SHOW_WARNINGS = _IMP_em.IMPEM_SHOW_WARNINGS
396 _object_types.append(
"DensityMap")
399 def _object_cast_to_DensityMap(o):
400 """_object_cast_to_DensityMap(Object o) -> DensityMap"""
401 return _IMP_em._object_cast_to_DensityMap(o)
403 _object_types.append(
"SampledDensityMap")
406 def _object_cast_to_SampledDensityMap(o):
407 """_object_cast_to_SampledDensityMap(Object o) -> SampledDensityMap"""
408 return _IMP_em._object_cast_to_SampledDensityMap(o)
410 _object_types.append(
"SurfaceShellDensityMap")
413 def _object_cast_to_SurfaceShellDensityMap(o):
414 """_object_cast_to_SurfaceShellDensityMap(Object o) -> SurfaceShellDensityMap"""
415 return _IMP_em._object_cast_to_SurfaceShellDensityMap(o)
417 _object_types.append(
"FitRestraint")
420 def _object_cast_to_FitRestraint(o):
421 """_object_cast_to_FitRestraint(Object o) -> FitRestraint"""
422 return _IMP_em._object_cast_to_FitRestraint(o)
424 _object_types.append(
"PCAFitRestraint")
427 def _object_cast_to_PCAFitRestraint(o):
428 """_object_cast_to_PCAFitRestraint(Object o) -> PCAFitRestraint"""
429 return _IMP_em._object_cast_to_PCAFitRestraint(o)
431 _object_types.append(
"EnvelopePenetrationRestraint")
434 def _object_cast_to_EnvelopePenetrationRestraint(o):
435 """_object_cast_to_EnvelopePenetrationRestraint(Object o) -> EnvelopePenetrationRestraint"""
436 return _IMP_em._object_cast_to_EnvelopePenetrationRestraint(o)
438 _object_types.append(
"EnvelopeFitRestraint")
441 def _object_cast_to_EnvelopeFitRestraint(o):
442 """_object_cast_to_EnvelopeFitRestraint(Object o) -> EnvelopeFitRestraint"""
443 return _IMP_em._object_cast_to_EnvelopeFitRestraint(o)
445 KernelParametersList=list
446 _plural_types.append(
"KernelParametersList")
447 _value_types.append(
"KernelParameters")
450 _object_types.append(
"HighDensityEmbedding")
453 def _object_cast_to_HighDensityEmbedding(o):
454 """_object_cast_to_HighDensityEmbedding(Object o) -> HighDensityEmbedding"""
455 return _IMP_em._object_cast_to_HighDensityEmbedding(o)
457 _object_types.append(
"MapReaderWriter")
460 def _object_cast_to_MapReaderWriter(o):
461 """_object_cast_to_MapReaderWriter(Object o) -> MapReaderWriter"""
462 return _IMP_em._object_cast_to_MapReaderWriter(o)
464 _object_types.append(
"MRCReaderWriter")
467 def _object_cast_to_MRCReaderWriter(o):
468 """_object_cast_to_MRCReaderWriter(Object o) -> MRCReaderWriter"""
469 return _IMP_em._object_cast_to_MRCReaderWriter(o)
471 _object_types.append(
"SpiderMapReaderWriter")
474 def _object_cast_to_SpiderMapReaderWriter(o):
475 """_object_cast_to_SpiderMapReaderWriter(Object o) -> SpiderMapReaderWriter"""
476 return _IMP_em._object_cast_to_SpiderMapReaderWriter(o)
478 _object_types.append(
"EMReaderWriter")
481 def _object_cast_to_EMReaderWriter(o):
482 """_object_cast_to_EMReaderWriter(Object o) -> EMReaderWriter"""
483 return _IMP_em._object_cast_to_EMReaderWriter(o)
485 _object_types.append(
"XplorReaderWriter")
488 def _object_cast_to_XplorReaderWriter(o):
489 """_object_cast_to_XplorReaderWriter(Object o) -> XplorReaderWriter"""
490 return _IMP_em._object_cast_to_XplorReaderWriter(o)
492 _object_types.append(
"CoarseCC")
495 def _object_cast_to_CoarseCC(o):
496 """_object_cast_to_CoarseCC(Object o) -> CoarseCC"""
497 return _IMP_em._object_cast_to_CoarseCC(o)
499 _object_types.append(
"CoarseCCatIntervals")
502 def _object_cast_to_CoarseCCatIntervals(o):
503 """_object_cast_to_CoarseCCatIntervals(Object o) -> CoarseCCatIntervals"""
504 return _IMP_em._object_cast_to_CoarseCCatIntervals(o)
506 FittingSolutionsList=list
507 _plural_types.append(
"FittingSolutionsList")
508 _value_types.append(
"FittingSolutions")
511 _object_types.append(
"MapDistanceTransform")
514 def _object_cast_to_MapDistanceTransform(o):
515 """_object_cast_to_MapDistanceTransform(Object o) -> MapDistanceTransform"""
516 return _IMP_em._object_cast_to_MapDistanceTransform(o)
518 _object_types.append(
"EnvelopeScore")
521 def _object_cast_to_EnvelopeScore(o):
522 """_object_cast_to_EnvelopeScore(Object o) -> EnvelopeScore"""
523 return _IMP_em._object_cast_to_EnvelopeScore(o)
525 """Proxy of C++ IMP::em::MapReaderWriter class."""
527 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
530 """__init__(IMP::em::MapReaderWriter self) -> MapReaderWriter"""
531 this = _IMP_em.new_MapReaderWriter()
533 self.this.append(this)
534 except __builtin__.Exception:
537 def get_version_info(self):
538 """get_version_info(MapReaderWriter self) -> VersionInfo"""
539 return _IMP_em.MapReaderWriter_get_version_info(self)
543 """__str__(MapReaderWriter self) -> std::string"""
544 return _IMP_em.MapReaderWriter___str__(self)
548 """__repr__(MapReaderWriter self) -> std::string"""
549 return _IMP_em.MapReaderWriter___repr__(self)
554 return _object_cast_to_MapReaderWriter(o)
556 MapReaderWriter_swigregister = _IMP_em.MapReaderWriter_swigregister
557 MapReaderWriter_swigregister(MapReaderWriter)
561 class DensityHeader(object):
562 """Proxy of C++ IMP::em::DensityHeader class."""
564 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
565 __repr__ = _swig_repr
568 """__init__(IMP::em::DensityHeader self) -> DensityHeader"""
569 this = _IMP_em.new_DensityHeader()
571 self.this.append(this)
572 except __builtin__.Exception:
575 def get_top(self, ind):
576 """get_top(DensityHeader self, int ind) -> IMP::em::emreal"""
577 return _IMP_em.DensityHeader_get_top(self, ind)
580 def compute_xyz_top(self, force=False):
582 compute_xyz_top(DensityHeader self, bool force=False)
583 compute_xyz_top(DensityHeader self)
585 return _IMP_em.DensityHeader_compute_xyz_top(self, force)
588 def update_map_dimensions(self, nnx, nny, nnz):
589 """update_map_dimensions(DensityHeader self, int nnx, int nny, int nnz)"""
590 return _IMP_em.DensityHeader_update_map_dimensions(self, nnx, nny, nnz)
593 def update_cell_dimensions(self):
594 """update_cell_dimensions(DensityHeader self)"""
595 return _IMP_em.DensityHeader_update_cell_dimensions(self)
598 def show(self, *args):
600 show(DensityHeader self, _ostream out)
601 show(DensityHeader self)
603 return _IMP_em.DensityHeader_show(self, *args)
605 MAP_FIELD_SIZE = _IMP_em.DensityHeader_MAP_FIELD_SIZE
606 USER_FIELD_SIZE = _IMP_em.DensityHeader_USER_FIELD_SIZE
607 COMMENT_FIELD_NUM_OF = _IMP_em.DensityHeader_COMMENT_FIELD_NUM_OF
608 COMMENT_FIELD_SINGLE_SIZE = _IMP_em.DensityHeader_COMMENT_FIELD_SINGLE_SIZE
609 nxstart = _swig_property(_IMP_em.DensityHeader_nxstart_get, _IMP_em.DensityHeader_nxstart_set)
610 nystart = _swig_property(_IMP_em.DensityHeader_nystart_get, _IMP_em.DensityHeader_nystart_set)
611 nzstart = _swig_property(_IMP_em.DensityHeader_nzstart_get, _IMP_em.DensityHeader_nzstart_set)
612 mx = _swig_property(_IMP_em.DensityHeader_mx_get, _IMP_em.DensityHeader_mx_set)
613 my = _swig_property(_IMP_em.DensityHeader_my_get, _IMP_em.DensityHeader_my_set)
614 mz = _swig_property(_IMP_em.DensityHeader_mz_get, _IMP_em.DensityHeader_mz_set)
615 xlen = _swig_property(_IMP_em.DensityHeader_xlen_get, _IMP_em.DensityHeader_xlen_set)
616 ylen = _swig_property(_IMP_em.DensityHeader_ylen_get, _IMP_em.DensityHeader_ylen_set)
617 zlen = _swig_property(_IMP_em.DensityHeader_zlen_get, _IMP_em.DensityHeader_zlen_set)
618 alpha = _swig_property(_IMP_em.DensityHeader_alpha_get, _IMP_em.DensityHeader_alpha_set)
619 beta = _swig_property(_IMP_em.DensityHeader_beta_get, _IMP_em.DensityHeader_beta_set)
620 gamma = _swig_property(_IMP_em.DensityHeader_gamma_get, _IMP_em.DensityHeader_gamma_set)
621 mapc = _swig_property(_IMP_em.DensityHeader_mapc_get, _IMP_em.DensityHeader_mapc_set)
622 mapr = _swig_property(_IMP_em.DensityHeader_mapr_get, _IMP_em.DensityHeader_mapr_set)
623 maps = _swig_property(_IMP_em.DensityHeader_maps_get, _IMP_em.DensityHeader_maps_set)
624 dmin = _swig_property(_IMP_em.DensityHeader_dmin_get, _IMP_em.DensityHeader_dmin_set)
625 dmax = _swig_property(_IMP_em.DensityHeader_dmax_get, _IMP_em.DensityHeader_dmax_set)
626 dmean = _swig_property(_IMP_em.DensityHeader_dmean_get, _IMP_em.DensityHeader_dmean_set)
627 ispg = _swig_property(_IMP_em.DensityHeader_ispg_get, _IMP_em.DensityHeader_ispg_set)
628 nsymbt = _swig_property(_IMP_em.DensityHeader_nsymbt_get, _IMP_em.DensityHeader_nsymbt_set)
629 user = _swig_property(_IMP_em.DensityHeader_user_get, _IMP_em.DensityHeader_user_set)
630 map = _swig_property(_IMP_em.DensityHeader_map_get, _IMP_em.DensityHeader_map_set)
631 machinestamp = _swig_property(_IMP_em.DensityHeader_machinestamp_get, _IMP_em.DensityHeader_machinestamp_set)
632 rms = _swig_property(_IMP_em.DensityHeader_rms_get, _IMP_em.DensityHeader_rms_set)
633 nlabl = _swig_property(_IMP_em.DensityHeader_nlabl_get, _IMP_em.DensityHeader_nlabl_set)
634 comments = _swig_property(_IMP_em.DensityHeader_comments_get, _IMP_em.DensityHeader_comments_set)
635 magic = _swig_property(_IMP_em.DensityHeader_magic_get, _IMP_em.DensityHeader_magic_set)
636 voltage = _swig_property(_IMP_em.DensityHeader_voltage_get, _IMP_em.DensityHeader_voltage_set)
637 Cs = _swig_property(_IMP_em.DensityHeader_Cs_get, _IMP_em.DensityHeader_Cs_set)
638 Aperture = _swig_property(_IMP_em.DensityHeader_Aperture_get, _IMP_em.DensityHeader_Aperture_set)
639 Magnification = _swig_property(_IMP_em.DensityHeader_Magnification_get, _IMP_em.DensityHeader_Magnification_set)
640 Postmagnification = _swig_property(_IMP_em.DensityHeader_Postmagnification_get, _IMP_em.DensityHeader_Postmagnification_set)
641 Exposuretime = _swig_property(_IMP_em.DensityHeader_Exposuretime_get, _IMP_em.DensityHeader_Exposuretime_set)
642 Microscope = _swig_property(_IMP_em.DensityHeader_Microscope_get, _IMP_em.DensityHeader_Microscope_set)
643 Pixelsize = _swig_property(_IMP_em.DensityHeader_Pixelsize_get, _IMP_em.DensityHeader_Pixelsize_set)
644 CCDArea = _swig_property(_IMP_em.DensityHeader_CCDArea_get, _IMP_em.DensityHeader_CCDArea_set)
645 Defocus = _swig_property(_IMP_em.DensityHeader_Defocus_get, _IMP_em.DensityHeader_Defocus_set)
646 Astigmatism = _swig_property(_IMP_em.DensityHeader_Astigmatism_get, _IMP_em.DensityHeader_Astigmatism_set)
647 AstigmatismAngle = _swig_property(_IMP_em.DensityHeader_AstigmatismAngle_get, _IMP_em.DensityHeader_AstigmatismAngle_set)
648 FocusIncrement = _swig_property(_IMP_em.DensityHeader_FocusIncrement_get, _IMP_em.DensityHeader_FocusIncrement_set)
649 CountsPerElectron = _swig_property(_IMP_em.DensityHeader_CountsPerElectron_get, _IMP_em.DensityHeader_CountsPerElectron_set)
650 Intensity = _swig_property(_IMP_em.DensityHeader_Intensity_get, _IMP_em.DensityHeader_Intensity_set)
651 EnergySlitwidth = _swig_property(_IMP_em.DensityHeader_EnergySlitwidth_get, _IMP_em.DensityHeader_EnergySlitwidth_set)
652 EnergyOffset = _swig_property(_IMP_em.DensityHeader_EnergyOffset_get, _IMP_em.DensityHeader_EnergyOffset_set)
653 Tiltangle = _swig_property(_IMP_em.DensityHeader_Tiltangle_get, _IMP_em.DensityHeader_Tiltangle_set)
654 Tiltaxis = _swig_property(_IMP_em.DensityHeader_Tiltaxis_get, _IMP_em.DensityHeader_Tiltaxis_set)
655 MarkerX = _swig_property(_IMP_em.DensityHeader_MarkerX_get, _IMP_em.DensityHeader_MarkerX_set)
656 MarkerY = _swig_property(_IMP_em.DensityHeader_MarkerY_get, _IMP_em.DensityHeader_MarkerY_set)
657 lswap = _swig_property(_IMP_em.DensityHeader_lswap_get, _IMP_em.DensityHeader_lswap_set)
660 """get_resolution(DensityHeader self) -> float"""
661 return _IMP_em.DensityHeader_get_resolution(self)
664 def get_has_resolution(self):
665 """get_has_resolution(DensityHeader self) -> bool"""
666 return _IMP_em.DensityHeader_get_has_resolution(self)
669 def set_resolution(self, resolution):
670 """set_resolution(DensityHeader self, float resolution)"""
671 return _IMP_em.DensityHeader_set_resolution(self, resolution)
674 def get_spacing(self):
675 """get_spacing(DensityHeader self) -> float"""
676 return _IMP_em.DensityHeader_get_spacing(self)
679 def get_xorigin(self):
680 """get_xorigin(DensityHeader self) -> float"""
681 return _IMP_em.DensityHeader_get_xorigin(self)
684 def get_yorigin(self):
685 """get_yorigin(DensityHeader self) -> float"""
686 return _IMP_em.DensityHeader_get_yorigin(self)
689 def get_zorigin(self):
690 """get_zorigin(DensityHeader self) -> float"""
691 return _IMP_em.DensityHeader_get_zorigin(self)
694 def get_origin(self, i):
695 """get_origin(DensityHeader self, int i) -> float"""
696 return _IMP_em.DensityHeader_get_origin(self, i)
699 def set_xorigin(self, x):
700 """set_xorigin(DensityHeader self, float x)"""
701 return _IMP_em.DensityHeader_set_xorigin(self, x)
704 def set_yorigin(self, y):
705 """set_yorigin(DensityHeader self, float y)"""
706 return _IMP_em.DensityHeader_set_yorigin(self, y)
709 def set_zorigin(self, z):
710 """set_zorigin(DensityHeader self, float z)"""
711 return _IMP_em.DensityHeader_set_zorigin(self, z)
714 def is_top_calculated(self):
715 """is_top_calculated(DensityHeader self) -> bool"""
716 return _IMP_em.DensityHeader_is_top_calculated(self)
718 Objectpixelsize_ = _swig_property(_IMP_em.DensityHeader_Objectpixelsize__get, _IMP_em.DensityHeader_Objectpixelsize__set)
721 """get_nx(DensityHeader self) -> int"""
722 return _IMP_em.DensityHeader_get_nx(self)
726 """get_ny(DensityHeader self) -> int"""
727 return _IMP_em.DensityHeader_get_ny(self)
731 """get_nz(DensityHeader self) -> int"""
732 return _IMP_em.DensityHeader_get_nz(self)
735 def get_number_of_voxels(self):
736 """get_number_of_voxels(DensityHeader self) -> int"""
737 return _IMP_em.DensityHeader_get_number_of_voxels(self)
740 def get_data_type(self):
741 """get_data_type(DensityHeader self) -> int"""
742 return _IMP_em.DensityHeader_get_data_type(self)
745 def set_data_type(self, data_type):
746 """set_data_type(DensityHeader self, int data_type)"""
747 return _IMP_em.DensityHeader_set_data_type(self, data_type)
749 __swig_destroy__ = _IMP_em.delete_DensityHeader
750 __del__ =
lambda self:
None
751 DensityHeader_swigregister = _IMP_em.DensityHeader_swigregister
752 DensityHeader_swigregister(DensityHeader)
756 """create_density_header(BoundingBox3D bb, float spacing) -> DensityHeader"""
757 return _IMP_em.create_density_header(bb, spacing)
761 read_map(std::string filename, MapReaderWriter reader) -> DensityMap
762 read_map(std::string filename) -> DensityMap
764 return _IMP_em.read_map(*args)
766 def write_map(*args):
768 write_map(DensityMap m, std::string filename, MapReaderWriter writer)
769 write_map(DensityMap m, std::string filename)
771 return _IMP_em.write_map(*args)
774 """approximate_molecular_mass(DensityMap m, IMP::Float threshold) -> IMP::Float"""
775 return _IMP_em.approximate_molecular_mass(m, threshold)
777 """Proxy of C++ IMP::em::DensityMap class."""
779 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
781 def __init__(self, *args):
783 __init__(IMP::em::DensityMap self, std::string name) -> DensityMap
784 __init__(IMP::em::DensityMap self) -> DensityMap
785 __init__(IMP::em::DensityMap self, DensityHeader header, std::string name) -> DensityMap
786 __init__(IMP::em::DensityMap self, DensityHeader header) -> DensityMap
788 this = _IMP_em.new_DensityMap(*args)
790 self.this.append(this)
791 except __builtin__.Exception:
794 def reset_data(self, value=0.0):
796 reset_data(DensityMap self, float value=0.0)
797 reset_data(DensityMap self)
799 return _IMP_em.DensityMap_reset_data(self, value)
803 """calcRMS(DensityMap self) -> IMP::em::emreal"""
804 return _IMP_em.DensityMap_calcRMS(self)
807 def std_normalize(self):
808 """std_normalize(DensityMap self)"""
809 return _IMP_em.DensityMap_std_normalize(self)
812 def is_normalized(self):
813 """is_normalized(DensityMap self) -> bool"""
814 return _IMP_em.DensityMap_is_normalized(self)
817 def get_location_in_dim_by_voxel(self, index, dim):
818 """get_location_in_dim_by_voxel(DensityMap self, long index, int dim) -> float"""
819 return _IMP_em.DensityMap_get_location_in_dim_by_voxel(self, index, dim)
822 def xyz_ind2voxel(self, x, y, z):
823 """xyz_ind2voxel(DensityMap self, int x, int y, int z) -> long"""
824 return _IMP_em.DensityMap_xyz_ind2voxel(self, x, y, z)
827 def get_voxel_by_location(self, *args):
829 get_voxel_by_location(DensityMap self, float x, float y, float z) -> long
830 get_voxel_by_location(DensityMap self, Vector3D v) -> long
832 return _IMP_em.DensityMap_get_voxel_by_location(self, *args)
835 def get_location_by_voxel(self, index):
836 """get_location_by_voxel(DensityMap self, long index) -> Vector3D"""
837 return _IMP_em.DensityMap_get_location_by_voxel(self, index)
840 def is_xyz_ind_part_of_volume(self, ix, iy, iz):
841 """is_xyz_ind_part_of_volume(DensityMap self, int ix, int iy, int iz) -> bool"""
842 return _IMP_em.DensityMap_is_xyz_ind_part_of_volume(self, ix, iy, iz)
845 def is_part_of_volume(self, *args):
847 is_part_of_volume(DensityMap self, float x, float y, float z) -> bool
848 is_part_of_volume(DensityMap self, Vector3D v) -> bool
850 return _IMP_em.DensityMap_is_part_of_volume(self, *args)
853 def get_value(self, *args):
855 get_value(DensityMap self, float x, float y, float z) -> IMP::em::emreal
856 get_value(DensityMap self, Vector3D point) -> IMP::em::emreal
857 get_value(DensityMap self, long index) -> IMP::em::emreal
859 return _IMP_em.DensityMap_get_value(self, *args)
862 def set_value(self, *args):
864 set_value(DensityMap self, long index, IMP::em::emreal value)
865 set_value(DensityMap self, float x, float y, float z, IMP::em::emreal value)
867 return _IMP_em.DensityMap_set_value(self, *args)
870 def set_origin(self, *args):
872 set_origin(DensityMap self, float x, float y, float z)
873 set_origin(DensityMap self, Vector3D v)
875 return _IMP_em.DensityMap_set_origin(self, *args)
878 def get_origin(self):
879 """get_origin(DensityMap self) -> Vector3D"""
880 return _IMP_em.DensityMap_get_origin(self)
884 """get_top(DensityMap self) -> Vector3D"""
885 return _IMP_em.DensityMap_get_top(self)
888 def get_header(self):
889 h = _IMP_em.DensityMap_get_header(self)
895 def get_header_writable(self):
896 h = _IMP_em.DensityMap_get_header_writable(self)
902 def same_origin(self, other):
903 """same_origin(DensityMap self, DensityMap other) -> bool"""
904 return _IMP_em.DensityMap_same_origin(self, other)
907 def same_dimensions(self, other):
908 """same_dimensions(DensityMap self, DensityMap other) -> bool"""
909 return _IMP_em.DensityMap_same_dimensions(self, other)
912 def same_voxel_size(self, other):
913 """same_voxel_size(DensityMap self, DensityMap other) -> bool"""
914 return _IMP_em.DensityMap_same_voxel_size(self, other)
919 get_centroid(DensityMap self, IMP::em::emreal threshold=0.0) -> Vector3D
920 get_centroid(DensityMap self) -> Vector3D
922 return _IMP_em.DensityMap_get_centroid(self, threshold)
925 def get_max_value(self):
926 """get_max_value(DensityMap self) -> IMP::em::emreal"""
927 return _IMP_em.DensityMap_get_max_value(self)
930 def get_min_value(self):
931 """get_min_value(DensityMap self) -> IMP::em::emreal"""
932 return _IMP_em.DensityMap_get_min_value(self)
935 def add(self, *args):
937 add(DensityMap self, DensityMap other)
938 add(DensityMap self, IMP::Float d)
940 return _IMP_em.DensityMap_add(self, *args)
943 def pick_max(self, other):
944 """pick_max(DensityMap self, DensityMap other)"""
945 return _IMP_em.DensityMap_pick_max(self, other)
948 def get_number_of_voxels(self):
949 """get_number_of_voxels(DensityMap self) -> long"""
950 return _IMP_em.DensityMap_get_number_of_voxels(self)
953 def set_void_map(self, nx, ny, nz):
954 """set_void_map(DensityMap self, int nx, int ny, int nz)"""
955 return _IMP_em.DensityMap_set_void_map(self, nx, ny, nz)
958 def pad(self, nx, ny, nz, val=0.0):
960 pad(DensityMap self, int nx, int ny, int nz, float val=0.0)
961 pad(DensityMap self, int nx, int ny, int nz)
963 return _IMP_em.DensityMap_pad(self, nx, ny, nz, val)
966 def pad_margin(self, mrg_x, mrg_y, mrg_z, val=0.0):
968 pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z, float val=0.0) -> DensityMap
969 pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z) -> DensityMap
971 return _IMP_em.DensityMap_pad_margin(self, mrg_x, mrg_y, mrg_z, val)
974 def get_cropped(self, *args):
976 get_cropped(DensityMap self, float threshold) -> DensityMap
977 get_cropped(DensityMap self, BoundingBox3D bb) -> DensityMap
979 return _IMP_em.DensityMap_get_cropped(self, *args)
982 def get_maximum_value_in_xy_plane(self, z_ind):
983 """get_maximum_value_in_xy_plane(DensityMap self, int z_ind) -> float"""
984 return _IMP_em.DensityMap_get_maximum_value_in_xy_plane(self, z_ind)
987 def get_maximum_value_in_xz_plane(self, y_ind):
988 """get_maximum_value_in_xz_plane(DensityMap self, int y_ind) -> float"""
989 return _IMP_em.DensityMap_get_maximum_value_in_xz_plane(self, y_ind)
992 def get_maximum_value_in_yz_plane(self, x_ind):
993 """get_maximum_value_in_yz_plane(DensityMap self, int x_ind) -> float"""
994 return _IMP_em.DensityMap_get_maximum_value_in_yz_plane(self, x_ind)
998 """multiply(DensityMap self, float factor)"""
999 return _IMP_em.DensityMap_multiply(self, factor)
1002 def get_locations_string(self, t):
1003 """get_locations_string(DensityMap self, float t) -> std::string"""
1004 return _IMP_em.DensityMap_get_locations_string(self, t)
1007 def update_voxel_size(self, new_apix):
1008 """update_voxel_size(DensityMap self, float new_apix)"""
1009 return _IMP_em.DensityMap_update_voxel_size(self, new_apix)
1012 def get_spacing(self):
1013 """get_spacing(DensityMap self) -> IMP::Float"""
1014 return _IMP_em.DensityMap_get_spacing(self)
1017 def calc_all_voxel2loc(self):
1018 """calc_all_voxel2loc(DensityMap self)"""
1019 return _IMP_em.DensityMap_calc_all_voxel2loc(self)
1022 def copy_map(self, other):
1023 """copy_map(DensityMap self, DensityMap other)"""
1024 return _IMP_em.DensityMap_copy_map(self, other)
1027 def get_version_info(self):
1028 """get_version_info(DensityMap self) -> VersionInfo"""
1029 return _IMP_em.DensityMap_get_version_info(self)
1032 def lower_voxel_shift(self, loc, kdist, orig, ndim):
1033 """lower_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
1034 return _IMP_em.DensityMap_lower_voxel_shift(self, loc, kdist, orig, ndim)
1037 def upper_voxel_shift(self, loc, kdist, orig, ndim):
1038 """upper_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
1039 return _IMP_em.DensityMap_upper_voxel_shift(self, loc, kdist, orig, ndim)
1042 def get_rms_calculated(self):
1043 """get_rms_calculated(DensityMap self) -> bool"""
1044 return _IMP_em.DensityMap_get_rms_calculated(self)
1047 def get_dim_index_by_location(self, *args):
1049 get_dim_index_by_location(DensityMap self, Vector3D v, int ind) -> int
1050 get_dim_index_by_location(DensityMap self, float loc_val, int ind) -> int
1052 return _IMP_em.DensityMap_get_dim_index_by_location(self, *args)
1056 """__str__(DensityMap self) -> std::string"""
1057 return _IMP_em.DensityMap___str__(self)
1061 """__repr__(DensityMap self) -> std::string"""
1062 return _IMP_em.DensityMap___repr__(self)
1067 return _object_cast_to_DensityMap(o)
1069 DensityMap_swigregister = _IMP_em.DensityMap_swigregister
1070 DensityMap_swigregister(DensityMap)
1075 get_bounding_box(DensityMap m, IMP::Float threshold) -> BoundingBox3D
1076 get_bounding_box(DensityMap m) -> BoundingBox3D
1078 return _IMP_em.get_bounding_box(*args)
1080 def get_density(m, v):
1081 """get_density(DensityMap m, Vector3D v) -> double"""
1082 return _IMP_em.get_density(m, v)
1084 def get_transformed(*args):
1086 get_transformed(DensityMap input, Transformation3D tr, double threshold) -> DensityMap
1087 get_transformed(DensityMap input, Transformation3D tr) -> DensityMap
1089 return _IMP_em.get_transformed(*args)
1091 def get_resampled(input, scaling):
1092 """get_resampled(DensityMap input, double scaling) -> DensityMap"""
1093 return _IMP_em.get_resampled(input, scaling)
1095 def get_transformed_into(source, tr, into, calc_rms=True):
1097 get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into, bool calc_rms=True)
1098 get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into)
1100 return _IMP_em.get_transformed_into(source, tr, into, calc_rms)
1102 def get_transformed_into2(source, tr, into):
1103 """get_transformed_into2(DensityMap source, Transformation3D tr, DensityMap into)"""
1104 return _IMP_em.get_transformed_into2(source, tr, into)
1106 def get_interiors_intersect(d1, d2):
1107 """get_interiors_intersect(DensityMap d1, DensityMap d2) -> bool"""
1108 return _IMP_em.get_interiors_intersect(d1, d2)
1112 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
1113 get_segment(DensityMap map_to_segment, IMP::algebra::Vector3Ds vecs, float dist) -> DensityMap
1115 return _IMP_em.get_segment(*args)
1118 """get_segment_by_masking(DensityMap map_to_segment, DensityMap mask, float mas_threshold) -> DensityMap"""
1119 return _IMP_em.get_segment_by_masking(map_to_segment, mask, mas_threshold)
1121 def binarize(orig_map, threshold, reverse=False):
1123 binarize(DensityMap orig_map, float threshold, bool reverse=False) -> DensityMap
1124 binarize(DensityMap orig_map, float threshold) -> DensityMap
1126 return _IMP_em.binarize(orig_map, threshold, reverse)
1129 """get_threshold_map(DensityMap orig_map, float threshold) -> DensityMap"""
1130 return _IMP_em.get_threshold_map(orig_map, threshold)
1133 """multiply(DensityMap m1, DensityMap m2) -> DensityMap"""
1134 return _IMP_em.multiply(m1, m2)
1137 """convolute(DensityMap m1, DensityMap m2) -> double"""
1138 return _IMP_em.convolute(m1, m2)
1141 """get_sum(DensityMap m1) -> double"""
1142 return _IMP_em.get_sum(m1)
1145 """get_max_map(IMP::em::DensityMaps maps) -> DensityMap"""
1146 return _IMP_em.get_max_map(maps)
1149 """interpolate_map(DensityMap in_map, double new_spacing) -> DensityMap"""
1150 return _IMP_em.interpolate_map(in_map, new_spacing)
1153 """get_grid(DensityMap in_map) -> IMP::algebra::GridD< 3,IMP::algebra::DenseGridStorageD< 3,float >,float,IMP::algebra::DefaultEmbeddingD< 3 > >"""
1154 return _IMP_em.get_grid(in_map)
1158 create_density_map(DensityMap other) -> DensityMap
1159 create_density_map(BoundingBox3D bb, double spacing) -> DensityMap
1160 create_density_map(int nx, int ny, int nz, double spacing) -> DensityMap
1161 create_density_map(DenseFloatGrid3D grid) -> DensityMap
1162 create_density_map(DenseDoubleGrid3D grid) -> DensityMap
1164 return _IMP_em.create_density_map(*args)
1166 def get_binarized_interior(dmap):
1167 """get_binarized_interior(DensityMap dmap) -> DensityMap"""
1168 return _IMP_em.get_binarized_interior(dmap)
1170 def add_to_map(dm, pis):
1171 """add_to_map(DensityMap dm, IMP::Particles const & pis)"""
1172 return _IMP_em.add_to_map(dm, pis)
1173 class RadiusDependentDistanceMask(object):
1174 """Proxy of C++ IMP::em::RadiusDependentDistanceMask class."""
1176 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1177 __repr__ = _swig_repr
1179 def __init__(self, sampling_radius, header):
1180 """__init__(IMP::em::RadiusDependentDistanceMask self, float sampling_radius, DensityHeader header) -> RadiusDependentDistanceMask"""
1181 this = _IMP_em.new_RadiusDependentDistanceMask(sampling_radius, header)
1183 self.this.append(this)
1184 except __builtin__.Exception:
1187 def get_neighbor_shift(self):
1188 """get_neighbor_shift(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1189 return _IMP_em.RadiusDependentDistanceMask_get_neighbor_shift(self)
1192 def get_neighbor_dist(self):
1193 """get_neighbor_dist(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1194 return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist(self)
1197 def get_neighbor_dist_exp(self):
1198 """get_neighbor_dist_exp(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1199 return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist_exp(self)
1202 def show(self, out):
1203 """show(RadiusDependentDistanceMask self, _ostream out)"""
1204 return _IMP_em.RadiusDependentDistanceMask_show(self, out)
1206 __swig_destroy__ = _IMP_em.delete_RadiusDependentDistanceMask
1207 __del__ =
lambda self:
None
1208 RadiusDependentDistanceMask_swigregister = _IMP_em.RadiusDependentDistanceMask_swigregister
1209 RadiusDependentDistanceMask_swigregister(RadiusDependentDistanceMask)
1211 class DistanceMask(object):
1212 """Proxy of C++ IMP::em::DistanceMask class."""
1214 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1215 __repr__ = _swig_repr
1217 def __init__(self, *args):
1219 __init__(IMP::em::DistanceMask self) -> DistanceMask
1220 __init__(IMP::em::DistanceMask self, DensityHeader header) -> DistanceMask
1222 this = _IMP_em.new_DistanceMask(*args)
1224 self.this.append(this)
1225 except __builtin__.Exception:
1228 def show(self, out):
1229 """show(DistanceMask self, _ostream out)"""
1230 return _IMP_em.DistanceMask_show(self, out)
1233 def is_mask_set(self, radius, eps=0.001):
1235 is_mask_set(DistanceMask self, float radius, float eps=0.001) -> bool
1236 is_mask_set(DistanceMask self, float radius) -> bool
1238 return _IMP_em.DistanceMask_is_mask_set(self, radius, eps)
1240 __swig_destroy__ = _IMP_em.delete_DistanceMask
1241 __del__ =
lambda self:
None
1242 DistanceMask_swigregister = _IMP_em.DistanceMask_swigregister
1243 DistanceMask_swigregister(DistanceMask)
1245 class EMReaderWriter(MapReaderWriter):
1246 """Proxy of C++ IMP::em::EMReaderWriter class."""
1248 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1251 """__str__(EMReaderWriter self) -> std::string"""
1252 return _IMP_em.EMReaderWriter___str__(self)
1256 """__repr__(EMReaderWriter self) -> std::string"""
1257 return _IMP_em.EMReaderWriter___repr__(self)
1262 return _object_cast_to_EMReaderWriter(o)
1266 """__init__(IMP::em::EMReaderWriter self) -> EMReaderWriter"""
1267 this = _IMP_em.new_EMReaderWriter()
1269 self.this.append(this)
1270 except __builtin__.Exception:
1272 EMReaderWriter_swigregister = _IMP_em.EMReaderWriter_swigregister
1273 EMReaderWriter_swigregister(EMReaderWriter)
1275 class XplorReaderWriter(MapReaderWriter):
1276 """Proxy of C++ IMP::em::XplorReaderWriter class."""
1278 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1281 """__str__(XplorReaderWriter self) -> std::string"""
1282 return _IMP_em.XplorReaderWriter___str__(self)
1286 """__repr__(XplorReaderWriter self) -> std::string"""
1287 return _IMP_em.XplorReaderWriter___repr__(self)
1292 return _object_cast_to_XplorReaderWriter(o)
1296 """__init__(IMP::em::XplorReaderWriter self) -> XplorReaderWriter"""
1297 this = _IMP_em.new_XplorReaderWriter()
1299 self.this.append(this)
1300 except __builtin__.Exception:
1302 XplorReaderWriter_swigregister = _IMP_em.XplorReaderWriter_swigregister
1303 XplorReaderWriter_swigregister(XplorReaderWriter)
1305 class MRCReaderWriter(MapReaderWriter):
1306 """Proxy of C++ IMP::em::MRCReaderWriter class."""
1308 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1310 def __init__(self, *args):
1312 __init__(IMP::em::MRCReaderWriter self) -> MRCReaderWriter
1313 __init__(IMP::em::MRCReaderWriter self, std::string fn) -> MRCReaderWriter
1315 this = _IMP_em.new_MRCReaderWriter(*args)
1317 self.this.append(this)
1318 except __builtin__.Exception:
1322 """__str__(MRCReaderWriter self) -> std::string"""
1323 return _IMP_em.MRCReaderWriter___str__(self)
1327 """__repr__(MRCReaderWriter self) -> std::string"""
1328 return _IMP_em.MRCReaderWriter___repr__(self)
1333 return _object_cast_to_MRCReaderWriter(o)
1335 MRCReaderWriter_swigregister = _IMP_em.MRCReaderWriter_swigregister
1336 MRCReaderWriter_swigregister(MRCReaderWriter)
1338 class KernelParameters(object):
1339 """Proxy of C++ IMP::em::KernelParameters class."""
1341 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1343 def __init__(self, *args):
1345 __init__(IMP::em::KernelParameters self) -> KernelParameters
1346 __init__(IMP::em::KernelParameters self, float resolution) -> KernelParameters
1348 this = _IMP_em.new_KernelParameters(*args)
1350 self.this.append(this)
1351 except __builtin__.Exception:
1353 __swig_destroy__ = _IMP_em.delete_KernelParameters
1354 __del__ =
lambda self:
None
1357 """get_rsig(KernelParameters self) -> float"""
1358 return _IMP_em.KernelParameters_get_rsig(self)
1361 def get_rsigsq(self):
1362 """get_rsigsq(KernelParameters self) -> float"""
1363 return _IMP_em.KernelParameters_get_rsigsq(self)
1366 def get_inv_rsigsq(self):
1367 """get_inv_rsigsq(KernelParameters self) -> float"""
1368 return _IMP_em.KernelParameters_get_inv_rsigsq(self)
1371 def get_timessig(self):
1372 """get_timessig(KernelParameters self) -> float"""
1373 return _IMP_em.KernelParameters_get_timessig(self)
1376 def get_sq2pi3(self):
1377 """get_sq2pi3(KernelParameters self) -> float"""
1378 return _IMP_em.KernelParameters_get_sq2pi3(self)
1381 def get_rnormfac(self):
1382 """get_rnormfac(KernelParameters self) -> float"""
1383 return _IMP_em.KernelParameters_get_rnormfac(self)
1386 def get_rkdist(self):
1387 """get_rkdist(KernelParameters self) -> float"""
1388 return _IMP_em.KernelParameters_get_rkdist(self)
1391 def get_rkdistsq(self):
1392 """get_rkdistsq(KernelParameters self) -> float"""
1393 return _IMP_em.KernelParameters_get_rkdistsq(self)
1397 """get_lim(KernelParameters self) -> float"""
1398 return _IMP_em.KernelParameters_get_lim(self)
1401 def show(self, *args):
1403 show(KernelParameters self, _ostream out)
1404 show(KernelParameters self)
1406 return _IMP_em.KernelParameters_show(self, *args)
1410 """__str__(KernelParameters self) -> std::string"""
1411 return _IMP_em.KernelParameters___str__(self)
1415 """__repr__(KernelParameters self) -> std::string"""
1416 return _IMP_em.KernelParameters___repr__(self)
1418 KernelParameters_swigregister = _IMP_em.KernelParameters_swigregister
1419 KernelParameters_swigregister(KernelParameters)
1421 GAUSSIAN = _IMP_em.GAUSSIAN
1422 BINARIZED_SPHERE = _IMP_em.BINARIZED_SPHERE
1423 SPHERE = _IMP_em.SPHERE
1424 class SampledDensityMap(DensityMap):
1425 """Proxy of C++ IMP::em::SampledDensityMap class."""
1427 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1429 def __init__(self, *args):
1431 __init__(IMP::em::SampledDensityMap self, IMP::em::KernelType kt) -> SampledDensityMap
1432 __init__(IMP::em::SampledDensityMap self) -> SampledDensityMap
1433 __init__(IMP::em::SampledDensityMap self, DensityHeader header, IMP::em::KernelType kt) -> SampledDensityMap
1434 __init__(IMP::em::SampledDensityMap self, DensityHeader header) -> SampledDensityMap
1435 __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
1436 __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
1437 __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size, FloatKey mass_key) -> SampledDensityMap
1438 __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size) -> SampledDensityMap
1440 this = _IMP_em.new_SampledDensityMap(*args)
1442 self.this.append(this)
1443 except __builtin__.Exception:
1447 """resample(SampledDensityMap self)"""
1448 return _IMP_em.SampledDensityMap_resample(self)
1451 def project(self, *args):
1453 project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin, Vector3D shift, FloatKey mass_key)
1454 project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin, Vector3D shift)
1455 project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin)
1457 return _IMP_em.SampledDensityMap_project(self, *args)
1460 def set_particles(self, *args):
1462 set_particles(SampledDensityMap self, IMP::ParticlesTemp const & ps, FloatKey mass_key)
1463 set_particles(SampledDensityMap self, IMP::ParticlesTemp const & ps)
1465 return _IMP_em.SampledDensityMap_set_particles(self, *args)
1468 def get_xyzr_particles(self):
1469 """get_xyzr_particles(SampledDensityMap self) -> IMP::core::XYZRs const &"""
1470 return _IMP_em.SampledDensityMap_get_xyzr_particles(self)
1473 def get_sampled_particles(self):
1474 """get_sampled_particles(SampledDensityMap self) -> IMP::Particles const &"""
1475 return _IMP_em.SampledDensityMap_get_sampled_particles(self)
1478 def get_weight_key(self):
1479 """get_weight_key(SampledDensityMap self) -> FloatKey"""
1480 return _IMP_em.SampledDensityMap_get_weight_key(self)
1483 def get_minimum_resampled_value(self):
1484 """get_minimum_resampled_value(SampledDensityMap self) -> float"""
1485 return _IMP_em.SampledDensityMap_get_minimum_resampled_value(self)
1488 def update_resolution(self, res):
1489 """update_resolution(SampledDensityMap self, IMP::Float res)"""
1490 return _IMP_em.SampledDensityMap_update_resolution(self, res)
1492 __swig_destroy__ = _IMP_em.delete_SampledDensityMap
1493 __del__ =
lambda self:
None
1496 """__str__(SampledDensityMap self) -> std::string"""
1497 return _IMP_em.SampledDensityMap___str__(self)
1501 """__repr__(SampledDensityMap self) -> std::string"""
1502 return _IMP_em.SampledDensityMap___repr__(self)
1507 return _object_cast_to_SampledDensityMap(o)
1509 SampledDensityMap_swigregister = _IMP_em.SampledDensityMap_swigregister
1510 SampledDensityMap_swigregister(SampledDensityMap)
1512 IMP_DEFAULT_NUM_SHELLS = _IMP_em.IMP_DEFAULT_NUM_SHELLS
1513 IMP_SIG_CUTOFF = _IMP_em.IMP_SIG_CUTOFF
1514 class SurfaceShellDensityMap(SampledDensityMap):
1515 """Proxy of C++ IMP::em::SurfaceShellDensityMap class."""
1517 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1519 def __init__(self, *args):
1521 __init__(IMP::em::SurfaceShellDensityMap self) -> SurfaceShellDensityMap
1522 __init__(IMP::em::SurfaceShellDensityMap self, DensityHeader header) -> SurfaceShellDensityMap
1523 __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key, int num_shells=5) -> SurfaceShellDensityMap
1524 __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key) -> SurfaceShellDensityMap
1525 __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size) -> SurfaceShellDensityMap
1527 this = _IMP_em.new_SurfaceShellDensityMap(*args)
1529 self.this.append(this)
1530 except __builtin__.Exception:
1534 """binarize(SurfaceShellDensityMap self, float scene_val)"""
1535 return _IMP_em.SurfaceShellDensityMap_binarize(self, scene_val)
1538 def has_background_neighbor(self, voxel_ind):
1539 """has_background_neighbor(SurfaceShellDensityMap self, long voxel_ind) -> bool"""
1540 return _IMP_em.SurfaceShellDensityMap_has_background_neighbor(self, voxel_ind)
1542 __swig_destroy__ = _IMP_em.delete_SurfaceShellDensityMap
1543 __del__ =
lambda self:
None
1546 """__str__(SurfaceShellDensityMap self) -> std::string"""
1547 return _IMP_em.SurfaceShellDensityMap___str__(self)
1551 """__repr__(SurfaceShellDensityMap self) -> std::string"""
1552 return _IMP_em.SurfaceShellDensityMap___repr__(self)
1557 return _object_cast_to_SurfaceShellDensityMap(o)
1559 SurfaceShellDensityMap_swigregister = _IMP_em.SurfaceShellDensityMap_swigregister
1560 SurfaceShellDensityMap_swigregister(SurfaceShellDensityMap)
1563 """Proxy of C++ IMP::em::CoarseCC class."""
1565 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1568 """__init__(IMP::em::CoarseCC self) -> CoarseCC"""
1569 this = _IMP_em.new_CoarseCC()
1571 self.this.append(this)
1572 except __builtin__.Exception:
1575 def calc_score(*args):
1577 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True, IMP::FloatPair norm_factors) -> float
1578 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True) -> float
1579 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1580 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1582 return _IMP_em.CoarseCC_calc_score(*args)
1584 calc_score = staticmethod(calc_score)
1586 def cross_correlation_coefficient(*args):
1588 cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False, IMP::FloatPair norm_factors) -> double
1589 cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1590 cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1592 return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1594 cross_correlation_coefficient = staticmethod(cross_correlation_coefficient)
1596 def local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold):
1597 """local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1598 return _IMP_em.CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold)
1600 local_cross_correlation_coefficient = staticmethod(local_cross_correlation_coefficient)
1602 def get_version_info(self):
1603 """get_version_info(CoarseCC self) -> VersionInfo"""
1604 return _IMP_em.CoarseCC_get_version_info(self)
1608 """__str__(CoarseCC self) -> std::string"""
1609 return _IMP_em.CoarseCC___str__(self)
1613 """__repr__(CoarseCC self) -> std::string"""
1614 return _IMP_em.CoarseCC___repr__(self)
1619 return _object_cast_to_CoarseCC(o)
1621 CoarseCC_swigregister = _IMP_em.CoarseCC_swigregister
1622 CoarseCC_swigregister(CoarseCC)
1624 def CoarseCC_calc_score(*args):
1626 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True, IMP::FloatPair norm_factors) -> float
1627 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True) -> float
1628 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1629 CoarseCC_calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1631 return _IMP_em.CoarseCC_calc_score(*args)
1633 def CoarseCC_cross_correlation_coefficient(*args):
1635 cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False, IMP::FloatPair norm_factors) -> double
1636 cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1637 CoarseCC_cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1639 return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1641 def CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold):
1642 """CoarseCC_local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1643 return _IMP_em.CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold)
1645 class CoarseConvolution(object):
1646 """Proxy of C++ IMP::em::CoarseConvolution class."""
1648 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1649 __repr__ = _swig_repr
1651 def convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac=True):
1653 convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1654 convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1656 return _IMP_em.CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac)
1658 convolution = staticmethod(convolution)
1661 """__init__(IMP::em::CoarseConvolution self) -> CoarseConvolution"""
1662 this = _IMP_em.new_CoarseConvolution()
1664 self.this.append(this)
1665 except __builtin__.Exception:
1667 __swig_destroy__ = _IMP_em.delete_CoarseConvolution
1668 __del__ =
lambda self:
None
1669 CoarseConvolution_swigregister = _IMP_em.CoarseConvolution_swigregister
1670 CoarseConvolution_swigregister(CoarseConvolution)
1672 def CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac=True):
1674 convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1675 CoarseConvolution_convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1677 return _IMP_em.CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac)
1679 class CoarseCCatIntervals(CoarseCC):
1680 """Proxy of C++ IMP::em::CoarseCCatIntervals class."""
1682 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1684 def __init__(self, *args):
1686 __init__(IMP::em::CoarseCCatIntervals self, int const & ncd) -> CoarseCCatIntervals
1687 __init__(IMP::em::CoarseCCatIntervals self) -> CoarseCCatIntervals
1689 this = _IMP_em.new_CoarseCCatIntervals(*args)
1691 self.this.append(this)
1692 except __builtin__.Exception:
1695 def evaluate(self, em_map, model_map, deriv, scalefac, lderiv, eval_interval):
1696 """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 >"""
1697 return _IMP_em.CoarseCCatIntervals_evaluate(self, em_map, model_map, deriv, scalefac, lderiv, eval_interval)
1701 """__str__(CoarseCCatIntervals self) -> std::string"""
1702 return _IMP_em.CoarseCCatIntervals___str__(self)
1706 """__repr__(CoarseCCatIntervals self) -> std::string"""
1707 return _IMP_em.CoarseCCatIntervals___repr__(self)
1712 return _object_cast_to_CoarseCCatIntervals(o)
1714 CoarseCCatIntervals_swigregister = _IMP_em.CoarseCCatIntervals_swigregister
1715 CoarseCCatIntervals_swigregister(CoarseCCatIntervals)
1718 """Proxy of C++ IMP::em::FitRestraint class."""
1720 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1722 def __init__(self, *args):
1724 __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
1725 __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
1726 __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key, float scale=1) -> FitRestraint
1727 __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key) -> FitRestraint
1728 __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors) -> FitRestraint
1729 __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map) -> FitRestraint
1731 this = _IMP_em.new_FitRestraint(*args)
1733 self.this.append(this)
1734 except __builtin__.Exception:
1737 def get_model_dens_map(self):
1738 """get_model_dens_map(FitRestraint self) -> SampledDensityMap"""
1739 return _IMP_em.FitRestraint_get_model_dens_map(self)
1742 def set_scale_factor(self, scale):
1743 """set_scale_factor(FitRestraint self, float scale)"""
1744 return _IMP_em.FitRestraint_set_scale_factor(self, scale)
1747 def get_scale_factor(self):
1748 """get_scale_factor(FitRestraint self) -> float"""
1749 return _IMP_em.FitRestraint_get_scale_factor(self)
1752 def do_get_inputs(self):
1753 """do_get_inputs(FitRestraint self) -> IMP::ModelObjectsTemp"""
1754 return _IMP_em.FitRestraint_do_get_inputs(self)
1757 def get_version_info(self):
1758 """get_version_info(FitRestraint self) -> VersionInfo"""
1759 return _IMP_em.FitRestraint_get_version_info(self)
1763 """__str__(FitRestraint self) -> std::string"""
1764 return _IMP_em.FitRestraint___str__(self)
1768 """__repr__(FitRestraint self) -> std::string"""
1769 return _IMP_em.FitRestraint___repr__(self)
1774 return _object_cast_to_FitRestraint(o)
1778 """cast(Restraint r) -> FitRestraint"""
1779 return _IMP_em.FitRestraint_cast(r)
1781 cast = staticmethod(cast)
1782 FitRestraint_swigregister = _IMP_em.FitRestraint_swigregister
1783 FitRestraint_swigregister(FitRestraint)
1785 def FitRestraint_cast(r):
1786 """FitRestraint_cast(Restraint r) -> FitRestraint"""
1787 return _IMP_em.FitRestraint_cast(r)
1792 density2particles(DensityMap dmap, IMP::Float threshold, Model m, int step=1) -> IMP::Particles
1793 density2particles(DensityMap dmap, IMP::Float threshold, Model m) -> IMP::Particles
1795 return _IMP_em.density2particles(dmap, threshold, m, step)
1798 """density2vectors(DensityMap dmap, IMP::Float threshold) -> IMP::algebra::Vector3Ds"""
1799 return _IMP_em.density2vectors(dmap, threshold)
1803 particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3, FloatKey weight_key) -> SampledDensityMap
1804 particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
1805 particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
1807 return _IMP_em.particles2density(*args)
1811 particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3, FloatKey weight_key) -> SampledDensityMap
1812 particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
1813 particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
1815 return _IMP_em.particles2binarized_density(*args)
1819 particles2surface(IMP::ParticlesTemp const & ps, IMP::Float apix, FloatKey weight_key) -> SurfaceShellDensityMap
1820 particles2surface(IMP::ParticlesTemp const & ps, IMP::Float apix) -> SurfaceShellDensityMap
1822 return _IMP_em.particles2surface(*args)
1824 def calculate_intersection_score(d1, d2):
1825 """calculate_intersection_score(SurfaceShellDensityMap d1, SurfaceShellDensityMap d2) -> IMP::Float"""
1826 return _IMP_em.calculate_intersection_score(d1, d2)
1827 class SpiderHeader(object):
1828 """Proxy of C++ IMP::em::SpiderHeader class."""
1830 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1831 __repr__ = _swig_repr
1832 fNslice = _swig_property(_IMP_em.SpiderHeader_fNslice_get, _IMP_em.SpiderHeader_fNslice_set)
1833 fNrow = _swig_property(_IMP_em.SpiderHeader_fNrow_get, _IMP_em.SpiderHeader_fNrow_set)
1834 fNrec = _swig_property(_IMP_em.SpiderHeader_fNrec_get, _IMP_em.SpiderHeader_fNrec_set)
1835 fNlabel = _swig_property(_IMP_em.SpiderHeader_fNlabel_get, _IMP_em.SpiderHeader_fNlabel_set)
1836 fIform = _swig_property(_IMP_em.SpiderHeader_fIform_get, _IMP_em.SpiderHeader_fIform_set)
1837 fImami = _swig_property(_IMP_em.SpiderHeader_fImami_get, _IMP_em.SpiderHeader_fImami_set)
1838 fFmax = _swig_property(_IMP_em.SpiderHeader_fFmax_get, _IMP_em.SpiderHeader_fFmax_set)
1839 fFmin = _swig_property(_IMP_em.SpiderHeader_fFmin_get, _IMP_em.SpiderHeader_fFmin_set)
1840 fAv = _swig_property(_IMP_em.SpiderHeader_fAv_get, _IMP_em.SpiderHeader_fAv_set)
1841 fSig = _swig_property(_IMP_em.SpiderHeader_fSig_get, _IMP_em.SpiderHeader_fSig_set)
1842 fIhist = _swig_property(_IMP_em.SpiderHeader_fIhist_get, _IMP_em.SpiderHeader_fIhist_set)
1843 fNcol = _swig_property(_IMP_em.SpiderHeader_fNcol_get, _IMP_em.SpiderHeader_fNcol_set)
1844 fLabrec = _swig_property(_IMP_em.SpiderHeader_fLabrec_get, _IMP_em.SpiderHeader_fLabrec_set)
1845 fIangle = _swig_property(_IMP_em.SpiderHeader_fIangle_get, _IMP_em.SpiderHeader_fIangle_set)
1846 fPhi = _swig_property(_IMP_em.SpiderHeader_fPhi_get, _IMP_em.SpiderHeader_fPhi_set)
1847 fTheta = _swig_property(_IMP_em.SpiderHeader_fTheta_get, _IMP_em.SpiderHeader_fTheta_set)
1848 fPsi = _swig_property(_IMP_em.SpiderHeader_fPsi_get, _IMP_em.SpiderHeader_fPsi_set)
1849 fXoff = _swig_property(_IMP_em.SpiderHeader_fXoff_get, _IMP_em.SpiderHeader_fXoff_set)
1850 fYoff = _swig_property(_IMP_em.SpiderHeader_fYoff_get, _IMP_em.SpiderHeader_fYoff_set)
1851 fZoff = _swig_property(_IMP_em.SpiderHeader_fZoff_get, _IMP_em.SpiderHeader_fZoff_set)
1852 fScale = _swig_property(_IMP_em.SpiderHeader_fScale_get, _IMP_em.SpiderHeader_fScale_set)
1853 fLabbyt = _swig_property(_IMP_em.SpiderHeader_fLabbyt_get, _IMP_em.SpiderHeader_fLabbyt_set)
1854 fLenbyt = _swig_property(_IMP_em.SpiderHeader_fLenbyt_get, _IMP_em.SpiderHeader_fLenbyt_set)
1855 fNothing = _swig_property(_IMP_em.SpiderHeader_fNothing_get, _IMP_em.SpiderHeader_fNothing_set)
1856 fFlag = _swig_property(_IMP_em.SpiderHeader_fFlag_get, _IMP_em.SpiderHeader_fFlag_set)
1857 fPhi1 = _swig_property(_IMP_em.SpiderHeader_fPhi1_get, _IMP_em.SpiderHeader_fPhi1_set)
1858 fTheta1 = _swig_property(_IMP_em.SpiderHeader_fTheta1_get, _IMP_em.SpiderHeader_fTheta1_set)
1859 fPsi1 = _swig_property(_IMP_em.SpiderHeader_fPsi1_get, _IMP_em.SpiderHeader_fPsi1_set)
1860 fPhi2 = _swig_property(_IMP_em.SpiderHeader_fPhi2_get, _IMP_em.SpiderHeader_fPhi2_set)
1861 fTheta2 = _swig_property(_IMP_em.SpiderHeader_fTheta2_get, _IMP_em.SpiderHeader_fTheta2_set)
1862 fPsi2 = _swig_property(_IMP_em.SpiderHeader_fPsi2_get, _IMP_em.SpiderHeader_fPsi2_set)
1863 fGeo_matrix = _swig_property(_IMP_em.SpiderHeader_fGeo_matrix_get, _IMP_em.SpiderHeader_fGeo_matrix_set)
1864 fAngle1 = _swig_property(_IMP_em.SpiderHeader_fAngle1_get, _IMP_em.SpiderHeader_fAngle1_set)
1865 fr1 = _swig_property(_IMP_em.SpiderHeader_fr1_get, _IMP_em.SpiderHeader_fr1_set)
1866 fr2 = _swig_property(_IMP_em.SpiderHeader_fr2_get, _IMP_em.SpiderHeader_fr2_set)
1867 RTflag = _swig_property(_IMP_em.SpiderHeader_RTflag_get, _IMP_em.SpiderHeader_RTflag_set)
1868 Astart = _swig_property(_IMP_em.SpiderHeader_Astart_get, _IMP_em.SpiderHeader_Astart_set)
1869 Aend = _swig_property(_IMP_em.SpiderHeader_Aend_get, _IMP_em.SpiderHeader_Aend_set)
1870 Ainc = _swig_property(_IMP_em.SpiderHeader_Ainc_get, _IMP_em.SpiderHeader_Ainc_set)
1871 Rsigma = _swig_property(_IMP_em.SpiderHeader_Rsigma_get, _IMP_em.SpiderHeader_Rsigma_set)
1872 Tstart = _swig_property(_IMP_em.SpiderHeader_Tstart_get, _IMP_em.SpiderHeader_Tstart_set)
1873 Tend = _swig_property(_IMP_em.SpiderHeader_Tend_get, _IMP_em.SpiderHeader_Tend_set)
1874 Tinc = _swig_property(_IMP_em.SpiderHeader_Tinc_get, _IMP_em.SpiderHeader_Tinc_set)
1875 Weight = _swig_property(_IMP_em.SpiderHeader_Weight_get, _IMP_em.SpiderHeader_Weight_set)
1876 Flip = _swig_property(_IMP_em.SpiderHeader_Flip_get, _IMP_em.SpiderHeader_Flip_set)
1877 empty = _swig_property(_IMP_em.SpiderHeader_empty_get, _IMP_em.SpiderHeader_empty_set)
1878 szIDat = _swig_property(_IMP_em.SpiderHeader_szIDat_get, _IMP_em.SpiderHeader_szIDat_set)
1879 szITim = _swig_property(_IMP_em.SpiderHeader_szITim_get, _IMP_em.SpiderHeader_szITim_set)
1880 szITit = _swig_property(_IMP_em.SpiderHeader_szITit_get, _IMP_em.SpiderHeader_szITit_set)
1882 def show(self, out):
1883 """show(SpiderHeader self, _ostream out)"""
1884 return _IMP_em.SpiderHeader_show(self, out)
1888 """__init__(IMP::em::SpiderHeader self) -> SpiderHeader"""
1889 this = _IMP_em.new_SpiderHeader()
1891 self.this.append(this)
1892 except __builtin__.Exception:
1894 __swig_destroy__ = _IMP_em.delete_SpiderHeader
1895 __del__ =
lambda self:
None
1896 SpiderHeader_swigregister = _IMP_em.SpiderHeader_swigregister
1897 SpiderHeader_swigregister(SpiderHeader)
1899 class ImageHeader(object):
1900 """Proxy of C++ IMP::em::ImageHeader class."""
1902 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1903 __repr__ = _swig_repr
1904 IMG_BYTE = _IMP_em.ImageHeader_IMG_BYTE
1905 IMG_IMPEM = _IMP_em.ImageHeader_IMG_IMPEM
1906 IMG_INT = _IMP_em.ImageHeader_IMG_INT
1907 VOL_BYTE = _IMP_em.ImageHeader_VOL_BYTE
1908 VOL_IMPEM = _IMP_em.ImageHeader_VOL_IMPEM
1909 VOL_INT = _IMP_em.ImageHeader_VOL_INT
1910 IMG_FOURIER = _IMP_em.ImageHeader_IMG_FOURIER
1911 VOL_FOURIER = _IMP_em.ImageHeader_VOL_FOURIER
1913 def __init__(self, *args):
1915 __init__(IMP::em::ImageHeader self) -> ImageHeader
1916 __init__(IMP::em::ImageHeader self, IMP::em::ImageHeader::img_type im) -> ImageHeader
1917 __init__(IMP::em::ImageHeader self, float im) -> ImageHeader
1919 this = _IMP_em.new_ImageHeader(*args)
1921 self.this.append(this)
1922 except __builtin__.Exception:
1925 def get_image_type(self):
1926 """get_image_type(ImageHeader self) -> float"""
1927 return _IMP_em.ImageHeader_get_image_type(self)
1930 def set_image_type(self, *args):
1932 set_image_type(ImageHeader self, IMP::em::ImageHeader::img_type im)
1933 set_image_type(ImageHeader self, float im)
1935 return _IMP_em.ImageHeader_set_image_type(self, *args)
1938 def do_show(self, out):
1939 """do_show(ImageHeader self, _ostream out)"""
1940 return _IMP_em.ImageHeader_do_show(self, out)
1943 def show(self, *args):
1945 show(ImageHeader self, _ostream out)
1946 show(ImageHeader self)
1948 return _IMP_em.ImageHeader_show(self, *args)
1951 def print_hard(self, out):
1952 """print_hard(ImageHeader self, _ostream out)"""
1953 return _IMP_em.ImageHeader_print_hard(self, out)
1956 def show_projection_params(self, out):
1957 """show_projection_params(ImageHeader self, _ostream out)"""
1958 return _IMP_em.ImageHeader_show_projection_params(self, out)
1961 def read(self, *args):
1963 read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False, bool skip_extra_checkings=False) -> int
1964 read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False) -> int
1965 read(ImageHeader self, IMP::String const filename, bool skip_type_check=False) -> int
1966 read(ImageHeader self, IMP::String const filename) -> int
1967 read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False, bool skip_extra_checkings=False) -> bool
1968 read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False) -> bool
1969 read(ImageHeader self, std::ifstream & f, bool skip_type_check=False) -> bool
1970 read(ImageHeader self, std::ifstream & f) -> bool
1972 return _IMP_em.ImageHeader_read(self, *args)
1975 def write(self, *args):
1977 write(ImageHeader self, IMP::String const & filename, bool force_reversed=False)
1978 write(ImageHeader self, IMP::String const & filename)
1979 write(ImageHeader self, std::ofstream & f, bool force_reversed=False)
1980 write(ImageHeader self, std::ofstream & f)
1982 return _IMP_em.ImageHeader_write(self, *args)
1986 """clear(ImageHeader self)"""
1987 return _IMP_em.ImageHeader_clear(self)
1990 def set_header(self):
1991 """set_header(ImageHeader self)"""
1992 return _IMP_em.ImageHeader_set_header(self)
1995 def get_reversed(self):
1996 """get_reversed(ImageHeader self) -> bool"""
1997 return _IMP_em.ImageHeader_get_reversed(self)
2000 def set_reversed(self, value):
2001 """set_reversed(ImageHeader self, bool value)"""
2002 return _IMP_em.ImageHeader_set_reversed(self, value)
2005 def get_number_of_slices(self):
2006 """get_number_of_slices(ImageHeader self) -> unsigned int"""
2007 return _IMP_em.ImageHeader_get_number_of_slices(self)
2010 def set_number_of_slices(self, n):
2011 """set_number_of_slices(ImageHeader self, unsigned int n)"""
2012 return _IMP_em.ImageHeader_set_number_of_slices(self, n)
2015 def get_number_of_rows(self):
2016 """get_number_of_rows(ImageHeader self) -> unsigned int"""
2017 return _IMP_em.ImageHeader_get_number_of_rows(self)
2020 def set_number_of_rows(self, n):
2021 """set_number_of_rows(ImageHeader self, unsigned int n)"""
2022 return _IMP_em.ImageHeader_set_number_of_rows(self, n)
2025 def get_number_of_columns(self):
2026 """get_number_of_columns(ImageHeader self) -> unsigned int"""
2027 return _IMP_em.ImageHeader_get_number_of_columns(self)
2030 def set_number_of_columns(self, n):
2031 """set_number_of_columns(ImageHeader self, unsigned int n)"""
2032 return _IMP_em.ImageHeader_set_number_of_columns(self, n)
2035 def get_old_rot(self):
2036 """get_old_rot(ImageHeader self) -> float"""
2037 return _IMP_em.ImageHeader_get_old_rot(self)
2040 def set_old_rot(self, value):
2041 """set_old_rot(ImageHeader self, float value)"""
2042 return _IMP_em.ImageHeader_set_old_rot(self, value)
2045 def get_fAngle1(self):
2046 """get_fAngle1(ImageHeader self) -> float"""
2047 return _IMP_em.ImageHeader_get_fAngle1(self)
2050 def set_fAngle1(self, value):
2051 """set_fAngle1(ImageHeader self, float value)"""
2052 return _IMP_em.ImageHeader_set_fAngle1(self, value)
2055 def get_Scale(self):
2056 """get_Scale(ImageHeader self) -> float"""
2057 return _IMP_em.ImageHeader_get_Scale(self)
2060 def set_Scale(self, value):
2061 """set_Scale(ImageHeader self, float value)"""
2062 return _IMP_em.ImageHeader_set_Scale(self, value)
2066 """get_Flip(ImageHeader self) -> float"""
2067 return _IMP_em.ImageHeader_get_Flip(self)
2070 def set_Flip(self, value):
2071 """set_Flip(ImageHeader self, float value)"""
2072 return _IMP_em.ImageHeader_set_Flip(self, value)
2075 def get_Weight(self):
2076 """get_Weight(ImageHeader self) -> float"""
2077 return _IMP_em.ImageHeader_get_Weight(self)
2080 def set_Weight(self, value):
2081 """set_Weight(ImageHeader self, float value)"""
2082 return _IMP_em.ImageHeader_set_Weight(self, value)
2085 def get_fNrec(self):
2086 """get_fNrec(ImageHeader self) -> float"""
2087 return _IMP_em.ImageHeader_get_fNrec(self)
2090 def set_fNrec(self, value):
2091 """set_fNrec(ImageHeader self, float value)"""
2092 return _IMP_em.ImageHeader_set_fNrec(self, value)
2095 def get_fNlabel(self):
2096 """get_fNlabel(ImageHeader self) -> float"""
2097 return _IMP_em.ImageHeader_get_fNlabel(self)
2100 def set_fNlabel(self, value):
2101 """set_fNlabel(ImageHeader self, float value)"""
2102 return _IMP_em.ImageHeader_set_fNlabel(self, value)
2105 def get_fIform(self):
2106 """get_fIform(ImageHeader self) -> float"""
2107 return _IMP_em.ImageHeader_get_fIform(self)
2110 def set_fIform(self, value):
2111 """set_fIform(ImageHeader self, float value)"""
2112 return _IMP_em.ImageHeader_set_fIform(self, value)
2115 def get_fImami(self):
2116 """get_fImami(ImageHeader self) -> float"""
2117 return _IMP_em.ImageHeader_get_fImami(self)
2120 def set_fImami(self, value):
2121 """set_fImami(ImageHeader self, float value)"""
2122 return _IMP_em.ImageHeader_set_fImami(self, value)
2125 def get_fFmax(self):
2126 """get_fFmax(ImageHeader self) -> float"""
2127 return _IMP_em.ImageHeader_get_fFmax(self)
2130 def set_fFmax(self, value):
2131 """set_fFmax(ImageHeader self, float value)"""
2132 return _IMP_em.ImageHeader_set_fFmax(self, value)
2135 def get_fFmin(self):
2136 """get_fFmin(ImageHeader self) -> float"""
2137 return _IMP_em.ImageHeader_get_fFmin(self)
2140 def set_fFmin(self, value):
2141 """set_fFmin(ImageHeader self, float value)"""
2142 return _IMP_em.ImageHeader_set_fFmin(self, value)
2146 """get_fAv(ImageHeader self) -> float"""
2147 return _IMP_em.ImageHeader_get_fAv(self)
2150 def set_fAv(self, value):
2151 """set_fAv(ImageHeader self, float value)"""
2152 return _IMP_em.ImageHeader_set_fAv(self, value)
2156 """get_fSig(ImageHeader self) -> float"""
2157 return _IMP_em.ImageHeader_get_fSig(self)
2160 def set_fSig(self, value):
2161 """set_fSig(ImageHeader self, float value)"""
2162 return _IMP_em.ImageHeader_set_fSig(self, value)
2165 def get_fIhist(self):
2166 """get_fIhist(ImageHeader self) -> float"""
2167 return _IMP_em.ImageHeader_get_fIhist(self)
2170 def set_fIhist(self, value):
2171 """set_fIhist(ImageHeader self, float value)"""
2172 return _IMP_em.ImageHeader_set_fIhist(self, value)
2175 def get_fLabrec(self):
2176 """get_fLabrec(ImageHeader self) -> float"""
2177 return _IMP_em.ImageHeader_get_fLabrec(self)
2180 def set_fLabrec(self, value):
2181 """set_fLabrec(ImageHeader self, float value)"""
2182 return _IMP_em.ImageHeader_set_fLabrec(self, value)
2185 def get_fIangle(self):
2186 """get_fIangle(ImageHeader self) -> float"""
2187 return _IMP_em.ImageHeader_get_fIangle(self)
2190 def set_fIangle(self, value):
2191 """set_fIangle(ImageHeader self, float value)"""
2192 return _IMP_em.ImageHeader_set_fIangle(self, value)
2195 def get_origin(self):
2196 """get_origin(ImageHeader self) -> Vector3D"""
2197 return _IMP_em.ImageHeader_get_origin(self)
2200 def set_origin(self, *args):
2202 set_origin(ImageHeader self, Vector3D v)
2203 set_origin(ImageHeader self, Vector2D v)
2205 return _IMP_em.ImageHeader_set_origin(self, *args)
2208 def get_object_pixel_size(self):
2209 """get_object_pixel_size(ImageHeader self) -> float"""
2210 return _IMP_em.ImageHeader_get_object_pixel_size(self)
2213 def set_object_pixel_size(self, value):
2214 """set_object_pixel_size(ImageHeader self, float value)"""
2215 return _IMP_em.ImageHeader_set_object_pixel_size(self, value)
2218 def get_fLabbyt(self):
2219 """get_fLabbyt(ImageHeader self) -> float"""
2220 return _IMP_em.ImageHeader_get_fLabbyt(self)
2223 def set_fLabbyt(self, value):
2224 """set_fLabbyt(ImageHeader self, float value)"""
2225 return _IMP_em.ImageHeader_set_fLabbyt(self, value)
2228 def get_fLenbyt(self):
2229 """get_fLenbyt(ImageHeader self) -> float"""
2230 return _IMP_em.ImageHeader_get_fLenbyt(self)
2233 def set_fLenbyt(self, value):
2234 """set_fLenbyt(ImageHeader self, float value)"""
2235 return _IMP_em.ImageHeader_set_fLenbyt(self, value)
2238 def get_fGeo_matrix(self, i, j):
2239 """get_fGeo_matrix(ImageHeader self, unsigned int i, unsigned int j) -> double"""
2240 return _IMP_em.ImageHeader_get_fGeo_matrix(self, i, j)
2243 def get_fFlag(self):
2244 """get_fFlag(ImageHeader self) -> float"""
2245 return _IMP_em.ImageHeader_get_fFlag(self)
2248 def set_fFlag(self, value):
2249 """set_fFlag(ImageHeader self, float value)"""
2250 return _IMP_em.ImageHeader_set_fFlag(self, value)
2253 def get_euler_angles(self):
2254 """get_euler_angles(ImageHeader self) -> Vector3D"""
2255 return _IMP_em.ImageHeader_get_euler_angles(self)
2258 def get_euler_angles1(self):
2259 """get_euler_angles1(ImageHeader self) -> Vector3D"""
2260 return _IMP_em.ImageHeader_get_euler_angles1(self)
2263 def get_euler_angles2(self):
2264 """get_euler_angles2(ImageHeader self) -> Vector3D"""
2265 return _IMP_em.ImageHeader_get_euler_angles2(self)
2268 def set_euler_angles(self, euler):
2269 """set_euler_angles(ImageHeader self, Vector3D euler)"""
2270 return _IMP_em.ImageHeader_set_euler_angles(self, euler)
2273 def set_euler_angles1(self, euler):
2274 """set_euler_angles1(ImageHeader self, Vector3D euler)"""
2275 return _IMP_em.ImageHeader_set_euler_angles1(self, euler)
2278 def set_euler_angles2(self, euler):
2279 """set_euler_angles2(ImageHeader self, Vector3D euler)"""
2280 return _IMP_em.ImageHeader_set_euler_angles2(self, euler)
2283 def is_normalized(self):
2284 """is_normalized(ImageHeader self) -> bool"""
2285 return _IMP_em.ImageHeader_is_normalized(self)
2289 """set_date(ImageHeader self)"""
2290 return _IMP_em.ImageHeader_set_date(self)
2294 """set_time(ImageHeader self)"""
2295 return _IMP_em.ImageHeader_set_time(self)
2298 def set_title(self, newName):
2299 """set_title(ImageHeader self, IMP::String newName)"""
2300 return _IMP_em.ImageHeader_set_title(self, newName)
2302 __swig_destroy__ = _IMP_em.delete_ImageHeader
2303 __del__ =
lambda self:
None
2304 ImageHeader_swigregister = _IMP_em.ImageHeader_swigregister
2305 ImageHeader_swigregister(ImageHeader)
2307 class SpiderMapReaderWriter(MapReaderWriter):
2308 """Proxy of C++ IMP::em::SpiderMapReaderWriter class."""
2310 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2311 filename_ = _swig_property(_IMP_em.SpiderMapReaderWriter_filename__get, _IMP_em.SpiderMapReaderWriter_filename__set)
2312 skip_type_check_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_type_check__get, _IMP_em.SpiderMapReaderWriter_skip_type_check__set)
2313 force_reversed_ = _swig_property(_IMP_em.SpiderMapReaderWriter_force_reversed__get, _IMP_em.SpiderMapReaderWriter_force_reversed__set)
2314 skip_extra_checkings_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_extra_checkings__get, _IMP_em.SpiderMapReaderWriter_skip_extra_checkings__set)
2316 def __init__(self, *args):
2318 __init__(IMP::em::SpiderMapReaderWriter self) -> SpiderMapReaderWriter
2319 __init__(IMP::em::SpiderMapReaderWriter self, IMP::String filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings) -> SpiderMapReaderWriter
2321 this = _IMP_em.new_SpiderMapReaderWriter(*args)
2323 self.this.append(this)
2324 except __builtin__.Exception:
2328 """__str__(SpiderMapReaderWriter self) -> std::string"""
2329 return _IMP_em.SpiderMapReaderWriter___str__(self)
2333 """__repr__(SpiderMapReaderWriter self) -> std::string"""
2334 return _IMP_em.SpiderMapReaderWriter___repr__(self)
2339 return _object_cast_to_SpiderMapReaderWriter(o)
2341 SpiderMapReaderWriter_swigregister = _IMP_em.SpiderMapReaderWriter_swigregister
2342 SpiderMapReaderWriter_swigregister(SpiderMapReaderWriter)
2344 class FittingSolutions(object):
2345 """Proxy of C++ IMP::em::FittingSolutions class."""
2347 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2350 """__init__(IMP::em::FittingSolutions self) -> FittingSolutions"""
2351 this = _IMP_em.new_FittingSolutions()
2353 self.this.append(this)
2354 except __builtin__.Exception:
2357 def get_number_of_solutions(self):
2358 """get_number_of_solutions(FittingSolutions self) -> int"""
2359 return _IMP_em.FittingSolutions_get_number_of_solutions(self)
2362 def get_transformation(self, i):
2363 """get_transformation(FittingSolutions self, unsigned int i) -> Transformation3D"""
2364 return _IMP_em.FittingSolutions_get_transformation(self, i)
2367 def get_score(self, i):
2368 """get_score(FittingSolutions self, unsigned int i) -> IMP::Float"""
2369 return _IMP_em.FittingSolutions_get_score(self, i)
2372 def set_score(self, i, score):
2373 """set_score(FittingSolutions self, unsigned int i, IMP::Float score)"""
2374 return _IMP_em.FittingSolutions_set_score(self, i, score)
2377 def add_solution(self, t, score):
2378 """add_solution(FittingSolutions self, Transformation3D t, IMP::Float score)"""
2379 return _IMP_em.FittingSolutions_add_solution(self, t, score)
2382 def sort(self, reverse=False):
2384 sort(FittingSolutions self, bool reverse=False)
2385 sort(FittingSolutions self)
2387 return _IMP_em.FittingSolutions_sort(self, reverse)
2391 """multiply(FittingSolutions self, Transformation3D t)"""
2392 return _IMP_em.FittingSolutions_multiply(self, t)
2395 def get_transformations(self):
2396 """get_transformations(FittingSolutions self) -> IMP::algebra::Transformation3Ds"""
2397 return _IMP_em.FittingSolutions_get_transformations(self)
2400 def show(self, *args):
2402 show(FittingSolutions self, _ostream out)
2403 show(FittingSolutions self)
2405 return _IMP_em.FittingSolutions_show(self, *args)
2409 """__str__(FittingSolutions self) -> std::string"""
2410 return _IMP_em.FittingSolutions___str__(self)
2414 """__repr__(FittingSolutions self) -> std::string"""
2415 return _IMP_em.FittingSolutions___repr__(self)
2417 __swig_destroy__ = _IMP_em.delete_FittingSolutions
2418 __del__ =
lambda self:
None
2419 FittingSolutions_swigregister = _IMP_em.FittingSolutions_swigregister
2420 FittingSolutions_swigregister(FittingSolutions)
2423 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):
2425 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
2426 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
2427 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
2428 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
2429 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
2430 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
2431 local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log) -> FittingSolutions
2433 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)
2435 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):
2437 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
2438 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
2439 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
2440 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
2441 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
2442 local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2443 local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log) -> FittingSolutions
2445 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)
2447 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):
2449 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
2450 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
2451 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
2452 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
2453 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
2454 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
2456 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)
2458 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):
2460 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
2461 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
2462 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
2463 local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2) -> FittingSolutions
2464 local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap) -> FittingSolutions
2466 return _IMP_em.local_rigid_fitting_grid_search(ps, wei_key, dmap, max_voxels_translation, translation_step, max_angle_in_radians, number_of_rotations)
2470 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
2471 compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations, bool fast_version=False, bool local_score=False) -> FittingSolutions
2472 compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations, bool fast_version=False) -> FittingSolutions
2473 compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2474 compute_fitting_scores(DensityMap em_map, RigidBody rb, Refiner refiner, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2476 return _IMP_em.compute_fitting_scores(*args)
2480 compute_fitting_score(IMP::ParticlesTemp const & ps, DensityMap em_map, FloatKey wei_key) -> IMP::Float
2481 compute_fitting_score(IMP::ParticlesTemp const & ps, DensityMap em_map) -> IMP::Float
2483 return _IMP_em.compute_fitting_score(*args)
2487 get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, Transformation3D t, float thr=0.0) -> long
2488 get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, Transformation3D t) -> long
2489 get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps) -> long
2491 return _IMP_em.get_number_of_particles_outside_of_the_density(*args)
2495 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
2496 get_numbers_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, IMP::algebra::Transformation3Ds const & transformations) -> IMP::Ints
2498 return _IMP_em.get_numbers_of_particles_outside_of_the_density(dmap, ps, transformations, thr)
2502 get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3., Transformation3D t, float thr=0.0) -> double
2503 get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3., Transformation3D t) -> double
2504 get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3.) -> double
2505 get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps) -> double
2507 return _IMP_em.get_percentage_of_voxels_covered_by_particles(*args)
2509 """Proxy of C++ IMP::em::HighDensityEmbedding class."""
2511 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2513 def __init__(self, dm, threshold):
2514 """__init__(IMP::em::HighDensityEmbedding self, DensityMap dm, double threshold) -> HighDensityEmbedding"""
2515 this = _IMP_em.new_HighDensityEmbedding(dm, threshold)
2517 self.this.append(this)
2518 except __builtin__.Exception:
2521 def get_version_info(self):
2522 """get_version_info(HighDensityEmbedding self) -> VersionInfo"""
2523 return _IMP_em.HighDensityEmbedding_get_version_info(self)
2527 """__str__(HighDensityEmbedding self) -> std::string"""
2528 return _IMP_em.HighDensityEmbedding___str__(self)
2532 """__repr__(HighDensityEmbedding self) -> std::string"""
2533 return _IMP_em.HighDensityEmbedding___repr__(self)
2538 return _object_cast_to_HighDensityEmbedding(o)
2540 HighDensityEmbedding_swigregister = _IMP_em.HighDensityEmbedding_swigregister
2541 HighDensityEmbedding_swigregister(HighDensityEmbedding)
2545 """mask_and_norm(DensityMap dmap, DensityMap mask) -> DensityMap"""
2546 return _IMP_em.mask_and_norm(dmap, mask)
2549 """get_volume_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float"""
2550 return _IMP_em.get_volume_at_threshold(m, threshold)
2554 get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold, IMP::atom::ProteinDensityReference ref) -> IMP::Float
2555 get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float
2557 return _IMP_em.get_molecular_mass_at_threshold(*args)
2560 """get_threshold_for_approximate_volume(DensityMap m, IMP::Float desired_volume) -> IMP::Float"""
2561 return _IMP_em.get_threshold_for_approximate_volume(m, desired_volume)
2565 get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass, IMP::atom::ProteinDensityReference ref) -> IMP::Float
2566 get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass) -> IMP::Float
2568 return _IMP_em.get_threshold_for_approximate_mass(*args)
2570 """Proxy of C++ IMP::em::EnvelopePenetrationRestraint class."""
2572 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2574 def __init__(self, ps, em_map, threshold):
2575 """__init__(IMP::em::EnvelopePenetrationRestraint self, IMP::Particles ps, DensityMap em_map, IMP::Float threshold) -> EnvelopePenetrationRestraint"""
2576 this = _IMP_em.new_EnvelopePenetrationRestraint(ps, em_map, threshold)
2578 self.this.append(this)
2579 except __builtin__.Exception:
2582 def do_get_inputs(self):
2583 """do_get_inputs(EnvelopePenetrationRestraint self) -> IMP::ModelObjectsTemp"""
2584 return _IMP_em.EnvelopePenetrationRestraint_do_get_inputs(self)
2587 def get_version_info(self):
2588 """get_version_info(EnvelopePenetrationRestraint self) -> VersionInfo"""
2589 return _IMP_em.EnvelopePenetrationRestraint_get_version_info(self)
2593 """__str__(EnvelopePenetrationRestraint self) -> std::string"""
2594 return _IMP_em.EnvelopePenetrationRestraint___str__(self)
2598 """__repr__(EnvelopePenetrationRestraint self) -> std::string"""
2599 return _IMP_em.EnvelopePenetrationRestraint___repr__(self)
2604 return _object_cast_to_EnvelopePenetrationRestraint(o)
2606 EnvelopePenetrationRestraint_swigregister = _IMP_em.EnvelopePenetrationRestraint_swigregister
2607 EnvelopePenetrationRestraint_swigregister(EnvelopePenetrationRestraint)
2610 """Proxy of C++ IMP::em::PCAFitRestraint class."""
2612 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2614 def __init__(self, *args):
2616 __init__(IMP::em::PCAFitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, float threshold, float max_pca_size_diff, float max_angle_diff, float max_centroid_diff, FloatKey weight_key) -> PCAFitRestraint
2617 __init__(IMP::em::PCAFitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, float threshold, float max_pca_size_diff, float max_angle_diff, float max_centroid_diff) -> PCAFitRestraint
2619 this = _IMP_em.new_PCAFitRestraint(*args)
2621 self.this.append(this)
2622 except __builtin__.Exception:
2625 def do_get_inputs(self):
2626 """do_get_inputs(PCAFitRestraint self) -> IMP::ModelObjectsTemp"""
2627 return _IMP_em.PCAFitRestraint_do_get_inputs(self)
2630 def get_version_info(self):
2631 """get_version_info(PCAFitRestraint self) -> VersionInfo"""
2632 return _IMP_em.PCAFitRestraint_get_version_info(self)
2636 """__str__(PCAFitRestraint self) -> std::string"""
2637 return _IMP_em.PCAFitRestraint___str__(self)
2641 """__repr__(PCAFitRestraint self) -> std::string"""
2642 return _IMP_em.PCAFitRestraint___repr__(self)
2647 return _object_cast_to_PCAFitRestraint(o)
2649 PCAFitRestraint_swigregister = _IMP_em.PCAFitRestraint_swigregister
2650 PCAFitRestraint_swigregister(PCAFitRestraint)
2653 """Proxy of C++ IMP::em::EnvelopeFitRestraint class."""
2655 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2657 def __init__(self, particles, em_map, density_threshold, penetration_threshold):
2658 """__init__(IMP::em::EnvelopeFitRestraint self, IMP::Particles particles, DensityMap em_map, double density_threshold, double penetration_threshold) -> EnvelopeFitRestraint"""
2659 this = _IMP_em.new_EnvelopeFitRestraint(particles, em_map, density_threshold, penetration_threshold)
2661 self.this.append(this)
2662 except __builtin__.Exception:
2665 def get_transformation(self):
2666 """get_transformation(EnvelopeFitRestraint self) -> Transformation3D"""
2667 return _IMP_em.EnvelopeFitRestraint_get_transformation(self)
2670 def apply_transformation(self):
2671 """apply_transformation(EnvelopeFitRestraint self)"""
2672 return _IMP_em.EnvelopeFitRestraint_apply_transformation(self)
2675 def do_get_inputs(self):
2676 """do_get_inputs(EnvelopeFitRestraint self) -> IMP::ModelObjectsTemp"""
2677 return _IMP_em.EnvelopeFitRestraint_do_get_inputs(self)
2680 def get_version_info(self):
2681 """get_version_info(EnvelopeFitRestraint self) -> VersionInfo"""
2682 return _IMP_em.EnvelopeFitRestraint_get_version_info(self)
2686 """__str__(EnvelopeFitRestraint self) -> std::string"""
2687 return _IMP_em.EnvelopeFitRestraint___str__(self)
2691 """__repr__(EnvelopeFitRestraint self) -> std::string"""
2692 return _IMP_em.EnvelopeFitRestraint___repr__(self)
2697 return _object_cast_to_EnvelopeFitRestraint(o)
2699 EnvelopeFitRestraint_swigregister = _IMP_em.EnvelopeFitRestraint_swigregister
2700 EnvelopeFitRestraint_swigregister(EnvelopeFitRestraint)
2702 class MapDistanceTransform(DensityMap):
2703 """Proxy of C++ IMP::em::MapDistanceTransform class."""
2705 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2707 def __init__(self, map, density_threshold, max_distance):
2708 """__init__(IMP::em::MapDistanceTransform self, DensityMap map, float density_threshold, float max_distance) -> MapDistanceTransform"""
2709 this = _IMP_em.new_MapDistanceTransform(map, density_threshold, max_distance)
2711 self.this.append(this)
2712 except __builtin__.Exception:
2715 def get_distance_from_envelope(self, v):
2716 """get_distance_from_envelope(MapDistanceTransform self, Vector3D v) -> float"""
2717 return _IMP_em.MapDistanceTransform_get_distance_from_envelope(self, v)
2721 """__str__(MapDistanceTransform self) -> std::string"""
2722 return _IMP_em.MapDistanceTransform___str__(self)
2726 """__repr__(MapDistanceTransform self) -> std::string"""
2727 return _IMP_em.MapDistanceTransform___repr__(self)
2732 return _object_cast_to_MapDistanceTransform(o)
2734 __swig_destroy__ = _IMP_em.delete_MapDistanceTransform
2735 __del__ =
lambda self:
None
2736 MapDistanceTransform_swigregister = _IMP_em.MapDistanceTransform_swigregister
2737 MapDistanceTransform_swigregister(MapDistanceTransform)
2740 """Proxy of C++ IMP::em::EnvelopeScore class."""
2742 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2744 def __init__(self, mdt):
2745 """__init__(IMP::em::EnvelopeScore self, MapDistanceTransform mdt) -> EnvelopeScore"""
2746 this = _IMP_em.new_EnvelopeScore(mdt)
2748 self.this.append(this)
2749 except __builtin__.Exception:
2752 def is_penetrating(self, *args):
2754 is_penetrating(EnvelopeScore self, IMP::algebra::Vector3Ds const & points, float penetration_thr) -> bool
2755 is_penetrating(EnvelopeScore self, IMP::algebra::Vector3Ds const & points, Transformation3D trans, float penetration_thr) -> bool
2757 return _IMP_em.EnvelopeScore_is_penetrating(self, *args)
2760 def score(self, *args):
2762 score(EnvelopeScore self, IMP::algebra::Vector3Ds const & points) -> double
2763 score(EnvelopeScore self, IMP::algebra::Vector3Ds const & points, Transformation3D trans) -> double
2765 return _IMP_em.EnvelopeScore_score(self, *args)
2767 __swig_destroy__ = _IMP_em.delete_EnvelopeScore
2768 __del__ =
lambda self:
None
2771 """__str__(EnvelopeScore self) -> std::string"""
2772 return _IMP_em.EnvelopeScore___str__(self)
2776 """__repr__(EnvelopeScore self) -> std::string"""
2777 return _IMP_em.EnvelopeScore___repr__(self)
2782 return _object_cast_to_EnvelopeScore(o)
2784 EnvelopeScore_swigregister = _IMP_em.EnvelopeScore_swigregister
2785 EnvelopeScore_swigregister(EnvelopeScore)
2791 """Write out principal components to a file in Chimera Marker format"""
2792 eigen_values = pca.get_principal_values()
2793 eigen_vecs = pca.get_principal_components()
2794 centroid = pca.get_centroid()
2796 fh.write(
"<marker_set>\n")
2797 fh.write(
"<!-- PCA with eigen values: (%g,%g,%g) and "
2798 "centroid (%g,%g,%g) -->\n"
2799 % (math.sqrt(eigen_values[0]),
2800 math.sqrt(eigen_values[1]),
2801 math.sqrt(eigen_values[2]),
2802 centroid[0], centroid[1], centroid[2]))
2807 val = math.sqrt(eigen_values[i])
2808 v1 = centroid - val * eigen_vecs[i]
2809 v2 = centroid + val * eigen_vecs[i]
2810 for markerid, v
in ((i*2+1, v1), (i*2+2, v2)):
2811 fh.write(
"<marker id=\"%d\" x=\"%g\" y=\"%g\" z=\"%g\" "
2813 % (markerid, v[0], v[1], v[2], radius))
2815 for i
in range(1, 7, 2):
2816 fh.write(
"<link id1= \"%d\" id2=\"%d\" radius=\"%g\"/>\n"
2818 fh.write(
"</marker_set>\n")
2822 """get_module_version() -> std::string const"""
2823 return _IMP_em.get_module_version()
2826 """get_example_path(std::string fname) -> std::string"""
2827 return _IMP_em.get_example_path(fname)
2830 """get_data_path(std::string fname) -> std::string"""
2831 return _IMP_em.get_data_path(fname)
2833 from .
import _version_check
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.
std::string get_module_version()
Return the version of this module, as a string.
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.