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IMP Reference Guide  2.15.0
The Integrative Modeling Platform
em/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.7
3 #
4 # Do not make changes to this file unless you know what you are doing--modify
5 # the SWIG interface file instead.
6 
7 # This wrapper is part of IMP,
8 # Copyright 2007-2021 IMP Inventors. All rights reserved.
9 
10 from __future__ import print_function, division, absolute_import
11 
12 
13 
14 
15 from sys import version_info
16 if version_info >= (2, 6, 0):
17  def swig_import_helper():
18  from os.path import dirname
19  import imp
20  fp = None
21  try:
22  fp, pathname, description = imp.find_module('_IMP_em', [dirname(__file__)])
23  except ImportError:
24  import _IMP_em
25  return _IMP_em
26  if fp is not None:
27  try:
28  _mod = imp.load_module('_IMP_em', fp, pathname, description)
29  finally:
30  fp.close()
31  return _mod
32  _IMP_em = swig_import_helper()
33  del swig_import_helper
34 else:
35  import _IMP_em
36 del version_info
37 try:
38  _swig_property = property
39 except NameError:
40  pass # Python < 2.2 doesn't have 'property'.
41 
42 
43 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
44  if (name == "thisown"):
45  return self.this.own(value)
46  if (name == "this"):
47  if type(value).__name__ == 'SwigPyObject':
48  self.__dict__[name] = value
49  return
50  method = class_type.__swig_setmethods__.get(name, None)
51  if method:
52  return method(self, value)
53  if (not static):
54  object.__setattr__(self, name, value)
55  else:
56  raise AttributeError("You cannot add attributes to %s" % self)
57 
58 
59 def _swig_setattr(self, class_type, name, value):
60  return _swig_setattr_nondynamic(self, class_type, name, value, 0)
61 
62 
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)
67  if method:
68  return method(self)
69  if (not static):
70  return object.__getattr__(self, name)
71  else:
72  raise AttributeError(name)
73 
74 def _swig_getattr(self, class_type, name):
75  return _swig_getattr_nondynamic(self, class_type, name, 0)
76 
77 
78 def _swig_repr(self):
79  try:
80  strthis = "proxy of " + self.this.__repr__()
81  except:
82  strthis = ""
83  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
84 
85 try:
86  _object = object
87  _newclass = 1
88 except AttributeError:
89  class _object:
90  pass
91  _newclass = 0
92 
93 
94 
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)
101  else:
102  raise AttributeError("You cannot add attributes to %s" % self)
103  return set_attr
104 
105 
106 try:
107  import weakref
108  weakref_proxy = weakref.proxy
109 except:
110  weakref_proxy = lambda x: x
111 
112 
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')
116 
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
122 
123  def value(self):
124  """value(IMP_EM_SwigPyIterator self) -> PyObject *"""
125  return _IMP_em.IMP_EM_SwigPyIterator_value(self)
126 
127 
128  def incr(self, n=1):
129  """
130  incr(IMP_EM_SwigPyIterator self, size_t n=1) -> IMP_EM_SwigPyIterator
131  incr(IMP_EM_SwigPyIterator self) -> IMP_EM_SwigPyIterator
132  """
133  return _IMP_em.IMP_EM_SwigPyIterator_incr(self, n)
134 
135 
136  def decr(self, n=1):
137  """
138  decr(IMP_EM_SwigPyIterator self, size_t n=1) -> IMP_EM_SwigPyIterator
139  decr(IMP_EM_SwigPyIterator self) -> IMP_EM_SwigPyIterator
140  """
141  return _IMP_em.IMP_EM_SwigPyIterator_decr(self, n)
142 
143 
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)
147 
148 
149  def equal(self, x):
150  """equal(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> bool"""
151  return _IMP_em.IMP_EM_SwigPyIterator_equal(self, x)
152 
153 
154  def copy(self):
155  """copy(IMP_EM_SwigPyIterator self) -> IMP_EM_SwigPyIterator"""
156  return _IMP_em.IMP_EM_SwigPyIterator_copy(self)
157 
158 
159  def next(self):
160  """next(IMP_EM_SwigPyIterator self) -> PyObject *"""
161  return _IMP_em.IMP_EM_SwigPyIterator_next(self)
162 
163 
164  def __next__(self):
165  """__next__(IMP_EM_SwigPyIterator self) -> PyObject *"""
166  return _IMP_em.IMP_EM_SwigPyIterator___next__(self)
167 
168 
169  def previous(self):
170  """previous(IMP_EM_SwigPyIterator self) -> PyObject *"""
171  return _IMP_em.IMP_EM_SwigPyIterator_previous(self)
172 
173 
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)
177 
178 
179  def __eq__(self, x):
180  """__eq__(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> bool"""
181  return _IMP_em.IMP_EM_SwigPyIterator___eq__(self, x)
182 
183 
184  def __ne__(self, x):
185  """__ne__(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> bool"""
186  return _IMP_em.IMP_EM_SwigPyIterator___ne__(self, x)
187 
188 
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)
192 
193 
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)
197 
198 
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)
202 
203 
204  def __sub__(self, *args):
205  """
206  __sub__(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator
207  __sub__(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> ptrdiff_t
208  """
209  return _IMP_em.IMP_EM_SwigPyIterator___sub__(self, *args)
210 
211  def __iter__(self):
212  return self
213 IMP_EM_SwigPyIterator_swigregister = _IMP_em.IMP_EM_SwigPyIterator_swigregister
214 IMP_EM_SwigPyIterator_swigregister(IMP_EM_SwigPyIterator)
215 
216 
217 _value_types=[]
218 _object_types=[]
219 _raii_types=[]
220 _plural_types=[]
221 
222 
223 _IMP_em.IMP_DEBUG_swigconstant(_IMP_em)
224 IMP_DEBUG = _IMP_em.IMP_DEBUG
225 
226 _IMP_em.IMP_RELEASE_swigconstant(_IMP_em)
227 IMP_RELEASE = _IMP_em.IMP_RELEASE
228 
229 _IMP_em.IMP_SILENT_swigconstant(_IMP_em)
230 IMP_SILENT = _IMP_em.IMP_SILENT
231 
232 _IMP_em.IMP_PROGRESS_swigconstant(_IMP_em)
233 IMP_PROGRESS = _IMP_em.IMP_PROGRESS
234 
235 _IMP_em.IMP_TERSE_swigconstant(_IMP_em)
236 IMP_TERSE = _IMP_em.IMP_TERSE
237 
238 _IMP_em.IMP_VERBOSE_swigconstant(_IMP_em)
239 IMP_VERBOSE = _IMP_em.IMP_VERBOSE
240 
241 _IMP_em.IMP_MEMORY_swigconstant(_IMP_em)
242 IMP_MEMORY = _IMP_em.IMP_MEMORY
243 
244 _IMP_em.IMP_NONE_swigconstant(_IMP_em)
245 IMP_NONE = _IMP_em.IMP_NONE
246 
247 _IMP_em.IMP_USAGE_swigconstant(_IMP_em)
248 IMP_USAGE = _IMP_em.IMP_USAGE
249 
250 _IMP_em.IMP_INTERNAL_swigconstant(_IMP_em)
251 IMP_INTERNAL = _IMP_em.IMP_INTERNAL
252 
253 _IMP_em.IMP_KERNEL_HAS_LOG4CXX_swigconstant(_IMP_em)
254 IMP_KERNEL_HAS_LOG4CXX = _IMP_em.IMP_KERNEL_HAS_LOG4CXX
255 
256 _IMP_em.IMP_COMPILER_HAS_AUTO_swigconstant(_IMP_em)
257 IMP_COMPILER_HAS_AUTO = _IMP_em.IMP_COMPILER_HAS_AUTO
258 
259 _IMP_em.IMP_COMPILER_HAS_DEBUG_VECTOR_swigconstant(_IMP_em)
260 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_em.IMP_COMPILER_HAS_DEBUG_VECTOR
261 
262 _IMP_em.IMP_COMPILER_HAS_UNIQUE_PTR_swigconstant(_IMP_em)
263 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_em.IMP_COMPILER_HAS_UNIQUE_PTR
264 
265 _IMP_em.IMP_KERNEL_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
266 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_em.IMP_KERNEL_HAS_BOOST_RANDOM
267 
268 _IMP_em.IMP_KERNEL_HAS_NUMPY_swigconstant(_IMP_em)
269 IMP_KERNEL_HAS_NUMPY = _IMP_em.IMP_KERNEL_HAS_NUMPY
270 
271 _IMP_em.IMP_KERNEL_HAS_GPERFTOOLS_swigconstant(_IMP_em)
272 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_em.IMP_KERNEL_HAS_GPERFTOOLS
273 
274 _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER_swigconstant(_IMP_em)
275 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
276 
277 _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER_swigconstant(_IMP_em)
278 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
279 
280 _IMP_em.IMPKERNEL_SHOW_WARNINGS_swigconstant(_IMP_em)
281 IMPKERNEL_SHOW_WARNINGS = _IMP_em.IMPKERNEL_SHOW_WARNINGS
282 
283 import sys
284 class _DirectorObjects(object):
285  """@internal Simple class to keep references to director objects
286  to prevent premature deletion."""
287  def __init__(self):
288  self._objects = []
289  def register(self, obj):
290  """Take a reference to a director object; will only work for
291  refcounted C++ classes"""
292  if hasattr(obj, 'get_ref_count'):
293  self._objects.append(obj)
294  def cleanup(self):
295  """Only drop our reference and allow cleanup by Python if no other
296  Python references exist (we hold 3 references: one in self._objects,
297  one in x, and one in the argument list for getrefcount) *and* no
298  other C++ references exist (the Python object always holds one)"""
299  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
300  or x.get_ref_count() > 1]
301 # Do in two steps so the references are kept until the end of the
302 # function (deleting references may trigger a fresh call to this method)
303  self._objects = objs
304  def get_object_count(self):
305  """Get number of director objects (useful for testing only)"""
306  return len(self._objects)
307 _director_objects = _DirectorObjects()
308 
309 class _ostream(object):
310  """Proxy of C++ std::ostream class"""
311  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
312 
313  def __init__(self, *args, **kwargs):
314  raise AttributeError("No constructor defined")
315  __repr__ = _swig_repr
316 
317  def write(self, osa_buf):
318  """write(_ostream self, char const * osa_buf)"""
319  return _IMP_em._ostream_write(self, osa_buf)
320 
321 _ostream_swigregister = _IMP_em._ostream_swigregister
322 _ostream_swigregister(_ostream)
323 
324 
325 _IMP_em.IMP_COMPILER_HAS_OVERRIDE_swigconstant(_IMP_em)
326 IMP_COMPILER_HAS_OVERRIDE = _IMP_em.IMP_COMPILER_HAS_OVERRIDE
327 
328 _IMP_em.IMP_COMPILER_HAS_FINAL_swigconstant(_IMP_em)
329 IMP_COMPILER_HAS_FINAL = _IMP_em.IMP_COMPILER_HAS_FINAL
330 
331 _IMP_em.IMP_HAS_NOEXCEPT_swigconstant(_IMP_em)
332 IMP_HAS_NOEXCEPT = _IMP_em.IMP_HAS_NOEXCEPT
333 
334 _IMP_em.IMP_C_OPEN_BINARY_swigconstant(_IMP_em)
335 IMP_C_OPEN_BINARY = _IMP_em.IMP_C_OPEN_BINARY
336 import IMP
337 
338 _IMP_em.IMP_CGAL_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
339 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CGAL_HAS_BOOST_FILESYSTEM
340 
341 _IMP_em.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
342 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
343 
344 _IMP_em.IMP_CGAL_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
345 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_em.IMP_CGAL_HAS_BOOST_RANDOM
346 
347 _IMP_em.IMP_CGAL_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
348 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_em.IMP_CGAL_HAS_BOOST_SYSTEM
349 
350 _IMP_em.IMP_CGAL_HAS_NUMPY_swigconstant(_IMP_em)
351 IMP_CGAL_HAS_NUMPY = _IMP_em.IMP_CGAL_HAS_NUMPY
352 
353 _IMP_em.IMPCGAL_SHOW_WARNINGS_swigconstant(_IMP_em)
354 IMPCGAL_SHOW_WARNINGS = _IMP_em.IMPCGAL_SHOW_WARNINGS
355 import IMP.cgal
356 
357 _IMP_em.IMP_ALGEBRA_HAS_IMP_CGAL_swigconstant(_IMP_em)
358 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_em.IMP_ALGEBRA_HAS_IMP_CGAL
359 
360 _IMP_em.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
361 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
362 
363 _IMP_em.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
364 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
365 
366 _IMP_em.IMP_ALGEBRA_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
367 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_RANDOM
368 
369 _IMP_em.IMP_ALGEBRA_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
370 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_SYSTEM
371 
372 _IMP_em.IMP_ALGEBRA_HAS_CGAL_swigconstant(_IMP_em)
373 IMP_ALGEBRA_HAS_CGAL = _IMP_em.IMP_ALGEBRA_HAS_CGAL
374 
375 _IMP_em.IMP_ALGEBRA_HAS_NUMPY_swigconstant(_IMP_em)
376 IMP_ALGEBRA_HAS_NUMPY = _IMP_em.IMP_ALGEBRA_HAS_NUMPY
377 
378 _IMP_em.IMP_ALGEBRA_HAS_ANN_swigconstant(_IMP_em)
379 IMP_ALGEBRA_HAS_ANN = _IMP_em.IMP_ALGEBRA_HAS_ANN
380 
381 _IMP_em.IMPALGEBRA_SHOW_WARNINGS_swigconstant(_IMP_em)
382 IMPALGEBRA_SHOW_WARNINGS = _IMP_em.IMPALGEBRA_SHOW_WARNINGS
383 import IMP.algebra
384 
385 _IMP_em.IMP_DISPLAY_HAS_IMP_CGAL_swigconstant(_IMP_em)
386 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_em.IMP_DISPLAY_HAS_IMP_CGAL
387 
388 _IMP_em.IMP_DISPLAY_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
389 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
390 
391 _IMP_em.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
392 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
393 
394 _IMP_em.IMP_DISPLAY_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
395 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_em.IMP_DISPLAY_HAS_BOOST_RANDOM
396 
397 _IMP_em.IMP_DISPLAY_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
398 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_em.IMP_DISPLAY_HAS_BOOST_SYSTEM
399 
400 _IMP_em.IMP_DISPLAY_HAS_CGAL_swigconstant(_IMP_em)
401 IMP_DISPLAY_HAS_CGAL = _IMP_em.IMP_DISPLAY_HAS_CGAL
402 
403 _IMP_em.IMP_DISPLAY_HAS_NUMPY_swigconstant(_IMP_em)
404 IMP_DISPLAY_HAS_NUMPY = _IMP_em.IMP_DISPLAY_HAS_NUMPY
405 
406 _IMP_em.IMPDISPLAY_SHOW_WARNINGS_swigconstant(_IMP_em)
407 IMPDISPLAY_SHOW_WARNINGS = _IMP_em.IMPDISPLAY_SHOW_WARNINGS
408 import IMP.display
409 
410 _IMP_em.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL_swigconstant(_IMP_em)
411 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_em.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
412 
413 _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
414 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
415 
416 _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
417 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
418 
419 _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
420 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
421 
422 _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
423 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
424 
425 _IMP_em.IMP_SCORE_FUNCTOR_HAS_CGAL_swigconstant(_IMP_em)
426 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_em.IMP_SCORE_FUNCTOR_HAS_CGAL
427 
428 _IMP_em.IMP_SCORE_FUNCTOR_HAS_HDF5_swigconstant(_IMP_em)
429 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_em.IMP_SCORE_FUNCTOR_HAS_HDF5
430 
431 _IMP_em.IMP_SCORE_FUNCTOR_HAS_NUMPY_swigconstant(_IMP_em)
432 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_em.IMP_SCORE_FUNCTOR_HAS_NUMPY
433 
434 _IMP_em.IMPSCOREFUNCTOR_SHOW_WARNINGS_swigconstant(_IMP_em)
435 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_em.IMPSCOREFUNCTOR_SHOW_WARNINGS
436 import IMP.score_functor
437 
438 _IMP_em.IMP_STATISTICS_HAS_IMP_CGAL_swigconstant(_IMP_em)
439 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_em.IMP_STATISTICS_HAS_IMP_CGAL
440 
441 _IMP_em.IMP_STATISTICS_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
442 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
443 
444 _IMP_em.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
445 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
446 
447 _IMP_em.IMP_STATISTICS_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
448 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_em.IMP_STATISTICS_HAS_BOOST_RANDOM
449 
450 _IMP_em.IMP_STATISTICS_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
451 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_SYSTEM
452 
453 _IMP_em.IMP_STATISTICS_HAS_CGAL_swigconstant(_IMP_em)
454 IMP_STATISTICS_HAS_CGAL = _IMP_em.IMP_STATISTICS_HAS_CGAL
455 
456 _IMP_em.IMP_STATISTICS_HAS_NUMPY_swigconstant(_IMP_em)
457 IMP_STATISTICS_HAS_NUMPY = _IMP_em.IMP_STATISTICS_HAS_NUMPY
458 
459 _IMP_em.IMPSTATISTICS_SHOW_WARNINGS_swigconstant(_IMP_em)
460 IMPSTATISTICS_SHOW_WARNINGS = _IMP_em.IMPSTATISTICS_SHOW_WARNINGS
461 import IMP.statistics
462 
463 _IMP_em.IMP_CORE_HAS_IMP_CGAL_swigconstant(_IMP_em)
464 IMP_CORE_HAS_IMP_CGAL = _IMP_em.IMP_CORE_HAS_IMP_CGAL
465 
466 _IMP_em.IMP_CORE_HAS_IMP_KERNEL_swigconstant(_IMP_em)
467 IMP_CORE_HAS_IMP_KERNEL = _IMP_em.IMP_CORE_HAS_IMP_KERNEL
468 
469 _IMP_em.IMP_CORE_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
470 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_FILESYSTEM
471 
472 _IMP_em.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
473 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
474 
475 _IMP_em.IMP_CORE_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
476 IMP_CORE_HAS_BOOST_RANDOM = _IMP_em.IMP_CORE_HAS_BOOST_RANDOM
477 
478 _IMP_em.IMP_CORE_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
479 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_SYSTEM
480 
481 _IMP_em.IMP_CORE_HAS_CGAL_swigconstant(_IMP_em)
482 IMP_CORE_HAS_CGAL = _IMP_em.IMP_CORE_HAS_CGAL
483 
484 _IMP_em.IMP_CORE_HAS_HDF5_swigconstant(_IMP_em)
485 IMP_CORE_HAS_HDF5 = _IMP_em.IMP_CORE_HAS_HDF5
486 
487 _IMP_em.IMP_CORE_HAS_NUMPY_swigconstant(_IMP_em)
488 IMP_CORE_HAS_NUMPY = _IMP_em.IMP_CORE_HAS_NUMPY
489 
490 _IMP_em.IMPCORE_SHOW_WARNINGS_swigconstant(_IMP_em)
491 IMPCORE_SHOW_WARNINGS = _IMP_em.IMPCORE_SHOW_WARNINGS
492 import IMP.core
493 
494 _IMP_em.IMP_CONTAINER_HAS_IMP_ALGEBRA_swigconstant(_IMP_em)
495 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_em.IMP_CONTAINER_HAS_IMP_ALGEBRA
496 
497 _IMP_em.IMP_CONTAINER_HAS_IMP_CGAL_swigconstant(_IMP_em)
498 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_em.IMP_CONTAINER_HAS_IMP_CGAL
499 
500 _IMP_em.IMP_CONTAINER_HAS_IMP_DISPLAY_swigconstant(_IMP_em)
501 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_em.IMP_CONTAINER_HAS_IMP_DISPLAY
502 
503 _IMP_em.IMP_CONTAINER_HAS_IMP_KERNEL_swigconstant(_IMP_em)
504 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_em.IMP_CONTAINER_HAS_IMP_KERNEL
505 
506 _IMP_em.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_em)
507 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
508 
509 _IMP_em.IMP_CONTAINER_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
510 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
511 
512 _IMP_em.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
513 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
514 
515 _IMP_em.IMP_CONTAINER_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
516 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_em.IMP_CONTAINER_HAS_BOOST_RANDOM
517 
518 _IMP_em.IMP_CONTAINER_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
519 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_SYSTEM
520 
521 _IMP_em.IMP_CONTAINER_HAS_CGAL_swigconstant(_IMP_em)
522 IMP_CONTAINER_HAS_CGAL = _IMP_em.IMP_CONTAINER_HAS_CGAL
523 
524 _IMP_em.IMP_CONTAINER_HAS_HDF5_swigconstant(_IMP_em)
525 IMP_CONTAINER_HAS_HDF5 = _IMP_em.IMP_CONTAINER_HAS_HDF5
526 
527 _IMP_em.IMP_CONTAINER_HAS_NUMPY_swigconstant(_IMP_em)
528 IMP_CONTAINER_HAS_NUMPY = _IMP_em.IMP_CONTAINER_HAS_NUMPY
529 
530 _IMP_em.IMP_CONTAINER_HAS_PYTHON_IHM_swigconstant(_IMP_em)
531 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_em.IMP_CONTAINER_HAS_PYTHON_IHM
532 
533 _IMP_em.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP_swigconstant(_IMP_em)
534 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_em.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
535 
536 _IMP_em.IMP_CONTAINER_HAS_ROBIN_MAP_swigconstant(_IMP_em)
537 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_em.IMP_CONTAINER_HAS_ROBIN_MAP
538 
539 _IMP_em.IMPCONTAINER_SHOW_WARNINGS_swigconstant(_IMP_em)
540 IMPCONTAINER_SHOW_WARNINGS = _IMP_em.IMPCONTAINER_SHOW_WARNINGS
541 import IMP.container
542 
543 _IMP_em.IMP_ATOM_HAS_IMP_CGAL_swigconstant(_IMP_em)
544 IMP_ATOM_HAS_IMP_CGAL = _IMP_em.IMP_ATOM_HAS_IMP_CGAL
545 
546 _IMP_em.IMP_ATOM_HAS_IMP_KERNEL_swigconstant(_IMP_em)
547 IMP_ATOM_HAS_IMP_KERNEL = _IMP_em.IMP_ATOM_HAS_IMP_KERNEL
548 
549 _IMP_em.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_em)
550 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
551 
552 _IMP_em.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
553 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
554 
555 _IMP_em.IMP_ATOM_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
556 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_em.IMP_ATOM_HAS_BOOST_RANDOM
557 
558 _IMP_em.IMP_ATOM_HAS_BOOST_REGEX_swigconstant(_IMP_em)
559 IMP_ATOM_HAS_BOOST_REGEX = _IMP_em.IMP_ATOM_HAS_BOOST_REGEX
560 
561 _IMP_em.IMP_ATOM_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
562 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_em.IMP_ATOM_HAS_BOOST_SYSTEM
563 
564 _IMP_em.IMP_ATOM_HAS_CGAL_swigconstant(_IMP_em)
565 IMP_ATOM_HAS_CGAL = _IMP_em.IMP_ATOM_HAS_CGAL
566 
567 _IMP_em.IMP_ATOM_HAS_HDF5_swigconstant(_IMP_em)
568 IMP_ATOM_HAS_HDF5 = _IMP_em.IMP_ATOM_HAS_HDF5
569 
570 _IMP_em.IMP_ATOM_HAS_NUMPY_swigconstant(_IMP_em)
571 IMP_ATOM_HAS_NUMPY = _IMP_em.IMP_ATOM_HAS_NUMPY
572 
573 _IMP_em.IMP_ATOM_HAS_PYTHON_IHM_swigconstant(_IMP_em)
574 IMP_ATOM_HAS_PYTHON_IHM = _IMP_em.IMP_ATOM_HAS_PYTHON_IHM
575 
576 _IMP_em.IMPATOM_SHOW_WARNINGS_swigconstant(_IMP_em)
577 IMPATOM_SHOW_WARNINGS = _IMP_em.IMPATOM_SHOW_WARNINGS
578 
579 _IMP_em.IMP_ATOM_TYPE_INDEX_swigconstant(_IMP_em)
580 IMP_ATOM_TYPE_INDEX = _IMP_em.IMP_ATOM_TYPE_INDEX
581 
582 _IMP_em.IMP_RESIDUE_TYPE_INDEX_swigconstant(_IMP_em)
583 IMP_RESIDUE_TYPE_INDEX = _IMP_em.IMP_RESIDUE_TYPE_INDEX
584 
585 _IMP_em.IMP_HIERARCHY_TYPE_INDEX_swigconstant(_IMP_em)
586 IMP_HIERARCHY_TYPE_INDEX = _IMP_em.IMP_HIERARCHY_TYPE_INDEX
587 
588 _IMP_em.IMP_CHAIN_TYPE_INDEX_swigconstant(_IMP_em)
589 IMP_CHAIN_TYPE_INDEX = _IMP_em.IMP_CHAIN_TYPE_INDEX
590 import IMP.atom
591 
592 _IMP_em.IMP_EM_HAS_IMP_CGAL_swigconstant(_IMP_em)
593 IMP_EM_HAS_IMP_CGAL = _IMP_em.IMP_EM_HAS_IMP_CGAL
594 
595 _IMP_em.IMP_EM_HAS_IMP_CONTAINER_swigconstant(_IMP_em)
596 IMP_EM_HAS_IMP_CONTAINER = _IMP_em.IMP_EM_HAS_IMP_CONTAINER
597 
598 _IMP_em.IMP_EM_HAS_IMP_DISPLAY_swigconstant(_IMP_em)
599 IMP_EM_HAS_IMP_DISPLAY = _IMP_em.IMP_EM_HAS_IMP_DISPLAY
600 
601 _IMP_em.IMP_EM_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_em)
602 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_EM_HAS_IMP_SCORE_FUNCTOR
603 
604 _IMP_em.IMP_EM_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
605 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_EM_HAS_BOOST_FILESYSTEM
606 
607 _IMP_em.IMP_EM_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
608 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
609 
610 _IMP_em.IMP_EM_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
611 IMP_EM_HAS_BOOST_RANDOM = _IMP_em.IMP_EM_HAS_BOOST_RANDOM
612 
613 _IMP_em.IMP_EM_HAS_BOOST_REGEX_swigconstant(_IMP_em)
614 IMP_EM_HAS_BOOST_REGEX = _IMP_em.IMP_EM_HAS_BOOST_REGEX
615 
616 _IMP_em.IMP_EM_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
617 IMP_EM_HAS_BOOST_SYSTEM = _IMP_em.IMP_EM_HAS_BOOST_SYSTEM
618 
619 _IMP_em.IMP_EM_HAS_CGAL_swigconstant(_IMP_em)
620 IMP_EM_HAS_CGAL = _IMP_em.IMP_EM_HAS_CGAL
621 
622 _IMP_em.IMP_EM_HAS_HDF5_swigconstant(_IMP_em)
623 IMP_EM_HAS_HDF5 = _IMP_em.IMP_EM_HAS_HDF5
624 
625 _IMP_em.IMP_EM_HAS_NUMPY_swigconstant(_IMP_em)
626 IMP_EM_HAS_NUMPY = _IMP_em.IMP_EM_HAS_NUMPY
627 
628 _IMP_em.IMP_EM_HAS_PYTHON_IHM_swigconstant(_IMP_em)
629 IMP_EM_HAS_PYTHON_IHM = _IMP_em.IMP_EM_HAS_PYTHON_IHM
630 
631 _IMP_em.IMPEM_SHOW_WARNINGS_swigconstant(_IMP_em)
632 IMPEM_SHOW_WARNINGS = _IMP_em.IMPEM_SHOW_WARNINGS
633 
634 _object_types.append("DensityMap")
635 
636 
637 def _object_cast_to_DensityMap(o):
638  """_object_cast_to_DensityMap(Object o) -> DensityMap"""
639  return _IMP_em._object_cast_to_DensityMap(o)
640 
641 _object_types.append("SampledDensityMap")
642 
643 
644 def _object_cast_to_SampledDensityMap(o):
645  """_object_cast_to_SampledDensityMap(Object o) -> SampledDensityMap"""
646  return _IMP_em._object_cast_to_SampledDensityMap(o)
647 
648 _object_types.append("SurfaceShellDensityMap")
649 
650 
651 def _object_cast_to_SurfaceShellDensityMap(o):
652  """_object_cast_to_SurfaceShellDensityMap(Object o) -> SurfaceShellDensityMap"""
653  return _IMP_em._object_cast_to_SurfaceShellDensityMap(o)
654 
655 _object_types.append("FitRestraint")
656 
657 
658 def _object_cast_to_FitRestraint(o):
659  """_object_cast_to_FitRestraint(Object o) -> FitRestraint"""
660  return _IMP_em._object_cast_to_FitRestraint(o)
661 
662 _object_types.append("FitRestraintBayesEM3D")
663 
664 
665 def _object_cast_to_FitRestraintBayesEM3D(o):
666  """_object_cast_to_FitRestraintBayesEM3D(Object o) -> FitRestraintBayesEM3D"""
667  return _IMP_em._object_cast_to_FitRestraintBayesEM3D(o)
668 
669 _object_types.append("PCAFitRestraint")
670 
671 
672 def _object_cast_to_PCAFitRestraint(o):
673  """_object_cast_to_PCAFitRestraint(Object o) -> PCAFitRestraint"""
674  return _IMP_em._object_cast_to_PCAFitRestraint(o)
675 
676 _object_types.append("EnvelopePenetrationRestraint")
677 
678 
679 def _object_cast_to_EnvelopePenetrationRestraint(o):
680  """_object_cast_to_EnvelopePenetrationRestraint(Object o) -> EnvelopePenetrationRestraint"""
681  return _IMP_em._object_cast_to_EnvelopePenetrationRestraint(o)
682 
683 _object_types.append("EnvelopeFitRestraint")
684 
685 
686 def _object_cast_to_EnvelopeFitRestraint(o):
687  """_object_cast_to_EnvelopeFitRestraint(Object o) -> EnvelopeFitRestraint"""
688  return _IMP_em._object_cast_to_EnvelopeFitRestraint(o)
689 
690 KernelParametersList=list
691 _plural_types.append("KernelParametersList")
692 _value_types.append("KernelParameters")
693 
694 
695 _object_types.append("HighDensityEmbedding")
696 
697 
698 def _object_cast_to_HighDensityEmbedding(o):
699  """_object_cast_to_HighDensityEmbedding(Object o) -> HighDensityEmbedding"""
700  return _IMP_em._object_cast_to_HighDensityEmbedding(o)
701 
702 _object_types.append("MapReaderWriter")
703 
704 
705 def _object_cast_to_MapReaderWriter(o):
706  """_object_cast_to_MapReaderWriter(Object o) -> MapReaderWriter"""
707  return _IMP_em._object_cast_to_MapReaderWriter(o)
708 
709 _object_types.append("MRCReaderWriter")
710 
711 
712 def _object_cast_to_MRCReaderWriter(o):
713  """_object_cast_to_MRCReaderWriter(Object o) -> MRCReaderWriter"""
714  return _IMP_em._object_cast_to_MRCReaderWriter(o)
715 
716 _object_types.append("SpiderMapReaderWriter")
717 
718 
719 def _object_cast_to_SpiderMapReaderWriter(o):
720  """_object_cast_to_SpiderMapReaderWriter(Object o) -> SpiderMapReaderWriter"""
721  return _IMP_em._object_cast_to_SpiderMapReaderWriter(o)
722 
723 _object_types.append("EMReaderWriter")
724 
725 
726 def _object_cast_to_EMReaderWriter(o):
727  """_object_cast_to_EMReaderWriter(Object o) -> EMReaderWriter"""
728  return _IMP_em._object_cast_to_EMReaderWriter(o)
729 
730 _object_types.append("XplorReaderWriter")
731 
732 
733 def _object_cast_to_XplorReaderWriter(o):
734  """_object_cast_to_XplorReaderWriter(Object o) -> XplorReaderWriter"""
735  return _IMP_em._object_cast_to_XplorReaderWriter(o)
736 
737 _object_types.append("CoarseCC")
738 
739 
740 def _object_cast_to_CoarseCC(o):
741  """_object_cast_to_CoarseCC(Object o) -> CoarseCC"""
742  return _IMP_em._object_cast_to_CoarseCC(o)
743 
744 _object_types.append("CoarseCCatIntervals")
745 
746 
747 def _object_cast_to_CoarseCCatIntervals(o):
748  """_object_cast_to_CoarseCCatIntervals(Object o) -> CoarseCCatIntervals"""
749  return _IMP_em._object_cast_to_CoarseCCatIntervals(o)
750 
751 FittingSolutionsList=list
752 _plural_types.append("FittingSolutionsList")
753 _value_types.append("FittingSolutions")
754 
755 
756 _object_types.append("MapDistanceTransform")
757 
758 
759 def _object_cast_to_MapDistanceTransform(o):
760  """_object_cast_to_MapDistanceTransform(Object o) -> MapDistanceTransform"""
761  return _IMP_em._object_cast_to_MapDistanceTransform(o)
762 
763 _object_types.append("EnvelopeScore")
764 
765 
766 def _object_cast_to_EnvelopeScore(o):
767  """_object_cast_to_EnvelopeScore(Object o) -> EnvelopeScore"""
768  return _IMP_em._object_cast_to_EnvelopeScore(o)
769 class MapReaderWriter(IMP.Object):
770  """Proxy of C++ IMP::em::MapReaderWriter class"""
771  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
772 
773  def __init__(self):
774  """__init__(IMP::em::MapReaderWriter self) -> MapReaderWriter"""
775  this = _IMP_em.new_MapReaderWriter()
776  try:
777  self.this.append(this)
778  except:
779  self.this = this
780 
781  def get_version_info(self):
782  """get_version_info(MapReaderWriter self) -> VersionInfo"""
783  return _IMP_em.MapReaderWriter_get_version_info(self)
784 
785 
786  def __str__(self):
787  """__str__(MapReaderWriter self) -> std::string"""
788  return _IMP_em.MapReaderWriter___str__(self)
789 
790 
791  def __repr__(self):
792  """__repr__(MapReaderWriter self) -> std::string"""
793  return _IMP_em.MapReaderWriter___repr__(self)
794 
795 
796  @staticmethod
797  def get_from(o):
798  return _object_cast_to_MapReaderWriter(o)
799 
800 MapReaderWriter_swigregister = _IMP_em.MapReaderWriter_swigregister
801 MapReaderWriter_swigregister(MapReaderWriter)
802 cvar = _IMP_em.cvar
803 EPS = cvar.EPS
804 
805 class DensityHeader(object):
806  """Proxy of C++ IMP::em::DensityHeader class"""
807  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
808  __repr__ = _swig_repr
809 
810  def __init__(self):
811  """__init__(IMP::em::DensityHeader self) -> DensityHeader"""
812  this = _IMP_em.new_DensityHeader()
813  try:
814  self.this.append(this)
815  except:
816  self.this = this
817 
818  def get_top(self, ind):
819  """get_top(DensityHeader self, int ind) -> IMP::em::emreal"""
820  return _IMP_em.DensityHeader_get_top(self, ind)
821 
822 
823  def compute_xyz_top(self, force=False):
824  """
825  compute_xyz_top(DensityHeader self, bool force=False)
826  compute_xyz_top(DensityHeader self)
827  """
828  return _IMP_em.DensityHeader_compute_xyz_top(self, force)
829 
830 
831  def update_map_dimensions(self, nnx, nny, nnz):
832  """update_map_dimensions(DensityHeader self, int nnx, int nny, int nnz)"""
833  return _IMP_em.DensityHeader_update_map_dimensions(self, nnx, nny, nnz)
834 
835 
836  def update_cell_dimensions(self):
837  """update_cell_dimensions(DensityHeader self)"""
838  return _IMP_em.DensityHeader_update_cell_dimensions(self)
839 
840 
841  def show(self, *args):
842  """
843  show(DensityHeader self, _ostream out)
844  show(DensityHeader self)
845  """
846  return _IMP_em.DensityHeader_show(self, *args)
847 
848  MAP_FIELD_SIZE = _IMP_em.DensityHeader_MAP_FIELD_SIZE
849  USER_FIELD_SIZE = _IMP_em.DensityHeader_USER_FIELD_SIZE
850  COMMENT_FIELD_NUM_OF = _IMP_em.DensityHeader_COMMENT_FIELD_NUM_OF
851  COMMENT_FIELD_SINGLE_SIZE = _IMP_em.DensityHeader_COMMENT_FIELD_SINGLE_SIZE
852  nxstart = _swig_property(_IMP_em.DensityHeader_nxstart_get, _IMP_em.DensityHeader_nxstart_set)
853  nystart = _swig_property(_IMP_em.DensityHeader_nystart_get, _IMP_em.DensityHeader_nystart_set)
854  nzstart = _swig_property(_IMP_em.DensityHeader_nzstart_get, _IMP_em.DensityHeader_nzstart_set)
855  mx = _swig_property(_IMP_em.DensityHeader_mx_get, _IMP_em.DensityHeader_mx_set)
856  my = _swig_property(_IMP_em.DensityHeader_my_get, _IMP_em.DensityHeader_my_set)
857  mz = _swig_property(_IMP_em.DensityHeader_mz_get, _IMP_em.DensityHeader_mz_set)
858  xlen = _swig_property(_IMP_em.DensityHeader_xlen_get, _IMP_em.DensityHeader_xlen_set)
859  ylen = _swig_property(_IMP_em.DensityHeader_ylen_get, _IMP_em.DensityHeader_ylen_set)
860  zlen = _swig_property(_IMP_em.DensityHeader_zlen_get, _IMP_em.DensityHeader_zlen_set)
861  alpha = _swig_property(_IMP_em.DensityHeader_alpha_get, _IMP_em.DensityHeader_alpha_set)
862  beta = _swig_property(_IMP_em.DensityHeader_beta_get, _IMP_em.DensityHeader_beta_set)
863  gamma = _swig_property(_IMP_em.DensityHeader_gamma_get, _IMP_em.DensityHeader_gamma_set)
864  mapc = _swig_property(_IMP_em.DensityHeader_mapc_get, _IMP_em.DensityHeader_mapc_set)
865  mapr = _swig_property(_IMP_em.DensityHeader_mapr_get, _IMP_em.DensityHeader_mapr_set)
866  maps = _swig_property(_IMP_em.DensityHeader_maps_get, _IMP_em.DensityHeader_maps_set)
867  dmin = _swig_property(_IMP_em.DensityHeader_dmin_get, _IMP_em.DensityHeader_dmin_set)
868  dmax = _swig_property(_IMP_em.DensityHeader_dmax_get, _IMP_em.DensityHeader_dmax_set)
869  dmean = _swig_property(_IMP_em.DensityHeader_dmean_get, _IMP_em.DensityHeader_dmean_set)
870  ispg = _swig_property(_IMP_em.DensityHeader_ispg_get, _IMP_em.DensityHeader_ispg_set)
871  nsymbt = _swig_property(_IMP_em.DensityHeader_nsymbt_get, _IMP_em.DensityHeader_nsymbt_set)
872  user = _swig_property(_IMP_em.DensityHeader_user_get, _IMP_em.DensityHeader_user_set)
873  map = _swig_property(_IMP_em.DensityHeader_map_get, _IMP_em.DensityHeader_map_set)
874  machinestamp = _swig_property(_IMP_em.DensityHeader_machinestamp_get, _IMP_em.DensityHeader_machinestamp_set)
875  rms = _swig_property(_IMP_em.DensityHeader_rms_get, _IMP_em.DensityHeader_rms_set)
876  nlabl = _swig_property(_IMP_em.DensityHeader_nlabl_get, _IMP_em.DensityHeader_nlabl_set)
877  comments = _swig_property(_IMP_em.DensityHeader_comments_get, _IMP_em.DensityHeader_comments_set)
878  magic = _swig_property(_IMP_em.DensityHeader_magic_get, _IMP_em.DensityHeader_magic_set)
879  voltage = _swig_property(_IMP_em.DensityHeader_voltage_get, _IMP_em.DensityHeader_voltage_set)
880  Cs = _swig_property(_IMP_em.DensityHeader_Cs_get, _IMP_em.DensityHeader_Cs_set)
881  Aperture = _swig_property(_IMP_em.DensityHeader_Aperture_get, _IMP_em.DensityHeader_Aperture_set)
882  Magnification = _swig_property(_IMP_em.DensityHeader_Magnification_get, _IMP_em.DensityHeader_Magnification_set)
883  Postmagnification = _swig_property(_IMP_em.DensityHeader_Postmagnification_get, _IMP_em.DensityHeader_Postmagnification_set)
884  Exposuretime = _swig_property(_IMP_em.DensityHeader_Exposuretime_get, _IMP_em.DensityHeader_Exposuretime_set)
885  Microscope = _swig_property(_IMP_em.DensityHeader_Microscope_get, _IMP_em.DensityHeader_Microscope_set)
886  Pixelsize = _swig_property(_IMP_em.DensityHeader_Pixelsize_get, _IMP_em.DensityHeader_Pixelsize_set)
887  CCDArea = _swig_property(_IMP_em.DensityHeader_CCDArea_get, _IMP_em.DensityHeader_CCDArea_set)
888  Defocus = _swig_property(_IMP_em.DensityHeader_Defocus_get, _IMP_em.DensityHeader_Defocus_set)
889  Astigmatism = _swig_property(_IMP_em.DensityHeader_Astigmatism_get, _IMP_em.DensityHeader_Astigmatism_set)
890  AstigmatismAngle = _swig_property(_IMP_em.DensityHeader_AstigmatismAngle_get, _IMP_em.DensityHeader_AstigmatismAngle_set)
891  FocusIncrement = _swig_property(_IMP_em.DensityHeader_FocusIncrement_get, _IMP_em.DensityHeader_FocusIncrement_set)
892  CountsPerElectron = _swig_property(_IMP_em.DensityHeader_CountsPerElectron_get, _IMP_em.DensityHeader_CountsPerElectron_set)
893  Intensity = _swig_property(_IMP_em.DensityHeader_Intensity_get, _IMP_em.DensityHeader_Intensity_set)
894  EnergySlitwidth = _swig_property(_IMP_em.DensityHeader_EnergySlitwidth_get, _IMP_em.DensityHeader_EnergySlitwidth_set)
895  EnergyOffset = _swig_property(_IMP_em.DensityHeader_EnergyOffset_get, _IMP_em.DensityHeader_EnergyOffset_set)
896  Tiltangle = _swig_property(_IMP_em.DensityHeader_Tiltangle_get, _IMP_em.DensityHeader_Tiltangle_set)
897  Tiltaxis = _swig_property(_IMP_em.DensityHeader_Tiltaxis_get, _IMP_em.DensityHeader_Tiltaxis_set)
898  MarkerX = _swig_property(_IMP_em.DensityHeader_MarkerX_get, _IMP_em.DensityHeader_MarkerX_set)
899  MarkerY = _swig_property(_IMP_em.DensityHeader_MarkerY_get, _IMP_em.DensityHeader_MarkerY_set)
900  lswap = _swig_property(_IMP_em.DensityHeader_lswap_get, _IMP_em.DensityHeader_lswap_set)
901 
902  def get_resolution(self):
903  """get_resolution(DensityHeader self) -> float"""
904  return _IMP_em.DensityHeader_get_resolution(self)
905 
906 
907  def get_has_resolution(self):
908  """get_has_resolution(DensityHeader self) -> bool"""
909  return _IMP_em.DensityHeader_get_has_resolution(self)
910 
911 
912  def set_resolution(self, resolution):
913  """set_resolution(DensityHeader self, float resolution)"""
914  return _IMP_em.DensityHeader_set_resolution(self, resolution)
915 
916 
917  def get_spacing(self):
918  """get_spacing(DensityHeader self) -> float"""
919  return _IMP_em.DensityHeader_get_spacing(self)
920 
921 
922  def get_xorigin(self):
923  """get_xorigin(DensityHeader self) -> float"""
924  return _IMP_em.DensityHeader_get_xorigin(self)
925 
926 
927  def get_yorigin(self):
928  """get_yorigin(DensityHeader self) -> float"""
929  return _IMP_em.DensityHeader_get_yorigin(self)
930 
931 
932  def get_zorigin(self):
933  """get_zorigin(DensityHeader self) -> float"""
934  return _IMP_em.DensityHeader_get_zorigin(self)
935 
936 
937  def get_origin(self, i):
938  """get_origin(DensityHeader self, int i) -> float"""
939  return _IMP_em.DensityHeader_get_origin(self, i)
940 
941 
942  def set_xorigin(self, x):
943  """set_xorigin(DensityHeader self, float x)"""
944  return _IMP_em.DensityHeader_set_xorigin(self, x)
945 
946 
947  def set_yorigin(self, y):
948  """set_yorigin(DensityHeader self, float y)"""
949  return _IMP_em.DensityHeader_set_yorigin(self, y)
950 
951 
952  def set_zorigin(self, z):
953  """set_zorigin(DensityHeader self, float z)"""
954  return _IMP_em.DensityHeader_set_zorigin(self, z)
955 
956 
957  def is_top_calculated(self):
958  """is_top_calculated(DensityHeader self) -> bool"""
959  return _IMP_em.DensityHeader_is_top_calculated(self)
960 
961  Objectpixelsize_ = _swig_property(_IMP_em.DensityHeader_Objectpixelsize__get, _IMP_em.DensityHeader_Objectpixelsize__set)
962 
963  def get_nx(self):
964  """get_nx(DensityHeader self) -> int"""
965  return _IMP_em.DensityHeader_get_nx(self)
966 
967 
968  def get_ny(self):
969  """get_ny(DensityHeader self) -> int"""
970  return _IMP_em.DensityHeader_get_ny(self)
971 
972 
973  def get_nz(self):
974  """get_nz(DensityHeader self) -> int"""
975  return _IMP_em.DensityHeader_get_nz(self)
976 
977 
978  def get_number_of_voxels(self):
979  """get_number_of_voxels(DensityHeader self) -> int"""
980  return _IMP_em.DensityHeader_get_number_of_voxels(self)
981 
982 
983  def get_data_type(self):
984  """get_data_type(DensityHeader self) -> int"""
985  return _IMP_em.DensityHeader_get_data_type(self)
986 
987 
988  def set_data_type(self, data_type):
989  """set_data_type(DensityHeader self, int data_type)"""
990  return _IMP_em.DensityHeader_set_data_type(self, data_type)
991 
992  __swig_destroy__ = _IMP_em.delete_DensityHeader
993  __del__ = lambda self: None
994 DensityHeader_swigregister = _IMP_em.DensityHeader_swigregister
995 DensityHeader_swigregister(DensityHeader)
996 
997 
998 def create_density_header(bb, spacing):
999  """create_density_header(BoundingBox3D bb, float spacing) -> DensityHeader"""
1000  return _IMP_em.create_density_header(bb, spacing)
1001 
1002 def read_map(*args):
1003  """
1004  read_map(std::string filename, MapReaderWriter reader) -> DensityMap
1005  read_map(std::string filename) -> DensityMap
1006  """
1007  return _IMP_em.read_map(*args)
1008 
1009 def write_map(*args):
1010  """
1011  write_map(DensityMap m, std::string filename, MapReaderWriter writer)
1012  write_map(DensityMap m, std::string filename)
1013  """
1014  return _IMP_em.write_map(*args)
1015 
1016 def approximate_molecular_mass(m, threshold):
1017  """approximate_molecular_mass(DensityMap m, IMP::Float threshold) -> IMP::Float"""
1018  return _IMP_em.approximate_molecular_mass(m, threshold)
1019 class DensityMap(IMP.Object):
1020  """Proxy of C++ IMP::em::DensityMap class"""
1021  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1022 
1023  def __init__(self, *args):
1024  """
1025  __init__(IMP::em::DensityMap self, std::string name) -> DensityMap
1026  __init__(IMP::em::DensityMap self) -> DensityMap
1027  __init__(IMP::em::DensityMap self, DensityHeader header, std::string name) -> DensityMap
1028  __init__(IMP::em::DensityMap self, DensityHeader header) -> DensityMap
1029  """
1030  this = _IMP_em.new_DensityMap(*args)
1031  try:
1032  self.this.append(this)
1033  except:
1034  self.this = this
1035 
1036  def reset_data(self, value=0.0):
1037  """
1038  reset_data(DensityMap self, float value=0.0)
1039  reset_data(DensityMap self)
1040  """
1041  return _IMP_em.DensityMap_reset_data(self, value)
1042 
1043 
1044  def calcRMS(self):
1045  """calcRMS(DensityMap self) -> IMP::em::emreal"""
1046  return _IMP_em.DensityMap_calcRMS(self)
1047 
1048 
1049  def std_normalize(self):
1050  """std_normalize(DensityMap self)"""
1051  return _IMP_em.DensityMap_std_normalize(self)
1052 
1053 
1054  def is_normalized(self):
1055  """is_normalized(DensityMap self) -> bool"""
1056  return _IMP_em.DensityMap_is_normalized(self)
1057 
1058 
1059  def get_location_in_dim_by_voxel(self, index, dim):
1060  """get_location_in_dim_by_voxel(DensityMap self, long index, int dim) -> float"""
1061  return _IMP_em.DensityMap_get_location_in_dim_by_voxel(self, index, dim)
1062 
1063 
1064  def xyz_ind2voxel(self, x, y, z):
1065  """xyz_ind2voxel(DensityMap self, int x, int y, int z) -> long"""
1066  return _IMP_em.DensityMap_xyz_ind2voxel(self, x, y, z)
1067 
1068 
1069  def get_voxel_by_location(self, *args):
1070  """
1071  get_voxel_by_location(DensityMap self, float x, float y, float z) -> long
1072  get_voxel_by_location(DensityMap self, Vector3D v) -> long
1073  """
1074  return _IMP_em.DensityMap_get_voxel_by_location(self, *args)
1075 
1076 
1077  def get_location_by_voxel(self, index):
1078  """get_location_by_voxel(DensityMap self, long index) -> Vector3D"""
1079  return _IMP_em.DensityMap_get_location_by_voxel(self, index)
1080 
1081 
1082  def is_xyz_ind_part_of_volume(self, ix, iy, iz):
1083  """is_xyz_ind_part_of_volume(DensityMap self, int ix, int iy, int iz) -> bool"""
1084  return _IMP_em.DensityMap_is_xyz_ind_part_of_volume(self, ix, iy, iz)
1085 
1086 
1087  def is_part_of_volume(self, *args):
1088  """
1089  is_part_of_volume(DensityMap self, float x, float y, float z) -> bool
1090  is_part_of_volume(DensityMap self, Vector3D v) -> bool
1091  """
1092  return _IMP_em.DensityMap_is_part_of_volume(self, *args)
1093 
1094 
1095  def get_value(self, *args):
1096  """
1097  get_value(DensityMap self, float x, float y, float z) -> IMP::em::emreal
1098  get_value(DensityMap self, Vector3D point) -> IMP::em::emreal
1099  get_value(DensityMap self, long index) -> IMP::em::emreal
1100  """
1101  return _IMP_em.DensityMap_get_value(self, *args)
1102 
1103 
1104  def set_value(self, *args):
1105  """
1106  set_value(DensityMap self, long index, IMP::em::emreal value)
1107  set_value(DensityMap self, float x, float y, float z, IMP::em::emreal value)
1108  """
1109  return _IMP_em.DensityMap_set_value(self, *args)
1110 
1111 
1112  def set_origin(self, *args):
1113  """
1114  set_origin(DensityMap self, float x, float y, float z)
1115  set_origin(DensityMap self, Vector3D v)
1116  """
1117  return _IMP_em.DensityMap_set_origin(self, *args)
1118 
1119 
1120  def get_origin(self):
1121  """get_origin(DensityMap self) -> Vector3D"""
1122  return _IMP_em.DensityMap_get_origin(self)
1123 
1124 
1125  def get_top(self):
1126  """get_top(DensityMap self) -> Vector3D"""
1127  return _IMP_em.DensityMap_get_top(self)
1128 
1129 
1130  def get_header(self):
1131  h = _IMP_em.DensityMap_get_header(self)
1132  h._owner = self
1133  return h
1134 
1135 
1136 
1137  def get_header_writable(self):
1138  h = _IMP_em.DensityMap_get_header_writable(self)
1139  h._owner = self
1140  return h
1141 
1142 
1143 
1144  def same_origin(self, other):
1145  """same_origin(DensityMap self, DensityMap other) -> bool"""
1146  return _IMP_em.DensityMap_same_origin(self, other)
1147 
1148 
1149  def same_dimensions(self, other):
1150  """same_dimensions(DensityMap self, DensityMap other) -> bool"""
1151  return _IMP_em.DensityMap_same_dimensions(self, other)
1152 
1153 
1154  def same_voxel_size(self, other):
1155  """same_voxel_size(DensityMap self, DensityMap other) -> bool"""
1156  return _IMP_em.DensityMap_same_voxel_size(self, other)
1157 
1158 
1159  def get_centroid(self, threshold=0.0):
1160  """
1161  get_centroid(DensityMap self, IMP::em::emreal threshold=0.0) -> Vector3D
1162  get_centroid(DensityMap self) -> Vector3D
1163  """
1164  return _IMP_em.DensityMap_get_centroid(self, threshold)
1165 
1166 
1167  def get_max_value(self):
1168  """get_max_value(DensityMap self) -> IMP::em::emreal"""
1169  return _IMP_em.DensityMap_get_max_value(self)
1170 
1171 
1172  def get_min_value(self):
1173  """get_min_value(DensityMap self) -> IMP::em::emreal"""
1174  return _IMP_em.DensityMap_get_min_value(self)
1175 
1176 
1177  def add(self, *args):
1178  """
1179  add(DensityMap self, DensityMap other)
1180  add(DensityMap self, IMP::Float d)
1181  """
1182  return _IMP_em.DensityMap_add(self, *args)
1183 
1184 
1185  def pick_max(self, other):
1186  """pick_max(DensityMap self, DensityMap other)"""
1187  return _IMP_em.DensityMap_pick_max(self, other)
1188 
1189 
1190  def get_number_of_voxels(self):
1191  """get_number_of_voxels(DensityMap self) -> long"""
1192  return _IMP_em.DensityMap_get_number_of_voxels(self)
1193 
1194 
1195  def set_void_map(self, nx, ny, nz):
1196  """set_void_map(DensityMap self, int nx, int ny, int nz)"""
1197  return _IMP_em.DensityMap_set_void_map(self, nx, ny, nz)
1198 
1199 
1200  def pad(self, nx, ny, nz, val=0.0):
1201  """
1202  pad(DensityMap self, int nx, int ny, int nz, float val=0.0)
1203  pad(DensityMap self, int nx, int ny, int nz)
1204  """
1205  return _IMP_em.DensityMap_pad(self, nx, ny, nz, val)
1206 
1207 
1208  def pad_margin(self, mrg_x, mrg_y, mrg_z, val=0.0):
1209  """
1210  pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z, float val=0.0) -> DensityMap
1211  pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z) -> DensityMap
1212  """
1213  return _IMP_em.DensityMap_pad_margin(self, mrg_x, mrg_y, mrg_z, val)
1214 
1215 
1216  def get_cropped(self, *args):
1217  """
1218  get_cropped(DensityMap self, float threshold) -> DensityMap
1219  get_cropped(DensityMap self, IMP::Particles ps, double distance, bool inverse=False, bool keep_map_dimensions=False) -> DensityMap
1220  get_cropped(DensityMap self, IMP::Particles ps, double distance, bool inverse=False) -> DensityMap
1221  get_cropped(DensityMap self, IMP::Particles ps, double distance) -> DensityMap
1222  get_cropped(DensityMap self, BoundingBox3D bb) -> DensityMap
1223  """
1224  return _IMP_em.DensityMap_get_cropped(self, *args)
1225 
1226 
1227  def get_maximum_value_in_xy_plane(self, z_ind):
1228  """get_maximum_value_in_xy_plane(DensityMap self, int z_ind) -> float"""
1229  return _IMP_em.DensityMap_get_maximum_value_in_xy_plane(self, z_ind)
1230 
1231 
1232  def get_maximum_value_in_xz_plane(self, y_ind):
1233  """get_maximum_value_in_xz_plane(DensityMap self, int y_ind) -> float"""
1234  return _IMP_em.DensityMap_get_maximum_value_in_xz_plane(self, y_ind)
1235 
1236 
1237  def get_maximum_value_in_yz_plane(self, x_ind):
1238  """get_maximum_value_in_yz_plane(DensityMap self, int x_ind) -> float"""
1239  return _IMP_em.DensityMap_get_maximum_value_in_yz_plane(self, x_ind)
1240 
1241 
1242  def multiply(self, factor):
1243  """multiply(DensityMap self, float factor)"""
1244  return _IMP_em.DensityMap_multiply(self, factor)
1245 
1246 
1247  def get_locations_string(self, t):
1248  """get_locations_string(DensityMap self, float t) -> std::string"""
1249  return _IMP_em.DensityMap_get_locations_string(self, t)
1250 
1251 
1252  def update_voxel_size(self, new_apix):
1253  """update_voxel_size(DensityMap self, float new_apix)"""
1254  return _IMP_em.DensityMap_update_voxel_size(self, new_apix)
1255 
1256 
1257  def get_spacing(self):
1258  """get_spacing(DensityMap self) -> IMP::Float"""
1259  return _IMP_em.DensityMap_get_spacing(self)
1260 
1261 
1262  def calc_all_voxel2loc(self):
1263  """calc_all_voxel2loc(DensityMap self)"""
1264  return _IMP_em.DensityMap_calc_all_voxel2loc(self)
1265 
1266 
1267  def copy_map(self, other):
1268  """copy_map(DensityMap self, DensityMap other)"""
1269  return _IMP_em.DensityMap_copy_map(self, other)
1270 
1271 
1272  def get_version_info(self):
1273  """get_version_info(DensityMap self) -> VersionInfo"""
1274  return _IMP_em.DensityMap_get_version_info(self)
1275 
1276 
1277  def lower_voxel_shift(self, loc, kdist, orig, ndim):
1278  """lower_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
1279  return _IMP_em.DensityMap_lower_voxel_shift(self, loc, kdist, orig, ndim)
1280 
1281 
1282  def upper_voxel_shift(self, loc, kdist, orig, ndim):
1283  """upper_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
1284  return _IMP_em.DensityMap_upper_voxel_shift(self, loc, kdist, orig, ndim)
1285 
1286 
1287  def get_rms_calculated(self):
1288  """get_rms_calculated(DensityMap self) -> bool"""
1289  return _IMP_em.DensityMap_get_rms_calculated(self)
1290 
1291 
1292  def get_dim_index_by_location(self, *args):
1293  """
1294  get_dim_index_by_location(DensityMap self, Vector3D v, int ind) -> int
1295  get_dim_index_by_location(DensityMap self, float loc_val, int ind) -> int
1296  """
1297  return _IMP_em.DensityMap_get_dim_index_by_location(self, *args)
1298 
1299 
1300  def __str__(self):
1301  """__str__(DensityMap self) -> std::string"""
1302  return _IMP_em.DensityMap___str__(self)
1303 
1304 
1305  def __repr__(self):
1306  """__repr__(DensityMap self) -> std::string"""
1307  return _IMP_em.DensityMap___repr__(self)
1308 
1309 
1310  @staticmethod
1311  def get_from(o):
1312  return _object_cast_to_DensityMap(o)
1313 
1314 DensityMap_swigregister = _IMP_em.DensityMap_swigregister
1315 DensityMap_swigregister(DensityMap)
1316 
1317 
1318 def get_bounding_box(*args):
1319  """
1320  get_bounding_box(DensityMap m, IMP::Float threshold) -> BoundingBox3D
1321  get_bounding_box(DensityMap m) -> BoundingBox3D
1322  """
1323  return _IMP_em.get_bounding_box(*args)
1324 
1325 def get_density(m, v):
1326  """get_density(DensityMap m, Vector3D v) -> double"""
1327  return _IMP_em.get_density(m, v)
1328 
1329 def get_transformed(*args):
1330  """
1331  get_transformed(DensityMap input, Transformation3D tr, double threshold) -> DensityMap
1332  get_transformed(DensityMap input, Transformation3D tr) -> DensityMap
1333  """
1334  return _IMP_em.get_transformed(*args)
1335 
1336 def get_resampled(input, scaling):
1337  """get_resampled(DensityMap input, double scaling) -> DensityMap"""
1338  return _IMP_em.get_resampled(input, scaling)
1339 
1340 def get_transformed_into(source, tr, into, calc_rms=True):
1341  """
1342  get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into, bool calc_rms=True)
1343  get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into)
1344  """
1345  return _IMP_em.get_transformed_into(source, tr, into, calc_rms)
1346 
1347 def get_transformed_into2(source, tr, into):
1348  """get_transformed_into2(DensityMap source, Transformation3D tr, DensityMap into)"""
1349  return _IMP_em.get_transformed_into2(source, tr, into)
1350 
1351 def get_interiors_intersect(d1, d2):
1352  """get_interiors_intersect(DensityMap d1, DensityMap d2) -> bool"""
1353  return _IMP_em.get_interiors_intersect(d1, d2)
1354 
1355 def get_segment(*args):
1356  """
1357  get_segment(DensityMap map_to_segment, int nx_start, int nx_end, int ny_start, int ny_end, int nz_start, int nz_end) -> DensityMap
1358  get_segment(DensityMap map_to_segment, IMP::algebra::Vector3Ds vecs, float dist) -> DensityMap
1359  """
1360  return _IMP_em.get_segment(*args)
1361 
1362 def get_segment_by_masking(map_to_segment, mask, mas_threshold):
1363  """get_segment_by_masking(DensityMap map_to_segment, DensityMap mask, float mas_threshold) -> DensityMap"""
1364  return _IMP_em.get_segment_by_masking(map_to_segment, mask, mas_threshold)
1365 
1366 def binarize(orig_map, threshold, reverse=False):
1367  """
1368  binarize(DensityMap orig_map, float threshold, bool reverse=False) -> DensityMap
1369  binarize(DensityMap orig_map, float threshold) -> DensityMap
1370  """
1371  return _IMP_em.binarize(orig_map, threshold, reverse)
1372 
1373 def get_threshold_map(orig_map, threshold):
1374  """get_threshold_map(DensityMap orig_map, float threshold) -> DensityMap"""
1375  return _IMP_em.get_threshold_map(orig_map, threshold)
1376 
1377 def multiply(m1, m2):
1378  """multiply(DensityMap m1, DensityMap m2) -> DensityMap"""
1379  return _IMP_em.multiply(m1, m2)
1380 
1381 def convolute(m1, m2):
1382  """convolute(DensityMap m1, DensityMap m2) -> double"""
1383  return _IMP_em.convolute(m1, m2)
1384 
1385 def get_sum(m1):
1386  """get_sum(DensityMap m1) -> double"""
1387  return _IMP_em.get_sum(m1)
1388 
1389 def get_max_map(maps):
1390  """get_max_map(IMP::em::DensityMaps maps) -> DensityMap"""
1391  return _IMP_em.get_max_map(maps)
1392 
1393 def interpolate_map(in_map, new_spacing):
1394  """interpolate_map(DensityMap in_map, double new_spacing) -> DensityMap"""
1395  return _IMP_em.interpolate_map(in_map, new_spacing)
1396 
1397 def get_grid(in_map):
1398  """get_grid(DensityMap in_map) -> IMP::algebra::GridD< 3,IMP::algebra::DenseGridStorageD< 3,float >,float,IMP::algebra::DefaultEmbeddingD< 3 > >"""
1399  return _IMP_em.get_grid(in_map)
1400 
1401 def create_density_map(*args):
1402  """
1403  create_density_map(DensityMap other) -> DensityMap
1404  create_density_map(BoundingBox3D bb, double spacing) -> DensityMap
1405  create_density_map(int nx, int ny, int nz, double spacing) -> DensityMap
1406  create_density_map(DenseFloatGrid3D grid) -> DensityMap
1407  create_density_map(DenseDoubleGrid3D grid) -> DensityMap
1408  """
1409  return _IMP_em.create_density_map(*args)
1410 
1411 def get_binarized_interior(dmap):
1412  """get_binarized_interior(DensityMap dmap) -> DensityMap"""
1413  return _IMP_em.get_binarized_interior(dmap)
1414 
1415 def add_to_map(dm, pis):
1416  """add_to_map(DensityMap dm, IMP::Particles const & pis)"""
1417  return _IMP_em.add_to_map(dm, pis)
1418 class RadiusDependentDistanceMask(object):
1419  """Proxy of C++ IMP::em::RadiusDependentDistanceMask class"""
1420  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1421  __repr__ = _swig_repr
1422 
1423  def __init__(self, sampling_radius, header):
1424  """__init__(IMP::em::RadiusDependentDistanceMask self, float sampling_radius, DensityHeader header) -> RadiusDependentDistanceMask"""
1425  this = _IMP_em.new_RadiusDependentDistanceMask(sampling_radius, header)
1426  try:
1427  self.this.append(this)
1428  except:
1429  self.this = this
1430 
1431  def get_neighbor_shift(self):
1432  """get_neighbor_shift(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1433  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_shift(self)
1434 
1435 
1436  def get_neighbor_dist(self):
1437  """get_neighbor_dist(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1438  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist(self)
1439 
1440 
1441  def get_neighbor_dist_exp(self):
1442  """get_neighbor_dist_exp(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1443  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist_exp(self)
1444 
1445 
1446  def show(self, out):
1447  """show(RadiusDependentDistanceMask self, _ostream out)"""
1448  return _IMP_em.RadiusDependentDistanceMask_show(self, out)
1449 
1450  __swig_destroy__ = _IMP_em.delete_RadiusDependentDistanceMask
1451  __del__ = lambda self: None
1452 RadiusDependentDistanceMask_swigregister = _IMP_em.RadiusDependentDistanceMask_swigregister
1453 RadiusDependentDistanceMask_swigregister(RadiusDependentDistanceMask)
1454 
1455 class DistanceMask(object):
1456  """Proxy of C++ IMP::em::DistanceMask class"""
1457  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1458  __repr__ = _swig_repr
1459 
1460  def __init__(self, *args):
1461  """
1462  __init__(IMP::em::DistanceMask self) -> DistanceMask
1463  __init__(IMP::em::DistanceMask self, DensityHeader header) -> DistanceMask
1464  """
1465  this = _IMP_em.new_DistanceMask(*args)
1466  try:
1467  self.this.append(this)
1468  except:
1469  self.this = this
1470 
1471  def show(self, out):
1472  """show(DistanceMask self, _ostream out)"""
1473  return _IMP_em.DistanceMask_show(self, out)
1474 
1475 
1476  def is_mask_set(self, radius, eps=0.001):
1477  """
1478  is_mask_set(DistanceMask self, float radius, float eps=0.001) -> bool
1479  is_mask_set(DistanceMask self, float radius) -> bool
1480  """
1481  return _IMP_em.DistanceMask_is_mask_set(self, radius, eps)
1482 
1483  __swig_destroy__ = _IMP_em.delete_DistanceMask
1484  __del__ = lambda self: None
1485 DistanceMask_swigregister = _IMP_em.DistanceMask_swigregister
1486 DistanceMask_swigregister(DistanceMask)
1487 
1488 class EMReaderWriter(MapReaderWriter):
1489  """Proxy of C++ IMP::em::EMReaderWriter class"""
1490  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1491 
1492  def __str__(self):
1493  """__str__(EMReaderWriter self) -> std::string"""
1494  return _IMP_em.EMReaderWriter___str__(self)
1495 
1496 
1497  def __repr__(self):
1498  """__repr__(EMReaderWriter self) -> std::string"""
1499  return _IMP_em.EMReaderWriter___repr__(self)
1500 
1501 
1502  @staticmethod
1503  def get_from(o):
1504  return _object_cast_to_EMReaderWriter(o)
1505 
1506 
1507  def __init__(self):
1508  """__init__(IMP::em::EMReaderWriter self) -> EMReaderWriter"""
1509  this = _IMP_em.new_EMReaderWriter()
1510  try:
1511  self.this.append(this)
1512  except:
1513  self.this = this
1514 EMReaderWriter_swigregister = _IMP_em.EMReaderWriter_swigregister
1515 EMReaderWriter_swigregister(EMReaderWriter)
1516 
1517 class XplorReaderWriter(MapReaderWriter):
1518  """Proxy of C++ IMP::em::XplorReaderWriter class"""
1519  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1520 
1521  def __str__(self):
1522  """__str__(XplorReaderWriter self) -> std::string"""
1523  return _IMP_em.XplorReaderWriter___str__(self)
1524 
1525 
1526  def __repr__(self):
1527  """__repr__(XplorReaderWriter self) -> std::string"""
1528  return _IMP_em.XplorReaderWriter___repr__(self)
1529 
1530 
1531  @staticmethod
1532  def get_from(o):
1533  return _object_cast_to_XplorReaderWriter(o)
1534 
1535 
1536  def __init__(self):
1537  """__init__(IMP::em::XplorReaderWriter self) -> XplorReaderWriter"""
1538  this = _IMP_em.new_XplorReaderWriter()
1539  try:
1540  self.this.append(this)
1541  except:
1542  self.this = this
1543 XplorReaderWriter_swigregister = _IMP_em.XplorReaderWriter_swigregister
1544 XplorReaderWriter_swigregister(XplorReaderWriter)
1545 
1546 class MRCReaderWriter(MapReaderWriter):
1547  """Proxy of C++ IMP::em::MRCReaderWriter class"""
1548  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1549 
1550  def __init__(self, *args):
1551  """
1552  __init__(IMP::em::MRCReaderWriter self) -> MRCReaderWriter
1553  __init__(IMP::em::MRCReaderWriter self, std::string fn) -> MRCReaderWriter
1554  """
1555  this = _IMP_em.new_MRCReaderWriter(*args)
1556  try:
1557  self.this.append(this)
1558  except:
1559  self.this = this
1560 
1561  def __str__(self):
1562  """__str__(MRCReaderWriter self) -> std::string"""
1563  return _IMP_em.MRCReaderWriter___str__(self)
1564 
1565 
1566  def __repr__(self):
1567  """__repr__(MRCReaderWriter self) -> std::string"""
1568  return _IMP_em.MRCReaderWriter___repr__(self)
1569 
1570 
1571  @staticmethod
1572  def get_from(o):
1573  return _object_cast_to_MRCReaderWriter(o)
1574 
1575 MRCReaderWriter_swigregister = _IMP_em.MRCReaderWriter_swigregister
1576 MRCReaderWriter_swigregister(MRCReaderWriter)
1577 
1578 class KernelParameters(object):
1579  """Proxy of C++ IMP::em::KernelParameters class"""
1580  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1581 
1582  def __init__(self, *args):
1583  """
1584  __init__(IMP::em::KernelParameters self) -> KernelParameters
1585  __init__(IMP::em::KernelParameters self, float resolution) -> KernelParameters
1586  """
1587  this = _IMP_em.new_KernelParameters(*args)
1588  try:
1589  self.this.append(this)
1590  except:
1591  self.this = this
1592  __swig_destroy__ = _IMP_em.delete_KernelParameters
1593  __del__ = lambda self: None
1594 
1595  def get_rsig(self):
1596  """get_rsig(KernelParameters self) -> float"""
1597  return _IMP_em.KernelParameters_get_rsig(self)
1598 
1599 
1600  def get_rsigsq(self):
1601  """get_rsigsq(KernelParameters self) -> float"""
1602  return _IMP_em.KernelParameters_get_rsigsq(self)
1603 
1604 
1605  def get_inv_rsigsq(self):
1606  """get_inv_rsigsq(KernelParameters self) -> float"""
1607  return _IMP_em.KernelParameters_get_inv_rsigsq(self)
1608 
1609 
1610  def get_timessig(self):
1611  """get_timessig(KernelParameters self) -> float"""
1612  return _IMP_em.KernelParameters_get_timessig(self)
1613 
1614 
1615  def get_sq2pi3(self):
1616  """get_sq2pi3(KernelParameters self) -> float"""
1617  return _IMP_em.KernelParameters_get_sq2pi3(self)
1618 
1619 
1620  def get_rnormfac(self):
1621  """get_rnormfac(KernelParameters self) -> float"""
1622  return _IMP_em.KernelParameters_get_rnormfac(self)
1623 
1624 
1625  def get_rkdist(self):
1626  """get_rkdist(KernelParameters self) -> float"""
1627  return _IMP_em.KernelParameters_get_rkdist(self)
1628 
1629 
1630  def get_rkdistsq(self):
1631  """get_rkdistsq(KernelParameters self) -> float"""
1632  return _IMP_em.KernelParameters_get_rkdistsq(self)
1633 
1634 
1635  def get_lim(self):
1636  """get_lim(KernelParameters self) -> float"""
1637  return _IMP_em.KernelParameters_get_lim(self)
1638 
1639 
1640  def show(self, *args):
1641  """
1642  show(KernelParameters self, _ostream out)
1643  show(KernelParameters self)
1644  """
1645  return _IMP_em.KernelParameters_show(self, *args)
1646 
1647 
1648  def __str__(self):
1649  """__str__(KernelParameters self) -> std::string"""
1650  return _IMP_em.KernelParameters___str__(self)
1651 
1652 
1653  def __repr__(self):
1654  """__repr__(KernelParameters self) -> std::string"""
1655  return _IMP_em.KernelParameters___repr__(self)
1656 
1657 KernelParameters_swigregister = _IMP_em.KernelParameters_swigregister
1658 KernelParameters_swigregister(KernelParameters)
1659 
1660 
1661 _IMP_em.GAUSSIAN_swigconstant(_IMP_em)
1662 GAUSSIAN = _IMP_em.GAUSSIAN
1663 
1664 _IMP_em.BINARIZED_SPHERE_swigconstant(_IMP_em)
1665 BINARIZED_SPHERE = _IMP_em.BINARIZED_SPHERE
1666 
1667 _IMP_em.SPHERE_swigconstant(_IMP_em)
1668 SPHERE = _IMP_em.SPHERE
1669 class SampledDensityMap(DensityMap):
1670  """Proxy of C++ IMP::em::SampledDensityMap class"""
1671  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1672 
1673  def __init__(self, *args):
1674  """
1675  __init__(IMP::em::SampledDensityMap self, IMP::em::KernelType kt) -> SampledDensityMap
1676  __init__(IMP::em::SampledDensityMap self) -> SampledDensityMap
1677  __init__(IMP::em::SampledDensityMap self, DensityHeader header, IMP::em::KernelType kt) -> SampledDensityMap
1678  __init__(IMP::em::SampledDensityMap self, DensityHeader header) -> SampledDensityMap
1679  __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size, FloatKey mass_key, int sig_cutoff=3, IMP::em::KernelType kt) -> SampledDensityMap
1680  __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size, FloatKey mass_key, int sig_cutoff=3) -> SampledDensityMap
1681  __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size, FloatKey mass_key) -> SampledDensityMap
1682  __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size) -> SampledDensityMap
1683  """
1684  this = _IMP_em.new_SampledDensityMap(*args)
1685  try:
1686  self.this.append(this)
1687  except:
1688  self.this = this
1689 
1690  def resample(self):
1691  """resample(SampledDensityMap self)"""
1692  return _IMP_em.SampledDensityMap_resample(self)
1693 
1694 
1695  def project(self, *args):
1696  """
1697  project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin, Vector3D shift, FloatKey mass_key)
1698  project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin, Vector3D shift)
1699  project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin)
1700  """
1701  return _IMP_em.SampledDensityMap_project(self, *args)
1702 
1703 
1704  def set_particles(self, *args):
1705  """
1706  set_particles(SampledDensityMap self, IMP::ParticlesTemp const & ps, FloatKey mass_key)
1707  set_particles(SampledDensityMap self, IMP::ParticlesTemp const & ps)
1708  """
1709  return _IMP_em.SampledDensityMap_set_particles(self, *args)
1710 
1711 
1712  def get_xyzr_particles(self):
1713  """get_xyzr_particles(SampledDensityMap self) -> IMP::core::XYZRs const &"""
1714  return _IMP_em.SampledDensityMap_get_xyzr_particles(self)
1715 
1716 
1717  def get_sampled_particles(self):
1718  """get_sampled_particles(SampledDensityMap self) -> IMP::Particles const &"""
1719  return _IMP_em.SampledDensityMap_get_sampled_particles(self)
1720 
1721 
1722  def get_weight_key(self):
1723  """get_weight_key(SampledDensityMap self) -> FloatKey"""
1724  return _IMP_em.SampledDensityMap_get_weight_key(self)
1725 
1726 
1727  def get_minimum_resampled_value(self):
1728  """get_minimum_resampled_value(SampledDensityMap self) -> float"""
1729  return _IMP_em.SampledDensityMap_get_minimum_resampled_value(self)
1730 
1731 
1732  def update_resolution(self, res):
1733  """update_resolution(SampledDensityMap self, IMP::Float res)"""
1734  return _IMP_em.SampledDensityMap_update_resolution(self, res)
1735 
1736  __swig_destroy__ = _IMP_em.delete_SampledDensityMap
1737  __del__ = lambda self: None
1738 
1739  def __str__(self):
1740  """__str__(SampledDensityMap self) -> std::string"""
1741  return _IMP_em.SampledDensityMap___str__(self)
1742 
1743 
1744  def __repr__(self):
1745  """__repr__(SampledDensityMap self) -> std::string"""
1746  return _IMP_em.SampledDensityMap___repr__(self)
1747 
1748 
1749  @staticmethod
1750  def get_from(o):
1751  return _object_cast_to_SampledDensityMap(o)
1752 
1753 SampledDensityMap_swigregister = _IMP_em.SampledDensityMap_swigregister
1754 SampledDensityMap_swigregister(SampledDensityMap)
1755 
1756 
1757 _IMP_em.IMP_DEFAULT_NUM_SHELLS_swigconstant(_IMP_em)
1758 IMP_DEFAULT_NUM_SHELLS = _IMP_em.IMP_DEFAULT_NUM_SHELLS
1759 
1760 _IMP_em.IMP_SIG_CUTOFF_swigconstant(_IMP_em)
1761 IMP_SIG_CUTOFF = _IMP_em.IMP_SIG_CUTOFF
1762 class SurfaceShellDensityMap(SampledDensityMap):
1763  """Proxy of C++ IMP::em::SurfaceShellDensityMap class"""
1764  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1765 
1766  def __init__(self, *args):
1767  """
1768  __init__(IMP::em::SurfaceShellDensityMap self) -> SurfaceShellDensityMap
1769  __init__(IMP::em::SurfaceShellDensityMap self, DensityHeader header) -> SurfaceShellDensityMap
1770  __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key, int num_shells=5) -> SurfaceShellDensityMap
1771  __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key) -> SurfaceShellDensityMap
1772  __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size) -> SurfaceShellDensityMap
1773  """
1774  this = _IMP_em.new_SurfaceShellDensityMap(*args)
1775  try:
1776  self.this.append(this)
1777  except:
1778  self.this = this
1779 
1780  def binarize(self, scene_val):
1781  """binarize(SurfaceShellDensityMap self, float scene_val)"""
1782  return _IMP_em.SurfaceShellDensityMap_binarize(self, scene_val)
1783 
1784 
1785  def has_background_neighbor(self, voxel_ind):
1786  """has_background_neighbor(SurfaceShellDensityMap self, long voxel_ind) -> bool"""
1787  return _IMP_em.SurfaceShellDensityMap_has_background_neighbor(self, voxel_ind)
1788 
1789  __swig_destroy__ = _IMP_em.delete_SurfaceShellDensityMap
1790  __del__ = lambda self: None
1791 
1792  def __str__(self):
1793  """__str__(SurfaceShellDensityMap self) -> std::string"""
1794  return _IMP_em.SurfaceShellDensityMap___str__(self)
1795 
1796 
1797  def __repr__(self):
1798  """__repr__(SurfaceShellDensityMap self) -> std::string"""
1799  return _IMP_em.SurfaceShellDensityMap___repr__(self)
1800 
1801 
1802  @staticmethod
1803  def get_from(o):
1804  return _object_cast_to_SurfaceShellDensityMap(o)
1805 
1806 SurfaceShellDensityMap_swigregister = _IMP_em.SurfaceShellDensityMap_swigregister
1807 SurfaceShellDensityMap_swigregister(SurfaceShellDensityMap)
1808 
1809 
1810 def get_coarse_cc_score(*args):
1811  """
1812  get_coarse_cc_score(DensityMap data, SampledDensityMap model_map, double scalefactor, bool recalc_rms=True, bool resample=True, IMP::FloatPair norm_factors) -> double
1813  get_coarse_cc_score(DensityMap data, SampledDensityMap model_map, double scalefactor, bool recalc_rms=True, bool resample=True) -> double
1814  get_coarse_cc_score(DensityMap data, SampledDensityMap model_map, double scalefactor, bool recalc_rms=True) -> double
1815  get_coarse_cc_score(DensityMap data, SampledDensityMap model_map, double scalefactor) -> double
1816  """
1817  return _IMP_em.get_coarse_cc_score(*args)
1818 
1819 def get_coarse_cc_coefficient(*args):
1820  """
1821  get_coarse_cc_coefficient(DensityMap grid1, DensityMap grid2, double grid2_voxel_data_threshold, bool allow_padding=False, IMP::FloatPair norm_factors) -> double
1822  get_coarse_cc_coefficient(DensityMap grid1, DensityMap grid2, double grid2_voxel_data_threshold, bool allow_padding=False) -> double
1823  get_coarse_cc_coefficient(DensityMap grid1, DensityMap grid2, double grid2_voxel_data_threshold) -> double
1824  """
1825  return _IMP_em.get_coarse_cc_coefficient(*args)
1826 
1827 def get_coarse_cc_local_coefficient(em_map, model_map, voxel_data_threshold):
1828  """get_coarse_cc_local_coefficient(DensityMap em_map, DensityMap model_map, double voxel_data_threshold) -> double"""
1829  return _IMP_em.get_coarse_cc_local_coefficient(em_map, model_map, voxel_data_threshold)
1830 class CoarseCC(IMP.Object):
1831  """Proxy of C++ IMP::em::CoarseCC class"""
1832  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1833 
1834  def __init__(self):
1835  """__init__(IMP::em::CoarseCC self) -> CoarseCC"""
1836  this = _IMP_em.new_CoarseCC()
1837  try:
1838  self.this.append(this)
1839  except:
1840  self.this = this
1841 
1842  def calc_score(*args):
1843  """
1844  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True, IMP::FloatPair norm_factors) -> float
1845  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True) -> float
1846  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1847  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1848  """
1849  return _IMP_em.CoarseCC_calc_score(*args)
1850 
1851  calc_score = staticmethod(calc_score)
1852 
1853  def cross_correlation_coefficient(*args):
1854  """
1855  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False, IMP::FloatPair norm_factors) -> double
1856  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1857  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1858  """
1859  return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1860 
1861  cross_correlation_coefficient = staticmethod(cross_correlation_coefficient)
1862 
1863  def local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold):
1864  """local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1865  return _IMP_em.CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold)
1866 
1867  local_cross_correlation_coefficient = staticmethod(local_cross_correlation_coefficient)
1868 
1869  def get_version_info(self):
1870  """get_version_info(CoarseCC self) -> VersionInfo"""
1871  return _IMP_em.CoarseCC_get_version_info(self)
1872 
1873 
1874  def __str__(self):
1875  """__str__(CoarseCC self) -> std::string"""
1876  return _IMP_em.CoarseCC___str__(self)
1877 
1878 
1879  def __repr__(self):
1880  """__repr__(CoarseCC self) -> std::string"""
1881  return _IMP_em.CoarseCC___repr__(self)
1882 
1883 
1884  @staticmethod
1885  def get_from(o):
1886  return _object_cast_to_CoarseCC(o)
1887 
1888 CoarseCC_swigregister = _IMP_em.CoarseCC_swigregister
1889 CoarseCC_swigregister(CoarseCC)
1890 
1891 def CoarseCC_calc_score(*args):
1892  """
1893  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True, IMP::FloatPair norm_factors) -> float
1894  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True) -> float
1895  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1896  CoarseCC_calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1897  """
1898  return _IMP_em.CoarseCC_calc_score(*args)
1899 
1900 def CoarseCC_cross_correlation_coefficient(*args):
1901  """
1902  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False, IMP::FloatPair norm_factors) -> double
1903  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1904  CoarseCC_cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1905  """
1906  return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1907 
1908 def CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold):
1909  """CoarseCC_local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1910  return _IMP_em.CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold)
1911 
1912 class CoarseConvolution(object):
1913  """Proxy of C++ IMP::em::CoarseConvolution class"""
1914  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1915  __repr__ = _swig_repr
1916 
1917  def convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac=True):
1918  """
1919  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1920  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1921  """
1922  return _IMP_em.CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac)
1923 
1924  convolution = staticmethod(convolution)
1925 
1926  def __init__(self):
1927  """__init__(IMP::em::CoarseConvolution self) -> CoarseConvolution"""
1928  this = _IMP_em.new_CoarseConvolution()
1929  try:
1930  self.this.append(this)
1931  except:
1932  self.this = this
1933  __swig_destroy__ = _IMP_em.delete_CoarseConvolution
1934  __del__ = lambda self: None
1935 CoarseConvolution_swigregister = _IMP_em.CoarseConvolution_swigregister
1936 CoarseConvolution_swigregister(CoarseConvolution)
1937 
1938 def CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac=True):
1939  """
1940  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1941  CoarseConvolution_convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1942  """
1943  return _IMP_em.CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac)
1944 
1945 class CoarseCCatIntervals(IMP.Object):
1946  """Proxy of C++ IMP::em::CoarseCCatIntervals class"""
1947  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1948 
1949  def __init__(self, *args):
1950  """
1951  __init__(IMP::em::CoarseCCatIntervals self, int const & ncd) -> CoarseCCatIntervals
1952  __init__(IMP::em::CoarseCCatIntervals self) -> CoarseCCatIntervals
1953  """
1954  this = _IMP_em.new_CoarseCCatIntervals(*args)
1955  try:
1956  self.this.append(this)
1957  except:
1958  self.this = this
1959 
1960  def evaluate(self, em_map, model_map, deriv, scalefac, lderiv, eval_interval):
1961  """evaluate(CoarseCCatIntervals self, DensityMap em_map, SampledDensityMap model_map, IMP::algebra::Vector3Ds const & deriv, float scalefac, bool lderiv, unsigned long eval_interval) -> std::pair< double,IMP::algebra::Vector3Ds >"""
1962  return _IMP_em.CoarseCCatIntervals_evaluate(self, em_map, model_map, deriv, scalefac, lderiv, eval_interval)
1963 
1964 
1965  def get_version_info(self):
1966  """get_version_info(CoarseCCatIntervals self) -> VersionInfo"""
1967  return _IMP_em.CoarseCCatIntervals_get_version_info(self)
1968 
1969 
1970  def __str__(self):
1971  """__str__(CoarseCCatIntervals self) -> std::string"""
1972  return _IMP_em.CoarseCCatIntervals___str__(self)
1973 
1974 
1975  def __repr__(self):
1976  """__repr__(CoarseCCatIntervals self) -> std::string"""
1977  return _IMP_em.CoarseCCatIntervals___repr__(self)
1978 
1979 
1980  @staticmethod
1981  def get_from(o):
1982  return _object_cast_to_CoarseCCatIntervals(o)
1983 
1984 CoarseCCatIntervals_swigregister = _IMP_em.CoarseCCatIntervals_swigregister
1985 CoarseCCatIntervals_swigregister(CoarseCCatIntervals)
1986 
1987 
1989  """bayesem3d_get_distinct_and_counts(DensityMap em) -> std::map< double,int >"""
1990  return _IMP_em.bayesem3d_get_distinct_and_counts(em)
1991 
1993  """bayesem3d_get_cumulative_sum(DensityMap em) -> IMP::Floats"""
1994  return _IMP_em.bayesem3d_get_cumulative_sum(em)
1995 
1997  """bayesem3d_get_cumulative_sum_with_reference(DensityMap em) -> std::map< double,double >"""
1998  return _IMP_em.bayesem3d_get_cumulative_sum_with_reference(em)
1999 
2000 def bayesem3d_linear_interpolate(x_data, y_data, x, extrapolate):
2001  """bayesem3d_linear_interpolate(IMP::Floats const & x_data, IMP::Floats const & y_data, double x, bool extrapolate) -> double"""
2002  return _IMP_em.bayesem3d_linear_interpolate(x_data, y_data, x, extrapolate)
2003 
2004 def bayesem3d_get_logabssumexp(x, y, sx, sy):
2005  """bayesem3d_get_logabssumexp(double x, double y, double sx, double sy) -> IMP::FloatPair"""
2006  return _IMP_em.bayesem3d_get_logabssumexp(x, y, sx, sy)
2007 
2008 def bayesem3d_get_logabssumprodexp(x, y, wx, wy):
2009  """bayesem3d_get_logabssumprodexp(double x, double y, double wx, double wy) -> IMP::FloatPair"""
2010  return _IMP_em.bayesem3d_get_logabssumprodexp(x, y, wx, wy)
2011 
2012 def bayesem3d_get_logsumexp(x, y):
2013  """bayesem3d_get_logsumexp(double x, double y) -> double"""
2014  return _IMP_em.bayesem3d_get_logsumexp(x, y)
2015 
2016 def bayesem3d_get_logsumprodexp(x, y, wx, wy):
2017  """bayesem3d_get_logsumprodexp(double x, double y, double wx, double wy) -> double"""
2018  return _IMP_em.bayesem3d_get_logsumprodexp(x, y, wx, wy)
2019 
2020 def bayesem3d_get_em_density_squared(em, number_of_voxels):
2021  """bayesem3d_get_em_density_squared(DensityMap em, long number_of_voxels) -> IMP::FloatPair"""
2022  return _IMP_em.bayesem3d_get_em_density_squared(em, number_of_voxels)
2023 
2024 def bayesem3d_get_value(p, pt, mass_ii, kps):
2025  """bayesem3d_get_value(Particle p, Vector3D pt, double mass_ii, KernelParameters kps) -> std::vector< double,std::allocator< double > >"""
2026  return _IMP_em.bayesem3d_get_value(p, pt, mass_ii, kps)
2027 
2028 def bayesem3d_get_value_no_deriv(p, pt, mass_ii, kps):
2029  """bayesem3d_get_value_no_deriv(Particle p, Vector3D pt, double mass_ii, KernelParameters kps) -> std::vector< double,std::allocator< double > >"""
2030  return _IMP_em.bayesem3d_get_value_no_deriv(p, pt, mass_ii, kps)
2031 
2032 def bayesem3d_get_density_from_particle(em, ps, resolution):
2033  """bayesem3d_get_density_from_particle(DensityMap em, IMP::ParticlesTemp const & ps, double resolution) -> DensityMap"""
2034  return _IMP_em.bayesem3d_get_density_from_particle(em, ps, resolution)
2035 
2037  """bayesem3d_get_cross_correlation_coefficient(DensityMap em1, DensityMap em2) -> double"""
2038  return _IMP_em.bayesem3d_get_cross_correlation_coefficient(em1, em2)
2039 
2040 def bayesem3d_get_score_and_derivative(em, ps, resolution, sigma):
2041  """bayesem3d_get_score_and_derivative(DensityMap em, IMP::ParticlesTemp const & ps, double resolution, double sigma) -> std::pair< double,IMP::algebra::Vector3Ds >"""
2042  return _IMP_em.bayesem3d_get_score_and_derivative(em, ps, resolution, sigma)
2043 
2044 def bayesem3d_get_normalized_intensities(em, ps, resolution):
2045  """bayesem3d_get_normalized_intensities(DensityMap em, IMP::ParticlesTemp const & ps, double resolution)"""
2046  return _IMP_em.bayesem3d_get_normalized_intensities(em, ps, resolution)
2047 class FitRestraint(IMP.Restraint):
2048  """Proxy of C++ IMP::em::FitRestraint class"""
2049  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2050 
2051  def __init__(self, *args):
2052  """
2053  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key, float scale=1, bool use_rigid_bodies=True, IMP::em::KernelType kt) -> FitRestraint
2054  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key, float scale=1, bool use_rigid_bodies=True) -> FitRestraint
2055  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key, float scale=1) -> FitRestraint
2056  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key) -> FitRestraint
2057  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors) -> FitRestraint
2058  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map) -> FitRestraint
2059  """
2060  this = _IMP_em.new_FitRestraint(*args)
2061  try:
2062  self.this.append(this)
2063  except:
2064  self.this = this
2065 
2066  def get_model_dens_map(self):
2067  """get_model_dens_map(FitRestraint self) -> SampledDensityMap"""
2068  return _IMP_em.FitRestraint_get_model_dens_map(self)
2069 
2070 
2071  def set_scale_factor(self, scale):
2072  """set_scale_factor(FitRestraint self, float scale)"""
2073  return _IMP_em.FitRestraint_set_scale_factor(self, scale)
2074 
2075 
2076  def get_scale_factor(self):
2077  """get_scale_factor(FitRestraint self) -> float"""
2078  return _IMP_em.FitRestraint_get_scale_factor(self)
2079 
2080 
2081  def do_get_inputs(self):
2082  """do_get_inputs(FitRestraint self) -> IMP::ModelObjectsTemp"""
2083  return _IMP_em.FitRestraint_do_get_inputs(self)
2084 
2085 
2086  def get_version_info(self):
2087  """get_version_info(FitRestraint self) -> VersionInfo"""
2088  return _IMP_em.FitRestraint_get_version_info(self)
2089 
2090 
2091  def __str__(self):
2092  """__str__(FitRestraint self) -> std::string"""
2093  return _IMP_em.FitRestraint___str__(self)
2094 
2095 
2096  def __repr__(self):
2097  """__repr__(FitRestraint self) -> std::string"""
2098  return _IMP_em.FitRestraint___repr__(self)
2099 
2100 
2101  @staticmethod
2102  def get_from(o):
2103  return _object_cast_to_FitRestraint(o)
2104 
2105 FitRestraint_swigregister = _IMP_em.FitRestraint_swigregister
2106 FitRestraint_swigregister(FitRestraint)
2107 
2108 class FitRestraintBayesEM3D(IMP.Restraint):
2109  """Proxy of C++ IMP::em::FitRestraintBayesEM3D class"""
2110  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2111 
2112  def __init__(self, *args):
2113  """
2114  __init__(IMP::em::FitRestraintBayesEM3D self, IMP::ParticlesTemp ps, DensityMap em_map, FloatKey weight_key, bool use_rigid_bodies=True, double sigma=.1) -> FitRestraintBayesEM3D
2115  __init__(IMP::em::FitRestraintBayesEM3D self, IMP::ParticlesTemp ps, DensityMap em_map, FloatKey weight_key, bool use_rigid_bodies=True) -> FitRestraintBayesEM3D
2116  __init__(IMP::em::FitRestraintBayesEM3D self, IMP::ParticlesTemp ps, DensityMap em_map, FloatKey weight_key) -> FitRestraintBayesEM3D
2117  __init__(IMP::em::FitRestraintBayesEM3D self, IMP::ParticlesTemp ps, DensityMap em_map) -> FitRestraintBayesEM3D
2118  """
2119  this = _IMP_em.new_FitRestraintBayesEM3D(*args)
2120  try:
2121  self.this.append(this)
2122  except:
2123  self.this = this
2124 
2125  def do_get_inputs(self):
2126  """do_get_inputs(FitRestraintBayesEM3D self) -> IMP::ModelObjectsTemp"""
2127  return _IMP_em.FitRestraintBayesEM3D_do_get_inputs(self)
2128 
2129 
2130  def get_version_info(self):
2131  """get_version_info(FitRestraintBayesEM3D self) -> VersionInfo"""
2132  return _IMP_em.FitRestraintBayesEM3D_get_version_info(self)
2133 
2134 
2135  def __str__(self):
2136  """__str__(FitRestraintBayesEM3D self) -> std::string"""
2137  return _IMP_em.FitRestraintBayesEM3D___str__(self)
2138 
2139 
2140  def __repr__(self):
2141  """__repr__(FitRestraintBayesEM3D self) -> std::string"""
2142  return _IMP_em.FitRestraintBayesEM3D___repr__(self)
2143 
2144 
2145  @staticmethod
2146  def get_from(o):
2147  return _object_cast_to_FitRestraintBayesEM3D(o)
2148 
2149 FitRestraintBayesEM3D_swigregister = _IMP_em.FitRestraintBayesEM3D_swigregister
2150 FitRestraintBayesEM3D_swigregister(FitRestraintBayesEM3D)
2151 
2152 
2153 def density2particles(dmap, threshold, m, step=1):
2154  """
2155  density2particles(DensityMap dmap, IMP::Float threshold, Model m, int step=1) -> IMP::Particles
2156  density2particles(DensityMap dmap, IMP::Float threshold, Model m) -> IMP::Particles
2157  """
2158  return _IMP_em.density2particles(dmap, threshold, m, step)
2159 
2160 def density2vectors(dmap, threshold):
2161  """density2vectors(DensityMap dmap, IMP::Float threshold) -> IMP::algebra::Vector3Ds"""
2162  return _IMP_em.density2vectors(dmap, threshold)
2163 
2164 def particles2density(*args):
2165  """
2166  particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3, FloatKey weight_key) -> SampledDensityMap
2167  particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
2168  particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
2169  """
2170  return _IMP_em.particles2density(*args)
2171 
2172 def particles2binarized_density(*args):
2173  """
2174  particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3, FloatKey weight_key) -> SampledDensityMap
2175  particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
2176  particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
2177  """
2178  return _IMP_em.particles2binarized_density(*args)
2179 
2180 def particles2surface(*args):
2181  """
2182  particles2surface(IMP::ParticlesTemp const & ps, IMP::Float apix, FloatKey weight_key) -> SurfaceShellDensityMap
2183  particles2surface(IMP::ParticlesTemp const & ps, IMP::Float apix) -> SurfaceShellDensityMap
2184  """
2185  return _IMP_em.particles2surface(*args)
2186 
2187 def calculate_intersection_score(d1, d2):
2188  """calculate_intersection_score(SurfaceShellDensityMap d1, SurfaceShellDensityMap d2) -> IMP::Float"""
2189  return _IMP_em.calculate_intersection_score(d1, d2)
2190 class SpiderHeader(object):
2191  """Proxy of C++ IMP::em::SpiderHeader class"""
2192  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2193  __repr__ = _swig_repr
2194  fNslice = _swig_property(_IMP_em.SpiderHeader_fNslice_get, _IMP_em.SpiderHeader_fNslice_set)
2195  fNrow = _swig_property(_IMP_em.SpiderHeader_fNrow_get, _IMP_em.SpiderHeader_fNrow_set)
2196  fNrec = _swig_property(_IMP_em.SpiderHeader_fNrec_get, _IMP_em.SpiderHeader_fNrec_set)
2197  fNlabel = _swig_property(_IMP_em.SpiderHeader_fNlabel_get, _IMP_em.SpiderHeader_fNlabel_set)
2198  fIform = _swig_property(_IMP_em.SpiderHeader_fIform_get, _IMP_em.SpiderHeader_fIform_set)
2199  fImami = _swig_property(_IMP_em.SpiderHeader_fImami_get, _IMP_em.SpiderHeader_fImami_set)
2200  fFmax = _swig_property(_IMP_em.SpiderHeader_fFmax_get, _IMP_em.SpiderHeader_fFmax_set)
2201  fFmin = _swig_property(_IMP_em.SpiderHeader_fFmin_get, _IMP_em.SpiderHeader_fFmin_set)
2202  fAv = _swig_property(_IMP_em.SpiderHeader_fAv_get, _IMP_em.SpiderHeader_fAv_set)
2203  fSig = _swig_property(_IMP_em.SpiderHeader_fSig_get, _IMP_em.SpiderHeader_fSig_set)
2204  fIhist = _swig_property(_IMP_em.SpiderHeader_fIhist_get, _IMP_em.SpiderHeader_fIhist_set)
2205  fNcol = _swig_property(_IMP_em.SpiderHeader_fNcol_get, _IMP_em.SpiderHeader_fNcol_set)
2206  fLabrec = _swig_property(_IMP_em.SpiderHeader_fLabrec_get, _IMP_em.SpiderHeader_fLabrec_set)
2207  fIangle = _swig_property(_IMP_em.SpiderHeader_fIangle_get, _IMP_em.SpiderHeader_fIangle_set)
2208  fPhi = _swig_property(_IMP_em.SpiderHeader_fPhi_get, _IMP_em.SpiderHeader_fPhi_set)
2209  fTheta = _swig_property(_IMP_em.SpiderHeader_fTheta_get, _IMP_em.SpiderHeader_fTheta_set)
2210  fPsi = _swig_property(_IMP_em.SpiderHeader_fPsi_get, _IMP_em.SpiderHeader_fPsi_set)
2211  fXoff = _swig_property(_IMP_em.SpiderHeader_fXoff_get, _IMP_em.SpiderHeader_fXoff_set)
2212  fYoff = _swig_property(_IMP_em.SpiderHeader_fYoff_get, _IMP_em.SpiderHeader_fYoff_set)
2213  fZoff = _swig_property(_IMP_em.SpiderHeader_fZoff_get, _IMP_em.SpiderHeader_fZoff_set)
2214  fScale = _swig_property(_IMP_em.SpiderHeader_fScale_get, _IMP_em.SpiderHeader_fScale_set)
2215  fLabbyt = _swig_property(_IMP_em.SpiderHeader_fLabbyt_get, _IMP_em.SpiderHeader_fLabbyt_set)
2216  fLenbyt = _swig_property(_IMP_em.SpiderHeader_fLenbyt_get, _IMP_em.SpiderHeader_fLenbyt_set)
2217  fNothing = _swig_property(_IMP_em.SpiderHeader_fNothing_get, _IMP_em.SpiderHeader_fNothing_set)
2218  fFlag = _swig_property(_IMP_em.SpiderHeader_fFlag_get, _IMP_em.SpiderHeader_fFlag_set)
2219  fPhi1 = _swig_property(_IMP_em.SpiderHeader_fPhi1_get, _IMP_em.SpiderHeader_fPhi1_set)
2220  fTheta1 = _swig_property(_IMP_em.SpiderHeader_fTheta1_get, _IMP_em.SpiderHeader_fTheta1_set)
2221  fPsi1 = _swig_property(_IMP_em.SpiderHeader_fPsi1_get, _IMP_em.SpiderHeader_fPsi1_set)
2222  fPhi2 = _swig_property(_IMP_em.SpiderHeader_fPhi2_get, _IMP_em.SpiderHeader_fPhi2_set)
2223  fTheta2 = _swig_property(_IMP_em.SpiderHeader_fTheta2_get, _IMP_em.SpiderHeader_fTheta2_set)
2224  fPsi2 = _swig_property(_IMP_em.SpiderHeader_fPsi2_get, _IMP_em.SpiderHeader_fPsi2_set)
2225  fGeo_matrix = _swig_property(_IMP_em.SpiderHeader_fGeo_matrix_get, _IMP_em.SpiderHeader_fGeo_matrix_set)
2226  fAngle1 = _swig_property(_IMP_em.SpiderHeader_fAngle1_get, _IMP_em.SpiderHeader_fAngle1_set)
2227  fr1 = _swig_property(_IMP_em.SpiderHeader_fr1_get, _IMP_em.SpiderHeader_fr1_set)
2228  fr2 = _swig_property(_IMP_em.SpiderHeader_fr2_get, _IMP_em.SpiderHeader_fr2_set)
2229  RTflag = _swig_property(_IMP_em.SpiderHeader_RTflag_get, _IMP_em.SpiderHeader_RTflag_set)
2230  Astart = _swig_property(_IMP_em.SpiderHeader_Astart_get, _IMP_em.SpiderHeader_Astart_set)
2231  Aend = _swig_property(_IMP_em.SpiderHeader_Aend_get, _IMP_em.SpiderHeader_Aend_set)
2232  Ainc = _swig_property(_IMP_em.SpiderHeader_Ainc_get, _IMP_em.SpiderHeader_Ainc_set)
2233  Rsigma = _swig_property(_IMP_em.SpiderHeader_Rsigma_get, _IMP_em.SpiderHeader_Rsigma_set)
2234  Tstart = _swig_property(_IMP_em.SpiderHeader_Tstart_get, _IMP_em.SpiderHeader_Tstart_set)
2235  Tend = _swig_property(_IMP_em.SpiderHeader_Tend_get, _IMP_em.SpiderHeader_Tend_set)
2236  Tinc = _swig_property(_IMP_em.SpiderHeader_Tinc_get, _IMP_em.SpiderHeader_Tinc_set)
2237  Weight = _swig_property(_IMP_em.SpiderHeader_Weight_get, _IMP_em.SpiderHeader_Weight_set)
2238  Flip = _swig_property(_IMP_em.SpiderHeader_Flip_get, _IMP_em.SpiderHeader_Flip_set)
2239  empty = _swig_property(_IMP_em.SpiderHeader_empty_get, _IMP_em.SpiderHeader_empty_set)
2240  szIDat = _swig_property(_IMP_em.SpiderHeader_szIDat_get, _IMP_em.SpiderHeader_szIDat_set)
2241  szITim = _swig_property(_IMP_em.SpiderHeader_szITim_get, _IMP_em.SpiderHeader_szITim_set)
2242  szITit = _swig_property(_IMP_em.SpiderHeader_szITit_get, _IMP_em.SpiderHeader_szITit_set)
2243 
2244  def show(self, out):
2245  """show(SpiderHeader self, _ostream out)"""
2246  return _IMP_em.SpiderHeader_show(self, out)
2247 
2248 
2249  def __init__(self):
2250  """__init__(IMP::em::SpiderHeader self) -> SpiderHeader"""
2251  this = _IMP_em.new_SpiderHeader()
2252  try:
2253  self.this.append(this)
2254  except:
2255  self.this = this
2256  __swig_destroy__ = _IMP_em.delete_SpiderHeader
2257  __del__ = lambda self: None
2258 SpiderHeader_swigregister = _IMP_em.SpiderHeader_swigregister
2259 SpiderHeader_swigregister(SpiderHeader)
2260 
2261 class ImageHeader(object):
2262  """Proxy of C++ IMP::em::ImageHeader class"""
2263  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2264  __repr__ = _swig_repr
2265  IMG_BYTE = _IMP_em.ImageHeader_IMG_BYTE
2266  IMG_IMPEM = _IMP_em.ImageHeader_IMG_IMPEM
2267  IMG_INT = _IMP_em.ImageHeader_IMG_INT
2268  VOL_BYTE = _IMP_em.ImageHeader_VOL_BYTE
2269  VOL_IMPEM = _IMP_em.ImageHeader_VOL_IMPEM
2270  VOL_INT = _IMP_em.ImageHeader_VOL_INT
2271  IMG_FOURIER = _IMP_em.ImageHeader_IMG_FOURIER
2272  VOL_FOURIER = _IMP_em.ImageHeader_VOL_FOURIER
2273 
2274  def __init__(self, *args):
2275  """
2276  __init__(IMP::em::ImageHeader self) -> ImageHeader
2277  __init__(IMP::em::ImageHeader self, IMP::em::ImageHeader::img_type im) -> ImageHeader
2278  __init__(IMP::em::ImageHeader self, float im) -> ImageHeader
2279  """
2280  this = _IMP_em.new_ImageHeader(*args)
2281  try:
2282  self.this.append(this)
2283  except:
2284  self.this = this
2285 
2286  def get_image_type(self):
2287  """get_image_type(ImageHeader self) -> float"""
2288  return _IMP_em.ImageHeader_get_image_type(self)
2289 
2290 
2291  def set_image_type(self, *args):
2292  """
2293  set_image_type(ImageHeader self, IMP::em::ImageHeader::img_type im)
2294  set_image_type(ImageHeader self, float im)
2295  """
2296  return _IMP_em.ImageHeader_set_image_type(self, *args)
2297 
2298 
2299  def do_show(self, out):
2300  """do_show(ImageHeader self, _ostream out)"""
2301  return _IMP_em.ImageHeader_do_show(self, out)
2302 
2303 
2304  def show(self, *args):
2305  """
2306  show(ImageHeader self, _ostream out)
2307  show(ImageHeader self)
2308  """
2309  return _IMP_em.ImageHeader_show(self, *args)
2310 
2311 
2312  def print_hard(self, out):
2313  """print_hard(ImageHeader self, _ostream out)"""
2314  return _IMP_em.ImageHeader_print_hard(self, out)
2315 
2316 
2317  def show_projection_params(self, out):
2318  """show_projection_params(ImageHeader self, _ostream out)"""
2319  return _IMP_em.ImageHeader_show_projection_params(self, out)
2320 
2321 
2322  def read(self, *args):
2323  """
2324  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False, bool skip_extra_checkings=False) -> int
2325  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False) -> int
2326  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False) -> int
2327  read(ImageHeader self, IMP::String const filename) -> int
2328  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False, bool skip_extra_checkings=False) -> bool
2329  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False) -> bool
2330  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False) -> bool
2331  read(ImageHeader self, std::ifstream & f) -> bool
2332  """
2333  return _IMP_em.ImageHeader_read(self, *args)
2334 
2335 
2336  def write(self, *args):
2337  """
2338  write(ImageHeader self, IMP::String const & filename, bool force_reversed=False)
2339  write(ImageHeader self, IMP::String const & filename)
2340  write(ImageHeader self, std::ofstream & f, bool force_reversed=False)
2341  write(ImageHeader self, std::ofstream & f)
2342  """
2343  return _IMP_em.ImageHeader_write(self, *args)
2344 
2345 
2346  def clear(self):
2347  """clear(ImageHeader self)"""
2348  return _IMP_em.ImageHeader_clear(self)
2349 
2350 
2351  def set_header(self):
2352  """set_header(ImageHeader self)"""
2353  return _IMP_em.ImageHeader_set_header(self)
2354 
2355 
2356  def get_reversed(self):
2357  """get_reversed(ImageHeader self) -> bool"""
2358  return _IMP_em.ImageHeader_get_reversed(self)
2359 
2360 
2361  def set_reversed(self, value):
2362  """set_reversed(ImageHeader self, bool value)"""
2363  return _IMP_em.ImageHeader_set_reversed(self, value)
2364 
2365 
2366  def get_number_of_slices(self):
2367  """get_number_of_slices(ImageHeader self) -> unsigned int"""
2368  return _IMP_em.ImageHeader_get_number_of_slices(self)
2369 
2370 
2371  def set_number_of_slices(self, n):
2372  """set_number_of_slices(ImageHeader self, unsigned int n)"""
2373  return _IMP_em.ImageHeader_set_number_of_slices(self, n)
2374 
2375 
2376  def get_number_of_rows(self):
2377  """get_number_of_rows(ImageHeader self) -> unsigned int"""
2378  return _IMP_em.ImageHeader_get_number_of_rows(self)
2379 
2380 
2381  def set_number_of_rows(self, n):
2382  """set_number_of_rows(ImageHeader self, unsigned int n)"""
2383  return _IMP_em.ImageHeader_set_number_of_rows(self, n)
2384 
2385 
2386  def get_number_of_columns(self):
2387  """get_number_of_columns(ImageHeader self) -> unsigned int"""
2388  return _IMP_em.ImageHeader_get_number_of_columns(self)
2389 
2390 
2391  def set_number_of_columns(self, n):
2392  """set_number_of_columns(ImageHeader self, unsigned int n)"""
2393  return _IMP_em.ImageHeader_set_number_of_columns(self, n)
2394 
2395 
2396  def get_old_rot(self):
2397  """get_old_rot(ImageHeader self) -> float"""
2398  return _IMP_em.ImageHeader_get_old_rot(self)
2399 
2400 
2401  def set_old_rot(self, value):
2402  """set_old_rot(ImageHeader self, float value)"""
2403  return _IMP_em.ImageHeader_set_old_rot(self, value)
2404 
2405 
2406  def get_fAngle1(self):
2407  """get_fAngle1(ImageHeader self) -> float"""
2408  return _IMP_em.ImageHeader_get_fAngle1(self)
2409 
2410 
2411  def set_fAngle1(self, value):
2412  """set_fAngle1(ImageHeader self, float value)"""
2413  return _IMP_em.ImageHeader_set_fAngle1(self, value)
2414 
2415 
2416  def get_Scale(self):
2417  """get_Scale(ImageHeader self) -> float"""
2418  return _IMP_em.ImageHeader_get_Scale(self)
2419 
2420 
2421  def set_Scale(self, value):
2422  """set_Scale(ImageHeader self, float value)"""
2423  return _IMP_em.ImageHeader_set_Scale(self, value)
2424 
2425 
2426  def get_Flip(self):
2427  """get_Flip(ImageHeader self) -> float"""
2428  return _IMP_em.ImageHeader_get_Flip(self)
2429 
2430 
2431  def set_Flip(self, value):
2432  """set_Flip(ImageHeader self, float value)"""
2433  return _IMP_em.ImageHeader_set_Flip(self, value)
2434 
2435 
2436  def get_Weight(self):
2437  """get_Weight(ImageHeader self) -> float"""
2438  return _IMP_em.ImageHeader_get_Weight(self)
2439 
2440 
2441  def set_Weight(self, value):
2442  """set_Weight(ImageHeader self, float value)"""
2443  return _IMP_em.ImageHeader_set_Weight(self, value)
2444 
2445 
2446  def get_fNrec(self):
2447  """get_fNrec(ImageHeader self) -> float"""
2448  return _IMP_em.ImageHeader_get_fNrec(self)
2449 
2450 
2451  def set_fNrec(self, value):
2452  """set_fNrec(ImageHeader self, float value)"""
2453  return _IMP_em.ImageHeader_set_fNrec(self, value)
2454 
2455 
2456  def get_fNlabel(self):
2457  """get_fNlabel(ImageHeader self) -> float"""
2458  return _IMP_em.ImageHeader_get_fNlabel(self)
2459 
2460 
2461  def set_fNlabel(self, value):
2462  """set_fNlabel(ImageHeader self, float value)"""
2463  return _IMP_em.ImageHeader_set_fNlabel(self, value)
2464 
2465 
2466  def get_fIform(self):
2467  """get_fIform(ImageHeader self) -> float"""
2468  return _IMP_em.ImageHeader_get_fIform(self)
2469 
2470 
2471  def set_fIform(self, value):
2472  """set_fIform(ImageHeader self, float value)"""
2473  return _IMP_em.ImageHeader_set_fIform(self, value)
2474 
2475 
2476  def get_fImami(self):
2477  """get_fImami(ImageHeader self) -> float"""
2478  return _IMP_em.ImageHeader_get_fImami(self)
2479 
2480 
2481  def set_fImami(self, value):
2482  """set_fImami(ImageHeader self, float value)"""
2483  return _IMP_em.ImageHeader_set_fImami(self, value)
2484 
2485 
2486  def get_fFmax(self):
2487  """get_fFmax(ImageHeader self) -> float"""
2488  return _IMP_em.ImageHeader_get_fFmax(self)
2489 
2490 
2491  def set_fFmax(self, value):
2492  """set_fFmax(ImageHeader self, float value)"""
2493  return _IMP_em.ImageHeader_set_fFmax(self, value)
2494 
2495 
2496  def get_fFmin(self):
2497  """get_fFmin(ImageHeader self) -> float"""
2498  return _IMP_em.ImageHeader_get_fFmin(self)
2499 
2500 
2501  def set_fFmin(self, value):
2502  """set_fFmin(ImageHeader self, float value)"""
2503  return _IMP_em.ImageHeader_set_fFmin(self, value)
2504 
2505 
2506  def get_fAv(self):
2507  """get_fAv(ImageHeader self) -> float"""
2508  return _IMP_em.ImageHeader_get_fAv(self)
2509 
2510 
2511  def set_fAv(self, value):
2512  """set_fAv(ImageHeader self, float value)"""
2513  return _IMP_em.ImageHeader_set_fAv(self, value)
2514 
2515 
2516  def get_fSig(self):
2517  """get_fSig(ImageHeader self) -> float"""
2518  return _IMP_em.ImageHeader_get_fSig(self)
2519 
2520 
2521  def set_fSig(self, value):
2522  """set_fSig(ImageHeader self, float value)"""
2523  return _IMP_em.ImageHeader_set_fSig(self, value)
2524 
2525 
2526  def get_fIhist(self):
2527  """get_fIhist(ImageHeader self) -> float"""
2528  return _IMP_em.ImageHeader_get_fIhist(self)
2529 
2530 
2531  def set_fIhist(self, value):
2532  """set_fIhist(ImageHeader self, float value)"""
2533  return _IMP_em.ImageHeader_set_fIhist(self, value)
2534 
2535 
2536  def get_fLabrec(self):
2537  """get_fLabrec(ImageHeader self) -> float"""
2538  return _IMP_em.ImageHeader_get_fLabrec(self)
2539 
2540 
2541  def set_fLabrec(self, value):
2542  """set_fLabrec(ImageHeader self, float value)"""
2543  return _IMP_em.ImageHeader_set_fLabrec(self, value)
2544 
2545 
2546  def get_fIangle(self):
2547  """get_fIangle(ImageHeader self) -> float"""
2548  return _IMP_em.ImageHeader_get_fIangle(self)
2549 
2550 
2551  def set_fIangle(self, value):
2552  """set_fIangle(ImageHeader self, float value)"""
2553  return _IMP_em.ImageHeader_set_fIangle(self, value)
2554 
2555 
2556  def get_origin(self):
2557  """get_origin(ImageHeader self) -> Vector3D"""
2558  return _IMP_em.ImageHeader_get_origin(self)
2559 
2560 
2561  def set_origin(self, *args):
2562  """
2563  set_origin(ImageHeader self, Vector3D v)
2564  set_origin(ImageHeader self, Vector2D v)
2565  """
2566  return _IMP_em.ImageHeader_set_origin(self, *args)
2567 
2568 
2569  def get_object_pixel_size(self):
2570  """get_object_pixel_size(ImageHeader self) -> float"""
2571  return _IMP_em.ImageHeader_get_object_pixel_size(self)
2572 
2573 
2574  def set_object_pixel_size(self, value):
2575  """set_object_pixel_size(ImageHeader self, float value)"""
2576  return _IMP_em.ImageHeader_set_object_pixel_size(self, value)
2577 
2578 
2579  def get_fLabbyt(self):
2580  """get_fLabbyt(ImageHeader self) -> float"""
2581  return _IMP_em.ImageHeader_get_fLabbyt(self)
2582 
2583 
2584  def set_fLabbyt(self, value):
2585  """set_fLabbyt(ImageHeader self, float value)"""
2586  return _IMP_em.ImageHeader_set_fLabbyt(self, value)
2587 
2588 
2589  def get_fLenbyt(self):
2590  """get_fLenbyt(ImageHeader self) -> float"""
2591  return _IMP_em.ImageHeader_get_fLenbyt(self)
2592 
2593 
2594  def set_fLenbyt(self, value):
2595  """set_fLenbyt(ImageHeader self, float value)"""
2596  return _IMP_em.ImageHeader_set_fLenbyt(self, value)
2597 
2598 
2599  def get_fGeo_matrix(self, i, j):
2600  """get_fGeo_matrix(ImageHeader self, unsigned int i, unsigned int j) -> double"""
2601  return _IMP_em.ImageHeader_get_fGeo_matrix(self, i, j)
2602 
2603 
2604  def get_fFlag(self):
2605  """get_fFlag(ImageHeader self) -> float"""
2606  return _IMP_em.ImageHeader_get_fFlag(self)
2607 
2608 
2609  def set_fFlag(self, value):
2610  """set_fFlag(ImageHeader self, float value)"""
2611  return _IMP_em.ImageHeader_set_fFlag(self, value)
2612 
2613 
2614  def get_euler_angles(self):
2615  """get_euler_angles(ImageHeader self) -> Vector3D"""
2616  return _IMP_em.ImageHeader_get_euler_angles(self)
2617 
2618 
2619  def get_euler_angles1(self):
2620  """get_euler_angles1(ImageHeader self) -> Vector3D"""
2621  return _IMP_em.ImageHeader_get_euler_angles1(self)
2622 
2623 
2624  def get_euler_angles2(self):
2625  """get_euler_angles2(ImageHeader self) -> Vector3D"""
2626  return _IMP_em.ImageHeader_get_euler_angles2(self)
2627 
2628 
2629  def set_euler_angles(self, euler):
2630  """set_euler_angles(ImageHeader self, Vector3D euler)"""
2631  return _IMP_em.ImageHeader_set_euler_angles(self, euler)
2632 
2633 
2634  def set_euler_angles1(self, euler):
2635  """set_euler_angles1(ImageHeader self, Vector3D euler)"""
2636  return _IMP_em.ImageHeader_set_euler_angles1(self, euler)
2637 
2638 
2639  def set_euler_angles2(self, euler):
2640  """set_euler_angles2(ImageHeader self, Vector3D euler)"""
2641  return _IMP_em.ImageHeader_set_euler_angles2(self, euler)
2642 
2643 
2644  def is_normalized(self):
2645  """is_normalized(ImageHeader self) -> bool"""
2646  return _IMP_em.ImageHeader_is_normalized(self)
2647 
2648 
2649  def set_date(self):
2650  """set_date(ImageHeader self)"""
2651  return _IMP_em.ImageHeader_set_date(self)
2652 
2653 
2654  def set_time(self):
2655  """set_time(ImageHeader self)"""
2656  return _IMP_em.ImageHeader_set_time(self)
2657 
2658 
2659  def set_title(self, newName):
2660  """set_title(ImageHeader self, IMP::String newName)"""
2661  return _IMP_em.ImageHeader_set_title(self, newName)
2662 
2663  __swig_destroy__ = _IMP_em.delete_ImageHeader
2664  __del__ = lambda self: None
2665 ImageHeader_swigregister = _IMP_em.ImageHeader_swigregister
2666 ImageHeader_swigregister(ImageHeader)
2667 
2668 class SpiderMapReaderWriter(MapReaderWriter):
2669  """Proxy of C++ IMP::em::SpiderMapReaderWriter class"""
2670  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2671  filename_ = _swig_property(_IMP_em.SpiderMapReaderWriter_filename__get, _IMP_em.SpiderMapReaderWriter_filename__set)
2672  skip_type_check_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_type_check__get, _IMP_em.SpiderMapReaderWriter_skip_type_check__set)
2673  force_reversed_ = _swig_property(_IMP_em.SpiderMapReaderWriter_force_reversed__get, _IMP_em.SpiderMapReaderWriter_force_reversed__set)
2674  skip_extra_checkings_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_extra_checkings__get, _IMP_em.SpiderMapReaderWriter_skip_extra_checkings__set)
2675 
2676  def __init__(self, *args):
2677  """
2678  __init__(IMP::em::SpiderMapReaderWriter self) -> SpiderMapReaderWriter
2679  __init__(IMP::em::SpiderMapReaderWriter self, IMP::String filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings) -> SpiderMapReaderWriter
2680  """
2681  this = _IMP_em.new_SpiderMapReaderWriter(*args)
2682  try:
2683  self.this.append(this)
2684  except:
2685  self.this = this
2686 
2687  def __str__(self):
2688  """__str__(SpiderMapReaderWriter self) -> std::string"""
2689  return _IMP_em.SpiderMapReaderWriter___str__(self)
2690 
2691 
2692  def __repr__(self):
2693  """__repr__(SpiderMapReaderWriter self) -> std::string"""
2694  return _IMP_em.SpiderMapReaderWriter___repr__(self)
2695 
2696 
2697  @staticmethod
2698  def get_from(o):
2699  return _object_cast_to_SpiderMapReaderWriter(o)
2700 
2701 SpiderMapReaderWriter_swigregister = _IMP_em.SpiderMapReaderWriter_swigregister
2702 SpiderMapReaderWriter_swigregister(SpiderMapReaderWriter)
2703 
2704 class FittingSolutions(object):
2705  """Proxy of C++ IMP::em::FittingSolutions class"""
2706  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2707 
2708  def __init__(self):
2709  """__init__(IMP::em::FittingSolutions self) -> FittingSolutions"""
2710  this = _IMP_em.new_FittingSolutions()
2711  try:
2712  self.this.append(this)
2713  except:
2714  self.this = this
2715 
2716  def get_number_of_solutions(self):
2717  """get_number_of_solutions(FittingSolutions self) -> int"""
2718  return _IMP_em.FittingSolutions_get_number_of_solutions(self)
2719 
2720 
2721  def get_transformation(self, i):
2722  """get_transformation(FittingSolutions self, unsigned int i) -> Transformation3D"""
2723  return _IMP_em.FittingSolutions_get_transformation(self, i)
2724 
2725 
2726  def get_score(self, i):
2727  """get_score(FittingSolutions self, unsigned int i) -> IMP::Float"""
2728  return _IMP_em.FittingSolutions_get_score(self, i)
2729 
2730 
2731  def set_score(self, i, score):
2732  """set_score(FittingSolutions self, unsigned int i, IMP::Float score)"""
2733  return _IMP_em.FittingSolutions_set_score(self, i, score)
2734 
2735 
2736  def add_solution(self, t, score):
2737  """add_solution(FittingSolutions self, Transformation3D t, IMP::Float score)"""
2738  return _IMP_em.FittingSolutions_add_solution(self, t, score)
2739 
2740 
2741  def sort(self, reverse=False):
2742  """
2743  sort(FittingSolutions self, bool reverse=False)
2744  sort(FittingSolutions self)
2745  """
2746  return _IMP_em.FittingSolutions_sort(self, reverse)
2747 
2748 
2749  def multiply(self, t):
2750  """multiply(FittingSolutions self, Transformation3D t)"""
2751  return _IMP_em.FittingSolutions_multiply(self, t)
2752 
2753 
2754  def get_transformations(self):
2755  """get_transformations(FittingSolutions self) -> IMP::algebra::Transformation3Ds"""
2756  return _IMP_em.FittingSolutions_get_transformations(self)
2757 
2758 
2759  def show(self, *args):
2760  """
2761  show(FittingSolutions self, _ostream out)
2762  show(FittingSolutions self)
2763  """
2764  return _IMP_em.FittingSolutions_show(self, *args)
2765 
2766 
2767  def __str__(self):
2768  """__str__(FittingSolutions self) -> std::string"""
2769  return _IMP_em.FittingSolutions___str__(self)
2770 
2771 
2772  def __repr__(self):
2773  """__repr__(FittingSolutions self) -> std::string"""
2774  return _IMP_em.FittingSolutions___repr__(self)
2775 
2776  __swig_destroy__ = _IMP_em.delete_FittingSolutions
2777  __del__ = lambda self: None
2778 FittingSolutions_swigregister = _IMP_em.FittingSolutions_swigregister
2779 FittingSolutions_swigregister(FittingSolutions)
2780 
2781 
2782 def local_rigid_fitting_around_point(p, refiner, weight_key, dmap, anchor_centroid, display_log, number_of_optimization_runs=5, number_of_mc_steps=10, number_of_cg_steps=100, max_translation=2., max_rotation=.3, fast=False):
2783  """
2784  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2., IMP::Float max_rotation=.3, bool fast=False) -> FittingSolutions
2785  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2., IMP::Float max_rotation=.3) -> FittingSolutions
2786  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2.) -> FittingSolutions
2787  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100) -> FittingSolutions
2788  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10) -> FittingSolutions
2789  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2790  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log) -> FittingSolutions
2791  """
2792  return _IMP_em.local_rigid_fitting_around_point(p, refiner, weight_key, dmap, anchor_centroid, display_log, number_of_optimization_runs, number_of_mc_steps, number_of_cg_steps, max_translation, max_rotation, fast)
2793 
2794 def local_rigid_fitting(p, refiner, weight_key, dmap, display_log, number_of_optimization_runs=5, number_of_mc_steps=10, number_of_cg_steps=100, max_translation=2., max_rotation=.3, fast=True):
2795  """
2796  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2., IMP::Float max_rotation=.3, bool fast=True) -> FittingSolutions
2797  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2., IMP::Float max_rotation=.3) -> FittingSolutions
2798  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2.) -> FittingSolutions
2799  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100) -> FittingSolutions
2800  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10) -> FittingSolutions
2801  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2802  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log) -> FittingSolutions
2803  """
2804  return _IMP_em.local_rigid_fitting(p, refiner, weight_key, dmap, display_log, number_of_optimization_runs, number_of_mc_steps, number_of_cg_steps, max_translation, max_rotation, fast)
2805 
2806 def local_rigid_fitting_around_points(p, refiner, wei_key, dmap, anchor_centroids, display_log, number_of_optimization_runs=5, number_of_mc_steps=10, number_of_cg_steps=100, max_translation=2., max_rotation=.3):
2807  """
2808  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2., IMP::Float max_rotation=.3) -> FittingSolutions
2809  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2.) -> FittingSolutions
2810  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100) -> FittingSolutions
2811  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10) -> FittingSolutions
2812  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2813  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids, IMP::OptimizerStates display_log) -> FittingSolutions
2814  """
2815  return _IMP_em.local_rigid_fitting_around_points(p, refiner, wei_key, dmap, anchor_centroids, display_log, number_of_optimization_runs, number_of_mc_steps, number_of_cg_steps, max_translation, max_rotation)
2816 
2817 def local_rigid_fitting_grid_search(ps, wei_key, dmap, max_voxels_translation=2, translation_step=1, max_angle_in_radians=0.174, number_of_rotations=100):
2818  """
2819  local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2, IMP::Int translation_step=1, IMP::Float max_angle_in_radians=0.174, IMP::Int number_of_rotations=100) -> FittingSolutions
2820  local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2, IMP::Int translation_step=1, IMP::Float max_angle_in_radians=0.174) -> FittingSolutions
2821  local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2, IMP::Int translation_step=1) -> FittingSolutions
2822  local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2) -> FittingSolutions
2823  local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap) -> FittingSolutions
2824  """
2825  return _IMP_em.local_rigid_fitting_grid_search(ps, wei_key, dmap, max_voxels_translation, translation_step, max_angle_in_radians, number_of_rotations)
2826 
2827 def compute_fitting_scores(*args):
2828  """
2829  compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations, bool fast_version=False, bool local_score=False, FloatKey wei_key) -> FittingSolutions
2830  compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations, bool fast_version=False, bool local_score=False) -> FittingSolutions
2831  compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations, bool fast_version=False) -> FittingSolutions
2832  compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2833  compute_fitting_scores(DensityMap em_map, RigidBody rb, Refiner refiner, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2834  """
2835  return _IMP_em.compute_fitting_scores(*args)
2836 
2837 def compute_fitting_score(*args):
2838  """
2839  compute_fitting_score(IMP::ParticlesTemp const & ps, DensityMap em_map, FloatKey wei_key) -> IMP::Float
2840  compute_fitting_score(IMP::ParticlesTemp const & ps, DensityMap em_map) -> IMP::Float
2841  """
2842  return _IMP_em.compute_fitting_score(*args)
2843 
2845  """
2846  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, Transformation3D t, float thr=0.0) -> long
2847  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, Transformation3D t) -> long
2848  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps) -> long
2849  """
2850  return _IMP_em.get_number_of_particles_outside_of_the_density(*args)
2851 
2852 def get_numbers_of_particles_outside_of_the_density(dmap, ps, transformations, thr=0.0):
2853  """
2854  get_numbers_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, IMP::algebra::Transformation3Ds const & transformations, float thr=0.0) -> IMP::Ints
2855  get_numbers_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, IMP::algebra::Transformation3Ds const & transformations) -> IMP::Ints
2856  """
2857  return _IMP_em.get_numbers_of_particles_outside_of_the_density(dmap, ps, transformations, thr)
2858 
2860  """
2861  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3., Transformation3D t, float thr=0.0) -> double
2862  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3., Transformation3D t) -> double
2863  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3.) -> double
2864  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps) -> double
2865  """
2866  return _IMP_em.get_percentage_of_voxels_covered_by_particles(*args)
2867 class HighDensityEmbedding(IMP.statistics.Embedding):
2868  """Proxy of C++ IMP::em::HighDensityEmbedding class"""
2869  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2870 
2871  def __init__(self, dm, threshold):
2872  """__init__(IMP::em::HighDensityEmbedding self, DensityMap dm, double threshold) -> HighDensityEmbedding"""
2873  this = _IMP_em.new_HighDensityEmbedding(dm, threshold)
2874  try:
2875  self.this.append(this)
2876  except:
2877  self.this = this
2878 
2879  def get_version_info(self):
2880  """get_version_info(HighDensityEmbedding self) -> VersionInfo"""
2881  return _IMP_em.HighDensityEmbedding_get_version_info(self)
2882 
2883 
2884  def __str__(self):
2885  """__str__(HighDensityEmbedding self) -> std::string"""
2886  return _IMP_em.HighDensityEmbedding___str__(self)
2887 
2888 
2889  def __repr__(self):
2890  """__repr__(HighDensityEmbedding self) -> std::string"""
2891  return _IMP_em.HighDensityEmbedding___repr__(self)
2892 
2893 
2894  @staticmethod
2895  def get_from(o):
2896  return _object_cast_to_HighDensityEmbedding(o)
2897 
2898 HighDensityEmbedding_swigregister = _IMP_em.HighDensityEmbedding_swigregister
2899 HighDensityEmbedding_swigregister(HighDensityEmbedding)
2900 
2901 
2902 def mask_and_norm(dmap, mask):
2903  """mask_and_norm(DensityMap dmap, DensityMap mask) -> DensityMap"""
2904  return _IMP_em.mask_and_norm(dmap, mask)
2905 
2906 def get_volume_at_threshold(m, threshold):
2907  """get_volume_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float"""
2908  return _IMP_em.get_volume_at_threshold(m, threshold)
2909 
2911  """
2912  get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold, IMP::atom::ProteinDensityReference ref) -> IMP::Float
2913  get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float
2914  """
2915  return _IMP_em.get_molecular_mass_at_threshold(*args)
2916 
2917 def get_threshold_for_approximate_volume(m, desired_volume):
2918  """get_threshold_for_approximate_volume(DensityMap m, IMP::Float desired_volume) -> IMP::Float"""
2919  return _IMP_em.get_threshold_for_approximate_volume(m, desired_volume)
2920 
2922  """
2923  get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass, IMP::atom::ProteinDensityReference ref) -> IMP::Float
2924  get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass) -> IMP::Float
2925  """
2926  return _IMP_em.get_threshold_for_approximate_mass(*args)
2927 class EnvelopePenetrationRestraint(IMP.Restraint):
2928  """Proxy of C++ IMP::em::EnvelopePenetrationRestraint class"""
2929  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2930 
2931  def __init__(self, ps, em_map, threshold):
2932  """__init__(IMP::em::EnvelopePenetrationRestraint self, IMP::Particles ps, DensityMap em_map, IMP::Float threshold) -> EnvelopePenetrationRestraint"""
2933  this = _IMP_em.new_EnvelopePenetrationRestraint(ps, em_map, threshold)
2934  try:
2935  self.this.append(this)
2936  except:
2937  self.this = this
2938 
2939  def do_get_inputs(self):
2940  """do_get_inputs(EnvelopePenetrationRestraint self) -> IMP::ModelObjectsTemp"""
2941  return _IMP_em.EnvelopePenetrationRestraint_do_get_inputs(self)
2942 
2943 
2944  def get_version_info(self):
2945  """get_version_info(EnvelopePenetrationRestraint self) -> VersionInfo"""
2946  return _IMP_em.EnvelopePenetrationRestraint_get_version_info(self)
2947 
2948 
2949  def __str__(self):
2950  """__str__(EnvelopePenetrationRestraint self) -> std::string"""
2951  return _IMP_em.EnvelopePenetrationRestraint___str__(self)
2952 
2953 
2954  def __repr__(self):
2955  """__repr__(EnvelopePenetrationRestraint self) -> std::string"""
2956  return _IMP_em.EnvelopePenetrationRestraint___repr__(self)
2957 
2958 
2959  @staticmethod
2960  def get_from(o):
2961  return _object_cast_to_EnvelopePenetrationRestraint(o)
2962 
2963 EnvelopePenetrationRestraint_swigregister = _IMP_em.EnvelopePenetrationRestraint_swigregister
2964 EnvelopePenetrationRestraint_swigregister(EnvelopePenetrationRestraint)
2965 
2966 class PCAFitRestraint(IMP.Restraint):
2967  """Proxy of C++ IMP::em::PCAFitRestraint class"""
2968  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2969 
2970  def __init__(self, *args):
2971  """
2972  __init__(IMP::em::PCAFitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, float threshold, float max_pca_size_diff, float max_angle_diff, float max_centroid_diff, FloatKey weight_key) -> PCAFitRestraint
2973  __init__(IMP::em::PCAFitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, float threshold, float max_pca_size_diff, float max_angle_diff, float max_centroid_diff) -> PCAFitRestraint
2974  """
2975  this = _IMP_em.new_PCAFitRestraint(*args)
2976  try:
2977  self.this.append(this)
2978  except:
2979  self.this = this
2980 
2981  def do_get_inputs(self):
2982  """do_get_inputs(PCAFitRestraint self) -> IMP::ModelObjectsTemp"""
2983  return _IMP_em.PCAFitRestraint_do_get_inputs(self)
2984 
2985 
2986  def get_version_info(self):
2987  """get_version_info(PCAFitRestraint self) -> VersionInfo"""
2988  return _IMP_em.PCAFitRestraint_get_version_info(self)
2989 
2990 
2991  def __str__(self):
2992  """__str__(PCAFitRestraint self) -> std::string"""
2993  return _IMP_em.PCAFitRestraint___str__(self)
2994 
2995 
2996  def __repr__(self):
2997  """__repr__(PCAFitRestraint self) -> std::string"""
2998  return _IMP_em.PCAFitRestraint___repr__(self)
2999 
3000 
3001  @staticmethod
3002  def get_from(o):
3003  return _object_cast_to_PCAFitRestraint(o)
3004 
3005 PCAFitRestraint_swigregister = _IMP_em.PCAFitRestraint_swigregister
3006 PCAFitRestraint_swigregister(PCAFitRestraint)
3007 
3008 class EnvelopeFitRestraint(IMP.Restraint):
3009  """Proxy of C++ IMP::em::EnvelopeFitRestraint class"""
3010  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3011 
3012  def __init__(self, particles, em_map, density_threshold, penetration_threshold):
3013  """__init__(IMP::em::EnvelopeFitRestraint self, IMP::Particles particles, DensityMap em_map, double density_threshold, double penetration_threshold) -> EnvelopeFitRestraint"""
3014  this = _IMP_em.new_EnvelopeFitRestraint(particles, em_map, density_threshold, penetration_threshold)
3015  try:
3016  self.this.append(this)
3017  except:
3018  self.this = this
3019 
3020  def get_transformation(self):
3021  """get_transformation(EnvelopeFitRestraint self) -> Transformation3D"""
3022  return _IMP_em.EnvelopeFitRestraint_get_transformation(self)
3023 
3024 
3025  def apply_transformation(self):
3026  """apply_transformation(EnvelopeFitRestraint self)"""
3027  return _IMP_em.EnvelopeFitRestraint_apply_transformation(self)
3028 
3029 
3030  def do_get_inputs(self):
3031  """do_get_inputs(EnvelopeFitRestraint self) -> IMP::ModelObjectsTemp"""
3032  return _IMP_em.EnvelopeFitRestraint_do_get_inputs(self)
3033 
3034 
3035  def get_version_info(self):
3036  """get_version_info(EnvelopeFitRestraint self) -> VersionInfo"""
3037  return _IMP_em.EnvelopeFitRestraint_get_version_info(self)
3038 
3039 
3040  def __str__(self):
3041  """__str__(EnvelopeFitRestraint self) -> std::string"""
3042  return _IMP_em.EnvelopeFitRestraint___str__(self)
3043 
3044 
3045  def __repr__(self):
3046  """__repr__(EnvelopeFitRestraint self) -> std::string"""
3047  return _IMP_em.EnvelopeFitRestraint___repr__(self)
3048 
3049 
3050  @staticmethod
3051  def get_from(o):
3052  return _object_cast_to_EnvelopeFitRestraint(o)
3053 
3054 EnvelopeFitRestraint_swigregister = _IMP_em.EnvelopeFitRestraint_swigregister
3055 EnvelopeFitRestraint_swigregister(EnvelopeFitRestraint)
3056 
3057 class MapDistanceTransform(DensityMap):
3058  """Proxy of C++ IMP::em::MapDistanceTransform class"""
3059  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3060 
3061  def __init__(self, map, density_threshold, max_distance):
3062  """__init__(IMP::em::MapDistanceTransform self, DensityMap map, float density_threshold, float max_distance) -> MapDistanceTransform"""
3063  this = _IMP_em.new_MapDistanceTransform(map, density_threshold, max_distance)
3064  try:
3065  self.this.append(this)
3066  except:
3067  self.this = this
3068 
3069  def get_distance_from_envelope(self, v):
3070  """get_distance_from_envelope(MapDistanceTransform self, Vector3D v) -> float"""
3071  return _IMP_em.MapDistanceTransform_get_distance_from_envelope(self, v)
3072 
3073 
3074  def __str__(self):
3075  """__str__(MapDistanceTransform self) -> std::string"""
3076  return _IMP_em.MapDistanceTransform___str__(self)
3077 
3078 
3079  def __repr__(self):
3080  """__repr__(MapDistanceTransform self) -> std::string"""
3081  return _IMP_em.MapDistanceTransform___repr__(self)
3082 
3083 
3084  @staticmethod
3085  def get_from(o):
3086  return _object_cast_to_MapDistanceTransform(o)
3087 
3088  __swig_destroy__ = _IMP_em.delete_MapDistanceTransform
3089  __del__ = lambda self: None
3090 MapDistanceTransform_swigregister = _IMP_em.MapDistanceTransform_swigregister
3091 MapDistanceTransform_swigregister(MapDistanceTransform)
3092 
3093 class EnvelopeScore(IMP.Object):
3094  """Proxy of C++ IMP::em::EnvelopeScore class"""
3095  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3096 
3097  def __init__(self, mdt):
3098  """__init__(IMP::em::EnvelopeScore self, MapDistanceTransform mdt) -> EnvelopeScore"""
3099  this = _IMP_em.new_EnvelopeScore(mdt)
3100  try:
3101  self.this.append(this)
3102  except:
3103  self.this = this
3104 
3105  def is_penetrating(self, *args):
3106  """
3107  is_penetrating(EnvelopeScore self, IMP::algebra::Vector3Ds const & points, float penetration_thr) -> bool
3108  is_penetrating(EnvelopeScore self, IMP::algebra::Vector3Ds const & points, Transformation3D trans, float penetration_thr) -> bool
3109  """
3110  return _IMP_em.EnvelopeScore_is_penetrating(self, *args)
3111 
3112 
3113  def score(self, *args):
3114  """
3115  score(EnvelopeScore self, IMP::algebra::Vector3Ds const & points) -> double
3116  score(EnvelopeScore self, IMP::algebra::Vector3Ds const & points, Transformation3D trans) -> double
3117  """
3118  return _IMP_em.EnvelopeScore_score(self, *args)
3119 
3120  __swig_destroy__ = _IMP_em.delete_EnvelopeScore
3121  __del__ = lambda self: None
3122 
3123  def __str__(self):
3124  """__str__(EnvelopeScore self) -> std::string"""
3125  return _IMP_em.EnvelopeScore___str__(self)
3126 
3127 
3128  def __repr__(self):
3129  """__repr__(EnvelopeScore self) -> std::string"""
3130  return _IMP_em.EnvelopeScore___repr__(self)
3131 
3132 
3133  @staticmethod
3134  def get_from(o):
3135  return _object_cast_to_EnvelopeScore(o)
3136 
3137 EnvelopeScore_swigregister = _IMP_em.EnvelopeScore_swigregister
3138 EnvelopeScore_swigregister(EnvelopeScore)
3139 
3140 
3141 import math
3142 
3143 def write_pca_cmm(pca, fh):
3144  """Write out principal components to a file in Chimera Marker format"""
3145  eigen_values = pca.get_principal_values()
3146  eigen_vecs = pca.get_principal_components()
3147  centroid = pca.get_centroid()
3148 
3149  fh.write("<marker_set>\n")
3150  fh.write("<!-- PCA with eigen values: (%g,%g,%g) and "
3151  "centroid (%g,%g,%g) -->\n"
3152  % (math.sqrt(eigen_values[0]),
3153  math.sqrt(eigen_values[1]),
3154  math.sqrt(eigen_values[2]),
3155  centroid[0], centroid[1], centroid[2]))
3156 
3157  radius = 2.
3158 
3159  for i in range(3):
3160  val = math.sqrt(eigen_values[i])
3161  v1 = centroid - val * eigen_vecs[i]
3162  v2 = centroid + val * eigen_vecs[i]
3163  for markerid, v in ((i*2+1, v1), (i*2+2, v2)):
3164  fh.write("<marker id=\"%d\" x=\"%g\" y=\"%g\" z=\"%g\" "
3165  "radius=\"%g\"/>\n"
3166  % (markerid, v[0], v[1], v[2], radius))
3167 
3168  for i in range(1, 7, 2):
3169  fh.write("<link id1= \"%d\" id2=\"%d\" radius=\"%g\"/>\n"
3170  % (i, i+1, radius))
3171  fh.write("</marker_set>\n")
3172 
3173 
3174 def get_module_version():
3175  """get_module_version() -> std::string const"""
3176  return _IMP_em.get_module_version()
3177 
3178 def get_example_path(fname):
3179  """get_example_path(std::string fname) -> std::string"""
3180  return _IMP_em.get_example_path(fname)
3181 
3182 def get_data_path(fname):
3183  """get_data_path(std::string fname) -> std::string"""
3184  return _IMP_em.get_data_path(fname)
3185 
3186 from . import _version_check
3187 _version_check.check_version(get_module_version())
3188 __version__ = get_module_version()
3189 
3190 
3191 
double bayesem3d_linear_interpolate(const Floats &x_data, const Floats &y_data, double x, bool extrapolate)
Basic linear interpolation given vectors of values.
Float get_threshold_for_approximate_mass(DensityMap *m, Float desired_mass, atom::ProteinDensityReference ref=atom::HARPAZ)
Computes the threshold to consider in an EM map to get a desired mass.
DensityMap * interpolate_map(DensityMap *in_map, double new_spacing)
Return a new map with an updated spacing.
Particles density2particles(DensityMap *dmap, Float threshold, Model *m, int step=1)
Convert a density grid to a set of particles.
algebra::Vector3Ds density2vectors(DensityMap *dmap, Float threshold)
Convert a density grid to a set of vectors.
algebra::BoundingBoxD< 3 > get_bounding_box(const DensityMap *m, Float threshold)
Get the bounding box for a map.
std::string get_module_version()
Return the version of this module, as a string.
Ints get_numbers_of_particles_outside_of_the_density(DensityMap *dmap, const Particles &ps, const IMP::algebra::Transformation3Ds &transformations, float thr=0.0)
Get numbers of particles (mult transforms) that are outside the density.
double bayesem3d_get_logsumexp(double x, double y)
Numerically stable logsumexp.
double get_coarse_cc_coefficient(const DensityMap *grid1, const DensityMap *grid2, double grid2_voxel_data_threshold, bool allow_padding=false, FloatPair norm_factors=FloatPair(0., 0.))
Calculates the cross correlation coefficient between two maps.
Various classes to hold sets of particles.
std::vector< double > bayesem3d_get_value(Particle *p, const algebra::Vector3D &pt, double mass_ii, const IMP::em::KernelParameters &kps)
Compute the score and derivatives for a particle at a given voxel.
DensityMap * binarize(DensityMap *orig_map, float threshold, bool reverse=false)
Return a map with 0 for all voxels below the threshold and 1 for those above.
DensityMap * bayesem3d_get_density_from_particle(DensityMap *em, const IMP::ParticlesTemp &ps, double resolution)
double get_sum(const DensityMap *m1)
Return the sum of all voxels.
SampledDensityMap * particles2binarized_density(const ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
Definition: converters.h:76
Make CGAL functionality available to IMP.
std::pair< double, algebra::Vector3Ds > bayesem3d_get_score_and_derivative(DensityMap *em, const IMP::ParticlesTemp &ps, double resolution, double sigma)
The function returns the negative log of the Normal distributed difference between a normalized EM de...
DensityMap * mask_and_norm(em::DensityMap *dmap, em::DensityMap *mask)
Return a masked density, and normalize the output map within the mask region.
FittingSolutions compute_fitting_scores(const ParticlesTemp &ps, DensityMap *em_map, const algebra::Transformation3Ds &transformations, bool fast_version=false, bool local_score=false, const FloatKey &wei_key=atom::Mass::get_mass_key())
Compute fitting scores for a given set of rigid transformations.
DensityMap * get_threshold_map(const DensityMap *orig_map, float threshold)
Return a map with 0 for all voxels below the threshold.
DensityMap * get_segment_by_masking(DensityMap *map_to_segment, DensityMap *mask, float mas_threshold)
Get a segment of the map covered by another map.
FloatPair bayesem3d_get_logabssumexp(double x, double y, double sx, double sy)
Numerically stable logabssumexp.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
SampledDensityMap * particles2density(const ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
Resample a set of particles into a density grid.
double get_coarse_cc_score(DensityMap *data, SampledDensityMap *model_map, double scalefactor, bool recalc_rms=true, bool resample=true, FloatPair norm_factors=FloatPair(0., 0.))
Calculates the value of the EM fitting term.
Composable functors to implement scores via compile-time composition.
Code to compute statistical measures.
algebra::GridD< 3, algebra::DenseGridStorageD< 3, float >, float > get_grid(DensityMap *in_map)
Return a dense grid containing the voxels of the passed density map.
void bayesem3d_get_normalized_intensities(DensityMap *em, const IMP::ParticlesTemp &ps, double resolution)
FloatPair bayesem3d_get_em_density_squared(DensityMap *em, long number_of_voxels)
Compute the sum of the density and the sum of the squares of the density.
def write_pca_cmm
Write out principal components to a file in Chimera Marker format.
double convolute(const DensityMap *m1, const DensityMap *m2)
Return a convolution between density maps m1 and m2.
Common base class for heavy weight IMP objects.
Definition: Object.h:106
DensityMap * multiply(const DensityMap *m1, const DensityMap *m2)
Return a density map for which voxel i contains the result of m1[i]*m2[i].
std::map< double, int > bayesem3d_get_distinct_and_counts(DensityMap *em)
Get histogram of density in EM map.
DensityHeader create_density_header(const algebra::BoundingBoxD< 3 > &bb, float spacing)
Create a header from a bounding box in 3D.
Float compute_fitting_score(const ParticlesTemp &ps, DensityMap *em_map, FloatKey wei_key=atom::Mass::get_mass_key())
Compute fitting scores for a given set of rigid transformations.
double get_coarse_cc_local_coefficient(const DensityMap *em_map, DensityMap *model_map, double voxel_data_threshold)
Local cross correlation function.
double bayesem3d_get_cross_correlation_coefficient(const DensityMap *em1, const DensityMap *em2)
Compute a normalized cross-correlation coefficient.
Floats bayesem3d_get_cumulative_sum(DensityMap *em)
Compute the cumulative sum of the histogram computed from EM map.
FittingSolutions local_rigid_fitting_around_point(Particle *p, Refiner *refiner, const FloatKey &weight_key, DensityMap *dmap, const algebra::Vector3D &anchor_centroid, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3, bool fast=false)
Local rigid fitting of a rigid body around a center point.
double bayesem3d_get_logsumprodexp(double x, double y, double wx, double wy)
Numerically stable logsumexpprod.
std::vector< double > bayesem3d_get_value_no_deriv(Particle *p, const algebra::Vector3D &pt, double mass_ii, const IMP::em::KernelParameters &kps)
Compute the score without its derivative.
long get_number_of_particles_outside_of_the_density(DensityMap *dmap, const Particles &ps, const IMP::algebra::Transformation3D &t=IMP::algebra::get_identity_transformation_3d(), float thr=0.0)
Get the number of particles that are outside of the density.
DensityMap * get_max_map(DensityMaps maps)
Return a map where each voxel is the maximum value from the input maps.
DensityMap * create_density_map(const DensityMap *other)
Create a copy of another map.
Store data to be clustered for embedding based algorithms.
Float approximate_molecular_mass(DensityMap *m, Float threshold)
Estimate the molecular mass from a map.
std::map< double, double > bayesem3d_get_cumulative_sum_with_reference(DensityMap *em)
Compute the cumulative sum of the histogram given a reference.
double get_percentage_of_voxels_covered_by_particles(DensityMap *dmap, const Particles &ps, float smoothing_radius=3., const IMP::algebra::Transformation3D &t=IMP::algebra::get_identity_transformation_3d(), float thr=0.0)
Get the number of density voxels that are not covered by particles.
Vector3D get_centroid(const Vector3Ds &ps)
Return the centroid of a set of vectors.
Definition: Vector3D.h:68
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.
Definition: Restraint.h:54
FloatPair bayesem3d_get_logabssumprodexp(double x, double y, double wx, double wy)
Numerically stable logabssumprodexp.