IMP logo
IMP Reference Guide  2.6.1
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 2007-2016 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_GPERFTOOLS_swigconstant(_IMP_em)
269 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_em.IMP_KERNEL_HAS_GPERFTOOLS
270 
271 _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER_swigconstant(_IMP_em)
272 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
273 
274 _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER_swigconstant(_IMP_em)
275 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
276 
277 _IMP_em.IMPKERNEL_SHOW_WARNINGS_swigconstant(_IMP_em)
278 IMPKERNEL_SHOW_WARNINGS = _IMP_em.IMPKERNEL_SHOW_WARNINGS
279 
280 import sys
281 class _DirectorObjects(object):
282  """@internal Simple class to keep references to director objects
283  to prevent premature deletion."""
284  def __init__(self):
285  self._objects = []
286  def register(self, obj):
287  """Take a reference to a director object; will only work for
288  refcounted C++ classes"""
289  if hasattr(obj, 'get_ref_count'):
290  self._objects.append(obj)
291  def cleanup(self):
292  """Only drop our reference and allow cleanup by Python if no other
293  Python references exist (we hold 3 references: one in self._objects,
294  one in x, and one in the argument list for getrefcount) *and* no
295  other C++ references exist (the Python object always holds one)"""
296  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
297  or x.get_ref_count() > 1]
298 # Do in two steps so the references are kept until the end of the
299 # function (deleting references may trigger a fresh call to this method)
300  self._objects = objs
301  def get_object_count(self):
302  """Get number of director objects (useful for testing only)"""
303  return len(self._objects)
304 _director_objects = _DirectorObjects()
305 
306 class _ostream(object):
307  """Proxy of C++ std::ostream class"""
308  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
309 
310  def __init__(self, *args, **kwargs):
311  raise AttributeError("No constructor defined")
312  __repr__ = _swig_repr
313 
314  def write(self, osa_buf):
315  """write(_ostream self, char const * osa_buf)"""
316  return _IMP_em._ostream_write(self, osa_buf)
317 
318 _ostream_swigregister = _IMP_em._ostream_swigregister
319 _ostream_swigregister(_ostream)
320 
321 
322 _IMP_em.IMP_COMPILER_HAS_OVERRIDE_swigconstant(_IMP_em)
323 IMP_COMPILER_HAS_OVERRIDE = _IMP_em.IMP_COMPILER_HAS_OVERRIDE
324 
325 _IMP_em.IMP_COMPILER_HAS_FINAL_swigconstant(_IMP_em)
326 IMP_COMPILER_HAS_FINAL = _IMP_em.IMP_COMPILER_HAS_FINAL
327 
328 _IMP_em.IMP_HAS_NOEXCEPT_swigconstant(_IMP_em)
329 IMP_HAS_NOEXCEPT = _IMP_em.IMP_HAS_NOEXCEPT
330 import IMP
331 
332 _IMP_em.IMP_CGAL_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
333 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CGAL_HAS_BOOST_FILESYSTEM
334 
335 _IMP_em.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
336 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
337 
338 _IMP_em.IMP_CGAL_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
339 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_em.IMP_CGAL_HAS_BOOST_RANDOM
340 
341 _IMP_em.IMP_CGAL_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
342 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_em.IMP_CGAL_HAS_BOOST_SYSTEM
343 
344 _IMP_em.IMPCGAL_SHOW_WARNINGS_swigconstant(_IMP_em)
345 IMPCGAL_SHOW_WARNINGS = _IMP_em.IMPCGAL_SHOW_WARNINGS
346 import IMP.cgal
347 
348 _IMP_em.IMP_ALGEBRA_HAS_IMP_CGAL_swigconstant(_IMP_em)
349 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_em.IMP_ALGEBRA_HAS_IMP_CGAL
350 
351 _IMP_em.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
352 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
353 
354 _IMP_em.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
355 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
356 
357 _IMP_em.IMP_ALGEBRA_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
358 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_RANDOM
359 
360 _IMP_em.IMP_ALGEBRA_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
361 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_SYSTEM
362 
363 _IMP_em.IMP_ALGEBRA_HAS_CGAL_swigconstant(_IMP_em)
364 IMP_ALGEBRA_HAS_CGAL = _IMP_em.IMP_ALGEBRA_HAS_CGAL
365 
366 _IMP_em.IMP_ALGEBRA_HAS_ANN_swigconstant(_IMP_em)
367 IMP_ALGEBRA_HAS_ANN = _IMP_em.IMP_ALGEBRA_HAS_ANN
368 
369 _IMP_em.IMPALGEBRA_SHOW_WARNINGS_swigconstant(_IMP_em)
370 IMPALGEBRA_SHOW_WARNINGS = _IMP_em.IMPALGEBRA_SHOW_WARNINGS
371 import IMP.algebra
372 
373 _IMP_em.IMP_DISPLAY_HAS_IMP_CGAL_swigconstant(_IMP_em)
374 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_em.IMP_DISPLAY_HAS_IMP_CGAL
375 
376 _IMP_em.IMP_DISPLAY_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
377 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
378 
379 _IMP_em.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
380 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
381 
382 _IMP_em.IMP_DISPLAY_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
383 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_em.IMP_DISPLAY_HAS_BOOST_RANDOM
384 
385 _IMP_em.IMP_DISPLAY_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
386 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_em.IMP_DISPLAY_HAS_BOOST_SYSTEM
387 
388 _IMP_em.IMP_DISPLAY_HAS_CGAL_swigconstant(_IMP_em)
389 IMP_DISPLAY_HAS_CGAL = _IMP_em.IMP_DISPLAY_HAS_CGAL
390 
391 _IMP_em.IMPDISPLAY_SHOW_WARNINGS_swigconstant(_IMP_em)
392 IMPDISPLAY_SHOW_WARNINGS = _IMP_em.IMPDISPLAY_SHOW_WARNINGS
393 import IMP.display
394 
395 _IMP_em.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL_swigconstant(_IMP_em)
396 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_em.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
397 
398 _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
399 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
400 
401 _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
402 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
403 
404 _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
405 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
406 
407 _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
408 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
409 
410 _IMP_em.IMP_SCORE_FUNCTOR_HAS_CGAL_swigconstant(_IMP_em)
411 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_em.IMP_SCORE_FUNCTOR_HAS_CGAL
412 
413 _IMP_em.IMP_SCORE_FUNCTOR_HAS_HDF5_swigconstant(_IMP_em)
414 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_em.IMP_SCORE_FUNCTOR_HAS_HDF5
415 
416 _IMP_em.IMPSCOREFUNCTOR_SHOW_WARNINGS_swigconstant(_IMP_em)
417 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_em.IMPSCOREFUNCTOR_SHOW_WARNINGS
418 import IMP.score_functor
419 
420 _IMP_em.IMP_STATISTICS_HAS_IMP_CGAL_swigconstant(_IMP_em)
421 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_em.IMP_STATISTICS_HAS_IMP_CGAL
422 
423 _IMP_em.IMP_STATISTICS_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
424 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
425 
426 _IMP_em.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
427 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
428 
429 _IMP_em.IMP_STATISTICS_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
430 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_em.IMP_STATISTICS_HAS_BOOST_RANDOM
431 
432 _IMP_em.IMP_STATISTICS_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
433 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_SYSTEM
434 
435 _IMP_em.IMP_STATISTICS_HAS_CGAL_swigconstant(_IMP_em)
436 IMP_STATISTICS_HAS_CGAL = _IMP_em.IMP_STATISTICS_HAS_CGAL
437 
438 _IMP_em.IMPSTATISTICS_SHOW_WARNINGS_swigconstant(_IMP_em)
439 IMPSTATISTICS_SHOW_WARNINGS = _IMP_em.IMPSTATISTICS_SHOW_WARNINGS
440 import IMP.statistics
441 
442 _IMP_em.IMP_CORE_HAS_IMP_CGAL_swigconstant(_IMP_em)
443 IMP_CORE_HAS_IMP_CGAL = _IMP_em.IMP_CORE_HAS_IMP_CGAL
444 
445 _IMP_em.IMP_CORE_HAS_IMP_KERNEL_swigconstant(_IMP_em)
446 IMP_CORE_HAS_IMP_KERNEL = _IMP_em.IMP_CORE_HAS_IMP_KERNEL
447 
448 _IMP_em.IMP_CORE_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
449 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_FILESYSTEM
450 
451 _IMP_em.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
452 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
453 
454 _IMP_em.IMP_CORE_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
455 IMP_CORE_HAS_BOOST_RANDOM = _IMP_em.IMP_CORE_HAS_BOOST_RANDOM
456 
457 _IMP_em.IMP_CORE_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
458 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_SYSTEM
459 
460 _IMP_em.IMP_CORE_HAS_CGAL_swigconstant(_IMP_em)
461 IMP_CORE_HAS_CGAL = _IMP_em.IMP_CORE_HAS_CGAL
462 
463 _IMP_em.IMP_CORE_HAS_HDF5_swigconstant(_IMP_em)
464 IMP_CORE_HAS_HDF5 = _IMP_em.IMP_CORE_HAS_HDF5
465 
466 _IMP_em.IMPCORE_SHOW_WARNINGS_swigconstant(_IMP_em)
467 IMPCORE_SHOW_WARNINGS = _IMP_em.IMPCORE_SHOW_WARNINGS
468 import IMP.core
469 
470 _IMP_em.IMP_CONTAINER_HAS_IMP_ALGEBRA_swigconstant(_IMP_em)
471 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_em.IMP_CONTAINER_HAS_IMP_ALGEBRA
472 
473 _IMP_em.IMP_CONTAINER_HAS_IMP_CGAL_swigconstant(_IMP_em)
474 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_em.IMP_CONTAINER_HAS_IMP_CGAL
475 
476 _IMP_em.IMP_CONTAINER_HAS_IMP_DISPLAY_swigconstant(_IMP_em)
477 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_em.IMP_CONTAINER_HAS_IMP_DISPLAY
478 
479 _IMP_em.IMP_CONTAINER_HAS_IMP_KERNEL_swigconstant(_IMP_em)
480 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_em.IMP_CONTAINER_HAS_IMP_KERNEL
481 
482 _IMP_em.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_em)
483 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
484 
485 _IMP_em.IMP_CONTAINER_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
486 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
487 
488 _IMP_em.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
489 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
490 
491 _IMP_em.IMP_CONTAINER_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
492 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_em.IMP_CONTAINER_HAS_BOOST_RANDOM
493 
494 _IMP_em.IMP_CONTAINER_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
495 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_SYSTEM
496 
497 _IMP_em.IMP_CONTAINER_HAS_CGAL_swigconstant(_IMP_em)
498 IMP_CONTAINER_HAS_CGAL = _IMP_em.IMP_CONTAINER_HAS_CGAL
499 
500 _IMP_em.IMP_CONTAINER_HAS_HDF5_swigconstant(_IMP_em)
501 IMP_CONTAINER_HAS_HDF5 = _IMP_em.IMP_CONTAINER_HAS_HDF5
502 
503 _IMP_em.IMPCONTAINER_SHOW_WARNINGS_swigconstant(_IMP_em)
504 IMPCONTAINER_SHOW_WARNINGS = _IMP_em.IMPCONTAINER_SHOW_WARNINGS
505 import IMP.container
506 
507 _IMP_em.IMP_ATOM_HAS_IMP_CGAL_swigconstant(_IMP_em)
508 IMP_ATOM_HAS_IMP_CGAL = _IMP_em.IMP_ATOM_HAS_IMP_CGAL
509 
510 _IMP_em.IMP_ATOM_HAS_IMP_KERNEL_swigconstant(_IMP_em)
511 IMP_ATOM_HAS_IMP_KERNEL = _IMP_em.IMP_ATOM_HAS_IMP_KERNEL
512 
513 _IMP_em.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_em)
514 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
515 
516 _IMP_em.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
517 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
518 
519 _IMP_em.IMP_ATOM_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
520 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_em.IMP_ATOM_HAS_BOOST_RANDOM
521 
522 _IMP_em.IMP_ATOM_HAS_BOOST_REGEX_swigconstant(_IMP_em)
523 IMP_ATOM_HAS_BOOST_REGEX = _IMP_em.IMP_ATOM_HAS_BOOST_REGEX
524 
525 _IMP_em.IMP_ATOM_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
526 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_em.IMP_ATOM_HAS_BOOST_SYSTEM
527 
528 _IMP_em.IMP_ATOM_HAS_CGAL_swigconstant(_IMP_em)
529 IMP_ATOM_HAS_CGAL = _IMP_em.IMP_ATOM_HAS_CGAL
530 
531 _IMP_em.IMP_ATOM_HAS_HDF5_swigconstant(_IMP_em)
532 IMP_ATOM_HAS_HDF5 = _IMP_em.IMP_ATOM_HAS_HDF5
533 
534 _IMP_em.IMPATOM_SHOW_WARNINGS_swigconstant(_IMP_em)
535 IMPATOM_SHOW_WARNINGS = _IMP_em.IMPATOM_SHOW_WARNINGS
536 
537 _IMP_em.IMP_ATOM_TYPE_INDEX_swigconstant(_IMP_em)
538 IMP_ATOM_TYPE_INDEX = _IMP_em.IMP_ATOM_TYPE_INDEX
539 
540 _IMP_em.IMP_RESIDUE_TYPE_INDEX_swigconstant(_IMP_em)
541 IMP_RESIDUE_TYPE_INDEX = _IMP_em.IMP_RESIDUE_TYPE_INDEX
542 
543 _IMP_em.IMP_HIERARCHY_TYPE_INDEX_swigconstant(_IMP_em)
544 IMP_HIERARCHY_TYPE_INDEX = _IMP_em.IMP_HIERARCHY_TYPE_INDEX
545 import IMP.atom
546 
547 _IMP_em.IMP_EM_HAS_IMP_CGAL_swigconstant(_IMP_em)
548 IMP_EM_HAS_IMP_CGAL = _IMP_em.IMP_EM_HAS_IMP_CGAL
549 
550 _IMP_em.IMP_EM_HAS_IMP_CONTAINER_swigconstant(_IMP_em)
551 IMP_EM_HAS_IMP_CONTAINER = _IMP_em.IMP_EM_HAS_IMP_CONTAINER
552 
553 _IMP_em.IMP_EM_HAS_IMP_DISPLAY_swigconstant(_IMP_em)
554 IMP_EM_HAS_IMP_DISPLAY = _IMP_em.IMP_EM_HAS_IMP_DISPLAY
555 
556 _IMP_em.IMP_EM_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_em)
557 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_EM_HAS_IMP_SCORE_FUNCTOR
558 
559 _IMP_em.IMP_EM_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_em)
560 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_EM_HAS_BOOST_FILESYSTEM
561 
562 _IMP_em.IMP_EM_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_em)
563 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
564 
565 _IMP_em.IMP_EM_HAS_BOOST_RANDOM_swigconstant(_IMP_em)
566 IMP_EM_HAS_BOOST_RANDOM = _IMP_em.IMP_EM_HAS_BOOST_RANDOM
567 
568 _IMP_em.IMP_EM_HAS_BOOST_REGEX_swigconstant(_IMP_em)
569 IMP_EM_HAS_BOOST_REGEX = _IMP_em.IMP_EM_HAS_BOOST_REGEX
570 
571 _IMP_em.IMP_EM_HAS_BOOST_SYSTEM_swigconstant(_IMP_em)
572 IMP_EM_HAS_BOOST_SYSTEM = _IMP_em.IMP_EM_HAS_BOOST_SYSTEM
573 
574 _IMP_em.IMP_EM_HAS_CGAL_swigconstant(_IMP_em)
575 IMP_EM_HAS_CGAL = _IMP_em.IMP_EM_HAS_CGAL
576 
577 _IMP_em.IMP_EM_HAS_HDF5_swigconstant(_IMP_em)
578 IMP_EM_HAS_HDF5 = _IMP_em.IMP_EM_HAS_HDF5
579 
580 _IMP_em.IMPEM_SHOW_WARNINGS_swigconstant(_IMP_em)
581 IMPEM_SHOW_WARNINGS = _IMP_em.IMPEM_SHOW_WARNINGS
582 
583 _object_types.append("DensityMap")
584 
585 
586 def _object_cast_to_DensityMap(o):
587  """_object_cast_to_DensityMap(Object o) -> DensityMap"""
588  return _IMP_em._object_cast_to_DensityMap(o)
589 
590 _object_types.append("SampledDensityMap")
591 
592 
593 def _object_cast_to_SampledDensityMap(o):
594  """_object_cast_to_SampledDensityMap(Object o) -> SampledDensityMap"""
595  return _IMP_em._object_cast_to_SampledDensityMap(o)
596 
597 _object_types.append("SurfaceShellDensityMap")
598 
599 
600 def _object_cast_to_SurfaceShellDensityMap(o):
601  """_object_cast_to_SurfaceShellDensityMap(Object o) -> SurfaceShellDensityMap"""
602  return _IMP_em._object_cast_to_SurfaceShellDensityMap(o)
603 
604 _object_types.append("FitRestraint")
605 
606 
607 def _object_cast_to_FitRestraint(o):
608  """_object_cast_to_FitRestraint(Object o) -> FitRestraint"""
609  return _IMP_em._object_cast_to_FitRestraint(o)
610 
611 _object_types.append("PCAFitRestraint")
612 
613 
614 def _object_cast_to_PCAFitRestraint(o):
615  """_object_cast_to_PCAFitRestraint(Object o) -> PCAFitRestraint"""
616  return _IMP_em._object_cast_to_PCAFitRestraint(o)
617 
618 _object_types.append("EnvelopePenetrationRestraint")
619 
620 
621 def _object_cast_to_EnvelopePenetrationRestraint(o):
622  """_object_cast_to_EnvelopePenetrationRestraint(Object o) -> EnvelopePenetrationRestraint"""
623  return _IMP_em._object_cast_to_EnvelopePenetrationRestraint(o)
624 
625 _object_types.append("EnvelopeFitRestraint")
626 
627 
628 def _object_cast_to_EnvelopeFitRestraint(o):
629  """_object_cast_to_EnvelopeFitRestraint(Object o) -> EnvelopeFitRestraint"""
630  return _IMP_em._object_cast_to_EnvelopeFitRestraint(o)
631 
632 KernelParametersList=list
633 _plural_types.append("KernelParametersList")
634 _value_types.append("KernelParameters")
635 
636 
637 _object_types.append("HighDensityEmbedding")
638 
639 
640 def _object_cast_to_HighDensityEmbedding(o):
641  """_object_cast_to_HighDensityEmbedding(Object o) -> HighDensityEmbedding"""
642  return _IMP_em._object_cast_to_HighDensityEmbedding(o)
643 
644 _object_types.append("MapReaderWriter")
645 
646 
647 def _object_cast_to_MapReaderWriter(o):
648  """_object_cast_to_MapReaderWriter(Object o) -> MapReaderWriter"""
649  return _IMP_em._object_cast_to_MapReaderWriter(o)
650 
651 _object_types.append("MRCReaderWriter")
652 
653 
654 def _object_cast_to_MRCReaderWriter(o):
655  """_object_cast_to_MRCReaderWriter(Object o) -> MRCReaderWriter"""
656  return _IMP_em._object_cast_to_MRCReaderWriter(o)
657 
658 _object_types.append("SpiderMapReaderWriter")
659 
660 
661 def _object_cast_to_SpiderMapReaderWriter(o):
662  """_object_cast_to_SpiderMapReaderWriter(Object o) -> SpiderMapReaderWriter"""
663  return _IMP_em._object_cast_to_SpiderMapReaderWriter(o)
664 
665 _object_types.append("EMReaderWriter")
666 
667 
668 def _object_cast_to_EMReaderWriter(o):
669  """_object_cast_to_EMReaderWriter(Object o) -> EMReaderWriter"""
670  return _IMP_em._object_cast_to_EMReaderWriter(o)
671 
672 _object_types.append("XplorReaderWriter")
673 
674 
675 def _object_cast_to_XplorReaderWriter(o):
676  """_object_cast_to_XplorReaderWriter(Object o) -> XplorReaderWriter"""
677  return _IMP_em._object_cast_to_XplorReaderWriter(o)
678 
679 _object_types.append("CoarseCC")
680 
681 
682 def _object_cast_to_CoarseCC(o):
683  """_object_cast_to_CoarseCC(Object o) -> CoarseCC"""
684  return _IMP_em._object_cast_to_CoarseCC(o)
685 
686 _object_types.append("CoarseCCatIntervals")
687 
688 
689 def _object_cast_to_CoarseCCatIntervals(o):
690  """_object_cast_to_CoarseCCatIntervals(Object o) -> CoarseCCatIntervals"""
691  return _IMP_em._object_cast_to_CoarseCCatIntervals(o)
692 
693 FittingSolutionsList=list
694 _plural_types.append("FittingSolutionsList")
695 _value_types.append("FittingSolutions")
696 
697 class MapReaderWriter(IMP.Object):
698  """Proxy of C++ IMP::em::MapReaderWriter class"""
699  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
700 
701  def __init__(self):
702  """__init__(IMP::em::MapReaderWriter self) -> MapReaderWriter"""
703  this = _IMP_em.new_MapReaderWriter()
704  try:
705  self.this.append(this)
706  except:
707  self.this = this
708 
709  def get_version_info(self):
710  """get_version_info(MapReaderWriter self) -> VersionInfo"""
711  return _IMP_em.MapReaderWriter_get_version_info(self)
712 
713 
714  def __str__(self):
715  """__str__(MapReaderWriter self) -> std::string"""
716  return _IMP_em.MapReaderWriter___str__(self)
717 
718 
719  def __repr__(self):
720  """__repr__(MapReaderWriter self) -> std::string"""
721  return _IMP_em.MapReaderWriter___repr__(self)
722 
723 
724  @staticmethod
725  def get_from(o):
726  return _object_cast_to_MapReaderWriter(o)
727 
728 MapReaderWriter_swigregister = _IMP_em.MapReaderWriter_swigregister
729 MapReaderWriter_swigregister(MapReaderWriter)
730 cvar = _IMP_em.cvar
731 EPS = cvar.EPS
732 
733 class DensityHeader(object):
734  """Proxy of C++ IMP::em::DensityHeader class"""
735  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
736  __repr__ = _swig_repr
737 
738  def __init__(self):
739  """__init__(IMP::em::DensityHeader self) -> DensityHeader"""
740  this = _IMP_em.new_DensityHeader()
741  try:
742  self.this.append(this)
743  except:
744  self.this = this
745 
746  def get_top(self, ind):
747  """get_top(DensityHeader self, int ind) -> IMP::em::emreal"""
748  return _IMP_em.DensityHeader_get_top(self, ind)
749 
750 
751  def compute_xyz_top(self, force=False):
752  """
753  compute_xyz_top(DensityHeader self, bool force=False)
754  compute_xyz_top(DensityHeader self)
755  """
756  return _IMP_em.DensityHeader_compute_xyz_top(self, force)
757 
758 
759  def update_map_dimensions(self, nnx, nny, nnz):
760  """update_map_dimensions(DensityHeader self, int nnx, int nny, int nnz)"""
761  return _IMP_em.DensityHeader_update_map_dimensions(self, nnx, nny, nnz)
762 
763 
764  def update_cell_dimensions(self):
765  """update_cell_dimensions(DensityHeader self)"""
766  return _IMP_em.DensityHeader_update_cell_dimensions(self)
767 
768 
769  def show(self, *args):
770  """
771  show(DensityHeader self, _ostream out)
772  show(DensityHeader self)
773  """
774  return _IMP_em.DensityHeader_show(self, *args)
775 
776  MAP_FIELD_SIZE = _IMP_em.DensityHeader_MAP_FIELD_SIZE
777  USER_FIELD_SIZE = _IMP_em.DensityHeader_USER_FIELD_SIZE
778  COMMENT_FIELD_NUM_OF = _IMP_em.DensityHeader_COMMENT_FIELD_NUM_OF
779  COMMENT_FIELD_SINGLE_SIZE = _IMP_em.DensityHeader_COMMENT_FIELD_SINGLE_SIZE
780  nxstart = _swig_property(_IMP_em.DensityHeader_nxstart_get, _IMP_em.DensityHeader_nxstart_set)
781  nystart = _swig_property(_IMP_em.DensityHeader_nystart_get, _IMP_em.DensityHeader_nystart_set)
782  nzstart = _swig_property(_IMP_em.DensityHeader_nzstart_get, _IMP_em.DensityHeader_nzstart_set)
783  mx = _swig_property(_IMP_em.DensityHeader_mx_get, _IMP_em.DensityHeader_mx_set)
784  my = _swig_property(_IMP_em.DensityHeader_my_get, _IMP_em.DensityHeader_my_set)
785  mz = _swig_property(_IMP_em.DensityHeader_mz_get, _IMP_em.DensityHeader_mz_set)
786  xlen = _swig_property(_IMP_em.DensityHeader_xlen_get, _IMP_em.DensityHeader_xlen_set)
787  ylen = _swig_property(_IMP_em.DensityHeader_ylen_get, _IMP_em.DensityHeader_ylen_set)
788  zlen = _swig_property(_IMP_em.DensityHeader_zlen_get, _IMP_em.DensityHeader_zlen_set)
789  alpha = _swig_property(_IMP_em.DensityHeader_alpha_get, _IMP_em.DensityHeader_alpha_set)
790  beta = _swig_property(_IMP_em.DensityHeader_beta_get, _IMP_em.DensityHeader_beta_set)
791  gamma = _swig_property(_IMP_em.DensityHeader_gamma_get, _IMP_em.DensityHeader_gamma_set)
792  mapc = _swig_property(_IMP_em.DensityHeader_mapc_get, _IMP_em.DensityHeader_mapc_set)
793  mapr = _swig_property(_IMP_em.DensityHeader_mapr_get, _IMP_em.DensityHeader_mapr_set)
794  maps = _swig_property(_IMP_em.DensityHeader_maps_get, _IMP_em.DensityHeader_maps_set)
795  dmin = _swig_property(_IMP_em.DensityHeader_dmin_get, _IMP_em.DensityHeader_dmin_set)
796  dmax = _swig_property(_IMP_em.DensityHeader_dmax_get, _IMP_em.DensityHeader_dmax_set)
797  dmean = _swig_property(_IMP_em.DensityHeader_dmean_get, _IMP_em.DensityHeader_dmean_set)
798  ispg = _swig_property(_IMP_em.DensityHeader_ispg_get, _IMP_em.DensityHeader_ispg_set)
799  nsymbt = _swig_property(_IMP_em.DensityHeader_nsymbt_get, _IMP_em.DensityHeader_nsymbt_set)
800  user = _swig_property(_IMP_em.DensityHeader_user_get, _IMP_em.DensityHeader_user_set)
801  map = _swig_property(_IMP_em.DensityHeader_map_get, _IMP_em.DensityHeader_map_set)
802  machinestamp = _swig_property(_IMP_em.DensityHeader_machinestamp_get, _IMP_em.DensityHeader_machinestamp_set)
803  rms = _swig_property(_IMP_em.DensityHeader_rms_get, _IMP_em.DensityHeader_rms_set)
804  nlabl = _swig_property(_IMP_em.DensityHeader_nlabl_get, _IMP_em.DensityHeader_nlabl_set)
805  comments = _swig_property(_IMP_em.DensityHeader_comments_get, _IMP_em.DensityHeader_comments_set)
806  magic = _swig_property(_IMP_em.DensityHeader_magic_get, _IMP_em.DensityHeader_magic_set)
807  voltage = _swig_property(_IMP_em.DensityHeader_voltage_get, _IMP_em.DensityHeader_voltage_set)
808  Cs = _swig_property(_IMP_em.DensityHeader_Cs_get, _IMP_em.DensityHeader_Cs_set)
809  Aperture = _swig_property(_IMP_em.DensityHeader_Aperture_get, _IMP_em.DensityHeader_Aperture_set)
810  Magnification = _swig_property(_IMP_em.DensityHeader_Magnification_get, _IMP_em.DensityHeader_Magnification_set)
811  Postmagnification = _swig_property(_IMP_em.DensityHeader_Postmagnification_get, _IMP_em.DensityHeader_Postmagnification_set)
812  Exposuretime = _swig_property(_IMP_em.DensityHeader_Exposuretime_get, _IMP_em.DensityHeader_Exposuretime_set)
813  Microscope = _swig_property(_IMP_em.DensityHeader_Microscope_get, _IMP_em.DensityHeader_Microscope_set)
814  Pixelsize = _swig_property(_IMP_em.DensityHeader_Pixelsize_get, _IMP_em.DensityHeader_Pixelsize_set)
815  CCDArea = _swig_property(_IMP_em.DensityHeader_CCDArea_get, _IMP_em.DensityHeader_CCDArea_set)
816  Defocus = _swig_property(_IMP_em.DensityHeader_Defocus_get, _IMP_em.DensityHeader_Defocus_set)
817  Astigmatism = _swig_property(_IMP_em.DensityHeader_Astigmatism_get, _IMP_em.DensityHeader_Astigmatism_set)
818  AstigmatismAngle = _swig_property(_IMP_em.DensityHeader_AstigmatismAngle_get, _IMP_em.DensityHeader_AstigmatismAngle_set)
819  FocusIncrement = _swig_property(_IMP_em.DensityHeader_FocusIncrement_get, _IMP_em.DensityHeader_FocusIncrement_set)
820  CountsPerElectron = _swig_property(_IMP_em.DensityHeader_CountsPerElectron_get, _IMP_em.DensityHeader_CountsPerElectron_set)
821  Intensity = _swig_property(_IMP_em.DensityHeader_Intensity_get, _IMP_em.DensityHeader_Intensity_set)
822  EnergySlitwidth = _swig_property(_IMP_em.DensityHeader_EnergySlitwidth_get, _IMP_em.DensityHeader_EnergySlitwidth_set)
823  EnergyOffset = _swig_property(_IMP_em.DensityHeader_EnergyOffset_get, _IMP_em.DensityHeader_EnergyOffset_set)
824  Tiltangle = _swig_property(_IMP_em.DensityHeader_Tiltangle_get, _IMP_em.DensityHeader_Tiltangle_set)
825  Tiltaxis = _swig_property(_IMP_em.DensityHeader_Tiltaxis_get, _IMP_em.DensityHeader_Tiltaxis_set)
826  MarkerX = _swig_property(_IMP_em.DensityHeader_MarkerX_get, _IMP_em.DensityHeader_MarkerX_set)
827  MarkerY = _swig_property(_IMP_em.DensityHeader_MarkerY_get, _IMP_em.DensityHeader_MarkerY_set)
828  lswap = _swig_property(_IMP_em.DensityHeader_lswap_get, _IMP_em.DensityHeader_lswap_set)
829 
830  def get_resolution(self):
831  """get_resolution(DensityHeader self) -> float"""
832  return _IMP_em.DensityHeader_get_resolution(self)
833 
834 
835  def get_has_resolution(self):
836  """get_has_resolution(DensityHeader self) -> bool"""
837  return _IMP_em.DensityHeader_get_has_resolution(self)
838 
839 
840  def set_resolution(self, resolution):
841  """set_resolution(DensityHeader self, float resolution)"""
842  return _IMP_em.DensityHeader_set_resolution(self, resolution)
843 
844 
845  def get_spacing(self):
846  """get_spacing(DensityHeader self) -> float"""
847  return _IMP_em.DensityHeader_get_spacing(self)
848 
849 
850  def get_xorigin(self):
851  """get_xorigin(DensityHeader self) -> float"""
852  return _IMP_em.DensityHeader_get_xorigin(self)
853 
854 
855  def get_yorigin(self):
856  """get_yorigin(DensityHeader self) -> float"""
857  return _IMP_em.DensityHeader_get_yorigin(self)
858 
859 
860  def get_zorigin(self):
861  """get_zorigin(DensityHeader self) -> float"""
862  return _IMP_em.DensityHeader_get_zorigin(self)
863 
864 
865  def get_origin(self, i):
866  """get_origin(DensityHeader self, int i) -> float"""
867  return _IMP_em.DensityHeader_get_origin(self, i)
868 
869 
870  def set_xorigin(self, x):
871  """set_xorigin(DensityHeader self, float x)"""
872  return _IMP_em.DensityHeader_set_xorigin(self, x)
873 
874 
875  def set_yorigin(self, y):
876  """set_yorigin(DensityHeader self, float y)"""
877  return _IMP_em.DensityHeader_set_yorigin(self, y)
878 
879 
880  def set_zorigin(self, z):
881  """set_zorigin(DensityHeader self, float z)"""
882  return _IMP_em.DensityHeader_set_zorigin(self, z)
883 
884 
885  def is_top_calculated(self):
886  """is_top_calculated(DensityHeader self) -> bool"""
887  return _IMP_em.DensityHeader_is_top_calculated(self)
888 
889  Objectpixelsize_ = _swig_property(_IMP_em.DensityHeader_Objectpixelsize__get, _IMP_em.DensityHeader_Objectpixelsize__set)
890 
891  def get_nx(self):
892  """get_nx(DensityHeader self) -> int"""
893  return _IMP_em.DensityHeader_get_nx(self)
894 
895 
896  def get_ny(self):
897  """get_ny(DensityHeader self) -> int"""
898  return _IMP_em.DensityHeader_get_ny(self)
899 
900 
901  def get_nz(self):
902  """get_nz(DensityHeader self) -> int"""
903  return _IMP_em.DensityHeader_get_nz(self)
904 
905 
906  def get_number_of_voxels(self):
907  """get_number_of_voxels(DensityHeader self) -> int"""
908  return _IMP_em.DensityHeader_get_number_of_voxels(self)
909 
910 
911  def get_data_type(self):
912  """get_data_type(DensityHeader self) -> int"""
913  return _IMP_em.DensityHeader_get_data_type(self)
914 
915 
916  def set_data_type(self, data_type):
917  """set_data_type(DensityHeader self, int data_type)"""
918  return _IMP_em.DensityHeader_set_data_type(self, data_type)
919 
920  __swig_destroy__ = _IMP_em.delete_DensityHeader
921  __del__ = lambda self: None
922 DensityHeader_swigregister = _IMP_em.DensityHeader_swigregister
923 DensityHeader_swigregister(DensityHeader)
924 
925 
926 def create_density_header(bb, spacing):
927  """create_density_header(BoundingBox3D bb, float spacing) -> DensityHeader"""
928  return _IMP_em.create_density_header(bb, spacing)
929 
930 def read_map(*args):
931  """
932  read_map(std::string filename, MapReaderWriter reader) -> DensityMap
933  read_map(std::string filename) -> DensityMap
934  """
935  return _IMP_em.read_map(*args)
936 
937 def write_map(*args):
938  """
939  write_map(DensityMap m, std::string filename, MapReaderWriter writer)
940  write_map(DensityMap m, std::string filename)
941  """
942  return _IMP_em.write_map(*args)
943 
944 def approximate_molecular_mass(m, threshold):
945  """approximate_molecular_mass(DensityMap m, IMP::Float threshold) -> IMP::Float"""
946  return _IMP_em.approximate_molecular_mass(m, threshold)
947 class DensityMap(IMP.Object):
948  """Proxy of C++ IMP::em::DensityMap class"""
949  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
950 
951  def __init__(self, *args):
952  """
953  __init__(IMP::em::DensityMap self, std::string name) -> DensityMap
954  __init__(IMP::em::DensityMap self) -> DensityMap
955  __init__(IMP::em::DensityMap self, DensityHeader header, std::string name) -> DensityMap
956  __init__(IMP::em::DensityMap self, DensityHeader header) -> DensityMap
957  """
958  this = _IMP_em.new_DensityMap(*args)
959  try:
960  self.this.append(this)
961  except:
962  self.this = this
963 
964  def reset_data(self, value=0.0):
965  """
966  reset_data(DensityMap self, float value=0.0)
967  reset_data(DensityMap self)
968  """
969  return _IMP_em.DensityMap_reset_data(self, value)
970 
971 
972  def calcRMS(self):
973  """calcRMS(DensityMap self) -> IMP::em::emreal"""
974  return _IMP_em.DensityMap_calcRMS(self)
975 
976 
977  def std_normalize(self):
978  """std_normalize(DensityMap self)"""
979  return _IMP_em.DensityMap_std_normalize(self)
980 
981 
982  def is_normalized(self):
983  """is_normalized(DensityMap self) -> bool"""
984  return _IMP_em.DensityMap_is_normalized(self)
985 
986 
987  def get_location_in_dim_by_voxel(self, index, dim):
988  """get_location_in_dim_by_voxel(DensityMap self, long index, int dim) -> float"""
989  return _IMP_em.DensityMap_get_location_in_dim_by_voxel(self, index, dim)
990 
991 
992  def xyz_ind2voxel(self, x, y, z):
993  """xyz_ind2voxel(DensityMap self, int x, int y, int z) -> long"""
994  return _IMP_em.DensityMap_xyz_ind2voxel(self, x, y, z)
995 
996 
997  def get_voxel_by_location(self, *args):
998  """
999  get_voxel_by_location(DensityMap self, float x, float y, float z) -> long
1000  get_voxel_by_location(DensityMap self, Vector3D v) -> long
1001  """
1002  return _IMP_em.DensityMap_get_voxel_by_location(self, *args)
1003 
1004 
1005  def get_location_by_voxel(self, index):
1006  """get_location_by_voxel(DensityMap self, long index) -> Vector3D"""
1007  return _IMP_em.DensityMap_get_location_by_voxel(self, index)
1008 
1009 
1010  def is_xyz_ind_part_of_volume(self, ix, iy, iz):
1011  """is_xyz_ind_part_of_volume(DensityMap self, int ix, int iy, int iz) -> bool"""
1012  return _IMP_em.DensityMap_is_xyz_ind_part_of_volume(self, ix, iy, iz)
1013 
1014 
1015  def is_part_of_volume(self, *args):
1016  """
1017  is_part_of_volume(DensityMap self, float x, float y, float z) -> bool
1018  is_part_of_volume(DensityMap self, Vector3D v) -> bool
1019  """
1020  return _IMP_em.DensityMap_is_part_of_volume(self, *args)
1021 
1022 
1023  def get_value(self, *args):
1024  """
1025  get_value(DensityMap self, float x, float y, float z) -> IMP::em::emreal
1026  get_value(DensityMap self, Vector3D point) -> IMP::em::emreal
1027  get_value(DensityMap self, long index) -> IMP::em::emreal
1028  """
1029  return _IMP_em.DensityMap_get_value(self, *args)
1030 
1031 
1032  def set_value(self, *args):
1033  """
1034  set_value(DensityMap self, long index, IMP::em::emreal value)
1035  set_value(DensityMap self, float x, float y, float z, IMP::em::emreal value)
1036  """
1037  return _IMP_em.DensityMap_set_value(self, *args)
1038 
1039 
1040  def set_origin(self, *args):
1041  """
1042  set_origin(DensityMap self, float x, float y, float z)
1043  set_origin(DensityMap self, Vector3D v)
1044  """
1045  return _IMP_em.DensityMap_set_origin(self, *args)
1046 
1047 
1048  def get_origin(self):
1049  """get_origin(DensityMap self) -> Vector3D"""
1050  return _IMP_em.DensityMap_get_origin(self)
1051 
1052 
1053  def get_top(self):
1054  """get_top(DensityMap self) -> Vector3D"""
1055  return _IMP_em.DensityMap_get_top(self)
1056 
1057 
1058  def get_header(self):
1059  h = _IMP_em.DensityMap_get_header(self)
1060  h._owner = self
1061  return h
1062 
1063 
1064 
1065  def get_header_writable(self):
1066  h = _IMP_em.DensityMap_get_header_writable(self)
1067  h._owner = self
1068  return h
1069 
1070 
1071 
1072  def same_origin(self, other):
1073  """same_origin(DensityMap self, DensityMap other) -> bool"""
1074  return _IMP_em.DensityMap_same_origin(self, other)
1075 
1076 
1077  def same_dimensions(self, other):
1078  """same_dimensions(DensityMap self, DensityMap other) -> bool"""
1079  return _IMP_em.DensityMap_same_dimensions(self, other)
1080 
1081 
1082  def same_voxel_size(self, other):
1083  """same_voxel_size(DensityMap self, DensityMap other) -> bool"""
1084  return _IMP_em.DensityMap_same_voxel_size(self, other)
1085 
1086 
1087  def get_centroid(self, threshold=0.0):
1088  """
1089  get_centroid(DensityMap self, IMP::em::emreal threshold=0.0) -> Vector3D
1090  get_centroid(DensityMap self) -> Vector3D
1091  """
1092  return _IMP_em.DensityMap_get_centroid(self, threshold)
1093 
1094 
1095  def get_max_value(self):
1096  """get_max_value(DensityMap self) -> IMP::em::emreal"""
1097  return _IMP_em.DensityMap_get_max_value(self)
1098 
1099 
1100  def get_min_value(self):
1101  """get_min_value(DensityMap self) -> IMP::em::emreal"""
1102  return _IMP_em.DensityMap_get_min_value(self)
1103 
1104 
1105  def add(self, other):
1106  """add(DensityMap self, DensityMap other)"""
1107  return _IMP_em.DensityMap_add(self, other)
1108 
1109 
1110  def pick_max(self, other):
1111  """pick_max(DensityMap self, DensityMap other)"""
1112  return _IMP_em.DensityMap_pick_max(self, other)
1113 
1114 
1115  def get_number_of_voxels(self):
1116  """get_number_of_voxels(DensityMap self) -> long"""
1117  return _IMP_em.DensityMap_get_number_of_voxels(self)
1118 
1119 
1120  def set_void_map(self, nx, ny, nz):
1121  """set_void_map(DensityMap self, int nx, int ny, int nz)"""
1122  return _IMP_em.DensityMap_set_void_map(self, nx, ny, nz)
1123 
1124 
1125  def pad(self, nx, ny, nz, val=0.0):
1126  """
1127  pad(DensityMap self, int nx, int ny, int nz, float val=0.0)
1128  pad(DensityMap self, int nx, int ny, int nz)
1129  """
1130  return _IMP_em.DensityMap_pad(self, nx, ny, nz, val)
1131 
1132 
1133  def pad_margin(self, mrg_x, mrg_y, mrg_z, val=0.0):
1134  """
1135  pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z, float val=0.0) -> DensityMap
1136  pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z) -> DensityMap
1137  """
1138  return _IMP_em.DensityMap_pad_margin(self, mrg_x, mrg_y, mrg_z, val)
1139 
1140 
1141  def get_cropped(self, *args):
1142  """
1143  get_cropped(DensityMap self, float threshold) -> DensityMap
1144  get_cropped(DensityMap self, BoundingBox3D bb) -> DensityMap
1145  """
1146  return _IMP_em.DensityMap_get_cropped(self, *args)
1147 
1148 
1149  def get_maximum_value_in_xy_plane(self, z_ind):
1150  """get_maximum_value_in_xy_plane(DensityMap self, int z_ind) -> float"""
1151  return _IMP_em.DensityMap_get_maximum_value_in_xy_plane(self, z_ind)
1152 
1153 
1154  def get_maximum_value_in_xz_plane(self, y_ind):
1155  """get_maximum_value_in_xz_plane(DensityMap self, int y_ind) -> float"""
1156  return _IMP_em.DensityMap_get_maximum_value_in_xz_plane(self, y_ind)
1157 
1158 
1159  def get_maximum_value_in_yz_plane(self, x_ind):
1160  """get_maximum_value_in_yz_plane(DensityMap self, int x_ind) -> float"""
1161  return _IMP_em.DensityMap_get_maximum_value_in_yz_plane(self, x_ind)
1162 
1163 
1164  def multiply(self, factor):
1165  """multiply(DensityMap self, float factor)"""
1166  return _IMP_em.DensityMap_multiply(self, factor)
1167 
1168 
1169  def get_locations_string(self, t):
1170  """get_locations_string(DensityMap self, float t) -> std::string"""
1171  return _IMP_em.DensityMap_get_locations_string(self, t)
1172 
1173 
1174  def update_voxel_size(self, new_apix):
1175  """update_voxel_size(DensityMap self, float new_apix)"""
1176  return _IMP_em.DensityMap_update_voxel_size(self, new_apix)
1177 
1178 
1179  def get_spacing(self):
1180  """get_spacing(DensityMap self) -> IMP::Float"""
1181  return _IMP_em.DensityMap_get_spacing(self)
1182 
1183 
1184  def calc_all_voxel2loc(self):
1185  """calc_all_voxel2loc(DensityMap self)"""
1186  return _IMP_em.DensityMap_calc_all_voxel2loc(self)
1187 
1188 
1189  def copy_map(self, other):
1190  """copy_map(DensityMap self, DensityMap other)"""
1191  return _IMP_em.DensityMap_copy_map(self, other)
1192 
1193 
1194  def get_version_info(self):
1195  """get_version_info(DensityMap self) -> VersionInfo"""
1196  return _IMP_em.DensityMap_get_version_info(self)
1197 
1198 
1199  def lower_voxel_shift(self, loc, kdist, orig, ndim):
1200  """lower_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
1201  return _IMP_em.DensityMap_lower_voxel_shift(self, loc, kdist, orig, ndim)
1202 
1203 
1204  def upper_voxel_shift(self, loc, kdist, orig, ndim):
1205  """upper_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
1206  return _IMP_em.DensityMap_upper_voxel_shift(self, loc, kdist, orig, ndim)
1207 
1208 
1209  def get_rms_calculated(self):
1210  """get_rms_calculated(DensityMap self) -> bool"""
1211  return _IMP_em.DensityMap_get_rms_calculated(self)
1212 
1213 
1214  def get_dim_index_by_location(self, *args):
1215  """
1216  get_dim_index_by_location(DensityMap self, Vector3D v, int ind) -> int
1217  get_dim_index_by_location(DensityMap self, float loc_val, int ind) -> int
1218  """
1219  return _IMP_em.DensityMap_get_dim_index_by_location(self, *args)
1220 
1221 
1222  def __str__(self):
1223  """__str__(DensityMap self) -> std::string"""
1224  return _IMP_em.DensityMap___str__(self)
1225 
1226 
1227  def __repr__(self):
1228  """__repr__(DensityMap self) -> std::string"""
1229  return _IMP_em.DensityMap___repr__(self)
1230 
1231 
1232  @staticmethod
1233  def get_from(o):
1234  return _object_cast_to_DensityMap(o)
1235 
1236 DensityMap_swigregister = _IMP_em.DensityMap_swigregister
1237 DensityMap_swigregister(DensityMap)
1238 
1239 
1240 def get_bounding_box(*args):
1241  """
1242  get_bounding_box(DensityMap m, IMP::Float threshold) -> BoundingBox3D
1243  get_bounding_box(DensityMap m) -> BoundingBox3D
1244  """
1245  return _IMP_em.get_bounding_box(*args)
1246 
1247 def get_density(m, v):
1248  """get_density(DensityMap m, Vector3D v) -> double"""
1249  return _IMP_em.get_density(m, v)
1250 
1251 def get_transformed(*args):
1252  """
1253  get_transformed(DensityMap input, Transformation3D tr, double threshold) -> DensityMap
1254  get_transformed(DensityMap input, Transformation3D tr) -> DensityMap
1255  """
1256  return _IMP_em.get_transformed(*args)
1257 
1258 def get_resampled(input, scaling):
1259  """get_resampled(DensityMap input, double scaling) -> DensityMap"""
1260  return _IMP_em.get_resampled(input, scaling)
1261 
1262 def get_transformed_into(source, tr, into, calc_rms=True):
1263  """
1264  get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into, bool calc_rms=True)
1265  get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into)
1266  """
1267  return _IMP_em.get_transformed_into(source, tr, into, calc_rms)
1268 
1269 def get_transformed_into2(source, tr, into):
1270  """get_transformed_into2(DensityMap source, Transformation3D tr, DensityMap into)"""
1271  return _IMP_em.get_transformed_into2(source, tr, into)
1272 
1273 def get_interiors_intersect(d1, d2):
1274  """get_interiors_intersect(DensityMap d1, DensityMap d2) -> bool"""
1275  return _IMP_em.get_interiors_intersect(d1, d2)
1276 
1277 def get_segment(*args):
1278  """
1279  get_segment(DensityMap map_to_segment, int nx_start, int nx_end, int ny_start, int ny_end, int nz_start, int nz_end) -> DensityMap
1280  get_segment(DensityMap map_to_segment, IMP::algebra::Vector3Ds vecs, float dist) -> DensityMap
1281  """
1282  return _IMP_em.get_segment(*args)
1283 
1284 def get_segment_by_masking(map_to_segment, mask, mas_threshold):
1285  """get_segment_by_masking(DensityMap map_to_segment, DensityMap mask, float mas_threshold) -> DensityMap"""
1286  return _IMP_em.get_segment_by_masking(map_to_segment, mask, mas_threshold)
1287 
1288 def binarize(orig_map, threshold, reverse=False):
1289  """
1290  binarize(DensityMap orig_map, float threshold, bool reverse=False) -> DensityMap
1291  binarize(DensityMap orig_map, float threshold) -> DensityMap
1292  """
1293  return _IMP_em.binarize(orig_map, threshold, reverse)
1294 
1295 def get_threshold_map(orig_map, threshold):
1296  """get_threshold_map(DensityMap orig_map, float threshold) -> DensityMap"""
1297  return _IMP_em.get_threshold_map(orig_map, threshold)
1298 
1299 def multiply(m1, m2):
1300  """multiply(DensityMap m1, DensityMap m2) -> DensityMap"""
1301  return _IMP_em.multiply(m1, m2)
1302 
1303 def convolute(m1, m2):
1304  """convolute(DensityMap m1, DensityMap m2) -> double"""
1305  return _IMP_em.convolute(m1, m2)
1306 
1307 def get_sum(m1):
1308  """get_sum(DensityMap m1) -> double"""
1309  return _IMP_em.get_sum(m1)
1310 
1311 def get_max_map(maps):
1312  """get_max_map(IMP::em::DensityMaps maps) -> DensityMap"""
1313  return _IMP_em.get_max_map(maps)
1314 
1315 def interpolate_map(in_map, new_spacing):
1316  """interpolate_map(DensityMap in_map, double new_spacing) -> DensityMap"""
1317  return _IMP_em.interpolate_map(in_map, new_spacing)
1318 
1319 def get_grid(in_map):
1320  """get_grid(DensityMap in_map) -> IMP::algebra::GridD< 3,IMP::algebra::DenseGridStorageD< 3,float >,float,IMP::algebra::DefaultEmbeddingD< 3 > >"""
1321  return _IMP_em.get_grid(in_map)
1322 
1323 def create_density_map(*args):
1324  """
1325  create_density_map(DensityMap other) -> DensityMap
1326  create_density_map(BoundingBox3D bb, double spacing) -> DensityMap
1327  create_density_map(int nx, int ny, int nz, double spacing) -> DensityMap
1328  create_density_map(IMP::algebra::GridD< 3,IMP::algebra::DenseGridStorageD< 3,float >,float,IMP::algebra::DefaultEmbeddingD< 3 > > const & grid) -> DensityMap
1329  """
1330  return _IMP_em.create_density_map(*args)
1331 
1332 def get_binarized_interior(dmap):
1333  """get_binarized_interior(DensityMap dmap) -> DensityMap"""
1334  return _IMP_em.get_binarized_interior(dmap)
1335 
1336 def add_to_map(dm, pis):
1337  """add_to_map(DensityMap dm, IMP::Particles const & pis)"""
1338  return _IMP_em.add_to_map(dm, pis)
1339 class RadiusDependentDistanceMask(object):
1340  """Proxy of C++ IMP::em::RadiusDependentDistanceMask class"""
1341  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1342  __repr__ = _swig_repr
1343 
1344  def __init__(self, sampling_radius, header):
1345  """__init__(IMP::em::RadiusDependentDistanceMask self, float sampling_radius, DensityHeader header) -> RadiusDependentDistanceMask"""
1346  this = _IMP_em.new_RadiusDependentDistanceMask(sampling_radius, header)
1347  try:
1348  self.this.append(this)
1349  except:
1350  self.this = this
1351 
1352  def get_neighbor_shift(self):
1353  """get_neighbor_shift(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1354  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_shift(self)
1355 
1356 
1357  def get_neighbor_dist(self):
1358  """get_neighbor_dist(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1359  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist(self)
1360 
1361 
1362  def get_neighbor_dist_exp(self):
1363  """get_neighbor_dist_exp(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1364  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist_exp(self)
1365 
1366 
1367  def show(self, out):
1368  """show(RadiusDependentDistanceMask self, _ostream out)"""
1369  return _IMP_em.RadiusDependentDistanceMask_show(self, out)
1370 
1371  __swig_destroy__ = _IMP_em.delete_RadiusDependentDistanceMask
1372  __del__ = lambda self: None
1373 RadiusDependentDistanceMask_swigregister = _IMP_em.RadiusDependentDistanceMask_swigregister
1374 RadiusDependentDistanceMask_swigregister(RadiusDependentDistanceMask)
1375 
1376 class DistanceMask(object):
1377  """Proxy of C++ IMP::em::DistanceMask class"""
1378  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1379  __repr__ = _swig_repr
1380 
1381  def __init__(self, *args):
1382  """
1383  __init__(IMP::em::DistanceMask self) -> DistanceMask
1384  __init__(IMP::em::DistanceMask self, DensityHeader header) -> DistanceMask
1385  """
1386  this = _IMP_em.new_DistanceMask(*args)
1387  try:
1388  self.this.append(this)
1389  except:
1390  self.this = this
1391 
1392  def show(self, out):
1393  """show(DistanceMask self, _ostream out)"""
1394  return _IMP_em.DistanceMask_show(self, out)
1395 
1396 
1397  def is_mask_set(self, radius, eps=0.001):
1398  """
1399  is_mask_set(DistanceMask self, float radius, float eps=0.001) -> bool
1400  is_mask_set(DistanceMask self, float radius) -> bool
1401  """
1402  return _IMP_em.DistanceMask_is_mask_set(self, radius, eps)
1403 
1404  __swig_destroy__ = _IMP_em.delete_DistanceMask
1405  __del__ = lambda self: None
1406 DistanceMask_swigregister = _IMP_em.DistanceMask_swigregister
1407 DistanceMask_swigregister(DistanceMask)
1408 
1409 class EMReaderWriter(MapReaderWriter):
1410  """Proxy of C++ IMP::em::EMReaderWriter class"""
1411  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1412 
1413  def __str__(self):
1414  """__str__(EMReaderWriter self) -> std::string"""
1415  return _IMP_em.EMReaderWriter___str__(self)
1416 
1417 
1418  def __repr__(self):
1419  """__repr__(EMReaderWriter self) -> std::string"""
1420  return _IMP_em.EMReaderWriter___repr__(self)
1421 
1422 
1423  @staticmethod
1424  def get_from(o):
1425  return _object_cast_to_EMReaderWriter(o)
1426 
1427 
1428  def __init__(self):
1429  """__init__(IMP::em::EMReaderWriter self) -> EMReaderWriter"""
1430  this = _IMP_em.new_EMReaderWriter()
1431  try:
1432  self.this.append(this)
1433  except:
1434  self.this = this
1435 EMReaderWriter_swigregister = _IMP_em.EMReaderWriter_swigregister
1436 EMReaderWriter_swigregister(EMReaderWriter)
1437 
1438 class XplorReaderWriter(MapReaderWriter):
1439  """Proxy of C++ IMP::em::XplorReaderWriter class"""
1440  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1441 
1442  def __str__(self):
1443  """__str__(XplorReaderWriter self) -> std::string"""
1444  return _IMP_em.XplorReaderWriter___str__(self)
1445 
1446 
1447  def __repr__(self):
1448  """__repr__(XplorReaderWriter self) -> std::string"""
1449  return _IMP_em.XplorReaderWriter___repr__(self)
1450 
1451 
1452  @staticmethod
1453  def get_from(o):
1454  return _object_cast_to_XplorReaderWriter(o)
1455 
1456 
1457  def __init__(self):
1458  """__init__(IMP::em::XplorReaderWriter self) -> XplorReaderWriter"""
1459  this = _IMP_em.new_XplorReaderWriter()
1460  try:
1461  self.this.append(this)
1462  except:
1463  self.this = this
1464 XplorReaderWriter_swigregister = _IMP_em.XplorReaderWriter_swigregister
1465 XplorReaderWriter_swigregister(XplorReaderWriter)
1466 
1467 class MRCReaderWriter(MapReaderWriter):
1468  """Proxy of C++ IMP::em::MRCReaderWriter class"""
1469  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1470 
1471  def __init__(self, *args):
1472  """
1473  __init__(IMP::em::MRCReaderWriter self) -> MRCReaderWriter
1474  __init__(IMP::em::MRCReaderWriter self, std::string fn) -> MRCReaderWriter
1475  """
1476  this = _IMP_em.new_MRCReaderWriter(*args)
1477  try:
1478  self.this.append(this)
1479  except:
1480  self.this = this
1481 
1482  def __str__(self):
1483  """__str__(MRCReaderWriter self) -> std::string"""
1484  return _IMP_em.MRCReaderWriter___str__(self)
1485 
1486 
1487  def __repr__(self):
1488  """__repr__(MRCReaderWriter self) -> std::string"""
1489  return _IMP_em.MRCReaderWriter___repr__(self)
1490 
1491 
1492  @staticmethod
1493  def get_from(o):
1494  return _object_cast_to_MRCReaderWriter(o)
1495 
1496 MRCReaderWriter_swigregister = _IMP_em.MRCReaderWriter_swigregister
1497 MRCReaderWriter_swigregister(MRCReaderWriter)
1498 
1499 class KernelParameters(object):
1500  """Proxy of C++ IMP::em::KernelParameters class"""
1501  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1502 
1503  def __init__(self, *args):
1504  """
1505  __init__(IMP::em::KernelParameters self) -> KernelParameters
1506  __init__(IMP::em::KernelParameters self, float resolution) -> KernelParameters
1507  """
1508  this = _IMP_em.new_KernelParameters(*args)
1509  try:
1510  self.this.append(this)
1511  except:
1512  self.this = this
1513  __swig_destroy__ = _IMP_em.delete_KernelParameters
1514  __del__ = lambda self: None
1515 
1516  def get_rsig(self):
1517  """get_rsig(KernelParameters self) -> float"""
1518  return _IMP_em.KernelParameters_get_rsig(self)
1519 
1520 
1521  def get_rsigsq(self):
1522  """get_rsigsq(KernelParameters self) -> float"""
1523  return _IMP_em.KernelParameters_get_rsigsq(self)
1524 
1525 
1526  def get_inv_rsigsq(self):
1527  """get_inv_rsigsq(KernelParameters self) -> float"""
1528  return _IMP_em.KernelParameters_get_inv_rsigsq(self)
1529 
1530 
1531  def get_timessig(self):
1532  """get_timessig(KernelParameters self) -> float"""
1533  return _IMP_em.KernelParameters_get_timessig(self)
1534 
1535 
1536  def get_sq2pi3(self):
1537  """get_sq2pi3(KernelParameters self) -> float"""
1538  return _IMP_em.KernelParameters_get_sq2pi3(self)
1539 
1540 
1541  def get_rnormfac(self):
1542  """get_rnormfac(KernelParameters self) -> float"""
1543  return _IMP_em.KernelParameters_get_rnormfac(self)
1544 
1545 
1546  def get_rkdist(self):
1547  """get_rkdist(KernelParameters self) -> float"""
1548  return _IMP_em.KernelParameters_get_rkdist(self)
1549 
1550 
1551  def get_rkdistsq(self):
1552  """get_rkdistsq(KernelParameters self) -> float"""
1553  return _IMP_em.KernelParameters_get_rkdistsq(self)
1554 
1555 
1556  def get_lim(self):
1557  """get_lim(KernelParameters self) -> float"""
1558  return _IMP_em.KernelParameters_get_lim(self)
1559 
1560 
1561  def show(self, *args):
1562  """
1563  show(KernelParameters self, _ostream out)
1564  show(KernelParameters self)
1565  """
1566  return _IMP_em.KernelParameters_show(self, *args)
1567 
1568 
1569  def __str__(self):
1570  """__str__(KernelParameters self) -> std::string"""
1571  return _IMP_em.KernelParameters___str__(self)
1572 
1573 
1574  def __repr__(self):
1575  """__repr__(KernelParameters self) -> std::string"""
1576  return _IMP_em.KernelParameters___repr__(self)
1577 
1578 KernelParameters_swigregister = _IMP_em.KernelParameters_swigregister
1579 KernelParameters_swigregister(KernelParameters)
1580 
1581 
1582 _IMP_em.GAUSSIAN_swigconstant(_IMP_em)
1583 GAUSSIAN = _IMP_em.GAUSSIAN
1584 
1585 _IMP_em.BINARIZED_SPHERE_swigconstant(_IMP_em)
1586 BINARIZED_SPHERE = _IMP_em.BINARIZED_SPHERE
1587 
1588 _IMP_em.SPHERE_swigconstant(_IMP_em)
1589 SPHERE = _IMP_em.SPHERE
1590 class SampledDensityMap(DensityMap):
1591  """Proxy of C++ IMP::em::SampledDensityMap class"""
1592  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1593 
1594  def __init__(self, *args):
1595  """
1596  __init__(IMP::em::SampledDensityMap self, IMP::em::KernelType kt) -> SampledDensityMap
1597  __init__(IMP::em::SampledDensityMap self) -> SampledDensityMap
1598  __init__(IMP::em::SampledDensityMap self, DensityHeader header, IMP::em::KernelType kt) -> SampledDensityMap
1599  __init__(IMP::em::SampledDensityMap self, DensityHeader header) -> SampledDensityMap
1600  __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size, FloatKey mass_key, int sig_cutoff=3, IMP::em::KernelType kt) -> SampledDensityMap
1601  __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size, FloatKey mass_key, int sig_cutoff=3) -> SampledDensityMap
1602  __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size, FloatKey mass_key) -> SampledDensityMap
1603  __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size) -> SampledDensityMap
1604  """
1605  this = _IMP_em.new_SampledDensityMap(*args)
1606  try:
1607  self.this.append(this)
1608  except:
1609  self.this = this
1610 
1611  def resample(self):
1612  """resample(SampledDensityMap self)"""
1613  return _IMP_em.SampledDensityMap_resample(self)
1614 
1615 
1616  def project(self, *args):
1617  """
1618  project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin, Vector3D shift, FloatKey mass_key)
1619  project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin, Vector3D shift)
1620  project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin)
1621  """
1622  return _IMP_em.SampledDensityMap_project(self, *args)
1623 
1624 
1625  def set_particles(self, *args):
1626  """
1627  set_particles(SampledDensityMap self, IMP::ParticlesTemp const & ps, FloatKey mass_key)
1628  set_particles(SampledDensityMap self, IMP::ParticlesTemp const & ps)
1629  """
1630  return _IMP_em.SampledDensityMap_set_particles(self, *args)
1631 
1632 
1633  def get_xyzr_particles(self):
1634  """get_xyzr_particles(SampledDensityMap self) -> IMP::core::XYZRs const &"""
1635  return _IMP_em.SampledDensityMap_get_xyzr_particles(self)
1636 
1637 
1638  def get_sampled_particles(self):
1639  """get_sampled_particles(SampledDensityMap self) -> IMP::Particles const &"""
1640  return _IMP_em.SampledDensityMap_get_sampled_particles(self)
1641 
1642 
1643  def get_weight_key(self):
1644  """get_weight_key(SampledDensityMap self) -> FloatKey"""
1645  return _IMP_em.SampledDensityMap_get_weight_key(self)
1646 
1647 
1648  def get_minimum_resampled_value(self):
1649  """get_minimum_resampled_value(SampledDensityMap self) -> float"""
1650  return _IMP_em.SampledDensityMap_get_minimum_resampled_value(self)
1651 
1652 
1653  def update_resolution(self, res):
1654  """update_resolution(SampledDensityMap self, IMP::Float res)"""
1655  return _IMP_em.SampledDensityMap_update_resolution(self, res)
1656 
1657  __swig_destroy__ = _IMP_em.delete_SampledDensityMap
1658  __del__ = lambda self: None
1659 
1660  def __str__(self):
1661  """__str__(SampledDensityMap self) -> std::string"""
1662  return _IMP_em.SampledDensityMap___str__(self)
1663 
1664 
1665  def __repr__(self):
1666  """__repr__(SampledDensityMap self) -> std::string"""
1667  return _IMP_em.SampledDensityMap___repr__(self)
1668 
1669 
1670  @staticmethod
1671  def get_from(o):
1672  return _object_cast_to_SampledDensityMap(o)
1673 
1674 SampledDensityMap_swigregister = _IMP_em.SampledDensityMap_swigregister
1675 SampledDensityMap_swigregister(SampledDensityMap)
1676 
1677 
1678 _IMP_em.IMP_DEFAULT_NUM_SHELLS_swigconstant(_IMP_em)
1679 IMP_DEFAULT_NUM_SHELLS = _IMP_em.IMP_DEFAULT_NUM_SHELLS
1680 
1681 _IMP_em.IMP_SIG_CUTOFF_swigconstant(_IMP_em)
1682 IMP_SIG_CUTOFF = _IMP_em.IMP_SIG_CUTOFF
1683 class SurfaceShellDensityMap(SampledDensityMap):
1684  """Proxy of C++ IMP::em::SurfaceShellDensityMap class"""
1685  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1686 
1687  def __init__(self, *args):
1688  """
1689  __init__(IMP::em::SurfaceShellDensityMap self) -> SurfaceShellDensityMap
1690  __init__(IMP::em::SurfaceShellDensityMap self, DensityHeader header) -> SurfaceShellDensityMap
1691  __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key, int num_shells=5) -> SurfaceShellDensityMap
1692  __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key) -> SurfaceShellDensityMap
1693  __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size) -> SurfaceShellDensityMap
1694  """
1695  this = _IMP_em.new_SurfaceShellDensityMap(*args)
1696  try:
1697  self.this.append(this)
1698  except:
1699  self.this = this
1700 
1701  def binarize(self, scene_val):
1702  """binarize(SurfaceShellDensityMap self, float scene_val)"""
1703  return _IMP_em.SurfaceShellDensityMap_binarize(self, scene_val)
1704 
1705 
1706  def binaries(self, scene_val):
1707  """binaries(SurfaceShellDensityMap self, float scene_val)"""
1708  return _IMP_em.SurfaceShellDensityMap_binaries(self, scene_val)
1709 
1710 
1711  def has_background_neighbor(self, voxel_ind):
1712  """has_background_neighbor(SurfaceShellDensityMap self, long voxel_ind) -> bool"""
1713  return _IMP_em.SurfaceShellDensityMap_has_background_neighbor(self, voxel_ind)
1714 
1715  __swig_destroy__ = _IMP_em.delete_SurfaceShellDensityMap
1716  __del__ = lambda self: None
1717 
1718  def __str__(self):
1719  """__str__(SurfaceShellDensityMap self) -> std::string"""
1720  return _IMP_em.SurfaceShellDensityMap___str__(self)
1721 
1722 
1723  def __repr__(self):
1724  """__repr__(SurfaceShellDensityMap self) -> std::string"""
1725  return _IMP_em.SurfaceShellDensityMap___repr__(self)
1726 
1727 
1728  @staticmethod
1729  def get_from(o):
1730  return _object_cast_to_SurfaceShellDensityMap(o)
1731 
1732 SurfaceShellDensityMap_swigregister = _IMP_em.SurfaceShellDensityMap_swigregister
1733 SurfaceShellDensityMap_swigregister(SurfaceShellDensityMap)
1734 
1735 class CoarseCC(IMP.Object):
1736  """Proxy of C++ IMP::em::CoarseCC class"""
1737  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1738 
1739  def __init__(self):
1740  """__init__(IMP::em::CoarseCC self) -> CoarseCC"""
1741  this = _IMP_em.new_CoarseCC()
1742  try:
1743  self.this.append(this)
1744  except:
1745  self.this = this
1746 
1747  def calc_score(*args):
1748  """
1749  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True, IMP::FloatPair norm_factors) -> float
1750  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True) -> float
1751  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1752  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1753  """
1754  return _IMP_em.CoarseCC_calc_score(*args)
1755 
1756  calc_score = staticmethod(calc_score)
1757 
1758  def cross_correlation_coefficient(*args):
1759  """
1760  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False, IMP::FloatPair norm_factors) -> double
1761  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1762  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1763  """
1764  return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1765 
1766  cross_correlation_coefficient = staticmethod(cross_correlation_coefficient)
1767 
1768  def local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold):
1769  """local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1770  return _IMP_em.CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold)
1771 
1772  local_cross_correlation_coefficient = staticmethod(local_cross_correlation_coefficient)
1773 
1774  def get_version_info(self):
1775  """get_version_info(CoarseCC self) -> VersionInfo"""
1776  return _IMP_em.CoarseCC_get_version_info(self)
1777 
1778 
1779  def __str__(self):
1780  """__str__(CoarseCC self) -> std::string"""
1781  return _IMP_em.CoarseCC___str__(self)
1782 
1783 
1784  def __repr__(self):
1785  """__repr__(CoarseCC self) -> std::string"""
1786  return _IMP_em.CoarseCC___repr__(self)
1787 
1788 
1789  @staticmethod
1790  def get_from(o):
1791  return _object_cast_to_CoarseCC(o)
1792 
1793 CoarseCC_swigregister = _IMP_em.CoarseCC_swigregister
1794 CoarseCC_swigregister(CoarseCC)
1795 
1796 def CoarseCC_calc_score(*args):
1797  """
1798  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True, IMP::FloatPair norm_factors) -> float
1799  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True) -> float
1800  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1801  CoarseCC_calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1802  """
1803  return _IMP_em.CoarseCC_calc_score(*args)
1804 
1805 def CoarseCC_cross_correlation_coefficient(*args):
1806  """
1807  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False, IMP::FloatPair norm_factors) -> double
1808  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1809  CoarseCC_cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1810  """
1811  return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1812 
1813 def CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold):
1814  """CoarseCC_local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1815  return _IMP_em.CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold)
1816 
1817 class CoarseConvolution(object):
1818  """Proxy of C++ IMP::em::CoarseConvolution class"""
1819  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1820  __repr__ = _swig_repr
1821 
1822  def convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac=True):
1823  """
1824  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1825  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1826  """
1827  return _IMP_em.CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac)
1828 
1829  convolution = staticmethod(convolution)
1830 
1831  def __init__(self):
1832  """__init__(IMP::em::CoarseConvolution self) -> CoarseConvolution"""
1833  this = _IMP_em.new_CoarseConvolution()
1834  try:
1835  self.this.append(this)
1836  except:
1837  self.this = this
1838  __swig_destroy__ = _IMP_em.delete_CoarseConvolution
1839  __del__ = lambda self: None
1840 CoarseConvolution_swigregister = _IMP_em.CoarseConvolution_swigregister
1841 CoarseConvolution_swigregister(CoarseConvolution)
1842 
1843 def CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac=True):
1844  """
1845  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1846  CoarseConvolution_convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1847  """
1848  return _IMP_em.CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac)
1849 
1850 class CoarseCCatIntervals(CoarseCC):
1851  """Proxy of C++ IMP::em::CoarseCCatIntervals class"""
1852  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1853 
1854  def __init__(self, *args):
1855  """
1856  __init__(IMP::em::CoarseCCatIntervals self, int const & ncd) -> CoarseCCatIntervals
1857  __init__(IMP::em::CoarseCCatIntervals self) -> CoarseCCatIntervals
1858  """
1859  this = _IMP_em.new_CoarseCCatIntervals(*args)
1860  try:
1861  self.this.append(this)
1862  except:
1863  self.this = this
1864 
1865  def evaluate(self, em_map, model_map, deriv, scalefac, lderiv, eval_interval):
1866  """evaluate(CoarseCCatIntervals self, DensityMap em_map, SampledDensityMap model_map, IMP::algebra::Vector3Ds const & deriv, float scalefac, bool lderiv, unsigned long eval_interval) -> std::pair< double,IMP::algebra::Vector3Ds >"""
1867  return _IMP_em.CoarseCCatIntervals_evaluate(self, em_map, model_map, deriv, scalefac, lderiv, eval_interval)
1868 
1869 
1870  def __str__(self):
1871  """__str__(CoarseCCatIntervals self) -> std::string"""
1872  return _IMP_em.CoarseCCatIntervals___str__(self)
1873 
1874 
1875  def __repr__(self):
1876  """__repr__(CoarseCCatIntervals self) -> std::string"""
1877  return _IMP_em.CoarseCCatIntervals___repr__(self)
1878 
1879 
1880  @staticmethod
1881  def get_from(o):
1882  return _object_cast_to_CoarseCCatIntervals(o)
1883 
1884 CoarseCCatIntervals_swigregister = _IMP_em.CoarseCCatIntervals_swigregister
1885 CoarseCCatIntervals_swigregister(CoarseCCatIntervals)
1886 
1887 class FitRestraint(IMP.Restraint):
1888  """Proxy of C++ IMP::em::FitRestraint class"""
1889  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1890 
1891  def __init__(self, *args):
1892  """
1893  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key, float scale=1, bool use_rigid_bodies=True, IMP::em::KernelType kt) -> FitRestraint
1894  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key, float scale=1, bool use_rigid_bodies=True) -> FitRestraint
1895  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key, float scale=1) -> FitRestraint
1896  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key) -> FitRestraint
1897  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors) -> FitRestraint
1898  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map) -> FitRestraint
1899  """
1900  this = _IMP_em.new_FitRestraint(*args)
1901  try:
1902  self.this.append(this)
1903  except:
1904  self.this = this
1905 
1906  def get_model_dens_map(self):
1907  """get_model_dens_map(FitRestraint self) -> SampledDensityMap"""
1908  return _IMP_em.FitRestraint_get_model_dens_map(self)
1909 
1910 
1911  def set_scale_factor(self, scale):
1912  """set_scale_factor(FitRestraint self, float scale)"""
1913  return _IMP_em.FitRestraint_set_scale_factor(self, scale)
1914 
1915 
1916  def get_scale_factor(self):
1917  """get_scale_factor(FitRestraint self) -> float"""
1918  return _IMP_em.FitRestraint_get_scale_factor(self)
1919 
1920 
1921  def do_get_inputs(self):
1922  """do_get_inputs(FitRestraint self) -> IMP::ModelObjectsTemp"""
1923  return _IMP_em.FitRestraint_do_get_inputs(self)
1924 
1925 
1926  def get_version_info(self):
1927  """get_version_info(FitRestraint self) -> VersionInfo"""
1928  return _IMP_em.FitRestraint_get_version_info(self)
1929 
1930 
1931  def __str__(self):
1932  """__str__(FitRestraint self) -> std::string"""
1933  return _IMP_em.FitRestraint___str__(self)
1934 
1935 
1936  def __repr__(self):
1937  """__repr__(FitRestraint self) -> std::string"""
1938  return _IMP_em.FitRestraint___repr__(self)
1939 
1940 
1941  @staticmethod
1942  def get_from(o):
1943  return _object_cast_to_FitRestraint(o)
1944 
1945 
1946  def cast(r):
1947  """cast(Restraint r) -> FitRestraint"""
1948  return _IMP_em.FitRestraint_cast(r)
1949 
1950  cast = staticmethod(cast)
1951 FitRestraint_swigregister = _IMP_em.FitRestraint_swigregister
1952 FitRestraint_swigregister(FitRestraint)
1953 
1954 def FitRestraint_cast(r):
1955  """FitRestraint_cast(Restraint r) -> FitRestraint"""
1956  return _IMP_em.FitRestraint_cast(r)
1957 
1958 
1959 def density2particles(dmap, threshold, m, step=1):
1960  """
1961  density2particles(DensityMap dmap, IMP::Float threshold, Model m, int step=1) -> IMP::Particles
1962  density2particles(DensityMap dmap, IMP::Float threshold, Model m) -> IMP::Particles
1963  """
1964  return _IMP_em.density2particles(dmap, threshold, m, step)
1965 
1966 def density2vectors(dmap, threshold):
1967  """density2vectors(DensityMap dmap, IMP::Float threshold) -> IMP::algebra::Vector3Ds"""
1968  return _IMP_em.density2vectors(dmap, threshold)
1969 
1970 def particles2density(*args):
1971  """
1972  particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3, FloatKey weight_key) -> SampledDensityMap
1973  particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
1974  particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
1975  """
1976  return _IMP_em.particles2density(*args)
1977 
1978 def particles2binarized_density(*args):
1979  """
1980  particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3, FloatKey weight_key) -> SampledDensityMap
1981  particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
1982  particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
1983  """
1984  return _IMP_em.particles2binarized_density(*args)
1985 
1986 def particles2surface(*args):
1987  """
1988  particles2surface(IMP::ParticlesTemp const & ps, IMP::Float apix, FloatKey weight_key) -> SurfaceShellDensityMap
1989  particles2surface(IMP::ParticlesTemp const & ps, IMP::Float apix) -> SurfaceShellDensityMap
1990  """
1991  return _IMP_em.particles2surface(*args)
1992 
1993 def calculate_intersection_score(d1, d2):
1994  """calculate_intersection_score(SurfaceShellDensityMap d1, SurfaceShellDensityMap d2) -> IMP::Float"""
1995  return _IMP_em.calculate_intersection_score(d1, d2)
1996 class SpiderHeader(object):
1997  """Proxy of C++ IMP::em::SpiderHeader class"""
1998  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1999  __repr__ = _swig_repr
2000  fNslice = _swig_property(_IMP_em.SpiderHeader_fNslice_get, _IMP_em.SpiderHeader_fNslice_set)
2001  fNrow = _swig_property(_IMP_em.SpiderHeader_fNrow_get, _IMP_em.SpiderHeader_fNrow_set)
2002  fNrec = _swig_property(_IMP_em.SpiderHeader_fNrec_get, _IMP_em.SpiderHeader_fNrec_set)
2003  fNlabel = _swig_property(_IMP_em.SpiderHeader_fNlabel_get, _IMP_em.SpiderHeader_fNlabel_set)
2004  fIform = _swig_property(_IMP_em.SpiderHeader_fIform_get, _IMP_em.SpiderHeader_fIform_set)
2005  fImami = _swig_property(_IMP_em.SpiderHeader_fImami_get, _IMP_em.SpiderHeader_fImami_set)
2006  fFmax = _swig_property(_IMP_em.SpiderHeader_fFmax_get, _IMP_em.SpiderHeader_fFmax_set)
2007  fFmin = _swig_property(_IMP_em.SpiderHeader_fFmin_get, _IMP_em.SpiderHeader_fFmin_set)
2008  fAv = _swig_property(_IMP_em.SpiderHeader_fAv_get, _IMP_em.SpiderHeader_fAv_set)
2009  fSig = _swig_property(_IMP_em.SpiderHeader_fSig_get, _IMP_em.SpiderHeader_fSig_set)
2010  fIhist = _swig_property(_IMP_em.SpiderHeader_fIhist_get, _IMP_em.SpiderHeader_fIhist_set)
2011  fNcol = _swig_property(_IMP_em.SpiderHeader_fNcol_get, _IMP_em.SpiderHeader_fNcol_set)
2012  fLabrec = _swig_property(_IMP_em.SpiderHeader_fLabrec_get, _IMP_em.SpiderHeader_fLabrec_set)
2013  fIangle = _swig_property(_IMP_em.SpiderHeader_fIangle_get, _IMP_em.SpiderHeader_fIangle_set)
2014  fPhi = _swig_property(_IMP_em.SpiderHeader_fPhi_get, _IMP_em.SpiderHeader_fPhi_set)
2015  fTheta = _swig_property(_IMP_em.SpiderHeader_fTheta_get, _IMP_em.SpiderHeader_fTheta_set)
2016  fPsi = _swig_property(_IMP_em.SpiderHeader_fPsi_get, _IMP_em.SpiderHeader_fPsi_set)
2017  fXoff = _swig_property(_IMP_em.SpiderHeader_fXoff_get, _IMP_em.SpiderHeader_fXoff_set)
2018  fYoff = _swig_property(_IMP_em.SpiderHeader_fYoff_get, _IMP_em.SpiderHeader_fYoff_set)
2019  fZoff = _swig_property(_IMP_em.SpiderHeader_fZoff_get, _IMP_em.SpiderHeader_fZoff_set)
2020  fScale = _swig_property(_IMP_em.SpiderHeader_fScale_get, _IMP_em.SpiderHeader_fScale_set)
2021  fLabbyt = _swig_property(_IMP_em.SpiderHeader_fLabbyt_get, _IMP_em.SpiderHeader_fLabbyt_set)
2022  fLenbyt = _swig_property(_IMP_em.SpiderHeader_fLenbyt_get, _IMP_em.SpiderHeader_fLenbyt_set)
2023  fNothing = _swig_property(_IMP_em.SpiderHeader_fNothing_get, _IMP_em.SpiderHeader_fNothing_set)
2024  fFlag = _swig_property(_IMP_em.SpiderHeader_fFlag_get, _IMP_em.SpiderHeader_fFlag_set)
2025  fPhi1 = _swig_property(_IMP_em.SpiderHeader_fPhi1_get, _IMP_em.SpiderHeader_fPhi1_set)
2026  fTheta1 = _swig_property(_IMP_em.SpiderHeader_fTheta1_get, _IMP_em.SpiderHeader_fTheta1_set)
2027  fPsi1 = _swig_property(_IMP_em.SpiderHeader_fPsi1_get, _IMP_em.SpiderHeader_fPsi1_set)
2028  fPhi2 = _swig_property(_IMP_em.SpiderHeader_fPhi2_get, _IMP_em.SpiderHeader_fPhi2_set)
2029  fTheta2 = _swig_property(_IMP_em.SpiderHeader_fTheta2_get, _IMP_em.SpiderHeader_fTheta2_set)
2030  fPsi2 = _swig_property(_IMP_em.SpiderHeader_fPsi2_get, _IMP_em.SpiderHeader_fPsi2_set)
2031  fGeo_matrix = _swig_property(_IMP_em.SpiderHeader_fGeo_matrix_get, _IMP_em.SpiderHeader_fGeo_matrix_set)
2032  fAngle1 = _swig_property(_IMP_em.SpiderHeader_fAngle1_get, _IMP_em.SpiderHeader_fAngle1_set)
2033  fr1 = _swig_property(_IMP_em.SpiderHeader_fr1_get, _IMP_em.SpiderHeader_fr1_set)
2034  fr2 = _swig_property(_IMP_em.SpiderHeader_fr2_get, _IMP_em.SpiderHeader_fr2_set)
2035  RTflag = _swig_property(_IMP_em.SpiderHeader_RTflag_get, _IMP_em.SpiderHeader_RTflag_set)
2036  Astart = _swig_property(_IMP_em.SpiderHeader_Astart_get, _IMP_em.SpiderHeader_Astart_set)
2037  Aend = _swig_property(_IMP_em.SpiderHeader_Aend_get, _IMP_em.SpiderHeader_Aend_set)
2038  Ainc = _swig_property(_IMP_em.SpiderHeader_Ainc_get, _IMP_em.SpiderHeader_Ainc_set)
2039  Rsigma = _swig_property(_IMP_em.SpiderHeader_Rsigma_get, _IMP_em.SpiderHeader_Rsigma_set)
2040  Tstart = _swig_property(_IMP_em.SpiderHeader_Tstart_get, _IMP_em.SpiderHeader_Tstart_set)
2041  Tend = _swig_property(_IMP_em.SpiderHeader_Tend_get, _IMP_em.SpiderHeader_Tend_set)
2042  Tinc = _swig_property(_IMP_em.SpiderHeader_Tinc_get, _IMP_em.SpiderHeader_Tinc_set)
2043  Weight = _swig_property(_IMP_em.SpiderHeader_Weight_get, _IMP_em.SpiderHeader_Weight_set)
2044  Flip = _swig_property(_IMP_em.SpiderHeader_Flip_get, _IMP_em.SpiderHeader_Flip_set)
2045  empty = _swig_property(_IMP_em.SpiderHeader_empty_get, _IMP_em.SpiderHeader_empty_set)
2046  szIDat = _swig_property(_IMP_em.SpiderHeader_szIDat_get, _IMP_em.SpiderHeader_szIDat_set)
2047  szITim = _swig_property(_IMP_em.SpiderHeader_szITim_get, _IMP_em.SpiderHeader_szITim_set)
2048  szITit = _swig_property(_IMP_em.SpiderHeader_szITit_get, _IMP_em.SpiderHeader_szITit_set)
2049 
2050  def show(self, out):
2051  """show(SpiderHeader self, _ostream out)"""
2052  return _IMP_em.SpiderHeader_show(self, out)
2053 
2054 
2055  def __init__(self):
2056  """__init__(IMP::em::SpiderHeader self) -> SpiderHeader"""
2057  this = _IMP_em.new_SpiderHeader()
2058  try:
2059  self.this.append(this)
2060  except:
2061  self.this = this
2062  __swig_destroy__ = _IMP_em.delete_SpiderHeader
2063  __del__ = lambda self: None
2064 SpiderHeader_swigregister = _IMP_em.SpiderHeader_swigregister
2065 SpiderHeader_swigregister(SpiderHeader)
2066 
2067 class ImageHeader(object):
2068  """Proxy of C++ IMP::em::ImageHeader class"""
2069  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2070  __repr__ = _swig_repr
2071  IMG_BYTE = _IMP_em.ImageHeader_IMG_BYTE
2072  IMG_IMPEM = _IMP_em.ImageHeader_IMG_IMPEM
2073  IMG_INT = _IMP_em.ImageHeader_IMG_INT
2074  VOL_BYTE = _IMP_em.ImageHeader_VOL_BYTE
2075  VOL_IMPEM = _IMP_em.ImageHeader_VOL_IMPEM
2076  VOL_INT = _IMP_em.ImageHeader_VOL_INT
2077  IMG_FOURIER = _IMP_em.ImageHeader_IMG_FOURIER
2078  VOL_FOURIER = _IMP_em.ImageHeader_VOL_FOURIER
2079 
2080  def __init__(self, *args):
2081  """
2082  __init__(IMP::em::ImageHeader self) -> ImageHeader
2083  __init__(IMP::em::ImageHeader self, IMP::em::ImageHeader::img_type im) -> ImageHeader
2084  __init__(IMP::em::ImageHeader self, float im) -> ImageHeader
2085  """
2086  this = _IMP_em.new_ImageHeader(*args)
2087  try:
2088  self.this.append(this)
2089  except:
2090  self.this = this
2091 
2092  def get_image_type(self):
2093  """get_image_type(ImageHeader self) -> float"""
2094  return _IMP_em.ImageHeader_get_image_type(self)
2095 
2096 
2097  def set_image_type(self, *args):
2098  """
2099  set_image_type(ImageHeader self, IMP::em::ImageHeader::img_type im)
2100  set_image_type(ImageHeader self, float im)
2101  """
2102  return _IMP_em.ImageHeader_set_image_type(self, *args)
2103 
2104 
2105  def do_show(self, out):
2106  """do_show(ImageHeader self, _ostream out)"""
2107  return _IMP_em.ImageHeader_do_show(self, out)
2108 
2109 
2110  def show(self, *args):
2111  """
2112  show(ImageHeader self, _ostream out)
2113  show(ImageHeader self)
2114  """
2115  return _IMP_em.ImageHeader_show(self, *args)
2116 
2117 
2118  def print_hard(self, out):
2119  """print_hard(ImageHeader self, _ostream out)"""
2120  return _IMP_em.ImageHeader_print_hard(self, out)
2121 
2122 
2123  def show_projection_params(self, out):
2124  """show_projection_params(ImageHeader self, _ostream out)"""
2125  return _IMP_em.ImageHeader_show_projection_params(self, out)
2126 
2127 
2128  def read(self, *args):
2129  """
2130  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False, bool skip_extra_checkings=False) -> int
2131  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False) -> int
2132  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False) -> int
2133  read(ImageHeader self, IMP::String const filename) -> int
2134  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False, bool skip_extra_checkings=False) -> bool
2135  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False) -> bool
2136  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False) -> bool
2137  read(ImageHeader self, std::ifstream & f) -> bool
2138  """
2139  return _IMP_em.ImageHeader_read(self, *args)
2140 
2141 
2142  def write(self, *args):
2143  """
2144  write(ImageHeader self, IMP::String const & filename, bool force_reversed=False)
2145  write(ImageHeader self, IMP::String const & filename)
2146  write(ImageHeader self, std::ofstream & f, bool force_reversed=False)
2147  write(ImageHeader self, std::ofstream & f)
2148  """
2149  return _IMP_em.ImageHeader_write(self, *args)
2150 
2151 
2152  def clear(self):
2153  """clear(ImageHeader self)"""
2154  return _IMP_em.ImageHeader_clear(self)
2155 
2156 
2157  def set_header(self):
2158  """set_header(ImageHeader self)"""
2159  return _IMP_em.ImageHeader_set_header(self)
2160 
2161 
2162  def get_reversed(self):
2163  """get_reversed(ImageHeader self) -> bool"""
2164  return _IMP_em.ImageHeader_get_reversed(self)
2165 
2166 
2167  def set_reversed(self, value):
2168  """set_reversed(ImageHeader self, bool value)"""
2169  return _IMP_em.ImageHeader_set_reversed(self, value)
2170 
2171 
2172  def get_number_of_slices(self):
2173  """get_number_of_slices(ImageHeader self) -> unsigned int"""
2174  return _IMP_em.ImageHeader_get_number_of_slices(self)
2175 
2176 
2177  def set_number_of_slices(self, n):
2178  """set_number_of_slices(ImageHeader self, unsigned int n)"""
2179  return _IMP_em.ImageHeader_set_number_of_slices(self, n)
2180 
2181 
2182  def get_number_of_rows(self):
2183  """get_number_of_rows(ImageHeader self) -> unsigned int"""
2184  return _IMP_em.ImageHeader_get_number_of_rows(self)
2185 
2186 
2187  def set_number_of_rows(self, n):
2188  """set_number_of_rows(ImageHeader self, unsigned int n)"""
2189  return _IMP_em.ImageHeader_set_number_of_rows(self, n)
2190 
2191 
2192  def get_number_of_columns(self):
2193  """get_number_of_columns(ImageHeader self) -> unsigned int"""
2194  return _IMP_em.ImageHeader_get_number_of_columns(self)
2195 
2196 
2197  def set_number_of_columns(self, n):
2198  """set_number_of_columns(ImageHeader self, unsigned int n)"""
2199  return _IMP_em.ImageHeader_set_number_of_columns(self, n)
2200 
2201 
2202  def get_old_rot(self):
2203  """get_old_rot(ImageHeader self) -> float"""
2204  return _IMP_em.ImageHeader_get_old_rot(self)
2205 
2206 
2207  def set_old_rot(self, value):
2208  """set_old_rot(ImageHeader self, float value)"""
2209  return _IMP_em.ImageHeader_set_old_rot(self, value)
2210 
2211 
2212  def get_fAngle1(self):
2213  """get_fAngle1(ImageHeader self) -> float"""
2214  return _IMP_em.ImageHeader_get_fAngle1(self)
2215 
2216 
2217  def set_fAngle1(self, value):
2218  """set_fAngle1(ImageHeader self, float value)"""
2219  return _IMP_em.ImageHeader_set_fAngle1(self, value)
2220 
2221 
2222  def get_Scale(self):
2223  """get_Scale(ImageHeader self) -> float"""
2224  return _IMP_em.ImageHeader_get_Scale(self)
2225 
2226 
2227  def set_Scale(self, value):
2228  """set_Scale(ImageHeader self, float value)"""
2229  return _IMP_em.ImageHeader_set_Scale(self, value)
2230 
2231 
2232  def get_Flip(self):
2233  """get_Flip(ImageHeader self) -> float"""
2234  return _IMP_em.ImageHeader_get_Flip(self)
2235 
2236 
2237  def set_Flip(self, value):
2238  """set_Flip(ImageHeader self, float value)"""
2239  return _IMP_em.ImageHeader_set_Flip(self, value)
2240 
2241 
2242  def get_Weight(self):
2243  """get_Weight(ImageHeader self) -> float"""
2244  return _IMP_em.ImageHeader_get_Weight(self)
2245 
2246 
2247  def set_Weight(self, value):
2248  """set_Weight(ImageHeader self, float value)"""
2249  return _IMP_em.ImageHeader_set_Weight(self, value)
2250 
2251 
2252  def get_fNrec(self):
2253  """get_fNrec(ImageHeader self) -> float"""
2254  return _IMP_em.ImageHeader_get_fNrec(self)
2255 
2256 
2257  def set_fNrec(self, value):
2258  """set_fNrec(ImageHeader self, float value)"""
2259  return _IMP_em.ImageHeader_set_fNrec(self, value)
2260 
2261 
2262  def get_fNlabel(self):
2263  """get_fNlabel(ImageHeader self) -> float"""
2264  return _IMP_em.ImageHeader_get_fNlabel(self)
2265 
2266 
2267  def set_fNlabel(self, value):
2268  """set_fNlabel(ImageHeader self, float value)"""
2269  return _IMP_em.ImageHeader_set_fNlabel(self, value)
2270 
2271 
2272  def get_fIform(self):
2273  """get_fIform(ImageHeader self) -> float"""
2274  return _IMP_em.ImageHeader_get_fIform(self)
2275 
2276 
2277  def set_fIform(self, value):
2278  """set_fIform(ImageHeader self, float value)"""
2279  return _IMP_em.ImageHeader_set_fIform(self, value)
2280 
2281 
2282  def get_fImami(self):
2283  """get_fImami(ImageHeader self) -> float"""
2284  return _IMP_em.ImageHeader_get_fImami(self)
2285 
2286 
2287  def set_fImami(self, value):
2288  """set_fImami(ImageHeader self, float value)"""
2289  return _IMP_em.ImageHeader_set_fImami(self, value)
2290 
2291 
2292  def get_fFmax(self):
2293  """get_fFmax(ImageHeader self) -> float"""
2294  return _IMP_em.ImageHeader_get_fFmax(self)
2295 
2296 
2297  def set_fFmax(self, value):
2298  """set_fFmax(ImageHeader self, float value)"""
2299  return _IMP_em.ImageHeader_set_fFmax(self, value)
2300 
2301 
2302  def get_fFmin(self):
2303  """get_fFmin(ImageHeader self) -> float"""
2304  return _IMP_em.ImageHeader_get_fFmin(self)
2305 
2306 
2307  def set_fFmin(self, value):
2308  """set_fFmin(ImageHeader self, float value)"""
2309  return _IMP_em.ImageHeader_set_fFmin(self, value)
2310 
2311 
2312  def get_fAv(self):
2313  """get_fAv(ImageHeader self) -> float"""
2314  return _IMP_em.ImageHeader_get_fAv(self)
2315 
2316 
2317  def set_fAv(self, value):
2318  """set_fAv(ImageHeader self, float value)"""
2319  return _IMP_em.ImageHeader_set_fAv(self, value)
2320 
2321 
2322  def get_fSig(self):
2323  """get_fSig(ImageHeader self) -> float"""
2324  return _IMP_em.ImageHeader_get_fSig(self)
2325 
2326 
2327  def set_fSig(self, value):
2328  """set_fSig(ImageHeader self, float value)"""
2329  return _IMP_em.ImageHeader_set_fSig(self, value)
2330 
2331 
2332  def get_fIhist(self):
2333  """get_fIhist(ImageHeader self) -> float"""
2334  return _IMP_em.ImageHeader_get_fIhist(self)
2335 
2336 
2337  def set_fIhist(self, value):
2338  """set_fIhist(ImageHeader self, float value)"""
2339  return _IMP_em.ImageHeader_set_fIhist(self, value)
2340 
2341 
2342  def get_fLabrec(self):
2343  """get_fLabrec(ImageHeader self) -> float"""
2344  return _IMP_em.ImageHeader_get_fLabrec(self)
2345 
2346 
2347  def set_fLabrec(self, value):
2348  """set_fLabrec(ImageHeader self, float value)"""
2349  return _IMP_em.ImageHeader_set_fLabrec(self, value)
2350 
2351 
2352  def get_fIangle(self):
2353  """get_fIangle(ImageHeader self) -> float"""
2354  return _IMP_em.ImageHeader_get_fIangle(self)
2355 
2356 
2357  def set_fIangle(self, value):
2358  """set_fIangle(ImageHeader self, float value)"""
2359  return _IMP_em.ImageHeader_set_fIangle(self, value)
2360 
2361 
2362  def get_origin(self):
2363  """get_origin(ImageHeader self) -> Vector3D"""
2364  return _IMP_em.ImageHeader_get_origin(self)
2365 
2366 
2367  def set_origin(self, *args):
2368  """
2369  set_origin(ImageHeader self, Vector3D v)
2370  set_origin(ImageHeader self, Vector2D v)
2371  """
2372  return _IMP_em.ImageHeader_set_origin(self, *args)
2373 
2374 
2375  def get_object_pixel_size(self):
2376  """get_object_pixel_size(ImageHeader self) -> float"""
2377  return _IMP_em.ImageHeader_get_object_pixel_size(self)
2378 
2379 
2380  def set_object_pixel_size(self, value):
2381  """set_object_pixel_size(ImageHeader self, float value)"""
2382  return _IMP_em.ImageHeader_set_object_pixel_size(self, value)
2383 
2384 
2385  def get_fLabbyt(self):
2386  """get_fLabbyt(ImageHeader self) -> float"""
2387  return _IMP_em.ImageHeader_get_fLabbyt(self)
2388 
2389 
2390  def set_fLabbyt(self, value):
2391  """set_fLabbyt(ImageHeader self, float value)"""
2392  return _IMP_em.ImageHeader_set_fLabbyt(self, value)
2393 
2394 
2395  def get_fLenbyt(self):
2396  """get_fLenbyt(ImageHeader self) -> float"""
2397  return _IMP_em.ImageHeader_get_fLenbyt(self)
2398 
2399 
2400  def set_fLenbyt(self, value):
2401  """set_fLenbyt(ImageHeader self, float value)"""
2402  return _IMP_em.ImageHeader_set_fLenbyt(self, value)
2403 
2404 
2405  def get_fGeo_matrix(self, i, j):
2406  """get_fGeo_matrix(ImageHeader self, unsigned int i, unsigned int j) -> double"""
2407  return _IMP_em.ImageHeader_get_fGeo_matrix(self, i, j)
2408 
2409 
2410  def get_fFlag(self):
2411  """get_fFlag(ImageHeader self) -> float"""
2412  return _IMP_em.ImageHeader_get_fFlag(self)
2413 
2414 
2415  def set_fFlag(self, value):
2416  """set_fFlag(ImageHeader self, float value)"""
2417  return _IMP_em.ImageHeader_set_fFlag(self, value)
2418 
2419 
2420  def get_euler_angles(self):
2421  """get_euler_angles(ImageHeader self) -> Vector3D"""
2422  return _IMP_em.ImageHeader_get_euler_angles(self)
2423 
2424 
2425  def get_euler_angles1(self):
2426  """get_euler_angles1(ImageHeader self) -> Vector3D"""
2427  return _IMP_em.ImageHeader_get_euler_angles1(self)
2428 
2429 
2430  def get_euler_angles2(self):
2431  """get_euler_angles2(ImageHeader self) -> Vector3D"""
2432  return _IMP_em.ImageHeader_get_euler_angles2(self)
2433 
2434 
2435  def set_euler_angles(self, euler):
2436  """set_euler_angles(ImageHeader self, Vector3D euler)"""
2437  return _IMP_em.ImageHeader_set_euler_angles(self, euler)
2438 
2439 
2440  def set_euler_angles1(self, euler):
2441  """set_euler_angles1(ImageHeader self, Vector3D euler)"""
2442  return _IMP_em.ImageHeader_set_euler_angles1(self, euler)
2443 
2444 
2445  def set_euler_angles2(self, euler):
2446  """set_euler_angles2(ImageHeader self, Vector3D euler)"""
2447  return _IMP_em.ImageHeader_set_euler_angles2(self, euler)
2448 
2449 
2450  def is_normalized(self):
2451  """is_normalized(ImageHeader self) -> bool"""
2452  return _IMP_em.ImageHeader_is_normalized(self)
2453 
2454 
2455  def set_date(self):
2456  """set_date(ImageHeader self)"""
2457  return _IMP_em.ImageHeader_set_date(self)
2458 
2459 
2460  def set_time(self):
2461  """set_time(ImageHeader self)"""
2462  return _IMP_em.ImageHeader_set_time(self)
2463 
2464 
2465  def set_title(self, newName):
2466  """set_title(ImageHeader self, IMP::String newName)"""
2467  return _IMP_em.ImageHeader_set_title(self, newName)
2468 
2469  __swig_destroy__ = _IMP_em.delete_ImageHeader
2470  __del__ = lambda self: None
2471 ImageHeader_swigregister = _IMP_em.ImageHeader_swigregister
2472 ImageHeader_swigregister(ImageHeader)
2473 
2474 class SpiderMapReaderWriter(MapReaderWriter):
2475  """Proxy of C++ IMP::em::SpiderMapReaderWriter class"""
2476  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2477  filename_ = _swig_property(_IMP_em.SpiderMapReaderWriter_filename__get, _IMP_em.SpiderMapReaderWriter_filename__set)
2478  skip_type_check_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_type_check__get, _IMP_em.SpiderMapReaderWriter_skip_type_check__set)
2479  force_reversed_ = _swig_property(_IMP_em.SpiderMapReaderWriter_force_reversed__get, _IMP_em.SpiderMapReaderWriter_force_reversed__set)
2480  skip_extra_checkings_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_extra_checkings__get, _IMP_em.SpiderMapReaderWriter_skip_extra_checkings__set)
2481 
2482  def __init__(self, *args):
2483  """
2484  __init__(IMP::em::SpiderMapReaderWriter self) -> SpiderMapReaderWriter
2485  __init__(IMP::em::SpiderMapReaderWriter self, IMP::String filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings) -> SpiderMapReaderWriter
2486  """
2487  this = _IMP_em.new_SpiderMapReaderWriter(*args)
2488  try:
2489  self.this.append(this)
2490  except:
2491  self.this = this
2492 
2493  def __str__(self):
2494  """__str__(SpiderMapReaderWriter self) -> std::string"""
2495  return _IMP_em.SpiderMapReaderWriter___str__(self)
2496 
2497 
2498  def __repr__(self):
2499  """__repr__(SpiderMapReaderWriter self) -> std::string"""
2500  return _IMP_em.SpiderMapReaderWriter___repr__(self)
2501 
2502 
2503  @staticmethod
2504  def get_from(o):
2505  return _object_cast_to_SpiderMapReaderWriter(o)
2506 
2507 SpiderMapReaderWriter_swigregister = _IMP_em.SpiderMapReaderWriter_swigregister
2508 SpiderMapReaderWriter_swigregister(SpiderMapReaderWriter)
2509 
2510 class FittingSolutions(object):
2511  """Proxy of C++ IMP::em::FittingSolutions class"""
2512  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2513 
2514  def __init__(self):
2515  """__init__(IMP::em::FittingSolutions self) -> FittingSolutions"""
2516  this = _IMP_em.new_FittingSolutions()
2517  try:
2518  self.this.append(this)
2519  except:
2520  self.this = this
2521 
2522  def get_number_of_solutions(self):
2523  """get_number_of_solutions(FittingSolutions self) -> int"""
2524  return _IMP_em.FittingSolutions_get_number_of_solutions(self)
2525 
2526 
2527  def get_transformation(self, i):
2528  """get_transformation(FittingSolutions self, unsigned int i) -> Transformation3D"""
2529  return _IMP_em.FittingSolutions_get_transformation(self, i)
2530 
2531 
2532  def get_score(self, i):
2533  """get_score(FittingSolutions self, unsigned int i) -> IMP::Float"""
2534  return _IMP_em.FittingSolutions_get_score(self, i)
2535 
2536 
2537  def set_score(self, i, score):
2538  """set_score(FittingSolutions self, unsigned int i, IMP::Float score)"""
2539  return _IMP_em.FittingSolutions_set_score(self, i, score)
2540 
2541 
2542  def add_solution(self, t, score):
2543  """add_solution(FittingSolutions self, Transformation3D t, IMP::Float score)"""
2544  return _IMP_em.FittingSolutions_add_solution(self, t, score)
2545 
2546 
2547  def sort(self, reverse=False):
2548  """
2549  sort(FittingSolutions self, bool reverse=False)
2550  sort(FittingSolutions self)
2551  """
2552  return _IMP_em.FittingSolutions_sort(self, reverse)
2553 
2554 
2555  def multiply(self, t):
2556  """multiply(FittingSolutions self, Transformation3D t)"""
2557  return _IMP_em.FittingSolutions_multiply(self, t)
2558 
2559 
2560  def get_transformations(self):
2561  """get_transformations(FittingSolutions self) -> IMP::algebra::Transformation3Ds"""
2562  return _IMP_em.FittingSolutions_get_transformations(self)
2563 
2564 
2565  def show(self, *args):
2566  """
2567  show(FittingSolutions self, _ostream out)
2568  show(FittingSolutions self)
2569  """
2570  return _IMP_em.FittingSolutions_show(self, *args)
2571 
2572 
2573  def __str__(self):
2574  """__str__(FittingSolutions self) -> std::string"""
2575  return _IMP_em.FittingSolutions___str__(self)
2576 
2577 
2578  def __repr__(self):
2579  """__repr__(FittingSolutions self) -> std::string"""
2580  return _IMP_em.FittingSolutions___repr__(self)
2581 
2582  __swig_destroy__ = _IMP_em.delete_FittingSolutions
2583  __del__ = lambda self: None
2584 FittingSolutions_swigregister = _IMP_em.FittingSolutions_swigregister
2585 FittingSolutions_swigregister(FittingSolutions)
2586 
2587 
2588 def local_rigid_fitting_around_point(p, refiner, weight_key, dmap, anchor_centroid, display_log, number_of_optimization_runs=5, number_of_mc_steps=10, number_of_cg_steps=100, max_translation=2., max_rotation=.3, fast=False):
2589  """
2590  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2., IMP::Float max_rotation=.3, bool fast=False) -> FittingSolutions
2591  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2., IMP::Float max_rotation=.3) -> FittingSolutions
2592  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2.) -> FittingSolutions
2593  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100) -> FittingSolutions
2594  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10) -> FittingSolutions
2595  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2596  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log) -> FittingSolutions
2597  """
2598  return _IMP_em.local_rigid_fitting_around_point(p, refiner, weight_key, dmap, anchor_centroid, display_log, number_of_optimization_runs, number_of_mc_steps, number_of_cg_steps, max_translation, max_rotation, fast)
2599 
2600 def local_rigid_fitting(p, refiner, weight_key, dmap, display_log, number_of_optimization_runs=5, number_of_mc_steps=10, number_of_cg_steps=100, max_translation=2., max_rotation=.3, fast=True):
2601  """
2602  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2., IMP::Float max_rotation=.3, bool fast=True) -> FittingSolutions
2603  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2., IMP::Float max_rotation=.3) -> FittingSolutions
2604  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2.) -> FittingSolutions
2605  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100) -> FittingSolutions
2606  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10) -> FittingSolutions
2607  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2608  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log) -> FittingSolutions
2609  """
2610  return _IMP_em.local_rigid_fitting(p, refiner, weight_key, dmap, display_log, number_of_optimization_runs, number_of_mc_steps, number_of_cg_steps, max_translation, max_rotation, fast)
2611 
2612 def local_rigid_fitting_around_points(p, refiner, wei_key, dmap, anchor_centroids, display_log, number_of_optimization_runs=5, number_of_mc_steps=10, number_of_cg_steps=100, max_translation=2., max_rotation=.3):
2613  """
2614  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2., IMP::Float max_rotation=.3) -> FittingSolutions
2615  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2.) -> FittingSolutions
2616  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100) -> FittingSolutions
2617  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10) -> FittingSolutions
2618  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2619  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids, IMP::OptimizerStates display_log) -> FittingSolutions
2620  """
2621  return _IMP_em.local_rigid_fitting_around_points(p, refiner, wei_key, dmap, anchor_centroids, display_log, number_of_optimization_runs, number_of_mc_steps, number_of_cg_steps, max_translation, max_rotation)
2622 
2623 def local_rigid_fitting_grid_search(ps, wei_key, dmap, max_voxels_translation=2, translation_step=1, max_angle_in_radians=0.174, number_of_rotations=100):
2624  """
2625  local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2, IMP::Int translation_step=1, IMP::Float max_angle_in_radians=0.174, IMP::Int number_of_rotations=100) -> FittingSolutions
2626  local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2, IMP::Int translation_step=1, IMP::Float max_angle_in_radians=0.174) -> FittingSolutions
2627  local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2, IMP::Int translation_step=1) -> FittingSolutions
2628  local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2) -> FittingSolutions
2629  local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap) -> FittingSolutions
2630  """
2631  return _IMP_em.local_rigid_fitting_grid_search(ps, wei_key, dmap, max_voxels_translation, translation_step, max_angle_in_radians, number_of_rotations)
2632 
2633 def compute_fitting_scores(*args):
2634  """
2635  compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations, bool fast_version=False, bool local_score=False, FloatKey wei_key) -> FittingSolutions
2636  compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations, bool fast_version=False, bool local_score=False) -> FittingSolutions
2637  compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations, bool fast_version=False) -> FittingSolutions
2638  compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2639  compute_fitting_scores(DensityMap em_map, RigidBody rb, Refiner refiner, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2640  """
2641  return _IMP_em.compute_fitting_scores(*args)
2642 
2643 def compute_fitting_score(*args):
2644  """
2645  compute_fitting_score(IMP::ParticlesTemp const & ps, DensityMap em_map, FloatKey wei_key) -> IMP::Float
2646  compute_fitting_score(IMP::ParticlesTemp const & ps, DensityMap em_map) -> IMP::Float
2647  """
2648  return _IMP_em.compute_fitting_score(*args)
2649 
2651  """
2652  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, Transformation3D t, float thr=0.0) -> long
2653  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, Transformation3D t) -> long
2654  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps) -> long
2655  """
2656  return _IMP_em.get_number_of_particles_outside_of_the_density(*args)
2657 
2658 def get_numbers_of_particles_outside_of_the_density(dmap, ps, transformations, thr=0.0):
2659  """
2660  get_numbers_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, IMP::algebra::Transformation3Ds const & transformations, float thr=0.0) -> IMP::Ints
2661  get_numbers_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, IMP::algebra::Transformation3Ds const & transformations) -> IMP::Ints
2662  """
2663  return _IMP_em.get_numbers_of_particles_outside_of_the_density(dmap, ps, transformations, thr)
2664 
2666  """
2667  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3., Transformation3D t, float thr=0.0) -> double
2668  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3., Transformation3D t) -> double
2669  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3.) -> double
2670  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps) -> double
2671  """
2672  return _IMP_em.get_percentage_of_voxels_covered_by_particles(*args)
2673 class HighDensityEmbedding(IMP.statistics.Embedding):
2674  """Proxy of C++ IMP::em::HighDensityEmbedding class"""
2675  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2676 
2677  def __init__(self, dm, threshold):
2678  """__init__(IMP::em::HighDensityEmbedding self, DensityMap dm, double threshold) -> HighDensityEmbedding"""
2679  this = _IMP_em.new_HighDensityEmbedding(dm, threshold)
2680  try:
2681  self.this.append(this)
2682  except:
2683  self.this = this
2684 
2685  def get_version_info(self):
2686  """get_version_info(HighDensityEmbedding self) -> VersionInfo"""
2687  return _IMP_em.HighDensityEmbedding_get_version_info(self)
2688 
2689 
2690  def __str__(self):
2691  """__str__(HighDensityEmbedding self) -> std::string"""
2692  return _IMP_em.HighDensityEmbedding___str__(self)
2693 
2694 
2695  def __repr__(self):
2696  """__repr__(HighDensityEmbedding self) -> std::string"""
2697  return _IMP_em.HighDensityEmbedding___repr__(self)
2698 
2699 
2700  @staticmethod
2701  def get_from(o):
2702  return _object_cast_to_HighDensityEmbedding(o)
2703 
2704 HighDensityEmbedding_swigregister = _IMP_em.HighDensityEmbedding_swigregister
2705 HighDensityEmbedding_swigregister(HighDensityEmbedding)
2706 
2707 
2708 def mask_and_norm(dmap, mask):
2709  """mask_and_norm(DensityMap dmap, DensityMap mask) -> DensityMap"""
2710  return _IMP_em.mask_and_norm(dmap, mask)
2711 
2712 def get_volume_at_threshold(m, threshold):
2713  """get_volume_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float"""
2714  return _IMP_em.get_volume_at_threshold(m, threshold)
2715 
2717  """
2718  get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold, IMP::atom::ProteinDensityReference ref) -> IMP::Float
2719  get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float
2720  """
2721  return _IMP_em.get_molecular_mass_at_threshold(*args)
2722 
2723 def get_threshold_for_approximate_volume(m, desired_volume):
2724  """get_threshold_for_approximate_volume(DensityMap m, IMP::Float desired_volume) -> IMP::Float"""
2725  return _IMP_em.get_threshold_for_approximate_volume(m, desired_volume)
2726 
2728  """
2729  get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass, IMP::atom::ProteinDensityReference ref) -> IMP::Float
2730  get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass) -> IMP::Float
2731  """
2732  return _IMP_em.get_threshold_for_approximate_mass(*args)
2733 class EnvelopePenetrationRestraint(IMP.Restraint):
2734  """Proxy of C++ IMP::em::EnvelopePenetrationRestraint class"""
2735  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2736 
2737  def __init__(self, ps, em_map, threshold):
2738  """__init__(IMP::em::EnvelopePenetrationRestraint self, IMP::Particles ps, DensityMap em_map, IMP::Float threshold) -> EnvelopePenetrationRestraint"""
2739  this = _IMP_em.new_EnvelopePenetrationRestraint(ps, em_map, threshold)
2740  try:
2741  self.this.append(this)
2742  except:
2743  self.this = this
2744 
2745  def do_get_inputs(self):
2746  """do_get_inputs(EnvelopePenetrationRestraint self) -> IMP::ModelObjectsTemp"""
2747  return _IMP_em.EnvelopePenetrationRestraint_do_get_inputs(self)
2748 
2749 
2750  def get_version_info(self):
2751  """get_version_info(EnvelopePenetrationRestraint self) -> VersionInfo"""
2752  return _IMP_em.EnvelopePenetrationRestraint_get_version_info(self)
2753 
2754 
2755  def __str__(self):
2756  """__str__(EnvelopePenetrationRestraint self) -> std::string"""
2757  return _IMP_em.EnvelopePenetrationRestraint___str__(self)
2758 
2759 
2760  def __repr__(self):
2761  """__repr__(EnvelopePenetrationRestraint self) -> std::string"""
2762  return _IMP_em.EnvelopePenetrationRestraint___repr__(self)
2763 
2764 
2765  @staticmethod
2766  def get_from(o):
2767  return _object_cast_to_EnvelopePenetrationRestraint(o)
2768 
2769 EnvelopePenetrationRestraint_swigregister = _IMP_em.EnvelopePenetrationRestraint_swigregister
2770 EnvelopePenetrationRestraint_swigregister(EnvelopePenetrationRestraint)
2771 
2772 class PCAFitRestraint(IMP.Restraint):
2773  """Proxy of C++ IMP::em::PCAFitRestraint class"""
2774  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2775 
2776  def __init__(self, *args):
2777  """
2778  __init__(IMP::em::PCAFitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, float threahold, float max_pca_size_diff, float max_angle_diff, float max_centroid_diff, FloatKey weight_key) -> PCAFitRestraint
2779  __init__(IMP::em::PCAFitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, float threahold, float max_pca_size_diff, float max_angle_diff, float max_centroid_diff) -> PCAFitRestraint
2780  """
2781  this = _IMP_em.new_PCAFitRestraint(*args)
2782  try:
2783  self.this.append(this)
2784  except:
2785  self.this = this
2786 
2787  def do_get_inputs(self):
2788  """do_get_inputs(PCAFitRestraint self) -> IMP::ModelObjectsTemp"""
2789  return _IMP_em.PCAFitRestraint_do_get_inputs(self)
2790 
2791 
2792  def get_version_info(self):
2793  """get_version_info(PCAFitRestraint self) -> VersionInfo"""
2794  return _IMP_em.PCAFitRestraint_get_version_info(self)
2795 
2796 
2797  def __str__(self):
2798  """__str__(PCAFitRestraint self) -> std::string"""
2799  return _IMP_em.PCAFitRestraint___str__(self)
2800 
2801 
2802  def __repr__(self):
2803  """__repr__(PCAFitRestraint self) -> std::string"""
2804  return _IMP_em.PCAFitRestraint___repr__(self)
2805 
2806 
2807  @staticmethod
2808  def get_from(o):
2809  return _object_cast_to_PCAFitRestraint(o)
2810 
2811 PCAFitRestraint_swigregister = _IMP_em.PCAFitRestraint_swigregister
2812 PCAFitRestraint_swigregister(PCAFitRestraint)
2813 
2814 class EnvelopeFitRestraint(IMP.Restraint):
2815  """Proxy of C++ IMP::em::EnvelopeFitRestraint class"""
2816  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2817 
2818  def __init__(self, particles, em_map, density_threshold, penetration_threshold):
2819  """__init__(IMP::em::EnvelopeFitRestraint self, IMP::Particles particles, DensityMap em_map, double density_threshold, double penetration_threshold) -> EnvelopeFitRestraint"""
2820  this = _IMP_em.new_EnvelopeFitRestraint(particles, em_map, density_threshold, penetration_threshold)
2821  try:
2822  self.this.append(this)
2823  except:
2824  self.this = this
2825 
2826  def get_transformation(self):
2827  """get_transformation(EnvelopeFitRestraint self) -> Transformation3D"""
2828  return _IMP_em.EnvelopeFitRestraint_get_transformation(self)
2829 
2830 
2831  def apply_transformation(self):
2832  """apply_transformation(EnvelopeFitRestraint self)"""
2833  return _IMP_em.EnvelopeFitRestraint_apply_transformation(self)
2834 
2835 
2836  def do_get_inputs(self):
2837  """do_get_inputs(EnvelopeFitRestraint self) -> IMP::ModelObjectsTemp"""
2838  return _IMP_em.EnvelopeFitRestraint_do_get_inputs(self)
2839 
2840 
2841  def get_version_info(self):
2842  """get_version_info(EnvelopeFitRestraint self) -> VersionInfo"""
2843  return _IMP_em.EnvelopeFitRestraint_get_version_info(self)
2844 
2845 
2846  def __str__(self):
2847  """__str__(EnvelopeFitRestraint self) -> std::string"""
2848  return _IMP_em.EnvelopeFitRestraint___str__(self)
2849 
2850 
2851  def __repr__(self):
2852  """__repr__(EnvelopeFitRestraint self) -> std::string"""
2853  return _IMP_em.EnvelopeFitRestraint___repr__(self)
2854 
2855 
2856  @staticmethod
2857  def get_from(o):
2858  return _object_cast_to_EnvelopeFitRestraint(o)
2859 
2860 EnvelopeFitRestraint_swigregister = _IMP_em.EnvelopeFitRestraint_swigregister
2861 EnvelopeFitRestraint_swigregister(EnvelopeFitRestraint)
2862 
2863 
2864 import math
2865 
2866 def write_pca_cmm(pca, fh):
2867  """Write out principal components to a file in Chimera Marker format"""
2868  eigen_values = pca.get_principal_values()
2869  eigen_vecs = pca.get_principal_components()
2870  centroid = pca.get_centroid()
2871 
2872  fh.write("<marker_set>\n")
2873  fh.write("<!-- PCA with eigen values: (%g,%g,%g) and "
2874  "centroid (%g,%g,%g) -->\n"
2875  % (math.sqrt(eigen_values[0]),
2876  math.sqrt(eigen_values[1]),
2877  math.sqrt(eigen_values[2]),
2878  centroid[0], centroid[1], centroid[2]))
2879 
2880  radius = 2.
2881 
2882  for i in range(3):
2883  val = math.sqrt(eigen_values[i])
2884  v1 = centroid - val * eigen_vecs[i]
2885  v2 = centroid + val * eigen_vecs[i]
2886  for markerid, v in ((i*2+1, v1), (i*2+2, v2)):
2887  fh.write("<marker id=\"%d\" x=\"%g\" y=\"%g\" z=\"%g\" "
2888  "radius=\"%g\"/>\n"
2889  % (markerid, v[0], v[1], v[2], radius))
2890 
2891  for i in range(1, 7, 2):
2892  fh.write("<link id1= \"%d\" id2=\"%d\" radius=\"%g\"/>\n"
2893  % (i, i+1, radius))
2894  fh.write("</marker_set>\n")
2895 
2896 
2897 def get_module_version():
2898  """get_module_version() -> std::string const"""
2899  return _IMP_em.get_module_version()
2900 
2901 def get_example_path(fname):
2902  """get_example_path(std::string fname) -> std::string"""
2903  return _IMP_em.get_example_path(fname)
2904 
2905 def get_data_path(fname):
2906  """get_data_path(std::string fname) -> std::string"""
2907  return _IMP_em.get_data_path(fname)
2908 
2909 from . import _version_check
2910 _version_check.check_version(get_module_version())
2911 __version__ = get_module_version()
2912 
2913 
2914 
Float get_threshold_for_approximate_mass(DensityMap *m, Float desired_mass, atom::ProteinDensityReference ref=atom::HARPAZ)
Computes the threshold to consider in an EM map to get a desired mass.
DensityMap * interpolate_map(DensityMap *in_map, double new_spacing)
Return a new map with an updated spacing.
Particles density2particles(DensityMap *dmap, Float threshold, Model *m, int step=1)
Convert a density grid to a set of particles.
algebra::Vector3Ds density2vectors(DensityMap *dmap, Float threshold)
Convert a density grid to a set of vectors.
algebra::BoundingBoxD< 3 > get_bounding_box(const DensityMap *m, Float threshold)
Get the bounding box for a map.
Ints get_numbers_of_particles_outside_of_the_density(DensityMap *dmap, const Particles &ps, const IMP::algebra::Transformation3Ds &transformations, float thr=0.0)
Get numbers of particles (mult transforms) that are outside the density.
Various classes to hold sets of particles.
DensityMap * binarize(DensityMap *orig_map, float threshold, bool reverse=false)
Return a map with 0 for all voxels below the threshold and 1 for those above.
double get_sum(const DensityMap *m1)
Return the sum of all voxels.
SampledDensityMap * particles2binarized_density(const ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
Definition: converters.h:76
Make CGAL functionality available to IMP.
DensityMap * mask_and_norm(em::DensityMap *dmap, em::DensityMap *mask)
Return a masked density, and normalize the output map within the mask region.
FittingSolutions compute_fitting_scores(const ParticlesTemp &ps, DensityMap *em_map, const algebra::Transformation3Ds &transformations, bool fast_version=false, bool local_score=false, const FloatKey &wei_key=atom::Mass::get_mass_key())
Compute fitting scores for a given set of rigid transformations.
DensityMap * get_threshold_map(const DensityMap *orig_map, float threshold)
Return a map with 0 for all voxels below the threshold.
DensityMap * get_segment_by_masking(DensityMap *map_to_segment, DensityMap *mask, float mas_threshold)
Get a segment of the map covered by another map.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
SampledDensityMap * particles2density(const ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
Resample a set of particles into a density grid.
Composable functors to implement scores via compile-time composition.
Code to compute statistical measures.
algebra::GridD< 3, algebra::DenseGridStorageD< 3, float >, float > get_grid(DensityMap *in_map)
Return a dense grid containing the voxels of the passed density map.
def write_pca_cmm
Write out principal components to a file in Chimera Marker format.
double convolute(const DensityMap *m1, const DensityMap *m2)
Return a convolution between density maps m1 and m2.
Common base class for heavy weight IMP objects.
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].
DensityHeader create_density_header(const algebra::BoundingBoxD< 3 > &bb, float spacing)
Create a header from a bounding box in 3D.
Float compute_fitting_score(const ParticlesTemp &ps, DensityMap *em_map, FloatKey wei_key=atom::Mass::get_mass_key())
Compute fitting scores for a given set of rigid transformations.
FittingSolutions local_rigid_fitting_around_point(Particle *p, Refiner *refiner, const FloatKey &weight_key, DensityMap *dmap, const algebra::Vector3D &anchor_centroid, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3, bool fast=false)
Local rigid fitting of a rigid body around a center point.
long get_number_of_particles_outside_of_the_density(DensityMap *dmap, const Particles &ps, const IMP::algebra::Transformation3D &t=IMP::algebra::get_identity_transformation_3d(), float thr=0.0)
Get the number of particles that are outside of the density.
DensityMap * get_max_map(DensityMaps maps)
Return a map where each voxel is the maximum value from the input maps.
DensityMap * create_density_map(const DensityMap *other)
Create a copy of another map.
Store data to be clustered for embedding based algorithms.
Float approximate_molecular_mass(DensityMap *m, Float threshold)
Estimate the molecular mass from a map.
double get_percentage_of_voxels_covered_by_particles(DensityMap *dmap, const Particles &ps, float smoothing_radius=3., const IMP::algebra::Transformation3D &t=IMP::algebra::get_identity_transformation_3d(), float thr=0.0)
Get the number of density voxels that are not covered by particles.
Vector3D get_centroid(const Vector3Ds &ps)
Returns the centroid of a set of vectors.
Definition: Vector3D.h:56
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:52