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_GPERFTOOLS_swigconstant(_IMP_em)
269 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_em.IMP_KERNEL_HAS_GPERFTOOLS
271 _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER_swigconstant(_IMP_em)
272 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
274 _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER_swigconstant(_IMP_em)
275 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
277 _IMP_em.IMPKERNEL_SHOW_WARNINGS_swigconstant(_IMP_em)
278 IMPKERNEL_SHOW_WARNINGS = _IMP_em.IMPKERNEL_SHOW_WARNINGS
281 class _DirectorObjects(object):
282 """@internal Simple class to keep references to director objects
283 to prevent premature deletion."""
286 def register(self, obj):
287 """Take a reference to a director object; will only work for
288 refcounted C++ classes"""
289 if hasattr(obj,
'get_ref_count'):
290 self._objects.append(obj)
292 """Only drop our reference and allow cleanup by Python if no other
293 Python references exist (we hold 3 references: one in self._objects,
294 one in x, and one in the argument list for getrefcount) *and* no
295 other C++ references exist (the Python object always holds one)"""
296 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
297 or x.get_ref_count() > 1]
301 def get_object_count(self):
302 """Get number of director objects (useful for testing only)"""
303 return len(self._objects)
304 _director_objects = _DirectorObjects()
306 class _ostream(object):
307 """Proxy of C++ std::ostream class"""
308 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
310 def __init__(self, *args, **kwargs):
311 raise AttributeError(
"No constructor defined")
312 __repr__ = _swig_repr
314 def write(self, osa_buf):
315 """write(_ostream self, char const * osa_buf)"""
316 return _IMP_em._ostream_write(self, osa_buf)
318 _ostream_swigregister = _IMP_em._ostream_swigregister
319 _ostream_swigregister(_ostream)
322 _IMP_em.IMP_COMPILER_HAS_OVERRIDE_swigconstant(_IMP_em)
323 IMP_COMPILER_HAS_OVERRIDE = _IMP_em.IMP_COMPILER_HAS_OVERRIDE
325 _IMP_em.IMP_COMPILER_HAS_FINAL_swigconstant(_IMP_em)
326 IMP_COMPILER_HAS_FINAL = _IMP_em.IMP_COMPILER_HAS_FINAL
328 _IMP_em.IMP_HAS_NOEXCEPT_swigconstant(_IMP_em)
329 IMP_HAS_NOEXCEPT = _IMP_em.IMP_HAS_NOEXCEPT
332 _IMP_em.IMP_CGAL_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
333 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CGAL_HAS_BOOST_FILESYSTEM
335 _IMP_em.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
336 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
338 _IMP_em.IMP_CGAL_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
339 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_em.IMP_CGAL_HAS_BOOST_RANDOM
341 _IMP_em.IMP_CGAL_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
342 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_em.IMP_CGAL_HAS_BOOST_SYSTEM
344 _IMP_em.IMPCGAL_SHOW_WARNINGS_swigconstant(_IMP_em)
345 IMPCGAL_SHOW_WARNINGS = _IMP_em.IMPCGAL_SHOW_WARNINGS
348 _IMP_em.IMP_ALGEBRA_HAS_IMP_CGAL_swigconstant(_IMP_em)
349 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_em.IMP_ALGEBRA_HAS_IMP_CGAL
351 _IMP_em.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
352 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
354 _IMP_em.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
355 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
357 _IMP_em.IMP_ALGEBRA_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
358 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_RANDOM
360 _IMP_em.IMP_ALGEBRA_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
361 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_SYSTEM
363 _IMP_em.IMP_ALGEBRA_HAS_CGAL_swigconstant(_IMP_em)
364 IMP_ALGEBRA_HAS_CGAL = _IMP_em.IMP_ALGEBRA_HAS_CGAL
366 _IMP_em.IMP_ALGEBRA_HAS_ANN_swigconstant(_IMP_em)
367 IMP_ALGEBRA_HAS_ANN = _IMP_em.IMP_ALGEBRA_HAS_ANN
369 _IMP_em.IMPALGEBRA_SHOW_WARNINGS_swigconstant(_IMP_em)
370 IMPALGEBRA_SHOW_WARNINGS = _IMP_em.IMPALGEBRA_SHOW_WARNINGS
373 _IMP_em.IMP_DISPLAY_HAS_IMP_CGAL_swigconstant(_IMP_em)
374 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_em.IMP_DISPLAY_HAS_IMP_CGAL
376 _IMP_em.IMP_DISPLAY_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
377 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
379 _IMP_em.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
380 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
382 _IMP_em.IMP_DISPLAY_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
383 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_em.IMP_DISPLAY_HAS_BOOST_RANDOM
385 _IMP_em.IMP_DISPLAY_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
386 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_em.IMP_DISPLAY_HAS_BOOST_SYSTEM
388 _IMP_em.IMP_DISPLAY_HAS_CGAL_swigconstant(_IMP_em)
389 IMP_DISPLAY_HAS_CGAL = _IMP_em.IMP_DISPLAY_HAS_CGAL
391 _IMP_em.IMPDISPLAY_SHOW_WARNINGS_swigconstant(_IMP_em)
392 IMPDISPLAY_SHOW_WARNINGS = _IMP_em.IMPDISPLAY_SHOW_WARNINGS
395 _IMP_em.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL_swigconstant(_IMP_em)
396 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_em.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
398 _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
399 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
401 _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
402 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
404 _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
405 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
407 _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
408 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
410 _IMP_em.IMP_SCORE_FUNCTOR_HAS_CGAL_swigconstant(_IMP_em)
411 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_em.IMP_SCORE_FUNCTOR_HAS_CGAL
413 _IMP_em.IMP_SCORE_FUNCTOR_HAS_HDF5_swigconstant(_IMP_em)
414 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_em.IMP_SCORE_FUNCTOR_HAS_HDF5
416 _IMP_em.IMPSCOREFUNCTOR_SHOW_WARNINGS_swigconstant(_IMP_em)
417 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_em.IMPSCOREFUNCTOR_SHOW_WARNINGS
420 _IMP_em.IMP_STATISTICS_HAS_IMP_CGAL_swigconstant(_IMP_em)
421 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_em.IMP_STATISTICS_HAS_IMP_CGAL
423 _IMP_em.IMP_STATISTICS_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
424 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
426 _IMP_em.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
427 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
429 _IMP_em.IMP_STATISTICS_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
430 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_em.IMP_STATISTICS_HAS_BOOST_RANDOM
432 _IMP_em.IMP_STATISTICS_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
433 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_SYSTEM
435 _IMP_em.IMP_STATISTICS_HAS_CGAL_swigconstant(_IMP_em)
436 IMP_STATISTICS_HAS_CGAL = _IMP_em.IMP_STATISTICS_HAS_CGAL
438 _IMP_em.IMPSTATISTICS_SHOW_WARNINGS_swigconstant(_IMP_em)
439 IMPSTATISTICS_SHOW_WARNINGS = _IMP_em.IMPSTATISTICS_SHOW_WARNINGS
442 _IMP_em.IMP_CORE_HAS_IMP_CGAL_swigconstant(_IMP_em)
443 IMP_CORE_HAS_IMP_CGAL = _IMP_em.IMP_CORE_HAS_IMP_CGAL
445 _IMP_em.IMP_CORE_HAS_IMP_KERNEL_swigconstant(_IMP_em)
446 IMP_CORE_HAS_IMP_KERNEL = _IMP_em.IMP_CORE_HAS_IMP_KERNEL
448 _IMP_em.IMP_CORE_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
449 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_FILESYSTEM
451 _IMP_em.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
452 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
454 _IMP_em.IMP_CORE_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
455 IMP_CORE_HAS_BOOST_RANDOM = _IMP_em.IMP_CORE_HAS_BOOST_RANDOM
457 _IMP_em.IMP_CORE_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
458 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_SYSTEM
460 _IMP_em.IMP_CORE_HAS_CGAL_swigconstant(_IMP_em)
461 IMP_CORE_HAS_CGAL = _IMP_em.IMP_CORE_HAS_CGAL
463 _IMP_em.IMP_CORE_HAS_HDF5_swigconstant(_IMP_em)
464 IMP_CORE_HAS_HDF5 = _IMP_em.IMP_CORE_HAS_HDF5
466 _IMP_em.IMPCORE_SHOW_WARNINGS_swigconstant(_IMP_em)
467 IMPCORE_SHOW_WARNINGS = _IMP_em.IMPCORE_SHOW_WARNINGS
470 _IMP_em.IMP_CONTAINER_HAS_IMP_ALGEBRA_swigconstant(_IMP_em)
471 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_em.IMP_CONTAINER_HAS_IMP_ALGEBRA
473 _IMP_em.IMP_CONTAINER_HAS_IMP_CGAL_swigconstant(_IMP_em)
474 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_em.IMP_CONTAINER_HAS_IMP_CGAL
476 _IMP_em.IMP_CONTAINER_HAS_IMP_DISPLAY_swigconstant(_IMP_em)
477 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_em.IMP_CONTAINER_HAS_IMP_DISPLAY
479 _IMP_em.IMP_CONTAINER_HAS_IMP_KERNEL_swigconstant(_IMP_em)
480 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_em.IMP_CONTAINER_HAS_IMP_KERNEL
482 _IMP_em.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_em)
483 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
485 _IMP_em.IMP_CONTAINER_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
486 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
488 _IMP_em.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
489 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
491 _IMP_em.IMP_CONTAINER_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
492 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_em.IMP_CONTAINER_HAS_BOOST_RANDOM
494 _IMP_em.IMP_CONTAINER_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
495 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_SYSTEM
497 _IMP_em.IMP_CONTAINER_HAS_CGAL_swigconstant(_IMP_em)
498 IMP_CONTAINER_HAS_CGAL = _IMP_em.IMP_CONTAINER_HAS_CGAL
500 _IMP_em.IMP_CONTAINER_HAS_HDF5_swigconstant(_IMP_em)
501 IMP_CONTAINER_HAS_HDF5 = _IMP_em.IMP_CONTAINER_HAS_HDF5
503 _IMP_em.IMPCONTAINER_SHOW_WARNINGS_swigconstant(_IMP_em)
504 IMPCONTAINER_SHOW_WARNINGS = _IMP_em.IMPCONTAINER_SHOW_WARNINGS
507 _IMP_em.IMP_ATOM_HAS_IMP_CGAL_swigconstant(_IMP_em)
508 IMP_ATOM_HAS_IMP_CGAL = _IMP_em.IMP_ATOM_HAS_IMP_CGAL
510 _IMP_em.IMP_ATOM_HAS_IMP_KERNEL_swigconstant(_IMP_em)
511 IMP_ATOM_HAS_IMP_KERNEL = _IMP_em.IMP_ATOM_HAS_IMP_KERNEL
513 _IMP_em.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_em)
514 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
516 _IMP_em.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
517 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
519 _IMP_em.IMP_ATOM_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
520 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_em.IMP_ATOM_HAS_BOOST_RANDOM
522 _IMP_em.IMP_ATOM_HAS_BOOST_REGEX_swigconstant(_IMP_em)
523 IMP_ATOM_HAS_BOOST_REGEX = _IMP_em.IMP_ATOM_HAS_BOOST_REGEX
525 _IMP_em.IMP_ATOM_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
526 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_em.IMP_ATOM_HAS_BOOST_SYSTEM
528 _IMP_em.IMP_ATOM_HAS_CGAL_swigconstant(_IMP_em)
529 IMP_ATOM_HAS_CGAL = _IMP_em.IMP_ATOM_HAS_CGAL
531 _IMP_em.IMP_ATOM_HAS_HDF5_swigconstant(_IMP_em)
532 IMP_ATOM_HAS_HDF5 = _IMP_em.IMP_ATOM_HAS_HDF5
534 _IMP_em.IMPATOM_SHOW_WARNINGS_swigconstant(_IMP_em)
535 IMPATOM_SHOW_WARNINGS = _IMP_em.IMPATOM_SHOW_WARNINGS
537 _IMP_em.IMP_ATOM_TYPE_INDEX_swigconstant(_IMP_em)
538 IMP_ATOM_TYPE_INDEX = _IMP_em.IMP_ATOM_TYPE_INDEX
540 _IMP_em.IMP_RESIDUE_TYPE_INDEX_swigconstant(_IMP_em)
541 IMP_RESIDUE_TYPE_INDEX = _IMP_em.IMP_RESIDUE_TYPE_INDEX
543 _IMP_em.IMP_HIERARCHY_TYPE_INDEX_swigconstant(_IMP_em)
544 IMP_HIERARCHY_TYPE_INDEX = _IMP_em.IMP_HIERARCHY_TYPE_INDEX
547 _IMP_em.IMP_EM_HAS_IMP_CGAL_swigconstant(_IMP_em)
548 IMP_EM_HAS_IMP_CGAL = _IMP_em.IMP_EM_HAS_IMP_CGAL
550 _IMP_em.IMP_EM_HAS_IMP_CONTAINER_swigconstant(_IMP_em)
551 IMP_EM_HAS_IMP_CONTAINER = _IMP_em.IMP_EM_HAS_IMP_CONTAINER
553 _IMP_em.IMP_EM_HAS_IMP_DISPLAY_swigconstant(_IMP_em)
554 IMP_EM_HAS_IMP_DISPLAY = _IMP_em.IMP_EM_HAS_IMP_DISPLAY
556 _IMP_em.IMP_EM_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_em)
557 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_EM_HAS_IMP_SCORE_FUNCTOR
559 _IMP_em.IMP_EM_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
560 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_EM_HAS_BOOST_FILESYSTEM
562 _IMP_em.IMP_EM_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
563 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
565 _IMP_em.IMP_EM_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
566 IMP_EM_HAS_BOOST_RANDOM = _IMP_em.IMP_EM_HAS_BOOST_RANDOM
568 _IMP_em.IMP_EM_HAS_BOOST_REGEX_swigconstant(_IMP_em)
569 IMP_EM_HAS_BOOST_REGEX = _IMP_em.IMP_EM_HAS_BOOST_REGEX
571 _IMP_em.IMP_EM_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
572 IMP_EM_HAS_BOOST_SYSTEM = _IMP_em.IMP_EM_HAS_BOOST_SYSTEM
574 _IMP_em.IMP_EM_HAS_CGAL_swigconstant(_IMP_em)
575 IMP_EM_HAS_CGAL = _IMP_em.IMP_EM_HAS_CGAL
577 _IMP_em.IMP_EM_HAS_HDF5_swigconstant(_IMP_em)
578 IMP_EM_HAS_HDF5 = _IMP_em.IMP_EM_HAS_HDF5
580 _IMP_em.IMPEM_SHOW_WARNINGS_swigconstant(_IMP_em)
581 IMPEM_SHOW_WARNINGS = _IMP_em.IMPEM_SHOW_WARNINGS
583 _object_types.append(
"DensityMap")
586 def _object_cast_to_DensityMap(o):
587 """_object_cast_to_DensityMap(Object o) -> DensityMap"""
588 return _IMP_em._object_cast_to_DensityMap(o)
590 _object_types.append(
"SampledDensityMap")
593 def _object_cast_to_SampledDensityMap(o):
594 """_object_cast_to_SampledDensityMap(Object o) -> SampledDensityMap"""
595 return _IMP_em._object_cast_to_SampledDensityMap(o)
597 _object_types.append(
"SurfaceShellDensityMap")
600 def _object_cast_to_SurfaceShellDensityMap(o):
601 """_object_cast_to_SurfaceShellDensityMap(Object o) -> SurfaceShellDensityMap"""
602 return _IMP_em._object_cast_to_SurfaceShellDensityMap(o)
604 _object_types.append(
"FitRestraint")
607 def _object_cast_to_FitRestraint(o):
608 """_object_cast_to_FitRestraint(Object o) -> FitRestraint"""
609 return _IMP_em._object_cast_to_FitRestraint(o)
611 _object_types.append(
"PCAFitRestraint")
614 def _object_cast_to_PCAFitRestraint(o):
615 """_object_cast_to_PCAFitRestraint(Object o) -> PCAFitRestraint"""
616 return _IMP_em._object_cast_to_PCAFitRestraint(o)
618 _object_types.append(
"EnvelopePenetrationRestraint")
621 def _object_cast_to_EnvelopePenetrationRestraint(o):
622 """_object_cast_to_EnvelopePenetrationRestraint(Object o) -> EnvelopePenetrationRestraint"""
623 return _IMP_em._object_cast_to_EnvelopePenetrationRestraint(o)
625 _object_types.append(
"EnvelopeFitRestraint")
628 def _object_cast_to_EnvelopeFitRestraint(o):
629 """_object_cast_to_EnvelopeFitRestraint(Object o) -> EnvelopeFitRestraint"""
630 return _IMP_em._object_cast_to_EnvelopeFitRestraint(o)
632 KernelParametersList=list
633 _plural_types.append(
"KernelParametersList")
634 _value_types.append(
"KernelParameters")
637 _object_types.append(
"HighDensityEmbedding")
640 def _object_cast_to_HighDensityEmbedding(o):
641 """_object_cast_to_HighDensityEmbedding(Object o) -> HighDensityEmbedding"""
642 return _IMP_em._object_cast_to_HighDensityEmbedding(o)
644 _object_types.append(
"MapReaderWriter")
647 def _object_cast_to_MapReaderWriter(o):
648 """_object_cast_to_MapReaderWriter(Object o) -> MapReaderWriter"""
649 return _IMP_em._object_cast_to_MapReaderWriter(o)
651 _object_types.append(
"MRCReaderWriter")
654 def _object_cast_to_MRCReaderWriter(o):
655 """_object_cast_to_MRCReaderWriter(Object o) -> MRCReaderWriter"""
656 return _IMP_em._object_cast_to_MRCReaderWriter(o)
658 _object_types.append(
"SpiderMapReaderWriter")
661 def _object_cast_to_SpiderMapReaderWriter(o):
662 """_object_cast_to_SpiderMapReaderWriter(Object o) -> SpiderMapReaderWriter"""
663 return _IMP_em._object_cast_to_SpiderMapReaderWriter(o)
665 _object_types.append(
"EMReaderWriter")
668 def _object_cast_to_EMReaderWriter(o):
669 """_object_cast_to_EMReaderWriter(Object o) -> EMReaderWriter"""
670 return _IMP_em._object_cast_to_EMReaderWriter(o)
672 _object_types.append(
"XplorReaderWriter")
675 def _object_cast_to_XplorReaderWriter(o):
676 """_object_cast_to_XplorReaderWriter(Object o) -> XplorReaderWriter"""
677 return _IMP_em._object_cast_to_XplorReaderWriter(o)
679 _object_types.append(
"CoarseCC")
682 def _object_cast_to_CoarseCC(o):
683 """_object_cast_to_CoarseCC(Object o) -> CoarseCC"""
684 return _IMP_em._object_cast_to_CoarseCC(o)
686 _object_types.append(
"CoarseCCatIntervals")
689 def _object_cast_to_CoarseCCatIntervals(o):
690 """_object_cast_to_CoarseCCatIntervals(Object o) -> CoarseCCatIntervals"""
691 return _IMP_em._object_cast_to_CoarseCCatIntervals(o)
693 FittingSolutionsList=list
694 _plural_types.append(
"FittingSolutionsList")
695 _value_types.append(
"FittingSolutions")
698 """Proxy of C++ IMP::em::MapReaderWriter class"""
699 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
702 """__init__(IMP::em::MapReaderWriter self) -> MapReaderWriter"""
703 this = _IMP_em.new_MapReaderWriter()
705 self.this.append(this)
709 def get_version_info(self):
710 """get_version_info(MapReaderWriter self) -> VersionInfo"""
711 return _IMP_em.MapReaderWriter_get_version_info(self)
715 """__str__(MapReaderWriter self) -> std::string"""
716 return _IMP_em.MapReaderWriter___str__(self)
720 """__repr__(MapReaderWriter self) -> std::string"""
721 return _IMP_em.MapReaderWriter___repr__(self)
726 return _object_cast_to_MapReaderWriter(o)
728 MapReaderWriter_swigregister = _IMP_em.MapReaderWriter_swigregister
729 MapReaderWriter_swigregister(MapReaderWriter)
733 class DensityHeader(object):
734 """Proxy of C++ IMP::em::DensityHeader class"""
735 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
736 __repr__ = _swig_repr
739 """__init__(IMP::em::DensityHeader self) -> DensityHeader"""
740 this = _IMP_em.new_DensityHeader()
742 self.this.append(this)
746 def get_top(self, ind):
747 """get_top(DensityHeader self, int ind) -> IMP::em::emreal"""
748 return _IMP_em.DensityHeader_get_top(self, ind)
751 def compute_xyz_top(self, force=False):
753 compute_xyz_top(DensityHeader self, bool force=False)
754 compute_xyz_top(DensityHeader self)
756 return _IMP_em.DensityHeader_compute_xyz_top(self, force)
759 def update_map_dimensions(self, nnx, nny, nnz):
760 """update_map_dimensions(DensityHeader self, int nnx, int nny, int nnz)"""
761 return _IMP_em.DensityHeader_update_map_dimensions(self, nnx, nny, nnz)
764 def update_cell_dimensions(self):
765 """update_cell_dimensions(DensityHeader self)"""
766 return _IMP_em.DensityHeader_update_cell_dimensions(self)
769 def show(self, *args):
771 show(DensityHeader self, _ostream out)
772 show(DensityHeader self)
774 return _IMP_em.DensityHeader_show(self, *args)
776 MAP_FIELD_SIZE = _IMP_em.DensityHeader_MAP_FIELD_SIZE
777 USER_FIELD_SIZE = _IMP_em.DensityHeader_USER_FIELD_SIZE
778 COMMENT_FIELD_NUM_OF = _IMP_em.DensityHeader_COMMENT_FIELD_NUM_OF
779 COMMENT_FIELD_SINGLE_SIZE = _IMP_em.DensityHeader_COMMENT_FIELD_SINGLE_SIZE
780 nxstart = _swig_property(_IMP_em.DensityHeader_nxstart_get, _IMP_em.DensityHeader_nxstart_set)
781 nystart = _swig_property(_IMP_em.DensityHeader_nystart_get, _IMP_em.DensityHeader_nystart_set)
782 nzstart = _swig_property(_IMP_em.DensityHeader_nzstart_get, _IMP_em.DensityHeader_nzstart_set)
783 mx = _swig_property(_IMP_em.DensityHeader_mx_get, _IMP_em.DensityHeader_mx_set)
784 my = _swig_property(_IMP_em.DensityHeader_my_get, _IMP_em.DensityHeader_my_set)
785 mz = _swig_property(_IMP_em.DensityHeader_mz_get, _IMP_em.DensityHeader_mz_set)
786 xlen = _swig_property(_IMP_em.DensityHeader_xlen_get, _IMP_em.DensityHeader_xlen_set)
787 ylen = _swig_property(_IMP_em.DensityHeader_ylen_get, _IMP_em.DensityHeader_ylen_set)
788 zlen = _swig_property(_IMP_em.DensityHeader_zlen_get, _IMP_em.DensityHeader_zlen_set)
789 alpha = _swig_property(_IMP_em.DensityHeader_alpha_get, _IMP_em.DensityHeader_alpha_set)
790 beta = _swig_property(_IMP_em.DensityHeader_beta_get, _IMP_em.DensityHeader_beta_set)
791 gamma = _swig_property(_IMP_em.DensityHeader_gamma_get, _IMP_em.DensityHeader_gamma_set)
792 mapc = _swig_property(_IMP_em.DensityHeader_mapc_get, _IMP_em.DensityHeader_mapc_set)
793 mapr = _swig_property(_IMP_em.DensityHeader_mapr_get, _IMP_em.DensityHeader_mapr_set)
794 maps = _swig_property(_IMP_em.DensityHeader_maps_get, _IMP_em.DensityHeader_maps_set)
795 dmin = _swig_property(_IMP_em.DensityHeader_dmin_get, _IMP_em.DensityHeader_dmin_set)
796 dmax = _swig_property(_IMP_em.DensityHeader_dmax_get, _IMP_em.DensityHeader_dmax_set)
797 dmean = _swig_property(_IMP_em.DensityHeader_dmean_get, _IMP_em.DensityHeader_dmean_set)
798 ispg = _swig_property(_IMP_em.DensityHeader_ispg_get, _IMP_em.DensityHeader_ispg_set)
799 nsymbt = _swig_property(_IMP_em.DensityHeader_nsymbt_get, _IMP_em.DensityHeader_nsymbt_set)
800 user = _swig_property(_IMP_em.DensityHeader_user_get, _IMP_em.DensityHeader_user_set)
801 map = _swig_property(_IMP_em.DensityHeader_map_get, _IMP_em.DensityHeader_map_set)
802 machinestamp = _swig_property(_IMP_em.DensityHeader_machinestamp_get, _IMP_em.DensityHeader_machinestamp_set)
803 rms = _swig_property(_IMP_em.DensityHeader_rms_get, _IMP_em.DensityHeader_rms_set)
804 nlabl = _swig_property(_IMP_em.DensityHeader_nlabl_get, _IMP_em.DensityHeader_nlabl_set)
805 comments = _swig_property(_IMP_em.DensityHeader_comments_get, _IMP_em.DensityHeader_comments_set)
806 magic = _swig_property(_IMP_em.DensityHeader_magic_get, _IMP_em.DensityHeader_magic_set)
807 voltage = _swig_property(_IMP_em.DensityHeader_voltage_get, _IMP_em.DensityHeader_voltage_set)
808 Cs = _swig_property(_IMP_em.DensityHeader_Cs_get, _IMP_em.DensityHeader_Cs_set)
809 Aperture = _swig_property(_IMP_em.DensityHeader_Aperture_get, _IMP_em.DensityHeader_Aperture_set)
810 Magnification = _swig_property(_IMP_em.DensityHeader_Magnification_get, _IMP_em.DensityHeader_Magnification_set)
811 Postmagnification = _swig_property(_IMP_em.DensityHeader_Postmagnification_get, _IMP_em.DensityHeader_Postmagnification_set)
812 Exposuretime = _swig_property(_IMP_em.DensityHeader_Exposuretime_get, _IMP_em.DensityHeader_Exposuretime_set)
813 Microscope = _swig_property(_IMP_em.DensityHeader_Microscope_get, _IMP_em.DensityHeader_Microscope_set)
814 Pixelsize = _swig_property(_IMP_em.DensityHeader_Pixelsize_get, _IMP_em.DensityHeader_Pixelsize_set)
815 CCDArea = _swig_property(_IMP_em.DensityHeader_CCDArea_get, _IMP_em.DensityHeader_CCDArea_set)
816 Defocus = _swig_property(_IMP_em.DensityHeader_Defocus_get, _IMP_em.DensityHeader_Defocus_set)
817 Astigmatism = _swig_property(_IMP_em.DensityHeader_Astigmatism_get, _IMP_em.DensityHeader_Astigmatism_set)
818 AstigmatismAngle = _swig_property(_IMP_em.DensityHeader_AstigmatismAngle_get, _IMP_em.DensityHeader_AstigmatismAngle_set)
819 FocusIncrement = _swig_property(_IMP_em.DensityHeader_FocusIncrement_get, _IMP_em.DensityHeader_FocusIncrement_set)
820 CountsPerElectron = _swig_property(_IMP_em.DensityHeader_CountsPerElectron_get, _IMP_em.DensityHeader_CountsPerElectron_set)
821 Intensity = _swig_property(_IMP_em.DensityHeader_Intensity_get, _IMP_em.DensityHeader_Intensity_set)
822 EnergySlitwidth = _swig_property(_IMP_em.DensityHeader_EnergySlitwidth_get, _IMP_em.DensityHeader_EnergySlitwidth_set)
823 EnergyOffset = _swig_property(_IMP_em.DensityHeader_EnergyOffset_get, _IMP_em.DensityHeader_EnergyOffset_set)
824 Tiltangle = _swig_property(_IMP_em.DensityHeader_Tiltangle_get, _IMP_em.DensityHeader_Tiltangle_set)
825 Tiltaxis = _swig_property(_IMP_em.DensityHeader_Tiltaxis_get, _IMP_em.DensityHeader_Tiltaxis_set)
826 MarkerX = _swig_property(_IMP_em.DensityHeader_MarkerX_get, _IMP_em.DensityHeader_MarkerX_set)
827 MarkerY = _swig_property(_IMP_em.DensityHeader_MarkerY_get, _IMP_em.DensityHeader_MarkerY_set)
828 lswap = _swig_property(_IMP_em.DensityHeader_lswap_get, _IMP_em.DensityHeader_lswap_set)
831 """get_resolution(DensityHeader self) -> float"""
832 return _IMP_em.DensityHeader_get_resolution(self)
835 def get_has_resolution(self):
836 """get_has_resolution(DensityHeader self) -> bool"""
837 return _IMP_em.DensityHeader_get_has_resolution(self)
840 def set_resolution(self, resolution):
841 """set_resolution(DensityHeader self, float resolution)"""
842 return _IMP_em.DensityHeader_set_resolution(self, resolution)
845 def get_spacing(self):
846 """get_spacing(DensityHeader self) -> float"""
847 return _IMP_em.DensityHeader_get_spacing(self)
850 def get_xorigin(self):
851 """get_xorigin(DensityHeader self) -> float"""
852 return _IMP_em.DensityHeader_get_xorigin(self)
855 def get_yorigin(self):
856 """get_yorigin(DensityHeader self) -> float"""
857 return _IMP_em.DensityHeader_get_yorigin(self)
860 def get_zorigin(self):
861 """get_zorigin(DensityHeader self) -> float"""
862 return _IMP_em.DensityHeader_get_zorigin(self)
865 def get_origin(self, i):
866 """get_origin(DensityHeader self, int i) -> float"""
867 return _IMP_em.DensityHeader_get_origin(self, i)
870 def set_xorigin(self, x):
871 """set_xorigin(DensityHeader self, float x)"""
872 return _IMP_em.DensityHeader_set_xorigin(self, x)
875 def set_yorigin(self, y):
876 """set_yorigin(DensityHeader self, float y)"""
877 return _IMP_em.DensityHeader_set_yorigin(self, y)
880 def set_zorigin(self, z):
881 """set_zorigin(DensityHeader self, float z)"""
882 return _IMP_em.DensityHeader_set_zorigin(self, z)
885 def is_top_calculated(self):
886 """is_top_calculated(DensityHeader self) -> bool"""
887 return _IMP_em.DensityHeader_is_top_calculated(self)
889 Objectpixelsize_ = _swig_property(_IMP_em.DensityHeader_Objectpixelsize__get, _IMP_em.DensityHeader_Objectpixelsize__set)
892 """get_nx(DensityHeader self) -> int"""
893 return _IMP_em.DensityHeader_get_nx(self)
897 """get_ny(DensityHeader self) -> int"""
898 return _IMP_em.DensityHeader_get_ny(self)
902 """get_nz(DensityHeader self) -> int"""
903 return _IMP_em.DensityHeader_get_nz(self)
906 def get_number_of_voxels(self):
907 """get_number_of_voxels(DensityHeader self) -> int"""
908 return _IMP_em.DensityHeader_get_number_of_voxels(self)
911 def get_data_type(self):
912 """get_data_type(DensityHeader self) -> int"""
913 return _IMP_em.DensityHeader_get_data_type(self)
916 def set_data_type(self, data_type):
917 """set_data_type(DensityHeader self, int data_type)"""
918 return _IMP_em.DensityHeader_set_data_type(self, data_type)
920 __swig_destroy__ = _IMP_em.delete_DensityHeader
921 __del__ =
lambda self:
None
922 DensityHeader_swigregister = _IMP_em.DensityHeader_swigregister
923 DensityHeader_swigregister(DensityHeader)
927 """create_density_header(BoundingBox3D bb, float spacing) -> DensityHeader"""
928 return _IMP_em.create_density_header(bb, spacing)
932 read_map(std::string filename, MapReaderWriter reader) -> DensityMap
933 read_map(std::string filename) -> DensityMap
935 return _IMP_em.read_map(*args)
937 def write_map(*args):
939 write_map(DensityMap m, std::string filename, MapReaderWriter writer)
940 write_map(DensityMap m, std::string filename)
942 return _IMP_em.write_map(*args)
945 """approximate_molecular_mass(DensityMap m, IMP::Float threshold) -> IMP::Float"""
946 return _IMP_em.approximate_molecular_mass(m, threshold)
948 """Proxy of C++ IMP::em::DensityMap class"""
949 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
951 def __init__(self, *args):
953 __init__(IMP::em::DensityMap self, std::string name) -> DensityMap
954 __init__(IMP::em::DensityMap self) -> DensityMap
955 __init__(IMP::em::DensityMap self, DensityHeader header, std::string name) -> DensityMap
956 __init__(IMP::em::DensityMap self, DensityHeader header) -> DensityMap
958 this = _IMP_em.new_DensityMap(*args)
960 self.this.append(this)
964 def reset_data(self, value=0.0):
966 reset_data(DensityMap self, float value=0.0)
967 reset_data(DensityMap self)
969 return _IMP_em.DensityMap_reset_data(self, value)
973 """calcRMS(DensityMap self) -> IMP::em::emreal"""
974 return _IMP_em.DensityMap_calcRMS(self)
977 def std_normalize(self):
978 """std_normalize(DensityMap self)"""
979 return _IMP_em.DensityMap_std_normalize(self)
982 def is_normalized(self):
983 """is_normalized(DensityMap self) -> bool"""
984 return _IMP_em.DensityMap_is_normalized(self)
987 def get_location_in_dim_by_voxel(self, index, dim):
988 """get_location_in_dim_by_voxel(DensityMap self, long index, int dim) -> float"""
989 return _IMP_em.DensityMap_get_location_in_dim_by_voxel(self, index, dim)
992 def xyz_ind2voxel(self, x, y, z):
993 """xyz_ind2voxel(DensityMap self, int x, int y, int z) -> long"""
994 return _IMP_em.DensityMap_xyz_ind2voxel(self, x, y, z)
997 def get_voxel_by_location(self, *args):
999 get_voxel_by_location(DensityMap self, float x, float y, float z) -> long
1000 get_voxel_by_location(DensityMap self, Vector3D v) -> long
1002 return _IMP_em.DensityMap_get_voxel_by_location(self, *args)
1005 def get_location_by_voxel(self, index):
1006 """get_location_by_voxel(DensityMap self, long index) -> Vector3D"""
1007 return _IMP_em.DensityMap_get_location_by_voxel(self, index)
1010 def is_xyz_ind_part_of_volume(self, ix, iy, iz):
1011 """is_xyz_ind_part_of_volume(DensityMap self, int ix, int iy, int iz) -> bool"""
1012 return _IMP_em.DensityMap_is_xyz_ind_part_of_volume(self, ix, iy, iz)
1015 def is_part_of_volume(self, *args):
1017 is_part_of_volume(DensityMap self, float x, float y, float z) -> bool
1018 is_part_of_volume(DensityMap self, Vector3D v) -> bool
1020 return _IMP_em.DensityMap_is_part_of_volume(self, *args)
1023 def get_value(self, *args):
1025 get_value(DensityMap self, float x, float y, float z) -> IMP::em::emreal
1026 get_value(DensityMap self, Vector3D point) -> IMP::em::emreal
1027 get_value(DensityMap self, long index) -> IMP::em::emreal
1029 return _IMP_em.DensityMap_get_value(self, *args)
1032 def set_value(self, *args):
1034 set_value(DensityMap self, long index, IMP::em::emreal value)
1035 set_value(DensityMap self, float x, float y, float z, IMP::em::emreal value)
1037 return _IMP_em.DensityMap_set_value(self, *args)
1040 def set_origin(self, *args):
1042 set_origin(DensityMap self, float x, float y, float z)
1043 set_origin(DensityMap self, Vector3D v)
1045 return _IMP_em.DensityMap_set_origin(self, *args)
1048 def get_origin(self):
1049 """get_origin(DensityMap self) -> Vector3D"""
1050 return _IMP_em.DensityMap_get_origin(self)
1054 """get_top(DensityMap self) -> Vector3D"""
1055 return _IMP_em.DensityMap_get_top(self)
1058 def get_header(self):
1059 h = _IMP_em.DensityMap_get_header(self)
1065 def get_header_writable(self):
1066 h = _IMP_em.DensityMap_get_header_writable(self)
1072 def same_origin(self, other):
1073 """same_origin(DensityMap self, DensityMap other) -> bool"""
1074 return _IMP_em.DensityMap_same_origin(self, other)
1077 def same_dimensions(self, other):
1078 """same_dimensions(DensityMap self, DensityMap other) -> bool"""
1079 return _IMP_em.DensityMap_same_dimensions(self, other)
1082 def same_voxel_size(self, other):
1083 """same_voxel_size(DensityMap self, DensityMap other) -> bool"""
1084 return _IMP_em.DensityMap_same_voxel_size(self, other)
1089 get_centroid(DensityMap self, IMP::em::emreal threshold=0.0) -> Vector3D
1090 get_centroid(DensityMap self) -> Vector3D
1092 return _IMP_em.DensityMap_get_centroid(self, threshold)
1095 def get_max_value(self):
1096 """get_max_value(DensityMap self) -> IMP::em::emreal"""
1097 return _IMP_em.DensityMap_get_max_value(self)
1100 def get_min_value(self):
1101 """get_min_value(DensityMap self) -> IMP::em::emreal"""
1102 return _IMP_em.DensityMap_get_min_value(self)
1105 def add(self, other):
1106 """add(DensityMap self, DensityMap other)"""
1107 return _IMP_em.DensityMap_add(self, other)
1110 def pick_max(self, other):
1111 """pick_max(DensityMap self, DensityMap other)"""
1112 return _IMP_em.DensityMap_pick_max(self, other)
1115 def get_number_of_voxels(self):
1116 """get_number_of_voxels(DensityMap self) -> long"""
1117 return _IMP_em.DensityMap_get_number_of_voxels(self)
1120 def set_void_map(self, nx, ny, nz):
1121 """set_void_map(DensityMap self, int nx, int ny, int nz)"""
1122 return _IMP_em.DensityMap_set_void_map(self, nx, ny, nz)
1125 def pad(self, nx, ny, nz, val=0.0):
1127 pad(DensityMap self, int nx, int ny, int nz, float val=0.0)
1128 pad(DensityMap self, int nx, int ny, int nz)
1130 return _IMP_em.DensityMap_pad(self, nx, ny, nz, val)
1133 def pad_margin(self, mrg_x, mrg_y, mrg_z, val=0.0):
1135 pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z, float val=0.0) -> DensityMap
1136 pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z) -> DensityMap
1138 return _IMP_em.DensityMap_pad_margin(self, mrg_x, mrg_y, mrg_z, val)
1141 def get_cropped(self, *args):
1143 get_cropped(DensityMap self, float threshold) -> DensityMap
1144 get_cropped(DensityMap self, BoundingBox3D bb) -> DensityMap
1146 return _IMP_em.DensityMap_get_cropped(self, *args)
1149 def get_maximum_value_in_xy_plane(self, z_ind):
1150 """get_maximum_value_in_xy_plane(DensityMap self, int z_ind) -> float"""
1151 return _IMP_em.DensityMap_get_maximum_value_in_xy_plane(self, z_ind)
1154 def get_maximum_value_in_xz_plane(self, y_ind):
1155 """get_maximum_value_in_xz_plane(DensityMap self, int y_ind) -> float"""
1156 return _IMP_em.DensityMap_get_maximum_value_in_xz_plane(self, y_ind)
1159 def get_maximum_value_in_yz_plane(self, x_ind):
1160 """get_maximum_value_in_yz_plane(DensityMap self, int x_ind) -> float"""
1161 return _IMP_em.DensityMap_get_maximum_value_in_yz_plane(self, x_ind)
1165 """multiply(DensityMap self, float factor)"""
1166 return _IMP_em.DensityMap_multiply(self, factor)
1169 def get_locations_string(self, t):
1170 """get_locations_string(DensityMap self, float t) -> std::string"""
1171 return _IMP_em.DensityMap_get_locations_string(self, t)
1174 def update_voxel_size(self, new_apix):
1175 """update_voxel_size(DensityMap self, float new_apix)"""
1176 return _IMP_em.DensityMap_update_voxel_size(self, new_apix)
1179 def get_spacing(self):
1180 """get_spacing(DensityMap self) -> IMP::Float"""
1181 return _IMP_em.DensityMap_get_spacing(self)
1184 def calc_all_voxel2loc(self):
1185 """calc_all_voxel2loc(DensityMap self)"""
1186 return _IMP_em.DensityMap_calc_all_voxel2loc(self)
1189 def copy_map(self, other):
1190 """copy_map(DensityMap self, DensityMap other)"""
1191 return _IMP_em.DensityMap_copy_map(self, other)
1194 def get_version_info(self):
1195 """get_version_info(DensityMap self) -> VersionInfo"""
1196 return _IMP_em.DensityMap_get_version_info(self)
1199 def lower_voxel_shift(self, loc, kdist, orig, ndim):
1200 """lower_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
1201 return _IMP_em.DensityMap_lower_voxel_shift(self, loc, kdist, orig, ndim)
1204 def upper_voxel_shift(self, loc, kdist, orig, ndim):
1205 """upper_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
1206 return _IMP_em.DensityMap_upper_voxel_shift(self, loc, kdist, orig, ndim)
1209 def get_rms_calculated(self):
1210 """get_rms_calculated(DensityMap self) -> bool"""
1211 return _IMP_em.DensityMap_get_rms_calculated(self)
1214 def get_dim_index_by_location(self, *args):
1216 get_dim_index_by_location(DensityMap self, Vector3D v, int ind) -> int
1217 get_dim_index_by_location(DensityMap self, float loc_val, int ind) -> int
1219 return _IMP_em.DensityMap_get_dim_index_by_location(self, *args)
1223 """__str__(DensityMap self) -> std::string"""
1224 return _IMP_em.DensityMap___str__(self)
1228 """__repr__(DensityMap self) -> std::string"""
1229 return _IMP_em.DensityMap___repr__(self)
1234 return _object_cast_to_DensityMap(o)
1236 DensityMap_swigregister = _IMP_em.DensityMap_swigregister
1237 DensityMap_swigregister(DensityMap)
1242 get_bounding_box(DensityMap m, IMP::Float threshold) -> BoundingBox3D
1243 get_bounding_box(DensityMap m) -> BoundingBox3D
1245 return _IMP_em.get_bounding_box(*args)
1247 def get_density(m, v):
1248 """get_density(DensityMap m, Vector3D v) -> double"""
1249 return _IMP_em.get_density(m, v)
1251 def get_transformed(*args):
1253 get_transformed(DensityMap input, Transformation3D tr, double threshold) -> DensityMap
1254 get_transformed(DensityMap input, Transformation3D tr) -> DensityMap
1256 return _IMP_em.get_transformed(*args)
1258 def get_resampled(input, scaling):
1259 """get_resampled(DensityMap input, double scaling) -> DensityMap"""
1260 return _IMP_em.get_resampled(input, scaling)
1262 def get_transformed_into(source, tr, into, calc_rms=True):
1264 get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into, bool calc_rms=True)
1265 get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into)
1267 return _IMP_em.get_transformed_into(source, tr, into, calc_rms)
1269 def get_transformed_into2(source, tr, into):
1270 """get_transformed_into2(DensityMap source, Transformation3D tr, DensityMap into)"""
1271 return _IMP_em.get_transformed_into2(source, tr, into)
1273 def get_interiors_intersect(d1, d2):
1274 """get_interiors_intersect(DensityMap d1, DensityMap d2) -> bool"""
1275 return _IMP_em.get_interiors_intersect(d1, d2)
1279 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
1280 get_segment(DensityMap map_to_segment, IMP::algebra::Vector3Ds vecs, float dist) -> DensityMap
1282 return _IMP_em.get_segment(*args)
1285 """get_segment_by_masking(DensityMap map_to_segment, DensityMap mask, float mas_threshold) -> DensityMap"""
1286 return _IMP_em.get_segment_by_masking(map_to_segment, mask, mas_threshold)
1288 def binarize(orig_map, threshold, reverse=False):
1290 binarize(DensityMap orig_map, float threshold, bool reverse=False) -> DensityMap
1291 binarize(DensityMap orig_map, float threshold) -> DensityMap
1293 return _IMP_em.binarize(orig_map, threshold, reverse)
1296 """get_threshold_map(DensityMap orig_map, float threshold) -> DensityMap"""
1297 return _IMP_em.get_threshold_map(orig_map, threshold)
1300 """multiply(DensityMap m1, DensityMap m2) -> DensityMap"""
1301 return _IMP_em.multiply(m1, m2)
1304 """convolute(DensityMap m1, DensityMap m2) -> double"""
1305 return _IMP_em.convolute(m1, m2)
1308 """get_sum(DensityMap m1) -> double"""
1309 return _IMP_em.get_sum(m1)
1312 """get_max_map(IMP::em::DensityMaps maps) -> DensityMap"""
1313 return _IMP_em.get_max_map(maps)
1316 """interpolate_map(DensityMap in_map, double new_spacing) -> DensityMap"""
1317 return _IMP_em.interpolate_map(in_map, new_spacing)
1320 """get_grid(DensityMap in_map) -> IMP::algebra::GridD< 3,IMP::algebra::DenseGridStorageD< 3,float >,float,IMP::algebra::DefaultEmbeddingD< 3 > >"""
1321 return _IMP_em.get_grid(in_map)
1325 create_density_map(DensityMap other) -> DensityMap
1326 create_density_map(BoundingBox3D bb, double spacing) -> DensityMap
1327 create_density_map(int nx, int ny, int nz, double spacing) -> DensityMap
1328 create_density_map(IMP::algebra::GridD< 3,IMP::algebra::DenseGridStorageD< 3,float >,float,IMP::algebra::DefaultEmbeddingD< 3 > > const & grid) -> DensityMap
1330 return _IMP_em.create_density_map(*args)
1332 def get_binarized_interior(dmap):
1333 """get_binarized_interior(DensityMap dmap) -> DensityMap"""
1334 return _IMP_em.get_binarized_interior(dmap)
1336 def add_to_map(dm, pis):
1337 """add_to_map(DensityMap dm, IMP::Particles const & pis)"""
1338 return _IMP_em.add_to_map(dm, pis)
1339 class RadiusDependentDistanceMask(object):
1340 """Proxy of C++ IMP::em::RadiusDependentDistanceMask class"""
1341 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1342 __repr__ = _swig_repr
1344 def __init__(self, sampling_radius, header):
1345 """__init__(IMP::em::RadiusDependentDistanceMask self, float sampling_radius, DensityHeader header) -> RadiusDependentDistanceMask"""
1346 this = _IMP_em.new_RadiusDependentDistanceMask(sampling_radius, header)
1348 self.this.append(this)
1352 def get_neighbor_shift(self):
1353 """get_neighbor_shift(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1354 return _IMP_em.RadiusDependentDistanceMask_get_neighbor_shift(self)
1357 def get_neighbor_dist(self):
1358 """get_neighbor_dist(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1359 return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist(self)
1362 def get_neighbor_dist_exp(self):
1363 """get_neighbor_dist_exp(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1364 return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist_exp(self)
1367 def show(self, out):
1368 """show(RadiusDependentDistanceMask self, _ostream out)"""
1369 return _IMP_em.RadiusDependentDistanceMask_show(self, out)
1371 __swig_destroy__ = _IMP_em.delete_RadiusDependentDistanceMask
1372 __del__ =
lambda self:
None
1373 RadiusDependentDistanceMask_swigregister = _IMP_em.RadiusDependentDistanceMask_swigregister
1374 RadiusDependentDistanceMask_swigregister(RadiusDependentDistanceMask)
1376 class DistanceMask(object):
1377 """Proxy of C++ IMP::em::DistanceMask class"""
1378 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1379 __repr__ = _swig_repr
1381 def __init__(self, *args):
1383 __init__(IMP::em::DistanceMask self) -> DistanceMask
1384 __init__(IMP::em::DistanceMask self, DensityHeader header) -> DistanceMask
1386 this = _IMP_em.new_DistanceMask(*args)
1388 self.this.append(this)
1392 def show(self, out):
1393 """show(DistanceMask self, _ostream out)"""
1394 return _IMP_em.DistanceMask_show(self, out)
1397 def is_mask_set(self, radius, eps=0.001):
1399 is_mask_set(DistanceMask self, float radius, float eps=0.001) -> bool
1400 is_mask_set(DistanceMask self, float radius) -> bool
1402 return _IMP_em.DistanceMask_is_mask_set(self, radius, eps)
1404 __swig_destroy__ = _IMP_em.delete_DistanceMask
1405 __del__ =
lambda self:
None
1406 DistanceMask_swigregister = _IMP_em.DistanceMask_swigregister
1407 DistanceMask_swigregister(DistanceMask)
1409 class EMReaderWriter(MapReaderWriter):
1410 """Proxy of C++ IMP::em::EMReaderWriter class"""
1411 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1414 """__str__(EMReaderWriter self) -> std::string"""
1415 return _IMP_em.EMReaderWriter___str__(self)
1419 """__repr__(EMReaderWriter self) -> std::string"""
1420 return _IMP_em.EMReaderWriter___repr__(self)
1425 return _object_cast_to_EMReaderWriter(o)
1429 """__init__(IMP::em::EMReaderWriter self) -> EMReaderWriter"""
1430 this = _IMP_em.new_EMReaderWriter()
1432 self.this.append(this)
1435 EMReaderWriter_swigregister = _IMP_em.EMReaderWriter_swigregister
1436 EMReaderWriter_swigregister(EMReaderWriter)
1438 class XplorReaderWriter(MapReaderWriter):
1439 """Proxy of C++ IMP::em::XplorReaderWriter class"""
1440 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1443 """__str__(XplorReaderWriter self) -> std::string"""
1444 return _IMP_em.XplorReaderWriter___str__(self)
1448 """__repr__(XplorReaderWriter self) -> std::string"""
1449 return _IMP_em.XplorReaderWriter___repr__(self)
1454 return _object_cast_to_XplorReaderWriter(o)
1458 """__init__(IMP::em::XplorReaderWriter self) -> XplorReaderWriter"""
1459 this = _IMP_em.new_XplorReaderWriter()
1461 self.this.append(this)
1464 XplorReaderWriter_swigregister = _IMP_em.XplorReaderWriter_swigregister
1465 XplorReaderWriter_swigregister(XplorReaderWriter)
1467 class MRCReaderWriter(MapReaderWriter):
1468 """Proxy of C++ IMP::em::MRCReaderWriter class"""
1469 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1471 def __init__(self, *args):
1473 __init__(IMP::em::MRCReaderWriter self) -> MRCReaderWriter
1474 __init__(IMP::em::MRCReaderWriter self, std::string fn) -> MRCReaderWriter
1476 this = _IMP_em.new_MRCReaderWriter(*args)
1478 self.this.append(this)
1483 """__str__(MRCReaderWriter self) -> std::string"""
1484 return _IMP_em.MRCReaderWriter___str__(self)
1488 """__repr__(MRCReaderWriter self) -> std::string"""
1489 return _IMP_em.MRCReaderWriter___repr__(self)
1494 return _object_cast_to_MRCReaderWriter(o)
1496 MRCReaderWriter_swigregister = _IMP_em.MRCReaderWriter_swigregister
1497 MRCReaderWriter_swigregister(MRCReaderWriter)
1499 class KernelParameters(object):
1500 """Proxy of C++ IMP::em::KernelParameters class"""
1501 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1503 def __init__(self, *args):
1505 __init__(IMP::em::KernelParameters self) -> KernelParameters
1506 __init__(IMP::em::KernelParameters self, float resolution) -> KernelParameters
1508 this = _IMP_em.new_KernelParameters(*args)
1510 self.this.append(this)
1513 __swig_destroy__ = _IMP_em.delete_KernelParameters
1514 __del__ =
lambda self:
None
1517 """get_rsig(KernelParameters self) -> float"""
1518 return _IMP_em.KernelParameters_get_rsig(self)
1521 def get_rsigsq(self):
1522 """get_rsigsq(KernelParameters self) -> float"""
1523 return _IMP_em.KernelParameters_get_rsigsq(self)
1526 def get_inv_rsigsq(self):
1527 """get_inv_rsigsq(KernelParameters self) -> float"""
1528 return _IMP_em.KernelParameters_get_inv_rsigsq(self)
1531 def get_timessig(self):
1532 """get_timessig(KernelParameters self) -> float"""
1533 return _IMP_em.KernelParameters_get_timessig(self)
1536 def get_sq2pi3(self):
1537 """get_sq2pi3(KernelParameters self) -> float"""
1538 return _IMP_em.KernelParameters_get_sq2pi3(self)
1541 def get_rnormfac(self):
1542 """get_rnormfac(KernelParameters self) -> float"""
1543 return _IMP_em.KernelParameters_get_rnormfac(self)
1546 def get_rkdist(self):
1547 """get_rkdist(KernelParameters self) -> float"""
1548 return _IMP_em.KernelParameters_get_rkdist(self)
1551 def get_rkdistsq(self):
1552 """get_rkdistsq(KernelParameters self) -> float"""
1553 return _IMP_em.KernelParameters_get_rkdistsq(self)
1557 """get_lim(KernelParameters self) -> float"""
1558 return _IMP_em.KernelParameters_get_lim(self)
1561 def show(self, *args):
1563 show(KernelParameters self, _ostream out)
1564 show(KernelParameters self)
1566 return _IMP_em.KernelParameters_show(self, *args)
1570 """__str__(KernelParameters self) -> std::string"""
1571 return _IMP_em.KernelParameters___str__(self)
1575 """__repr__(KernelParameters self) -> std::string"""
1576 return _IMP_em.KernelParameters___repr__(self)
1578 KernelParameters_swigregister = _IMP_em.KernelParameters_swigregister
1579 KernelParameters_swigregister(KernelParameters)
1582 _IMP_em.GAUSSIAN_swigconstant(_IMP_em)
1583 GAUSSIAN = _IMP_em.GAUSSIAN
1585 _IMP_em.BINARIZED_SPHERE_swigconstant(_IMP_em)
1586 BINARIZED_SPHERE = _IMP_em.BINARIZED_SPHERE
1588 _IMP_em.SPHERE_swigconstant(_IMP_em)
1589 SPHERE = _IMP_em.SPHERE
1590 class SampledDensityMap(DensityMap):
1591 """Proxy of C++ IMP::em::SampledDensityMap class"""
1592 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1594 def __init__(self, *args):
1596 __init__(IMP::em::SampledDensityMap self, IMP::em::KernelType kt) -> SampledDensityMap
1597 __init__(IMP::em::SampledDensityMap self) -> SampledDensityMap
1598 __init__(IMP::em::SampledDensityMap self, DensityHeader header, IMP::em::KernelType kt) -> SampledDensityMap
1599 __init__(IMP::em::SampledDensityMap self, DensityHeader header) -> SampledDensityMap
1600 __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
1601 __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
1602 __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size, FloatKey mass_key) -> SampledDensityMap
1603 __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size) -> SampledDensityMap
1605 this = _IMP_em.new_SampledDensityMap(*args)
1607 self.this.append(this)
1612 """resample(SampledDensityMap self)"""
1613 return _IMP_em.SampledDensityMap_resample(self)
1616 def project(self, *args):
1618 project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin, Vector3D shift, FloatKey mass_key)
1619 project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin, Vector3D shift)
1620 project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin)
1622 return _IMP_em.SampledDensityMap_project(self, *args)
1625 def set_particles(self, *args):
1627 set_particles(SampledDensityMap self, IMP::ParticlesTemp const & ps, FloatKey mass_key)
1628 set_particles(SampledDensityMap self, IMP::ParticlesTemp const & ps)
1630 return _IMP_em.SampledDensityMap_set_particles(self, *args)
1633 def get_xyzr_particles(self):
1634 """get_xyzr_particles(SampledDensityMap self) -> IMP::core::XYZRs const &"""
1635 return _IMP_em.SampledDensityMap_get_xyzr_particles(self)
1638 def get_sampled_particles(self):
1639 """get_sampled_particles(SampledDensityMap self) -> IMP::Particles const &"""
1640 return _IMP_em.SampledDensityMap_get_sampled_particles(self)
1643 def get_weight_key(self):
1644 """get_weight_key(SampledDensityMap self) -> FloatKey"""
1645 return _IMP_em.SampledDensityMap_get_weight_key(self)
1648 def get_minimum_resampled_value(self):
1649 """get_minimum_resampled_value(SampledDensityMap self) -> float"""
1650 return _IMP_em.SampledDensityMap_get_minimum_resampled_value(self)
1653 def update_resolution(self, res):
1654 """update_resolution(SampledDensityMap self, IMP::Float res)"""
1655 return _IMP_em.SampledDensityMap_update_resolution(self, res)
1657 __swig_destroy__ = _IMP_em.delete_SampledDensityMap
1658 __del__ =
lambda self:
None
1661 """__str__(SampledDensityMap self) -> std::string"""
1662 return _IMP_em.SampledDensityMap___str__(self)
1666 """__repr__(SampledDensityMap self) -> std::string"""
1667 return _IMP_em.SampledDensityMap___repr__(self)
1672 return _object_cast_to_SampledDensityMap(o)
1674 SampledDensityMap_swigregister = _IMP_em.SampledDensityMap_swigregister
1675 SampledDensityMap_swigregister(SampledDensityMap)
1678 _IMP_em.IMP_DEFAULT_NUM_SHELLS_swigconstant(_IMP_em)
1679 IMP_DEFAULT_NUM_SHELLS = _IMP_em.IMP_DEFAULT_NUM_SHELLS
1681 _IMP_em.IMP_SIG_CUTOFF_swigconstant(_IMP_em)
1682 IMP_SIG_CUTOFF = _IMP_em.IMP_SIG_CUTOFF
1683 class SurfaceShellDensityMap(SampledDensityMap):
1684 """Proxy of C++ IMP::em::SurfaceShellDensityMap class"""
1685 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1687 def __init__(self, *args):
1689 __init__(IMP::em::SurfaceShellDensityMap self) -> SurfaceShellDensityMap
1690 __init__(IMP::em::SurfaceShellDensityMap self, DensityHeader header) -> SurfaceShellDensityMap
1691 __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key, int num_shells=5) -> SurfaceShellDensityMap
1692 __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key) -> SurfaceShellDensityMap
1693 __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size) -> SurfaceShellDensityMap
1695 this = _IMP_em.new_SurfaceShellDensityMap(*args)
1697 self.this.append(this)
1702 """binarize(SurfaceShellDensityMap self, float scene_val)"""
1703 return _IMP_em.SurfaceShellDensityMap_binarize(self, scene_val)
1706 def binaries(self, scene_val):
1707 """binaries(SurfaceShellDensityMap self, float scene_val)"""
1708 return _IMP_em.SurfaceShellDensityMap_binaries(self, scene_val)
1711 def has_background_neighbor(self, voxel_ind):
1712 """has_background_neighbor(SurfaceShellDensityMap self, long voxel_ind) -> bool"""
1713 return _IMP_em.SurfaceShellDensityMap_has_background_neighbor(self, voxel_ind)
1715 __swig_destroy__ = _IMP_em.delete_SurfaceShellDensityMap
1716 __del__ =
lambda self:
None
1719 """__str__(SurfaceShellDensityMap self) -> std::string"""
1720 return _IMP_em.SurfaceShellDensityMap___str__(self)
1724 """__repr__(SurfaceShellDensityMap self) -> std::string"""
1725 return _IMP_em.SurfaceShellDensityMap___repr__(self)
1730 return _object_cast_to_SurfaceShellDensityMap(o)
1732 SurfaceShellDensityMap_swigregister = _IMP_em.SurfaceShellDensityMap_swigregister
1733 SurfaceShellDensityMap_swigregister(SurfaceShellDensityMap)
1736 """Proxy of C++ IMP::em::CoarseCC class"""
1737 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1740 """__init__(IMP::em::CoarseCC self) -> CoarseCC"""
1741 this = _IMP_em.new_CoarseCC()
1743 self.this.append(this)
1747 def calc_score(*args):
1749 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True, IMP::FloatPair norm_factors) -> float
1750 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True) -> float
1751 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1752 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1754 return _IMP_em.CoarseCC_calc_score(*args)
1756 calc_score = staticmethod(calc_score)
1758 def cross_correlation_coefficient(*args):
1760 cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False, IMP::FloatPair norm_factors) -> double
1761 cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1762 cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1764 return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1766 cross_correlation_coefficient = staticmethod(cross_correlation_coefficient)
1768 def local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold):
1769 """local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1770 return _IMP_em.CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold)
1772 local_cross_correlation_coefficient = staticmethod(local_cross_correlation_coefficient)
1774 def get_version_info(self):
1775 """get_version_info(CoarseCC self) -> VersionInfo"""
1776 return _IMP_em.CoarseCC_get_version_info(self)
1780 """__str__(CoarseCC self) -> std::string"""
1781 return _IMP_em.CoarseCC___str__(self)
1785 """__repr__(CoarseCC self) -> std::string"""
1786 return _IMP_em.CoarseCC___repr__(self)
1791 return _object_cast_to_CoarseCC(o)
1793 CoarseCC_swigregister = _IMP_em.CoarseCC_swigregister
1794 CoarseCC_swigregister(CoarseCC)
1796 def CoarseCC_calc_score(*args):
1798 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True, IMP::FloatPair norm_factors) -> float
1799 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True) -> float
1800 calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1801 CoarseCC_calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1803 return _IMP_em.CoarseCC_calc_score(*args)
1805 def CoarseCC_cross_correlation_coefficient(*args):
1807 cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False, IMP::FloatPair norm_factors) -> double
1808 cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1809 CoarseCC_cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1811 return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1813 def CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold):
1814 """CoarseCC_local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1815 return _IMP_em.CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold)
1817 class CoarseConvolution(object):
1818 """Proxy of C++ IMP::em::CoarseConvolution class"""
1819 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1820 __repr__ = _swig_repr
1822 def convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac=True):
1824 convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1825 convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1827 return _IMP_em.CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac)
1829 convolution = staticmethod(convolution)
1832 """__init__(IMP::em::CoarseConvolution self) -> CoarseConvolution"""
1833 this = _IMP_em.new_CoarseConvolution()
1835 self.this.append(this)
1838 __swig_destroy__ = _IMP_em.delete_CoarseConvolution
1839 __del__ =
lambda self:
None
1840 CoarseConvolution_swigregister = _IMP_em.CoarseConvolution_swigregister
1841 CoarseConvolution_swigregister(CoarseConvolution)
1843 def CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac=True):
1845 convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1846 CoarseConvolution_convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1848 return _IMP_em.CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac)
1850 class CoarseCCatIntervals(CoarseCC):
1851 """Proxy of C++ IMP::em::CoarseCCatIntervals class"""
1852 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1854 def __init__(self, *args):
1856 __init__(IMP::em::CoarseCCatIntervals self, int const & ncd) -> CoarseCCatIntervals
1857 __init__(IMP::em::CoarseCCatIntervals self) -> CoarseCCatIntervals
1859 this = _IMP_em.new_CoarseCCatIntervals(*args)
1861 self.this.append(this)
1865 def evaluate(self, em_map, model_map, deriv, scalefac, lderiv, eval_interval):
1866 """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 >"""
1867 return _IMP_em.CoarseCCatIntervals_evaluate(self, em_map, model_map, deriv, scalefac, lderiv, eval_interval)
1871 """__str__(CoarseCCatIntervals self) -> std::string"""
1872 return _IMP_em.CoarseCCatIntervals___str__(self)
1876 """__repr__(CoarseCCatIntervals self) -> std::string"""
1877 return _IMP_em.CoarseCCatIntervals___repr__(self)
1882 return _object_cast_to_CoarseCCatIntervals(o)
1884 CoarseCCatIntervals_swigregister = _IMP_em.CoarseCCatIntervals_swigregister
1885 CoarseCCatIntervals_swigregister(CoarseCCatIntervals)
1888 """Proxy of C++ IMP::em::FitRestraint class"""
1889 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1891 def __init__(self, *args):
1893 __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
1894 __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
1895 __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key, float scale=1) -> FitRestraint
1896 __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key) -> FitRestraint
1897 __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors) -> FitRestraint
1898 __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map) -> FitRestraint
1900 this = _IMP_em.new_FitRestraint(*args)
1902 self.this.append(this)
1906 def get_model_dens_map(self):
1907 """get_model_dens_map(FitRestraint self) -> SampledDensityMap"""
1908 return _IMP_em.FitRestraint_get_model_dens_map(self)
1911 def set_scale_factor(self, scale):
1912 """set_scale_factor(FitRestraint self, float scale)"""
1913 return _IMP_em.FitRestraint_set_scale_factor(self, scale)
1916 def get_scale_factor(self):
1917 """get_scale_factor(FitRestraint self) -> float"""
1918 return _IMP_em.FitRestraint_get_scale_factor(self)
1921 def do_get_inputs(self):
1922 """do_get_inputs(FitRestraint self) -> IMP::ModelObjectsTemp"""
1923 return _IMP_em.FitRestraint_do_get_inputs(self)
1926 def get_version_info(self):
1927 """get_version_info(FitRestraint self) -> VersionInfo"""
1928 return _IMP_em.FitRestraint_get_version_info(self)
1932 """__str__(FitRestraint self) -> std::string"""
1933 return _IMP_em.FitRestraint___str__(self)
1937 """__repr__(FitRestraint self) -> std::string"""
1938 return _IMP_em.FitRestraint___repr__(self)
1943 return _object_cast_to_FitRestraint(o)
1947 """cast(Restraint r) -> FitRestraint"""
1948 return _IMP_em.FitRestraint_cast(r)
1950 cast = staticmethod(cast)
1951 FitRestraint_swigregister = _IMP_em.FitRestraint_swigregister
1952 FitRestraint_swigregister(FitRestraint)
1954 def FitRestraint_cast(r):
1955 """FitRestraint_cast(Restraint r) -> FitRestraint"""
1956 return _IMP_em.FitRestraint_cast(r)
1961 density2particles(DensityMap dmap, IMP::Float threshold, Model m, int step=1) -> IMP::Particles
1962 density2particles(DensityMap dmap, IMP::Float threshold, Model m) -> IMP::Particles
1964 return _IMP_em.density2particles(dmap, threshold, m, step)
1967 """density2vectors(DensityMap dmap, IMP::Float threshold) -> IMP::algebra::Vector3Ds"""
1968 return _IMP_em.density2vectors(dmap, threshold)
1972 particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3, FloatKey weight_key) -> SampledDensityMap
1973 particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
1974 particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
1976 return _IMP_em.particles2density(*args)
1980 particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3, FloatKey weight_key) -> SampledDensityMap
1981 particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
1982 particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
1984 return _IMP_em.particles2binarized_density(*args)
1988 particles2surface(IMP::ParticlesTemp const & ps, IMP::Float apix, FloatKey weight_key) -> SurfaceShellDensityMap
1989 particles2surface(IMP::ParticlesTemp const & ps, IMP::Float apix) -> SurfaceShellDensityMap
1991 return _IMP_em.particles2surface(*args)
1993 def calculate_intersection_score(d1, d2):
1994 """calculate_intersection_score(SurfaceShellDensityMap d1, SurfaceShellDensityMap d2) -> IMP::Float"""
1995 return _IMP_em.calculate_intersection_score(d1, d2)
1996 class SpiderHeader(object):
1997 """Proxy of C++ IMP::em::SpiderHeader class"""
1998 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1999 __repr__ = _swig_repr
2000 fNslice = _swig_property(_IMP_em.SpiderHeader_fNslice_get, _IMP_em.SpiderHeader_fNslice_set)
2001 fNrow = _swig_property(_IMP_em.SpiderHeader_fNrow_get, _IMP_em.SpiderHeader_fNrow_set)
2002 fNrec = _swig_property(_IMP_em.SpiderHeader_fNrec_get, _IMP_em.SpiderHeader_fNrec_set)
2003 fNlabel = _swig_property(_IMP_em.SpiderHeader_fNlabel_get, _IMP_em.SpiderHeader_fNlabel_set)
2004 fIform = _swig_property(_IMP_em.SpiderHeader_fIform_get, _IMP_em.SpiderHeader_fIform_set)
2005 fImami = _swig_property(_IMP_em.SpiderHeader_fImami_get, _IMP_em.SpiderHeader_fImami_set)
2006 fFmax = _swig_property(_IMP_em.SpiderHeader_fFmax_get, _IMP_em.SpiderHeader_fFmax_set)
2007 fFmin = _swig_property(_IMP_em.SpiderHeader_fFmin_get, _IMP_em.SpiderHeader_fFmin_set)
2008 fAv = _swig_property(_IMP_em.SpiderHeader_fAv_get, _IMP_em.SpiderHeader_fAv_set)
2009 fSig = _swig_property(_IMP_em.SpiderHeader_fSig_get, _IMP_em.SpiderHeader_fSig_set)
2010 fIhist = _swig_property(_IMP_em.SpiderHeader_fIhist_get, _IMP_em.SpiderHeader_fIhist_set)
2011 fNcol = _swig_property(_IMP_em.SpiderHeader_fNcol_get, _IMP_em.SpiderHeader_fNcol_set)
2012 fLabrec = _swig_property(_IMP_em.SpiderHeader_fLabrec_get, _IMP_em.SpiderHeader_fLabrec_set)
2013 fIangle = _swig_property(_IMP_em.SpiderHeader_fIangle_get, _IMP_em.SpiderHeader_fIangle_set)
2014 fPhi = _swig_property(_IMP_em.SpiderHeader_fPhi_get, _IMP_em.SpiderHeader_fPhi_set)
2015 fTheta = _swig_property(_IMP_em.SpiderHeader_fTheta_get, _IMP_em.SpiderHeader_fTheta_set)
2016 fPsi = _swig_property(_IMP_em.SpiderHeader_fPsi_get, _IMP_em.SpiderHeader_fPsi_set)
2017 fXoff = _swig_property(_IMP_em.SpiderHeader_fXoff_get, _IMP_em.SpiderHeader_fXoff_set)
2018 fYoff = _swig_property(_IMP_em.SpiderHeader_fYoff_get, _IMP_em.SpiderHeader_fYoff_set)
2019 fZoff = _swig_property(_IMP_em.SpiderHeader_fZoff_get, _IMP_em.SpiderHeader_fZoff_set)
2020 fScale = _swig_property(_IMP_em.SpiderHeader_fScale_get, _IMP_em.SpiderHeader_fScale_set)
2021 fLabbyt = _swig_property(_IMP_em.SpiderHeader_fLabbyt_get, _IMP_em.SpiderHeader_fLabbyt_set)
2022 fLenbyt = _swig_property(_IMP_em.SpiderHeader_fLenbyt_get, _IMP_em.SpiderHeader_fLenbyt_set)
2023 fNothing = _swig_property(_IMP_em.SpiderHeader_fNothing_get, _IMP_em.SpiderHeader_fNothing_set)
2024 fFlag = _swig_property(_IMP_em.SpiderHeader_fFlag_get, _IMP_em.SpiderHeader_fFlag_set)
2025 fPhi1 = _swig_property(_IMP_em.SpiderHeader_fPhi1_get, _IMP_em.SpiderHeader_fPhi1_set)
2026 fTheta1 = _swig_property(_IMP_em.SpiderHeader_fTheta1_get, _IMP_em.SpiderHeader_fTheta1_set)
2027 fPsi1 = _swig_property(_IMP_em.SpiderHeader_fPsi1_get, _IMP_em.SpiderHeader_fPsi1_set)
2028 fPhi2 = _swig_property(_IMP_em.SpiderHeader_fPhi2_get, _IMP_em.SpiderHeader_fPhi2_set)
2029 fTheta2 = _swig_property(_IMP_em.SpiderHeader_fTheta2_get, _IMP_em.SpiderHeader_fTheta2_set)
2030 fPsi2 = _swig_property(_IMP_em.SpiderHeader_fPsi2_get, _IMP_em.SpiderHeader_fPsi2_set)
2031 fGeo_matrix = _swig_property(_IMP_em.SpiderHeader_fGeo_matrix_get, _IMP_em.SpiderHeader_fGeo_matrix_set)
2032 fAngle1 = _swig_property(_IMP_em.SpiderHeader_fAngle1_get, _IMP_em.SpiderHeader_fAngle1_set)
2033 fr1 = _swig_property(_IMP_em.SpiderHeader_fr1_get, _IMP_em.SpiderHeader_fr1_set)
2034 fr2 = _swig_property(_IMP_em.SpiderHeader_fr2_get, _IMP_em.SpiderHeader_fr2_set)
2035 RTflag = _swig_property(_IMP_em.SpiderHeader_RTflag_get, _IMP_em.SpiderHeader_RTflag_set)
2036 Astart = _swig_property(_IMP_em.SpiderHeader_Astart_get, _IMP_em.SpiderHeader_Astart_set)
2037 Aend = _swig_property(_IMP_em.SpiderHeader_Aend_get, _IMP_em.SpiderHeader_Aend_set)
2038 Ainc = _swig_property(_IMP_em.SpiderHeader_Ainc_get, _IMP_em.SpiderHeader_Ainc_set)
2039 Rsigma = _swig_property(_IMP_em.SpiderHeader_Rsigma_get, _IMP_em.SpiderHeader_Rsigma_set)
2040 Tstart = _swig_property(_IMP_em.SpiderHeader_Tstart_get, _IMP_em.SpiderHeader_Tstart_set)
2041 Tend = _swig_property(_IMP_em.SpiderHeader_Tend_get, _IMP_em.SpiderHeader_Tend_set)
2042 Tinc = _swig_property(_IMP_em.SpiderHeader_Tinc_get, _IMP_em.SpiderHeader_Tinc_set)
2043 Weight = _swig_property(_IMP_em.SpiderHeader_Weight_get, _IMP_em.SpiderHeader_Weight_set)
2044 Flip = _swig_property(_IMP_em.SpiderHeader_Flip_get, _IMP_em.SpiderHeader_Flip_set)
2045 empty = _swig_property(_IMP_em.SpiderHeader_empty_get, _IMP_em.SpiderHeader_empty_set)
2046 szIDat = _swig_property(_IMP_em.SpiderHeader_szIDat_get, _IMP_em.SpiderHeader_szIDat_set)
2047 szITim = _swig_property(_IMP_em.SpiderHeader_szITim_get, _IMP_em.SpiderHeader_szITim_set)
2048 szITit = _swig_property(_IMP_em.SpiderHeader_szITit_get, _IMP_em.SpiderHeader_szITit_set)
2050 def show(self, out):
2051 """show(SpiderHeader self, _ostream out)"""
2052 return _IMP_em.SpiderHeader_show(self, out)
2056 """__init__(IMP::em::SpiderHeader self) -> SpiderHeader"""
2057 this = _IMP_em.new_SpiderHeader()
2059 self.this.append(this)
2062 __swig_destroy__ = _IMP_em.delete_SpiderHeader
2063 __del__ =
lambda self:
None
2064 SpiderHeader_swigregister = _IMP_em.SpiderHeader_swigregister
2065 SpiderHeader_swigregister(SpiderHeader)
2067 class ImageHeader(object):
2068 """Proxy of C++ IMP::em::ImageHeader class"""
2069 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2070 __repr__ = _swig_repr
2071 IMG_BYTE = _IMP_em.ImageHeader_IMG_BYTE
2072 IMG_IMPEM = _IMP_em.ImageHeader_IMG_IMPEM
2073 IMG_INT = _IMP_em.ImageHeader_IMG_INT
2074 VOL_BYTE = _IMP_em.ImageHeader_VOL_BYTE
2075 VOL_IMPEM = _IMP_em.ImageHeader_VOL_IMPEM
2076 VOL_INT = _IMP_em.ImageHeader_VOL_INT
2077 IMG_FOURIER = _IMP_em.ImageHeader_IMG_FOURIER
2078 VOL_FOURIER = _IMP_em.ImageHeader_VOL_FOURIER
2080 def __init__(self, *args):
2082 __init__(IMP::em::ImageHeader self) -> ImageHeader
2083 __init__(IMP::em::ImageHeader self, IMP::em::ImageHeader::img_type im) -> ImageHeader
2084 __init__(IMP::em::ImageHeader self, float im) -> ImageHeader
2086 this = _IMP_em.new_ImageHeader(*args)
2088 self.this.append(this)
2092 def get_image_type(self):
2093 """get_image_type(ImageHeader self) -> float"""
2094 return _IMP_em.ImageHeader_get_image_type(self)
2097 def set_image_type(self, *args):
2099 set_image_type(ImageHeader self, IMP::em::ImageHeader::img_type im)
2100 set_image_type(ImageHeader self, float im)
2102 return _IMP_em.ImageHeader_set_image_type(self, *args)
2105 def do_show(self, out):
2106 """do_show(ImageHeader self, _ostream out)"""
2107 return _IMP_em.ImageHeader_do_show(self, out)
2110 def show(self, *args):
2112 show(ImageHeader self, _ostream out)
2113 show(ImageHeader self)
2115 return _IMP_em.ImageHeader_show(self, *args)
2118 def print_hard(self, out):
2119 """print_hard(ImageHeader self, _ostream out)"""
2120 return _IMP_em.ImageHeader_print_hard(self, out)
2123 def show_projection_params(self, out):
2124 """show_projection_params(ImageHeader self, _ostream out)"""
2125 return _IMP_em.ImageHeader_show_projection_params(self, out)
2128 def read(self, *args):
2130 read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False, bool skip_extra_checkings=False) -> int
2131 read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False) -> int
2132 read(ImageHeader self, IMP::String const filename, bool skip_type_check=False) -> int
2133 read(ImageHeader self, IMP::String const filename) -> int
2134 read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False, bool skip_extra_checkings=False) -> bool
2135 read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False) -> bool
2136 read(ImageHeader self, std::ifstream & f, bool skip_type_check=False) -> bool
2137 read(ImageHeader self, std::ifstream & f) -> bool
2139 return _IMP_em.ImageHeader_read(self, *args)
2142 def write(self, *args):
2144 write(ImageHeader self, IMP::String const & filename, bool force_reversed=False)
2145 write(ImageHeader self, IMP::String const & filename)
2146 write(ImageHeader self, std::ofstream & f, bool force_reversed=False)
2147 write(ImageHeader self, std::ofstream & f)
2149 return _IMP_em.ImageHeader_write(self, *args)
2153 """clear(ImageHeader self)"""
2154 return _IMP_em.ImageHeader_clear(self)
2157 def set_header(self):
2158 """set_header(ImageHeader self)"""
2159 return _IMP_em.ImageHeader_set_header(self)
2162 def get_reversed(self):
2163 """get_reversed(ImageHeader self) -> bool"""
2164 return _IMP_em.ImageHeader_get_reversed(self)
2167 def set_reversed(self, value):
2168 """set_reversed(ImageHeader self, bool value)"""
2169 return _IMP_em.ImageHeader_set_reversed(self, value)
2172 def get_number_of_slices(self):
2173 """get_number_of_slices(ImageHeader self) -> unsigned int"""
2174 return _IMP_em.ImageHeader_get_number_of_slices(self)
2177 def set_number_of_slices(self, n):
2178 """set_number_of_slices(ImageHeader self, unsigned int n)"""
2179 return _IMP_em.ImageHeader_set_number_of_slices(self, n)
2182 def get_number_of_rows(self):
2183 """get_number_of_rows(ImageHeader self) -> unsigned int"""
2184 return _IMP_em.ImageHeader_get_number_of_rows(self)
2187 def set_number_of_rows(self, n):
2188 """set_number_of_rows(ImageHeader self, unsigned int n)"""
2189 return _IMP_em.ImageHeader_set_number_of_rows(self, n)
2192 def get_number_of_columns(self):
2193 """get_number_of_columns(ImageHeader self) -> unsigned int"""
2194 return _IMP_em.ImageHeader_get_number_of_columns(self)
2197 def set_number_of_columns(self, n):
2198 """set_number_of_columns(ImageHeader self, unsigned int n)"""
2199 return _IMP_em.ImageHeader_set_number_of_columns(self, n)
2202 def get_old_rot(self):
2203 """get_old_rot(ImageHeader self) -> float"""
2204 return _IMP_em.ImageHeader_get_old_rot(self)
2207 def set_old_rot(self, value):
2208 """set_old_rot(ImageHeader self, float value)"""
2209 return _IMP_em.ImageHeader_set_old_rot(self, value)
2212 def get_fAngle1(self):
2213 """get_fAngle1(ImageHeader self) -> float"""
2214 return _IMP_em.ImageHeader_get_fAngle1(self)
2217 def set_fAngle1(self, value):
2218 """set_fAngle1(ImageHeader self, float value)"""
2219 return _IMP_em.ImageHeader_set_fAngle1(self, value)
2222 def get_Scale(self):
2223 """get_Scale(ImageHeader self) -> float"""
2224 return _IMP_em.ImageHeader_get_Scale(self)
2227 def set_Scale(self, value):
2228 """set_Scale(ImageHeader self, float value)"""
2229 return _IMP_em.ImageHeader_set_Scale(self, value)
2233 """get_Flip(ImageHeader self) -> float"""
2234 return _IMP_em.ImageHeader_get_Flip(self)
2237 def set_Flip(self, value):
2238 """set_Flip(ImageHeader self, float value)"""
2239 return _IMP_em.ImageHeader_set_Flip(self, value)
2242 def get_Weight(self):
2243 """get_Weight(ImageHeader self) -> float"""
2244 return _IMP_em.ImageHeader_get_Weight(self)
2247 def set_Weight(self, value):
2248 """set_Weight(ImageHeader self, float value)"""
2249 return _IMP_em.ImageHeader_set_Weight(self, value)
2252 def get_fNrec(self):
2253 """get_fNrec(ImageHeader self) -> float"""
2254 return _IMP_em.ImageHeader_get_fNrec(self)
2257 def set_fNrec(self, value):
2258 """set_fNrec(ImageHeader self, float value)"""
2259 return _IMP_em.ImageHeader_set_fNrec(self, value)
2262 def get_fNlabel(self):
2263 """get_fNlabel(ImageHeader self) -> float"""
2264 return _IMP_em.ImageHeader_get_fNlabel(self)
2267 def set_fNlabel(self, value):
2268 """set_fNlabel(ImageHeader self, float value)"""
2269 return _IMP_em.ImageHeader_set_fNlabel(self, value)
2272 def get_fIform(self):
2273 """get_fIform(ImageHeader self) -> float"""
2274 return _IMP_em.ImageHeader_get_fIform(self)
2277 def set_fIform(self, value):
2278 """set_fIform(ImageHeader self, float value)"""
2279 return _IMP_em.ImageHeader_set_fIform(self, value)
2282 def get_fImami(self):
2283 """get_fImami(ImageHeader self) -> float"""
2284 return _IMP_em.ImageHeader_get_fImami(self)
2287 def set_fImami(self, value):
2288 """set_fImami(ImageHeader self, float value)"""
2289 return _IMP_em.ImageHeader_set_fImami(self, value)
2292 def get_fFmax(self):
2293 """get_fFmax(ImageHeader self) -> float"""
2294 return _IMP_em.ImageHeader_get_fFmax(self)
2297 def set_fFmax(self, value):
2298 """set_fFmax(ImageHeader self, float value)"""
2299 return _IMP_em.ImageHeader_set_fFmax(self, value)
2302 def get_fFmin(self):
2303 """get_fFmin(ImageHeader self) -> float"""
2304 return _IMP_em.ImageHeader_get_fFmin(self)
2307 def set_fFmin(self, value):
2308 """set_fFmin(ImageHeader self, float value)"""
2309 return _IMP_em.ImageHeader_set_fFmin(self, value)
2313 """get_fAv(ImageHeader self) -> float"""
2314 return _IMP_em.ImageHeader_get_fAv(self)
2317 def set_fAv(self, value):
2318 """set_fAv(ImageHeader self, float value)"""
2319 return _IMP_em.ImageHeader_set_fAv(self, value)
2323 """get_fSig(ImageHeader self) -> float"""
2324 return _IMP_em.ImageHeader_get_fSig(self)
2327 def set_fSig(self, value):
2328 """set_fSig(ImageHeader self, float value)"""
2329 return _IMP_em.ImageHeader_set_fSig(self, value)
2332 def get_fIhist(self):
2333 """get_fIhist(ImageHeader self) -> float"""
2334 return _IMP_em.ImageHeader_get_fIhist(self)
2337 def set_fIhist(self, value):
2338 """set_fIhist(ImageHeader self, float value)"""
2339 return _IMP_em.ImageHeader_set_fIhist(self, value)
2342 def get_fLabrec(self):
2343 """get_fLabrec(ImageHeader self) -> float"""
2344 return _IMP_em.ImageHeader_get_fLabrec(self)
2347 def set_fLabrec(self, value):
2348 """set_fLabrec(ImageHeader self, float value)"""
2349 return _IMP_em.ImageHeader_set_fLabrec(self, value)
2352 def get_fIangle(self):
2353 """get_fIangle(ImageHeader self) -> float"""
2354 return _IMP_em.ImageHeader_get_fIangle(self)
2357 def set_fIangle(self, value):
2358 """set_fIangle(ImageHeader self, float value)"""
2359 return _IMP_em.ImageHeader_set_fIangle(self, value)
2362 def get_origin(self):
2363 """get_origin(ImageHeader self) -> Vector3D"""
2364 return _IMP_em.ImageHeader_get_origin(self)
2367 def set_origin(self, *args):
2369 set_origin(ImageHeader self, Vector3D v)
2370 set_origin(ImageHeader self, Vector2D v)
2372 return _IMP_em.ImageHeader_set_origin(self, *args)
2375 def get_object_pixel_size(self):
2376 """get_object_pixel_size(ImageHeader self) -> float"""
2377 return _IMP_em.ImageHeader_get_object_pixel_size(self)
2380 def set_object_pixel_size(self, value):
2381 """set_object_pixel_size(ImageHeader self, float value)"""
2382 return _IMP_em.ImageHeader_set_object_pixel_size(self, value)
2385 def get_fLabbyt(self):
2386 """get_fLabbyt(ImageHeader self) -> float"""
2387 return _IMP_em.ImageHeader_get_fLabbyt(self)
2390 def set_fLabbyt(self, value):
2391 """set_fLabbyt(ImageHeader self, float value)"""
2392 return _IMP_em.ImageHeader_set_fLabbyt(self, value)
2395 def get_fLenbyt(self):
2396 """get_fLenbyt(ImageHeader self) -> float"""
2397 return _IMP_em.ImageHeader_get_fLenbyt(self)
2400 def set_fLenbyt(self, value):
2401 """set_fLenbyt(ImageHeader self, float value)"""
2402 return _IMP_em.ImageHeader_set_fLenbyt(self, value)
2405 def get_fGeo_matrix(self, i, j):
2406 """get_fGeo_matrix(ImageHeader self, unsigned int i, unsigned int j) -> double"""
2407 return _IMP_em.ImageHeader_get_fGeo_matrix(self, i, j)
2410 def get_fFlag(self):
2411 """get_fFlag(ImageHeader self) -> float"""
2412 return _IMP_em.ImageHeader_get_fFlag(self)
2415 def set_fFlag(self, value):
2416 """set_fFlag(ImageHeader self, float value)"""
2417 return _IMP_em.ImageHeader_set_fFlag(self, value)
2420 def get_euler_angles(self):
2421 """get_euler_angles(ImageHeader self) -> Vector3D"""
2422 return _IMP_em.ImageHeader_get_euler_angles(self)
2425 def get_euler_angles1(self):
2426 """get_euler_angles1(ImageHeader self) -> Vector3D"""
2427 return _IMP_em.ImageHeader_get_euler_angles1(self)
2430 def get_euler_angles2(self):
2431 """get_euler_angles2(ImageHeader self) -> Vector3D"""
2432 return _IMP_em.ImageHeader_get_euler_angles2(self)
2435 def set_euler_angles(self, euler):
2436 """set_euler_angles(ImageHeader self, Vector3D euler)"""
2437 return _IMP_em.ImageHeader_set_euler_angles(self, euler)
2440 def set_euler_angles1(self, euler):
2441 """set_euler_angles1(ImageHeader self, Vector3D euler)"""
2442 return _IMP_em.ImageHeader_set_euler_angles1(self, euler)
2445 def set_euler_angles2(self, euler):
2446 """set_euler_angles2(ImageHeader self, Vector3D euler)"""
2447 return _IMP_em.ImageHeader_set_euler_angles2(self, euler)
2450 def is_normalized(self):
2451 """is_normalized(ImageHeader self) -> bool"""
2452 return _IMP_em.ImageHeader_is_normalized(self)
2456 """set_date(ImageHeader self)"""
2457 return _IMP_em.ImageHeader_set_date(self)
2461 """set_time(ImageHeader self)"""
2462 return _IMP_em.ImageHeader_set_time(self)
2465 def set_title(self, newName):
2466 """set_title(ImageHeader self, IMP::String newName)"""
2467 return _IMP_em.ImageHeader_set_title(self, newName)
2469 __swig_destroy__ = _IMP_em.delete_ImageHeader
2470 __del__ =
lambda self:
None
2471 ImageHeader_swigregister = _IMP_em.ImageHeader_swigregister
2472 ImageHeader_swigregister(ImageHeader)
2474 class SpiderMapReaderWriter(MapReaderWriter):
2475 """Proxy of C++ IMP::em::SpiderMapReaderWriter class"""
2476 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2477 filename_ = _swig_property(_IMP_em.SpiderMapReaderWriter_filename__get, _IMP_em.SpiderMapReaderWriter_filename__set)
2478 skip_type_check_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_type_check__get, _IMP_em.SpiderMapReaderWriter_skip_type_check__set)
2479 force_reversed_ = _swig_property(_IMP_em.SpiderMapReaderWriter_force_reversed__get, _IMP_em.SpiderMapReaderWriter_force_reversed__set)
2480 skip_extra_checkings_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_extra_checkings__get, _IMP_em.SpiderMapReaderWriter_skip_extra_checkings__set)
2482 def __init__(self, *args):
2484 __init__(IMP::em::SpiderMapReaderWriter self) -> SpiderMapReaderWriter
2485 __init__(IMP::em::SpiderMapReaderWriter self, IMP::String filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings) -> SpiderMapReaderWriter
2487 this = _IMP_em.new_SpiderMapReaderWriter(*args)
2489 self.this.append(this)
2494 """__str__(SpiderMapReaderWriter self) -> std::string"""
2495 return _IMP_em.SpiderMapReaderWriter___str__(self)
2499 """__repr__(SpiderMapReaderWriter self) -> std::string"""
2500 return _IMP_em.SpiderMapReaderWriter___repr__(self)
2505 return _object_cast_to_SpiderMapReaderWriter(o)
2507 SpiderMapReaderWriter_swigregister = _IMP_em.SpiderMapReaderWriter_swigregister
2508 SpiderMapReaderWriter_swigregister(SpiderMapReaderWriter)
2510 class FittingSolutions(object):
2511 """Proxy of C++ IMP::em::FittingSolutions class"""
2512 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2515 """__init__(IMP::em::FittingSolutions self) -> FittingSolutions"""
2516 this = _IMP_em.new_FittingSolutions()
2518 self.this.append(this)
2522 def get_number_of_solutions(self):
2523 """get_number_of_solutions(FittingSolutions self) -> int"""
2524 return _IMP_em.FittingSolutions_get_number_of_solutions(self)
2527 def get_transformation(self, i):
2528 """get_transformation(FittingSolutions self, unsigned int i) -> Transformation3D"""
2529 return _IMP_em.FittingSolutions_get_transformation(self, i)
2532 def get_score(self, i):
2533 """get_score(FittingSolutions self, unsigned int i) -> IMP::Float"""
2534 return _IMP_em.FittingSolutions_get_score(self, i)
2537 def set_score(self, i, score):
2538 """set_score(FittingSolutions self, unsigned int i, IMP::Float score)"""
2539 return _IMP_em.FittingSolutions_set_score(self, i, score)
2542 def add_solution(self, t, score):
2543 """add_solution(FittingSolutions self, Transformation3D t, IMP::Float score)"""
2544 return _IMP_em.FittingSolutions_add_solution(self, t, score)
2547 def sort(self, reverse=False):
2549 sort(FittingSolutions self, bool reverse=False)
2550 sort(FittingSolutions self)
2552 return _IMP_em.FittingSolutions_sort(self, reverse)
2556 """multiply(FittingSolutions self, Transformation3D t)"""
2557 return _IMP_em.FittingSolutions_multiply(self, t)
2560 def get_transformations(self):
2561 """get_transformations(FittingSolutions self) -> IMP::algebra::Transformation3Ds"""
2562 return _IMP_em.FittingSolutions_get_transformations(self)
2565 def show(self, *args):
2567 show(FittingSolutions self, _ostream out)
2568 show(FittingSolutions self)
2570 return _IMP_em.FittingSolutions_show(self, *args)
2574 """__str__(FittingSolutions self) -> std::string"""
2575 return _IMP_em.FittingSolutions___str__(self)
2579 """__repr__(FittingSolutions self) -> std::string"""
2580 return _IMP_em.FittingSolutions___repr__(self)
2582 __swig_destroy__ = _IMP_em.delete_FittingSolutions
2583 __del__ =
lambda self:
None
2584 FittingSolutions_swigregister = _IMP_em.FittingSolutions_swigregister
2585 FittingSolutions_swigregister(FittingSolutions)
2588 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):
2590 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
2591 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
2592 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
2593 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
2594 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
2595 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
2596 local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log) -> FittingSolutions
2598 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)
2600 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):
2602 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
2603 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
2604 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
2605 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
2606 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
2607 local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2608 local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log) -> FittingSolutions
2610 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)
2612 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):
2614 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
2615 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
2616 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
2617 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
2618 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
2619 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
2621 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)
2623 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):
2625 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
2626 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
2627 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
2628 local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2) -> FittingSolutions
2629 local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap) -> FittingSolutions
2631 return _IMP_em.local_rigid_fitting_grid_search(ps, wei_key, dmap, max_voxels_translation, translation_step, max_angle_in_radians, number_of_rotations)
2635 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
2636 compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations, bool fast_version=False, bool local_score=False) -> FittingSolutions
2637 compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations, bool fast_version=False) -> FittingSolutions
2638 compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2639 compute_fitting_scores(DensityMap em_map, RigidBody rb, Refiner refiner, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2641 return _IMP_em.compute_fitting_scores(*args)
2645 compute_fitting_score(IMP::ParticlesTemp const & ps, DensityMap em_map, FloatKey wei_key) -> IMP::Float
2646 compute_fitting_score(IMP::ParticlesTemp const & ps, DensityMap em_map) -> IMP::Float
2648 return _IMP_em.compute_fitting_score(*args)
2652 get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, Transformation3D t, float thr=0.0) -> long
2653 get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, Transformation3D t) -> long
2654 get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps) -> long
2656 return _IMP_em.get_number_of_particles_outside_of_the_density(*args)
2660 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
2661 get_numbers_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, IMP::algebra::Transformation3Ds const & transformations) -> IMP::Ints
2663 return _IMP_em.get_numbers_of_particles_outside_of_the_density(dmap, ps, transformations, thr)
2667 get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3., Transformation3D t, float thr=0.0) -> double
2668 get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3., Transformation3D t) -> double
2669 get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3.) -> double
2670 get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps) -> double
2672 return _IMP_em.get_percentage_of_voxels_covered_by_particles(*args)
2674 """Proxy of C++ IMP::em::HighDensityEmbedding class"""
2675 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2677 def __init__(self, dm, threshold):
2678 """__init__(IMP::em::HighDensityEmbedding self, DensityMap dm, double threshold) -> HighDensityEmbedding"""
2679 this = _IMP_em.new_HighDensityEmbedding(dm, threshold)
2681 self.this.append(this)
2685 def get_version_info(self):
2686 """get_version_info(HighDensityEmbedding self) -> VersionInfo"""
2687 return _IMP_em.HighDensityEmbedding_get_version_info(self)
2691 """__str__(HighDensityEmbedding self) -> std::string"""
2692 return _IMP_em.HighDensityEmbedding___str__(self)
2696 """__repr__(HighDensityEmbedding self) -> std::string"""
2697 return _IMP_em.HighDensityEmbedding___repr__(self)
2702 return _object_cast_to_HighDensityEmbedding(o)
2704 HighDensityEmbedding_swigregister = _IMP_em.HighDensityEmbedding_swigregister
2705 HighDensityEmbedding_swigregister(HighDensityEmbedding)
2709 """mask_and_norm(DensityMap dmap, DensityMap mask) -> DensityMap"""
2710 return _IMP_em.mask_and_norm(dmap, mask)
2713 """get_volume_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float"""
2714 return _IMP_em.get_volume_at_threshold(m, threshold)
2718 get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold, IMP::atom::ProteinDensityReference ref) -> IMP::Float
2719 get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float
2721 return _IMP_em.get_molecular_mass_at_threshold(*args)
2724 """get_threshold_for_approximate_volume(DensityMap m, IMP::Float desired_volume) -> IMP::Float"""
2725 return _IMP_em.get_threshold_for_approximate_volume(m, desired_volume)
2729 get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass, IMP::atom::ProteinDensityReference ref) -> IMP::Float
2730 get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass) -> IMP::Float
2732 return _IMP_em.get_threshold_for_approximate_mass(*args)
2734 """Proxy of C++ IMP::em::EnvelopePenetrationRestraint class"""
2735 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2737 def __init__(self, ps, em_map, threshold):
2738 """__init__(IMP::em::EnvelopePenetrationRestraint self, IMP::Particles ps, DensityMap em_map, IMP::Float threshold) -> EnvelopePenetrationRestraint"""
2739 this = _IMP_em.new_EnvelopePenetrationRestraint(ps, em_map, threshold)
2741 self.this.append(this)
2745 def do_get_inputs(self):
2746 """do_get_inputs(EnvelopePenetrationRestraint self) -> IMP::ModelObjectsTemp"""
2747 return _IMP_em.EnvelopePenetrationRestraint_do_get_inputs(self)
2750 def get_version_info(self):
2751 """get_version_info(EnvelopePenetrationRestraint self) -> VersionInfo"""
2752 return _IMP_em.EnvelopePenetrationRestraint_get_version_info(self)
2756 """__str__(EnvelopePenetrationRestraint self) -> std::string"""
2757 return _IMP_em.EnvelopePenetrationRestraint___str__(self)
2761 """__repr__(EnvelopePenetrationRestraint self) -> std::string"""
2762 return _IMP_em.EnvelopePenetrationRestraint___repr__(self)
2767 return _object_cast_to_EnvelopePenetrationRestraint(o)
2769 EnvelopePenetrationRestraint_swigregister = _IMP_em.EnvelopePenetrationRestraint_swigregister
2770 EnvelopePenetrationRestraint_swigregister(EnvelopePenetrationRestraint)
2773 """Proxy of C++ IMP::em::PCAFitRestraint class"""
2774 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2776 def __init__(self, *args):
2778 __init__(IMP::em::PCAFitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, float threahold, float max_pca_size_diff, float max_angle_diff, float max_centroid_diff, FloatKey weight_key) -> PCAFitRestraint
2779 __init__(IMP::em::PCAFitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, float threahold, float max_pca_size_diff, float max_angle_diff, float max_centroid_diff) -> PCAFitRestraint
2781 this = _IMP_em.new_PCAFitRestraint(*args)
2783 self.this.append(this)
2787 def do_get_inputs(self):
2788 """do_get_inputs(PCAFitRestraint self) -> IMP::ModelObjectsTemp"""
2789 return _IMP_em.PCAFitRestraint_do_get_inputs(self)
2792 def get_version_info(self):
2793 """get_version_info(PCAFitRestraint self) -> VersionInfo"""
2794 return _IMP_em.PCAFitRestraint_get_version_info(self)
2798 """__str__(PCAFitRestraint self) -> std::string"""
2799 return _IMP_em.PCAFitRestraint___str__(self)
2803 """__repr__(PCAFitRestraint self) -> std::string"""
2804 return _IMP_em.PCAFitRestraint___repr__(self)
2809 return _object_cast_to_PCAFitRestraint(o)
2811 PCAFitRestraint_swigregister = _IMP_em.PCAFitRestraint_swigregister
2812 PCAFitRestraint_swigregister(PCAFitRestraint)
2815 """Proxy of C++ IMP::em::EnvelopeFitRestraint class"""
2816 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2818 def __init__(self, particles, em_map, density_threshold, penetration_threshold):
2819 """__init__(IMP::em::EnvelopeFitRestraint self, IMP::Particles particles, DensityMap em_map, double density_threshold, double penetration_threshold) -> EnvelopeFitRestraint"""
2820 this = _IMP_em.new_EnvelopeFitRestraint(particles, em_map, density_threshold, penetration_threshold)
2822 self.this.append(this)
2826 def get_transformation(self):
2827 """get_transformation(EnvelopeFitRestraint self) -> Transformation3D"""
2828 return _IMP_em.EnvelopeFitRestraint_get_transformation(self)
2831 def apply_transformation(self):
2832 """apply_transformation(EnvelopeFitRestraint self)"""
2833 return _IMP_em.EnvelopeFitRestraint_apply_transformation(self)
2836 def do_get_inputs(self):
2837 """do_get_inputs(EnvelopeFitRestraint self) -> IMP::ModelObjectsTemp"""
2838 return _IMP_em.EnvelopeFitRestraint_do_get_inputs(self)
2841 def get_version_info(self):
2842 """get_version_info(EnvelopeFitRestraint self) -> VersionInfo"""
2843 return _IMP_em.EnvelopeFitRestraint_get_version_info(self)
2847 """__str__(EnvelopeFitRestraint self) -> std::string"""
2848 return _IMP_em.EnvelopeFitRestraint___str__(self)
2852 """__repr__(EnvelopeFitRestraint self) -> std::string"""
2853 return _IMP_em.EnvelopeFitRestraint___repr__(self)
2858 return _object_cast_to_EnvelopeFitRestraint(o)
2860 EnvelopeFitRestraint_swigregister = _IMP_em.EnvelopeFitRestraint_swigregister
2861 EnvelopeFitRestraint_swigregister(EnvelopeFitRestraint)
2867 """Write out principal components to a file in Chimera Marker format"""
2868 eigen_values = pca.get_principal_values()
2869 eigen_vecs = pca.get_principal_components()
2870 centroid = pca.get_centroid()
2872 fh.write(
"<marker_set>\n")
2873 fh.write(
"<!-- PCA with eigen values: (%g,%g,%g) and "
2874 "centroid (%g,%g,%g) -->\n"
2875 % (math.sqrt(eigen_values[0]),
2876 math.sqrt(eigen_values[1]),
2877 math.sqrt(eigen_values[2]),
2878 centroid[0], centroid[1], centroid[2]))
2883 val = math.sqrt(eigen_values[i])
2884 v1 = centroid - val * eigen_vecs[i]
2885 v2 = centroid + val * eigen_vecs[i]
2886 for markerid, v
in ((i*2+1, v1), (i*2+2, v2)):
2887 fh.write(
"<marker id=\"%d\" x=\"%g\" y=\"%g\" z=\"%g\" "
2889 % (markerid, v[0], v[1], v[2], radius))
2891 for i
in range(1, 7, 2):
2892 fh.write(
"<link id1= \"%d\" id2=\"%d\" radius=\"%g\"/>\n"
2894 fh.write(
"</marker_set>\n")
2897 def get_module_version():
2898 """get_module_version() -> std::string const"""
2899 return _IMP_em.get_module_version()
2902 """get_example_path(std::string fname) -> std::string"""
2903 return _IMP_em.get_example_path(fname)
2906 """get_data_path(std::string fname) -> std::string"""
2907 return _IMP_em.get_data_path(fname)
2909 from .
import _version_check
2910 _version_check.check_version(get_module_version())
2911 __version__ = get_module_version()
Float get_threshold_for_approximate_mass(DensityMap *m, Float desired_mass, atom::ProteinDensityReference ref=atom::HARPAZ)
Computes the threshold to consider in an EM map to get a desired mass.
DensityMap * interpolate_map(DensityMap *in_map, double new_spacing)
Return a new map with an updated spacing.
Particles density2particles(DensityMap *dmap, Float threshold, Model *m, int step=1)
Convert a density grid to a set of particles.
algebra::Vector3Ds density2vectors(DensityMap *dmap, Float threshold)
Convert a density grid to a set of vectors.
algebra::BoundingBoxD< 3 > get_bounding_box(const DensityMap *m, Float threshold)
Get the bounding box for a map.
Ints get_numbers_of_particles_outside_of_the_density(DensityMap *dmap, const Particles &ps, const IMP::algebra::Transformation3Ds &transformations, float thr=0.0)
Get numbers of particles (mult transforms) that are outside the density.
Various classes to hold sets of particles.
DensityMap * binarize(DensityMap *orig_map, float threshold, bool reverse=false)
Return a map with 0 for all voxels below the threshold and 1 for those above.
double get_sum(const DensityMap *m1)
Return the sum of all voxels.
SampledDensityMap * particles2binarized_density(const ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
Make CGAL functionality available to IMP.
DensityMap * mask_and_norm(em::DensityMap *dmap, em::DensityMap *mask)
Return a masked density, and normalize the output map within the mask region.
FittingSolutions compute_fitting_scores(const ParticlesTemp &ps, DensityMap *em_map, const algebra::Transformation3Ds &transformations, bool fast_version=false, bool local_score=false, const FloatKey &wei_key=atom::Mass::get_mass_key())
Compute fitting scores for a given set of rigid transformations.
DensityMap * get_threshold_map(const DensityMap *orig_map, float threshold)
Return a map with 0 for all voxels below the threshold.
DensityMap * get_segment_by_masking(DensityMap *map_to_segment, DensityMap *mask, float mas_threshold)
Get a segment of the map covered by another map.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
SampledDensityMap * particles2density(const ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
Resample a set of particles into a density grid.
Composable functors to implement scores via compile-time composition.
Code to compute statistical measures.
algebra::GridD< 3, algebra::DenseGridStorageD< 3, float >, float > get_grid(DensityMap *in_map)
Return a dense grid containing the voxels of the passed density map.
def write_pca_cmm
Write out principal components to a file in Chimera Marker format.
double convolute(const DensityMap *m1, const DensityMap *m2)
Return a convolution between density maps m1 and m2.
Common base class for heavy weight IMP objects.
DensityMap * multiply(const DensityMap *m1, const DensityMap *m2)
Return a density map for which voxel i contains the result of m1[i]*m2[i].
DensityHeader create_density_header(const algebra::BoundingBoxD< 3 > &bb, float spacing)
Create a header from a bounding box in 3D.
Float compute_fitting_score(const ParticlesTemp &ps, DensityMap *em_map, FloatKey wei_key=atom::Mass::get_mass_key())
Compute fitting scores for a given set of rigid transformations.
FittingSolutions local_rigid_fitting_around_point(Particle *p, Refiner *refiner, const FloatKey &weight_key, DensityMap *dmap, const algebra::Vector3D &anchor_centroid, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3, bool fast=false)
Local rigid fitting of a rigid body around a center point.
long get_number_of_particles_outside_of_the_density(DensityMap *dmap, const Particles &ps, const IMP::algebra::Transformation3D &t=IMP::algebra::get_identity_transformation_3d(), float thr=0.0)
Get the number of particles that are outside of the density.
DensityMap * get_max_map(DensityMaps maps)
Return a map where each voxel is the maximum value from the input maps.
DensityMap * create_density_map(const DensityMap *other)
Create a copy of another map.
Store data to be clustered for embedding based algorithms.
Float approximate_molecular_mass(DensityMap *m, Float threshold)
Estimate the molecular mass from a map.
double get_percentage_of_voxels_covered_by_particles(DensityMap *dmap, const Particles &ps, float smoothing_radius=3., const IMP::algebra::Transformation3D &t=IMP::algebra::get_identity_transformation_3d(), float thr=0.0)
Get the number of density voxels that are not covered by particles.
Vector3D get_centroid(const Vector3Ds &ps)
Returns 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.