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IMP Reference Guide  2.10.0
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 2007-2018 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 IMP_C_OPEN_BINARY = _IMP_em.IMP_C_OPEN_BINARY
289 import IMP
290 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CGAL_HAS_BOOST_FILESYSTEM
291 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
292 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_em.IMP_CGAL_HAS_BOOST_RANDOM
293 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_em.IMP_CGAL_HAS_BOOST_SYSTEM
294 IMPCGAL_SHOW_WARNINGS = _IMP_em.IMPCGAL_SHOW_WARNINGS
295 import IMP.cgal
296 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_em.IMP_ALGEBRA_HAS_IMP_CGAL
297 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
298 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
299 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_RANDOM
300 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_SYSTEM
301 IMP_ALGEBRA_HAS_CGAL = _IMP_em.IMP_ALGEBRA_HAS_CGAL
302 IMP_ALGEBRA_HAS_ANN = _IMP_em.IMP_ALGEBRA_HAS_ANN
303 IMPALGEBRA_SHOW_WARNINGS = _IMP_em.IMPALGEBRA_SHOW_WARNINGS
304 import IMP.algebra
305 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_em.IMP_DISPLAY_HAS_IMP_CGAL
306 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
307 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
308 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_em.IMP_DISPLAY_HAS_BOOST_RANDOM
309 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_em.IMP_DISPLAY_HAS_BOOST_SYSTEM
310 IMP_DISPLAY_HAS_CGAL = _IMP_em.IMP_DISPLAY_HAS_CGAL
311 IMPDISPLAY_SHOW_WARNINGS = _IMP_em.IMPDISPLAY_SHOW_WARNINGS
312 import IMP.display
313 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_em.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
314 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
315 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
316 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
317 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
318 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_em.IMP_SCORE_FUNCTOR_HAS_CGAL
319 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_em.IMP_SCORE_FUNCTOR_HAS_HDF5
320 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_em.IMPSCOREFUNCTOR_SHOW_WARNINGS
321 import IMP.score_functor
322 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_em.IMP_STATISTICS_HAS_IMP_CGAL
323 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
324 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
325 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_em.IMP_STATISTICS_HAS_BOOST_RANDOM
326 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_SYSTEM
327 IMP_STATISTICS_HAS_CGAL = _IMP_em.IMP_STATISTICS_HAS_CGAL
328 IMPSTATISTICS_SHOW_WARNINGS = _IMP_em.IMPSTATISTICS_SHOW_WARNINGS
329 import IMP.statistics
330 IMP_CORE_HAS_IMP_CGAL = _IMP_em.IMP_CORE_HAS_IMP_CGAL
331 IMP_CORE_HAS_IMP_KERNEL = _IMP_em.IMP_CORE_HAS_IMP_KERNEL
332 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_FILESYSTEM
333 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
334 IMP_CORE_HAS_BOOST_RANDOM = _IMP_em.IMP_CORE_HAS_BOOST_RANDOM
335 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_SYSTEM
336 IMP_CORE_HAS_CGAL = _IMP_em.IMP_CORE_HAS_CGAL
337 IMP_CORE_HAS_HDF5 = _IMP_em.IMP_CORE_HAS_HDF5
338 IMPCORE_SHOW_WARNINGS = _IMP_em.IMPCORE_SHOW_WARNINGS
339 import IMP.core
340 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_em.IMP_CONTAINER_HAS_IMP_ALGEBRA
341 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_em.IMP_CONTAINER_HAS_IMP_CGAL
342 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_em.IMP_CONTAINER_HAS_IMP_DISPLAY
343 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_em.IMP_CONTAINER_HAS_IMP_KERNEL
344 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
345 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
346 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
347 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_em.IMP_CONTAINER_HAS_BOOST_RANDOM
348 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_SYSTEM
349 IMP_CONTAINER_HAS_CGAL = _IMP_em.IMP_CONTAINER_HAS_CGAL
350 IMP_CONTAINER_HAS_HDF5 = _IMP_em.IMP_CONTAINER_HAS_HDF5
351 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_em.IMP_CONTAINER_HAS_PYTHON_IHM
352 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_em.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
353 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_em.IMP_CONTAINER_HAS_ROBIN_MAP
354 IMPCONTAINER_SHOW_WARNINGS = _IMP_em.IMPCONTAINER_SHOW_WARNINGS
355 import IMP.container
356 IMP_ATOM_HAS_IMP_CGAL = _IMP_em.IMP_ATOM_HAS_IMP_CGAL
357 IMP_ATOM_HAS_IMP_KERNEL = _IMP_em.IMP_ATOM_HAS_IMP_KERNEL
358 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
359 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
360 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_em.IMP_ATOM_HAS_BOOST_RANDOM
361 IMP_ATOM_HAS_BOOST_REGEX = _IMP_em.IMP_ATOM_HAS_BOOST_REGEX
362 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_em.IMP_ATOM_HAS_BOOST_SYSTEM
363 IMP_ATOM_HAS_CGAL = _IMP_em.IMP_ATOM_HAS_CGAL
364 IMP_ATOM_HAS_HDF5 = _IMP_em.IMP_ATOM_HAS_HDF5
365 IMP_ATOM_HAS_PYTHON_IHM = _IMP_em.IMP_ATOM_HAS_PYTHON_IHM
366 IMPATOM_SHOW_WARNINGS = _IMP_em.IMPATOM_SHOW_WARNINGS
367 IMP_ATOM_TYPE_INDEX = _IMP_em.IMP_ATOM_TYPE_INDEX
368 IMP_RESIDUE_TYPE_INDEX = _IMP_em.IMP_RESIDUE_TYPE_INDEX
369 IMP_HIERARCHY_TYPE_INDEX = _IMP_em.IMP_HIERARCHY_TYPE_INDEX
370 IMP_CHAIN_TYPE_INDEX = _IMP_em.IMP_CHAIN_TYPE_INDEX
371 import IMP.atom
372 IMP_EM_HAS_IMP_CGAL = _IMP_em.IMP_EM_HAS_IMP_CGAL
373 IMP_EM_HAS_IMP_CONTAINER = _IMP_em.IMP_EM_HAS_IMP_CONTAINER
374 IMP_EM_HAS_IMP_DISPLAY = _IMP_em.IMP_EM_HAS_IMP_DISPLAY
375 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_EM_HAS_IMP_SCORE_FUNCTOR
376 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_EM_HAS_BOOST_FILESYSTEM
377 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
378 IMP_EM_HAS_BOOST_RANDOM = _IMP_em.IMP_EM_HAS_BOOST_RANDOM
379 IMP_EM_HAS_BOOST_REGEX = _IMP_em.IMP_EM_HAS_BOOST_REGEX
380 IMP_EM_HAS_BOOST_SYSTEM = _IMP_em.IMP_EM_HAS_BOOST_SYSTEM
381 IMP_EM_HAS_CGAL = _IMP_em.IMP_EM_HAS_CGAL
382 IMP_EM_HAS_HDF5 = _IMP_em.IMP_EM_HAS_HDF5
383 IMP_EM_HAS_PYTHON_IHM = _IMP_em.IMP_EM_HAS_PYTHON_IHM
384 IMPEM_SHOW_WARNINGS = _IMP_em.IMPEM_SHOW_WARNINGS
385 
386 _object_types.append("DensityMap")
387 
388 
389 def _object_cast_to_DensityMap(o):
390  """_object_cast_to_DensityMap(Object o) -> DensityMap"""
391  return _IMP_em._object_cast_to_DensityMap(o)
392 
393 _object_types.append("SampledDensityMap")
394 
395 
396 def _object_cast_to_SampledDensityMap(o):
397  """_object_cast_to_SampledDensityMap(Object o) -> SampledDensityMap"""
398  return _IMP_em._object_cast_to_SampledDensityMap(o)
399 
400 _object_types.append("SurfaceShellDensityMap")
401 
402 
403 def _object_cast_to_SurfaceShellDensityMap(o):
404  """_object_cast_to_SurfaceShellDensityMap(Object o) -> SurfaceShellDensityMap"""
405  return _IMP_em._object_cast_to_SurfaceShellDensityMap(o)
406 
407 _object_types.append("FitRestraint")
408 
409 
410 def _object_cast_to_FitRestraint(o):
411  """_object_cast_to_FitRestraint(Object o) -> FitRestraint"""
412  return _IMP_em._object_cast_to_FitRestraint(o)
413 
414 _object_types.append("PCAFitRestraint")
415 
416 
417 def _object_cast_to_PCAFitRestraint(o):
418  """_object_cast_to_PCAFitRestraint(Object o) -> PCAFitRestraint"""
419  return _IMP_em._object_cast_to_PCAFitRestraint(o)
420 
421 _object_types.append("EnvelopePenetrationRestraint")
422 
423 
424 def _object_cast_to_EnvelopePenetrationRestraint(o):
425  """_object_cast_to_EnvelopePenetrationRestraint(Object o) -> EnvelopePenetrationRestraint"""
426  return _IMP_em._object_cast_to_EnvelopePenetrationRestraint(o)
427 
428 _object_types.append("EnvelopeFitRestraint")
429 
430 
431 def _object_cast_to_EnvelopeFitRestraint(o):
432  """_object_cast_to_EnvelopeFitRestraint(Object o) -> EnvelopeFitRestraint"""
433  return _IMP_em._object_cast_to_EnvelopeFitRestraint(o)
434 
435 KernelParametersList=list
436 _plural_types.append("KernelParametersList")
437 _value_types.append("KernelParameters")
438 
439 
440 _object_types.append("HighDensityEmbedding")
441 
442 
443 def _object_cast_to_HighDensityEmbedding(o):
444  """_object_cast_to_HighDensityEmbedding(Object o) -> HighDensityEmbedding"""
445  return _IMP_em._object_cast_to_HighDensityEmbedding(o)
446 
447 _object_types.append("MapReaderWriter")
448 
449 
450 def _object_cast_to_MapReaderWriter(o):
451  """_object_cast_to_MapReaderWriter(Object o) -> MapReaderWriter"""
452  return _IMP_em._object_cast_to_MapReaderWriter(o)
453 
454 _object_types.append("MRCReaderWriter")
455 
456 
457 def _object_cast_to_MRCReaderWriter(o):
458  """_object_cast_to_MRCReaderWriter(Object o) -> MRCReaderWriter"""
459  return _IMP_em._object_cast_to_MRCReaderWriter(o)
460 
461 _object_types.append("SpiderMapReaderWriter")
462 
463 
464 def _object_cast_to_SpiderMapReaderWriter(o):
465  """_object_cast_to_SpiderMapReaderWriter(Object o) -> SpiderMapReaderWriter"""
466  return _IMP_em._object_cast_to_SpiderMapReaderWriter(o)
467 
468 _object_types.append("EMReaderWriter")
469 
470 
471 def _object_cast_to_EMReaderWriter(o):
472  """_object_cast_to_EMReaderWriter(Object o) -> EMReaderWriter"""
473  return _IMP_em._object_cast_to_EMReaderWriter(o)
474 
475 _object_types.append("XplorReaderWriter")
476 
477 
478 def _object_cast_to_XplorReaderWriter(o):
479  """_object_cast_to_XplorReaderWriter(Object o) -> XplorReaderWriter"""
480  return _IMP_em._object_cast_to_XplorReaderWriter(o)
481 
482 _object_types.append("CoarseCC")
483 
484 
485 def _object_cast_to_CoarseCC(o):
486  """_object_cast_to_CoarseCC(Object o) -> CoarseCC"""
487  return _IMP_em._object_cast_to_CoarseCC(o)
488 
489 _object_types.append("CoarseCCatIntervals")
490 
491 
492 def _object_cast_to_CoarseCCatIntervals(o):
493  """_object_cast_to_CoarseCCatIntervals(Object o) -> CoarseCCatIntervals"""
494  return _IMP_em._object_cast_to_CoarseCCatIntervals(o)
495 
496 FittingSolutionsList=list
497 _plural_types.append("FittingSolutionsList")
498 _value_types.append("FittingSolutions")
499 
500 class MapReaderWriter(IMP.Object):
501  """Proxy of C++ IMP::em::MapReaderWriter class."""
502 
503  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
504 
505  def __init__(self):
506  """__init__(IMP::em::MapReaderWriter self) -> MapReaderWriter"""
507  this = _IMP_em.new_MapReaderWriter()
508  try:
509  self.this.append(this)
510  except __builtin__.Exception:
511  self.this = this
512 
513  def get_version_info(self):
514  """get_version_info(MapReaderWriter self) -> VersionInfo"""
515  return _IMP_em.MapReaderWriter_get_version_info(self)
516 
517 
518  def __str__(self):
519  """__str__(MapReaderWriter self) -> std::string"""
520  return _IMP_em.MapReaderWriter___str__(self)
521 
522 
523  def __repr__(self):
524  """__repr__(MapReaderWriter self) -> std::string"""
525  return _IMP_em.MapReaderWriter___repr__(self)
526 
527 
528  @staticmethod
529  def get_from(o):
530  return _object_cast_to_MapReaderWriter(o)
531 
532 MapReaderWriter_swigregister = _IMP_em.MapReaderWriter_swigregister
533 MapReaderWriter_swigregister(MapReaderWriter)
534 cvar = _IMP_em.cvar
535 EPS = cvar.EPS
536 
537 class DensityHeader(object):
538  """Proxy of C++ IMP::em::DensityHeader class."""
539 
540  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
541  __repr__ = _swig_repr
542 
543  def __init__(self):
544  """__init__(IMP::em::DensityHeader self) -> DensityHeader"""
545  this = _IMP_em.new_DensityHeader()
546  try:
547  self.this.append(this)
548  except __builtin__.Exception:
549  self.this = this
550 
551  def get_top(self, ind):
552  """get_top(DensityHeader self, int ind) -> IMP::em::emreal"""
553  return _IMP_em.DensityHeader_get_top(self, ind)
554 
555 
556  def compute_xyz_top(self, force=False):
557  """
558  compute_xyz_top(DensityHeader self, bool force=False)
559  compute_xyz_top(DensityHeader self)
560  """
561  return _IMP_em.DensityHeader_compute_xyz_top(self, force)
562 
563 
564  def update_map_dimensions(self, nnx, nny, nnz):
565  """update_map_dimensions(DensityHeader self, int nnx, int nny, int nnz)"""
566  return _IMP_em.DensityHeader_update_map_dimensions(self, nnx, nny, nnz)
567 
568 
569  def update_cell_dimensions(self):
570  """update_cell_dimensions(DensityHeader self)"""
571  return _IMP_em.DensityHeader_update_cell_dimensions(self)
572 
573 
574  def show(self, *args):
575  """
576  show(DensityHeader self, _ostream out)
577  show(DensityHeader self)
578  """
579  return _IMP_em.DensityHeader_show(self, *args)
580 
581  MAP_FIELD_SIZE = _IMP_em.DensityHeader_MAP_FIELD_SIZE
582  USER_FIELD_SIZE = _IMP_em.DensityHeader_USER_FIELD_SIZE
583  COMMENT_FIELD_NUM_OF = _IMP_em.DensityHeader_COMMENT_FIELD_NUM_OF
584  COMMENT_FIELD_SINGLE_SIZE = _IMP_em.DensityHeader_COMMENT_FIELD_SINGLE_SIZE
585  nxstart = _swig_property(_IMP_em.DensityHeader_nxstart_get, _IMP_em.DensityHeader_nxstart_set)
586  nystart = _swig_property(_IMP_em.DensityHeader_nystart_get, _IMP_em.DensityHeader_nystart_set)
587  nzstart = _swig_property(_IMP_em.DensityHeader_nzstart_get, _IMP_em.DensityHeader_nzstart_set)
588  mx = _swig_property(_IMP_em.DensityHeader_mx_get, _IMP_em.DensityHeader_mx_set)
589  my = _swig_property(_IMP_em.DensityHeader_my_get, _IMP_em.DensityHeader_my_set)
590  mz = _swig_property(_IMP_em.DensityHeader_mz_get, _IMP_em.DensityHeader_mz_set)
591  xlen = _swig_property(_IMP_em.DensityHeader_xlen_get, _IMP_em.DensityHeader_xlen_set)
592  ylen = _swig_property(_IMP_em.DensityHeader_ylen_get, _IMP_em.DensityHeader_ylen_set)
593  zlen = _swig_property(_IMP_em.DensityHeader_zlen_get, _IMP_em.DensityHeader_zlen_set)
594  alpha = _swig_property(_IMP_em.DensityHeader_alpha_get, _IMP_em.DensityHeader_alpha_set)
595  beta = _swig_property(_IMP_em.DensityHeader_beta_get, _IMP_em.DensityHeader_beta_set)
596  gamma = _swig_property(_IMP_em.DensityHeader_gamma_get, _IMP_em.DensityHeader_gamma_set)
597  mapc = _swig_property(_IMP_em.DensityHeader_mapc_get, _IMP_em.DensityHeader_mapc_set)
598  mapr = _swig_property(_IMP_em.DensityHeader_mapr_get, _IMP_em.DensityHeader_mapr_set)
599  maps = _swig_property(_IMP_em.DensityHeader_maps_get, _IMP_em.DensityHeader_maps_set)
600  dmin = _swig_property(_IMP_em.DensityHeader_dmin_get, _IMP_em.DensityHeader_dmin_set)
601  dmax = _swig_property(_IMP_em.DensityHeader_dmax_get, _IMP_em.DensityHeader_dmax_set)
602  dmean = _swig_property(_IMP_em.DensityHeader_dmean_get, _IMP_em.DensityHeader_dmean_set)
603  ispg = _swig_property(_IMP_em.DensityHeader_ispg_get, _IMP_em.DensityHeader_ispg_set)
604  nsymbt = _swig_property(_IMP_em.DensityHeader_nsymbt_get, _IMP_em.DensityHeader_nsymbt_set)
605  user = _swig_property(_IMP_em.DensityHeader_user_get, _IMP_em.DensityHeader_user_set)
606  map = _swig_property(_IMP_em.DensityHeader_map_get, _IMP_em.DensityHeader_map_set)
607  machinestamp = _swig_property(_IMP_em.DensityHeader_machinestamp_get, _IMP_em.DensityHeader_machinestamp_set)
608  rms = _swig_property(_IMP_em.DensityHeader_rms_get, _IMP_em.DensityHeader_rms_set)
609  nlabl = _swig_property(_IMP_em.DensityHeader_nlabl_get, _IMP_em.DensityHeader_nlabl_set)
610  comments = _swig_property(_IMP_em.DensityHeader_comments_get, _IMP_em.DensityHeader_comments_set)
611  magic = _swig_property(_IMP_em.DensityHeader_magic_get, _IMP_em.DensityHeader_magic_set)
612  voltage = _swig_property(_IMP_em.DensityHeader_voltage_get, _IMP_em.DensityHeader_voltage_set)
613  Cs = _swig_property(_IMP_em.DensityHeader_Cs_get, _IMP_em.DensityHeader_Cs_set)
614  Aperture = _swig_property(_IMP_em.DensityHeader_Aperture_get, _IMP_em.DensityHeader_Aperture_set)
615  Magnification = _swig_property(_IMP_em.DensityHeader_Magnification_get, _IMP_em.DensityHeader_Magnification_set)
616  Postmagnification = _swig_property(_IMP_em.DensityHeader_Postmagnification_get, _IMP_em.DensityHeader_Postmagnification_set)
617  Exposuretime = _swig_property(_IMP_em.DensityHeader_Exposuretime_get, _IMP_em.DensityHeader_Exposuretime_set)
618  Microscope = _swig_property(_IMP_em.DensityHeader_Microscope_get, _IMP_em.DensityHeader_Microscope_set)
619  Pixelsize = _swig_property(_IMP_em.DensityHeader_Pixelsize_get, _IMP_em.DensityHeader_Pixelsize_set)
620  CCDArea = _swig_property(_IMP_em.DensityHeader_CCDArea_get, _IMP_em.DensityHeader_CCDArea_set)
621  Defocus = _swig_property(_IMP_em.DensityHeader_Defocus_get, _IMP_em.DensityHeader_Defocus_set)
622  Astigmatism = _swig_property(_IMP_em.DensityHeader_Astigmatism_get, _IMP_em.DensityHeader_Astigmatism_set)
623  AstigmatismAngle = _swig_property(_IMP_em.DensityHeader_AstigmatismAngle_get, _IMP_em.DensityHeader_AstigmatismAngle_set)
624  FocusIncrement = _swig_property(_IMP_em.DensityHeader_FocusIncrement_get, _IMP_em.DensityHeader_FocusIncrement_set)
625  CountsPerElectron = _swig_property(_IMP_em.DensityHeader_CountsPerElectron_get, _IMP_em.DensityHeader_CountsPerElectron_set)
626  Intensity = _swig_property(_IMP_em.DensityHeader_Intensity_get, _IMP_em.DensityHeader_Intensity_set)
627  EnergySlitwidth = _swig_property(_IMP_em.DensityHeader_EnergySlitwidth_get, _IMP_em.DensityHeader_EnergySlitwidth_set)
628  EnergyOffset = _swig_property(_IMP_em.DensityHeader_EnergyOffset_get, _IMP_em.DensityHeader_EnergyOffset_set)
629  Tiltangle = _swig_property(_IMP_em.DensityHeader_Tiltangle_get, _IMP_em.DensityHeader_Tiltangle_set)
630  Tiltaxis = _swig_property(_IMP_em.DensityHeader_Tiltaxis_get, _IMP_em.DensityHeader_Tiltaxis_set)
631  MarkerX = _swig_property(_IMP_em.DensityHeader_MarkerX_get, _IMP_em.DensityHeader_MarkerX_set)
632  MarkerY = _swig_property(_IMP_em.DensityHeader_MarkerY_get, _IMP_em.DensityHeader_MarkerY_set)
633  lswap = _swig_property(_IMP_em.DensityHeader_lswap_get, _IMP_em.DensityHeader_lswap_set)
634 
635  def get_resolution(self):
636  """get_resolution(DensityHeader self) -> float"""
637  return _IMP_em.DensityHeader_get_resolution(self)
638 
639 
640  def get_has_resolution(self):
641  """get_has_resolution(DensityHeader self) -> bool"""
642  return _IMP_em.DensityHeader_get_has_resolution(self)
643 
644 
645  def set_resolution(self, resolution):
646  """set_resolution(DensityHeader self, float resolution)"""
647  return _IMP_em.DensityHeader_set_resolution(self, resolution)
648 
649 
650  def get_spacing(self):
651  """get_spacing(DensityHeader self) -> float"""
652  return _IMP_em.DensityHeader_get_spacing(self)
653 
654 
655  def get_xorigin(self):
656  """get_xorigin(DensityHeader self) -> float"""
657  return _IMP_em.DensityHeader_get_xorigin(self)
658 
659 
660  def get_yorigin(self):
661  """get_yorigin(DensityHeader self) -> float"""
662  return _IMP_em.DensityHeader_get_yorigin(self)
663 
664 
665  def get_zorigin(self):
666  """get_zorigin(DensityHeader self) -> float"""
667  return _IMP_em.DensityHeader_get_zorigin(self)
668 
669 
670  def get_origin(self, i):
671  """get_origin(DensityHeader self, int i) -> float"""
672  return _IMP_em.DensityHeader_get_origin(self, i)
673 
674 
675  def set_xorigin(self, x):
676  """set_xorigin(DensityHeader self, float x)"""
677  return _IMP_em.DensityHeader_set_xorigin(self, x)
678 
679 
680  def set_yorigin(self, y):
681  """set_yorigin(DensityHeader self, float y)"""
682  return _IMP_em.DensityHeader_set_yorigin(self, y)
683 
684 
685  def set_zorigin(self, z):
686  """set_zorigin(DensityHeader self, float z)"""
687  return _IMP_em.DensityHeader_set_zorigin(self, z)
688 
689 
690  def is_top_calculated(self):
691  """is_top_calculated(DensityHeader self) -> bool"""
692  return _IMP_em.DensityHeader_is_top_calculated(self)
693 
694  Objectpixelsize_ = _swig_property(_IMP_em.DensityHeader_Objectpixelsize__get, _IMP_em.DensityHeader_Objectpixelsize__set)
695 
696  def get_nx(self):
697  """get_nx(DensityHeader self) -> int"""
698  return _IMP_em.DensityHeader_get_nx(self)
699 
700 
701  def get_ny(self):
702  """get_ny(DensityHeader self) -> int"""
703  return _IMP_em.DensityHeader_get_ny(self)
704 
705 
706  def get_nz(self):
707  """get_nz(DensityHeader self) -> int"""
708  return _IMP_em.DensityHeader_get_nz(self)
709 
710 
711  def get_number_of_voxels(self):
712  """get_number_of_voxels(DensityHeader self) -> int"""
713  return _IMP_em.DensityHeader_get_number_of_voxels(self)
714 
715 
716  def get_data_type(self):
717  """get_data_type(DensityHeader self) -> int"""
718  return _IMP_em.DensityHeader_get_data_type(self)
719 
720 
721  def set_data_type(self, data_type):
722  """set_data_type(DensityHeader self, int data_type)"""
723  return _IMP_em.DensityHeader_set_data_type(self, data_type)
724 
725  __swig_destroy__ = _IMP_em.delete_DensityHeader
726  __del__ = lambda self: None
727 DensityHeader_swigregister = _IMP_em.DensityHeader_swigregister
728 DensityHeader_swigregister(DensityHeader)
729 
730 
731 def create_density_header(bb, spacing):
732  """create_density_header(BoundingBox3D bb, float spacing) -> DensityHeader"""
733  return _IMP_em.create_density_header(bb, spacing)
734 
735 def read_map(*args):
736  """
737  read_map(std::string filename, MapReaderWriter reader) -> DensityMap
738  read_map(std::string filename) -> DensityMap
739  """
740  return _IMP_em.read_map(*args)
741 
742 def write_map(*args):
743  """
744  write_map(DensityMap m, std::string filename, MapReaderWriter writer)
745  write_map(DensityMap m, std::string filename)
746  """
747  return _IMP_em.write_map(*args)
748 
749 def approximate_molecular_mass(m, threshold):
750  """approximate_molecular_mass(DensityMap m, IMP::Float threshold) -> IMP::Float"""
751  return _IMP_em.approximate_molecular_mass(m, threshold)
752 class DensityMap(IMP.Object):
753  """Proxy of C++ IMP::em::DensityMap class."""
754 
755  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
756 
757  def __init__(self, *args):
758  """
759  __init__(IMP::em::DensityMap self, std::string name) -> DensityMap
760  __init__(IMP::em::DensityMap self) -> DensityMap
761  __init__(IMP::em::DensityMap self, DensityHeader header, std::string name) -> DensityMap
762  __init__(IMP::em::DensityMap self, DensityHeader header) -> DensityMap
763  """
764  this = _IMP_em.new_DensityMap(*args)
765  try:
766  self.this.append(this)
767  except __builtin__.Exception:
768  self.this = this
769 
770  def reset_data(self, value=0.0):
771  """
772  reset_data(DensityMap self, float value=0.0)
773  reset_data(DensityMap self)
774  """
775  return _IMP_em.DensityMap_reset_data(self, value)
776 
777 
778  def calcRMS(self):
779  """calcRMS(DensityMap self) -> IMP::em::emreal"""
780  return _IMP_em.DensityMap_calcRMS(self)
781 
782 
783  def std_normalize(self):
784  """std_normalize(DensityMap self)"""
785  return _IMP_em.DensityMap_std_normalize(self)
786 
787 
788  def is_normalized(self):
789  """is_normalized(DensityMap self) -> bool"""
790  return _IMP_em.DensityMap_is_normalized(self)
791 
792 
793  def get_location_in_dim_by_voxel(self, index, dim):
794  """get_location_in_dim_by_voxel(DensityMap self, long index, int dim) -> float"""
795  return _IMP_em.DensityMap_get_location_in_dim_by_voxel(self, index, dim)
796 
797 
798  def xyz_ind2voxel(self, x, y, z):
799  """xyz_ind2voxel(DensityMap self, int x, int y, int z) -> long"""
800  return _IMP_em.DensityMap_xyz_ind2voxel(self, x, y, z)
801 
802 
803  def get_voxel_by_location(self, *args):
804  """
805  get_voxel_by_location(DensityMap self, float x, float y, float z) -> long
806  get_voxel_by_location(DensityMap self, Vector3D v) -> long
807  """
808  return _IMP_em.DensityMap_get_voxel_by_location(self, *args)
809 
810 
811  def get_location_by_voxel(self, index):
812  """get_location_by_voxel(DensityMap self, long index) -> Vector3D"""
813  return _IMP_em.DensityMap_get_location_by_voxel(self, index)
814 
815 
816  def is_xyz_ind_part_of_volume(self, ix, iy, iz):
817  """is_xyz_ind_part_of_volume(DensityMap self, int ix, int iy, int iz) -> bool"""
818  return _IMP_em.DensityMap_is_xyz_ind_part_of_volume(self, ix, iy, iz)
819 
820 
821  def is_part_of_volume(self, *args):
822  """
823  is_part_of_volume(DensityMap self, float x, float y, float z) -> bool
824  is_part_of_volume(DensityMap self, Vector3D v) -> bool
825  """
826  return _IMP_em.DensityMap_is_part_of_volume(self, *args)
827 
828 
829  def get_value(self, *args):
830  """
831  get_value(DensityMap self, float x, float y, float z) -> IMP::em::emreal
832  get_value(DensityMap self, Vector3D point) -> IMP::em::emreal
833  get_value(DensityMap self, long index) -> IMP::em::emreal
834  """
835  return _IMP_em.DensityMap_get_value(self, *args)
836 
837 
838  def set_value(self, *args):
839  """
840  set_value(DensityMap self, long index, IMP::em::emreal value)
841  set_value(DensityMap self, float x, float y, float z, IMP::em::emreal value)
842  """
843  return _IMP_em.DensityMap_set_value(self, *args)
844 
845 
846  def set_origin(self, *args):
847  """
848  set_origin(DensityMap self, float x, float y, float z)
849  set_origin(DensityMap self, Vector3D v)
850  """
851  return _IMP_em.DensityMap_set_origin(self, *args)
852 
853 
854  def get_origin(self):
855  """get_origin(DensityMap self) -> Vector3D"""
856  return _IMP_em.DensityMap_get_origin(self)
857 
858 
859  def get_top(self):
860  """get_top(DensityMap self) -> Vector3D"""
861  return _IMP_em.DensityMap_get_top(self)
862 
863 
864  def get_header(self):
865  h = _IMP_em.DensityMap_get_header(self)
866  h._owner = self
867  return h
868 
869 
870 
871  def get_header_writable(self):
872  h = _IMP_em.DensityMap_get_header_writable(self)
873  h._owner = self
874  return h
875 
876 
877 
878  def same_origin(self, other):
879  """same_origin(DensityMap self, DensityMap other) -> bool"""
880  return _IMP_em.DensityMap_same_origin(self, other)
881 
882 
883  def same_dimensions(self, other):
884  """same_dimensions(DensityMap self, DensityMap other) -> bool"""
885  return _IMP_em.DensityMap_same_dimensions(self, other)
886 
887 
888  def same_voxel_size(self, other):
889  """same_voxel_size(DensityMap self, DensityMap other) -> bool"""
890  return _IMP_em.DensityMap_same_voxel_size(self, other)
891 
892 
893  def get_centroid(self, threshold=0.0):
894  """
895  get_centroid(DensityMap self, IMP::em::emreal threshold=0.0) -> Vector3D
896  get_centroid(DensityMap self) -> Vector3D
897  """
898  return _IMP_em.DensityMap_get_centroid(self, threshold)
899 
900 
901  def get_max_value(self):
902  """get_max_value(DensityMap self) -> IMP::em::emreal"""
903  return _IMP_em.DensityMap_get_max_value(self)
904 
905 
906  def get_min_value(self):
907  """get_min_value(DensityMap self) -> IMP::em::emreal"""
908  return _IMP_em.DensityMap_get_min_value(self)
909 
910 
911  def add(self, *args):
912  """
913  add(DensityMap self, DensityMap other)
914  add(DensityMap self, IMP::Float d)
915  """
916  return _IMP_em.DensityMap_add(self, *args)
917 
918 
919  def pick_max(self, other):
920  """pick_max(DensityMap self, DensityMap other)"""
921  return _IMP_em.DensityMap_pick_max(self, other)
922 
923 
924  def get_number_of_voxels(self):
925  """get_number_of_voxels(DensityMap self) -> long"""
926  return _IMP_em.DensityMap_get_number_of_voxels(self)
927 
928 
929  def set_void_map(self, nx, ny, nz):
930  """set_void_map(DensityMap self, int nx, int ny, int nz)"""
931  return _IMP_em.DensityMap_set_void_map(self, nx, ny, nz)
932 
933 
934  def pad(self, nx, ny, nz, val=0.0):
935  """
936  pad(DensityMap self, int nx, int ny, int nz, float val=0.0)
937  pad(DensityMap self, int nx, int ny, int nz)
938  """
939  return _IMP_em.DensityMap_pad(self, nx, ny, nz, val)
940 
941 
942  def pad_margin(self, mrg_x, mrg_y, mrg_z, val=0.0):
943  """
944  pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z, float val=0.0) -> DensityMap
945  pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z) -> DensityMap
946  """
947  return _IMP_em.DensityMap_pad_margin(self, mrg_x, mrg_y, mrg_z, val)
948 
949 
950  def get_cropped(self, *args):
951  """
952  get_cropped(DensityMap self, float threshold) -> DensityMap
953  get_cropped(DensityMap self, BoundingBox3D bb) -> DensityMap
954  """
955  return _IMP_em.DensityMap_get_cropped(self, *args)
956 
957 
958  def get_maximum_value_in_xy_plane(self, z_ind):
959  """get_maximum_value_in_xy_plane(DensityMap self, int z_ind) -> float"""
960  return _IMP_em.DensityMap_get_maximum_value_in_xy_plane(self, z_ind)
961 
962 
963  def get_maximum_value_in_xz_plane(self, y_ind):
964  """get_maximum_value_in_xz_plane(DensityMap self, int y_ind) -> float"""
965  return _IMP_em.DensityMap_get_maximum_value_in_xz_plane(self, y_ind)
966 
967 
968  def get_maximum_value_in_yz_plane(self, x_ind):
969  """get_maximum_value_in_yz_plane(DensityMap self, int x_ind) -> float"""
970  return _IMP_em.DensityMap_get_maximum_value_in_yz_plane(self, x_ind)
971 
972 
973  def multiply(self, factor):
974  """multiply(DensityMap self, float factor)"""
975  return _IMP_em.DensityMap_multiply(self, factor)
976 
977 
978  def get_locations_string(self, t):
979  """get_locations_string(DensityMap self, float t) -> std::string"""
980  return _IMP_em.DensityMap_get_locations_string(self, t)
981 
982 
983  def update_voxel_size(self, new_apix):
984  """update_voxel_size(DensityMap self, float new_apix)"""
985  return _IMP_em.DensityMap_update_voxel_size(self, new_apix)
986 
987 
988  def get_spacing(self):
989  """get_spacing(DensityMap self) -> IMP::Float"""
990  return _IMP_em.DensityMap_get_spacing(self)
991 
992 
993  def calc_all_voxel2loc(self):
994  """calc_all_voxel2loc(DensityMap self)"""
995  return _IMP_em.DensityMap_calc_all_voxel2loc(self)
996 
997 
998  def copy_map(self, other):
999  """copy_map(DensityMap self, DensityMap other)"""
1000  return _IMP_em.DensityMap_copy_map(self, other)
1001 
1002 
1003  def get_version_info(self):
1004  """get_version_info(DensityMap self) -> VersionInfo"""
1005  return _IMP_em.DensityMap_get_version_info(self)
1006 
1007 
1008  def lower_voxel_shift(self, loc, kdist, orig, ndim):
1009  """lower_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
1010  return _IMP_em.DensityMap_lower_voxel_shift(self, loc, kdist, orig, ndim)
1011 
1012 
1013  def upper_voxel_shift(self, loc, kdist, orig, ndim):
1014  """upper_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
1015  return _IMP_em.DensityMap_upper_voxel_shift(self, loc, kdist, orig, ndim)
1016 
1017 
1018  def get_rms_calculated(self):
1019  """get_rms_calculated(DensityMap self) -> bool"""
1020  return _IMP_em.DensityMap_get_rms_calculated(self)
1021 
1022 
1023  def get_dim_index_by_location(self, *args):
1024  """
1025  get_dim_index_by_location(DensityMap self, Vector3D v, int ind) -> int
1026  get_dim_index_by_location(DensityMap self, float loc_val, int ind) -> int
1027  """
1028  return _IMP_em.DensityMap_get_dim_index_by_location(self, *args)
1029 
1030 
1031  def __str__(self):
1032  """__str__(DensityMap self) -> std::string"""
1033  return _IMP_em.DensityMap___str__(self)
1034 
1035 
1036  def __repr__(self):
1037  """__repr__(DensityMap self) -> std::string"""
1038  return _IMP_em.DensityMap___repr__(self)
1039 
1040 
1041  @staticmethod
1042  def get_from(o):
1043  return _object_cast_to_DensityMap(o)
1044 
1045 DensityMap_swigregister = _IMP_em.DensityMap_swigregister
1046 DensityMap_swigregister(DensityMap)
1047 
1048 
1049 def get_bounding_box(*args):
1050  """
1051  get_bounding_box(DensityMap m, IMP::Float threshold) -> BoundingBox3D
1052  get_bounding_box(DensityMap m) -> BoundingBox3D
1053  """
1054  return _IMP_em.get_bounding_box(*args)
1055 
1056 def get_density(m, v):
1057  """get_density(DensityMap m, Vector3D v) -> double"""
1058  return _IMP_em.get_density(m, v)
1059 
1060 def get_transformed(*args):
1061  """
1062  get_transformed(DensityMap input, Transformation3D tr, double threshold) -> DensityMap
1063  get_transformed(DensityMap input, Transformation3D tr) -> DensityMap
1064  """
1065  return _IMP_em.get_transformed(*args)
1066 
1067 def get_resampled(input, scaling):
1068  """get_resampled(DensityMap input, double scaling) -> DensityMap"""
1069  return _IMP_em.get_resampled(input, scaling)
1070 
1071 def get_transformed_into(source, tr, into, calc_rms=True):
1072  """
1073  get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into, bool calc_rms=True)
1074  get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into)
1075  """
1076  return _IMP_em.get_transformed_into(source, tr, into, calc_rms)
1077 
1078 def get_transformed_into2(source, tr, into):
1079  """get_transformed_into2(DensityMap source, Transformation3D tr, DensityMap into)"""
1080  return _IMP_em.get_transformed_into2(source, tr, into)
1081 
1082 def get_interiors_intersect(d1, d2):
1083  """get_interiors_intersect(DensityMap d1, DensityMap d2) -> bool"""
1084  return _IMP_em.get_interiors_intersect(d1, d2)
1085 
1086 def get_segment(*args):
1087  """
1088  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
1089  get_segment(DensityMap map_to_segment, IMP::algebra::Vector3Ds vecs, float dist) -> DensityMap
1090  """
1091  return _IMP_em.get_segment(*args)
1092 
1093 def get_segment_by_masking(map_to_segment, mask, mas_threshold):
1094  """get_segment_by_masking(DensityMap map_to_segment, DensityMap mask, float mas_threshold) -> DensityMap"""
1095  return _IMP_em.get_segment_by_masking(map_to_segment, mask, mas_threshold)
1096 
1097 def binarize(orig_map, threshold, reverse=False):
1098  """
1099  binarize(DensityMap orig_map, float threshold, bool reverse=False) -> DensityMap
1100  binarize(DensityMap orig_map, float threshold) -> DensityMap
1101  """
1102  return _IMP_em.binarize(orig_map, threshold, reverse)
1103 
1104 def get_threshold_map(orig_map, threshold):
1105  """get_threshold_map(DensityMap orig_map, float threshold) -> DensityMap"""
1106  return _IMP_em.get_threshold_map(orig_map, threshold)
1107 
1108 def multiply(m1, m2):
1109  """multiply(DensityMap m1, DensityMap m2) -> DensityMap"""
1110  return _IMP_em.multiply(m1, m2)
1111 
1112 def convolute(m1, m2):
1113  """convolute(DensityMap m1, DensityMap m2) -> double"""
1114  return _IMP_em.convolute(m1, m2)
1115 
1116 def get_sum(m1):
1117  """get_sum(DensityMap m1) -> double"""
1118  return _IMP_em.get_sum(m1)
1119 
1120 def get_max_map(maps):
1121  """get_max_map(IMP::em::DensityMaps maps) -> DensityMap"""
1122  return _IMP_em.get_max_map(maps)
1123 
1124 def interpolate_map(in_map, new_spacing):
1125  """interpolate_map(DensityMap in_map, double new_spacing) -> DensityMap"""
1126  return _IMP_em.interpolate_map(in_map, new_spacing)
1127 
1128 def get_grid(in_map):
1129  """get_grid(DensityMap in_map) -> IMP::algebra::GridD< 3,IMP::algebra::DenseGridStorageD< 3,float >,float,IMP::algebra::DefaultEmbeddingD< 3 > >"""
1130  return _IMP_em.get_grid(in_map)
1131 
1132 def create_density_map(*args):
1133  """
1134  create_density_map(DensityMap other) -> DensityMap
1135  create_density_map(BoundingBox3D bb, double spacing) -> DensityMap
1136  create_density_map(int nx, int ny, int nz, double spacing) -> DensityMap
1137  create_density_map(DenseFloatGrid3D grid) -> DensityMap
1138  create_density_map(DenseDoubleGrid3D grid) -> DensityMap
1139  """
1140  return _IMP_em.create_density_map(*args)
1141 
1142 def get_binarized_interior(dmap):
1143  """get_binarized_interior(DensityMap dmap) -> DensityMap"""
1144  return _IMP_em.get_binarized_interior(dmap)
1145 
1146 def add_to_map(dm, pis):
1147  """add_to_map(DensityMap dm, IMP::Particles const & pis)"""
1148  return _IMP_em.add_to_map(dm, pis)
1149 class RadiusDependentDistanceMask(object):
1150  """Proxy of C++ IMP::em::RadiusDependentDistanceMask class."""
1151 
1152  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1153  __repr__ = _swig_repr
1154 
1155  def __init__(self, sampling_radius, header):
1156  """__init__(IMP::em::RadiusDependentDistanceMask self, float sampling_radius, DensityHeader header) -> RadiusDependentDistanceMask"""
1157  this = _IMP_em.new_RadiusDependentDistanceMask(sampling_radius, header)
1158  try:
1159  self.this.append(this)
1160  except __builtin__.Exception:
1161  self.this = this
1162 
1163  def get_neighbor_shift(self):
1164  """get_neighbor_shift(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1165  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_shift(self)
1166 
1167 
1168  def get_neighbor_dist(self):
1169  """get_neighbor_dist(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1170  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist(self)
1171 
1172 
1173  def get_neighbor_dist_exp(self):
1174  """get_neighbor_dist_exp(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1175  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist_exp(self)
1176 
1177 
1178  def show(self, out):
1179  """show(RadiusDependentDistanceMask self, _ostream out)"""
1180  return _IMP_em.RadiusDependentDistanceMask_show(self, out)
1181 
1182  __swig_destroy__ = _IMP_em.delete_RadiusDependentDistanceMask
1183  __del__ = lambda self: None
1184 RadiusDependentDistanceMask_swigregister = _IMP_em.RadiusDependentDistanceMask_swigregister
1185 RadiusDependentDistanceMask_swigregister(RadiusDependentDistanceMask)
1186 
1187 class DistanceMask(object):
1188  """Proxy of C++ IMP::em::DistanceMask class."""
1189 
1190  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1191  __repr__ = _swig_repr
1192 
1193  def __init__(self, *args):
1194  """
1195  __init__(IMP::em::DistanceMask self) -> DistanceMask
1196  __init__(IMP::em::DistanceMask self, DensityHeader header) -> DistanceMask
1197  """
1198  this = _IMP_em.new_DistanceMask(*args)
1199  try:
1200  self.this.append(this)
1201  except __builtin__.Exception:
1202  self.this = this
1203 
1204  def show(self, out):
1205  """show(DistanceMask self, _ostream out)"""
1206  return _IMP_em.DistanceMask_show(self, out)
1207 
1208 
1209  def is_mask_set(self, radius, eps=0.001):
1210  """
1211  is_mask_set(DistanceMask self, float radius, float eps=0.001) -> bool
1212  is_mask_set(DistanceMask self, float radius) -> bool
1213  """
1214  return _IMP_em.DistanceMask_is_mask_set(self, radius, eps)
1215 
1216  __swig_destroy__ = _IMP_em.delete_DistanceMask
1217  __del__ = lambda self: None
1218 DistanceMask_swigregister = _IMP_em.DistanceMask_swigregister
1219 DistanceMask_swigregister(DistanceMask)
1220 
1221 class EMReaderWriter(MapReaderWriter):
1222  """Proxy of C++ IMP::em::EMReaderWriter class."""
1223 
1224  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1225 
1226  def __str__(self):
1227  """__str__(EMReaderWriter self) -> std::string"""
1228  return _IMP_em.EMReaderWriter___str__(self)
1229 
1230 
1231  def __repr__(self):
1232  """__repr__(EMReaderWriter self) -> std::string"""
1233  return _IMP_em.EMReaderWriter___repr__(self)
1234 
1235 
1236  @staticmethod
1237  def get_from(o):
1238  return _object_cast_to_EMReaderWriter(o)
1239 
1240 
1241  def __init__(self):
1242  """__init__(IMP::em::EMReaderWriter self) -> EMReaderWriter"""
1243  this = _IMP_em.new_EMReaderWriter()
1244  try:
1245  self.this.append(this)
1246  except __builtin__.Exception:
1247  self.this = this
1248 EMReaderWriter_swigregister = _IMP_em.EMReaderWriter_swigregister
1249 EMReaderWriter_swigregister(EMReaderWriter)
1250 
1251 class XplorReaderWriter(MapReaderWriter):
1252  """Proxy of C++ IMP::em::XplorReaderWriter class."""
1253 
1254  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1255 
1256  def __str__(self):
1257  """__str__(XplorReaderWriter self) -> std::string"""
1258  return _IMP_em.XplorReaderWriter___str__(self)
1259 
1260 
1261  def __repr__(self):
1262  """__repr__(XplorReaderWriter self) -> std::string"""
1263  return _IMP_em.XplorReaderWriter___repr__(self)
1264 
1265 
1266  @staticmethod
1267  def get_from(o):
1268  return _object_cast_to_XplorReaderWriter(o)
1269 
1270 
1271  def __init__(self):
1272  """__init__(IMP::em::XplorReaderWriter self) -> XplorReaderWriter"""
1273  this = _IMP_em.new_XplorReaderWriter()
1274  try:
1275  self.this.append(this)
1276  except __builtin__.Exception:
1277  self.this = this
1278 XplorReaderWriter_swigregister = _IMP_em.XplorReaderWriter_swigregister
1279 XplorReaderWriter_swigregister(XplorReaderWriter)
1280 
1281 class MRCReaderWriter(MapReaderWriter):
1282  """Proxy of C++ IMP::em::MRCReaderWriter class."""
1283 
1284  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1285 
1286  def __init__(self, *args):
1287  """
1288  __init__(IMP::em::MRCReaderWriter self) -> MRCReaderWriter
1289  __init__(IMP::em::MRCReaderWriter self, std::string fn) -> MRCReaderWriter
1290  """
1291  this = _IMP_em.new_MRCReaderWriter(*args)
1292  try:
1293  self.this.append(this)
1294  except __builtin__.Exception:
1295  self.this = this
1296 
1297  def __str__(self):
1298  """__str__(MRCReaderWriter self) -> std::string"""
1299  return _IMP_em.MRCReaderWriter___str__(self)
1300 
1301 
1302  def __repr__(self):
1303  """__repr__(MRCReaderWriter self) -> std::string"""
1304  return _IMP_em.MRCReaderWriter___repr__(self)
1305 
1306 
1307  @staticmethod
1308  def get_from(o):
1309  return _object_cast_to_MRCReaderWriter(o)
1310 
1311 MRCReaderWriter_swigregister = _IMP_em.MRCReaderWriter_swigregister
1312 MRCReaderWriter_swigregister(MRCReaderWriter)
1313 
1314 class KernelParameters(object):
1315  """Proxy of C++ IMP::em::KernelParameters class."""
1316 
1317  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1318 
1319  def __init__(self, *args):
1320  """
1321  __init__(IMP::em::KernelParameters self) -> KernelParameters
1322  __init__(IMP::em::KernelParameters self, float resolution) -> KernelParameters
1323  """
1324  this = _IMP_em.new_KernelParameters(*args)
1325  try:
1326  self.this.append(this)
1327  except __builtin__.Exception:
1328  self.this = this
1329  __swig_destroy__ = _IMP_em.delete_KernelParameters
1330  __del__ = lambda self: None
1331 
1332  def get_rsig(self):
1333  """get_rsig(KernelParameters self) -> float"""
1334  return _IMP_em.KernelParameters_get_rsig(self)
1335 
1336 
1337  def get_rsigsq(self):
1338  """get_rsigsq(KernelParameters self) -> float"""
1339  return _IMP_em.KernelParameters_get_rsigsq(self)
1340 
1341 
1342  def get_inv_rsigsq(self):
1343  """get_inv_rsigsq(KernelParameters self) -> float"""
1344  return _IMP_em.KernelParameters_get_inv_rsigsq(self)
1345 
1346 
1347  def get_timessig(self):
1348  """get_timessig(KernelParameters self) -> float"""
1349  return _IMP_em.KernelParameters_get_timessig(self)
1350 
1351 
1352  def get_sq2pi3(self):
1353  """get_sq2pi3(KernelParameters self) -> float"""
1354  return _IMP_em.KernelParameters_get_sq2pi3(self)
1355 
1356 
1357  def get_rnormfac(self):
1358  """get_rnormfac(KernelParameters self) -> float"""
1359  return _IMP_em.KernelParameters_get_rnormfac(self)
1360 
1361 
1362  def get_rkdist(self):
1363  """get_rkdist(KernelParameters self) -> float"""
1364  return _IMP_em.KernelParameters_get_rkdist(self)
1365 
1366 
1367  def get_rkdistsq(self):
1368  """get_rkdistsq(KernelParameters self) -> float"""
1369  return _IMP_em.KernelParameters_get_rkdistsq(self)
1370 
1371 
1372  def get_lim(self):
1373  """get_lim(KernelParameters self) -> float"""
1374  return _IMP_em.KernelParameters_get_lim(self)
1375 
1376 
1377  def show(self, *args):
1378  """
1379  show(KernelParameters self, _ostream out)
1380  show(KernelParameters self)
1381  """
1382  return _IMP_em.KernelParameters_show(self, *args)
1383 
1384 
1385  def __str__(self):
1386  """__str__(KernelParameters self) -> std::string"""
1387  return _IMP_em.KernelParameters___str__(self)
1388 
1389 
1390  def __repr__(self):
1391  """__repr__(KernelParameters self) -> std::string"""
1392  return _IMP_em.KernelParameters___repr__(self)
1393 
1394 KernelParameters_swigregister = _IMP_em.KernelParameters_swigregister
1395 KernelParameters_swigregister(KernelParameters)
1396 
1397 GAUSSIAN = _IMP_em.GAUSSIAN
1398 BINARIZED_SPHERE = _IMP_em.BINARIZED_SPHERE
1399 SPHERE = _IMP_em.SPHERE
1400 class SampledDensityMap(DensityMap):
1401  """Proxy of C++ IMP::em::SampledDensityMap class."""
1402 
1403  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1404 
1405  def __init__(self, *args):
1406  """
1407  __init__(IMP::em::SampledDensityMap self, IMP::em::KernelType kt) -> SampledDensityMap
1408  __init__(IMP::em::SampledDensityMap self) -> SampledDensityMap
1409  __init__(IMP::em::SampledDensityMap self, DensityHeader header, IMP::em::KernelType kt) -> SampledDensityMap
1410  __init__(IMP::em::SampledDensityMap self, DensityHeader header) -> SampledDensityMap
1411  __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
1412  __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
1413  __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size, FloatKey mass_key) -> SampledDensityMap
1414  __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size) -> SampledDensityMap
1415  """
1416  this = _IMP_em.new_SampledDensityMap(*args)
1417  try:
1418  self.this.append(this)
1419  except __builtin__.Exception:
1420  self.this = this
1421 
1422  def resample(self):
1423  """resample(SampledDensityMap self)"""
1424  return _IMP_em.SampledDensityMap_resample(self)
1425 
1426 
1427  def project(self, *args):
1428  """
1429  project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin, Vector3D shift, FloatKey mass_key)
1430  project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin, Vector3D shift)
1431  project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin)
1432  """
1433  return _IMP_em.SampledDensityMap_project(self, *args)
1434 
1435 
1436  def set_particles(self, *args):
1437  """
1438  set_particles(SampledDensityMap self, IMP::ParticlesTemp const & ps, FloatKey mass_key)
1439  set_particles(SampledDensityMap self, IMP::ParticlesTemp const & ps)
1440  """
1441  return _IMP_em.SampledDensityMap_set_particles(self, *args)
1442 
1443 
1444  def get_xyzr_particles(self):
1445  """get_xyzr_particles(SampledDensityMap self) -> IMP::core::XYZRs const &"""
1446  return _IMP_em.SampledDensityMap_get_xyzr_particles(self)
1447 
1448 
1449  def get_sampled_particles(self):
1450  """get_sampled_particles(SampledDensityMap self) -> IMP::Particles const &"""
1451  return _IMP_em.SampledDensityMap_get_sampled_particles(self)
1452 
1453 
1454  def get_weight_key(self):
1455  """get_weight_key(SampledDensityMap self) -> FloatKey"""
1456  return _IMP_em.SampledDensityMap_get_weight_key(self)
1457 
1458 
1459  def get_minimum_resampled_value(self):
1460  """get_minimum_resampled_value(SampledDensityMap self) -> float"""
1461  return _IMP_em.SampledDensityMap_get_minimum_resampled_value(self)
1462 
1463 
1464  def update_resolution(self, res):
1465  """update_resolution(SampledDensityMap self, IMP::Float res)"""
1466  return _IMP_em.SampledDensityMap_update_resolution(self, res)
1467 
1468  __swig_destroy__ = _IMP_em.delete_SampledDensityMap
1469  __del__ = lambda self: None
1470 
1471  def __str__(self):
1472  """__str__(SampledDensityMap self) -> std::string"""
1473  return _IMP_em.SampledDensityMap___str__(self)
1474 
1475 
1476  def __repr__(self):
1477  """__repr__(SampledDensityMap self) -> std::string"""
1478  return _IMP_em.SampledDensityMap___repr__(self)
1479 
1480 
1481  @staticmethod
1482  def get_from(o):
1483  return _object_cast_to_SampledDensityMap(o)
1484 
1485 SampledDensityMap_swigregister = _IMP_em.SampledDensityMap_swigregister
1486 SampledDensityMap_swigregister(SampledDensityMap)
1487 
1488 IMP_DEFAULT_NUM_SHELLS = _IMP_em.IMP_DEFAULT_NUM_SHELLS
1489 IMP_SIG_CUTOFF = _IMP_em.IMP_SIG_CUTOFF
1490 class SurfaceShellDensityMap(SampledDensityMap):
1491  """Proxy of C++ IMP::em::SurfaceShellDensityMap class."""
1492 
1493  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1494 
1495  def __init__(self, *args):
1496  """
1497  __init__(IMP::em::SurfaceShellDensityMap self) -> SurfaceShellDensityMap
1498  __init__(IMP::em::SurfaceShellDensityMap self, DensityHeader header) -> SurfaceShellDensityMap
1499  __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key, int num_shells=5) -> SurfaceShellDensityMap
1500  __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key) -> SurfaceShellDensityMap
1501  __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size) -> SurfaceShellDensityMap
1502  """
1503  this = _IMP_em.new_SurfaceShellDensityMap(*args)
1504  try:
1505  self.this.append(this)
1506  except __builtin__.Exception:
1507  self.this = this
1508 
1509  def binarize(self, scene_val):
1510  """binarize(SurfaceShellDensityMap self, float scene_val)"""
1511  return _IMP_em.SurfaceShellDensityMap_binarize(self, scene_val)
1512 
1513 
1514  def has_background_neighbor(self, voxel_ind):
1515  """has_background_neighbor(SurfaceShellDensityMap self, long voxel_ind) -> bool"""
1516  return _IMP_em.SurfaceShellDensityMap_has_background_neighbor(self, voxel_ind)
1517 
1518  __swig_destroy__ = _IMP_em.delete_SurfaceShellDensityMap
1519  __del__ = lambda self: None
1520 
1521  def __str__(self):
1522  """__str__(SurfaceShellDensityMap self) -> std::string"""
1523  return _IMP_em.SurfaceShellDensityMap___str__(self)
1524 
1525 
1526  def __repr__(self):
1527  """__repr__(SurfaceShellDensityMap self) -> std::string"""
1528  return _IMP_em.SurfaceShellDensityMap___repr__(self)
1529 
1530 
1531  @staticmethod
1532  def get_from(o):
1533  return _object_cast_to_SurfaceShellDensityMap(o)
1534 
1535 SurfaceShellDensityMap_swigregister = _IMP_em.SurfaceShellDensityMap_swigregister
1536 SurfaceShellDensityMap_swigregister(SurfaceShellDensityMap)
1537 
1538 class CoarseCC(IMP.Object):
1539  """Proxy of C++ IMP::em::CoarseCC class."""
1540 
1541  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1542 
1543  def __init__(self):
1544  """__init__(IMP::em::CoarseCC self) -> CoarseCC"""
1545  this = _IMP_em.new_CoarseCC()
1546  try:
1547  self.this.append(this)
1548  except __builtin__.Exception:
1549  self.this = this
1550 
1551  def calc_score(*args):
1552  """
1553  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True, IMP::FloatPair norm_factors) -> float
1554  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True) -> float
1555  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1556  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1557  """
1558  return _IMP_em.CoarseCC_calc_score(*args)
1559 
1560  calc_score = staticmethod(calc_score)
1561 
1562  def cross_correlation_coefficient(*args):
1563  """
1564  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False, IMP::FloatPair norm_factors) -> double
1565  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1566  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1567  """
1568  return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1569 
1570  cross_correlation_coefficient = staticmethod(cross_correlation_coefficient)
1571 
1572  def local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold):
1573  """local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1574  return _IMP_em.CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold)
1575 
1576  local_cross_correlation_coefficient = staticmethod(local_cross_correlation_coefficient)
1577 
1578  def get_version_info(self):
1579  """get_version_info(CoarseCC self) -> VersionInfo"""
1580  return _IMP_em.CoarseCC_get_version_info(self)
1581 
1582 
1583  def __str__(self):
1584  """__str__(CoarseCC self) -> std::string"""
1585  return _IMP_em.CoarseCC___str__(self)
1586 
1587 
1588  def __repr__(self):
1589  """__repr__(CoarseCC self) -> std::string"""
1590  return _IMP_em.CoarseCC___repr__(self)
1591 
1592 
1593  @staticmethod
1594  def get_from(o):
1595  return _object_cast_to_CoarseCC(o)
1596 
1597 CoarseCC_swigregister = _IMP_em.CoarseCC_swigregister
1598 CoarseCC_swigregister(CoarseCC)
1599 
1600 def CoarseCC_calc_score(*args):
1601  """
1602  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True, IMP::FloatPair norm_factors) -> float
1603  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True) -> float
1604  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1605  CoarseCC_calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1606  """
1607  return _IMP_em.CoarseCC_calc_score(*args)
1608 
1609 def CoarseCC_cross_correlation_coefficient(*args):
1610  """
1611  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False, IMP::FloatPair norm_factors) -> double
1612  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1613  CoarseCC_cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1614  """
1615  return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1616 
1617 def CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold):
1618  """CoarseCC_local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1619  return _IMP_em.CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold)
1620 
1621 class CoarseConvolution(object):
1622  """Proxy of C++ IMP::em::CoarseConvolution class."""
1623 
1624  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1625  __repr__ = _swig_repr
1626 
1627  def convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac=True):
1628  """
1629  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1630  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1631  """
1632  return _IMP_em.CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac)
1633 
1634  convolution = staticmethod(convolution)
1635 
1636  def __init__(self):
1637  """__init__(IMP::em::CoarseConvolution self) -> CoarseConvolution"""
1638  this = _IMP_em.new_CoarseConvolution()
1639  try:
1640  self.this.append(this)
1641  except __builtin__.Exception:
1642  self.this = this
1643  __swig_destroy__ = _IMP_em.delete_CoarseConvolution
1644  __del__ = lambda self: None
1645 CoarseConvolution_swigregister = _IMP_em.CoarseConvolution_swigregister
1646 CoarseConvolution_swigregister(CoarseConvolution)
1647 
1648 def CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac=True):
1649  """
1650  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1651  CoarseConvolution_convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1652  """
1653  return _IMP_em.CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac)
1654 
1655 class CoarseCCatIntervals(CoarseCC):
1656  """Proxy of C++ IMP::em::CoarseCCatIntervals class."""
1657 
1658  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1659 
1660  def __init__(self, *args):
1661  """
1662  __init__(IMP::em::CoarseCCatIntervals self, int const & ncd) -> CoarseCCatIntervals
1663  __init__(IMP::em::CoarseCCatIntervals self) -> CoarseCCatIntervals
1664  """
1665  this = _IMP_em.new_CoarseCCatIntervals(*args)
1666  try:
1667  self.this.append(this)
1668  except __builtin__.Exception:
1669  self.this = this
1670 
1671  def evaluate(self, em_map, model_map, deriv, scalefac, lderiv, eval_interval):
1672  """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 >"""
1673  return _IMP_em.CoarseCCatIntervals_evaluate(self, em_map, model_map, deriv, scalefac, lderiv, eval_interval)
1674 
1675 
1676  def __str__(self):
1677  """__str__(CoarseCCatIntervals self) -> std::string"""
1678  return _IMP_em.CoarseCCatIntervals___str__(self)
1679 
1680 
1681  def __repr__(self):
1682  """__repr__(CoarseCCatIntervals self) -> std::string"""
1683  return _IMP_em.CoarseCCatIntervals___repr__(self)
1684 
1685 
1686  @staticmethod
1687  def get_from(o):
1688  return _object_cast_to_CoarseCCatIntervals(o)
1689 
1690 CoarseCCatIntervals_swigregister = _IMP_em.CoarseCCatIntervals_swigregister
1691 CoarseCCatIntervals_swigregister(CoarseCCatIntervals)
1692 
1693 class FitRestraint(IMP.Restraint):
1694  """Proxy of C++ IMP::em::FitRestraint class."""
1695 
1696  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1697 
1698  def __init__(self, *args):
1699  """
1700  __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
1701  __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
1702  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key, float scale=1) -> FitRestraint
1703  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key) -> FitRestraint
1704  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors) -> FitRestraint
1705  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map) -> FitRestraint
1706  """
1707  this = _IMP_em.new_FitRestraint(*args)
1708  try:
1709  self.this.append(this)
1710  except __builtin__.Exception:
1711  self.this = this
1712 
1713  def get_model_dens_map(self):
1714  """get_model_dens_map(FitRestraint self) -> SampledDensityMap"""
1715  return _IMP_em.FitRestraint_get_model_dens_map(self)
1716 
1717 
1718  def set_scale_factor(self, scale):
1719  """set_scale_factor(FitRestraint self, float scale)"""
1720  return _IMP_em.FitRestraint_set_scale_factor(self, scale)
1721 
1722 
1723  def get_scale_factor(self):
1724  """get_scale_factor(FitRestraint self) -> float"""
1725  return _IMP_em.FitRestraint_get_scale_factor(self)
1726 
1727 
1728  def do_get_inputs(self):
1729  """do_get_inputs(FitRestraint self) -> IMP::ModelObjectsTemp"""
1730  return _IMP_em.FitRestraint_do_get_inputs(self)
1731 
1732 
1733  def get_version_info(self):
1734  """get_version_info(FitRestraint self) -> VersionInfo"""
1735  return _IMP_em.FitRestraint_get_version_info(self)
1736 
1737 
1738  def __str__(self):
1739  """__str__(FitRestraint self) -> std::string"""
1740  return _IMP_em.FitRestraint___str__(self)
1741 
1742 
1743  def __repr__(self):
1744  """__repr__(FitRestraint self) -> std::string"""
1745  return _IMP_em.FitRestraint___repr__(self)
1746 
1747 
1748  @staticmethod
1749  def get_from(o):
1750  return _object_cast_to_FitRestraint(o)
1751 
1752 
1753  def cast(r):
1754  """cast(Restraint r) -> FitRestraint"""
1755  return _IMP_em.FitRestraint_cast(r)
1756 
1757  cast = staticmethod(cast)
1758 FitRestraint_swigregister = _IMP_em.FitRestraint_swigregister
1759 FitRestraint_swigregister(FitRestraint)
1760 
1761 def FitRestraint_cast(r):
1762  """FitRestraint_cast(Restraint r) -> FitRestraint"""
1763  return _IMP_em.FitRestraint_cast(r)
1764 
1765 
1766 def density2particles(dmap, threshold, m, step=1):
1767  """
1768  density2particles(DensityMap dmap, IMP::Float threshold, Model m, int step=1) -> IMP::Particles
1769  density2particles(DensityMap dmap, IMP::Float threshold, Model m) -> IMP::Particles
1770  """
1771  return _IMP_em.density2particles(dmap, threshold, m, step)
1772 
1773 def density2vectors(dmap, threshold):
1774  """density2vectors(DensityMap dmap, IMP::Float threshold) -> IMP::algebra::Vector3Ds"""
1775  return _IMP_em.density2vectors(dmap, threshold)
1776 
1777 def particles2density(*args):
1778  """
1779  particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3, FloatKey weight_key) -> SampledDensityMap
1780  particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
1781  particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
1782  """
1783  return _IMP_em.particles2density(*args)
1784 
1785 def particles2binarized_density(*args):
1786  """
1787  particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3, FloatKey weight_key) -> SampledDensityMap
1788  particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
1789  particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
1790  """
1791  return _IMP_em.particles2binarized_density(*args)
1792 
1793 def particles2surface(*args):
1794  """
1795  particles2surface(IMP::ParticlesTemp const & ps, IMP::Float apix, FloatKey weight_key) -> SurfaceShellDensityMap
1796  particles2surface(IMP::ParticlesTemp const & ps, IMP::Float apix) -> SurfaceShellDensityMap
1797  """
1798  return _IMP_em.particles2surface(*args)
1799 
1800 def calculate_intersection_score(d1, d2):
1801  """calculate_intersection_score(SurfaceShellDensityMap d1, SurfaceShellDensityMap d2) -> IMP::Float"""
1802  return _IMP_em.calculate_intersection_score(d1, d2)
1803 class SpiderHeader(object):
1804  """Proxy of C++ IMP::em::SpiderHeader class."""
1805 
1806  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1807  __repr__ = _swig_repr
1808  fNslice = _swig_property(_IMP_em.SpiderHeader_fNslice_get, _IMP_em.SpiderHeader_fNslice_set)
1809  fNrow = _swig_property(_IMP_em.SpiderHeader_fNrow_get, _IMP_em.SpiderHeader_fNrow_set)
1810  fNrec = _swig_property(_IMP_em.SpiderHeader_fNrec_get, _IMP_em.SpiderHeader_fNrec_set)
1811  fNlabel = _swig_property(_IMP_em.SpiderHeader_fNlabel_get, _IMP_em.SpiderHeader_fNlabel_set)
1812  fIform = _swig_property(_IMP_em.SpiderHeader_fIform_get, _IMP_em.SpiderHeader_fIform_set)
1813  fImami = _swig_property(_IMP_em.SpiderHeader_fImami_get, _IMP_em.SpiderHeader_fImami_set)
1814  fFmax = _swig_property(_IMP_em.SpiderHeader_fFmax_get, _IMP_em.SpiderHeader_fFmax_set)
1815  fFmin = _swig_property(_IMP_em.SpiderHeader_fFmin_get, _IMP_em.SpiderHeader_fFmin_set)
1816  fAv = _swig_property(_IMP_em.SpiderHeader_fAv_get, _IMP_em.SpiderHeader_fAv_set)
1817  fSig = _swig_property(_IMP_em.SpiderHeader_fSig_get, _IMP_em.SpiderHeader_fSig_set)
1818  fIhist = _swig_property(_IMP_em.SpiderHeader_fIhist_get, _IMP_em.SpiderHeader_fIhist_set)
1819  fNcol = _swig_property(_IMP_em.SpiderHeader_fNcol_get, _IMP_em.SpiderHeader_fNcol_set)
1820  fLabrec = _swig_property(_IMP_em.SpiderHeader_fLabrec_get, _IMP_em.SpiderHeader_fLabrec_set)
1821  fIangle = _swig_property(_IMP_em.SpiderHeader_fIangle_get, _IMP_em.SpiderHeader_fIangle_set)
1822  fPhi = _swig_property(_IMP_em.SpiderHeader_fPhi_get, _IMP_em.SpiderHeader_fPhi_set)
1823  fTheta = _swig_property(_IMP_em.SpiderHeader_fTheta_get, _IMP_em.SpiderHeader_fTheta_set)
1824  fPsi = _swig_property(_IMP_em.SpiderHeader_fPsi_get, _IMP_em.SpiderHeader_fPsi_set)
1825  fXoff = _swig_property(_IMP_em.SpiderHeader_fXoff_get, _IMP_em.SpiderHeader_fXoff_set)
1826  fYoff = _swig_property(_IMP_em.SpiderHeader_fYoff_get, _IMP_em.SpiderHeader_fYoff_set)
1827  fZoff = _swig_property(_IMP_em.SpiderHeader_fZoff_get, _IMP_em.SpiderHeader_fZoff_set)
1828  fScale = _swig_property(_IMP_em.SpiderHeader_fScale_get, _IMP_em.SpiderHeader_fScale_set)
1829  fLabbyt = _swig_property(_IMP_em.SpiderHeader_fLabbyt_get, _IMP_em.SpiderHeader_fLabbyt_set)
1830  fLenbyt = _swig_property(_IMP_em.SpiderHeader_fLenbyt_get, _IMP_em.SpiderHeader_fLenbyt_set)
1831  fNothing = _swig_property(_IMP_em.SpiderHeader_fNothing_get, _IMP_em.SpiderHeader_fNothing_set)
1832  fFlag = _swig_property(_IMP_em.SpiderHeader_fFlag_get, _IMP_em.SpiderHeader_fFlag_set)
1833  fPhi1 = _swig_property(_IMP_em.SpiderHeader_fPhi1_get, _IMP_em.SpiderHeader_fPhi1_set)
1834  fTheta1 = _swig_property(_IMP_em.SpiderHeader_fTheta1_get, _IMP_em.SpiderHeader_fTheta1_set)
1835  fPsi1 = _swig_property(_IMP_em.SpiderHeader_fPsi1_get, _IMP_em.SpiderHeader_fPsi1_set)
1836  fPhi2 = _swig_property(_IMP_em.SpiderHeader_fPhi2_get, _IMP_em.SpiderHeader_fPhi2_set)
1837  fTheta2 = _swig_property(_IMP_em.SpiderHeader_fTheta2_get, _IMP_em.SpiderHeader_fTheta2_set)
1838  fPsi2 = _swig_property(_IMP_em.SpiderHeader_fPsi2_get, _IMP_em.SpiderHeader_fPsi2_set)
1839  fGeo_matrix = _swig_property(_IMP_em.SpiderHeader_fGeo_matrix_get, _IMP_em.SpiderHeader_fGeo_matrix_set)
1840  fAngle1 = _swig_property(_IMP_em.SpiderHeader_fAngle1_get, _IMP_em.SpiderHeader_fAngle1_set)
1841  fr1 = _swig_property(_IMP_em.SpiderHeader_fr1_get, _IMP_em.SpiderHeader_fr1_set)
1842  fr2 = _swig_property(_IMP_em.SpiderHeader_fr2_get, _IMP_em.SpiderHeader_fr2_set)
1843  RTflag = _swig_property(_IMP_em.SpiderHeader_RTflag_get, _IMP_em.SpiderHeader_RTflag_set)
1844  Astart = _swig_property(_IMP_em.SpiderHeader_Astart_get, _IMP_em.SpiderHeader_Astart_set)
1845  Aend = _swig_property(_IMP_em.SpiderHeader_Aend_get, _IMP_em.SpiderHeader_Aend_set)
1846  Ainc = _swig_property(_IMP_em.SpiderHeader_Ainc_get, _IMP_em.SpiderHeader_Ainc_set)
1847  Rsigma = _swig_property(_IMP_em.SpiderHeader_Rsigma_get, _IMP_em.SpiderHeader_Rsigma_set)
1848  Tstart = _swig_property(_IMP_em.SpiderHeader_Tstart_get, _IMP_em.SpiderHeader_Tstart_set)
1849  Tend = _swig_property(_IMP_em.SpiderHeader_Tend_get, _IMP_em.SpiderHeader_Tend_set)
1850  Tinc = _swig_property(_IMP_em.SpiderHeader_Tinc_get, _IMP_em.SpiderHeader_Tinc_set)
1851  Weight = _swig_property(_IMP_em.SpiderHeader_Weight_get, _IMP_em.SpiderHeader_Weight_set)
1852  Flip = _swig_property(_IMP_em.SpiderHeader_Flip_get, _IMP_em.SpiderHeader_Flip_set)
1853  empty = _swig_property(_IMP_em.SpiderHeader_empty_get, _IMP_em.SpiderHeader_empty_set)
1854  szIDat = _swig_property(_IMP_em.SpiderHeader_szIDat_get, _IMP_em.SpiderHeader_szIDat_set)
1855  szITim = _swig_property(_IMP_em.SpiderHeader_szITim_get, _IMP_em.SpiderHeader_szITim_set)
1856  szITit = _swig_property(_IMP_em.SpiderHeader_szITit_get, _IMP_em.SpiderHeader_szITit_set)
1857 
1858  def show(self, out):
1859  """show(SpiderHeader self, _ostream out)"""
1860  return _IMP_em.SpiderHeader_show(self, out)
1861 
1862 
1863  def __init__(self):
1864  """__init__(IMP::em::SpiderHeader self) -> SpiderHeader"""
1865  this = _IMP_em.new_SpiderHeader()
1866  try:
1867  self.this.append(this)
1868  except __builtin__.Exception:
1869  self.this = this
1870  __swig_destroy__ = _IMP_em.delete_SpiderHeader
1871  __del__ = lambda self: None
1872 SpiderHeader_swigregister = _IMP_em.SpiderHeader_swigregister
1873 SpiderHeader_swigregister(SpiderHeader)
1874 
1875 class ImageHeader(object):
1876  """Proxy of C++ IMP::em::ImageHeader class."""
1877 
1878  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1879  __repr__ = _swig_repr
1880  IMG_BYTE = _IMP_em.ImageHeader_IMG_BYTE
1881  IMG_IMPEM = _IMP_em.ImageHeader_IMG_IMPEM
1882  IMG_INT = _IMP_em.ImageHeader_IMG_INT
1883  VOL_BYTE = _IMP_em.ImageHeader_VOL_BYTE
1884  VOL_IMPEM = _IMP_em.ImageHeader_VOL_IMPEM
1885  VOL_INT = _IMP_em.ImageHeader_VOL_INT
1886  IMG_FOURIER = _IMP_em.ImageHeader_IMG_FOURIER
1887  VOL_FOURIER = _IMP_em.ImageHeader_VOL_FOURIER
1888 
1889  def __init__(self, *args):
1890  """
1891  __init__(IMP::em::ImageHeader self) -> ImageHeader
1892  __init__(IMP::em::ImageHeader self, IMP::em::ImageHeader::img_type im) -> ImageHeader
1893  __init__(IMP::em::ImageHeader self, float im) -> ImageHeader
1894  """
1895  this = _IMP_em.new_ImageHeader(*args)
1896  try:
1897  self.this.append(this)
1898  except __builtin__.Exception:
1899  self.this = this
1900 
1901  def get_image_type(self):
1902  """get_image_type(ImageHeader self) -> float"""
1903  return _IMP_em.ImageHeader_get_image_type(self)
1904 
1905 
1906  def set_image_type(self, *args):
1907  """
1908  set_image_type(ImageHeader self, IMP::em::ImageHeader::img_type im)
1909  set_image_type(ImageHeader self, float im)
1910  """
1911  return _IMP_em.ImageHeader_set_image_type(self, *args)
1912 
1913 
1914  def do_show(self, out):
1915  """do_show(ImageHeader self, _ostream out)"""
1916  return _IMP_em.ImageHeader_do_show(self, out)
1917 
1918 
1919  def show(self, *args):
1920  """
1921  show(ImageHeader self, _ostream out)
1922  show(ImageHeader self)
1923  """
1924  return _IMP_em.ImageHeader_show(self, *args)
1925 
1926 
1927  def print_hard(self, out):
1928  """print_hard(ImageHeader self, _ostream out)"""
1929  return _IMP_em.ImageHeader_print_hard(self, out)
1930 
1931 
1932  def show_projection_params(self, out):
1933  """show_projection_params(ImageHeader self, _ostream out)"""
1934  return _IMP_em.ImageHeader_show_projection_params(self, out)
1935 
1936 
1937  def read(self, *args):
1938  """
1939  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False, bool skip_extra_checkings=False) -> int
1940  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False) -> int
1941  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False) -> int
1942  read(ImageHeader self, IMP::String const filename) -> int
1943  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False, bool skip_extra_checkings=False) -> bool
1944  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False) -> bool
1945  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False) -> bool
1946  read(ImageHeader self, std::ifstream & f) -> bool
1947  """
1948  return _IMP_em.ImageHeader_read(self, *args)
1949 
1950 
1951  def write(self, *args):
1952  """
1953  write(ImageHeader self, IMP::String const & filename, bool force_reversed=False)
1954  write(ImageHeader self, IMP::String const & filename)
1955  write(ImageHeader self, std::ofstream & f, bool force_reversed=False)
1956  write(ImageHeader self, std::ofstream & f)
1957  """
1958  return _IMP_em.ImageHeader_write(self, *args)
1959 
1960 
1961  def clear(self):
1962  """clear(ImageHeader self)"""
1963  return _IMP_em.ImageHeader_clear(self)
1964 
1965 
1966  def set_header(self):
1967  """set_header(ImageHeader self)"""
1968  return _IMP_em.ImageHeader_set_header(self)
1969 
1970 
1971  def get_reversed(self):
1972  """get_reversed(ImageHeader self) -> bool"""
1973  return _IMP_em.ImageHeader_get_reversed(self)
1974 
1975 
1976  def set_reversed(self, value):
1977  """set_reversed(ImageHeader self, bool value)"""
1978  return _IMP_em.ImageHeader_set_reversed(self, value)
1979 
1980 
1981  def get_number_of_slices(self):
1982  """get_number_of_slices(ImageHeader self) -> unsigned int"""
1983  return _IMP_em.ImageHeader_get_number_of_slices(self)
1984 
1985 
1986  def set_number_of_slices(self, n):
1987  """set_number_of_slices(ImageHeader self, unsigned int n)"""
1988  return _IMP_em.ImageHeader_set_number_of_slices(self, n)
1989 
1990 
1991  def get_number_of_rows(self):
1992  """get_number_of_rows(ImageHeader self) -> unsigned int"""
1993  return _IMP_em.ImageHeader_get_number_of_rows(self)
1994 
1995 
1996  def set_number_of_rows(self, n):
1997  """set_number_of_rows(ImageHeader self, unsigned int n)"""
1998  return _IMP_em.ImageHeader_set_number_of_rows(self, n)
1999 
2000 
2001  def get_number_of_columns(self):
2002  """get_number_of_columns(ImageHeader self) -> unsigned int"""
2003  return _IMP_em.ImageHeader_get_number_of_columns(self)
2004 
2005 
2006  def set_number_of_columns(self, n):
2007  """set_number_of_columns(ImageHeader self, unsigned int n)"""
2008  return _IMP_em.ImageHeader_set_number_of_columns(self, n)
2009 
2010 
2011  def get_old_rot(self):
2012  """get_old_rot(ImageHeader self) -> float"""
2013  return _IMP_em.ImageHeader_get_old_rot(self)
2014 
2015 
2016  def set_old_rot(self, value):
2017  """set_old_rot(ImageHeader self, float value)"""
2018  return _IMP_em.ImageHeader_set_old_rot(self, value)
2019 
2020 
2021  def get_fAngle1(self):
2022  """get_fAngle1(ImageHeader self) -> float"""
2023  return _IMP_em.ImageHeader_get_fAngle1(self)
2024 
2025 
2026  def set_fAngle1(self, value):
2027  """set_fAngle1(ImageHeader self, float value)"""
2028  return _IMP_em.ImageHeader_set_fAngle1(self, value)
2029 
2030 
2031  def get_Scale(self):
2032  """get_Scale(ImageHeader self) -> float"""
2033  return _IMP_em.ImageHeader_get_Scale(self)
2034 
2035 
2036  def set_Scale(self, value):
2037  """set_Scale(ImageHeader self, float value)"""
2038  return _IMP_em.ImageHeader_set_Scale(self, value)
2039 
2040 
2041  def get_Flip(self):
2042  """get_Flip(ImageHeader self) -> float"""
2043  return _IMP_em.ImageHeader_get_Flip(self)
2044 
2045 
2046  def set_Flip(self, value):
2047  """set_Flip(ImageHeader self, float value)"""
2048  return _IMP_em.ImageHeader_set_Flip(self, value)
2049 
2050 
2051  def get_Weight(self):
2052  """get_Weight(ImageHeader self) -> float"""
2053  return _IMP_em.ImageHeader_get_Weight(self)
2054 
2055 
2056  def set_Weight(self, value):
2057  """set_Weight(ImageHeader self, float value)"""
2058  return _IMP_em.ImageHeader_set_Weight(self, value)
2059 
2060 
2061  def get_fNrec(self):
2062  """get_fNrec(ImageHeader self) -> float"""
2063  return _IMP_em.ImageHeader_get_fNrec(self)
2064 
2065 
2066  def set_fNrec(self, value):
2067  """set_fNrec(ImageHeader self, float value)"""
2068  return _IMP_em.ImageHeader_set_fNrec(self, value)
2069 
2070 
2071  def get_fNlabel(self):
2072  """get_fNlabel(ImageHeader self) -> float"""
2073  return _IMP_em.ImageHeader_get_fNlabel(self)
2074 
2075 
2076  def set_fNlabel(self, value):
2077  """set_fNlabel(ImageHeader self, float value)"""
2078  return _IMP_em.ImageHeader_set_fNlabel(self, value)
2079 
2080 
2081  def get_fIform(self):
2082  """get_fIform(ImageHeader self) -> float"""
2083  return _IMP_em.ImageHeader_get_fIform(self)
2084 
2085 
2086  def set_fIform(self, value):
2087  """set_fIform(ImageHeader self, float value)"""
2088  return _IMP_em.ImageHeader_set_fIform(self, value)
2089 
2090 
2091  def get_fImami(self):
2092  """get_fImami(ImageHeader self) -> float"""
2093  return _IMP_em.ImageHeader_get_fImami(self)
2094 
2095 
2096  def set_fImami(self, value):
2097  """set_fImami(ImageHeader self, float value)"""
2098  return _IMP_em.ImageHeader_set_fImami(self, value)
2099 
2100 
2101  def get_fFmax(self):
2102  """get_fFmax(ImageHeader self) -> float"""
2103  return _IMP_em.ImageHeader_get_fFmax(self)
2104 
2105 
2106  def set_fFmax(self, value):
2107  """set_fFmax(ImageHeader self, float value)"""
2108  return _IMP_em.ImageHeader_set_fFmax(self, value)
2109 
2110 
2111  def get_fFmin(self):
2112  """get_fFmin(ImageHeader self) -> float"""
2113  return _IMP_em.ImageHeader_get_fFmin(self)
2114 
2115 
2116  def set_fFmin(self, value):
2117  """set_fFmin(ImageHeader self, float value)"""
2118  return _IMP_em.ImageHeader_set_fFmin(self, value)
2119 
2120 
2121  def get_fAv(self):
2122  """get_fAv(ImageHeader self) -> float"""
2123  return _IMP_em.ImageHeader_get_fAv(self)
2124 
2125 
2126  def set_fAv(self, value):
2127  """set_fAv(ImageHeader self, float value)"""
2128  return _IMP_em.ImageHeader_set_fAv(self, value)
2129 
2130 
2131  def get_fSig(self):
2132  """get_fSig(ImageHeader self) -> float"""
2133  return _IMP_em.ImageHeader_get_fSig(self)
2134 
2135 
2136  def set_fSig(self, value):
2137  """set_fSig(ImageHeader self, float value)"""
2138  return _IMP_em.ImageHeader_set_fSig(self, value)
2139 
2140 
2141  def get_fIhist(self):
2142  """get_fIhist(ImageHeader self) -> float"""
2143  return _IMP_em.ImageHeader_get_fIhist(self)
2144 
2145 
2146  def set_fIhist(self, value):
2147  """set_fIhist(ImageHeader self, float value)"""
2148  return _IMP_em.ImageHeader_set_fIhist(self, value)
2149 
2150 
2151  def get_fLabrec(self):
2152  """get_fLabrec(ImageHeader self) -> float"""
2153  return _IMP_em.ImageHeader_get_fLabrec(self)
2154 
2155 
2156  def set_fLabrec(self, value):
2157  """set_fLabrec(ImageHeader self, float value)"""
2158  return _IMP_em.ImageHeader_set_fLabrec(self, value)
2159 
2160 
2161  def get_fIangle(self):
2162  """get_fIangle(ImageHeader self) -> float"""
2163  return _IMP_em.ImageHeader_get_fIangle(self)
2164 
2165 
2166  def set_fIangle(self, value):
2167  """set_fIangle(ImageHeader self, float value)"""
2168  return _IMP_em.ImageHeader_set_fIangle(self, value)
2169 
2170 
2171  def get_origin(self):
2172  """get_origin(ImageHeader self) -> Vector3D"""
2173  return _IMP_em.ImageHeader_get_origin(self)
2174 
2175 
2176  def set_origin(self, *args):
2177  """
2178  set_origin(ImageHeader self, Vector3D v)
2179  set_origin(ImageHeader self, Vector2D v)
2180  """
2181  return _IMP_em.ImageHeader_set_origin(self, *args)
2182 
2183 
2184  def get_object_pixel_size(self):
2185  """get_object_pixel_size(ImageHeader self) -> float"""
2186  return _IMP_em.ImageHeader_get_object_pixel_size(self)
2187 
2188 
2189  def set_object_pixel_size(self, value):
2190  """set_object_pixel_size(ImageHeader self, float value)"""
2191  return _IMP_em.ImageHeader_set_object_pixel_size(self, value)
2192 
2193 
2194  def get_fLabbyt(self):
2195  """get_fLabbyt(ImageHeader self) -> float"""
2196  return _IMP_em.ImageHeader_get_fLabbyt(self)
2197 
2198 
2199  def set_fLabbyt(self, value):
2200  """set_fLabbyt(ImageHeader self, float value)"""
2201  return _IMP_em.ImageHeader_set_fLabbyt(self, value)
2202 
2203 
2204  def get_fLenbyt(self):
2205  """get_fLenbyt(ImageHeader self) -> float"""
2206  return _IMP_em.ImageHeader_get_fLenbyt(self)
2207 
2208 
2209  def set_fLenbyt(self, value):
2210  """set_fLenbyt(ImageHeader self, float value)"""
2211  return _IMP_em.ImageHeader_set_fLenbyt(self, value)
2212 
2213 
2214  def get_fGeo_matrix(self, i, j):
2215  """get_fGeo_matrix(ImageHeader self, unsigned int i, unsigned int j) -> double"""
2216  return _IMP_em.ImageHeader_get_fGeo_matrix(self, i, j)
2217 
2218 
2219  def get_fFlag(self):
2220  """get_fFlag(ImageHeader self) -> float"""
2221  return _IMP_em.ImageHeader_get_fFlag(self)
2222 
2223 
2224  def set_fFlag(self, value):
2225  """set_fFlag(ImageHeader self, float value)"""
2226  return _IMP_em.ImageHeader_set_fFlag(self, value)
2227 
2228 
2229  def get_euler_angles(self):
2230  """get_euler_angles(ImageHeader self) -> Vector3D"""
2231  return _IMP_em.ImageHeader_get_euler_angles(self)
2232 
2233 
2234  def get_euler_angles1(self):
2235  """get_euler_angles1(ImageHeader self) -> Vector3D"""
2236  return _IMP_em.ImageHeader_get_euler_angles1(self)
2237 
2238 
2239  def get_euler_angles2(self):
2240  """get_euler_angles2(ImageHeader self) -> Vector3D"""
2241  return _IMP_em.ImageHeader_get_euler_angles2(self)
2242 
2243 
2244  def set_euler_angles(self, euler):
2245  """set_euler_angles(ImageHeader self, Vector3D euler)"""
2246  return _IMP_em.ImageHeader_set_euler_angles(self, euler)
2247 
2248 
2249  def set_euler_angles1(self, euler):
2250  """set_euler_angles1(ImageHeader self, Vector3D euler)"""
2251  return _IMP_em.ImageHeader_set_euler_angles1(self, euler)
2252 
2253 
2254  def set_euler_angles2(self, euler):
2255  """set_euler_angles2(ImageHeader self, Vector3D euler)"""
2256  return _IMP_em.ImageHeader_set_euler_angles2(self, euler)
2257 
2258 
2259  def is_normalized(self):
2260  """is_normalized(ImageHeader self) -> bool"""
2261  return _IMP_em.ImageHeader_is_normalized(self)
2262 
2263 
2264  def set_date(self):
2265  """set_date(ImageHeader self)"""
2266  return _IMP_em.ImageHeader_set_date(self)
2267 
2268 
2269  def set_time(self):
2270  """set_time(ImageHeader self)"""
2271  return _IMP_em.ImageHeader_set_time(self)
2272 
2273 
2274  def set_title(self, newName):
2275  """set_title(ImageHeader self, IMP::String newName)"""
2276  return _IMP_em.ImageHeader_set_title(self, newName)
2277 
2278  __swig_destroy__ = _IMP_em.delete_ImageHeader
2279  __del__ = lambda self: None
2280 ImageHeader_swigregister = _IMP_em.ImageHeader_swigregister
2281 ImageHeader_swigregister(ImageHeader)
2282 
2283 class SpiderMapReaderWriter(MapReaderWriter):
2284  """Proxy of C++ IMP::em::SpiderMapReaderWriter class."""
2285 
2286  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2287  filename_ = _swig_property(_IMP_em.SpiderMapReaderWriter_filename__get, _IMP_em.SpiderMapReaderWriter_filename__set)
2288  skip_type_check_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_type_check__get, _IMP_em.SpiderMapReaderWriter_skip_type_check__set)
2289  force_reversed_ = _swig_property(_IMP_em.SpiderMapReaderWriter_force_reversed__get, _IMP_em.SpiderMapReaderWriter_force_reversed__set)
2290  skip_extra_checkings_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_extra_checkings__get, _IMP_em.SpiderMapReaderWriter_skip_extra_checkings__set)
2291 
2292  def __init__(self, *args):
2293  """
2294  __init__(IMP::em::SpiderMapReaderWriter self) -> SpiderMapReaderWriter
2295  __init__(IMP::em::SpiderMapReaderWriter self, IMP::String filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings) -> SpiderMapReaderWriter
2296  """
2297  this = _IMP_em.new_SpiderMapReaderWriter(*args)
2298  try:
2299  self.this.append(this)
2300  except __builtin__.Exception:
2301  self.this = this
2302 
2303  def __str__(self):
2304  """__str__(SpiderMapReaderWriter self) -> std::string"""
2305  return _IMP_em.SpiderMapReaderWriter___str__(self)
2306 
2307 
2308  def __repr__(self):
2309  """__repr__(SpiderMapReaderWriter self) -> std::string"""
2310  return _IMP_em.SpiderMapReaderWriter___repr__(self)
2311 
2312 
2313  @staticmethod
2314  def get_from(o):
2315  return _object_cast_to_SpiderMapReaderWriter(o)
2316 
2317 SpiderMapReaderWriter_swigregister = _IMP_em.SpiderMapReaderWriter_swigregister
2318 SpiderMapReaderWriter_swigregister(SpiderMapReaderWriter)
2319 
2320 class FittingSolutions(object):
2321  """Proxy of C++ IMP::em::FittingSolutions class."""
2322 
2323  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2324 
2325  def __init__(self):
2326  """__init__(IMP::em::FittingSolutions self) -> FittingSolutions"""
2327  this = _IMP_em.new_FittingSolutions()
2328  try:
2329  self.this.append(this)
2330  except __builtin__.Exception:
2331  self.this = this
2332 
2333  def get_number_of_solutions(self):
2334  """get_number_of_solutions(FittingSolutions self) -> int"""
2335  return _IMP_em.FittingSolutions_get_number_of_solutions(self)
2336 
2337 
2338  def get_transformation(self, i):
2339  """get_transformation(FittingSolutions self, unsigned int i) -> Transformation3D"""
2340  return _IMP_em.FittingSolutions_get_transformation(self, i)
2341 
2342 
2343  def get_score(self, i):
2344  """get_score(FittingSolutions self, unsigned int i) -> IMP::Float"""
2345  return _IMP_em.FittingSolutions_get_score(self, i)
2346 
2347 
2348  def set_score(self, i, score):
2349  """set_score(FittingSolutions self, unsigned int i, IMP::Float score)"""
2350  return _IMP_em.FittingSolutions_set_score(self, i, score)
2351 
2352 
2353  def add_solution(self, t, score):
2354  """add_solution(FittingSolutions self, Transformation3D t, IMP::Float score)"""
2355  return _IMP_em.FittingSolutions_add_solution(self, t, score)
2356 
2357 
2358  def sort(self, reverse=False):
2359  """
2360  sort(FittingSolutions self, bool reverse=False)
2361  sort(FittingSolutions self)
2362  """
2363  return _IMP_em.FittingSolutions_sort(self, reverse)
2364 
2365 
2366  def multiply(self, t):
2367  """multiply(FittingSolutions self, Transformation3D t)"""
2368  return _IMP_em.FittingSolutions_multiply(self, t)
2369 
2370 
2371  def get_transformations(self):
2372  """get_transformations(FittingSolutions self) -> IMP::algebra::Transformation3Ds"""
2373  return _IMP_em.FittingSolutions_get_transformations(self)
2374 
2375 
2376  def show(self, *args):
2377  """
2378  show(FittingSolutions self, _ostream out)
2379  show(FittingSolutions self)
2380  """
2381  return _IMP_em.FittingSolutions_show(self, *args)
2382 
2383 
2384  def __str__(self):
2385  """__str__(FittingSolutions self) -> std::string"""
2386  return _IMP_em.FittingSolutions___str__(self)
2387 
2388 
2389  def __repr__(self):
2390  """__repr__(FittingSolutions self) -> std::string"""
2391  return _IMP_em.FittingSolutions___repr__(self)
2392 
2393  __swig_destroy__ = _IMP_em.delete_FittingSolutions
2394  __del__ = lambda self: None
2395 FittingSolutions_swigregister = _IMP_em.FittingSolutions_swigregister
2396 FittingSolutions_swigregister(FittingSolutions)
2397 
2398 
2399 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):
2400  """
2401  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
2402  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
2403  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
2404  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
2405  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
2406  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
2407  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log) -> FittingSolutions
2408  """
2409  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)
2410 
2411 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):
2412  """
2413  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
2414  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
2415  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
2416  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
2417  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
2418  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2419  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log) -> FittingSolutions
2420  """
2421  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)
2422 
2423 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):
2424  """
2425  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
2426  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
2427  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
2428  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
2429  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
2430  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
2431  """
2432  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)
2433 
2434 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):
2435  """
2436  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
2437  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
2438  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
2439  local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2) -> FittingSolutions
2440  local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap) -> FittingSolutions
2441  """
2442  return _IMP_em.local_rigid_fitting_grid_search(ps, wei_key, dmap, max_voxels_translation, translation_step, max_angle_in_radians, number_of_rotations)
2443 
2444 def compute_fitting_scores(*args):
2445  """
2446  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
2447  compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations, bool fast_version=False, bool local_score=False) -> FittingSolutions
2448  compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations, bool fast_version=False) -> FittingSolutions
2449  compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2450  compute_fitting_scores(DensityMap em_map, RigidBody rb, Refiner refiner, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2451  """
2452  return _IMP_em.compute_fitting_scores(*args)
2453 
2454 def compute_fitting_score(*args):
2455  """
2456  compute_fitting_score(IMP::ParticlesTemp const & ps, DensityMap em_map, FloatKey wei_key) -> IMP::Float
2457  compute_fitting_score(IMP::ParticlesTemp const & ps, DensityMap em_map) -> IMP::Float
2458  """
2459  return _IMP_em.compute_fitting_score(*args)
2460 
2462  """
2463  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, Transformation3D t, float thr=0.0) -> long
2464  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, Transformation3D t) -> long
2465  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps) -> long
2466  """
2467  return _IMP_em.get_number_of_particles_outside_of_the_density(*args)
2468 
2469 def get_numbers_of_particles_outside_of_the_density(dmap, ps, transformations, thr=0.0):
2470  """
2471  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
2472  get_numbers_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, IMP::algebra::Transformation3Ds const & transformations) -> IMP::Ints
2473  """
2474  return _IMP_em.get_numbers_of_particles_outside_of_the_density(dmap, ps, transformations, thr)
2475 
2477  """
2478  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3., Transformation3D t, float thr=0.0) -> double
2479  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3., Transformation3D t) -> double
2480  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3.) -> double
2481  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps) -> double
2482  """
2483  return _IMP_em.get_percentage_of_voxels_covered_by_particles(*args)
2484 class HighDensityEmbedding(IMP.statistics.Embedding):
2485  """Proxy of C++ IMP::em::HighDensityEmbedding class."""
2486 
2487  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2488 
2489  def __init__(self, dm, threshold):
2490  """__init__(IMP::em::HighDensityEmbedding self, DensityMap dm, double threshold) -> HighDensityEmbedding"""
2491  this = _IMP_em.new_HighDensityEmbedding(dm, threshold)
2492  try:
2493  self.this.append(this)
2494  except __builtin__.Exception:
2495  self.this = this
2496 
2497  def get_version_info(self):
2498  """get_version_info(HighDensityEmbedding self) -> VersionInfo"""
2499  return _IMP_em.HighDensityEmbedding_get_version_info(self)
2500 
2501 
2502  def __str__(self):
2503  """__str__(HighDensityEmbedding self) -> std::string"""
2504  return _IMP_em.HighDensityEmbedding___str__(self)
2505 
2506 
2507  def __repr__(self):
2508  """__repr__(HighDensityEmbedding self) -> std::string"""
2509  return _IMP_em.HighDensityEmbedding___repr__(self)
2510 
2511 
2512  @staticmethod
2513  def get_from(o):
2514  return _object_cast_to_HighDensityEmbedding(o)
2515 
2516 HighDensityEmbedding_swigregister = _IMP_em.HighDensityEmbedding_swigregister
2517 HighDensityEmbedding_swigregister(HighDensityEmbedding)
2518 
2519 
2520 def mask_and_norm(dmap, mask):
2521  """mask_and_norm(DensityMap dmap, DensityMap mask) -> DensityMap"""
2522  return _IMP_em.mask_and_norm(dmap, mask)
2523 
2524 def get_volume_at_threshold(m, threshold):
2525  """get_volume_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float"""
2526  return _IMP_em.get_volume_at_threshold(m, threshold)
2527 
2529  """
2530  get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold, IMP::atom::ProteinDensityReference ref) -> IMP::Float
2531  get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float
2532  """
2533  return _IMP_em.get_molecular_mass_at_threshold(*args)
2534 
2535 def get_threshold_for_approximate_volume(m, desired_volume):
2536  """get_threshold_for_approximate_volume(DensityMap m, IMP::Float desired_volume) -> IMP::Float"""
2537  return _IMP_em.get_threshold_for_approximate_volume(m, desired_volume)
2538 
2540  """
2541  get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass, IMP::atom::ProteinDensityReference ref) -> IMP::Float
2542  get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass) -> IMP::Float
2543  """
2544  return _IMP_em.get_threshold_for_approximate_mass(*args)
2545 class EnvelopePenetrationRestraint(IMP.Restraint):
2546  """Proxy of C++ IMP::em::EnvelopePenetrationRestraint class."""
2547 
2548  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2549 
2550  def __init__(self, ps, em_map, threshold):
2551  """__init__(IMP::em::EnvelopePenetrationRestraint self, IMP::Particles ps, DensityMap em_map, IMP::Float threshold) -> EnvelopePenetrationRestraint"""
2552  this = _IMP_em.new_EnvelopePenetrationRestraint(ps, em_map, threshold)
2553  try:
2554  self.this.append(this)
2555  except __builtin__.Exception:
2556  self.this = this
2557 
2558  def do_get_inputs(self):
2559  """do_get_inputs(EnvelopePenetrationRestraint self) -> IMP::ModelObjectsTemp"""
2560  return _IMP_em.EnvelopePenetrationRestraint_do_get_inputs(self)
2561 
2562 
2563  def get_version_info(self):
2564  """get_version_info(EnvelopePenetrationRestraint self) -> VersionInfo"""
2565  return _IMP_em.EnvelopePenetrationRestraint_get_version_info(self)
2566 
2567 
2568  def __str__(self):
2569  """__str__(EnvelopePenetrationRestraint self) -> std::string"""
2570  return _IMP_em.EnvelopePenetrationRestraint___str__(self)
2571 
2572 
2573  def __repr__(self):
2574  """__repr__(EnvelopePenetrationRestraint self) -> std::string"""
2575  return _IMP_em.EnvelopePenetrationRestraint___repr__(self)
2576 
2577 
2578  @staticmethod
2579  def get_from(o):
2580  return _object_cast_to_EnvelopePenetrationRestraint(o)
2581 
2582 EnvelopePenetrationRestraint_swigregister = _IMP_em.EnvelopePenetrationRestraint_swigregister
2583 EnvelopePenetrationRestraint_swigregister(EnvelopePenetrationRestraint)
2584 
2585 class PCAFitRestraint(IMP.Restraint):
2586  """Proxy of C++ IMP::em::PCAFitRestraint class."""
2587 
2588  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2589 
2590  def __init__(self, *args):
2591  """
2592  __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
2593  __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
2594  """
2595  this = _IMP_em.new_PCAFitRestraint(*args)
2596  try:
2597  self.this.append(this)
2598  except __builtin__.Exception:
2599  self.this = this
2600 
2601  def do_get_inputs(self):
2602  """do_get_inputs(PCAFitRestraint self) -> IMP::ModelObjectsTemp"""
2603  return _IMP_em.PCAFitRestraint_do_get_inputs(self)
2604 
2605 
2606  def get_version_info(self):
2607  """get_version_info(PCAFitRestraint self) -> VersionInfo"""
2608  return _IMP_em.PCAFitRestraint_get_version_info(self)
2609 
2610 
2611  def __str__(self):
2612  """__str__(PCAFitRestraint self) -> std::string"""
2613  return _IMP_em.PCAFitRestraint___str__(self)
2614 
2615 
2616  def __repr__(self):
2617  """__repr__(PCAFitRestraint self) -> std::string"""
2618  return _IMP_em.PCAFitRestraint___repr__(self)
2619 
2620 
2621  @staticmethod
2622  def get_from(o):
2623  return _object_cast_to_PCAFitRestraint(o)
2624 
2625 PCAFitRestraint_swigregister = _IMP_em.PCAFitRestraint_swigregister
2626 PCAFitRestraint_swigregister(PCAFitRestraint)
2627 
2628 class EnvelopeFitRestraint(IMP.Restraint):
2629  """Proxy of C++ IMP::em::EnvelopeFitRestraint class."""
2630 
2631  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2632 
2633  def __init__(self, particles, em_map, density_threshold, penetration_threshold):
2634  """__init__(IMP::em::EnvelopeFitRestraint self, IMP::Particles particles, DensityMap em_map, double density_threshold, double penetration_threshold) -> EnvelopeFitRestraint"""
2635  this = _IMP_em.new_EnvelopeFitRestraint(particles, em_map, density_threshold, penetration_threshold)
2636  try:
2637  self.this.append(this)
2638  except __builtin__.Exception:
2639  self.this = this
2640 
2641  def get_transformation(self):
2642  """get_transformation(EnvelopeFitRestraint self) -> Transformation3D"""
2643  return _IMP_em.EnvelopeFitRestraint_get_transformation(self)
2644 
2645 
2646  def apply_transformation(self):
2647  """apply_transformation(EnvelopeFitRestraint self)"""
2648  return _IMP_em.EnvelopeFitRestraint_apply_transformation(self)
2649 
2650 
2651  def do_get_inputs(self):
2652  """do_get_inputs(EnvelopeFitRestraint self) -> IMP::ModelObjectsTemp"""
2653  return _IMP_em.EnvelopeFitRestraint_do_get_inputs(self)
2654 
2655 
2656  def get_version_info(self):
2657  """get_version_info(EnvelopeFitRestraint self) -> VersionInfo"""
2658  return _IMP_em.EnvelopeFitRestraint_get_version_info(self)
2659 
2660 
2661  def __str__(self):
2662  """__str__(EnvelopeFitRestraint self) -> std::string"""
2663  return _IMP_em.EnvelopeFitRestraint___str__(self)
2664 
2665 
2666  def __repr__(self):
2667  """__repr__(EnvelopeFitRestraint self) -> std::string"""
2668  return _IMP_em.EnvelopeFitRestraint___repr__(self)
2669 
2670 
2671  @staticmethod
2672  def get_from(o):
2673  return _object_cast_to_EnvelopeFitRestraint(o)
2674 
2675 EnvelopeFitRestraint_swigregister = _IMP_em.EnvelopeFitRestraint_swigregister
2676 EnvelopeFitRestraint_swigregister(EnvelopeFitRestraint)
2677 
2678 
2679 import math
2680 
2681 def write_pca_cmm(pca, fh):
2682  """Write out principal components to a file in Chimera Marker format"""
2683  eigen_values = pca.get_principal_values()
2684  eigen_vecs = pca.get_principal_components()
2685  centroid = pca.get_centroid()
2686 
2687  fh.write("<marker_set>\n")
2688  fh.write("<!-- PCA with eigen values: (%g,%g,%g) and "
2689  "centroid (%g,%g,%g) -->\n"
2690  % (math.sqrt(eigen_values[0]),
2691  math.sqrt(eigen_values[1]),
2692  math.sqrt(eigen_values[2]),
2693  centroid[0], centroid[1], centroid[2]))
2694 
2695  radius = 2.
2696 
2697  for i in range(3):
2698  val = math.sqrt(eigen_values[i])
2699  v1 = centroid - val * eigen_vecs[i]
2700  v2 = centroid + val * eigen_vecs[i]
2701  for markerid, v in ((i*2+1, v1), (i*2+2, v2)):
2702  fh.write("<marker id=\"%d\" x=\"%g\" y=\"%g\" z=\"%g\" "
2703  "radius=\"%g\"/>\n"
2704  % (markerid, v[0], v[1], v[2], radius))
2705 
2706  for i in range(1, 7, 2):
2707  fh.write("<link id1= \"%d\" id2=\"%d\" radius=\"%g\"/>\n"
2708  % (i, i+1, radius))
2709  fh.write("</marker_set>\n")
2710 
2711 
2712 def get_module_version():
2713  """get_module_version() -> std::string const"""
2714  return _IMP_em.get_module_version()
2715 
2716 def get_example_path(fname):
2717  """get_example_path(std::string fname) -> std::string"""
2718  return _IMP_em.get_example_path(fname)
2719 
2720 def get_data_path(fname):
2721  """get_data_path(std::string fname) -> std::string"""
2722  return _IMP_em.get_data_path(fname)
2723 
2724 from . import _version_check
2725 _version_check.check_version(get_module_version())
2726 __version__ = get_module_version()
2727 
2728 
2729 
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:54