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IMP Reference Guide  2.8.0
The Integrative Modeling Platform
em/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.10
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 2007-2017 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 as _swig_python_version_info
16 if _swig_python_version_info >= (2, 7, 0):
17  def swig_import_helper():
18  import importlib
19  pkg = __name__.rpartition('.')[0]
20  mname = '.'.join((pkg, '_IMP_em')).lstrip('.')
21  try:
22  return importlib.import_module(mname)
23  except ImportError:
24  return importlib.import_module('_IMP_em')
25  _IMP_em = swig_import_helper()
26  del swig_import_helper
27 elif _swig_python_version_info >= (2, 6, 0):
28  def swig_import_helper():
29  from os.path import dirname
30  import imp
31  fp = None
32  try:
33  fp, pathname, description = imp.find_module('_IMP_em', [dirname(__file__)])
34  except ImportError:
35  import _IMP_em
36  return _IMP_em
37  if fp is not None:
38  try:
39  _mod = imp.load_module('_IMP_em', fp, pathname, description)
40  finally:
41  fp.close()
42  return _mod
43  _IMP_em = swig_import_helper()
44  del swig_import_helper
45 else:
46  import _IMP_em
47 del _swig_python_version_info
48 try:
49  _swig_property = property
50 except NameError:
51  pass # Python < 2.2 doesn't have 'property'.
52 
53 try:
54  import builtins as __builtin__
55 except ImportError:
56  import __builtin__
57 
58 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
59  if (name == "thisown"):
60  return self.this.own(value)
61  if (name == "this"):
62  if type(value).__name__ == 'SwigPyObject':
63  self.__dict__[name] = value
64  return
65  method = class_type.__swig_setmethods__.get(name, None)
66  if method:
67  return method(self, value)
68  if (not static):
69  object.__setattr__(self, name, value)
70  else:
71  raise AttributeError("You cannot add attributes to %s" % self)
72 
73 
74 def _swig_setattr(self, class_type, name, value):
75  return _swig_setattr_nondynamic(self, class_type, name, value, 0)
76 
77 
78 def _swig_getattr(self, class_type, name):
79  if (name == "thisown"):
80  return self.this.own()
81  method = class_type.__swig_getmethods__.get(name, None)
82  if method:
83  return method(self)
84  raise AttributeError("'%s' object has no attribute '%s'" % (class_type.__name__, name))
85 
86 
87 def _swig_repr(self):
88  try:
89  strthis = "proxy of " + self.this.__repr__()
90  except __builtin__.Exception:
91  strthis = ""
92  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
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 __builtin__.Exception:
110  weakref_proxy = lambda x: x
111 
112 
113 class IMP_EM_SwigPyIterator(object):
114  """Proxy of C++ swig::IMP_EM_SwigPyIterator class."""
115 
116  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
117 
118  def __init__(self, *args, **kwargs):
119  raise AttributeError("No constructor defined - class is abstract")
120  __repr__ = _swig_repr
121  __swig_destroy__ = _IMP_em.delete_IMP_EM_SwigPyIterator
122  __del__ = lambda self: None
123 
124  def value(self):
125  """value(IMP_EM_SwigPyIterator self) -> PyObject *"""
126  return _IMP_em.IMP_EM_SwigPyIterator_value(self)
127 
128 
129  def incr(self, n=1):
130  """
131  incr(IMP_EM_SwigPyIterator self, size_t n=1) -> IMP_EM_SwigPyIterator
132  incr(IMP_EM_SwigPyIterator self) -> IMP_EM_SwigPyIterator
133  """
134  return _IMP_em.IMP_EM_SwigPyIterator_incr(self, n)
135 
136 
137  def decr(self, n=1):
138  """
139  decr(IMP_EM_SwigPyIterator self, size_t n=1) -> IMP_EM_SwigPyIterator
140  decr(IMP_EM_SwigPyIterator self) -> IMP_EM_SwigPyIterator
141  """
142  return _IMP_em.IMP_EM_SwigPyIterator_decr(self, n)
143 
144 
145  def distance(self, x):
146  """distance(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> ptrdiff_t"""
147  return _IMP_em.IMP_EM_SwigPyIterator_distance(self, x)
148 
149 
150  def equal(self, x):
151  """equal(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> bool"""
152  return _IMP_em.IMP_EM_SwigPyIterator_equal(self, x)
153 
154 
155  def copy(self):
156  """copy(IMP_EM_SwigPyIterator self) -> IMP_EM_SwigPyIterator"""
157  return _IMP_em.IMP_EM_SwigPyIterator_copy(self)
158 
159 
160  def next(self):
161  """next(IMP_EM_SwigPyIterator self) -> PyObject *"""
162  return _IMP_em.IMP_EM_SwigPyIterator_next(self)
163 
164 
165  def __next__(self):
166  """__next__(IMP_EM_SwigPyIterator self) -> PyObject *"""
167  return _IMP_em.IMP_EM_SwigPyIterator___next__(self)
168 
169 
170  def previous(self):
171  """previous(IMP_EM_SwigPyIterator self) -> PyObject *"""
172  return _IMP_em.IMP_EM_SwigPyIterator_previous(self)
173 
174 
175  def advance(self, n):
176  """advance(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator"""
177  return _IMP_em.IMP_EM_SwigPyIterator_advance(self, n)
178 
179 
180  def __eq__(self, x):
181  """__eq__(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> bool"""
182  return _IMP_em.IMP_EM_SwigPyIterator___eq__(self, x)
183 
184 
185  def __ne__(self, x):
186  """__ne__(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> bool"""
187  return _IMP_em.IMP_EM_SwigPyIterator___ne__(self, x)
188 
189 
190  def __iadd__(self, n):
191  """__iadd__(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator"""
192  return _IMP_em.IMP_EM_SwigPyIterator___iadd__(self, n)
193 
194 
195  def __isub__(self, n):
196  """__isub__(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator"""
197  return _IMP_em.IMP_EM_SwigPyIterator___isub__(self, n)
198 
199 
200  def __add__(self, n):
201  """__add__(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator"""
202  return _IMP_em.IMP_EM_SwigPyIterator___add__(self, n)
203 
204 
205  def __sub__(self, *args):
206  """
207  __sub__(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator
208  __sub__(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> ptrdiff_t
209  """
210  return _IMP_em.IMP_EM_SwigPyIterator___sub__(self, *args)
211 
212  def __iter__(self):
213  return self
214 IMP_EM_SwigPyIterator_swigregister = _IMP_em.IMP_EM_SwigPyIterator_swigregister
215 IMP_EM_SwigPyIterator_swigregister(IMP_EM_SwigPyIterator)
216 
217 
218 _value_types=[]
219 _object_types=[]
220 _raii_types=[]
221 _plural_types=[]
222 
223 IMP_DEBUG = _IMP_em.IMP_DEBUG
224 IMP_RELEASE = _IMP_em.IMP_RELEASE
225 IMP_SILENT = _IMP_em.IMP_SILENT
226 IMP_PROGRESS = _IMP_em.IMP_PROGRESS
227 IMP_TERSE = _IMP_em.IMP_TERSE
228 IMP_VERBOSE = _IMP_em.IMP_VERBOSE
229 IMP_MEMORY = _IMP_em.IMP_MEMORY
230 IMP_NONE = _IMP_em.IMP_NONE
231 IMP_USAGE = _IMP_em.IMP_USAGE
232 IMP_INTERNAL = _IMP_em.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_em.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_em.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_em.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_em.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_em.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_em.IMP_KERNEL_HAS_GPERFTOOLS
239 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
240 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
241 IMPKERNEL_SHOW_WARNINGS = _IMP_em.IMPKERNEL_SHOW_WARNINGS
242 
243 import sys
244 class _DirectorObjects(object):
245  """@internal Simple class to keep references to director objects
246  to prevent premature deletion."""
247  def __init__(self):
248  self._objects = []
249  def register(self, obj):
250  """Take a reference to a director object; will only work for
251  refcounted C++ classes"""
252  if hasattr(obj, 'get_ref_count'):
253  self._objects.append(obj)
254  def cleanup(self):
255  """Only drop our reference and allow cleanup by Python if no other
256  Python references exist (we hold 3 references: one in self._objects,
257  one in x, and one in the argument list for getrefcount) *and* no
258  other C++ references exist (the Python object always holds one)"""
259  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
260  or x.get_ref_count() > 1]
261 # Do in two steps so the references are kept until the end of the
262 # function (deleting references may trigger a fresh call to this method)
263  self._objects = objs
264  def get_object_count(self):
265  """Get number of director objects (useful for testing only)"""
266  return len(self._objects)
267 _director_objects = _DirectorObjects()
268 
269 class _ostream(object):
270  """Proxy of C++ std::ostream class."""
271 
272  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
273 
274  def __init__(self, *args, **kwargs):
275  raise AttributeError("No constructor defined")
276  __repr__ = _swig_repr
277 
278  def write(self, osa_buf):
279  """write(_ostream self, char const * osa_buf)"""
280  return _IMP_em._ostream_write(self, osa_buf)
281 
282 _ostream_swigregister = _IMP_em._ostream_swigregister
283 _ostream_swigregister(_ostream)
284 
285 IMP_COMPILER_HAS_OVERRIDE = _IMP_em.IMP_COMPILER_HAS_OVERRIDE
286 IMP_COMPILER_HAS_FINAL = _IMP_em.IMP_COMPILER_HAS_FINAL
287 IMP_HAS_NOEXCEPT = _IMP_em.IMP_HAS_NOEXCEPT
288 import IMP
289 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CGAL_HAS_BOOST_FILESYSTEM
290 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
291 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_em.IMP_CGAL_HAS_BOOST_RANDOM
292 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_em.IMP_CGAL_HAS_BOOST_SYSTEM
293 IMPCGAL_SHOW_WARNINGS = _IMP_em.IMPCGAL_SHOW_WARNINGS
294 import IMP.cgal
295 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_em.IMP_ALGEBRA_HAS_IMP_CGAL
296 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
297 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
298 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_RANDOM
299 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_SYSTEM
300 IMP_ALGEBRA_HAS_CGAL = _IMP_em.IMP_ALGEBRA_HAS_CGAL
301 IMP_ALGEBRA_HAS_ANN = _IMP_em.IMP_ALGEBRA_HAS_ANN
302 IMPALGEBRA_SHOW_WARNINGS = _IMP_em.IMPALGEBRA_SHOW_WARNINGS
303 import IMP.algebra
304 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_em.IMP_DISPLAY_HAS_IMP_CGAL
305 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
306 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
307 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_em.IMP_DISPLAY_HAS_BOOST_RANDOM
308 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_em.IMP_DISPLAY_HAS_BOOST_SYSTEM
309 IMP_DISPLAY_HAS_CGAL = _IMP_em.IMP_DISPLAY_HAS_CGAL
310 IMPDISPLAY_SHOW_WARNINGS = _IMP_em.IMPDISPLAY_SHOW_WARNINGS
311 import IMP.display
312 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_em.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
313 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
314 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
315 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
316 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
317 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_em.IMP_SCORE_FUNCTOR_HAS_CGAL
318 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_em.IMP_SCORE_FUNCTOR_HAS_HDF5
319 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_em.IMPSCOREFUNCTOR_SHOW_WARNINGS
320 import IMP.score_functor
321 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_em.IMP_STATISTICS_HAS_IMP_CGAL
322 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
323 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
324 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_em.IMP_STATISTICS_HAS_BOOST_RANDOM
325 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_SYSTEM
326 IMP_STATISTICS_HAS_CGAL = _IMP_em.IMP_STATISTICS_HAS_CGAL
327 IMPSTATISTICS_SHOW_WARNINGS = _IMP_em.IMPSTATISTICS_SHOW_WARNINGS
328 import IMP.statistics
329 IMP_CORE_HAS_IMP_CGAL = _IMP_em.IMP_CORE_HAS_IMP_CGAL
330 IMP_CORE_HAS_IMP_KERNEL = _IMP_em.IMP_CORE_HAS_IMP_KERNEL
331 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_FILESYSTEM
332 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
333 IMP_CORE_HAS_BOOST_RANDOM = _IMP_em.IMP_CORE_HAS_BOOST_RANDOM
334 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_SYSTEM
335 IMP_CORE_HAS_CGAL = _IMP_em.IMP_CORE_HAS_CGAL
336 IMP_CORE_HAS_HDF5 = _IMP_em.IMP_CORE_HAS_HDF5
337 IMPCORE_SHOW_WARNINGS = _IMP_em.IMPCORE_SHOW_WARNINGS
338 import IMP.core
339 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_em.IMP_CONTAINER_HAS_IMP_ALGEBRA
340 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_em.IMP_CONTAINER_HAS_IMP_CGAL
341 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_em.IMP_CONTAINER_HAS_IMP_DISPLAY
342 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_em.IMP_CONTAINER_HAS_IMP_KERNEL
343 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
344 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
345 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
346 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_em.IMP_CONTAINER_HAS_BOOST_RANDOM
347 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_SYSTEM
348 IMP_CONTAINER_HAS_CGAL = _IMP_em.IMP_CONTAINER_HAS_CGAL
349 IMP_CONTAINER_HAS_HDF5 = _IMP_em.IMP_CONTAINER_HAS_HDF5
350 IMPCONTAINER_SHOW_WARNINGS = _IMP_em.IMPCONTAINER_SHOW_WARNINGS
351 import IMP.container
352 IMP_ATOM_HAS_IMP_CGAL = _IMP_em.IMP_ATOM_HAS_IMP_CGAL
353 IMP_ATOM_HAS_IMP_KERNEL = _IMP_em.IMP_ATOM_HAS_IMP_KERNEL
354 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
355 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
356 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_em.IMP_ATOM_HAS_BOOST_RANDOM
357 IMP_ATOM_HAS_BOOST_REGEX = _IMP_em.IMP_ATOM_HAS_BOOST_REGEX
358 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_em.IMP_ATOM_HAS_BOOST_SYSTEM
359 IMP_ATOM_HAS_CGAL = _IMP_em.IMP_ATOM_HAS_CGAL
360 IMP_ATOM_HAS_HDF5 = _IMP_em.IMP_ATOM_HAS_HDF5
361 IMPATOM_SHOW_WARNINGS = _IMP_em.IMPATOM_SHOW_WARNINGS
362 IMP_ATOM_TYPE_INDEX = _IMP_em.IMP_ATOM_TYPE_INDEX
363 IMP_RESIDUE_TYPE_INDEX = _IMP_em.IMP_RESIDUE_TYPE_INDEX
364 IMP_HIERARCHY_TYPE_INDEX = _IMP_em.IMP_HIERARCHY_TYPE_INDEX
365 import IMP.atom
366 IMP_EM_HAS_IMP_CGAL = _IMP_em.IMP_EM_HAS_IMP_CGAL
367 IMP_EM_HAS_IMP_CONTAINER = _IMP_em.IMP_EM_HAS_IMP_CONTAINER
368 IMP_EM_HAS_IMP_DISPLAY = _IMP_em.IMP_EM_HAS_IMP_DISPLAY
369 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_EM_HAS_IMP_SCORE_FUNCTOR
370 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_EM_HAS_BOOST_FILESYSTEM
371 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
372 IMP_EM_HAS_BOOST_RANDOM = _IMP_em.IMP_EM_HAS_BOOST_RANDOM
373 IMP_EM_HAS_BOOST_REGEX = _IMP_em.IMP_EM_HAS_BOOST_REGEX
374 IMP_EM_HAS_BOOST_SYSTEM = _IMP_em.IMP_EM_HAS_BOOST_SYSTEM
375 IMP_EM_HAS_CGAL = _IMP_em.IMP_EM_HAS_CGAL
376 IMP_EM_HAS_HDF5 = _IMP_em.IMP_EM_HAS_HDF5
377 IMPEM_SHOW_WARNINGS = _IMP_em.IMPEM_SHOW_WARNINGS
378 
379 _object_types.append("DensityMap")
380 
381 
382 def _object_cast_to_DensityMap(o):
383  """_object_cast_to_DensityMap(Object o) -> DensityMap"""
384  return _IMP_em._object_cast_to_DensityMap(o)
385 
386 _object_types.append("SampledDensityMap")
387 
388 
389 def _object_cast_to_SampledDensityMap(o):
390  """_object_cast_to_SampledDensityMap(Object o) -> SampledDensityMap"""
391  return _IMP_em._object_cast_to_SampledDensityMap(o)
392 
393 _object_types.append("SurfaceShellDensityMap")
394 
395 
396 def _object_cast_to_SurfaceShellDensityMap(o):
397  """_object_cast_to_SurfaceShellDensityMap(Object o) -> SurfaceShellDensityMap"""
398  return _IMP_em._object_cast_to_SurfaceShellDensityMap(o)
399 
400 _object_types.append("FitRestraint")
401 
402 
403 def _object_cast_to_FitRestraint(o):
404  """_object_cast_to_FitRestraint(Object o) -> FitRestraint"""
405  return _IMP_em._object_cast_to_FitRestraint(o)
406 
407 _object_types.append("PCAFitRestraint")
408 
409 
410 def _object_cast_to_PCAFitRestraint(o):
411  """_object_cast_to_PCAFitRestraint(Object o) -> PCAFitRestraint"""
412  return _IMP_em._object_cast_to_PCAFitRestraint(o)
413 
414 _object_types.append("EnvelopePenetrationRestraint")
415 
416 
417 def _object_cast_to_EnvelopePenetrationRestraint(o):
418  """_object_cast_to_EnvelopePenetrationRestraint(Object o) -> EnvelopePenetrationRestraint"""
419  return _IMP_em._object_cast_to_EnvelopePenetrationRestraint(o)
420 
421 _object_types.append("EnvelopeFitRestraint")
422 
423 
424 def _object_cast_to_EnvelopeFitRestraint(o):
425  """_object_cast_to_EnvelopeFitRestraint(Object o) -> EnvelopeFitRestraint"""
426  return _IMP_em._object_cast_to_EnvelopeFitRestraint(o)
427 
428 KernelParametersList=list
429 _plural_types.append("KernelParametersList")
430 _value_types.append("KernelParameters")
431 
432 
433 _object_types.append("HighDensityEmbedding")
434 
435 
436 def _object_cast_to_HighDensityEmbedding(o):
437  """_object_cast_to_HighDensityEmbedding(Object o) -> HighDensityEmbedding"""
438  return _IMP_em._object_cast_to_HighDensityEmbedding(o)
439 
440 _object_types.append("MapReaderWriter")
441 
442 
443 def _object_cast_to_MapReaderWriter(o):
444  """_object_cast_to_MapReaderWriter(Object o) -> MapReaderWriter"""
445  return _IMP_em._object_cast_to_MapReaderWriter(o)
446 
447 _object_types.append("MRCReaderWriter")
448 
449 
450 def _object_cast_to_MRCReaderWriter(o):
451  """_object_cast_to_MRCReaderWriter(Object o) -> MRCReaderWriter"""
452  return _IMP_em._object_cast_to_MRCReaderWriter(o)
453 
454 _object_types.append("SpiderMapReaderWriter")
455 
456 
457 def _object_cast_to_SpiderMapReaderWriter(o):
458  """_object_cast_to_SpiderMapReaderWriter(Object o) -> SpiderMapReaderWriter"""
459  return _IMP_em._object_cast_to_SpiderMapReaderWriter(o)
460 
461 _object_types.append("EMReaderWriter")
462 
463 
464 def _object_cast_to_EMReaderWriter(o):
465  """_object_cast_to_EMReaderWriter(Object o) -> EMReaderWriter"""
466  return _IMP_em._object_cast_to_EMReaderWriter(o)
467 
468 _object_types.append("XplorReaderWriter")
469 
470 
471 def _object_cast_to_XplorReaderWriter(o):
472  """_object_cast_to_XplorReaderWriter(Object o) -> XplorReaderWriter"""
473  return _IMP_em._object_cast_to_XplorReaderWriter(o)
474 
475 _object_types.append("CoarseCC")
476 
477 
478 def _object_cast_to_CoarseCC(o):
479  """_object_cast_to_CoarseCC(Object o) -> CoarseCC"""
480  return _IMP_em._object_cast_to_CoarseCC(o)
481 
482 _object_types.append("CoarseCCatIntervals")
483 
484 
485 def _object_cast_to_CoarseCCatIntervals(o):
486  """_object_cast_to_CoarseCCatIntervals(Object o) -> CoarseCCatIntervals"""
487  return _IMP_em._object_cast_to_CoarseCCatIntervals(o)
488 
489 FittingSolutionsList=list
490 _plural_types.append("FittingSolutionsList")
491 _value_types.append("FittingSolutions")
492 
493 class MapReaderWriter(IMP.Object):
494  """Proxy of C++ IMP::em::MapReaderWriter class."""
495 
496  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
497 
498  def __init__(self):
499  """__init__(IMP::em::MapReaderWriter self) -> MapReaderWriter"""
500  this = _IMP_em.new_MapReaderWriter()
501  try:
502  self.this.append(this)
503  except __builtin__.Exception:
504  self.this = this
505 
506  def get_version_info(self):
507  """get_version_info(MapReaderWriter self) -> VersionInfo"""
508  return _IMP_em.MapReaderWriter_get_version_info(self)
509 
510 
511  def __str__(self):
512  """__str__(MapReaderWriter self) -> std::string"""
513  return _IMP_em.MapReaderWriter___str__(self)
514 
515 
516  def __repr__(self):
517  """__repr__(MapReaderWriter self) -> std::string"""
518  return _IMP_em.MapReaderWriter___repr__(self)
519 
520 
521  @staticmethod
522  def get_from(o):
523  return _object_cast_to_MapReaderWriter(o)
524 
525 MapReaderWriter_swigregister = _IMP_em.MapReaderWriter_swigregister
526 MapReaderWriter_swigregister(MapReaderWriter)
527 cvar = _IMP_em.cvar
528 EPS = cvar.EPS
529 
530 class DensityHeader(object):
531  """Proxy of C++ IMP::em::DensityHeader class."""
532 
533  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
534  __repr__ = _swig_repr
535 
536  def __init__(self):
537  """__init__(IMP::em::DensityHeader self) -> DensityHeader"""
538  this = _IMP_em.new_DensityHeader()
539  try:
540  self.this.append(this)
541  except __builtin__.Exception:
542  self.this = this
543 
544  def get_top(self, ind):
545  """get_top(DensityHeader self, int ind) -> IMP::em::emreal"""
546  return _IMP_em.DensityHeader_get_top(self, ind)
547 
548 
549  def compute_xyz_top(self, force=False):
550  """
551  compute_xyz_top(DensityHeader self, bool force=False)
552  compute_xyz_top(DensityHeader self)
553  """
554  return _IMP_em.DensityHeader_compute_xyz_top(self, force)
555 
556 
557  def update_map_dimensions(self, nnx, nny, nnz):
558  """update_map_dimensions(DensityHeader self, int nnx, int nny, int nnz)"""
559  return _IMP_em.DensityHeader_update_map_dimensions(self, nnx, nny, nnz)
560 
561 
562  def update_cell_dimensions(self):
563  """update_cell_dimensions(DensityHeader self)"""
564  return _IMP_em.DensityHeader_update_cell_dimensions(self)
565 
566 
567  def show(self, *args):
568  """
569  show(DensityHeader self, _ostream out)
570  show(DensityHeader self)
571  """
572  return _IMP_em.DensityHeader_show(self, *args)
573 
574  MAP_FIELD_SIZE = _IMP_em.DensityHeader_MAP_FIELD_SIZE
575  USER_FIELD_SIZE = _IMP_em.DensityHeader_USER_FIELD_SIZE
576  COMMENT_FIELD_NUM_OF = _IMP_em.DensityHeader_COMMENT_FIELD_NUM_OF
577  COMMENT_FIELD_SINGLE_SIZE = _IMP_em.DensityHeader_COMMENT_FIELD_SINGLE_SIZE
578  nxstart = _swig_property(_IMP_em.DensityHeader_nxstart_get, _IMP_em.DensityHeader_nxstart_set)
579  nystart = _swig_property(_IMP_em.DensityHeader_nystart_get, _IMP_em.DensityHeader_nystart_set)
580  nzstart = _swig_property(_IMP_em.DensityHeader_nzstart_get, _IMP_em.DensityHeader_nzstart_set)
581  mx = _swig_property(_IMP_em.DensityHeader_mx_get, _IMP_em.DensityHeader_mx_set)
582  my = _swig_property(_IMP_em.DensityHeader_my_get, _IMP_em.DensityHeader_my_set)
583  mz = _swig_property(_IMP_em.DensityHeader_mz_get, _IMP_em.DensityHeader_mz_set)
584  xlen = _swig_property(_IMP_em.DensityHeader_xlen_get, _IMP_em.DensityHeader_xlen_set)
585  ylen = _swig_property(_IMP_em.DensityHeader_ylen_get, _IMP_em.DensityHeader_ylen_set)
586  zlen = _swig_property(_IMP_em.DensityHeader_zlen_get, _IMP_em.DensityHeader_zlen_set)
587  alpha = _swig_property(_IMP_em.DensityHeader_alpha_get, _IMP_em.DensityHeader_alpha_set)
588  beta = _swig_property(_IMP_em.DensityHeader_beta_get, _IMP_em.DensityHeader_beta_set)
589  gamma = _swig_property(_IMP_em.DensityHeader_gamma_get, _IMP_em.DensityHeader_gamma_set)
590  mapc = _swig_property(_IMP_em.DensityHeader_mapc_get, _IMP_em.DensityHeader_mapc_set)
591  mapr = _swig_property(_IMP_em.DensityHeader_mapr_get, _IMP_em.DensityHeader_mapr_set)
592  maps = _swig_property(_IMP_em.DensityHeader_maps_get, _IMP_em.DensityHeader_maps_set)
593  dmin = _swig_property(_IMP_em.DensityHeader_dmin_get, _IMP_em.DensityHeader_dmin_set)
594  dmax = _swig_property(_IMP_em.DensityHeader_dmax_get, _IMP_em.DensityHeader_dmax_set)
595  dmean = _swig_property(_IMP_em.DensityHeader_dmean_get, _IMP_em.DensityHeader_dmean_set)
596  ispg = _swig_property(_IMP_em.DensityHeader_ispg_get, _IMP_em.DensityHeader_ispg_set)
597  nsymbt = _swig_property(_IMP_em.DensityHeader_nsymbt_get, _IMP_em.DensityHeader_nsymbt_set)
598  user = _swig_property(_IMP_em.DensityHeader_user_get, _IMP_em.DensityHeader_user_set)
599  map = _swig_property(_IMP_em.DensityHeader_map_get, _IMP_em.DensityHeader_map_set)
600  machinestamp = _swig_property(_IMP_em.DensityHeader_machinestamp_get, _IMP_em.DensityHeader_machinestamp_set)
601  rms = _swig_property(_IMP_em.DensityHeader_rms_get, _IMP_em.DensityHeader_rms_set)
602  nlabl = _swig_property(_IMP_em.DensityHeader_nlabl_get, _IMP_em.DensityHeader_nlabl_set)
603  comments = _swig_property(_IMP_em.DensityHeader_comments_get, _IMP_em.DensityHeader_comments_set)
604  magic = _swig_property(_IMP_em.DensityHeader_magic_get, _IMP_em.DensityHeader_magic_set)
605  voltage = _swig_property(_IMP_em.DensityHeader_voltage_get, _IMP_em.DensityHeader_voltage_set)
606  Cs = _swig_property(_IMP_em.DensityHeader_Cs_get, _IMP_em.DensityHeader_Cs_set)
607  Aperture = _swig_property(_IMP_em.DensityHeader_Aperture_get, _IMP_em.DensityHeader_Aperture_set)
608  Magnification = _swig_property(_IMP_em.DensityHeader_Magnification_get, _IMP_em.DensityHeader_Magnification_set)
609  Postmagnification = _swig_property(_IMP_em.DensityHeader_Postmagnification_get, _IMP_em.DensityHeader_Postmagnification_set)
610  Exposuretime = _swig_property(_IMP_em.DensityHeader_Exposuretime_get, _IMP_em.DensityHeader_Exposuretime_set)
611  Microscope = _swig_property(_IMP_em.DensityHeader_Microscope_get, _IMP_em.DensityHeader_Microscope_set)
612  Pixelsize = _swig_property(_IMP_em.DensityHeader_Pixelsize_get, _IMP_em.DensityHeader_Pixelsize_set)
613  CCDArea = _swig_property(_IMP_em.DensityHeader_CCDArea_get, _IMP_em.DensityHeader_CCDArea_set)
614  Defocus = _swig_property(_IMP_em.DensityHeader_Defocus_get, _IMP_em.DensityHeader_Defocus_set)
615  Astigmatism = _swig_property(_IMP_em.DensityHeader_Astigmatism_get, _IMP_em.DensityHeader_Astigmatism_set)
616  AstigmatismAngle = _swig_property(_IMP_em.DensityHeader_AstigmatismAngle_get, _IMP_em.DensityHeader_AstigmatismAngle_set)
617  FocusIncrement = _swig_property(_IMP_em.DensityHeader_FocusIncrement_get, _IMP_em.DensityHeader_FocusIncrement_set)
618  CountsPerElectron = _swig_property(_IMP_em.DensityHeader_CountsPerElectron_get, _IMP_em.DensityHeader_CountsPerElectron_set)
619  Intensity = _swig_property(_IMP_em.DensityHeader_Intensity_get, _IMP_em.DensityHeader_Intensity_set)
620  EnergySlitwidth = _swig_property(_IMP_em.DensityHeader_EnergySlitwidth_get, _IMP_em.DensityHeader_EnergySlitwidth_set)
621  EnergyOffset = _swig_property(_IMP_em.DensityHeader_EnergyOffset_get, _IMP_em.DensityHeader_EnergyOffset_set)
622  Tiltangle = _swig_property(_IMP_em.DensityHeader_Tiltangle_get, _IMP_em.DensityHeader_Tiltangle_set)
623  Tiltaxis = _swig_property(_IMP_em.DensityHeader_Tiltaxis_get, _IMP_em.DensityHeader_Tiltaxis_set)
624  MarkerX = _swig_property(_IMP_em.DensityHeader_MarkerX_get, _IMP_em.DensityHeader_MarkerX_set)
625  MarkerY = _swig_property(_IMP_em.DensityHeader_MarkerY_get, _IMP_em.DensityHeader_MarkerY_set)
626  lswap = _swig_property(_IMP_em.DensityHeader_lswap_get, _IMP_em.DensityHeader_lswap_set)
627 
628  def get_resolution(self):
629  """get_resolution(DensityHeader self) -> float"""
630  return _IMP_em.DensityHeader_get_resolution(self)
631 
632 
633  def get_has_resolution(self):
634  """get_has_resolution(DensityHeader self) -> bool"""
635  return _IMP_em.DensityHeader_get_has_resolution(self)
636 
637 
638  def set_resolution(self, resolution):
639  """set_resolution(DensityHeader self, float resolution)"""
640  return _IMP_em.DensityHeader_set_resolution(self, resolution)
641 
642 
643  def get_spacing(self):
644  """get_spacing(DensityHeader self) -> float"""
645  return _IMP_em.DensityHeader_get_spacing(self)
646 
647 
648  def get_xorigin(self):
649  """get_xorigin(DensityHeader self) -> float"""
650  return _IMP_em.DensityHeader_get_xorigin(self)
651 
652 
653  def get_yorigin(self):
654  """get_yorigin(DensityHeader self) -> float"""
655  return _IMP_em.DensityHeader_get_yorigin(self)
656 
657 
658  def get_zorigin(self):
659  """get_zorigin(DensityHeader self) -> float"""
660  return _IMP_em.DensityHeader_get_zorigin(self)
661 
662 
663  def get_origin(self, i):
664  """get_origin(DensityHeader self, int i) -> float"""
665  return _IMP_em.DensityHeader_get_origin(self, i)
666 
667 
668  def set_xorigin(self, x):
669  """set_xorigin(DensityHeader self, float x)"""
670  return _IMP_em.DensityHeader_set_xorigin(self, x)
671 
672 
673  def set_yorigin(self, y):
674  """set_yorigin(DensityHeader self, float y)"""
675  return _IMP_em.DensityHeader_set_yorigin(self, y)
676 
677 
678  def set_zorigin(self, z):
679  """set_zorigin(DensityHeader self, float z)"""
680  return _IMP_em.DensityHeader_set_zorigin(self, z)
681 
682 
683  def is_top_calculated(self):
684  """is_top_calculated(DensityHeader self) -> bool"""
685  return _IMP_em.DensityHeader_is_top_calculated(self)
686 
687  Objectpixelsize_ = _swig_property(_IMP_em.DensityHeader_Objectpixelsize__get, _IMP_em.DensityHeader_Objectpixelsize__set)
688 
689  def get_nx(self):
690  """get_nx(DensityHeader self) -> int"""
691  return _IMP_em.DensityHeader_get_nx(self)
692 
693 
694  def get_ny(self):
695  """get_ny(DensityHeader self) -> int"""
696  return _IMP_em.DensityHeader_get_ny(self)
697 
698 
699  def get_nz(self):
700  """get_nz(DensityHeader self) -> int"""
701  return _IMP_em.DensityHeader_get_nz(self)
702 
703 
704  def get_number_of_voxels(self):
705  """get_number_of_voxels(DensityHeader self) -> int"""
706  return _IMP_em.DensityHeader_get_number_of_voxels(self)
707 
708 
709  def get_data_type(self):
710  """get_data_type(DensityHeader self) -> int"""
711  return _IMP_em.DensityHeader_get_data_type(self)
712 
713 
714  def set_data_type(self, data_type):
715  """set_data_type(DensityHeader self, int data_type)"""
716  return _IMP_em.DensityHeader_set_data_type(self, data_type)
717 
718  __swig_destroy__ = _IMP_em.delete_DensityHeader
719  __del__ = lambda self: None
720 DensityHeader_swigregister = _IMP_em.DensityHeader_swigregister
721 DensityHeader_swigregister(DensityHeader)
722 
723 
724 def create_density_header(bb, spacing):
725  """create_density_header(BoundingBox3D bb, float spacing) -> DensityHeader"""
726  return _IMP_em.create_density_header(bb, spacing)
727 
728 def read_map(*args):
729  """
730  read_map(std::string filename, MapReaderWriter reader) -> DensityMap
731  read_map(std::string filename) -> DensityMap
732  """
733  return _IMP_em.read_map(*args)
734 
735 def write_map(*args):
736  """
737  write_map(DensityMap m, std::string filename, MapReaderWriter writer)
738  write_map(DensityMap m, std::string filename)
739  """
740  return _IMP_em.write_map(*args)
741 
742 def approximate_molecular_mass(m, threshold):
743  """approximate_molecular_mass(DensityMap m, IMP::Float threshold) -> IMP::Float"""
744  return _IMP_em.approximate_molecular_mass(m, threshold)
745 class DensityMap(IMP.Object):
746  """Proxy of C++ IMP::em::DensityMap class."""
747 
748  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
749 
750  def __init__(self, *args):
751  """
752  __init__(IMP::em::DensityMap self, std::string name) -> DensityMap
753  __init__(IMP::em::DensityMap self) -> DensityMap
754  __init__(IMP::em::DensityMap self, DensityHeader header, std::string name) -> DensityMap
755  __init__(IMP::em::DensityMap self, DensityHeader header) -> DensityMap
756  """
757  this = _IMP_em.new_DensityMap(*args)
758  try:
759  self.this.append(this)
760  except __builtin__.Exception:
761  self.this = this
762 
763  def reset_data(self, value=0.0):
764  """
765  reset_data(DensityMap self, float value=0.0)
766  reset_data(DensityMap self)
767  """
768  return _IMP_em.DensityMap_reset_data(self, value)
769 
770 
771  def calcRMS(self):
772  """calcRMS(DensityMap self) -> IMP::em::emreal"""
773  return _IMP_em.DensityMap_calcRMS(self)
774 
775 
776  def std_normalize(self):
777  """std_normalize(DensityMap self)"""
778  return _IMP_em.DensityMap_std_normalize(self)
779 
780 
781  def is_normalized(self):
782  """is_normalized(DensityMap self) -> bool"""
783  return _IMP_em.DensityMap_is_normalized(self)
784 
785 
786  def get_location_in_dim_by_voxel(self, index, dim):
787  """get_location_in_dim_by_voxel(DensityMap self, long index, int dim) -> float"""
788  return _IMP_em.DensityMap_get_location_in_dim_by_voxel(self, index, dim)
789 
790 
791  def xyz_ind2voxel(self, x, y, z):
792  """xyz_ind2voxel(DensityMap self, int x, int y, int z) -> long"""
793  return _IMP_em.DensityMap_xyz_ind2voxel(self, x, y, z)
794 
795 
796  def get_voxel_by_location(self, *args):
797  """
798  get_voxel_by_location(DensityMap self, float x, float y, float z) -> long
799  get_voxel_by_location(DensityMap self, Vector3D v) -> long
800  """
801  return _IMP_em.DensityMap_get_voxel_by_location(self, *args)
802 
803 
804  def get_location_by_voxel(self, index):
805  """get_location_by_voxel(DensityMap self, long index) -> Vector3D"""
806  return _IMP_em.DensityMap_get_location_by_voxel(self, index)
807 
808 
809  def is_xyz_ind_part_of_volume(self, ix, iy, iz):
810  """is_xyz_ind_part_of_volume(DensityMap self, int ix, int iy, int iz) -> bool"""
811  return _IMP_em.DensityMap_is_xyz_ind_part_of_volume(self, ix, iy, iz)
812 
813 
814  def is_part_of_volume(self, *args):
815  """
816  is_part_of_volume(DensityMap self, float x, float y, float z) -> bool
817  is_part_of_volume(DensityMap self, Vector3D v) -> bool
818  """
819  return _IMP_em.DensityMap_is_part_of_volume(self, *args)
820 
821 
822  def get_value(self, *args):
823  """
824  get_value(DensityMap self, float x, float y, float z) -> IMP::em::emreal
825  get_value(DensityMap self, Vector3D point) -> IMP::em::emreal
826  get_value(DensityMap self, long index) -> IMP::em::emreal
827  """
828  return _IMP_em.DensityMap_get_value(self, *args)
829 
830 
831  def set_value(self, *args):
832  """
833  set_value(DensityMap self, long index, IMP::em::emreal value)
834  set_value(DensityMap self, float x, float y, float z, IMP::em::emreal value)
835  """
836  return _IMP_em.DensityMap_set_value(self, *args)
837 
838 
839  def set_origin(self, *args):
840  """
841  set_origin(DensityMap self, float x, float y, float z)
842  set_origin(DensityMap self, Vector3D v)
843  """
844  return _IMP_em.DensityMap_set_origin(self, *args)
845 
846 
847  def get_origin(self):
848  """get_origin(DensityMap self) -> Vector3D"""
849  return _IMP_em.DensityMap_get_origin(self)
850 
851 
852  def get_top(self):
853  """get_top(DensityMap self) -> Vector3D"""
854  return _IMP_em.DensityMap_get_top(self)
855 
856 
857  def get_header(self):
858  h = _IMP_em.DensityMap_get_header(self)
859  h._owner = self
860  return h
861 
862 
863 
864  def get_header_writable(self):
865  h = _IMP_em.DensityMap_get_header_writable(self)
866  h._owner = self
867  return h
868 
869 
870 
871  def same_origin(self, other):
872  """same_origin(DensityMap self, DensityMap other) -> bool"""
873  return _IMP_em.DensityMap_same_origin(self, other)
874 
875 
876  def same_dimensions(self, other):
877  """same_dimensions(DensityMap self, DensityMap other) -> bool"""
878  return _IMP_em.DensityMap_same_dimensions(self, other)
879 
880 
881  def same_voxel_size(self, other):
882  """same_voxel_size(DensityMap self, DensityMap other) -> bool"""
883  return _IMP_em.DensityMap_same_voxel_size(self, other)
884 
885 
886  def get_centroid(self, threshold=0.0):
887  """
888  get_centroid(DensityMap self, IMP::em::emreal threshold=0.0) -> Vector3D
889  get_centroid(DensityMap self) -> Vector3D
890  """
891  return _IMP_em.DensityMap_get_centroid(self, threshold)
892 
893 
894  def get_max_value(self):
895  """get_max_value(DensityMap self) -> IMP::em::emreal"""
896  return _IMP_em.DensityMap_get_max_value(self)
897 
898 
899  def get_min_value(self):
900  """get_min_value(DensityMap self) -> IMP::em::emreal"""
901  return _IMP_em.DensityMap_get_min_value(self)
902 
903 
904  def add(self, *args):
905  """
906  add(DensityMap self, DensityMap other)
907  add(DensityMap self, IMP::Float d)
908  """
909  return _IMP_em.DensityMap_add(self, *args)
910 
911 
912  def pick_max(self, other):
913  """pick_max(DensityMap self, DensityMap other)"""
914  return _IMP_em.DensityMap_pick_max(self, other)
915 
916 
917  def get_number_of_voxels(self):
918  """get_number_of_voxels(DensityMap self) -> long"""
919  return _IMP_em.DensityMap_get_number_of_voxels(self)
920 
921 
922  def set_void_map(self, nx, ny, nz):
923  """set_void_map(DensityMap self, int nx, int ny, int nz)"""
924  return _IMP_em.DensityMap_set_void_map(self, nx, ny, nz)
925 
926 
927  def pad(self, nx, ny, nz, val=0.0):
928  """
929  pad(DensityMap self, int nx, int ny, int nz, float val=0.0)
930  pad(DensityMap self, int nx, int ny, int nz)
931  """
932  return _IMP_em.DensityMap_pad(self, nx, ny, nz, val)
933 
934 
935  def pad_margin(self, mrg_x, mrg_y, mrg_z, val=0.0):
936  """
937  pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z, float val=0.0) -> DensityMap
938  pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z) -> DensityMap
939  """
940  return _IMP_em.DensityMap_pad_margin(self, mrg_x, mrg_y, mrg_z, val)
941 
942 
943  def get_cropped(self, *args):
944  """
945  get_cropped(DensityMap self, float threshold) -> DensityMap
946  get_cropped(DensityMap self, BoundingBox3D bb) -> DensityMap
947  """
948  return _IMP_em.DensityMap_get_cropped(self, *args)
949 
950 
951  def get_maximum_value_in_xy_plane(self, z_ind):
952  """get_maximum_value_in_xy_plane(DensityMap self, int z_ind) -> float"""
953  return _IMP_em.DensityMap_get_maximum_value_in_xy_plane(self, z_ind)
954 
955 
956  def get_maximum_value_in_xz_plane(self, y_ind):
957  """get_maximum_value_in_xz_plane(DensityMap self, int y_ind) -> float"""
958  return _IMP_em.DensityMap_get_maximum_value_in_xz_plane(self, y_ind)
959 
960 
961  def get_maximum_value_in_yz_plane(self, x_ind):
962  """get_maximum_value_in_yz_plane(DensityMap self, int x_ind) -> float"""
963  return _IMP_em.DensityMap_get_maximum_value_in_yz_plane(self, x_ind)
964 
965 
966  def multiply(self, factor):
967  """multiply(DensityMap self, float factor)"""
968  return _IMP_em.DensityMap_multiply(self, factor)
969 
970 
971  def get_locations_string(self, t):
972  """get_locations_string(DensityMap self, float t) -> std::string"""
973  return _IMP_em.DensityMap_get_locations_string(self, t)
974 
975 
976  def update_voxel_size(self, new_apix):
977  """update_voxel_size(DensityMap self, float new_apix)"""
978  return _IMP_em.DensityMap_update_voxel_size(self, new_apix)
979 
980 
981  def get_spacing(self):
982  """get_spacing(DensityMap self) -> IMP::Float"""
983  return _IMP_em.DensityMap_get_spacing(self)
984 
985 
986  def calc_all_voxel2loc(self):
987  """calc_all_voxel2loc(DensityMap self)"""
988  return _IMP_em.DensityMap_calc_all_voxel2loc(self)
989 
990 
991  def copy_map(self, other):
992  """copy_map(DensityMap self, DensityMap other)"""
993  return _IMP_em.DensityMap_copy_map(self, other)
994 
995 
996  def get_version_info(self):
997  """get_version_info(DensityMap self) -> VersionInfo"""
998  return _IMP_em.DensityMap_get_version_info(self)
999 
1000 
1001  def lower_voxel_shift(self, loc, kdist, orig, ndim):
1002  """lower_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
1003  return _IMP_em.DensityMap_lower_voxel_shift(self, loc, kdist, orig, ndim)
1004 
1005 
1006  def upper_voxel_shift(self, loc, kdist, orig, ndim):
1007  """upper_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
1008  return _IMP_em.DensityMap_upper_voxel_shift(self, loc, kdist, orig, ndim)
1009 
1010 
1011  def get_rms_calculated(self):
1012  """get_rms_calculated(DensityMap self) -> bool"""
1013  return _IMP_em.DensityMap_get_rms_calculated(self)
1014 
1015 
1016  def get_dim_index_by_location(self, *args):
1017  """
1018  get_dim_index_by_location(DensityMap self, Vector3D v, int ind) -> int
1019  get_dim_index_by_location(DensityMap self, float loc_val, int ind) -> int
1020  """
1021  return _IMP_em.DensityMap_get_dim_index_by_location(self, *args)
1022 
1023 
1024  def __str__(self):
1025  """__str__(DensityMap self) -> std::string"""
1026  return _IMP_em.DensityMap___str__(self)
1027 
1028 
1029  def __repr__(self):
1030  """__repr__(DensityMap self) -> std::string"""
1031  return _IMP_em.DensityMap___repr__(self)
1032 
1033 
1034  @staticmethod
1035  def get_from(o):
1036  return _object_cast_to_DensityMap(o)
1037 
1038 DensityMap_swigregister = _IMP_em.DensityMap_swigregister
1039 DensityMap_swigregister(DensityMap)
1040 
1041 
1042 def get_bounding_box(*args):
1043  """
1044  get_bounding_box(DensityMap m, IMP::Float threshold) -> BoundingBox3D
1045  get_bounding_box(DensityMap m) -> BoundingBox3D
1046  """
1047  return _IMP_em.get_bounding_box(*args)
1048 
1049 def get_density(m, v):
1050  """get_density(DensityMap m, Vector3D v) -> double"""
1051  return _IMP_em.get_density(m, v)
1052 
1053 def get_transformed(*args):
1054  """
1055  get_transformed(DensityMap input, Transformation3D tr, double threshold) -> DensityMap
1056  get_transformed(DensityMap input, Transformation3D tr) -> DensityMap
1057  """
1058  return _IMP_em.get_transformed(*args)
1059 
1060 def get_resampled(input, scaling):
1061  """get_resampled(DensityMap input, double scaling) -> DensityMap"""
1062  return _IMP_em.get_resampled(input, scaling)
1063 
1064 def get_transformed_into(source, tr, into, calc_rms=True):
1065  """
1066  get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into, bool calc_rms=True)
1067  get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into)
1068  """
1069  return _IMP_em.get_transformed_into(source, tr, into, calc_rms)
1070 
1071 def get_transformed_into2(source, tr, into):
1072  """get_transformed_into2(DensityMap source, Transformation3D tr, DensityMap into)"""
1073  return _IMP_em.get_transformed_into2(source, tr, into)
1074 
1075 def get_interiors_intersect(d1, d2):
1076  """get_interiors_intersect(DensityMap d1, DensityMap d2) -> bool"""
1077  return _IMP_em.get_interiors_intersect(d1, d2)
1078 
1079 def get_segment(*args):
1080  """
1081  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
1082  get_segment(DensityMap map_to_segment, IMP::algebra::Vector3Ds vecs, float dist) -> DensityMap
1083  """
1084  return _IMP_em.get_segment(*args)
1085 
1086 def get_segment_by_masking(map_to_segment, mask, mas_threshold):
1087  """get_segment_by_masking(DensityMap map_to_segment, DensityMap mask, float mas_threshold) -> DensityMap"""
1088  return _IMP_em.get_segment_by_masking(map_to_segment, mask, mas_threshold)
1089 
1090 def binarize(orig_map, threshold, reverse=False):
1091  """
1092  binarize(DensityMap orig_map, float threshold, bool reverse=False) -> DensityMap
1093  binarize(DensityMap orig_map, float threshold) -> DensityMap
1094  """
1095  return _IMP_em.binarize(orig_map, threshold, reverse)
1096 
1097 def get_threshold_map(orig_map, threshold):
1098  """get_threshold_map(DensityMap orig_map, float threshold) -> DensityMap"""
1099  return _IMP_em.get_threshold_map(orig_map, threshold)
1100 
1101 def multiply(m1, m2):
1102  """multiply(DensityMap m1, DensityMap m2) -> DensityMap"""
1103  return _IMP_em.multiply(m1, m2)
1104 
1105 def convolute(m1, m2):
1106  """convolute(DensityMap m1, DensityMap m2) -> double"""
1107  return _IMP_em.convolute(m1, m2)
1108 
1109 def get_sum(m1):
1110  """get_sum(DensityMap m1) -> double"""
1111  return _IMP_em.get_sum(m1)
1112 
1113 def get_max_map(maps):
1114  """get_max_map(IMP::em::DensityMaps maps) -> DensityMap"""
1115  return _IMP_em.get_max_map(maps)
1116 
1117 def interpolate_map(in_map, new_spacing):
1118  """interpolate_map(DensityMap in_map, double new_spacing) -> DensityMap"""
1119  return _IMP_em.interpolate_map(in_map, new_spacing)
1120 
1121 def get_grid(in_map):
1122  """get_grid(DensityMap in_map) -> IMP::algebra::GridD< 3,IMP::algebra::DenseGridStorageD< 3,float >,float,IMP::algebra::DefaultEmbeddingD< 3 > >"""
1123  return _IMP_em.get_grid(in_map)
1124 
1125 def create_density_map(*args):
1126  """
1127  create_density_map(DensityMap other) -> DensityMap
1128  create_density_map(BoundingBox3D bb, double spacing) -> DensityMap
1129  create_density_map(int nx, int ny, int nz, double spacing) -> DensityMap
1130  create_density_map(DenseFloatGrid3D grid) -> DensityMap
1131  create_density_map(DenseDoubleGrid3D grid) -> DensityMap
1132  """
1133  return _IMP_em.create_density_map(*args)
1134 
1135 def get_binarized_interior(dmap):
1136  """get_binarized_interior(DensityMap dmap) -> DensityMap"""
1137  return _IMP_em.get_binarized_interior(dmap)
1138 
1139 def add_to_map(dm, pis):
1140  """add_to_map(DensityMap dm, IMP::Particles const & pis)"""
1141  return _IMP_em.add_to_map(dm, pis)
1142 class RadiusDependentDistanceMask(object):
1143  """Proxy of C++ IMP::em::RadiusDependentDistanceMask class."""
1144 
1145  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1146  __repr__ = _swig_repr
1147 
1148  def __init__(self, sampling_radius, header):
1149  """__init__(IMP::em::RadiusDependentDistanceMask self, float sampling_radius, DensityHeader header) -> RadiusDependentDistanceMask"""
1150  this = _IMP_em.new_RadiusDependentDistanceMask(sampling_radius, header)
1151  try:
1152  self.this.append(this)
1153  except __builtin__.Exception:
1154  self.this = this
1155 
1156  def get_neighbor_shift(self):
1157  """get_neighbor_shift(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1158  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_shift(self)
1159 
1160 
1161  def get_neighbor_dist(self):
1162  """get_neighbor_dist(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1163  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist(self)
1164 
1165 
1166  def get_neighbor_dist_exp(self):
1167  """get_neighbor_dist_exp(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1168  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist_exp(self)
1169 
1170 
1171  def show(self, out):
1172  """show(RadiusDependentDistanceMask self, _ostream out)"""
1173  return _IMP_em.RadiusDependentDistanceMask_show(self, out)
1174 
1175  __swig_destroy__ = _IMP_em.delete_RadiusDependentDistanceMask
1176  __del__ = lambda self: None
1177 RadiusDependentDistanceMask_swigregister = _IMP_em.RadiusDependentDistanceMask_swigregister
1178 RadiusDependentDistanceMask_swigregister(RadiusDependentDistanceMask)
1179 
1180 class DistanceMask(object):
1181  """Proxy of C++ IMP::em::DistanceMask class."""
1182 
1183  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1184  __repr__ = _swig_repr
1185 
1186  def __init__(self, *args):
1187  """
1188  __init__(IMP::em::DistanceMask self) -> DistanceMask
1189  __init__(IMP::em::DistanceMask self, DensityHeader header) -> DistanceMask
1190  """
1191  this = _IMP_em.new_DistanceMask(*args)
1192  try:
1193  self.this.append(this)
1194  except __builtin__.Exception:
1195  self.this = this
1196 
1197  def show(self, out):
1198  """show(DistanceMask self, _ostream out)"""
1199  return _IMP_em.DistanceMask_show(self, out)
1200 
1201 
1202  def is_mask_set(self, radius, eps=0.001):
1203  """
1204  is_mask_set(DistanceMask self, float radius, float eps=0.001) -> bool
1205  is_mask_set(DistanceMask self, float radius) -> bool
1206  """
1207  return _IMP_em.DistanceMask_is_mask_set(self, radius, eps)
1208 
1209  __swig_destroy__ = _IMP_em.delete_DistanceMask
1210  __del__ = lambda self: None
1211 DistanceMask_swigregister = _IMP_em.DistanceMask_swigregister
1212 DistanceMask_swigregister(DistanceMask)
1213 
1214 class EMReaderWriter(MapReaderWriter):
1215  """Proxy of C++ IMP::em::EMReaderWriter class."""
1216 
1217  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1218 
1219  def __str__(self):
1220  """__str__(EMReaderWriter self) -> std::string"""
1221  return _IMP_em.EMReaderWriter___str__(self)
1222 
1223 
1224  def __repr__(self):
1225  """__repr__(EMReaderWriter self) -> std::string"""
1226  return _IMP_em.EMReaderWriter___repr__(self)
1227 
1228 
1229  @staticmethod
1230  def get_from(o):
1231  return _object_cast_to_EMReaderWriter(o)
1232 
1233 
1234  def __init__(self):
1235  """__init__(IMP::em::EMReaderWriter self) -> EMReaderWriter"""
1236  this = _IMP_em.new_EMReaderWriter()
1237  try:
1238  self.this.append(this)
1239  except __builtin__.Exception:
1240  self.this = this
1241 EMReaderWriter_swigregister = _IMP_em.EMReaderWriter_swigregister
1242 EMReaderWriter_swigregister(EMReaderWriter)
1243 
1244 class XplorReaderWriter(MapReaderWriter):
1245  """Proxy of C++ IMP::em::XplorReaderWriter class."""
1246 
1247  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1248 
1249  def __str__(self):
1250  """__str__(XplorReaderWriter self) -> std::string"""
1251  return _IMP_em.XplorReaderWriter___str__(self)
1252 
1253 
1254  def __repr__(self):
1255  """__repr__(XplorReaderWriter self) -> std::string"""
1256  return _IMP_em.XplorReaderWriter___repr__(self)
1257 
1258 
1259  @staticmethod
1260  def get_from(o):
1261  return _object_cast_to_XplorReaderWriter(o)
1262 
1263 
1264  def __init__(self):
1265  """__init__(IMP::em::XplorReaderWriter self) -> XplorReaderWriter"""
1266  this = _IMP_em.new_XplorReaderWriter()
1267  try:
1268  self.this.append(this)
1269  except __builtin__.Exception:
1270  self.this = this
1271 XplorReaderWriter_swigregister = _IMP_em.XplorReaderWriter_swigregister
1272 XplorReaderWriter_swigregister(XplorReaderWriter)
1273 
1274 class MRCReaderWriter(MapReaderWriter):
1275  """Proxy of C++ IMP::em::MRCReaderWriter class."""
1276 
1277  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1278 
1279  def __init__(self, *args):
1280  """
1281  __init__(IMP::em::MRCReaderWriter self) -> MRCReaderWriter
1282  __init__(IMP::em::MRCReaderWriter self, std::string fn) -> MRCReaderWriter
1283  """
1284  this = _IMP_em.new_MRCReaderWriter(*args)
1285  try:
1286  self.this.append(this)
1287  except __builtin__.Exception:
1288  self.this = this
1289 
1290  def __str__(self):
1291  """__str__(MRCReaderWriter self) -> std::string"""
1292  return _IMP_em.MRCReaderWriter___str__(self)
1293 
1294 
1295  def __repr__(self):
1296  """__repr__(MRCReaderWriter self) -> std::string"""
1297  return _IMP_em.MRCReaderWriter___repr__(self)
1298 
1299 
1300  @staticmethod
1301  def get_from(o):
1302  return _object_cast_to_MRCReaderWriter(o)
1303 
1304 MRCReaderWriter_swigregister = _IMP_em.MRCReaderWriter_swigregister
1305 MRCReaderWriter_swigregister(MRCReaderWriter)
1306 
1307 class KernelParameters(object):
1308  """Proxy of C++ IMP::em::KernelParameters class."""
1309 
1310  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1311 
1312  def __init__(self, *args):
1313  """
1314  __init__(IMP::em::KernelParameters self) -> KernelParameters
1315  __init__(IMP::em::KernelParameters self, float resolution) -> KernelParameters
1316  """
1317  this = _IMP_em.new_KernelParameters(*args)
1318  try:
1319  self.this.append(this)
1320  except __builtin__.Exception:
1321  self.this = this
1322  __swig_destroy__ = _IMP_em.delete_KernelParameters
1323  __del__ = lambda self: None
1324 
1325  def get_rsig(self):
1326  """get_rsig(KernelParameters self) -> float"""
1327  return _IMP_em.KernelParameters_get_rsig(self)
1328 
1329 
1330  def get_rsigsq(self):
1331  """get_rsigsq(KernelParameters self) -> float"""
1332  return _IMP_em.KernelParameters_get_rsigsq(self)
1333 
1334 
1335  def get_inv_rsigsq(self):
1336  """get_inv_rsigsq(KernelParameters self) -> float"""
1337  return _IMP_em.KernelParameters_get_inv_rsigsq(self)
1338 
1339 
1340  def get_timessig(self):
1341  """get_timessig(KernelParameters self) -> float"""
1342  return _IMP_em.KernelParameters_get_timessig(self)
1343 
1344 
1345  def get_sq2pi3(self):
1346  """get_sq2pi3(KernelParameters self) -> float"""
1347  return _IMP_em.KernelParameters_get_sq2pi3(self)
1348 
1349 
1350  def get_rnormfac(self):
1351  """get_rnormfac(KernelParameters self) -> float"""
1352  return _IMP_em.KernelParameters_get_rnormfac(self)
1353 
1354 
1355  def get_rkdist(self):
1356  """get_rkdist(KernelParameters self) -> float"""
1357  return _IMP_em.KernelParameters_get_rkdist(self)
1358 
1359 
1360  def get_rkdistsq(self):
1361  """get_rkdistsq(KernelParameters self) -> float"""
1362  return _IMP_em.KernelParameters_get_rkdistsq(self)
1363 
1364 
1365  def get_lim(self):
1366  """get_lim(KernelParameters self) -> float"""
1367  return _IMP_em.KernelParameters_get_lim(self)
1368 
1369 
1370  def show(self, *args):
1371  """
1372  show(KernelParameters self, _ostream out)
1373  show(KernelParameters self)
1374  """
1375  return _IMP_em.KernelParameters_show(self, *args)
1376 
1377 
1378  def __str__(self):
1379  """__str__(KernelParameters self) -> std::string"""
1380  return _IMP_em.KernelParameters___str__(self)
1381 
1382 
1383  def __repr__(self):
1384  """__repr__(KernelParameters self) -> std::string"""
1385  return _IMP_em.KernelParameters___repr__(self)
1386 
1387 KernelParameters_swigregister = _IMP_em.KernelParameters_swigregister
1388 KernelParameters_swigregister(KernelParameters)
1389 
1390 GAUSSIAN = _IMP_em.GAUSSIAN
1391 BINARIZED_SPHERE = _IMP_em.BINARIZED_SPHERE
1392 SPHERE = _IMP_em.SPHERE
1393 class SampledDensityMap(DensityMap):
1394  """Proxy of C++ IMP::em::SampledDensityMap class."""
1395 
1396  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1397 
1398  def __init__(self, *args):
1399  """
1400  __init__(IMP::em::SampledDensityMap self, IMP::em::KernelType kt) -> SampledDensityMap
1401  __init__(IMP::em::SampledDensityMap self) -> SampledDensityMap
1402  __init__(IMP::em::SampledDensityMap self, DensityHeader header, IMP::em::KernelType kt) -> SampledDensityMap
1403  __init__(IMP::em::SampledDensityMap self, DensityHeader header) -> SampledDensityMap
1404  __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
1405  __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
1406  __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size, FloatKey mass_key) -> SampledDensityMap
1407  __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size) -> SampledDensityMap
1408  """
1409  this = _IMP_em.new_SampledDensityMap(*args)
1410  try:
1411  self.this.append(this)
1412  except __builtin__.Exception:
1413  self.this = this
1414 
1415  def resample(self):
1416  """resample(SampledDensityMap self)"""
1417  return _IMP_em.SampledDensityMap_resample(self)
1418 
1419 
1420  def project(self, *args):
1421  """
1422  project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin, Vector3D shift, FloatKey mass_key)
1423  project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin, Vector3D shift)
1424  project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin)
1425  """
1426  return _IMP_em.SampledDensityMap_project(self, *args)
1427 
1428 
1429  def set_particles(self, *args):
1430  """
1431  set_particles(SampledDensityMap self, IMP::ParticlesTemp const & ps, FloatKey mass_key)
1432  set_particles(SampledDensityMap self, IMP::ParticlesTemp const & ps)
1433  """
1434  return _IMP_em.SampledDensityMap_set_particles(self, *args)
1435 
1436 
1437  def get_xyzr_particles(self):
1438  """get_xyzr_particles(SampledDensityMap self) -> IMP::core::XYZRs const &"""
1439  return _IMP_em.SampledDensityMap_get_xyzr_particles(self)
1440 
1441 
1442  def get_sampled_particles(self):
1443  """get_sampled_particles(SampledDensityMap self) -> IMP::Particles const &"""
1444  return _IMP_em.SampledDensityMap_get_sampled_particles(self)
1445 
1446 
1447  def get_weight_key(self):
1448  """get_weight_key(SampledDensityMap self) -> FloatKey"""
1449  return _IMP_em.SampledDensityMap_get_weight_key(self)
1450 
1451 
1452  def get_minimum_resampled_value(self):
1453  """get_minimum_resampled_value(SampledDensityMap self) -> float"""
1454  return _IMP_em.SampledDensityMap_get_minimum_resampled_value(self)
1455 
1456 
1457  def update_resolution(self, res):
1458  """update_resolution(SampledDensityMap self, IMP::Float res)"""
1459  return _IMP_em.SampledDensityMap_update_resolution(self, res)
1460 
1461  __swig_destroy__ = _IMP_em.delete_SampledDensityMap
1462  __del__ = lambda self: None
1463 
1464  def __str__(self):
1465  """__str__(SampledDensityMap self) -> std::string"""
1466  return _IMP_em.SampledDensityMap___str__(self)
1467 
1468 
1469  def __repr__(self):
1470  """__repr__(SampledDensityMap self) -> std::string"""
1471  return _IMP_em.SampledDensityMap___repr__(self)
1472 
1473 
1474  @staticmethod
1475  def get_from(o):
1476  return _object_cast_to_SampledDensityMap(o)
1477 
1478 SampledDensityMap_swigregister = _IMP_em.SampledDensityMap_swigregister
1479 SampledDensityMap_swigregister(SampledDensityMap)
1480 
1481 IMP_DEFAULT_NUM_SHELLS = _IMP_em.IMP_DEFAULT_NUM_SHELLS
1482 IMP_SIG_CUTOFF = _IMP_em.IMP_SIG_CUTOFF
1483 class SurfaceShellDensityMap(SampledDensityMap):
1484  """Proxy of C++ IMP::em::SurfaceShellDensityMap class."""
1485 
1486  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1487 
1488  def __init__(self, *args):
1489  """
1490  __init__(IMP::em::SurfaceShellDensityMap self) -> SurfaceShellDensityMap
1491  __init__(IMP::em::SurfaceShellDensityMap self, DensityHeader header) -> SurfaceShellDensityMap
1492  __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key, int num_shells=5) -> SurfaceShellDensityMap
1493  __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key) -> SurfaceShellDensityMap
1494  __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size) -> SurfaceShellDensityMap
1495  """
1496  this = _IMP_em.new_SurfaceShellDensityMap(*args)
1497  try:
1498  self.this.append(this)
1499  except __builtin__.Exception:
1500  self.this = this
1501 
1502  def binarize(self, scene_val):
1503  """binarize(SurfaceShellDensityMap self, float scene_val)"""
1504  return _IMP_em.SurfaceShellDensityMap_binarize(self, scene_val)
1505 
1506 
1507  def has_background_neighbor(self, voxel_ind):
1508  """has_background_neighbor(SurfaceShellDensityMap self, long voxel_ind) -> bool"""
1509  return _IMP_em.SurfaceShellDensityMap_has_background_neighbor(self, voxel_ind)
1510 
1511  __swig_destroy__ = _IMP_em.delete_SurfaceShellDensityMap
1512  __del__ = lambda self: None
1513 
1514  def __str__(self):
1515  """__str__(SurfaceShellDensityMap self) -> std::string"""
1516  return _IMP_em.SurfaceShellDensityMap___str__(self)
1517 
1518 
1519  def __repr__(self):
1520  """__repr__(SurfaceShellDensityMap self) -> std::string"""
1521  return _IMP_em.SurfaceShellDensityMap___repr__(self)
1522 
1523 
1524  @staticmethod
1525  def get_from(o):
1526  return _object_cast_to_SurfaceShellDensityMap(o)
1527 
1528 SurfaceShellDensityMap_swigregister = _IMP_em.SurfaceShellDensityMap_swigregister
1529 SurfaceShellDensityMap_swigregister(SurfaceShellDensityMap)
1530 
1531 class CoarseCC(IMP.Object):
1532  """Proxy of C++ IMP::em::CoarseCC class."""
1533 
1534  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1535 
1536  def __init__(self):
1537  """__init__(IMP::em::CoarseCC self) -> CoarseCC"""
1538  this = _IMP_em.new_CoarseCC()
1539  try:
1540  self.this.append(this)
1541  except __builtin__.Exception:
1542  self.this = this
1543 
1544  def calc_score(*args):
1545  """
1546  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True, IMP::FloatPair norm_factors) -> float
1547  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True) -> float
1548  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1549  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1550  """
1551  return _IMP_em.CoarseCC_calc_score(*args)
1552 
1553  calc_score = staticmethod(calc_score)
1554 
1555  def cross_correlation_coefficient(*args):
1556  """
1557  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False, IMP::FloatPair norm_factors) -> double
1558  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1559  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1560  """
1561  return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1562 
1563  cross_correlation_coefficient = staticmethod(cross_correlation_coefficient)
1564 
1565  def local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold):
1566  """local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1567  return _IMP_em.CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold)
1568 
1569  local_cross_correlation_coefficient = staticmethod(local_cross_correlation_coefficient)
1570 
1571  def get_version_info(self):
1572  """get_version_info(CoarseCC self) -> VersionInfo"""
1573  return _IMP_em.CoarseCC_get_version_info(self)
1574 
1575 
1576  def __str__(self):
1577  """__str__(CoarseCC self) -> std::string"""
1578  return _IMP_em.CoarseCC___str__(self)
1579 
1580 
1581  def __repr__(self):
1582  """__repr__(CoarseCC self) -> std::string"""
1583  return _IMP_em.CoarseCC___repr__(self)
1584 
1585 
1586  @staticmethod
1587  def get_from(o):
1588  return _object_cast_to_CoarseCC(o)
1589 
1590 CoarseCC_swigregister = _IMP_em.CoarseCC_swigregister
1591 CoarseCC_swigregister(CoarseCC)
1592 
1593 def CoarseCC_calc_score(*args):
1594  """
1595  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True, IMP::FloatPair norm_factors) -> float
1596  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True) -> float
1597  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1598  CoarseCC_calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1599  """
1600  return _IMP_em.CoarseCC_calc_score(*args)
1601 
1602 def CoarseCC_cross_correlation_coefficient(*args):
1603  """
1604  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False, IMP::FloatPair norm_factors) -> double
1605  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1606  CoarseCC_cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1607  """
1608  return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1609 
1610 def CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold):
1611  """CoarseCC_local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1612  return _IMP_em.CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold)
1613 
1614 class CoarseConvolution(object):
1615  """Proxy of C++ IMP::em::CoarseConvolution class."""
1616 
1617  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1618  __repr__ = _swig_repr
1619 
1620  def convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac=True):
1621  """
1622  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1623  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1624  """
1625  return _IMP_em.CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac)
1626 
1627  convolution = staticmethod(convolution)
1628 
1629  def __init__(self):
1630  """__init__(IMP::em::CoarseConvolution self) -> CoarseConvolution"""
1631  this = _IMP_em.new_CoarseConvolution()
1632  try:
1633  self.this.append(this)
1634  except __builtin__.Exception:
1635  self.this = this
1636  __swig_destroy__ = _IMP_em.delete_CoarseConvolution
1637  __del__ = lambda self: None
1638 CoarseConvolution_swigregister = _IMP_em.CoarseConvolution_swigregister
1639 CoarseConvolution_swigregister(CoarseConvolution)
1640 
1641 def CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac=True):
1642  """
1643  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1644  CoarseConvolution_convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1645  """
1646  return _IMP_em.CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac)
1647 
1648 class CoarseCCatIntervals(CoarseCC):
1649  """Proxy of C++ IMP::em::CoarseCCatIntervals class."""
1650 
1651  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1652 
1653  def __init__(self, *args):
1654  """
1655  __init__(IMP::em::CoarseCCatIntervals self, int const & ncd) -> CoarseCCatIntervals
1656  __init__(IMP::em::CoarseCCatIntervals self) -> CoarseCCatIntervals
1657  """
1658  this = _IMP_em.new_CoarseCCatIntervals(*args)
1659  try:
1660  self.this.append(this)
1661  except __builtin__.Exception:
1662  self.this = this
1663 
1664  def evaluate(self, em_map, model_map, deriv, scalefac, lderiv, eval_interval):
1665  """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 >"""
1666  return _IMP_em.CoarseCCatIntervals_evaluate(self, em_map, model_map, deriv, scalefac, lderiv, eval_interval)
1667 
1668 
1669  def __str__(self):
1670  """__str__(CoarseCCatIntervals self) -> std::string"""
1671  return _IMP_em.CoarseCCatIntervals___str__(self)
1672 
1673 
1674  def __repr__(self):
1675  """__repr__(CoarseCCatIntervals self) -> std::string"""
1676  return _IMP_em.CoarseCCatIntervals___repr__(self)
1677 
1678 
1679  @staticmethod
1680  def get_from(o):
1681  return _object_cast_to_CoarseCCatIntervals(o)
1682 
1683 CoarseCCatIntervals_swigregister = _IMP_em.CoarseCCatIntervals_swigregister
1684 CoarseCCatIntervals_swigregister(CoarseCCatIntervals)
1685 
1686 class FitRestraint(IMP.Restraint):
1687  """Proxy of C++ IMP::em::FitRestraint class."""
1688 
1689  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1690 
1691  def __init__(self, *args):
1692  """
1693  __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
1694  __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
1695  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key, float scale=1) -> FitRestraint
1696  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key) -> FitRestraint
1697  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors) -> FitRestraint
1698  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map) -> FitRestraint
1699  """
1700  this = _IMP_em.new_FitRestraint(*args)
1701  try:
1702  self.this.append(this)
1703  except __builtin__.Exception:
1704  self.this = this
1705 
1706  def get_model_dens_map(self):
1707  """get_model_dens_map(FitRestraint self) -> SampledDensityMap"""
1708  return _IMP_em.FitRestraint_get_model_dens_map(self)
1709 
1710 
1711  def set_scale_factor(self, scale):
1712  """set_scale_factor(FitRestraint self, float scale)"""
1713  return _IMP_em.FitRestraint_set_scale_factor(self, scale)
1714 
1715 
1716  def get_scale_factor(self):
1717  """get_scale_factor(FitRestraint self) -> float"""
1718  return _IMP_em.FitRestraint_get_scale_factor(self)
1719 
1720 
1721  def do_get_inputs(self):
1722  """do_get_inputs(FitRestraint self) -> IMP::ModelObjectsTemp"""
1723  return _IMP_em.FitRestraint_do_get_inputs(self)
1724 
1725 
1726  def get_version_info(self):
1727  """get_version_info(FitRestraint self) -> VersionInfo"""
1728  return _IMP_em.FitRestraint_get_version_info(self)
1729 
1730 
1731  def __str__(self):
1732  """__str__(FitRestraint self) -> std::string"""
1733  return _IMP_em.FitRestraint___str__(self)
1734 
1735 
1736  def __repr__(self):
1737  """__repr__(FitRestraint self) -> std::string"""
1738  return _IMP_em.FitRestraint___repr__(self)
1739 
1740 
1741  @staticmethod
1742  def get_from(o):
1743  return _object_cast_to_FitRestraint(o)
1744 
1745 
1746  def cast(r):
1747  """cast(Restraint r) -> FitRestraint"""
1748  return _IMP_em.FitRestraint_cast(r)
1749 
1750  cast = staticmethod(cast)
1751 FitRestraint_swigregister = _IMP_em.FitRestraint_swigregister
1752 FitRestraint_swigregister(FitRestraint)
1753 
1754 def FitRestraint_cast(r):
1755  """FitRestraint_cast(Restraint r) -> FitRestraint"""
1756  return _IMP_em.FitRestraint_cast(r)
1757 
1758 
1759 def density2particles(dmap, threshold, m, step=1):
1760  """
1761  density2particles(DensityMap dmap, IMP::Float threshold, Model m, int step=1) -> IMP::Particles
1762  density2particles(DensityMap dmap, IMP::Float threshold, Model m) -> IMP::Particles
1763  """
1764  return _IMP_em.density2particles(dmap, threshold, m, step)
1765 
1766 def density2vectors(dmap, threshold):
1767  """density2vectors(DensityMap dmap, IMP::Float threshold) -> IMP::algebra::Vector3Ds"""
1768  return _IMP_em.density2vectors(dmap, threshold)
1769 
1770 def particles2density(*args):
1771  """
1772  particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3, FloatKey weight_key) -> SampledDensityMap
1773  particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
1774  particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
1775  """
1776  return _IMP_em.particles2density(*args)
1777 
1778 def particles2binarized_density(*args):
1779  """
1780  particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3, FloatKey weight_key) -> SampledDensityMap
1781  particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
1782  particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
1783  """
1784  return _IMP_em.particles2binarized_density(*args)
1785 
1786 def particles2surface(*args):
1787  """
1788  particles2surface(IMP::ParticlesTemp const & ps, IMP::Float apix, FloatKey weight_key) -> SurfaceShellDensityMap
1789  particles2surface(IMP::ParticlesTemp const & ps, IMP::Float apix) -> SurfaceShellDensityMap
1790  """
1791  return _IMP_em.particles2surface(*args)
1792 
1793 def calculate_intersection_score(d1, d2):
1794  """calculate_intersection_score(SurfaceShellDensityMap d1, SurfaceShellDensityMap d2) -> IMP::Float"""
1795  return _IMP_em.calculate_intersection_score(d1, d2)
1796 class SpiderHeader(object):
1797  """Proxy of C++ IMP::em::SpiderHeader class."""
1798 
1799  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1800  __repr__ = _swig_repr
1801  fNslice = _swig_property(_IMP_em.SpiderHeader_fNslice_get, _IMP_em.SpiderHeader_fNslice_set)
1802  fNrow = _swig_property(_IMP_em.SpiderHeader_fNrow_get, _IMP_em.SpiderHeader_fNrow_set)
1803  fNrec = _swig_property(_IMP_em.SpiderHeader_fNrec_get, _IMP_em.SpiderHeader_fNrec_set)
1804  fNlabel = _swig_property(_IMP_em.SpiderHeader_fNlabel_get, _IMP_em.SpiderHeader_fNlabel_set)
1805  fIform = _swig_property(_IMP_em.SpiderHeader_fIform_get, _IMP_em.SpiderHeader_fIform_set)
1806  fImami = _swig_property(_IMP_em.SpiderHeader_fImami_get, _IMP_em.SpiderHeader_fImami_set)
1807  fFmax = _swig_property(_IMP_em.SpiderHeader_fFmax_get, _IMP_em.SpiderHeader_fFmax_set)
1808  fFmin = _swig_property(_IMP_em.SpiderHeader_fFmin_get, _IMP_em.SpiderHeader_fFmin_set)
1809  fAv = _swig_property(_IMP_em.SpiderHeader_fAv_get, _IMP_em.SpiderHeader_fAv_set)
1810  fSig = _swig_property(_IMP_em.SpiderHeader_fSig_get, _IMP_em.SpiderHeader_fSig_set)
1811  fIhist = _swig_property(_IMP_em.SpiderHeader_fIhist_get, _IMP_em.SpiderHeader_fIhist_set)
1812  fNcol = _swig_property(_IMP_em.SpiderHeader_fNcol_get, _IMP_em.SpiderHeader_fNcol_set)
1813  fLabrec = _swig_property(_IMP_em.SpiderHeader_fLabrec_get, _IMP_em.SpiderHeader_fLabrec_set)
1814  fIangle = _swig_property(_IMP_em.SpiderHeader_fIangle_get, _IMP_em.SpiderHeader_fIangle_set)
1815  fPhi = _swig_property(_IMP_em.SpiderHeader_fPhi_get, _IMP_em.SpiderHeader_fPhi_set)
1816  fTheta = _swig_property(_IMP_em.SpiderHeader_fTheta_get, _IMP_em.SpiderHeader_fTheta_set)
1817  fPsi = _swig_property(_IMP_em.SpiderHeader_fPsi_get, _IMP_em.SpiderHeader_fPsi_set)
1818  fXoff = _swig_property(_IMP_em.SpiderHeader_fXoff_get, _IMP_em.SpiderHeader_fXoff_set)
1819  fYoff = _swig_property(_IMP_em.SpiderHeader_fYoff_get, _IMP_em.SpiderHeader_fYoff_set)
1820  fZoff = _swig_property(_IMP_em.SpiderHeader_fZoff_get, _IMP_em.SpiderHeader_fZoff_set)
1821  fScale = _swig_property(_IMP_em.SpiderHeader_fScale_get, _IMP_em.SpiderHeader_fScale_set)
1822  fLabbyt = _swig_property(_IMP_em.SpiderHeader_fLabbyt_get, _IMP_em.SpiderHeader_fLabbyt_set)
1823  fLenbyt = _swig_property(_IMP_em.SpiderHeader_fLenbyt_get, _IMP_em.SpiderHeader_fLenbyt_set)
1824  fNothing = _swig_property(_IMP_em.SpiderHeader_fNothing_get, _IMP_em.SpiderHeader_fNothing_set)
1825  fFlag = _swig_property(_IMP_em.SpiderHeader_fFlag_get, _IMP_em.SpiderHeader_fFlag_set)
1826  fPhi1 = _swig_property(_IMP_em.SpiderHeader_fPhi1_get, _IMP_em.SpiderHeader_fPhi1_set)
1827  fTheta1 = _swig_property(_IMP_em.SpiderHeader_fTheta1_get, _IMP_em.SpiderHeader_fTheta1_set)
1828  fPsi1 = _swig_property(_IMP_em.SpiderHeader_fPsi1_get, _IMP_em.SpiderHeader_fPsi1_set)
1829  fPhi2 = _swig_property(_IMP_em.SpiderHeader_fPhi2_get, _IMP_em.SpiderHeader_fPhi2_set)
1830  fTheta2 = _swig_property(_IMP_em.SpiderHeader_fTheta2_get, _IMP_em.SpiderHeader_fTheta2_set)
1831  fPsi2 = _swig_property(_IMP_em.SpiderHeader_fPsi2_get, _IMP_em.SpiderHeader_fPsi2_set)
1832  fGeo_matrix = _swig_property(_IMP_em.SpiderHeader_fGeo_matrix_get, _IMP_em.SpiderHeader_fGeo_matrix_set)
1833  fAngle1 = _swig_property(_IMP_em.SpiderHeader_fAngle1_get, _IMP_em.SpiderHeader_fAngle1_set)
1834  fr1 = _swig_property(_IMP_em.SpiderHeader_fr1_get, _IMP_em.SpiderHeader_fr1_set)
1835  fr2 = _swig_property(_IMP_em.SpiderHeader_fr2_get, _IMP_em.SpiderHeader_fr2_set)
1836  RTflag = _swig_property(_IMP_em.SpiderHeader_RTflag_get, _IMP_em.SpiderHeader_RTflag_set)
1837  Astart = _swig_property(_IMP_em.SpiderHeader_Astart_get, _IMP_em.SpiderHeader_Astart_set)
1838  Aend = _swig_property(_IMP_em.SpiderHeader_Aend_get, _IMP_em.SpiderHeader_Aend_set)
1839  Ainc = _swig_property(_IMP_em.SpiderHeader_Ainc_get, _IMP_em.SpiderHeader_Ainc_set)
1840  Rsigma = _swig_property(_IMP_em.SpiderHeader_Rsigma_get, _IMP_em.SpiderHeader_Rsigma_set)
1841  Tstart = _swig_property(_IMP_em.SpiderHeader_Tstart_get, _IMP_em.SpiderHeader_Tstart_set)
1842  Tend = _swig_property(_IMP_em.SpiderHeader_Tend_get, _IMP_em.SpiderHeader_Tend_set)
1843  Tinc = _swig_property(_IMP_em.SpiderHeader_Tinc_get, _IMP_em.SpiderHeader_Tinc_set)
1844  Weight = _swig_property(_IMP_em.SpiderHeader_Weight_get, _IMP_em.SpiderHeader_Weight_set)
1845  Flip = _swig_property(_IMP_em.SpiderHeader_Flip_get, _IMP_em.SpiderHeader_Flip_set)
1846  empty = _swig_property(_IMP_em.SpiderHeader_empty_get, _IMP_em.SpiderHeader_empty_set)
1847  szIDat = _swig_property(_IMP_em.SpiderHeader_szIDat_get, _IMP_em.SpiderHeader_szIDat_set)
1848  szITim = _swig_property(_IMP_em.SpiderHeader_szITim_get, _IMP_em.SpiderHeader_szITim_set)
1849  szITit = _swig_property(_IMP_em.SpiderHeader_szITit_get, _IMP_em.SpiderHeader_szITit_set)
1850 
1851  def show(self, out):
1852  """show(SpiderHeader self, _ostream out)"""
1853  return _IMP_em.SpiderHeader_show(self, out)
1854 
1855 
1856  def __init__(self):
1857  """__init__(IMP::em::SpiderHeader self) -> SpiderHeader"""
1858  this = _IMP_em.new_SpiderHeader()
1859  try:
1860  self.this.append(this)
1861  except __builtin__.Exception:
1862  self.this = this
1863  __swig_destroy__ = _IMP_em.delete_SpiderHeader
1864  __del__ = lambda self: None
1865 SpiderHeader_swigregister = _IMP_em.SpiderHeader_swigregister
1866 SpiderHeader_swigregister(SpiderHeader)
1867 
1868 class ImageHeader(object):
1869  """Proxy of C++ IMP::em::ImageHeader class."""
1870 
1871  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1872  __repr__ = _swig_repr
1873  IMG_BYTE = _IMP_em.ImageHeader_IMG_BYTE
1874  IMG_IMPEM = _IMP_em.ImageHeader_IMG_IMPEM
1875  IMG_INT = _IMP_em.ImageHeader_IMG_INT
1876  VOL_BYTE = _IMP_em.ImageHeader_VOL_BYTE
1877  VOL_IMPEM = _IMP_em.ImageHeader_VOL_IMPEM
1878  VOL_INT = _IMP_em.ImageHeader_VOL_INT
1879  IMG_FOURIER = _IMP_em.ImageHeader_IMG_FOURIER
1880  VOL_FOURIER = _IMP_em.ImageHeader_VOL_FOURIER
1881 
1882  def __init__(self, *args):
1883  """
1884  __init__(IMP::em::ImageHeader self) -> ImageHeader
1885  __init__(IMP::em::ImageHeader self, IMP::em::ImageHeader::img_type im) -> ImageHeader
1886  __init__(IMP::em::ImageHeader self, float im) -> ImageHeader
1887  """
1888  this = _IMP_em.new_ImageHeader(*args)
1889  try:
1890  self.this.append(this)
1891  except __builtin__.Exception:
1892  self.this = this
1893 
1894  def get_image_type(self):
1895  """get_image_type(ImageHeader self) -> float"""
1896  return _IMP_em.ImageHeader_get_image_type(self)
1897 
1898 
1899  def set_image_type(self, *args):
1900  """
1901  set_image_type(ImageHeader self, IMP::em::ImageHeader::img_type im)
1902  set_image_type(ImageHeader self, float im)
1903  """
1904  return _IMP_em.ImageHeader_set_image_type(self, *args)
1905 
1906 
1907  def do_show(self, out):
1908  """do_show(ImageHeader self, _ostream out)"""
1909  return _IMP_em.ImageHeader_do_show(self, out)
1910 
1911 
1912  def show(self, *args):
1913  """
1914  show(ImageHeader self, _ostream out)
1915  show(ImageHeader self)
1916  """
1917  return _IMP_em.ImageHeader_show(self, *args)
1918 
1919 
1920  def print_hard(self, out):
1921  """print_hard(ImageHeader self, _ostream out)"""
1922  return _IMP_em.ImageHeader_print_hard(self, out)
1923 
1924 
1925  def show_projection_params(self, out):
1926  """show_projection_params(ImageHeader self, _ostream out)"""
1927  return _IMP_em.ImageHeader_show_projection_params(self, out)
1928 
1929 
1930  def read(self, *args):
1931  """
1932  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False, bool skip_extra_checkings=False) -> int
1933  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False) -> int
1934  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False) -> int
1935  read(ImageHeader self, IMP::String const filename) -> int
1936  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False, bool skip_extra_checkings=False) -> bool
1937  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False) -> bool
1938  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False) -> bool
1939  read(ImageHeader self, std::ifstream & f) -> bool
1940  """
1941  return _IMP_em.ImageHeader_read(self, *args)
1942 
1943 
1944  def write(self, *args):
1945  """
1946  write(ImageHeader self, IMP::String const & filename, bool force_reversed=False)
1947  write(ImageHeader self, IMP::String const & filename)
1948  write(ImageHeader self, std::ofstream & f, bool force_reversed=False)
1949  write(ImageHeader self, std::ofstream & f)
1950  """
1951  return _IMP_em.ImageHeader_write(self, *args)
1952 
1953 
1954  def clear(self):
1955  """clear(ImageHeader self)"""
1956  return _IMP_em.ImageHeader_clear(self)
1957 
1958 
1959  def set_header(self):
1960  """set_header(ImageHeader self)"""
1961  return _IMP_em.ImageHeader_set_header(self)
1962 
1963 
1964  def get_reversed(self):
1965  """get_reversed(ImageHeader self) -> bool"""
1966  return _IMP_em.ImageHeader_get_reversed(self)
1967 
1968 
1969  def set_reversed(self, value):
1970  """set_reversed(ImageHeader self, bool value)"""
1971  return _IMP_em.ImageHeader_set_reversed(self, value)
1972 
1973 
1974  def get_number_of_slices(self):
1975  """get_number_of_slices(ImageHeader self) -> unsigned int"""
1976  return _IMP_em.ImageHeader_get_number_of_slices(self)
1977 
1978 
1979  def set_number_of_slices(self, n):
1980  """set_number_of_slices(ImageHeader self, unsigned int n)"""
1981  return _IMP_em.ImageHeader_set_number_of_slices(self, n)
1982 
1983 
1984  def get_number_of_rows(self):
1985  """get_number_of_rows(ImageHeader self) -> unsigned int"""
1986  return _IMP_em.ImageHeader_get_number_of_rows(self)
1987 
1988 
1989  def set_number_of_rows(self, n):
1990  """set_number_of_rows(ImageHeader self, unsigned int n)"""
1991  return _IMP_em.ImageHeader_set_number_of_rows(self, n)
1992 
1993 
1994  def get_number_of_columns(self):
1995  """get_number_of_columns(ImageHeader self) -> unsigned int"""
1996  return _IMP_em.ImageHeader_get_number_of_columns(self)
1997 
1998 
1999  def set_number_of_columns(self, n):
2000  """set_number_of_columns(ImageHeader self, unsigned int n)"""
2001  return _IMP_em.ImageHeader_set_number_of_columns(self, n)
2002 
2003 
2004  def get_old_rot(self):
2005  """get_old_rot(ImageHeader self) -> float"""
2006  return _IMP_em.ImageHeader_get_old_rot(self)
2007 
2008 
2009  def set_old_rot(self, value):
2010  """set_old_rot(ImageHeader self, float value)"""
2011  return _IMP_em.ImageHeader_set_old_rot(self, value)
2012 
2013 
2014  def get_fAngle1(self):
2015  """get_fAngle1(ImageHeader self) -> float"""
2016  return _IMP_em.ImageHeader_get_fAngle1(self)
2017 
2018 
2019  def set_fAngle1(self, value):
2020  """set_fAngle1(ImageHeader self, float value)"""
2021  return _IMP_em.ImageHeader_set_fAngle1(self, value)
2022 
2023 
2024  def get_Scale(self):
2025  """get_Scale(ImageHeader self) -> float"""
2026  return _IMP_em.ImageHeader_get_Scale(self)
2027 
2028 
2029  def set_Scale(self, value):
2030  """set_Scale(ImageHeader self, float value)"""
2031  return _IMP_em.ImageHeader_set_Scale(self, value)
2032 
2033 
2034  def get_Flip(self):
2035  """get_Flip(ImageHeader self) -> float"""
2036  return _IMP_em.ImageHeader_get_Flip(self)
2037 
2038 
2039  def set_Flip(self, value):
2040  """set_Flip(ImageHeader self, float value)"""
2041  return _IMP_em.ImageHeader_set_Flip(self, value)
2042 
2043 
2044  def get_Weight(self):
2045  """get_Weight(ImageHeader self) -> float"""
2046  return _IMP_em.ImageHeader_get_Weight(self)
2047 
2048 
2049  def set_Weight(self, value):
2050  """set_Weight(ImageHeader self, float value)"""
2051  return _IMP_em.ImageHeader_set_Weight(self, value)
2052 
2053 
2054  def get_fNrec(self):
2055  """get_fNrec(ImageHeader self) -> float"""
2056  return _IMP_em.ImageHeader_get_fNrec(self)
2057 
2058 
2059  def set_fNrec(self, value):
2060  """set_fNrec(ImageHeader self, float value)"""
2061  return _IMP_em.ImageHeader_set_fNrec(self, value)
2062 
2063 
2064  def get_fNlabel(self):
2065  """get_fNlabel(ImageHeader self) -> float"""
2066  return _IMP_em.ImageHeader_get_fNlabel(self)
2067 
2068 
2069  def set_fNlabel(self, value):
2070  """set_fNlabel(ImageHeader self, float value)"""
2071  return _IMP_em.ImageHeader_set_fNlabel(self, value)
2072 
2073 
2074  def get_fIform(self):
2075  """get_fIform(ImageHeader self) -> float"""
2076  return _IMP_em.ImageHeader_get_fIform(self)
2077 
2078 
2079  def set_fIform(self, value):
2080  """set_fIform(ImageHeader self, float value)"""
2081  return _IMP_em.ImageHeader_set_fIform(self, value)
2082 
2083 
2084  def get_fImami(self):
2085  """get_fImami(ImageHeader self) -> float"""
2086  return _IMP_em.ImageHeader_get_fImami(self)
2087 
2088 
2089  def set_fImami(self, value):
2090  """set_fImami(ImageHeader self, float value)"""
2091  return _IMP_em.ImageHeader_set_fImami(self, value)
2092 
2093 
2094  def get_fFmax(self):
2095  """get_fFmax(ImageHeader self) -> float"""
2096  return _IMP_em.ImageHeader_get_fFmax(self)
2097 
2098 
2099  def set_fFmax(self, value):
2100  """set_fFmax(ImageHeader self, float value)"""
2101  return _IMP_em.ImageHeader_set_fFmax(self, value)
2102 
2103 
2104  def get_fFmin(self):
2105  """get_fFmin(ImageHeader self) -> float"""
2106  return _IMP_em.ImageHeader_get_fFmin(self)
2107 
2108 
2109  def set_fFmin(self, value):
2110  """set_fFmin(ImageHeader self, float value)"""
2111  return _IMP_em.ImageHeader_set_fFmin(self, value)
2112 
2113 
2114  def get_fAv(self):
2115  """get_fAv(ImageHeader self) -> float"""
2116  return _IMP_em.ImageHeader_get_fAv(self)
2117 
2118 
2119  def set_fAv(self, value):
2120  """set_fAv(ImageHeader self, float value)"""
2121  return _IMP_em.ImageHeader_set_fAv(self, value)
2122 
2123 
2124  def get_fSig(self):
2125  """get_fSig(ImageHeader self) -> float"""
2126  return _IMP_em.ImageHeader_get_fSig(self)
2127 
2128 
2129  def set_fSig(self, value):
2130  """set_fSig(ImageHeader self, float value)"""
2131  return _IMP_em.ImageHeader_set_fSig(self, value)
2132 
2133 
2134  def get_fIhist(self):
2135  """get_fIhist(ImageHeader self) -> float"""
2136  return _IMP_em.ImageHeader_get_fIhist(self)
2137 
2138 
2139  def set_fIhist(self, value):
2140  """set_fIhist(ImageHeader self, float value)"""
2141  return _IMP_em.ImageHeader_set_fIhist(self, value)
2142 
2143 
2144  def get_fLabrec(self):
2145  """get_fLabrec(ImageHeader self) -> float"""
2146  return _IMP_em.ImageHeader_get_fLabrec(self)
2147 
2148 
2149  def set_fLabrec(self, value):
2150  """set_fLabrec(ImageHeader self, float value)"""
2151  return _IMP_em.ImageHeader_set_fLabrec(self, value)
2152 
2153 
2154  def get_fIangle(self):
2155  """get_fIangle(ImageHeader self) -> float"""
2156  return _IMP_em.ImageHeader_get_fIangle(self)
2157 
2158 
2159  def set_fIangle(self, value):
2160  """set_fIangle(ImageHeader self, float value)"""
2161  return _IMP_em.ImageHeader_set_fIangle(self, value)
2162 
2163 
2164  def get_origin(self):
2165  """get_origin(ImageHeader self) -> Vector3D"""
2166  return _IMP_em.ImageHeader_get_origin(self)
2167 
2168 
2169  def set_origin(self, *args):
2170  """
2171  set_origin(ImageHeader self, Vector3D v)
2172  set_origin(ImageHeader self, Vector2D v)
2173  """
2174  return _IMP_em.ImageHeader_set_origin(self, *args)
2175 
2176 
2177  def get_object_pixel_size(self):
2178  """get_object_pixel_size(ImageHeader self) -> float"""
2179  return _IMP_em.ImageHeader_get_object_pixel_size(self)
2180 
2181 
2182  def set_object_pixel_size(self, value):
2183  """set_object_pixel_size(ImageHeader self, float value)"""
2184  return _IMP_em.ImageHeader_set_object_pixel_size(self, value)
2185 
2186 
2187  def get_fLabbyt(self):
2188  """get_fLabbyt(ImageHeader self) -> float"""
2189  return _IMP_em.ImageHeader_get_fLabbyt(self)
2190 
2191 
2192  def set_fLabbyt(self, value):
2193  """set_fLabbyt(ImageHeader self, float value)"""
2194  return _IMP_em.ImageHeader_set_fLabbyt(self, value)
2195 
2196 
2197  def get_fLenbyt(self):
2198  """get_fLenbyt(ImageHeader self) -> float"""
2199  return _IMP_em.ImageHeader_get_fLenbyt(self)
2200 
2201 
2202  def set_fLenbyt(self, value):
2203  """set_fLenbyt(ImageHeader self, float value)"""
2204  return _IMP_em.ImageHeader_set_fLenbyt(self, value)
2205 
2206 
2207  def get_fGeo_matrix(self, i, j):
2208  """get_fGeo_matrix(ImageHeader self, unsigned int i, unsigned int j) -> double"""
2209  return _IMP_em.ImageHeader_get_fGeo_matrix(self, i, j)
2210 
2211 
2212  def get_fFlag(self):
2213  """get_fFlag(ImageHeader self) -> float"""
2214  return _IMP_em.ImageHeader_get_fFlag(self)
2215 
2216 
2217  def set_fFlag(self, value):
2218  """set_fFlag(ImageHeader self, float value)"""
2219  return _IMP_em.ImageHeader_set_fFlag(self, value)
2220 
2221 
2222  def get_euler_angles(self):
2223  """get_euler_angles(ImageHeader self) -> Vector3D"""
2224  return _IMP_em.ImageHeader_get_euler_angles(self)
2225 
2226 
2227  def get_euler_angles1(self):
2228  """get_euler_angles1(ImageHeader self) -> Vector3D"""
2229  return _IMP_em.ImageHeader_get_euler_angles1(self)
2230 
2231 
2232  def get_euler_angles2(self):
2233  """get_euler_angles2(ImageHeader self) -> Vector3D"""
2234  return _IMP_em.ImageHeader_get_euler_angles2(self)
2235 
2236 
2237  def set_euler_angles(self, euler):
2238  """set_euler_angles(ImageHeader self, Vector3D euler)"""
2239  return _IMP_em.ImageHeader_set_euler_angles(self, euler)
2240 
2241 
2242  def set_euler_angles1(self, euler):
2243  """set_euler_angles1(ImageHeader self, Vector3D euler)"""
2244  return _IMP_em.ImageHeader_set_euler_angles1(self, euler)
2245 
2246 
2247  def set_euler_angles2(self, euler):
2248  """set_euler_angles2(ImageHeader self, Vector3D euler)"""
2249  return _IMP_em.ImageHeader_set_euler_angles2(self, euler)
2250 
2251 
2252  def is_normalized(self):
2253  """is_normalized(ImageHeader self) -> bool"""
2254  return _IMP_em.ImageHeader_is_normalized(self)
2255 
2256 
2257  def set_date(self):
2258  """set_date(ImageHeader self)"""
2259  return _IMP_em.ImageHeader_set_date(self)
2260 
2261 
2262  def set_time(self):
2263  """set_time(ImageHeader self)"""
2264  return _IMP_em.ImageHeader_set_time(self)
2265 
2266 
2267  def set_title(self, newName):
2268  """set_title(ImageHeader self, IMP::String newName)"""
2269  return _IMP_em.ImageHeader_set_title(self, newName)
2270 
2271  __swig_destroy__ = _IMP_em.delete_ImageHeader
2272  __del__ = lambda self: None
2273 ImageHeader_swigregister = _IMP_em.ImageHeader_swigregister
2274 ImageHeader_swigregister(ImageHeader)
2275 
2276 class SpiderMapReaderWriter(MapReaderWriter):
2277  """Proxy of C++ IMP::em::SpiderMapReaderWriter class."""
2278 
2279  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2280  filename_ = _swig_property(_IMP_em.SpiderMapReaderWriter_filename__get, _IMP_em.SpiderMapReaderWriter_filename__set)
2281  skip_type_check_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_type_check__get, _IMP_em.SpiderMapReaderWriter_skip_type_check__set)
2282  force_reversed_ = _swig_property(_IMP_em.SpiderMapReaderWriter_force_reversed__get, _IMP_em.SpiderMapReaderWriter_force_reversed__set)
2283  skip_extra_checkings_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_extra_checkings__get, _IMP_em.SpiderMapReaderWriter_skip_extra_checkings__set)
2284 
2285  def __init__(self, *args):
2286  """
2287  __init__(IMP::em::SpiderMapReaderWriter self) -> SpiderMapReaderWriter
2288  __init__(IMP::em::SpiderMapReaderWriter self, IMP::String filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings) -> SpiderMapReaderWriter
2289  """
2290  this = _IMP_em.new_SpiderMapReaderWriter(*args)
2291  try:
2292  self.this.append(this)
2293  except __builtin__.Exception:
2294  self.this = this
2295 
2296  def __str__(self):
2297  """__str__(SpiderMapReaderWriter self) -> std::string"""
2298  return _IMP_em.SpiderMapReaderWriter___str__(self)
2299 
2300 
2301  def __repr__(self):
2302  """__repr__(SpiderMapReaderWriter self) -> std::string"""
2303  return _IMP_em.SpiderMapReaderWriter___repr__(self)
2304 
2305 
2306  @staticmethod
2307  def get_from(o):
2308  return _object_cast_to_SpiderMapReaderWriter(o)
2309 
2310 SpiderMapReaderWriter_swigregister = _IMP_em.SpiderMapReaderWriter_swigregister
2311 SpiderMapReaderWriter_swigregister(SpiderMapReaderWriter)
2312 
2313 class FittingSolutions(object):
2314  """Proxy of C++ IMP::em::FittingSolutions class."""
2315 
2316  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2317 
2318  def __init__(self):
2319  """__init__(IMP::em::FittingSolutions self) -> FittingSolutions"""
2320  this = _IMP_em.new_FittingSolutions()
2321  try:
2322  self.this.append(this)
2323  except __builtin__.Exception:
2324  self.this = this
2325 
2326  def get_number_of_solutions(self):
2327  """get_number_of_solutions(FittingSolutions self) -> int"""
2328  return _IMP_em.FittingSolutions_get_number_of_solutions(self)
2329 
2330 
2331  def get_transformation(self, i):
2332  """get_transformation(FittingSolutions self, unsigned int i) -> Transformation3D"""
2333  return _IMP_em.FittingSolutions_get_transformation(self, i)
2334 
2335 
2336  def get_score(self, i):
2337  """get_score(FittingSolutions self, unsigned int i) -> IMP::Float"""
2338  return _IMP_em.FittingSolutions_get_score(self, i)
2339 
2340 
2341  def set_score(self, i, score):
2342  """set_score(FittingSolutions self, unsigned int i, IMP::Float score)"""
2343  return _IMP_em.FittingSolutions_set_score(self, i, score)
2344 
2345 
2346  def add_solution(self, t, score):
2347  """add_solution(FittingSolutions self, Transformation3D t, IMP::Float score)"""
2348  return _IMP_em.FittingSolutions_add_solution(self, t, score)
2349 
2350 
2351  def sort(self, reverse=False):
2352  """
2353  sort(FittingSolutions self, bool reverse=False)
2354  sort(FittingSolutions self)
2355  """
2356  return _IMP_em.FittingSolutions_sort(self, reverse)
2357 
2358 
2359  def multiply(self, t):
2360  """multiply(FittingSolutions self, Transformation3D t)"""
2361  return _IMP_em.FittingSolutions_multiply(self, t)
2362 
2363 
2364  def get_transformations(self):
2365  """get_transformations(FittingSolutions self) -> IMP::algebra::Transformation3Ds"""
2366  return _IMP_em.FittingSolutions_get_transformations(self)
2367 
2368 
2369  def show(self, *args):
2370  """
2371  show(FittingSolutions self, _ostream out)
2372  show(FittingSolutions self)
2373  """
2374  return _IMP_em.FittingSolutions_show(self, *args)
2375 
2376 
2377  def __str__(self):
2378  """__str__(FittingSolutions self) -> std::string"""
2379  return _IMP_em.FittingSolutions___str__(self)
2380 
2381 
2382  def __repr__(self):
2383  """__repr__(FittingSolutions self) -> std::string"""
2384  return _IMP_em.FittingSolutions___repr__(self)
2385 
2386  __swig_destroy__ = _IMP_em.delete_FittingSolutions
2387  __del__ = lambda self: None
2388 FittingSolutions_swigregister = _IMP_em.FittingSolutions_swigregister
2389 FittingSolutions_swigregister(FittingSolutions)
2390 
2391 
2392 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):
2393  """
2394  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
2395  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
2396  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
2397  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
2398  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
2399  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
2400  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log) -> FittingSolutions
2401  """
2402  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)
2403 
2404 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):
2405  """
2406  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
2407  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
2408  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
2409  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
2410  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
2411  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2412  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log) -> FittingSolutions
2413  """
2414  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)
2415 
2416 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):
2417  """
2418  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
2419  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
2420  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
2421  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
2422  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
2423  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
2424  """
2425  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)
2426 
2427 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):
2428  """
2429  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
2430  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
2431  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
2432  local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2) -> FittingSolutions
2433  local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap) -> FittingSolutions
2434  """
2435  return _IMP_em.local_rigid_fitting_grid_search(ps, wei_key, dmap, max_voxels_translation, translation_step, max_angle_in_radians, number_of_rotations)
2436 
2437 def compute_fitting_scores(*args):
2438  """
2439  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
2440  compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations, bool fast_version=False, bool local_score=False) -> FittingSolutions
2441  compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations, bool fast_version=False) -> FittingSolutions
2442  compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2443  compute_fitting_scores(DensityMap em_map, RigidBody rb, Refiner refiner, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2444  """
2445  return _IMP_em.compute_fitting_scores(*args)
2446 
2447 def compute_fitting_score(*args):
2448  """
2449  compute_fitting_score(IMP::ParticlesTemp const & ps, DensityMap em_map, FloatKey wei_key) -> IMP::Float
2450  compute_fitting_score(IMP::ParticlesTemp const & ps, DensityMap em_map) -> IMP::Float
2451  """
2452  return _IMP_em.compute_fitting_score(*args)
2453 
2455  """
2456  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, Transformation3D t, float thr=0.0) -> long
2457  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, Transformation3D t) -> long
2458  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps) -> long
2459  """
2460  return _IMP_em.get_number_of_particles_outside_of_the_density(*args)
2461 
2462 def get_numbers_of_particles_outside_of_the_density(dmap, ps, transformations, thr=0.0):
2463  """
2464  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
2465  get_numbers_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, IMP::algebra::Transformation3Ds const & transformations) -> IMP::Ints
2466  """
2467  return _IMP_em.get_numbers_of_particles_outside_of_the_density(dmap, ps, transformations, thr)
2468 
2470  """
2471  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3., Transformation3D t, float thr=0.0) -> double
2472  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3., Transformation3D t) -> double
2473  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3.) -> double
2474  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps) -> double
2475  """
2476  return _IMP_em.get_percentage_of_voxels_covered_by_particles(*args)
2477 class HighDensityEmbedding(IMP.statistics.Embedding):
2478  """Proxy of C++ IMP::em::HighDensityEmbedding class."""
2479 
2480  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2481 
2482  def __init__(self, dm, threshold):
2483  """__init__(IMP::em::HighDensityEmbedding self, DensityMap dm, double threshold) -> HighDensityEmbedding"""
2484  this = _IMP_em.new_HighDensityEmbedding(dm, threshold)
2485  try:
2486  self.this.append(this)
2487  except __builtin__.Exception:
2488  self.this = this
2489 
2490  def get_version_info(self):
2491  """get_version_info(HighDensityEmbedding self) -> VersionInfo"""
2492  return _IMP_em.HighDensityEmbedding_get_version_info(self)
2493 
2494 
2495  def __str__(self):
2496  """__str__(HighDensityEmbedding self) -> std::string"""
2497  return _IMP_em.HighDensityEmbedding___str__(self)
2498 
2499 
2500  def __repr__(self):
2501  """__repr__(HighDensityEmbedding self) -> std::string"""
2502  return _IMP_em.HighDensityEmbedding___repr__(self)
2503 
2504 
2505  @staticmethod
2506  def get_from(o):
2507  return _object_cast_to_HighDensityEmbedding(o)
2508 
2509 HighDensityEmbedding_swigregister = _IMP_em.HighDensityEmbedding_swigregister
2510 HighDensityEmbedding_swigregister(HighDensityEmbedding)
2511 
2512 
2513 def mask_and_norm(dmap, mask):
2514  """mask_and_norm(DensityMap dmap, DensityMap mask) -> DensityMap"""
2515  return _IMP_em.mask_and_norm(dmap, mask)
2516 
2517 def get_volume_at_threshold(m, threshold):
2518  """get_volume_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float"""
2519  return _IMP_em.get_volume_at_threshold(m, threshold)
2520 
2522  """
2523  get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold, IMP::atom::ProteinDensityReference ref) -> IMP::Float
2524  get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float
2525  """
2526  return _IMP_em.get_molecular_mass_at_threshold(*args)
2527 
2528 def get_threshold_for_approximate_volume(m, desired_volume):
2529  """get_threshold_for_approximate_volume(DensityMap m, IMP::Float desired_volume) -> IMP::Float"""
2530  return _IMP_em.get_threshold_for_approximate_volume(m, desired_volume)
2531 
2533  """
2534  get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass, IMP::atom::ProteinDensityReference ref) -> IMP::Float
2535  get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass) -> IMP::Float
2536  """
2537  return _IMP_em.get_threshold_for_approximate_mass(*args)
2538 class EnvelopePenetrationRestraint(IMP.Restraint):
2539  """Proxy of C++ IMP::em::EnvelopePenetrationRestraint class."""
2540 
2541  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2542 
2543  def __init__(self, ps, em_map, threshold):
2544  """__init__(IMP::em::EnvelopePenetrationRestraint self, IMP::Particles ps, DensityMap em_map, IMP::Float threshold) -> EnvelopePenetrationRestraint"""
2545  this = _IMP_em.new_EnvelopePenetrationRestraint(ps, em_map, threshold)
2546  try:
2547  self.this.append(this)
2548  except __builtin__.Exception:
2549  self.this = this
2550 
2551  def do_get_inputs(self):
2552  """do_get_inputs(EnvelopePenetrationRestraint self) -> IMP::ModelObjectsTemp"""
2553  return _IMP_em.EnvelopePenetrationRestraint_do_get_inputs(self)
2554 
2555 
2556  def get_version_info(self):
2557  """get_version_info(EnvelopePenetrationRestraint self) -> VersionInfo"""
2558  return _IMP_em.EnvelopePenetrationRestraint_get_version_info(self)
2559 
2560 
2561  def __str__(self):
2562  """__str__(EnvelopePenetrationRestraint self) -> std::string"""
2563  return _IMP_em.EnvelopePenetrationRestraint___str__(self)
2564 
2565 
2566  def __repr__(self):
2567  """__repr__(EnvelopePenetrationRestraint self) -> std::string"""
2568  return _IMP_em.EnvelopePenetrationRestraint___repr__(self)
2569 
2570 
2571  @staticmethod
2572  def get_from(o):
2573  return _object_cast_to_EnvelopePenetrationRestraint(o)
2574 
2575 EnvelopePenetrationRestraint_swigregister = _IMP_em.EnvelopePenetrationRestraint_swigregister
2576 EnvelopePenetrationRestraint_swigregister(EnvelopePenetrationRestraint)
2577 
2578 class PCAFitRestraint(IMP.Restraint):
2579  """Proxy of C++ IMP::em::PCAFitRestraint class."""
2580 
2581  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2582 
2583  def __init__(self, *args):
2584  """
2585  __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
2586  __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
2587  """
2588  this = _IMP_em.new_PCAFitRestraint(*args)
2589  try:
2590  self.this.append(this)
2591  except __builtin__.Exception:
2592  self.this = this
2593 
2594  def do_get_inputs(self):
2595  """do_get_inputs(PCAFitRestraint self) -> IMP::ModelObjectsTemp"""
2596  return _IMP_em.PCAFitRestraint_do_get_inputs(self)
2597 
2598 
2599  def get_version_info(self):
2600  """get_version_info(PCAFitRestraint self) -> VersionInfo"""
2601  return _IMP_em.PCAFitRestraint_get_version_info(self)
2602 
2603 
2604  def __str__(self):
2605  """__str__(PCAFitRestraint self) -> std::string"""
2606  return _IMP_em.PCAFitRestraint___str__(self)
2607 
2608 
2609  def __repr__(self):
2610  """__repr__(PCAFitRestraint self) -> std::string"""
2611  return _IMP_em.PCAFitRestraint___repr__(self)
2612 
2613 
2614  @staticmethod
2615  def get_from(o):
2616  return _object_cast_to_PCAFitRestraint(o)
2617 
2618 PCAFitRestraint_swigregister = _IMP_em.PCAFitRestraint_swigregister
2619 PCAFitRestraint_swigregister(PCAFitRestraint)
2620 
2621 class EnvelopeFitRestraint(IMP.Restraint):
2622  """Proxy of C++ IMP::em::EnvelopeFitRestraint class."""
2623 
2624  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2625 
2626  def __init__(self, particles, em_map, density_threshold, penetration_threshold):
2627  """__init__(IMP::em::EnvelopeFitRestraint self, IMP::Particles particles, DensityMap em_map, double density_threshold, double penetration_threshold) -> EnvelopeFitRestraint"""
2628  this = _IMP_em.new_EnvelopeFitRestraint(particles, em_map, density_threshold, penetration_threshold)
2629  try:
2630  self.this.append(this)
2631  except __builtin__.Exception:
2632  self.this = this
2633 
2634  def get_transformation(self):
2635  """get_transformation(EnvelopeFitRestraint self) -> Transformation3D"""
2636  return _IMP_em.EnvelopeFitRestraint_get_transformation(self)
2637 
2638 
2639  def apply_transformation(self):
2640  """apply_transformation(EnvelopeFitRestraint self)"""
2641  return _IMP_em.EnvelopeFitRestraint_apply_transformation(self)
2642 
2643 
2644  def do_get_inputs(self):
2645  """do_get_inputs(EnvelopeFitRestraint self) -> IMP::ModelObjectsTemp"""
2646  return _IMP_em.EnvelopeFitRestraint_do_get_inputs(self)
2647 
2648 
2649  def get_version_info(self):
2650  """get_version_info(EnvelopeFitRestraint self) -> VersionInfo"""
2651  return _IMP_em.EnvelopeFitRestraint_get_version_info(self)
2652 
2653 
2654  def __str__(self):
2655  """__str__(EnvelopeFitRestraint self) -> std::string"""
2656  return _IMP_em.EnvelopeFitRestraint___str__(self)
2657 
2658 
2659  def __repr__(self):
2660  """__repr__(EnvelopeFitRestraint self) -> std::string"""
2661  return _IMP_em.EnvelopeFitRestraint___repr__(self)
2662 
2663 
2664  @staticmethod
2665  def get_from(o):
2666  return _object_cast_to_EnvelopeFitRestraint(o)
2667 
2668 EnvelopeFitRestraint_swigregister = _IMP_em.EnvelopeFitRestraint_swigregister
2669 EnvelopeFitRestraint_swigregister(EnvelopeFitRestraint)
2670 
2671 
2672 import math
2673 
2674 def write_pca_cmm(pca, fh):
2675  """Write out principal components to a file in Chimera Marker format"""
2676  eigen_values = pca.get_principal_values()
2677  eigen_vecs = pca.get_principal_components()
2678  centroid = pca.get_centroid()
2679 
2680  fh.write("<marker_set>\n")
2681  fh.write("<!-- PCA with eigen values: (%g,%g,%g) and "
2682  "centroid (%g,%g,%g) -->\n"
2683  % (math.sqrt(eigen_values[0]),
2684  math.sqrt(eigen_values[1]),
2685  math.sqrt(eigen_values[2]),
2686  centroid[0], centroid[1], centroid[2]))
2687 
2688  radius = 2.
2689 
2690  for i in range(3):
2691  val = math.sqrt(eigen_values[i])
2692  v1 = centroid - val * eigen_vecs[i]
2693  v2 = centroid + val * eigen_vecs[i]
2694  for markerid, v in ((i*2+1, v1), (i*2+2, v2)):
2695  fh.write("<marker id=\"%d\" x=\"%g\" y=\"%g\" z=\"%g\" "
2696  "radius=\"%g\"/>\n"
2697  % (markerid, v[0], v[1], v[2], radius))
2698 
2699  for i in range(1, 7, 2):
2700  fh.write("<link id1= \"%d\" id2=\"%d\" radius=\"%g\"/>\n"
2701  % (i, i+1, radius))
2702  fh.write("</marker_set>\n")
2703 
2704 
2705 def get_module_version():
2706  """get_module_version() -> std::string const"""
2707  return _IMP_em.get_module_version()
2708 
2709 def get_example_path(fname):
2710  """get_example_path(std::string fname) -> std::string"""
2711  return _IMP_em.get_example_path(fname)
2712 
2713 def get_data_path(fname):
2714  """get_data_path(std::string fname) -> std::string"""
2715  return _IMP_em.get_data_path(fname)
2716 
2717 from . import _version_check
2718 _version_check.check_version(get_module_version())
2719 __version__ = get_module_version()
2720 
2721 
2722 
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)
Return the centroid of a set of vectors.
Definition: Vector3D.h:68
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
FittingSolutions local_rigid_fitting(Particle *p, Refiner *refiner, const FloatKey &weight_key, DensityMap *dmap, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3, bool fast=true)
Local rigid fitting of a rigid body.
Basic functionality that is expected to be used by a wide variety of IMP users.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
SurfaceShellDensityMap * particles2surface(const ParticlesTemp &ps, Float apix, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
Resample a set of particles into a density grid.
FittingSolutions local_rigid_fitting_around_points(Particle *p, Refiner *refiner, const FloatKey &wei_key, DensityMap *dmap, const algebra::Vector3Ds &anchor_centroids, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3)
Local rigid fitting of a rigid body around a set of center points.
FittingSolutions local_rigid_fitting_grid_search(const ParticlesTemp &ps, const FloatKey &wei_key, DensityMap *dmap, Int max_voxels_translation=2, Int translation_step=1, Float max_angle_in_radians=0.174, Int number_of_rotations=100)
Local grid search rigid fitting.
double get_resolution(Model *m, ParticleIndex pi)
Estimate the resolution of the hierarchy as used by Representation.
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
Float get_molecular_mass_at_threshold(DensityMap *m, Float threshold, atom::ProteinDensityReference ref=atom::HARPAZ)
Compute an approximate molecular mass.
DensityMap * get_segment(DensityMap *map_to_segment, int nx_start, int nx_end, int ny_start, int ny_end, int nz_start, int nz_end)
Get a segment of the map according to xyz indexes.
Float get_threshold_for_approximate_volume(DensityMap *m, Float desired_volume)
Computes the threshold consider in an EM map to get a desired volume.
Float get_volume_at_threshold(DensityMap *m, Float threshold)
Compute an approximate volume.
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:52