10 from __future__
import print_function, division, absolute_import
15 from sys
import version_info
16 if version_info >= (2, 6, 0):
17 def swig_import_helper():
18 from os.path
import dirname
22 fp, pathname, description = imp.find_module(
'_IMP_em', [dirname(__file__)])
28 _mod = imp.load_module(
'_IMP_em', fp, pathname, description)
32 _IMP_em = swig_import_helper()
33 del swig_import_helper
38 _swig_property = property
43 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
44 if (name ==
"thisown"):
45 return self.this.own(value)
47 if type(value).__name__ ==
'SwigPyObject':
48 self.__dict__[name] = value
50 method = class_type.__swig_setmethods__.get(name,
None)
52 return method(self, value)
54 object.__setattr__(self, name, value)
56 raise AttributeError(
"You cannot add attributes to %s" % self)
59 def _swig_setattr(self, class_type, name, value):
60 return _swig_setattr_nondynamic(self, class_type, name, value, 0)
63 def _swig_getattr_nondynamic(self, class_type, name, static=1):
64 if (name ==
"thisown"):
65 return self.this.own()
66 method = class_type.__swig_getmethods__.get(name,
None)
70 return object.__getattr__(self, name)
72 raise AttributeError(name)
74 def _swig_getattr(self, class_type, name):
75 return _swig_getattr_nondynamic(self, class_type, name, 0)
80 strthis =
"proxy of " + self.this.__repr__()
83 return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
88 except AttributeError:
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
110 weakref_proxy =
lambda x: x
113 class IMP_EM_SwigPyIterator(object):
114 """Proxy of C++ swig::IMP_EM_SwigPyIterator class"""
115 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
117 def __init__(self, *args, **kwargs):
118 raise AttributeError(
"No constructor defined - class is abstract")
119 __repr__ = _swig_repr
120 __swig_destroy__ = _IMP_em.delete_IMP_EM_SwigPyIterator
121 __del__ =
lambda self:
None
124 """value(IMP_EM_SwigPyIterator self) -> PyObject *"""
125 return _IMP_em.IMP_EM_SwigPyIterator_value(self)
130 incr(IMP_EM_SwigPyIterator self, size_t n=1) -> IMP_EM_SwigPyIterator
131 incr(IMP_EM_SwigPyIterator self) -> IMP_EM_SwigPyIterator
133 return _IMP_em.IMP_EM_SwigPyIterator_incr(self, n)
138 decr(IMP_EM_SwigPyIterator self, size_t n=1) -> IMP_EM_SwigPyIterator
139 decr(IMP_EM_SwigPyIterator self) -> IMP_EM_SwigPyIterator
141 return _IMP_em.IMP_EM_SwigPyIterator_decr(self, n)
144 def distance(self, x):
145 """distance(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> ptrdiff_t"""
146 return _IMP_em.IMP_EM_SwigPyIterator_distance(self, x)
150 """equal(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> bool"""
151 return _IMP_em.IMP_EM_SwigPyIterator_equal(self, x)
155 """copy(IMP_EM_SwigPyIterator self) -> IMP_EM_SwigPyIterator"""
156 return _IMP_em.IMP_EM_SwigPyIterator_copy(self)
160 """next(IMP_EM_SwigPyIterator self) -> PyObject *"""
161 return _IMP_em.IMP_EM_SwigPyIterator_next(self)
165 """__next__(IMP_EM_SwigPyIterator self) -> PyObject *"""
166 return _IMP_em.IMP_EM_SwigPyIterator___next__(self)
170 """previous(IMP_EM_SwigPyIterator self) -> PyObject *"""
171 return _IMP_em.IMP_EM_SwigPyIterator_previous(self)
174 def advance(self, n):
175 """advance(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator"""
176 return _IMP_em.IMP_EM_SwigPyIterator_advance(self, n)
180 """__eq__(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> bool"""
181 return _IMP_em.IMP_EM_SwigPyIterator___eq__(self, x)
185 """__ne__(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> bool"""
186 return _IMP_em.IMP_EM_SwigPyIterator___ne__(self, x)
189 def __iadd__(self, n):
190 """__iadd__(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator"""
191 return _IMP_em.IMP_EM_SwigPyIterator___iadd__(self, n)
194 def __isub__(self, n):
195 """__isub__(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator"""
196 return _IMP_em.IMP_EM_SwigPyIterator___isub__(self, n)
199 def __add__(self, n):
200 """__add__(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator"""
201 return _IMP_em.IMP_EM_SwigPyIterator___add__(self, n)
204 def __sub__(self, *args):
206 __sub__(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator
207 __sub__(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> ptrdiff_t
209 return _IMP_em.IMP_EM_SwigPyIterator___sub__(self, *args)
213 IMP_EM_SwigPyIterator_swigregister = _IMP_em.IMP_EM_SwigPyIterator_swigregister
214 IMP_EM_SwigPyIterator_swigregister(IMP_EM_SwigPyIterator)
223 _IMP_em.IMP_DEBUG_swigconstant(_IMP_em)
224 IMP_DEBUG = _IMP_em.IMP_DEBUG
226 _IMP_em.IMP_RELEASE_swigconstant(_IMP_em)
227 IMP_RELEASE = _IMP_em.IMP_RELEASE
229 _IMP_em.IMP_SILENT_swigconstant(_IMP_em)
230 IMP_SILENT = _IMP_em.IMP_SILENT
232 _IMP_em.IMP_PROGRESS_swigconstant(_IMP_em)
233 IMP_PROGRESS = _IMP_em.IMP_PROGRESS
235 _IMP_em.IMP_TERSE_swigconstant(_IMP_em)
236 IMP_TERSE = _IMP_em.IMP_TERSE
238 _IMP_em.IMP_VERBOSE_swigconstant(_IMP_em)
239 IMP_VERBOSE = _IMP_em.IMP_VERBOSE
241 _IMP_em.IMP_MEMORY_swigconstant(_IMP_em)
242 IMP_MEMORY = _IMP_em.IMP_MEMORY
244 _IMP_em.IMP_NONE_swigconstant(_IMP_em)
245 IMP_NONE = _IMP_em.IMP_NONE
247 _IMP_em.IMP_USAGE_swigconstant(_IMP_em)
248 IMP_USAGE = _IMP_em.IMP_USAGE
250 _IMP_em.IMP_INTERNAL_swigconstant(_IMP_em)
251 IMP_INTERNAL = _IMP_em.IMP_INTERNAL
253 _IMP_em.IMP_KERNEL_HAS_LOG4CXX_swigconstant(_IMP_em)
254 IMP_KERNEL_HAS_LOG4CXX = _IMP_em.IMP_KERNEL_HAS_LOG4CXX
256 _IMP_em.IMP_COMPILER_HAS_AUTO_swigconstant(_IMP_em)
257 IMP_COMPILER_HAS_AUTO = _IMP_em.IMP_COMPILER_HAS_AUTO
259 _IMP_em.IMP_COMPILER_HAS_DEBUG_VECTOR_swigconstant(_IMP_em)
260 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_em.IMP_COMPILER_HAS_DEBUG_VECTOR
262 _IMP_em.IMP_COMPILER_HAS_UNIQUE_PTR_swigconstant(_IMP_em)
263 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_em.IMP_COMPILER_HAS_UNIQUE_PTR
265 _IMP_em.IMP_KERNEL_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
266 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_em.IMP_KERNEL_HAS_BOOST_RANDOM
268 _IMP_em.IMP_KERNEL_HAS_NUMPY_swigconstant(_IMP_em)
269 IMP_KERNEL_HAS_NUMPY = _IMP_em.IMP_KERNEL_HAS_NUMPY
271 _IMP_em.IMP_KERNEL_HAS_GPERFTOOLS_swigconstant(_IMP_em)
272 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_em.IMP_KERNEL_HAS_GPERFTOOLS
274 _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER_swigconstant(_IMP_em)
275 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
277 _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER_swigconstant(_IMP_em)
278 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
280 _IMP_em.IMPKERNEL_SHOW_WARNINGS_swigconstant(_IMP_em)
281 IMPKERNEL_SHOW_WARNINGS = _IMP_em.IMPKERNEL_SHOW_WARNINGS
284 class _DirectorObjects(object):
285 """@internal Simple class to keep references to director objects
286 to prevent premature deletion."""
289 def register(self, obj):
290 """Take a reference to a director object; will only work for
291 refcounted C++ classes"""
292 if hasattr(obj,
'get_ref_count'):
293 self._objects.append(obj)
295 """Only drop our reference and allow cleanup by Python if no other
296 Python references exist (we hold 3 references: one in self._objects,
297 one in x, and one in the argument list for getrefcount) *and* no
298 other C++ references exist (the Python object always holds one)"""
299 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
300 or x.get_ref_count() > 1]
304 def get_object_count(self):
305 """Get number of director objects (useful for testing only)"""
306 return len(self._objects)
307 _director_objects = _DirectorObjects()
309 class _ostream(object):
310 """Proxy of C++ std::ostream class"""
311 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
313 def __init__(self, *args, **kwargs):
314 raise AttributeError(
"No constructor defined")
315 __repr__ = _swig_repr
317 def write(self, osa_buf):
318 """write(_ostream self, char const * osa_buf)"""
319 return _IMP_em._ostream_write(self, osa_buf)
321 _ostream_swigregister = _IMP_em._ostream_swigregister
322 _ostream_swigregister(_ostream)
325 _IMP_em.IMP_COMPILER_HAS_OVERRIDE_swigconstant(_IMP_em)
326 IMP_COMPILER_HAS_OVERRIDE = _IMP_em.IMP_COMPILER_HAS_OVERRIDE
328 _IMP_em.IMP_COMPILER_HAS_FINAL_swigconstant(_IMP_em)
329 IMP_COMPILER_HAS_FINAL = _IMP_em.IMP_COMPILER_HAS_FINAL
331 _IMP_em.IMP_HAS_NOEXCEPT_swigconstant(_IMP_em)
332 IMP_HAS_NOEXCEPT = _IMP_em.IMP_HAS_NOEXCEPT
334 _IMP_em.IMP_C_OPEN_BINARY_swigconstant(_IMP_em)
335 IMP_C_OPEN_BINARY = _IMP_em.IMP_C_OPEN_BINARY
338 _IMP_em.IMP_CGAL_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
339 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CGAL_HAS_BOOST_FILESYSTEM
341 _IMP_em.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
342 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
344 _IMP_em.IMP_CGAL_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
345 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_em.IMP_CGAL_HAS_BOOST_RANDOM
347 _IMP_em.IMP_CGAL_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
348 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_em.IMP_CGAL_HAS_BOOST_SYSTEM
350 _IMP_em.IMP_CGAL_HAS_NUMPY_swigconstant(_IMP_em)
351 IMP_CGAL_HAS_NUMPY = _IMP_em.IMP_CGAL_HAS_NUMPY
353 _IMP_em.IMPCGAL_SHOW_WARNINGS_swigconstant(_IMP_em)
354 IMPCGAL_SHOW_WARNINGS = _IMP_em.IMPCGAL_SHOW_WARNINGS
357 _IMP_em.IMP_ALGEBRA_HAS_IMP_CGAL_swigconstant(_IMP_em)
358 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_em.IMP_ALGEBRA_HAS_IMP_CGAL
360 _IMP_em.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
361 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
363 _IMP_em.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
364 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
366 _IMP_em.IMP_ALGEBRA_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
367 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_RANDOM
369 _IMP_em.IMP_ALGEBRA_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
370 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_SYSTEM
372 _IMP_em.IMP_ALGEBRA_HAS_CGAL_swigconstant(_IMP_em)
373 IMP_ALGEBRA_HAS_CGAL = _IMP_em.IMP_ALGEBRA_HAS_CGAL
375 _IMP_em.IMP_ALGEBRA_HAS_NUMPY_swigconstant(_IMP_em)
376 IMP_ALGEBRA_HAS_NUMPY = _IMP_em.IMP_ALGEBRA_HAS_NUMPY
378 _IMP_em.IMP_ALGEBRA_HAS_ANN_swigconstant(_IMP_em)
379 IMP_ALGEBRA_HAS_ANN = _IMP_em.IMP_ALGEBRA_HAS_ANN
381 _IMP_em.IMPALGEBRA_SHOW_WARNINGS_swigconstant(_IMP_em)
382 IMPALGEBRA_SHOW_WARNINGS = _IMP_em.IMPALGEBRA_SHOW_WARNINGS
385 _IMP_em.IMP_DISPLAY_HAS_IMP_CGAL_swigconstant(_IMP_em)
386 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_em.IMP_DISPLAY_HAS_IMP_CGAL
388 _IMP_em.IMP_DISPLAY_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
389 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
391 _IMP_em.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
392 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
394 _IMP_em.IMP_DISPLAY_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
395 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_em.IMP_DISPLAY_HAS_BOOST_RANDOM
397 _IMP_em.IMP_DISPLAY_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
398 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_em.IMP_DISPLAY_HAS_BOOST_SYSTEM
400 _IMP_em.IMP_DISPLAY_HAS_CGAL_swigconstant(_IMP_em)
401 IMP_DISPLAY_HAS_CGAL = _IMP_em.IMP_DISPLAY_HAS_CGAL
403 _IMP_em.IMP_DISPLAY_HAS_NUMPY_swigconstant(_IMP_em)
404 IMP_DISPLAY_HAS_NUMPY = _IMP_em.IMP_DISPLAY_HAS_NUMPY
406 _IMP_em.IMPDISPLAY_SHOW_WARNINGS_swigconstant(_IMP_em)
407 IMPDISPLAY_SHOW_WARNINGS = _IMP_em.IMPDISPLAY_SHOW_WARNINGS
410 _IMP_em.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL_swigconstant(_IMP_em)
411 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_em.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
413 _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
414 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
416 _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
417 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
419 _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
420 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
422 _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
423 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
425 _IMP_em.IMP_SCORE_FUNCTOR_HAS_CGAL_swigconstant(_IMP_em)
426 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_em.IMP_SCORE_FUNCTOR_HAS_CGAL
428 _IMP_em.IMP_SCORE_FUNCTOR_HAS_HDF5_swigconstant(_IMP_em)
429 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_em.IMP_SCORE_FUNCTOR_HAS_HDF5
431 _IMP_em.IMP_SCORE_FUNCTOR_HAS_NUMPY_swigconstant(_IMP_em)
432 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_em.IMP_SCORE_FUNCTOR_HAS_NUMPY
434 _IMP_em.IMPSCOREFUNCTOR_SHOW_WARNINGS_swigconstant(_IMP_em)
435 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_em.IMPSCOREFUNCTOR_SHOW_WARNINGS
438 _IMP_em.IMP_STATISTICS_HAS_IMP_CGAL_swigconstant(_IMP_em)
439 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_em.IMP_STATISTICS_HAS_IMP_CGAL
441 _IMP_em.IMP_STATISTICS_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
442 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
444 _IMP_em.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
445 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
447 _IMP_em.IMP_STATISTICS_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
448 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_em.IMP_STATISTICS_HAS_BOOST_RANDOM
450 _IMP_em.IMP_STATISTICS_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
451 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_SYSTEM
453 _IMP_em.IMP_STATISTICS_HAS_CGAL_swigconstant(_IMP_em)
454 IMP_STATISTICS_HAS_CGAL = _IMP_em.IMP_STATISTICS_HAS_CGAL
456 _IMP_em.IMP_STATISTICS_HAS_NUMPY_swigconstant(_IMP_em)
457 IMP_STATISTICS_HAS_NUMPY = _IMP_em.IMP_STATISTICS_HAS_NUMPY
459 _IMP_em.IMPSTATISTICS_SHOW_WARNINGS_swigconstant(_IMP_em)
460 IMPSTATISTICS_SHOW_WARNINGS = _IMP_em.IMPSTATISTICS_SHOW_WARNINGS
463 _IMP_em.IMP_CORE_HAS_IMP_CGAL_swigconstant(_IMP_em)
464 IMP_CORE_HAS_IMP_CGAL = _IMP_em.IMP_CORE_HAS_IMP_CGAL
466 _IMP_em.IMP_CORE_HAS_IMP_KERNEL_swigconstant(_IMP_em)
467 IMP_CORE_HAS_IMP_KERNEL = _IMP_em.IMP_CORE_HAS_IMP_KERNEL
469 _IMP_em.IMP_CORE_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
470 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_FILESYSTEM
472 _IMP_em.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
473 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
475 _IMP_em.IMP_CORE_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
476 IMP_CORE_HAS_BOOST_RANDOM = _IMP_em.IMP_CORE_HAS_BOOST_RANDOM
478 _IMP_em.IMP_CORE_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
479 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_SYSTEM
481 _IMP_em.IMP_CORE_HAS_CGAL_swigconstant(_IMP_em)
482 IMP_CORE_HAS_CGAL = _IMP_em.IMP_CORE_HAS_CGAL
484 _IMP_em.IMP_CORE_HAS_HDF5_swigconstant(_IMP_em)
485 IMP_CORE_HAS_HDF5 = _IMP_em.IMP_CORE_HAS_HDF5
487 _IMP_em.IMP_CORE_HAS_NUMPY_swigconstant(_IMP_em)
488 IMP_CORE_HAS_NUMPY = _IMP_em.IMP_CORE_HAS_NUMPY
490 _IMP_em.IMPCORE_SHOW_WARNINGS_swigconstant(_IMP_em)
491 IMPCORE_SHOW_WARNINGS = _IMP_em.IMPCORE_SHOW_WARNINGS
494 _IMP_em.IMP_CONTAINER_HAS_IMP_ALGEBRA_swigconstant(_IMP_em)
495 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_em.IMP_CONTAINER_HAS_IMP_ALGEBRA
497 _IMP_em.IMP_CONTAINER_HAS_IMP_CGAL_swigconstant(_IMP_em)
498 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_em.IMP_CONTAINER_HAS_IMP_CGAL
500 _IMP_em.IMP_CONTAINER_HAS_IMP_DISPLAY_swigconstant(_IMP_em)
501 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_em.IMP_CONTAINER_HAS_IMP_DISPLAY
503 _IMP_em.IMP_CONTAINER_HAS_IMP_KERNEL_swigconstant(_IMP_em)
504 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_em.IMP_CONTAINER_HAS_IMP_KERNEL
506 _IMP_em.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_em)
507 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
509 _IMP_em.IMP_CONTAINER_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
510 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
512 _IMP_em.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
513 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
515 _IMP_em.IMP_CONTAINER_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
516 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_em.IMP_CONTAINER_HAS_BOOST_RANDOM
518 _IMP_em.IMP_CONTAINER_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
519 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_SYSTEM
521 _IMP_em.IMP_CONTAINER_HAS_CGAL_swigconstant(_IMP_em)
522 IMP_CONTAINER_HAS_CGAL = _IMP_em.IMP_CONTAINER_HAS_CGAL
524 _IMP_em.IMP_CONTAINER_HAS_HDF5_swigconstant(_IMP_em)
525 IMP_CONTAINER_HAS_HDF5 = _IMP_em.IMP_CONTAINER_HAS_HDF5
527 _IMP_em.IMP_CONTAINER_HAS_NUMPY_swigconstant(_IMP_em)
528 IMP_CONTAINER_HAS_NUMPY = _IMP_em.IMP_CONTAINER_HAS_NUMPY
530 _IMP_em.IMP_CONTAINER_HAS_PYTHON_IHM_swigconstant(_IMP_em)
531 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_em.IMP_CONTAINER_HAS_PYTHON_IHM
533 _IMP_em.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP_swigconstant(_IMP_em)
534 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_em.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
536 _IMP_em.IMP_CONTAINER_HAS_ROBIN_MAP_swigconstant(_IMP_em)
537 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_em.IMP_CONTAINER_HAS_ROBIN_MAP
539 _IMP_em.IMPCONTAINER_SHOW_WARNINGS_swigconstant(_IMP_em)
540 IMPCONTAINER_SHOW_WARNINGS = _IMP_em.IMPCONTAINER_SHOW_WARNINGS
543 _IMP_em.IMP_ATOM_HAS_IMP_CGAL_swigconstant(_IMP_em)
544 IMP_ATOM_HAS_IMP_CGAL = _IMP_em.IMP_ATOM_HAS_IMP_CGAL
546 _IMP_em.IMP_ATOM_HAS_IMP_KERNEL_swigconstant(_IMP_em)
547 IMP_ATOM_HAS_IMP_KERNEL = _IMP_em.IMP_ATOM_HAS_IMP_KERNEL
549 _IMP_em.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_em)
550 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
552 _IMP_em.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
553 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
555 _IMP_em.IMP_ATOM_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
556 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_em.IMP_ATOM_HAS_BOOST_RANDOM
558 _IMP_em.IMP_ATOM_HAS_BOOST_REGEX_swigconstant(_IMP_em)
559 IMP_ATOM_HAS_BOOST_REGEX = _IMP_em.IMP_ATOM_HAS_BOOST_REGEX
561 _IMP_em.IMP_ATOM_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
562 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_em.IMP_ATOM_HAS_BOOST_SYSTEM
564 _IMP_em.IMP_ATOM_HAS_CGAL_swigconstant(_IMP_em)
565 IMP_ATOM_HAS_CGAL = _IMP_em.IMP_ATOM_HAS_CGAL
567 _IMP_em.IMP_ATOM_HAS_HDF5_swigconstant(_IMP_em)
568 IMP_ATOM_HAS_HDF5 = _IMP_em.IMP_ATOM_HAS_HDF5
570 _IMP_em.IMP_ATOM_HAS_NUMPY_swigconstant(_IMP_em)
571 IMP_ATOM_HAS_NUMPY = _IMP_em.IMP_ATOM_HAS_NUMPY
573 _IMP_em.IMP_ATOM_HAS_PYTHON_IHM_swigconstant(_IMP_em)
574 IMP_ATOM_HAS_PYTHON_IHM = _IMP_em.IMP_ATOM_HAS_PYTHON_IHM
576 _IMP_em.IMPATOM_SHOW_WARNINGS_swigconstant(_IMP_em)
577 IMPATOM_SHOW_WARNINGS = _IMP_em.IMPATOM_SHOW_WARNINGS
579 _IMP_em.IMP_ATOM_TYPE_INDEX_swigconstant(_IMP_em)
580 IMP_ATOM_TYPE_INDEX = _IMP_em.IMP_ATOM_TYPE_INDEX
582 _IMP_em.IMP_RESIDUE_TYPE_INDEX_swigconstant(_IMP_em)
583 IMP_RESIDUE_TYPE_INDEX = _IMP_em.IMP_RESIDUE_TYPE_INDEX
585 _IMP_em.IMP_HIERARCHY_TYPE_INDEX_swigconstant(_IMP_em)
586 IMP_HIERARCHY_TYPE_INDEX = _IMP_em.IMP_HIERARCHY_TYPE_INDEX
588 _IMP_em.IMP_CHAIN_TYPE_INDEX_swigconstant(_IMP_em)
589 IMP_CHAIN_TYPE_INDEX = _IMP_em.IMP_CHAIN_TYPE_INDEX
592 _IMP_em.IMP_EM_HAS_IMP_CGAL_swigconstant(_IMP_em)
593 IMP_EM_HAS_IMP_CGAL = _IMP_em.IMP_EM_HAS_IMP_CGAL
595 _IMP_em.IMP_EM_HAS_IMP_CONTAINER_swigconstant(_IMP_em)
596 IMP_EM_HAS_IMP_CONTAINER = _IMP_em.IMP_EM_HAS_IMP_CONTAINER
598 _IMP_em.IMP_EM_HAS_IMP_DISPLAY_swigconstant(_IMP_em)
599 IMP_EM_HAS_IMP_DISPLAY = _IMP_em.IMP_EM_HAS_IMP_DISPLAY
601 _IMP_em.IMP_EM_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_em)
602 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_EM_HAS_IMP_SCORE_FUNCTOR
604 _IMP_em.IMP_EM_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
605 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_EM_HAS_BOOST_FILESYSTEM
607 _IMP_em.IMP_EM_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
608 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
610 _IMP_em.IMP_EM_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
611 IMP_EM_HAS_BOOST_RANDOM = _IMP_em.IMP_EM_HAS_BOOST_RANDOM
613 _IMP_em.IMP_EM_HAS_BOOST_REGEX_swigconstant(_IMP_em)
614 IMP_EM_HAS_BOOST_REGEX = _IMP_em.IMP_EM_HAS_BOOST_REGEX
616 _IMP_em.IMP_EM_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
617 IMP_EM_HAS_BOOST_SYSTEM = _IMP_em.IMP_EM_HAS_BOOST_SYSTEM
619 _IMP_em.IMP_EM_HAS_CGAL_swigconstant(_IMP_em)
620 IMP_EM_HAS_CGAL = _IMP_em.IMP_EM_HAS_CGAL
622 _IMP_em.IMP_EM_HAS_HDF5_swigconstant(_IMP_em)
623 IMP_EM_HAS_HDF5 = _IMP_em.IMP_EM_HAS_HDF5
625 _IMP_em.IMP_EM_HAS_NUMPY_swigconstant(_IMP_em)
626 IMP_EM_HAS_NUMPY = _IMP_em.IMP_EM_HAS_NUMPY
628 _IMP_em.IMP_EM_HAS_PYTHON_IHM_swigconstant(_IMP_em)
629 IMP_EM_HAS_PYTHON_IHM = _IMP_em.IMP_EM_HAS_PYTHON_IHM
631 _IMP_em.IMPEM_SHOW_WARNINGS_swigconstant(_IMP_em)
632 IMPEM_SHOW_WARNINGS = _IMP_em.IMPEM_SHOW_WARNINGS
634 _object_types.append(
"DensityMap")
637 def _object_cast_to_DensityMap(o):
638 """_object_cast_to_DensityMap(Object o) -> DensityMap"""
639 return _IMP_em._object_cast_to_DensityMap(o)
641 _object_types.append(
"SampledDensityMap")
644 def _object_cast_to_SampledDensityMap(o):
645 """_object_cast_to_SampledDensityMap(Object o) -> SampledDensityMap"""
646 return _IMP_em._object_cast_to_SampledDensityMap(o)
648 _object_types.append(
"SurfaceShellDensityMap")
651 def _object_cast_to_SurfaceShellDensityMap(o):
652 """_object_cast_to_SurfaceShellDensityMap(Object o) -> SurfaceShellDensityMap"""
653 return _IMP_em._object_cast_to_SurfaceShellDensityMap(o)
655 _object_types.append(
"FitRestraint")
658 def _object_cast_to_FitRestraint(o):
659 """_object_cast_to_FitRestraint(Object o) -> FitRestraint"""
660 return _IMP_em._object_cast_to_FitRestraint(o)
662 _object_types.append(
"FitRestraintBayesEM3D")
665 def _object_cast_to_FitRestraintBayesEM3D(o):
666 """_object_cast_to_FitRestraintBayesEM3D(Object o) -> FitRestraintBayesEM3D"""
667 return _IMP_em._object_cast_to_FitRestraintBayesEM3D(o)
669 _object_types.append(
"PCAFitRestraint")
672 def _object_cast_to_PCAFitRestraint(o):
673 """_object_cast_to_PCAFitRestraint(Object o) -> PCAFitRestraint"""
674 return _IMP_em._object_cast_to_PCAFitRestraint(o)
676 _object_types.append(
"EnvelopePenetrationRestraint")
679 def _object_cast_to_EnvelopePenetrationRestraint(o):
680 """_object_cast_to_EnvelopePenetrationRestraint(Object o) -> EnvelopePenetrationRestraint"""
681 return _IMP_em._object_cast_to_EnvelopePenetrationRestraint(o)
683 _object_types.append(
"EnvelopeFitRestraint")
686 def _object_cast_to_EnvelopeFitRestraint(o):
687 """_object_cast_to_EnvelopeFitRestraint(Object o) -> EnvelopeFitRestraint"""
688 return _IMP_em._object_cast_to_EnvelopeFitRestraint(o)
690 KernelParametersList=list
691 _plural_types.append(
"KernelParametersList")
692 _value_types.append(
"KernelParameters")
695 _object_types.append(
"HighDensityEmbedding")
698 def _object_cast_to_HighDensityEmbedding(o):
699 """_object_cast_to_HighDensityEmbedding(Object o) -> HighDensityEmbedding"""
700 return _IMP_em._object_cast_to_HighDensityEmbedding(o)
702 _object_types.append(
"MapReaderWriter")
705 def _object_cast_to_MapReaderWriter(o):
706 """_object_cast_to_MapReaderWriter(Object o) -> MapReaderWriter"""
707 return _IMP_em._object_cast_to_MapReaderWriter(o)
709 _object_types.append(
"MRCReaderWriter")
712 def _object_cast_to_MRCReaderWriter(o):
713 """_object_cast_to_MRCReaderWriter(Object o) -> MRCReaderWriter"""
714 return _IMP_em._object_cast_to_MRCReaderWriter(o)
716 _object_types.append(
"SpiderMapReaderWriter")
719 def _object_cast_to_SpiderMapReaderWriter(o):
720 """_object_cast_to_SpiderMapReaderWriter(Object o) -> SpiderMapReaderWriter"""
721 return _IMP_em._object_cast_to_SpiderMapReaderWriter(o)
723 _object_types.append(
"EMReaderWriter")
726 def _object_cast_to_EMReaderWriter(o):
727 """_object_cast_to_EMReaderWriter(Object o) -> EMReaderWriter"""
728 return _IMP_em._object_cast_to_EMReaderWriter(o)
730 _object_types.append(
"XplorReaderWriter")
733 def _object_cast_to_XplorReaderWriter(o):
734 """_object_cast_to_XplorReaderWriter(Object o) -> XplorReaderWriter"""
735 return _IMP_em._object_cast_to_XplorReaderWriter(o)
737 _object_types.append(
"CoarseCC")
740 def _object_cast_to_CoarseCC(o):
741 """_object_cast_to_CoarseCC(Object o) -> CoarseCC"""
742 return _IMP_em._object_cast_to_CoarseCC(o)
744 _object_types.append(
"CoarseCCatIntervals")
747 def _object_cast_to_CoarseCCatIntervals(o):
748 """_object_cast_to_CoarseCCatIntervals(Object o) -> CoarseCCatIntervals"""
749 return _IMP_em._object_cast_to_CoarseCCatIntervals(o)
751 FittingSolutionsList=list
752 _plural_types.append(
"FittingSolutionsList")
753 _value_types.append(
"FittingSolutions")
756 _object_types.append(
"MapDistanceTransform")
759 def _object_cast_to_MapDistanceTransform(o):
760 """_object_cast_to_MapDistanceTransform(Object o) -> MapDistanceTransform"""
761 return _IMP_em._object_cast_to_MapDistanceTransform(o)
763 _object_types.append(
"EnvelopeScore")
766 def _object_cast_to_EnvelopeScore(o):
767 """_object_cast_to_EnvelopeScore(Object o) -> EnvelopeScore"""
768 return _IMP_em._object_cast_to_EnvelopeScore(o)
770 """Proxy of C++ IMP::em::MapReaderWriter class"""
771 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
774 """__init__(IMP::em::MapReaderWriter self) -> MapReaderWriter"""
775 this = _IMP_em.new_MapReaderWriter()
777 self.this.append(this)
781 def get_version_info(self):
782 """get_version_info(MapReaderWriter self) -> VersionInfo"""
783 return _IMP_em.MapReaderWriter_get_version_info(self)
787 """__str__(MapReaderWriter self) -> std::string"""
788 return _IMP_em.MapReaderWriter___str__(self)
792 """__repr__(MapReaderWriter self) -> std::string"""
793 return _IMP_em.MapReaderWriter___repr__(self)
798 return _object_cast_to_MapReaderWriter(o)
800 MapReaderWriter_swigregister = _IMP_em.MapReaderWriter_swigregister
801 MapReaderWriter_swigregister(MapReaderWriter)
805 class DensityHeader(object):
806 """Proxy of C++ IMP::em::DensityHeader class"""
807 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
808 __repr__ = _swig_repr
811 """__init__(IMP::em::DensityHeader self) -> DensityHeader"""
812 this = _IMP_em.new_DensityHeader()
814 self.this.append(this)
818 def get_top(self, ind):
819 """get_top(DensityHeader self, int ind) -> IMP::em::emreal"""
820 return _IMP_em.DensityHeader_get_top(self, ind)
823 def compute_xyz_top(self, force=False):
825 compute_xyz_top(DensityHeader self, bool force=False)
826 compute_xyz_top(DensityHeader self)
828 return _IMP_em.DensityHeader_compute_xyz_top(self, force)
831 def update_map_dimensions(self, nnx, nny, nnz):
832 """update_map_dimensions(DensityHeader self, int nnx, int nny, int nnz)"""
833 return _IMP_em.DensityHeader_update_map_dimensions(self, nnx, nny, nnz)
836 def update_cell_dimensions(self):
837 """update_cell_dimensions(DensityHeader self)"""
838 return _IMP_em.DensityHeader_update_cell_dimensions(self)
841 def show(self, *args):
843 show(DensityHeader self, _ostream out)
844 show(DensityHeader self)
846 return _IMP_em.DensityHeader_show(self, *args)
848 MAP_FIELD_SIZE = _IMP_em.DensityHeader_MAP_FIELD_SIZE
849 USER_FIELD_SIZE = _IMP_em.DensityHeader_USER_FIELD_SIZE
850 COMMENT_FIELD_NUM_OF = _IMP_em.DensityHeader_COMMENT_FIELD_NUM_OF
851 COMMENT_FIELD_SINGLE_SIZE = _IMP_em.DensityHeader_COMMENT_FIELD_SINGLE_SIZE
852 nxstart = _swig_property(_IMP_em.DensityHeader_nxstart_get, _IMP_em.DensityHeader_nxstart_set)
853 nystart = _swig_property(_IMP_em.DensityHeader_nystart_get, _IMP_em.DensityHeader_nystart_set)
854 nzstart = _swig_property(_IMP_em.DensityHeader_nzstart_get, _IMP_em.DensityHeader_nzstart_set)
855 mx = _swig_property(_IMP_em.DensityHeader_mx_get, _IMP_em.DensityHeader_mx_set)
856 my = _swig_property(_IMP_em.DensityHeader_my_get, _IMP_em.DensityHeader_my_set)
857 mz = _swig_property(_IMP_em.DensityHeader_mz_get, _IMP_em.DensityHeader_mz_set)
858 xlen = _swig_property(_IMP_em.DensityHeader_xlen_get, _IMP_em.DensityHeader_xlen_set)
859 ylen = _swig_property(_IMP_em.DensityHeader_ylen_get, _IMP_em.DensityHeader_ylen_set)
860 zlen = _swig_property(_IMP_em.DensityHeader_zlen_get, _IMP_em.DensityHeader_zlen_set)
861 alpha = _swig_property(_IMP_em.DensityHeader_alpha_get, _IMP_em.DensityHeader_alpha_set)
862 beta = _swig_property(_IMP_em.DensityHeader_beta_get, _IMP_em.DensityHeader_beta_set)
863 gamma = _swig_property(_IMP_em.DensityHeader_gamma_get, _IMP_em.DensityHeader_gamma_set)
864 mapc = _swig_property(_IMP_em.DensityHeader_mapc_get, _IMP_em.DensityHeader_mapc_set)
865 mapr = _swig_property(_IMP_em.DensityHeader_mapr_get, _IMP_em.DensityHeader_mapr_set)
866 maps = _swig_property(_IMP_em.DensityHeader_maps_get, _IMP_em.DensityHeader_maps_set)
867 dmin = _swig_property(_IMP_em.DensityHeader_dmin_get, _IMP_em.DensityHeader_dmin_set)
868 dmax = _swig_property(_IMP_em.DensityHeader_dmax_get, _IMP_em.DensityHeader_dmax_set)
869 dmean = _swig_property(_IMP_em.DensityHeader_dmean_get, _IMP_em.DensityHeader_dmean_set)
870 ispg = _swig_property(_IMP_em.DensityHeader_ispg_get, _IMP_em.DensityHeader_ispg_set)
871 nsymbt = _swig_property(_IMP_em.DensityHeader_nsymbt_get, _IMP_em.DensityHeader_nsymbt_set)
872 user = _swig_property(_IMP_em.DensityHeader_user_get, _IMP_em.DensityHeader_user_set)
873 map = _swig_property(_IMP_em.DensityHeader_map_get, _IMP_em.DensityHeader_map_set)
874 machinestamp = _swig_property(_IMP_em.DensityHeader_machinestamp_get, _IMP_em.DensityHeader_machinestamp_set)
875 rms = _swig_property(_IMP_em.DensityHeader_rms_get, _IMP_em.DensityHeader_rms_set)
876 nlabl = _swig_property(_IMP_em.DensityHeader_nlabl_get, _IMP_em.DensityHeader_nlabl_set)
877 comments = _swig_property(_IMP_em.DensityHeader_comments_get, _IMP_em.DensityHeader_comments_set)
878 magic = _swig_property(_IMP_em.DensityHeader_magic_get, _IMP_em.DensityHeader_magic_set)
879 voltage = _swig_property(_IMP_em.DensityHeader_voltage_get, _IMP_em.DensityHeader_voltage_set)
880 Cs = _swig_property(_IMP_em.DensityHeader_Cs_get, _IMP_em.DensityHeader_Cs_set)
881 Aperture = _swig_property(_IMP_em.DensityHeader_Aperture_get, _IMP_em.DensityHeader_Aperture_set)
882 Magnification = _swig_property(_IMP_em.DensityHeader_Magnification_get, _IMP_em.DensityHeader_Magnification_set)
883 Postmagnification = _swig_property(_IMP_em.DensityHeader_Postmagnification_get, _IMP_em.DensityHeader_Postmagnification_set)
884 Exposuretime = _swig_property(_IMP_em.DensityHeader_Exposuretime_get, _IMP_em.DensityHeader_Exposuretime_set)
885 Microscope = _swig_property(_IMP_em.DensityHeader_Microscope_get, _IMP_em.DensityHeader_Microscope_set)
886 Pixelsize = _swig_property(_IMP_em.DensityHeader_Pixelsize_get, _IMP_em.DensityHeader_Pixelsize_set)
887 CCDArea = _swig_property(_IMP_em.DensityHeader_CCDArea_get, _IMP_em.DensityHeader_CCDArea_set)
888 Defocus = _swig_property(_IMP_em.DensityHeader_Defocus_get, _IMP_em.DensityHeader_Defocus_set)
889 Astigmatism = _swig_property(_IMP_em.DensityHeader_Astigmatism_get, _IMP_em.DensityHeader_Astigmatism_set)
890 AstigmatismAngle = _swig_property(_IMP_em.DensityHeader_AstigmatismAngle_get, _IMP_em.DensityHeader_AstigmatismAngle_set)
891 FocusIncrement = _swig_property(_IMP_em.DensityHeader_FocusIncrement_get, _IMP_em.DensityHeader_FocusIncrement_set)
892 CountsPerElectron = _swig_property(_IMP_em.DensityHeader_CountsPerElectron_get, _IMP_em.DensityHeader_CountsPerElectron_set)
893 Intensity = _swig_property(_IMP_em.DensityHeader_Intensity_get, _IMP_em.DensityHeader_Intensity_set)
894 EnergySlitwidth = _swig_property(_IMP_em.DensityHeader_EnergySlitwidth_get, _IMP_em.DensityHeader_EnergySlitwidth_set)
895 EnergyOffset = _swig_property(_IMP_em.DensityHeader_EnergyOffset_get, _IMP_em.DensityHeader_EnergyOffset_set)
896 Tiltangle = _swig_property(_IMP_em.DensityHeader_Tiltangle_get, _IMP_em.DensityHeader_Tiltangle_set)
897 Tiltaxis = _swig_property(_IMP_em.DensityHeader_Tiltaxis_get, _IMP_em.DensityHeader_Tiltaxis_set)
898 MarkerX = _swig_property(_IMP_em.DensityHeader_MarkerX_get, _IMP_em.DensityHeader_MarkerX_set)
899 MarkerY = _swig_property(_IMP_em.DensityHeader_MarkerY_get, _IMP_em.DensityHeader_MarkerY_set)
900 lswap = _swig_property(_IMP_em.DensityHeader_lswap_get, _IMP_em.DensityHeader_lswap_set)
903 """get_resolution(DensityHeader self) -> float"""
904 return _IMP_em.DensityHeader_get_resolution(self)
907 def get_has_resolution(self):
908 """get_has_resolution(DensityHeader self) -> bool"""
909 return _IMP_em.DensityHeader_get_has_resolution(self)
912 def set_resolution(self, resolution):
913 """set_resolution(DensityHeader self, float resolution)"""
914 return _IMP_em.DensityHeader_set_resolution(self, resolution)
917 def get_spacing(self):
918 """get_spacing(DensityHeader self) -> float"""
919 return _IMP_em.DensityHeader_get_spacing(self)
922 def get_xorigin(self):
923 """get_xorigin(DensityHeader self) -> float"""
924 return _IMP_em.DensityHeader_get_xorigin(self)
927 def get_yorigin(self):
928 """get_yorigin(DensityHeader self) -> float"""
929 return _IMP_em.DensityHeader_get_yorigin(self)
932 def get_zorigin(self):
933 """get_zorigin(DensityHeader self) -> float"""
934 return _IMP_em.DensityHeader_get_zorigin(self)
937 def get_origin(self, i):
938 """get_origin(DensityHeader self, int i) -> float"""
939 return _IMP_em.DensityHeader_get_origin(self, i)
942 def set_xorigin(self, x):
943 """set_xorigin(DensityHeader self, float x)"""
944 return _IMP_em.DensityHeader_set_xorigin(self, x)
947 def set_yorigin(self, y):
948 """set_yorigin(DensityHeader self, float y)"""
949 return _IMP_em.DensityHeader_set_yorigin(self, y)
952 def set_zorigin(self, z):
953 """set_zorigin(DensityHeader self, float z)"""
954 return _IMP_em.DensityHeader_set_zorigin(self, z)
957 def is_top_calculated(self):
958 """is_top_calculated(DensityHeader self) -> bool"""
959 return _IMP_em.DensityHeader_is_top_calculated(self)
961 Objectpixelsize_ = _swig_property(_IMP_em.DensityHeader_Objectpixelsize__get, _IMP_em.DensityHeader_Objectpixelsize__set)
964 """get_nx(DensityHeader self) -> int"""
965 return _IMP_em.DensityHeader_get_nx(self)
969 """get_ny(DensityHeader self) -> int"""
970 return _IMP_em.DensityHeader_get_ny(self)
974 """get_nz(DensityHeader self) -> int"""
975 return _IMP_em.DensityHeader_get_nz(self)
978 def get_number_of_voxels(self):
979 """get_number_of_voxels(DensityHeader self) -> int"""
980 return _IMP_em.DensityHeader_get_number_of_voxels(self)
983 def get_data_type(self):
984 """get_data_type(DensityHeader self) -> int"""
985 return _IMP_em.DensityHeader_get_data_type(self)
988 def set_data_type(self, data_type):
989 """set_data_type(DensityHeader self, int data_type)"""
990 return _IMP_em.DensityHeader_set_data_type(self, data_type)
992 __swig_destroy__ = _IMP_em.delete_DensityHeader
993 __del__ =
lambda self:
None
994 DensityHeader_swigregister = _IMP_em.DensityHeader_swigregister
995 DensityHeader_swigregister(DensityHeader)
999 """create_density_header(BoundingBox3D bb, float spacing) -> DensityHeader"""
1000 return _IMP_em.create_density_header(bb, spacing)
1002 def read_map(*args):
1004 read_map(std::string filename, MapReaderWriter reader) -> DensityMap
1005 read_map(std::string filename) -> DensityMap
1007 return _IMP_em.read_map(*args)
1009 def write_map(*args):
1011 write_map(DensityMap m, std::string filename, MapReaderWriter writer)
1012 write_map(DensityMap m, std::string filename)
1014 return _IMP_em.write_map(*args)
1017 """approximate_molecular_mass(DensityMap m, IMP::Float threshold) -> IMP::Float"""
1018 return _IMP_em.approximate_molecular_mass(m, threshold)
1020 """Proxy of C++ IMP::em::DensityMap class"""
1021 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1023 def __init__(self, *args):
1025 __init__(IMP::em::DensityMap self, std::string name) -> DensityMap
1026 __init__(IMP::em::DensityMap self) -> DensityMap
1027 __init__(IMP::em::DensityMap self, DensityHeader header, std::string name) -> DensityMap
1028 __init__(IMP::em::DensityMap self, DensityHeader header) -> DensityMap
1030 this = _IMP_em.new_DensityMap(*args)
1032 self.this.append(this)
1036 def reset_data(self, value=0.0):
1038 reset_data(DensityMap self, float value=0.0)
1039 reset_data(DensityMap self)
1041 return _IMP_em.DensityMap_reset_data(self, value)
1045 """calcRMS(DensityMap self) -> IMP::em::emreal"""
1046 return _IMP_em.DensityMap_calcRMS(self)
1049 def std_normalize(self):
1050 """std_normalize(DensityMap self)"""
1051 return _IMP_em.DensityMap_std_normalize(self)
1054 def is_normalized(self):
1055 """is_normalized(DensityMap self) -> bool"""
1056 return _IMP_em.DensityMap_is_normalized(self)
1059 def get_location_in_dim_by_voxel(self, index, dim):
1060 """get_location_in_dim_by_voxel(DensityMap self, long index, int dim) -> float"""
1061 return _IMP_em.DensityMap_get_location_in_dim_by_voxel(self, index, dim)
1064 def xyz_ind2voxel(self, x, y, z):
1065 """xyz_ind2voxel(DensityMap self, int x, int y, int z) -> long"""
1066 return _IMP_em.DensityMap_xyz_ind2voxel(self, x, y, z)
1069 def get_voxel_by_location(self, *args):
1071 get_voxel_by_location(DensityMap self, float x, float y, float z) -> long
1072 get_voxel_by_location(DensityMap self, Vector3D v) -> long
1074 return _IMP_em.DensityMap_get_voxel_by_location(self, *args)
1077 def get_location_by_voxel(self, index):
1078 """get_location_by_voxel(DensityMap self, long index) -> Vector3D"""
1079 return _IMP_em.DensityMap_get_location_by_voxel(self, index)
1082 def is_xyz_ind_part_of_volume(self, ix, iy, iz):
1083 """is_xyz_ind_part_of_volume(DensityMap self, int ix, int iy, int iz) -> bool"""
1084 return _IMP_em.DensityMap_is_xyz_ind_part_of_volume(self, ix, iy, iz)
1087 def is_part_of_volume(self, *args):
1089 is_part_of_volume(DensityMap self, float x, float y, float z) -> bool
1090 is_part_of_volume(DensityMap self, Vector3D v) -> bool
1092 return _IMP_em.DensityMap_is_part_of_volume(self, *args)
1095 def get_value(self, *args):
1097 get_value(DensityMap self, float x, float y, float z) -> IMP::em::emreal
1098 get_value(DensityMap self, Vector3D point) -> IMP::em::emreal
1099 get_value(DensityMap self, long index) -> IMP::em::emreal
1101 return _IMP_em.DensityMap_get_value(self, *args)
1104 def set_value(self, *args):
1106 set_value(DensityMap self, long index, IMP::em::emreal value)
1107 set_value(DensityMap self, float x, float y, float z, IMP::em::emreal value)
1109 return _IMP_em.DensityMap_set_value(self, *args)
1112 def set_origin(self, *args):
1114 set_origin(DensityMap self, float x, float y, float z)
1115 set_origin(DensityMap self, Vector3D v)
1117 return _IMP_em.DensityMap_set_origin(self, *args)
1120 def get_origin(self):
1121 """get_origin(DensityMap self) -> Vector3D"""
1122 return _IMP_em.DensityMap_get_origin(self)
1126 """get_top(DensityMap self) -> Vector3D"""
1127 return _IMP_em.DensityMap_get_top(self)
1130 def get_header(self):
1131 h = _IMP_em.DensityMap_get_header(self)
1137 def get_header_writable(self):
1138 h = _IMP_em.DensityMap_get_header_writable(self)
1144 def same_origin(self, other):
1145 """same_origin(DensityMap self, DensityMap other) -> bool"""
1146 return _IMP_em.DensityMap_same_origin(self, other)
1149 def same_dimensions(self, other):
1150 """same_dimensions(DensityMap self, DensityMap other) -> bool"""
1151 return _IMP_em.DensityMap_same_dimensions(self, other)
1154 def same_voxel_size(self, other):
1155 """same_voxel_size(DensityMap self, DensityMap other) -> bool"""
1156 return _IMP_em.DensityMap_same_voxel_size(self, other)
1161 get_centroid(DensityMap self, IMP::em::emreal threshold=0.0) -> Vector3D
1162 get_centroid(DensityMap self) -> Vector3D
1164 return _IMP_em.DensityMap_get_centroid(self, threshold)
1167 def get_max_value(self):
1168 """get_max_value(DensityMap self) -> IMP::em::emreal"""
1169 return _IMP_em.DensityMap_get_max_value(self)
1172 def get_min_value(self):
1173 """get_min_value(DensityMap self) -> IMP::em::emreal"""
1174 return _IMP_em.DensityMap_get_min_value(self)
1177 def add(self, *args):
1179 add(DensityMap self, DensityMap other)
1180 add(DensityMap self, IMP::Float d)
1182 return _IMP_em.DensityMap_add(self, *args)
1185 def pick_max(self, other):
1186 """pick_max(DensityMap self, DensityMap other)"""
1187 return _IMP_em.DensityMap_pick_max(self, other)
1190 def get_number_of_voxels(self):
1191 """get_number_of_voxels(DensityMap self) -> long"""
1192 return _IMP_em.DensityMap_get_number_of_voxels(self)
1195 def set_void_map(self, nx, ny, nz):
1196 """set_void_map(DensityMap self, int nx, int ny, int nz)"""
1197 return _IMP_em.DensityMap_set_void_map(self, nx, ny, nz)
1200 def pad(self, nx, ny, nz, val=0.0):
1202 pad(DensityMap self, int nx, int ny, int nz, float val=0.0)
1203 pad(DensityMap self, int nx, int ny, int nz)
1205 return _IMP_em.DensityMap_pad(self, nx, ny, nz, val)
1208 def pad_margin(self, mrg_x, mrg_y, mrg_z, val=0.0):
1210 pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z, float val=0.0) -> DensityMap
1211 pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z) -> DensityMap
1213 return _IMP_em.DensityMap_pad_margin(self, mrg_x, mrg_y, mrg_z, val)
1216 def get_cropped(self, *args):
1218 get_cropped(DensityMap self, float threshold) -> DensityMap
1219 get_cropped(DensityMap self, IMP::Particles ps, double distance, bool inverse=False, bool keep_map_dimensions=False) -> DensityMap
1220 get_cropped(DensityMap self, IMP::Particles ps, double distance, bool inverse=False) -> DensityMap
1221 get_cropped(DensityMap self, IMP::Particles ps, double distance) -> DensityMap
1222 get_cropped(DensityMap self, BoundingBox3D bb) -> DensityMap
1224 return _IMP_em.DensityMap_get_cropped(self, *args)
1227 def get_maximum_value_in_xy_plane(self, z_ind):
1228 """get_maximum_value_in_xy_plane(DensityMap self, int z_ind) -> float"""
1229 return _IMP_em.DensityMap_get_maximum_value_in_xy_plane(self, z_ind)
1232 def get_maximum_value_in_xz_plane(self, y_ind):
1233 """get_maximum_value_in_xz_plane(DensityMap self, int y_ind) -> float"""
1234 return _IMP_em.DensityMap_get_maximum_value_in_xz_plane(self, y_ind)
1237 def get_maximum_value_in_yz_plane(self, x_ind):
1238 """get_maximum_value_in_yz_plane(DensityMap self, int x_ind) -> float"""
1239 return _IMP_em.DensityMap_get_maximum_value_in_yz_plane(self, x_ind)
1243 """multiply(DensityMap self, float factor)"""
1244 return _IMP_em.DensityMap_multiply(self, factor)
1247 def get_locations_string(self, t):
1248 """get_locations_string(DensityMap self, float t) -> std::string"""
1249 return _IMP_em.DensityMap_get_locations_string(self, t)
1252 def update_voxel_size(self, new_apix):
1253 """update_voxel_size(DensityMap self, float new_apix)"""
1254 return _IMP_em.DensityMap_update_voxel_size(self, new_apix)
1257 def get_spacing(self):
1258 """get_spacing(DensityMap self) -> IMP::Float"""
1259 return _IMP_em.DensityMap_get_spacing(self)
1262 def calc_all_voxel2loc(self):
1263 """calc_all_voxel2loc(DensityMap self)"""
1264 return _IMP_em.DensityMap_calc_all_voxel2loc(self)
1267 def copy_map(self, other):
1268 """copy_map(DensityMap self, DensityMap other)"""
1269 return _IMP_em.DensityMap_copy_map(self, other)
1272 def get_version_info(self):
1273 """get_version_info(DensityMap self) -> VersionInfo"""
1274 return _IMP_em.DensityMap_get_version_info(self)
1277 def lower_voxel_shift(self, loc, kdist, orig, ndim):
1278 """lower_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
1279 return _IMP_em.DensityMap_lower_voxel_shift(self, loc, kdist, orig, ndim)
1282 def upper_voxel_shift(self, loc, kdist, orig, ndim):
1283 """upper_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
1284 return _IMP_em.DensityMap_upper_voxel_shift(self, loc, kdist, orig, ndim)
1287 def get_rms_calculated(self):
1288 """get_rms_calculated(DensityMap self) -> bool"""
1289 return _IMP_em.DensityMap_get_rms_calculated(self)
1292 def get_dim_index_by_location(self, *args):
1294 get_dim_index_by_location(DensityMap self, Vector3D v, int ind) -> int
1295 get_dim_index_by_location(DensityMap self, float loc_val, int ind) -> int
1297 return _IMP_em.DensityMap_get_dim_index_by_location(self, *args)
1301 """__str__(DensityMap self) -> std::string"""
1302 return _IMP_em.DensityMap___str__(self)
1306 """__repr__(DensityMap self) -> std::string"""
1307 return _IMP_em.DensityMap___repr__(self)
1312 return _object_cast_to_DensityMap(o)
1314 DensityMap_swigregister = _IMP_em.DensityMap_swigregister
1315 DensityMap_swigregister(DensityMap)
1320 get_bounding_box(DensityMap m, IMP::Float threshold) -> BoundingBox3D
1321 get_bounding_box(DensityMap m) -> BoundingBox3D
1323 return _IMP_em.get_bounding_box(*args)
1325 def get_density(m, v):
1326 """get_density(DensityMap m, Vector3D v) -> double"""
1327 return _IMP_em.get_density(m, v)
1329 def get_transformed(*args):
1331 get_transformed(DensityMap input, Transformation3D tr, double threshold) -> DensityMap
1332 get_transformed(DensityMap input, Transformation3D tr) -> DensityMap
1334 return _IMP_em.get_transformed(*args)
1336 def get_resampled(input, scaling):
1337 """get_resampled(DensityMap input, double scaling) -> DensityMap"""
1338 return _IMP_em.get_resampled(input, scaling)
1340 def get_transformed_into(source, tr, into, calc_rms=True):
1342 get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into, bool calc_rms=True)
1343 get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into)
1345 return _IMP_em.get_transformed_into(source, tr, into, calc_rms)
1347 def get_transformed_into2(source, tr, into):
1348 """get_transformed_into2(DensityMap source, Transformation3D tr, DensityMap into)"""
1349 return _IMP_em.get_transformed_into2(source, tr, into)
1351 def get_interiors_intersect(d1, d2):
1352 """get_interiors_intersect(DensityMap d1, DensityMap d2) -> bool"""
1353 return _IMP_em.get_interiors_intersect(d1, d2)
1357 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
1358 get_segment(DensityMap map_to_segment, IMP::algebra::Vector3Ds vecs, float dist) -> DensityMap
1360 return _IMP_em.get_segment(*args)
1363 """get_segment_by_masking(DensityMap map_to_segment, DensityMap mask, float mas_threshold) -> DensityMap"""
1364 return _IMP_em.get_segment_by_masking(map_to_segment, mask, mas_threshold)
1366 def binarize(orig_map, threshold, reverse=False):
1368 binarize(DensityMap orig_map, float threshold, bool reverse=False) -> DensityMap
1369 binarize(DensityMap orig_map, float threshold) -> DensityMap
1371 return _IMP_em.binarize(orig_map, threshold, reverse)
1374 """get_threshold_map(DensityMap orig_map, float threshold) -> DensityMap"""
1375 return _IMP_em.get_threshold_map(orig_map, threshold)
1378 """multiply(DensityMap m1, DensityMap m2) -> DensityMap"""
1379 return _IMP_em.multiply(m1, m2)
1382 """convolute(DensityMap m1, DensityMap m2) -> double"""
1383 return _IMP_em.convolute(m1, m2)
1386 """get_sum(DensityMap m1) -> double"""
1387 return _IMP_em.get_sum(m1)
1390 """get_max_map(IMP::em::DensityMaps maps) -> DensityMap"""
1391 return _IMP_em.get_max_map(maps)
1394 """interpolate_map(DensityMap in_map, double new_spacing) -> DensityMap"""
1395 return _IMP_em.interpolate_map(in_map, new_spacing)
1398 """get_grid(DensityMap in_map) -> IMP::algebra::GridD< 3,IMP::algebra::DenseGridStorageD< 3,float >,float,IMP::algebra::DefaultEmbeddingD< 3 > >"""
1399 return _IMP_em.get_grid(in_map)
1403 create_density_map(DensityMap other) -> DensityMap
1404 create_density_map(BoundingBox3D bb, double spacing) -> DensityMap
1405 create_density_map(int nx, int ny, int nz, double spacing) -> DensityMap
1406 create_density_map(DenseFloatGrid3D grid) -> DensityMap
1407 create_density_map(DenseDoubleGrid3D grid) -> DensityMap
1409 return _IMP_em.create_density_map(*args)
1411 def get_binarized_interior(dmap):
1412 """get_binarized_interior(DensityMap dmap) -> DensityMap"""
1413 return _IMP_em.get_binarized_interior(dmap)
1415 def add_to_map(dm, pis):
1416 """add_to_map(DensityMap dm, IMP::Particles const & pis)"""
1417 return _IMP_em.add_to_map(dm, pis)
1418 class RadiusDependentDistanceMask(object):
1419 """Proxy of C++ IMP::em::RadiusDependentDistanceMask class"""
1420 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1421 __repr__ = _swig_repr
1423 def __init__(self, sampling_radius, header):
1424 """__init__(IMP::em::RadiusDependentDistanceMask self, float sampling_radius, DensityHeader header) -> RadiusDependentDistanceMask"""
1425 this = _IMP_em.new_RadiusDependentDistanceMask(sampling_radius, header)
1427 self.this.append(this)
1431 def get_neighbor_shift(self):
1432 """get_neighbor_shift(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1433 return _IMP_em.RadiusDependentDistanceMask_get_neighbor_shift(self)
1436 def get_neighbor_dist(self):
1437 """get_neighbor_dist(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1438 return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist(self)
1441 def get_neighbor_dist_exp(self):
1442 """get_neighbor_dist_exp(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1443 return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist_exp(self)
1446 def show(self, out):
1447 """show(RadiusDependentDistanceMask self, _ostream out)"""
1448 return _IMP_em.RadiusDependentDistanceMask_show(self, out)
1450 __swig_destroy__ = _IMP_em.delete_RadiusDependentDistanceMask
1451 __del__ =
lambda self:
None
1452 RadiusDependentDistanceMask_swigregister = _IMP_em.RadiusDependentDistanceMask_swigregister
1453 RadiusDependentDistanceMask_swigregister(RadiusDependentDistanceMask)
1455 class DistanceMask(object):
1456 """Proxy of C++ IMP::em::DistanceMask class"""
1457 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1458 __repr__ = _swig_repr
1460 def __init__(self, *args):
1462 __init__(IMP::em::DistanceMask self) -> DistanceMask
1463 __init__(IMP::em::DistanceMask self, DensityHeader header) -> DistanceMask
1465 this = _IMP_em.new_DistanceMask(*args)
1467 self.this.append(this)
1471 def show(self, out):
1472 """show(DistanceMask self, _ostream out)"""
1473 return _IMP_em.DistanceMask_show(self, out)
1476 def is_mask_set(self, radius, eps=0.001):
1478 is_mask_set(DistanceMask self, float radius, float eps=0.001) -> bool
1479 is_mask_set(DistanceMask self, float radius) -> bool
1481 return _IMP_em.DistanceMask_is_mask_set(self, radius, eps)
1483 __swig_destroy__ = _IMP_em.delete_DistanceMask
1484 __del__ =
lambda self:
None
1485 DistanceMask_swigregister = _IMP_em.DistanceMask_swigregister
1486 DistanceMask_swigregister(DistanceMask)
1488 class EMReaderWriter(MapReaderWriter):
1489 """Proxy of C++ IMP::em::EMReaderWriter class"""
1490 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1493 """__str__(EMReaderWriter self) -> std::string"""
1494 return _IMP_em.EMReaderWriter___str__(self)
1498 """__repr__(EMReaderWriter self) -> std::string"""
1499 return _IMP_em.EMReaderWriter___repr__(self)
1504 return _object_cast_to_EMReaderWriter(o)
1508 """__init__(IMP::em::EMReaderWriter self) -> EMReaderWriter"""
1509 this = _IMP_em.new_EMReaderWriter()
1511 self.this.append(this)
1514 EMReaderWriter_swigregister = _IMP_em.EMReaderWriter_swigregister
1515 EMReaderWriter_swigregister(EMReaderWriter)
1517 class XplorReaderWriter(MapReaderWriter):
1518 """Proxy of C++ IMP::em::XplorReaderWriter class"""
1519 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1522 """__str__(XplorReaderWriter self) -> std::string"""
1523 return _IMP_em.XplorReaderWriter___str__(self)
1527 """__repr__(XplorReaderWriter self) -> std::string"""
1528 return _IMP_em.XplorReaderWriter___repr__(self)
1533 return _object_cast_to_XplorReaderWriter(o)
1537 """__init__(IMP::em::XplorReaderWriter self) -> XplorReaderWriter"""
1538 this = _IMP_em.new_XplorReaderWriter()
1540 self.this.append(this)
1543 XplorReaderWriter_swigregister = _IMP_em.XplorReaderWriter_swigregister
1544 XplorReaderWriter_swigregister(XplorReaderWriter)
1546 class MRCReaderWriter(MapReaderWriter):
1547 """Proxy of C++ IMP::em::MRCReaderWriter class"""
1548 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1550 def __init__(self, *args):
1552 __init__(IMP::em::MRCReaderWriter self) -> MRCReaderWriter
1553 __init__(IMP::em::MRCReaderWriter self, std::string fn) -> MRCReaderWriter
1555 this = _IMP_em.new_MRCReaderWriter(*args)
1557 self.this.append(this)
1562 """__str__(MRCReaderWriter self) -> std::string"""
1563 return _IMP_em.MRCReaderWriter___str__(self)
1567 """__repr__(MRCReaderWriter self) -> std::string"""
1568 return _IMP_em.MRCReaderWriter___repr__(self)
1573 return _object_cast_to_MRCReaderWriter(o)
1575 MRCReaderWriter_swigregister = _IMP_em.MRCReaderWriter_swigregister
1576 MRCReaderWriter_swigregister(MRCReaderWriter)
1578 class KernelParameters(object):
1579 """Proxy of C++ IMP::em::KernelParameters class"""
1580 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1582 def __init__(self, *args):
1584 __init__(IMP::em::KernelParameters self) -> KernelParameters
1585 __init__(IMP::em::KernelParameters self, float resolution) -> KernelParameters
1587 this = _IMP_em.new_KernelParameters(*args)
1589 self.this.append(this)
1592 __swig_destroy__ = _IMP_em.delete_KernelParameters
1593 __del__ =
lambda self:
None
1596 """get_rsig(KernelParameters self) -> float"""
1597 return _IMP_em.KernelParameters_get_rsig(self)
1600 def get_rsigsq(self):
1601 """get_rsigsq(KernelParameters self) -> float"""
1602 return _IMP_em.KernelParameters_get_rsigsq(self)
1605 def get_inv_rsigsq(self):
1606 """get_inv_rsigsq(KernelParameters self) -> float"""
1607 return _IMP_em.KernelParameters_get_inv_rsigsq(self)
1610 def get_timessig(self):
1611 """get_timessig(KernelParameters self) -> float"""
1612 return _IMP_em.KernelParameters_get_timessig(self)
1615 def get_sq2pi3(self):
1616 """get_sq2pi3(KernelParameters self) -> float"""
1617 return _IMP_em.KernelParameters_get_sq2pi3(self)
1620 def get_rnormfac(self):
1621 """get_rnormfac(KernelParameters self) -> float"""
1622 return _IMP_em.KernelParameters_get_rnormfac(self)
1625 def get_rkdist(self):
1626 """get_rkdist(KernelParameters self) -> float"""
1627 return _IMP_em.KernelParameters_get_rkdist(self)
1630 def get_rkdistsq(self):
1631 """get_rkdistsq(KernelParameters self) -> float"""
1632 return _IMP_em.KernelParameters_get_rkdistsq(self)
1636 """get_lim(KernelParameters self) -> float"""
1637 return _IMP_em.KernelParameters_get_lim(self)
1640 def show(self, *args):
1642 show(KernelParameters self, _ostream out)
1643 show(KernelParameters self)
1645 return _IMP_em.KernelParameters_show(self, *args)
1649 """__str__(KernelParameters self) -> std::string"""
1650 return _IMP_em.KernelParameters___str__(self)
1654 """__repr__(KernelParameters self) -> std::string"""
1655 return _IMP_em.KernelParameters___repr__(self)
1657 KernelParameters_swigregister = _IMP_em.KernelParameters_swigregister
1658 KernelParameters_swigregister(KernelParameters)
1661 _IMP_em.GAUSSIAN_swigconstant(_IMP_em)
1662 GAUSSIAN = _IMP_em.GAUSSIAN
1664 _IMP_em.BINARIZED_SPHERE_swigconstant(_IMP_em)
1665 BINARIZED_SPHERE = _IMP_em.BINARIZED_SPHERE
1667 _IMP_em.SPHERE_swigconstant(_IMP_em)
1668 SPHERE = _IMP_em.SPHERE
1669 class SampledDensityMap(DensityMap):
1670 """Proxy of C++ IMP::em::SampledDensityMap class"""
1671 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1673 def __init__(self, *args):
1675 __init__(IMP::em::SampledDensityMap self, IMP::em::KernelType kt) -> SampledDensityMap
1676 __init__(IMP::em::SampledDensityMap self) -> SampledDensityMap
1677 __init__(IMP::em::SampledDensityMap self, DensityHeader header, IMP::em::KernelType kt) -> SampledDensityMap
1678 __init__(IMP::em::SampledDensityMap self, DensityHeader header) -> SampledDensityMap
1679 __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
1680 __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
1681 __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size, FloatKey mass_key) -> SampledDensityMap
1682 __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size) -> SampledDensityMap
1684 this = _IMP_em.new_SampledDensityMap(*args)
1686 self.this.append(this)
1691 """resample(SampledDensityMap self)"""
1692 return _IMP_em.SampledDensityMap_resample(self)
1695 def project(self, *args):
1697 project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin, Vector3D shift, FloatKey mass_key)
1698 project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin, Vector3D shift)
1699 project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin)
1701 return _IMP_em.SampledDensityMap_project(self, *args)
1704 def set_particles(self, *args):
1706 set_particles(SampledDensityMap self, IMP::ParticlesTemp const & ps, FloatKey mass_key)
1707 set_particles(SampledDensityMap self, IMP::ParticlesTemp const & ps)
1709 return _IMP_em.SampledDensityMap_set_particles(self, *args)
1712 def get_xyzr_particles(self):
1713 """get_xyzr_particles(SampledDensityMap self) -> IMP::core::XYZRs const &"""
1714 return _IMP_em.SampledDensityMap_get_xyzr_particles(self)
1717 def get_sampled_particles(self):
1718 """get_sampled_particles(SampledDensityMap self) -> IMP::Particles const &"""
1719 return _IMP_em.SampledDensityMap_get_sampled_particles(self)
1722 def get_weight_key(self):
1723 """get_weight_key(SampledDensityMap self) -> FloatKey"""
1724 return _IMP_em.SampledDensityMap_get_weight_key(self)
1727 def get_minimum_resampled_value(self):
1728 """get_minimum_resampled_value(SampledDensityMap self) -> float"""
1729 return _IMP_em.SampledDensityMap_get_minimum_resampled_value(self)
1732 def update_resolution(self, res):
1733 """update_resolution(SampledDensityMap self, IMP::Float res)"""
1734 return _IMP_em.SampledDensityMap_update_resolution(self, res)
1736 __swig_destroy__ = _IMP_em.delete_SampledDensityMap
1737 __del__ =
lambda self:
None
1740 """__str__(SampledDensityMap self) -> std::string"""
1741 return _IMP_em.SampledDensityMap___str__(self)
1745 """__repr__(SampledDensityMap self) -> std::string"""
1746 return _IMP_em.SampledDensityMap___repr__(self)
1751 return _object_cast_to_SampledDensityMap(o)
1753 SampledDensityMap_swigregister = _IMP_em.SampledDensityMap_swigregister
1754 SampledDensityMap_swigregister(SampledDensityMap)
1757 _IMP_em.IMP_DEFAULT_NUM_SHELLS_swigconstant(_IMP_em)
1758 IMP_DEFAULT_NUM_SHELLS = _IMP_em.IMP_DEFAULT_NUM_SHELLS
1760 _IMP_em.IMP_SIG_CUTOFF_swigconstant(_IMP_em)
1761 IMP_SIG_CUTOFF = _IMP_em.IMP_SIG_CUTOFF
1762 class SurfaceShellDensityMap(SampledDensityMap):
1763 """Proxy of C++ IMP::em::SurfaceShellDensityMap class"""
1764 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1766 def __init__(self, *args):
1768 __init__(IMP::em::SurfaceShellDensityMap self) -> SurfaceShellDensityMap
1769 __init__(IMP::em::SurfaceShellDensityMap self, DensityHeader header) -> SurfaceShellDensityMap
1770 __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key, int num_shells=5) -> SurfaceShellDensityMap
1771 __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key) -> SurfaceShellDensityMap
1772 __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size) -> SurfaceShellDensityMap
1774 this = _IMP_em.new_SurfaceShellDensityMap(*args)
1776 self.this.append(this)
1781 """binarize(SurfaceShellDensityMap self, float scene_val)"""
1782 return _IMP_em.SurfaceShellDensityMap_binarize(self, scene_val)
1785 def has_background_neighbor(self, voxel_ind):
1786 """has_background_neighbor(SurfaceShellDensityMap self, long voxel_ind) -> bool"""
1787 return _IMP_em.SurfaceShellDensityMap_has_background_neighbor(self, voxel_ind)
1789 __swig_destroy__ = _IMP_em.delete_SurfaceShellDensityMap
1790 __del__ =
lambda self:
None
1793 """__str__(SurfaceShellDensityMap self) -> std::string"""
1794 return _IMP_em.SurfaceShellDensityMap___str__(self)
1798 """__repr__(SurfaceShellDensityMap self) -> std::string"""
1799 return _IMP_em.SurfaceShellDensityMap___repr__(self)
1804 return _object_cast_to_SurfaceShellDensityMap(o)
1806 SurfaceShellDensityMap_swigregister = _IMP_em.SurfaceShellDensityMap_swigregister
1807 SurfaceShellDensityMap_swigregister(SurfaceShellDensityMap)
1812 get_coarse_cc_score(DensityMap data, SampledDensityMap model_map, double scalefactor, bool recalc_rms=True, bool resample=True, IMP::FloatPair norm_factors) -> double
1813 get_coarse_cc_score(DensityMap data, SampledDensityMap model_map, double scalefactor, bool recalc_rms=True, bool resample=True) -> double
1814 get_coarse_cc_score(DensityMap data, SampledDensityMap model_map, double scalefactor, bool recalc_rms=True) -> double
1815 get_coarse_cc_score(DensityMap data, SampledDensityMap model_map, double scalefactor) -> double
1817 return _IMP_em.get_coarse_cc_score(*args)
1821 get_coarse_cc_coefficient(DensityMap grid1, DensityMap grid2, double grid2_voxel_data_threshold, bool allow_padding=False, IMP::FloatPair norm_factors) -> double
1822 get_coarse_cc_coefficient(DensityMap grid1, DensityMap grid2, double grid2_voxel_data_threshold, bool allow_padding=False) -> double
1823 get_coarse_cc_coefficient(DensityMap grid1, DensityMap grid2, double grid2_voxel_data_threshold) -> double
1825 return _IMP_em.get_coarse_cc_coefficient(*args)
1828 """get_coarse_cc_local_coefficient(DensityMap em_map, DensityMap model_map, double voxel_data_threshold) -> double"""
1829 return _IMP_em.get_coarse_cc_local_coefficient(em_map, model_map, voxel_data_threshold)
1831 """Proxy of C++ IMP::em::CoarseCC class"""
1832 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1835 """__init__(IMP::em::CoarseCC self) -> CoarseCC"""
1836 this = _IMP_em.new_CoarseCC()
1838 self.this.append(this)
1842 def calc_score(*args):
1844 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True, IMP::FloatPair norm_factors) -> float
1845 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True) -> float
1846 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1847 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1849 return _IMP_em.CoarseCC_calc_score(*args)
1851 calc_score = staticmethod(calc_score)
1853 def cross_correlation_coefficient(*args):
1855 cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False, IMP::FloatPair norm_factors) -> double
1856 cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1857 cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1859 return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1861 cross_correlation_coefficient = staticmethod(cross_correlation_coefficient)
1863 def local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold):
1864 """local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1865 return _IMP_em.CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold)
1867 local_cross_correlation_coefficient = staticmethod(local_cross_correlation_coefficient)
1869 def get_version_info(self):
1870 """get_version_info(CoarseCC self) -> VersionInfo"""
1871 return _IMP_em.CoarseCC_get_version_info(self)
1875 """__str__(CoarseCC self) -> std::string"""
1876 return _IMP_em.CoarseCC___str__(self)
1880 """__repr__(CoarseCC self) -> std::string"""
1881 return _IMP_em.CoarseCC___repr__(self)
1886 return _object_cast_to_CoarseCC(o)
1888 CoarseCC_swigregister = _IMP_em.CoarseCC_swigregister
1889 CoarseCC_swigregister(CoarseCC)
1891 def CoarseCC_calc_score(*args):
1893 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True, IMP::FloatPair norm_factors) -> float
1894 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True) -> float
1895 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1896 CoarseCC_calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1898 return _IMP_em.CoarseCC_calc_score(*args)
1900 def CoarseCC_cross_correlation_coefficient(*args):
1902 cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False, IMP::FloatPair norm_factors) -> double
1903 cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1904 CoarseCC_cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1906 return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1908 def CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold):
1909 """CoarseCC_local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1910 return _IMP_em.CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold)
1912 class CoarseConvolution(object):
1913 """Proxy of C++ IMP::em::CoarseConvolution class"""
1914 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1915 __repr__ = _swig_repr
1917 def convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac=True):
1919 convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1920 convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1922 return _IMP_em.CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac)
1924 convolution = staticmethod(convolution)
1927 """__init__(IMP::em::CoarseConvolution self) -> CoarseConvolution"""
1928 this = _IMP_em.new_CoarseConvolution()
1930 self.this.append(this)
1933 __swig_destroy__ = _IMP_em.delete_CoarseConvolution
1934 __del__ =
lambda self:
None
1935 CoarseConvolution_swigregister = _IMP_em.CoarseConvolution_swigregister
1936 CoarseConvolution_swigregister(CoarseConvolution)
1938 def CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac=True):
1940 convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1941 CoarseConvolution_convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1943 return _IMP_em.CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac)
1946 """Proxy of C++ IMP::em::CoarseCCatIntervals class"""
1947 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1949 def __init__(self, *args):
1951 __init__(IMP::em::CoarseCCatIntervals self, int const & ncd) -> CoarseCCatIntervals
1952 __init__(IMP::em::CoarseCCatIntervals self) -> CoarseCCatIntervals
1954 this = _IMP_em.new_CoarseCCatIntervals(*args)
1956 self.this.append(this)
1960 def evaluate(self, em_map, model_map, deriv, scalefac, lderiv, eval_interval):
1961 """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 >"""
1962 return _IMP_em.CoarseCCatIntervals_evaluate(self, em_map, model_map, deriv, scalefac, lderiv, eval_interval)
1965 def get_version_info(self):
1966 """get_version_info(CoarseCCatIntervals self) -> VersionInfo"""
1967 return _IMP_em.CoarseCCatIntervals_get_version_info(self)
1971 """__str__(CoarseCCatIntervals self) -> std::string"""
1972 return _IMP_em.CoarseCCatIntervals___str__(self)
1976 """__repr__(CoarseCCatIntervals self) -> std::string"""
1977 return _IMP_em.CoarseCCatIntervals___repr__(self)
1982 return _object_cast_to_CoarseCCatIntervals(o)
1984 CoarseCCatIntervals_swigregister = _IMP_em.CoarseCCatIntervals_swigregister
1985 CoarseCCatIntervals_swigregister(CoarseCCatIntervals)
1989 """bayesem3d_get_distinct_and_counts(DensityMap em) -> std::map< double,int >"""
1990 return _IMP_em.bayesem3d_get_distinct_and_counts(em)
1993 """bayesem3d_get_cumulative_sum(DensityMap em) -> IMP::Floats"""
1994 return _IMP_em.bayesem3d_get_cumulative_sum(em)
1997 """bayesem3d_get_cumulative_sum_with_reference(DensityMap em) -> std::map< double,double >"""
1998 return _IMP_em.bayesem3d_get_cumulative_sum_with_reference(em)
2001 """bayesem3d_linear_interpolate(IMP::Floats const & x_data, IMP::Floats const & y_data, double x, bool extrapolate) -> double"""
2002 return _IMP_em.bayesem3d_linear_interpolate(x_data, y_data, x, extrapolate)
2005 """bayesem3d_get_logabssumexp(double x, double y, double sx, double sy) -> IMP::FloatPair"""
2006 return _IMP_em.bayesem3d_get_logabssumexp(x, y, sx, sy)
2009 """bayesem3d_get_logabssumprodexp(double x, double y, double wx, double wy) -> IMP::FloatPair"""
2010 return _IMP_em.bayesem3d_get_logabssumprodexp(x, y, wx, wy)
2013 """bayesem3d_get_logsumexp(double x, double y) -> double"""
2014 return _IMP_em.bayesem3d_get_logsumexp(x, y)
2017 """bayesem3d_get_logsumprodexp(double x, double y, double wx, double wy) -> double"""
2018 return _IMP_em.bayesem3d_get_logsumprodexp(x, y, wx, wy)
2021 """bayesem3d_get_em_density_squared(DensityMap em, long number_of_voxels) -> IMP::FloatPair"""
2022 return _IMP_em.bayesem3d_get_em_density_squared(em, number_of_voxels)
2025 """bayesem3d_get_value(Particle p, Vector3D pt, double mass_ii, KernelParameters kps) -> std::vector< double,std::allocator< double > >"""
2026 return _IMP_em.bayesem3d_get_value(p, pt, mass_ii, kps)
2029 """bayesem3d_get_value_no_deriv(Particle p, Vector3D pt, double mass_ii, KernelParameters kps) -> std::vector< double,std::allocator< double > >"""
2030 return _IMP_em.bayesem3d_get_value_no_deriv(p, pt, mass_ii, kps)
2033 """bayesem3d_get_density_from_particle(DensityMap em, IMP::ParticlesTemp const & ps, double resolution) -> DensityMap"""
2034 return _IMP_em.bayesem3d_get_density_from_particle(em, ps, resolution)
2037 """bayesem3d_get_cross_correlation_coefficient(DensityMap em1, DensityMap em2) -> double"""
2038 return _IMP_em.bayesem3d_get_cross_correlation_coefficient(em1, em2)
2041 """bayesem3d_get_score_and_derivative(DensityMap em, IMP::ParticlesTemp const & ps, double resolution, double sigma) -> std::pair< double,IMP::algebra::Vector3Ds >"""
2042 return _IMP_em.bayesem3d_get_score_and_derivative(em, ps, resolution, sigma)
2045 """bayesem3d_get_normalized_intensities(DensityMap em, IMP::ParticlesTemp const & ps, double resolution)"""
2046 return _IMP_em.bayesem3d_get_normalized_intensities(em, ps, resolution)
2048 """Proxy of C++ IMP::em::FitRestraint class"""
2049 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2051 def __init__(self, *args):
2053 __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
2054 __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
2055 __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key, float scale=1) -> FitRestraint
2056 __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key) -> FitRestraint
2057 __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors) -> FitRestraint
2058 __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map) -> FitRestraint
2060 this = _IMP_em.new_FitRestraint(*args)
2062 self.this.append(this)
2066 def get_model_dens_map(self):
2067 """get_model_dens_map(FitRestraint self) -> SampledDensityMap"""
2068 return _IMP_em.FitRestraint_get_model_dens_map(self)
2071 def set_scale_factor(self, scale):
2072 """set_scale_factor(FitRestraint self, float scale)"""
2073 return _IMP_em.FitRestraint_set_scale_factor(self, scale)
2076 def get_scale_factor(self):
2077 """get_scale_factor(FitRestraint self) -> float"""
2078 return _IMP_em.FitRestraint_get_scale_factor(self)
2081 def do_get_inputs(self):
2082 """do_get_inputs(FitRestraint self) -> IMP::ModelObjectsTemp"""
2083 return _IMP_em.FitRestraint_do_get_inputs(self)
2086 def get_version_info(self):
2087 """get_version_info(FitRestraint self) -> VersionInfo"""
2088 return _IMP_em.FitRestraint_get_version_info(self)
2092 """__str__(FitRestraint self) -> std::string"""
2093 return _IMP_em.FitRestraint___str__(self)
2097 """__repr__(FitRestraint self) -> std::string"""
2098 return _IMP_em.FitRestraint___repr__(self)
2103 return _object_cast_to_FitRestraint(o)
2105 FitRestraint_swigregister = _IMP_em.FitRestraint_swigregister
2106 FitRestraint_swigregister(FitRestraint)
2109 """Proxy of C++ IMP::em::FitRestraintBayesEM3D class"""
2110 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2112 def __init__(self, *args):
2114 __init__(IMP::em::FitRestraintBayesEM3D self, IMP::ParticlesTemp ps, DensityMap em_map, FloatKey weight_key, bool use_rigid_bodies=True, double sigma=.1) -> FitRestraintBayesEM3D
2115 __init__(IMP::em::FitRestraintBayesEM3D self, IMP::ParticlesTemp ps, DensityMap em_map, FloatKey weight_key, bool use_rigid_bodies=True) -> FitRestraintBayesEM3D
2116 __init__(IMP::em::FitRestraintBayesEM3D self, IMP::ParticlesTemp ps, DensityMap em_map, FloatKey weight_key) -> FitRestraintBayesEM3D
2117 __init__(IMP::em::FitRestraintBayesEM3D self, IMP::ParticlesTemp ps, DensityMap em_map) -> FitRestraintBayesEM3D
2119 this = _IMP_em.new_FitRestraintBayesEM3D(*args)
2121 self.this.append(this)
2125 def do_get_inputs(self):
2126 """do_get_inputs(FitRestraintBayesEM3D self) -> IMP::ModelObjectsTemp"""
2127 return _IMP_em.FitRestraintBayesEM3D_do_get_inputs(self)
2130 def get_version_info(self):
2131 """get_version_info(FitRestraintBayesEM3D self) -> VersionInfo"""
2132 return _IMP_em.FitRestraintBayesEM3D_get_version_info(self)
2136 """__str__(FitRestraintBayesEM3D self) -> std::string"""
2137 return _IMP_em.FitRestraintBayesEM3D___str__(self)
2141 """__repr__(FitRestraintBayesEM3D self) -> std::string"""
2142 return _IMP_em.FitRestraintBayesEM3D___repr__(self)
2147 return _object_cast_to_FitRestraintBayesEM3D(o)
2149 FitRestraintBayesEM3D_swigregister = _IMP_em.FitRestraintBayesEM3D_swigregister
2150 FitRestraintBayesEM3D_swigregister(FitRestraintBayesEM3D)
2155 density2particles(DensityMap dmap, IMP::Float threshold, Model m, int step=1) -> IMP::Particles
2156 density2particles(DensityMap dmap, IMP::Float threshold, Model m) -> IMP::Particles
2158 return _IMP_em.density2particles(dmap, threshold, m, step)
2161 """density2vectors(DensityMap dmap, IMP::Float threshold) -> IMP::algebra::Vector3Ds"""
2162 return _IMP_em.density2vectors(dmap, threshold)
2166 particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3, FloatKey weight_key) -> SampledDensityMap
2167 particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
2168 particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
2170 return _IMP_em.particles2density(*args)
2174 particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3, FloatKey weight_key) -> SampledDensityMap
2175 particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
2176 particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
2178 return _IMP_em.particles2binarized_density(*args)
2182 particles2surface(IMP::ParticlesTemp const & ps, IMP::Float apix, FloatKey weight_key) -> SurfaceShellDensityMap
2183 particles2surface(IMP::ParticlesTemp const & ps, IMP::Float apix) -> SurfaceShellDensityMap
2185 return _IMP_em.particles2surface(*args)
2187 def calculate_intersection_score(d1, d2):
2188 """calculate_intersection_score(SurfaceShellDensityMap d1, SurfaceShellDensityMap d2) -> IMP::Float"""
2189 return _IMP_em.calculate_intersection_score(d1, d2)
2190 class SpiderHeader(object):
2191 """Proxy of C++ IMP::em::SpiderHeader class"""
2192 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2193 __repr__ = _swig_repr
2194 fNslice = _swig_property(_IMP_em.SpiderHeader_fNslice_get, _IMP_em.SpiderHeader_fNslice_set)
2195 fNrow = _swig_property(_IMP_em.SpiderHeader_fNrow_get, _IMP_em.SpiderHeader_fNrow_set)
2196 fNrec = _swig_property(_IMP_em.SpiderHeader_fNrec_get, _IMP_em.SpiderHeader_fNrec_set)
2197 fNlabel = _swig_property(_IMP_em.SpiderHeader_fNlabel_get, _IMP_em.SpiderHeader_fNlabel_set)
2198 fIform = _swig_property(_IMP_em.SpiderHeader_fIform_get, _IMP_em.SpiderHeader_fIform_set)
2199 fImami = _swig_property(_IMP_em.SpiderHeader_fImami_get, _IMP_em.SpiderHeader_fImami_set)
2200 fFmax = _swig_property(_IMP_em.SpiderHeader_fFmax_get, _IMP_em.SpiderHeader_fFmax_set)
2201 fFmin = _swig_property(_IMP_em.SpiderHeader_fFmin_get, _IMP_em.SpiderHeader_fFmin_set)
2202 fAv = _swig_property(_IMP_em.SpiderHeader_fAv_get, _IMP_em.SpiderHeader_fAv_set)
2203 fSig = _swig_property(_IMP_em.SpiderHeader_fSig_get, _IMP_em.SpiderHeader_fSig_set)
2204 fIhist = _swig_property(_IMP_em.SpiderHeader_fIhist_get, _IMP_em.SpiderHeader_fIhist_set)
2205 fNcol = _swig_property(_IMP_em.SpiderHeader_fNcol_get, _IMP_em.SpiderHeader_fNcol_set)
2206 fLabrec = _swig_property(_IMP_em.SpiderHeader_fLabrec_get, _IMP_em.SpiderHeader_fLabrec_set)
2207 fIangle = _swig_property(_IMP_em.SpiderHeader_fIangle_get, _IMP_em.SpiderHeader_fIangle_set)
2208 fPhi = _swig_property(_IMP_em.SpiderHeader_fPhi_get, _IMP_em.SpiderHeader_fPhi_set)
2209 fTheta = _swig_property(_IMP_em.SpiderHeader_fTheta_get, _IMP_em.SpiderHeader_fTheta_set)
2210 fPsi = _swig_property(_IMP_em.SpiderHeader_fPsi_get, _IMP_em.SpiderHeader_fPsi_set)
2211 fXoff = _swig_property(_IMP_em.SpiderHeader_fXoff_get, _IMP_em.SpiderHeader_fXoff_set)
2212 fYoff = _swig_property(_IMP_em.SpiderHeader_fYoff_get, _IMP_em.SpiderHeader_fYoff_set)
2213 fZoff = _swig_property(_IMP_em.SpiderHeader_fZoff_get, _IMP_em.SpiderHeader_fZoff_set)
2214 fScale = _swig_property(_IMP_em.SpiderHeader_fScale_get, _IMP_em.SpiderHeader_fScale_set)
2215 fLabbyt = _swig_property(_IMP_em.SpiderHeader_fLabbyt_get, _IMP_em.SpiderHeader_fLabbyt_set)
2216 fLenbyt = _swig_property(_IMP_em.SpiderHeader_fLenbyt_get, _IMP_em.SpiderHeader_fLenbyt_set)
2217 fNothing = _swig_property(_IMP_em.SpiderHeader_fNothing_get, _IMP_em.SpiderHeader_fNothing_set)
2218 fFlag = _swig_property(_IMP_em.SpiderHeader_fFlag_get, _IMP_em.SpiderHeader_fFlag_set)
2219 fPhi1 = _swig_property(_IMP_em.SpiderHeader_fPhi1_get, _IMP_em.SpiderHeader_fPhi1_set)
2220 fTheta1 = _swig_property(_IMP_em.SpiderHeader_fTheta1_get, _IMP_em.SpiderHeader_fTheta1_set)
2221 fPsi1 = _swig_property(_IMP_em.SpiderHeader_fPsi1_get, _IMP_em.SpiderHeader_fPsi1_set)
2222 fPhi2 = _swig_property(_IMP_em.SpiderHeader_fPhi2_get, _IMP_em.SpiderHeader_fPhi2_set)
2223 fTheta2 = _swig_property(_IMP_em.SpiderHeader_fTheta2_get, _IMP_em.SpiderHeader_fTheta2_set)
2224 fPsi2 = _swig_property(_IMP_em.SpiderHeader_fPsi2_get, _IMP_em.SpiderHeader_fPsi2_set)
2225 fGeo_matrix = _swig_property(_IMP_em.SpiderHeader_fGeo_matrix_get, _IMP_em.SpiderHeader_fGeo_matrix_set)
2226 fAngle1 = _swig_property(_IMP_em.SpiderHeader_fAngle1_get, _IMP_em.SpiderHeader_fAngle1_set)
2227 fr1 = _swig_property(_IMP_em.SpiderHeader_fr1_get, _IMP_em.SpiderHeader_fr1_set)
2228 fr2 = _swig_property(_IMP_em.SpiderHeader_fr2_get, _IMP_em.SpiderHeader_fr2_set)
2229 RTflag = _swig_property(_IMP_em.SpiderHeader_RTflag_get, _IMP_em.SpiderHeader_RTflag_set)
2230 Astart = _swig_property(_IMP_em.SpiderHeader_Astart_get, _IMP_em.SpiderHeader_Astart_set)
2231 Aend = _swig_property(_IMP_em.SpiderHeader_Aend_get, _IMP_em.SpiderHeader_Aend_set)
2232 Ainc = _swig_property(_IMP_em.SpiderHeader_Ainc_get, _IMP_em.SpiderHeader_Ainc_set)
2233 Rsigma = _swig_property(_IMP_em.SpiderHeader_Rsigma_get, _IMP_em.SpiderHeader_Rsigma_set)
2234 Tstart = _swig_property(_IMP_em.SpiderHeader_Tstart_get, _IMP_em.SpiderHeader_Tstart_set)
2235 Tend = _swig_property(_IMP_em.SpiderHeader_Tend_get, _IMP_em.SpiderHeader_Tend_set)
2236 Tinc = _swig_property(_IMP_em.SpiderHeader_Tinc_get, _IMP_em.SpiderHeader_Tinc_set)
2237 Weight = _swig_property(_IMP_em.SpiderHeader_Weight_get, _IMP_em.SpiderHeader_Weight_set)
2238 Flip = _swig_property(_IMP_em.SpiderHeader_Flip_get, _IMP_em.SpiderHeader_Flip_set)
2239 empty = _swig_property(_IMP_em.SpiderHeader_empty_get, _IMP_em.SpiderHeader_empty_set)
2240 szIDat = _swig_property(_IMP_em.SpiderHeader_szIDat_get, _IMP_em.SpiderHeader_szIDat_set)
2241 szITim = _swig_property(_IMP_em.SpiderHeader_szITim_get, _IMP_em.SpiderHeader_szITim_set)
2242 szITit = _swig_property(_IMP_em.SpiderHeader_szITit_get, _IMP_em.SpiderHeader_szITit_set)
2244 def show(self, out):
2245 """show(SpiderHeader self, _ostream out)"""
2246 return _IMP_em.SpiderHeader_show(self, out)
2250 """__init__(IMP::em::SpiderHeader self) -> SpiderHeader"""
2251 this = _IMP_em.new_SpiderHeader()
2253 self.this.append(this)
2256 __swig_destroy__ = _IMP_em.delete_SpiderHeader
2257 __del__ =
lambda self:
None
2258 SpiderHeader_swigregister = _IMP_em.SpiderHeader_swigregister
2259 SpiderHeader_swigregister(SpiderHeader)
2261 class ImageHeader(object):
2262 """Proxy of C++ IMP::em::ImageHeader class"""
2263 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2264 __repr__ = _swig_repr
2265 IMG_BYTE = _IMP_em.ImageHeader_IMG_BYTE
2266 IMG_IMPEM = _IMP_em.ImageHeader_IMG_IMPEM
2267 IMG_INT = _IMP_em.ImageHeader_IMG_INT
2268 VOL_BYTE = _IMP_em.ImageHeader_VOL_BYTE
2269 VOL_IMPEM = _IMP_em.ImageHeader_VOL_IMPEM
2270 VOL_INT = _IMP_em.ImageHeader_VOL_INT
2271 IMG_FOURIER = _IMP_em.ImageHeader_IMG_FOURIER
2272 VOL_FOURIER = _IMP_em.ImageHeader_VOL_FOURIER
2274 def __init__(self, *args):
2276 __init__(IMP::em::ImageHeader self) -> ImageHeader
2277 __init__(IMP::em::ImageHeader self, IMP::em::ImageHeader::img_type im) -> ImageHeader
2278 __init__(IMP::em::ImageHeader self, float im) -> ImageHeader
2280 this = _IMP_em.new_ImageHeader(*args)
2282 self.this.append(this)
2286 def get_image_type(self):
2287 """get_image_type(ImageHeader self) -> float"""
2288 return _IMP_em.ImageHeader_get_image_type(self)
2291 def set_image_type(self, *args):
2293 set_image_type(ImageHeader self, IMP::em::ImageHeader::img_type im)
2294 set_image_type(ImageHeader self, float im)
2296 return _IMP_em.ImageHeader_set_image_type(self, *args)
2299 def do_show(self, out):
2300 """do_show(ImageHeader self, _ostream out)"""
2301 return _IMP_em.ImageHeader_do_show(self, out)
2304 def show(self, *args):
2306 show(ImageHeader self, _ostream out)
2307 show(ImageHeader self)
2309 return _IMP_em.ImageHeader_show(self, *args)
2312 def print_hard(self, out):
2313 """print_hard(ImageHeader self, _ostream out)"""
2314 return _IMP_em.ImageHeader_print_hard(self, out)
2317 def show_projection_params(self, out):
2318 """show_projection_params(ImageHeader self, _ostream out)"""
2319 return _IMP_em.ImageHeader_show_projection_params(self, out)
2322 def read(self, *args):
2324 read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False, bool skip_extra_checkings=False) -> int
2325 read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False) -> int
2326 read(ImageHeader self, IMP::String const filename, bool skip_type_check=False) -> int
2327 read(ImageHeader self, IMP::String const filename) -> int
2328 read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False, bool skip_extra_checkings=False) -> bool
2329 read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False) -> bool
2330 read(ImageHeader self, std::ifstream & f, bool skip_type_check=False) -> bool
2331 read(ImageHeader self, std::ifstream & f) -> bool
2333 return _IMP_em.ImageHeader_read(self, *args)
2336 def write(self, *args):
2338 write(ImageHeader self, IMP::String const & filename, bool force_reversed=False)
2339 write(ImageHeader self, IMP::String const & filename)
2340 write(ImageHeader self, std::ofstream & f, bool force_reversed=False)
2341 write(ImageHeader self, std::ofstream & f)
2343 return _IMP_em.ImageHeader_write(self, *args)
2347 """clear(ImageHeader self)"""
2348 return _IMP_em.ImageHeader_clear(self)
2351 def set_header(self):
2352 """set_header(ImageHeader self)"""
2353 return _IMP_em.ImageHeader_set_header(self)
2356 def get_reversed(self):
2357 """get_reversed(ImageHeader self) -> bool"""
2358 return _IMP_em.ImageHeader_get_reversed(self)
2361 def set_reversed(self, value):
2362 """set_reversed(ImageHeader self, bool value)"""
2363 return _IMP_em.ImageHeader_set_reversed(self, value)
2366 def get_number_of_slices(self):
2367 """get_number_of_slices(ImageHeader self) -> unsigned int"""
2368 return _IMP_em.ImageHeader_get_number_of_slices(self)
2371 def set_number_of_slices(self, n):
2372 """set_number_of_slices(ImageHeader self, unsigned int n)"""
2373 return _IMP_em.ImageHeader_set_number_of_slices(self, n)
2376 def get_number_of_rows(self):
2377 """get_number_of_rows(ImageHeader self) -> unsigned int"""
2378 return _IMP_em.ImageHeader_get_number_of_rows(self)
2381 def set_number_of_rows(self, n):
2382 """set_number_of_rows(ImageHeader self, unsigned int n)"""
2383 return _IMP_em.ImageHeader_set_number_of_rows(self, n)
2386 def get_number_of_columns(self):
2387 """get_number_of_columns(ImageHeader self) -> unsigned int"""
2388 return _IMP_em.ImageHeader_get_number_of_columns(self)
2391 def set_number_of_columns(self, n):
2392 """set_number_of_columns(ImageHeader self, unsigned int n)"""
2393 return _IMP_em.ImageHeader_set_number_of_columns(self, n)
2396 def get_old_rot(self):
2397 """get_old_rot(ImageHeader self) -> float"""
2398 return _IMP_em.ImageHeader_get_old_rot(self)
2401 def set_old_rot(self, value):
2402 """set_old_rot(ImageHeader self, float value)"""
2403 return _IMP_em.ImageHeader_set_old_rot(self, value)
2406 def get_fAngle1(self):
2407 """get_fAngle1(ImageHeader self) -> float"""
2408 return _IMP_em.ImageHeader_get_fAngle1(self)
2411 def set_fAngle1(self, value):
2412 """set_fAngle1(ImageHeader self, float value)"""
2413 return _IMP_em.ImageHeader_set_fAngle1(self, value)
2416 def get_Scale(self):
2417 """get_Scale(ImageHeader self) -> float"""
2418 return _IMP_em.ImageHeader_get_Scale(self)
2421 def set_Scale(self, value):
2422 """set_Scale(ImageHeader self, float value)"""
2423 return _IMP_em.ImageHeader_set_Scale(self, value)
2427 """get_Flip(ImageHeader self) -> float"""
2428 return _IMP_em.ImageHeader_get_Flip(self)
2431 def set_Flip(self, value):
2432 """set_Flip(ImageHeader self, float value)"""
2433 return _IMP_em.ImageHeader_set_Flip(self, value)
2436 def get_Weight(self):
2437 """get_Weight(ImageHeader self) -> float"""
2438 return _IMP_em.ImageHeader_get_Weight(self)
2441 def set_Weight(self, value):
2442 """set_Weight(ImageHeader self, float value)"""
2443 return _IMP_em.ImageHeader_set_Weight(self, value)
2446 def get_fNrec(self):
2447 """get_fNrec(ImageHeader self) -> float"""
2448 return _IMP_em.ImageHeader_get_fNrec(self)
2451 def set_fNrec(self, value):
2452 """set_fNrec(ImageHeader self, float value)"""
2453 return _IMP_em.ImageHeader_set_fNrec(self, value)
2456 def get_fNlabel(self):
2457 """get_fNlabel(ImageHeader self) -> float"""
2458 return _IMP_em.ImageHeader_get_fNlabel(self)
2461 def set_fNlabel(self, value):
2462 """set_fNlabel(ImageHeader self, float value)"""
2463 return _IMP_em.ImageHeader_set_fNlabel(self, value)
2466 def get_fIform(self):
2467 """get_fIform(ImageHeader self) -> float"""
2468 return _IMP_em.ImageHeader_get_fIform(self)
2471 def set_fIform(self, value):
2472 """set_fIform(ImageHeader self, float value)"""
2473 return _IMP_em.ImageHeader_set_fIform(self, value)
2476 def get_fImami(self):
2477 """get_fImami(ImageHeader self) -> float"""
2478 return _IMP_em.ImageHeader_get_fImami(self)
2481 def set_fImami(self, value):
2482 """set_fImami(ImageHeader self, float value)"""
2483 return _IMP_em.ImageHeader_set_fImami(self, value)
2486 def get_fFmax(self):
2487 """get_fFmax(ImageHeader self) -> float"""
2488 return _IMP_em.ImageHeader_get_fFmax(self)
2491 def set_fFmax(self, value):
2492 """set_fFmax(ImageHeader self, float value)"""
2493 return _IMP_em.ImageHeader_set_fFmax(self, value)
2496 def get_fFmin(self):
2497 """get_fFmin(ImageHeader self) -> float"""
2498 return _IMP_em.ImageHeader_get_fFmin(self)
2501 def set_fFmin(self, value):
2502 """set_fFmin(ImageHeader self, float value)"""
2503 return _IMP_em.ImageHeader_set_fFmin(self, value)
2507 """get_fAv(ImageHeader self) -> float"""
2508 return _IMP_em.ImageHeader_get_fAv(self)
2511 def set_fAv(self, value):
2512 """set_fAv(ImageHeader self, float value)"""
2513 return _IMP_em.ImageHeader_set_fAv(self, value)
2517 """get_fSig(ImageHeader self) -> float"""
2518 return _IMP_em.ImageHeader_get_fSig(self)
2521 def set_fSig(self, value):
2522 """set_fSig(ImageHeader self, float value)"""
2523 return _IMP_em.ImageHeader_set_fSig(self, value)
2526 def get_fIhist(self):
2527 """get_fIhist(ImageHeader self) -> float"""
2528 return _IMP_em.ImageHeader_get_fIhist(self)
2531 def set_fIhist(self, value):
2532 """set_fIhist(ImageHeader self, float value)"""
2533 return _IMP_em.ImageHeader_set_fIhist(self, value)
2536 def get_fLabrec(self):
2537 """get_fLabrec(ImageHeader self) -> float"""
2538 return _IMP_em.ImageHeader_get_fLabrec(self)
2541 def set_fLabrec(self, value):
2542 """set_fLabrec(ImageHeader self, float value)"""
2543 return _IMP_em.ImageHeader_set_fLabrec(self, value)
2546 def get_fIangle(self):
2547 """get_fIangle(ImageHeader self) -> float"""
2548 return _IMP_em.ImageHeader_get_fIangle(self)
2551 def set_fIangle(self, value):
2552 """set_fIangle(ImageHeader self, float value)"""
2553 return _IMP_em.ImageHeader_set_fIangle(self, value)
2556 def get_origin(self):
2557 """get_origin(ImageHeader self) -> Vector3D"""
2558 return _IMP_em.ImageHeader_get_origin(self)
2561 def set_origin(self, *args):
2563 set_origin(ImageHeader self, Vector3D v)
2564 set_origin(ImageHeader self, Vector2D v)
2566 return _IMP_em.ImageHeader_set_origin(self, *args)
2569 def get_object_pixel_size(self):
2570 """get_object_pixel_size(ImageHeader self) -> float"""
2571 return _IMP_em.ImageHeader_get_object_pixel_size(self)
2574 def set_object_pixel_size(self, value):
2575 """set_object_pixel_size(ImageHeader self, float value)"""
2576 return _IMP_em.ImageHeader_set_object_pixel_size(self, value)
2579 def get_fLabbyt(self):
2580 """get_fLabbyt(ImageHeader self) -> float"""
2581 return _IMP_em.ImageHeader_get_fLabbyt(self)
2584 def set_fLabbyt(self, value):
2585 """set_fLabbyt(ImageHeader self, float value)"""
2586 return _IMP_em.ImageHeader_set_fLabbyt(self, value)
2589 def get_fLenbyt(self):
2590 """get_fLenbyt(ImageHeader self) -> float"""
2591 return _IMP_em.ImageHeader_get_fLenbyt(self)
2594 def set_fLenbyt(self, value):
2595 """set_fLenbyt(ImageHeader self, float value)"""
2596 return _IMP_em.ImageHeader_set_fLenbyt(self, value)
2599 def get_fGeo_matrix(self, i, j):
2600 """get_fGeo_matrix(ImageHeader self, unsigned int i, unsigned int j) -> double"""
2601 return _IMP_em.ImageHeader_get_fGeo_matrix(self, i, j)
2604 def get_fFlag(self):
2605 """get_fFlag(ImageHeader self) -> float"""
2606 return _IMP_em.ImageHeader_get_fFlag(self)
2609 def set_fFlag(self, value):
2610 """set_fFlag(ImageHeader self, float value)"""
2611 return _IMP_em.ImageHeader_set_fFlag(self, value)
2614 def get_euler_angles(self):
2615 """get_euler_angles(ImageHeader self) -> Vector3D"""
2616 return _IMP_em.ImageHeader_get_euler_angles(self)
2619 def get_euler_angles1(self):
2620 """get_euler_angles1(ImageHeader self) -> Vector3D"""
2621 return _IMP_em.ImageHeader_get_euler_angles1(self)
2624 def get_euler_angles2(self):
2625 """get_euler_angles2(ImageHeader self) -> Vector3D"""
2626 return _IMP_em.ImageHeader_get_euler_angles2(self)
2629 def set_euler_angles(self, euler):
2630 """set_euler_angles(ImageHeader self, Vector3D euler)"""
2631 return _IMP_em.ImageHeader_set_euler_angles(self, euler)
2634 def set_euler_angles1(self, euler):
2635 """set_euler_angles1(ImageHeader self, Vector3D euler)"""
2636 return _IMP_em.ImageHeader_set_euler_angles1(self, euler)
2639 def set_euler_angles2(self, euler):
2640 """set_euler_angles2(ImageHeader self, Vector3D euler)"""
2641 return _IMP_em.ImageHeader_set_euler_angles2(self, euler)
2644 def is_normalized(self):
2645 """is_normalized(ImageHeader self) -> bool"""
2646 return _IMP_em.ImageHeader_is_normalized(self)
2650 """set_date(ImageHeader self)"""
2651 return _IMP_em.ImageHeader_set_date(self)
2655 """set_time(ImageHeader self)"""
2656 return _IMP_em.ImageHeader_set_time(self)
2659 def set_title(self, newName):
2660 """set_title(ImageHeader self, IMP::String newName)"""
2661 return _IMP_em.ImageHeader_set_title(self, newName)
2663 __swig_destroy__ = _IMP_em.delete_ImageHeader
2664 __del__ =
lambda self:
None
2665 ImageHeader_swigregister = _IMP_em.ImageHeader_swigregister
2666 ImageHeader_swigregister(ImageHeader)
2668 class SpiderMapReaderWriter(MapReaderWriter):
2669 """Proxy of C++ IMP::em::SpiderMapReaderWriter class"""
2670 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2671 filename_ = _swig_property(_IMP_em.SpiderMapReaderWriter_filename__get, _IMP_em.SpiderMapReaderWriter_filename__set)
2672 skip_type_check_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_type_check__get, _IMP_em.SpiderMapReaderWriter_skip_type_check__set)
2673 force_reversed_ = _swig_property(_IMP_em.SpiderMapReaderWriter_force_reversed__get, _IMP_em.SpiderMapReaderWriter_force_reversed__set)
2674 skip_extra_checkings_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_extra_checkings__get, _IMP_em.SpiderMapReaderWriter_skip_extra_checkings__set)
2676 def __init__(self, *args):
2678 __init__(IMP::em::SpiderMapReaderWriter self) -> SpiderMapReaderWriter
2679 __init__(IMP::em::SpiderMapReaderWriter self, IMP::String filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings) -> SpiderMapReaderWriter
2681 this = _IMP_em.new_SpiderMapReaderWriter(*args)
2683 self.this.append(this)
2688 """__str__(SpiderMapReaderWriter self) -> std::string"""
2689 return _IMP_em.SpiderMapReaderWriter___str__(self)
2693 """__repr__(SpiderMapReaderWriter self) -> std::string"""
2694 return _IMP_em.SpiderMapReaderWriter___repr__(self)
2699 return _object_cast_to_SpiderMapReaderWriter(o)
2701 SpiderMapReaderWriter_swigregister = _IMP_em.SpiderMapReaderWriter_swigregister
2702 SpiderMapReaderWriter_swigregister(SpiderMapReaderWriter)
2704 class FittingSolutions(object):
2705 """Proxy of C++ IMP::em::FittingSolutions class"""
2706 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2709 """__init__(IMP::em::FittingSolutions self) -> FittingSolutions"""
2710 this = _IMP_em.new_FittingSolutions()
2712 self.this.append(this)
2716 def get_number_of_solutions(self):
2717 """get_number_of_solutions(FittingSolutions self) -> int"""
2718 return _IMP_em.FittingSolutions_get_number_of_solutions(self)
2721 def get_transformation(self, i):
2722 """get_transformation(FittingSolutions self, unsigned int i) -> Transformation3D"""
2723 return _IMP_em.FittingSolutions_get_transformation(self, i)
2726 def get_score(self, i):
2727 """get_score(FittingSolutions self, unsigned int i) -> IMP::Float"""
2728 return _IMP_em.FittingSolutions_get_score(self, i)
2731 def set_score(self, i, score):
2732 """set_score(FittingSolutions self, unsigned int i, IMP::Float score)"""
2733 return _IMP_em.FittingSolutions_set_score(self, i, score)
2736 def add_solution(self, t, score):
2737 """add_solution(FittingSolutions self, Transformation3D t, IMP::Float score)"""
2738 return _IMP_em.FittingSolutions_add_solution(self, t, score)
2741 def sort(self, reverse=False):
2743 sort(FittingSolutions self, bool reverse=False)
2744 sort(FittingSolutions self)
2746 return _IMP_em.FittingSolutions_sort(self, reverse)
2750 """multiply(FittingSolutions self, Transformation3D t)"""
2751 return _IMP_em.FittingSolutions_multiply(self, t)
2754 def get_transformations(self):
2755 """get_transformations(FittingSolutions self) -> IMP::algebra::Transformation3Ds"""
2756 return _IMP_em.FittingSolutions_get_transformations(self)
2759 def show(self, *args):
2761 show(FittingSolutions self, _ostream out)
2762 show(FittingSolutions self)
2764 return _IMP_em.FittingSolutions_show(self, *args)
2768 """__str__(FittingSolutions self) -> std::string"""
2769 return _IMP_em.FittingSolutions___str__(self)
2773 """__repr__(FittingSolutions self) -> std::string"""
2774 return _IMP_em.FittingSolutions___repr__(self)
2776 __swig_destroy__ = _IMP_em.delete_FittingSolutions
2777 __del__ =
lambda self:
None
2778 FittingSolutions_swigregister = _IMP_em.FittingSolutions_swigregister
2779 FittingSolutions_swigregister(FittingSolutions)
2782 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):
2784 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
2785 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
2786 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
2787 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
2788 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
2789 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
2790 local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log) -> FittingSolutions
2792 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)
2794 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):
2796 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
2797 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
2798 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
2799 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
2800 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
2801 local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2802 local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log) -> FittingSolutions
2804 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)
2806 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):
2808 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
2809 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
2810 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
2811 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
2812 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
2813 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
2815 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)
2817 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):
2819 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
2820 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
2821 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
2822 local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2) -> FittingSolutions
2823 local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap) -> FittingSolutions
2825 return _IMP_em.local_rigid_fitting_grid_search(ps, wei_key, dmap, max_voxels_translation, translation_step, max_angle_in_radians, number_of_rotations)
2829 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
2830 compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations, bool fast_version=False, bool local_score=False) -> FittingSolutions
2831 compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations, bool fast_version=False) -> FittingSolutions
2832 compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2833 compute_fitting_scores(DensityMap em_map, RigidBody rb, Refiner refiner, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2835 return _IMP_em.compute_fitting_scores(*args)
2839 compute_fitting_score(IMP::ParticlesTemp const & ps, DensityMap em_map, FloatKey wei_key) -> IMP::Float
2840 compute_fitting_score(IMP::ParticlesTemp const & ps, DensityMap em_map) -> IMP::Float
2842 return _IMP_em.compute_fitting_score(*args)
2846 get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, Transformation3D t, float thr=0.0) -> long
2847 get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, Transformation3D t) -> long
2848 get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps) -> long
2850 return _IMP_em.get_number_of_particles_outside_of_the_density(*args)
2854 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
2855 get_numbers_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, IMP::algebra::Transformation3Ds const & transformations) -> IMP::Ints
2857 return _IMP_em.get_numbers_of_particles_outside_of_the_density(dmap, ps, transformations, thr)
2861 get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3., Transformation3D t, float thr=0.0) -> double
2862 get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3., Transformation3D t) -> double
2863 get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3.) -> double
2864 get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps) -> double
2866 return _IMP_em.get_percentage_of_voxels_covered_by_particles(*args)
2868 """Proxy of C++ IMP::em::HighDensityEmbedding class"""
2869 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2871 def __init__(self, dm, threshold):
2872 """__init__(IMP::em::HighDensityEmbedding self, DensityMap dm, double threshold) -> HighDensityEmbedding"""
2873 this = _IMP_em.new_HighDensityEmbedding(dm, threshold)
2875 self.this.append(this)
2879 def get_version_info(self):
2880 """get_version_info(HighDensityEmbedding self) -> VersionInfo"""
2881 return _IMP_em.HighDensityEmbedding_get_version_info(self)
2885 """__str__(HighDensityEmbedding self) -> std::string"""
2886 return _IMP_em.HighDensityEmbedding___str__(self)
2890 """__repr__(HighDensityEmbedding self) -> std::string"""
2891 return _IMP_em.HighDensityEmbedding___repr__(self)
2896 return _object_cast_to_HighDensityEmbedding(o)
2898 HighDensityEmbedding_swigregister = _IMP_em.HighDensityEmbedding_swigregister
2899 HighDensityEmbedding_swigregister(HighDensityEmbedding)
2903 """mask_and_norm(DensityMap dmap, DensityMap mask) -> DensityMap"""
2904 return _IMP_em.mask_and_norm(dmap, mask)
2907 """get_volume_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float"""
2908 return _IMP_em.get_volume_at_threshold(m, threshold)
2912 get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold, IMP::atom::ProteinDensityReference ref) -> IMP::Float
2913 get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float
2915 return _IMP_em.get_molecular_mass_at_threshold(*args)
2918 """get_threshold_for_approximate_volume(DensityMap m, IMP::Float desired_volume) -> IMP::Float"""
2919 return _IMP_em.get_threshold_for_approximate_volume(m, desired_volume)
2923 get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass, IMP::atom::ProteinDensityReference ref) -> IMP::Float
2924 get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass) -> IMP::Float
2926 return _IMP_em.get_threshold_for_approximate_mass(*args)
2928 """Proxy of C++ IMP::em::EnvelopePenetrationRestraint class"""
2929 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2931 def __init__(self, ps, em_map, threshold):
2932 """__init__(IMP::em::EnvelopePenetrationRestraint self, IMP::Particles ps, DensityMap em_map, IMP::Float threshold) -> EnvelopePenetrationRestraint"""
2933 this = _IMP_em.new_EnvelopePenetrationRestraint(ps, em_map, threshold)
2935 self.this.append(this)
2939 def do_get_inputs(self):
2940 """do_get_inputs(EnvelopePenetrationRestraint self) -> IMP::ModelObjectsTemp"""
2941 return _IMP_em.EnvelopePenetrationRestraint_do_get_inputs(self)
2944 def get_version_info(self):
2945 """get_version_info(EnvelopePenetrationRestraint self) -> VersionInfo"""
2946 return _IMP_em.EnvelopePenetrationRestraint_get_version_info(self)
2950 """__str__(EnvelopePenetrationRestraint self) -> std::string"""
2951 return _IMP_em.EnvelopePenetrationRestraint___str__(self)
2955 """__repr__(EnvelopePenetrationRestraint self) -> std::string"""
2956 return _IMP_em.EnvelopePenetrationRestraint___repr__(self)
2961 return _object_cast_to_EnvelopePenetrationRestraint(o)
2963 EnvelopePenetrationRestraint_swigregister = _IMP_em.EnvelopePenetrationRestraint_swigregister
2964 EnvelopePenetrationRestraint_swigregister(EnvelopePenetrationRestraint)
2967 """Proxy of C++ IMP::em::PCAFitRestraint class"""
2968 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2970 def __init__(self, *args):
2972 __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
2973 __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
2975 this = _IMP_em.new_PCAFitRestraint(*args)
2977 self.this.append(this)
2981 def do_get_inputs(self):
2982 """do_get_inputs(PCAFitRestraint self) -> IMP::ModelObjectsTemp"""
2983 return _IMP_em.PCAFitRestraint_do_get_inputs(self)
2986 def get_version_info(self):
2987 """get_version_info(PCAFitRestraint self) -> VersionInfo"""
2988 return _IMP_em.PCAFitRestraint_get_version_info(self)
2992 """__str__(PCAFitRestraint self) -> std::string"""
2993 return _IMP_em.PCAFitRestraint___str__(self)
2997 """__repr__(PCAFitRestraint self) -> std::string"""
2998 return _IMP_em.PCAFitRestraint___repr__(self)
3003 return _object_cast_to_PCAFitRestraint(o)
3005 PCAFitRestraint_swigregister = _IMP_em.PCAFitRestraint_swigregister
3006 PCAFitRestraint_swigregister(PCAFitRestraint)
3009 """Proxy of C++ IMP::em::EnvelopeFitRestraint class"""
3010 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3012 def __init__(self, particles, em_map, density_threshold, penetration_threshold):
3013 """__init__(IMP::em::EnvelopeFitRestraint self, IMP::Particles particles, DensityMap em_map, double density_threshold, double penetration_threshold) -> EnvelopeFitRestraint"""
3014 this = _IMP_em.new_EnvelopeFitRestraint(particles, em_map, density_threshold, penetration_threshold)
3016 self.this.append(this)
3020 def get_transformation(self):
3021 """get_transformation(EnvelopeFitRestraint self) -> Transformation3D"""
3022 return _IMP_em.EnvelopeFitRestraint_get_transformation(self)
3025 def apply_transformation(self):
3026 """apply_transformation(EnvelopeFitRestraint self)"""
3027 return _IMP_em.EnvelopeFitRestraint_apply_transformation(self)
3030 def do_get_inputs(self):
3031 """do_get_inputs(EnvelopeFitRestraint self) -> IMP::ModelObjectsTemp"""
3032 return _IMP_em.EnvelopeFitRestraint_do_get_inputs(self)
3035 def get_version_info(self):
3036 """get_version_info(EnvelopeFitRestraint self) -> VersionInfo"""
3037 return _IMP_em.EnvelopeFitRestraint_get_version_info(self)
3041 """__str__(EnvelopeFitRestraint self) -> std::string"""
3042 return _IMP_em.EnvelopeFitRestraint___str__(self)
3046 """__repr__(EnvelopeFitRestraint self) -> std::string"""
3047 return _IMP_em.EnvelopeFitRestraint___repr__(self)
3052 return _object_cast_to_EnvelopeFitRestraint(o)
3054 EnvelopeFitRestraint_swigregister = _IMP_em.EnvelopeFitRestraint_swigregister
3055 EnvelopeFitRestraint_swigregister(EnvelopeFitRestraint)
3057 class MapDistanceTransform(DensityMap):
3058 """Proxy of C++ IMP::em::MapDistanceTransform class"""
3059 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3061 def __init__(self, map, density_threshold, max_distance):
3062 """__init__(IMP::em::MapDistanceTransform self, DensityMap map, float density_threshold, float max_distance) -> MapDistanceTransform"""
3063 this = _IMP_em.new_MapDistanceTransform(map, density_threshold, max_distance)
3065 self.this.append(this)
3069 def get_distance_from_envelope(self, v):
3070 """get_distance_from_envelope(MapDistanceTransform self, Vector3D v) -> float"""
3071 return _IMP_em.MapDistanceTransform_get_distance_from_envelope(self, v)
3075 """__str__(MapDistanceTransform self) -> std::string"""
3076 return _IMP_em.MapDistanceTransform___str__(self)
3080 """__repr__(MapDistanceTransform self) -> std::string"""
3081 return _IMP_em.MapDistanceTransform___repr__(self)
3086 return _object_cast_to_MapDistanceTransform(o)
3088 __swig_destroy__ = _IMP_em.delete_MapDistanceTransform
3089 __del__ =
lambda self:
None
3090 MapDistanceTransform_swigregister = _IMP_em.MapDistanceTransform_swigregister
3091 MapDistanceTransform_swigregister(MapDistanceTransform)
3094 """Proxy of C++ IMP::em::EnvelopeScore class"""
3095 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3097 def __init__(self, mdt):
3098 """__init__(IMP::em::EnvelopeScore self, MapDistanceTransform mdt) -> EnvelopeScore"""
3099 this = _IMP_em.new_EnvelopeScore(mdt)
3101 self.this.append(this)
3105 def is_penetrating(self, *args):
3107 is_penetrating(EnvelopeScore self, IMP::algebra::Vector3Ds const & points, float penetration_thr) -> bool
3108 is_penetrating(EnvelopeScore self, IMP::algebra::Vector3Ds const & points, Transformation3D trans, float penetration_thr) -> bool
3110 return _IMP_em.EnvelopeScore_is_penetrating(self, *args)
3113 def score(self, *args):
3115 score(EnvelopeScore self, IMP::algebra::Vector3Ds const & points) -> double
3116 score(EnvelopeScore self, IMP::algebra::Vector3Ds const & points, Transformation3D trans) -> double
3118 return _IMP_em.EnvelopeScore_score(self, *args)
3120 __swig_destroy__ = _IMP_em.delete_EnvelopeScore
3121 __del__ =
lambda self:
None
3124 """__str__(EnvelopeScore self) -> std::string"""
3125 return _IMP_em.EnvelopeScore___str__(self)
3129 """__repr__(EnvelopeScore self) -> std::string"""
3130 return _IMP_em.EnvelopeScore___repr__(self)
3135 return _object_cast_to_EnvelopeScore(o)
3137 EnvelopeScore_swigregister = _IMP_em.EnvelopeScore_swigregister
3138 EnvelopeScore_swigregister(EnvelopeScore)
3144 """Write out principal components to a file in Chimera Marker format"""
3145 eigen_values = pca.get_principal_values()
3146 eigen_vecs = pca.get_principal_components()
3147 centroid = pca.get_centroid()
3149 fh.write(
"<marker_set>\n")
3150 fh.write(
"<!-- PCA with eigen values: (%g,%g,%g) and "
3151 "centroid (%g,%g,%g) -->\n"
3152 % (math.sqrt(eigen_values[0]),
3153 math.sqrt(eigen_values[1]),
3154 math.sqrt(eigen_values[2]),
3155 centroid[0], centroid[1], centroid[2]))
3160 val = math.sqrt(eigen_values[i])
3161 v1 = centroid - val * eigen_vecs[i]
3162 v2 = centroid + val * eigen_vecs[i]
3163 for markerid, v
in ((i*2+1, v1), (i*2+2, v2)):
3164 fh.write(
"<marker id=\"%d\" x=\"%g\" y=\"%g\" z=\"%g\" "
3166 % (markerid, v[0], v[1], v[2], radius))
3168 for i
in range(1, 7, 2):
3169 fh.write(
"<link id1= \"%d\" id2=\"%d\" radius=\"%g\"/>\n"
3171 fh.write(
"</marker_set>\n")
3175 """get_module_version() -> std::string const"""
3176 return _IMP_em.get_module_version()
3179 """get_example_path(std::string fname) -> std::string"""
3180 return _IMP_em.get_example_path(fname)
3183 """get_data_path(std::string fname) -> std::string"""
3184 return _IMP_em.get_data_path(fname)
3186 from .
import _version_check
double bayesem3d_linear_interpolate(const Floats &x_data, const Floats &y_data, double x, bool extrapolate)
Basic linear interpolation given vectors of values.
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.
double bayesem3d_get_logsumexp(double x, double y)
Numerically stable logsumexp.
double get_coarse_cc_coefficient(const DensityMap *grid1, const DensityMap *grid2, double grid2_voxel_data_threshold, bool allow_padding=false, FloatPair norm_factors=FloatPair(0., 0.))
Calculates the cross correlation coefficient between two maps.
Various classes to hold sets of particles.
std::vector< double > bayesem3d_get_value(Particle *p, const algebra::Vector3D &pt, double mass_ii, const IMP::em::KernelParameters &kps)
Compute the score and derivatives for a particle at a given voxel.
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.
DensityMap * bayesem3d_get_density_from_particle(DensityMap *em, const IMP::ParticlesTemp &ps, double resolution)
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.
std::pair< double, algebra::Vector3Ds > bayesem3d_get_score_and_derivative(DensityMap *em, const IMP::ParticlesTemp &ps, double resolution, double sigma)
The function returns the negative log of the Normal distributed difference between a normalized EM de...
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.
FloatPair bayesem3d_get_logabssumexp(double x, double y, double sx, double sy)
Numerically stable logabssumexp.
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.
double get_coarse_cc_score(DensityMap *data, SampledDensityMap *model_map, double scalefactor, bool recalc_rms=true, bool resample=true, FloatPair norm_factors=FloatPair(0., 0.))
Calculates the value of the EM fitting term.
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.
void bayesem3d_get_normalized_intensities(DensityMap *em, const IMP::ParticlesTemp &ps, double resolution)
FloatPair bayesem3d_get_em_density_squared(DensityMap *em, long number_of_voxels)
Compute the sum of the density and the sum of the squares of the density.
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].
std::map< double, int > bayesem3d_get_distinct_and_counts(DensityMap *em)
Get histogram of density in EM map.
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.
double get_coarse_cc_local_coefficient(const DensityMap *em_map, DensityMap *model_map, double voxel_data_threshold)
Local cross correlation function.
double bayesem3d_get_cross_correlation_coefficient(const DensityMap *em1, const DensityMap *em2)
Compute a normalized cross-correlation coefficient.
Floats bayesem3d_get_cumulative_sum(DensityMap *em)
Compute the cumulative sum of the histogram computed from EM map.
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.
double bayesem3d_get_logsumprodexp(double x, double y, double wx, double wy)
Numerically stable logsumexpprod.
std::vector< double > bayesem3d_get_value_no_deriv(Particle *p, const algebra::Vector3D &pt, double mass_ii, const IMP::em::KernelParameters &kps)
Compute the score without its derivative.
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.
std::map< double, double > bayesem3d_get_cumulative_sum_with_reference(DensityMap *em)
Compute the cumulative sum of the histogram given a reference.
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.
FloatPair bayesem3d_get_logabssumprodexp(double x, double y, double wx, double wy)
Numerically stable logabssumprodexp.