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IMP Reference Guide  2.14.0
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 2007-2020 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_NUMPY = _IMP_em.IMP_KERNEL_HAS_NUMPY
239 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_em.IMP_KERNEL_HAS_GPERFTOOLS
240 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
241 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_em.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
242 IMPKERNEL_SHOW_WARNINGS = _IMP_em.IMPKERNEL_SHOW_WARNINGS
243 
244 import sys
245 class _DirectorObjects(object):
246  """@internal Simple class to keep references to director objects
247  to prevent premature deletion."""
248  def __init__(self):
249  self._objects = []
250  def register(self, obj):
251  """Take a reference to a director object; will only work for
252  refcounted C++ classes"""
253  if hasattr(obj, 'get_ref_count'):
254  self._objects.append(obj)
255  def cleanup(self):
256  """Only drop our reference and allow cleanup by Python if no other
257  Python references exist (we hold 3 references: one in self._objects,
258  one in x, and one in the argument list for getrefcount) *and* no
259  other C++ references exist (the Python object always holds one)"""
260  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
261  or x.get_ref_count() > 1]
262 # Do in two steps so the references are kept until the end of the
263 # function (deleting references may trigger a fresh call to this method)
264  self._objects = objs
265  def get_object_count(self):
266  """Get number of director objects (useful for testing only)"""
267  return len(self._objects)
268 _director_objects = _DirectorObjects()
269 
270 class _ostream(object):
271  """Proxy of C++ std::ostream class."""
272 
273  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
274 
275  def __init__(self, *args, **kwargs):
276  raise AttributeError("No constructor defined")
277  __repr__ = _swig_repr
278 
279  def write(self, osa_buf):
280  """write(_ostream self, char const * osa_buf)"""
281  return _IMP_em._ostream_write(self, osa_buf)
282 
283 _ostream_swigregister = _IMP_em._ostream_swigregister
284 _ostream_swigregister(_ostream)
285 
286 IMP_COMPILER_HAS_OVERRIDE = _IMP_em.IMP_COMPILER_HAS_OVERRIDE
287 IMP_COMPILER_HAS_FINAL = _IMP_em.IMP_COMPILER_HAS_FINAL
288 IMP_HAS_NOEXCEPT = _IMP_em.IMP_HAS_NOEXCEPT
289 IMP_C_OPEN_BINARY = _IMP_em.IMP_C_OPEN_BINARY
290 import IMP
291 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CGAL_HAS_BOOST_FILESYSTEM
292 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
293 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_em.IMP_CGAL_HAS_BOOST_RANDOM
294 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_em.IMP_CGAL_HAS_BOOST_SYSTEM
295 IMP_CGAL_HAS_NUMPY = _IMP_em.IMP_CGAL_HAS_NUMPY
296 IMPCGAL_SHOW_WARNINGS = _IMP_em.IMPCGAL_SHOW_WARNINGS
297 import IMP.cgal
298 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_em.IMP_ALGEBRA_HAS_IMP_CGAL
299 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
300 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
301 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_RANDOM
302 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_SYSTEM
303 IMP_ALGEBRA_HAS_CGAL = _IMP_em.IMP_ALGEBRA_HAS_CGAL
304 IMP_ALGEBRA_HAS_NUMPY = _IMP_em.IMP_ALGEBRA_HAS_NUMPY
305 IMP_ALGEBRA_HAS_ANN = _IMP_em.IMP_ALGEBRA_HAS_ANN
306 IMPALGEBRA_SHOW_WARNINGS = _IMP_em.IMPALGEBRA_SHOW_WARNINGS
307 import IMP.algebra
308 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_em.IMP_DISPLAY_HAS_IMP_CGAL
309 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
310 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
311 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_em.IMP_DISPLAY_HAS_BOOST_RANDOM
312 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_em.IMP_DISPLAY_HAS_BOOST_SYSTEM
313 IMP_DISPLAY_HAS_CGAL = _IMP_em.IMP_DISPLAY_HAS_CGAL
314 IMP_DISPLAY_HAS_NUMPY = _IMP_em.IMP_DISPLAY_HAS_NUMPY
315 IMPDISPLAY_SHOW_WARNINGS = _IMP_em.IMPDISPLAY_SHOW_WARNINGS
316 import IMP.display
317 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_em.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
318 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
319 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
320 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
321 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
322 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_em.IMP_SCORE_FUNCTOR_HAS_CGAL
323 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_em.IMP_SCORE_FUNCTOR_HAS_HDF5
324 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_em.IMP_SCORE_FUNCTOR_HAS_NUMPY
325 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_em.IMPSCOREFUNCTOR_SHOW_WARNINGS
326 import IMP.score_functor
327 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_em.IMP_STATISTICS_HAS_IMP_CGAL
328 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
329 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
330 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_em.IMP_STATISTICS_HAS_BOOST_RANDOM
331 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_SYSTEM
332 IMP_STATISTICS_HAS_CGAL = _IMP_em.IMP_STATISTICS_HAS_CGAL
333 IMP_STATISTICS_HAS_NUMPY = _IMP_em.IMP_STATISTICS_HAS_NUMPY
334 IMPSTATISTICS_SHOW_WARNINGS = _IMP_em.IMPSTATISTICS_SHOW_WARNINGS
335 import IMP.statistics
336 IMP_CORE_HAS_IMP_CGAL = _IMP_em.IMP_CORE_HAS_IMP_CGAL
337 IMP_CORE_HAS_IMP_KERNEL = _IMP_em.IMP_CORE_HAS_IMP_KERNEL
338 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_FILESYSTEM
339 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
340 IMP_CORE_HAS_BOOST_RANDOM = _IMP_em.IMP_CORE_HAS_BOOST_RANDOM
341 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_SYSTEM
342 IMP_CORE_HAS_CGAL = _IMP_em.IMP_CORE_HAS_CGAL
343 IMP_CORE_HAS_HDF5 = _IMP_em.IMP_CORE_HAS_HDF5
344 IMP_CORE_HAS_NUMPY = _IMP_em.IMP_CORE_HAS_NUMPY
345 IMPCORE_SHOW_WARNINGS = _IMP_em.IMPCORE_SHOW_WARNINGS
346 import IMP.core
347 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_em.IMP_CONTAINER_HAS_IMP_ALGEBRA
348 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_em.IMP_CONTAINER_HAS_IMP_CGAL
349 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_em.IMP_CONTAINER_HAS_IMP_DISPLAY
350 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_em.IMP_CONTAINER_HAS_IMP_KERNEL
351 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
352 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
353 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
354 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_em.IMP_CONTAINER_HAS_BOOST_RANDOM
355 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_SYSTEM
356 IMP_CONTAINER_HAS_CGAL = _IMP_em.IMP_CONTAINER_HAS_CGAL
357 IMP_CONTAINER_HAS_HDF5 = _IMP_em.IMP_CONTAINER_HAS_HDF5
358 IMP_CONTAINER_HAS_NUMPY = _IMP_em.IMP_CONTAINER_HAS_NUMPY
359 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_em.IMP_CONTAINER_HAS_PYTHON_IHM
360 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_em.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
361 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_em.IMP_CONTAINER_HAS_ROBIN_MAP
362 IMPCONTAINER_SHOW_WARNINGS = _IMP_em.IMPCONTAINER_SHOW_WARNINGS
363 import IMP.container
364 IMP_ATOM_HAS_IMP_CGAL = _IMP_em.IMP_ATOM_HAS_IMP_CGAL
365 IMP_ATOM_HAS_IMP_KERNEL = _IMP_em.IMP_ATOM_HAS_IMP_KERNEL
366 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
367 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
368 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_em.IMP_ATOM_HAS_BOOST_RANDOM
369 IMP_ATOM_HAS_BOOST_REGEX = _IMP_em.IMP_ATOM_HAS_BOOST_REGEX
370 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_em.IMP_ATOM_HAS_BOOST_SYSTEM
371 IMP_ATOM_HAS_CGAL = _IMP_em.IMP_ATOM_HAS_CGAL
372 IMP_ATOM_HAS_HDF5 = _IMP_em.IMP_ATOM_HAS_HDF5
373 IMP_ATOM_HAS_NUMPY = _IMP_em.IMP_ATOM_HAS_NUMPY
374 IMP_ATOM_HAS_PYTHON_IHM = _IMP_em.IMP_ATOM_HAS_PYTHON_IHM
375 IMPATOM_SHOW_WARNINGS = _IMP_em.IMPATOM_SHOW_WARNINGS
376 IMP_ATOM_TYPE_INDEX = _IMP_em.IMP_ATOM_TYPE_INDEX
377 IMP_RESIDUE_TYPE_INDEX = _IMP_em.IMP_RESIDUE_TYPE_INDEX
378 IMP_HIERARCHY_TYPE_INDEX = _IMP_em.IMP_HIERARCHY_TYPE_INDEX
379 IMP_CHAIN_TYPE_INDEX = _IMP_em.IMP_CHAIN_TYPE_INDEX
380 import IMP.atom
381 IMP_EM_HAS_IMP_CGAL = _IMP_em.IMP_EM_HAS_IMP_CGAL
382 IMP_EM_HAS_IMP_CONTAINER = _IMP_em.IMP_EM_HAS_IMP_CONTAINER
383 IMP_EM_HAS_IMP_DISPLAY = _IMP_em.IMP_EM_HAS_IMP_DISPLAY
384 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_EM_HAS_IMP_SCORE_FUNCTOR
385 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_EM_HAS_BOOST_FILESYSTEM
386 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
387 IMP_EM_HAS_BOOST_RANDOM = _IMP_em.IMP_EM_HAS_BOOST_RANDOM
388 IMP_EM_HAS_BOOST_REGEX = _IMP_em.IMP_EM_HAS_BOOST_REGEX
389 IMP_EM_HAS_BOOST_SYSTEM = _IMP_em.IMP_EM_HAS_BOOST_SYSTEM
390 IMP_EM_HAS_CGAL = _IMP_em.IMP_EM_HAS_CGAL
391 IMP_EM_HAS_HDF5 = _IMP_em.IMP_EM_HAS_HDF5
392 IMP_EM_HAS_NUMPY = _IMP_em.IMP_EM_HAS_NUMPY
393 IMP_EM_HAS_PYTHON_IHM = _IMP_em.IMP_EM_HAS_PYTHON_IHM
394 IMPEM_SHOW_WARNINGS = _IMP_em.IMPEM_SHOW_WARNINGS
395 
396 _object_types.append("DensityMap")
397 
398 
399 def _object_cast_to_DensityMap(o):
400  """_object_cast_to_DensityMap(Object o) -> DensityMap"""
401  return _IMP_em._object_cast_to_DensityMap(o)
402 
403 _object_types.append("SampledDensityMap")
404 
405 
406 def _object_cast_to_SampledDensityMap(o):
407  """_object_cast_to_SampledDensityMap(Object o) -> SampledDensityMap"""
408  return _IMP_em._object_cast_to_SampledDensityMap(o)
409 
410 _object_types.append("SurfaceShellDensityMap")
411 
412 
413 def _object_cast_to_SurfaceShellDensityMap(o):
414  """_object_cast_to_SurfaceShellDensityMap(Object o) -> SurfaceShellDensityMap"""
415  return _IMP_em._object_cast_to_SurfaceShellDensityMap(o)
416 
417 _object_types.append("FitRestraint")
418 
419 
420 def _object_cast_to_FitRestraint(o):
421  """_object_cast_to_FitRestraint(Object o) -> FitRestraint"""
422  return _IMP_em._object_cast_to_FitRestraint(o)
423 
424 _object_types.append("PCAFitRestraint")
425 
426 
427 def _object_cast_to_PCAFitRestraint(o):
428  """_object_cast_to_PCAFitRestraint(Object o) -> PCAFitRestraint"""
429  return _IMP_em._object_cast_to_PCAFitRestraint(o)
430 
431 _object_types.append("EnvelopePenetrationRestraint")
432 
433 
434 def _object_cast_to_EnvelopePenetrationRestraint(o):
435  """_object_cast_to_EnvelopePenetrationRestraint(Object o) -> EnvelopePenetrationRestraint"""
436  return _IMP_em._object_cast_to_EnvelopePenetrationRestraint(o)
437 
438 _object_types.append("EnvelopeFitRestraint")
439 
440 
441 def _object_cast_to_EnvelopeFitRestraint(o):
442  """_object_cast_to_EnvelopeFitRestraint(Object o) -> EnvelopeFitRestraint"""
443  return _IMP_em._object_cast_to_EnvelopeFitRestraint(o)
444 
445 KernelParametersList=list
446 _plural_types.append("KernelParametersList")
447 _value_types.append("KernelParameters")
448 
449 
450 _object_types.append("HighDensityEmbedding")
451 
452 
453 def _object_cast_to_HighDensityEmbedding(o):
454  """_object_cast_to_HighDensityEmbedding(Object o) -> HighDensityEmbedding"""
455  return _IMP_em._object_cast_to_HighDensityEmbedding(o)
456 
457 _object_types.append("MapReaderWriter")
458 
459 
460 def _object_cast_to_MapReaderWriter(o):
461  """_object_cast_to_MapReaderWriter(Object o) -> MapReaderWriter"""
462  return _IMP_em._object_cast_to_MapReaderWriter(o)
463 
464 _object_types.append("MRCReaderWriter")
465 
466 
467 def _object_cast_to_MRCReaderWriter(o):
468  """_object_cast_to_MRCReaderWriter(Object o) -> MRCReaderWriter"""
469  return _IMP_em._object_cast_to_MRCReaderWriter(o)
470 
471 _object_types.append("SpiderMapReaderWriter")
472 
473 
474 def _object_cast_to_SpiderMapReaderWriter(o):
475  """_object_cast_to_SpiderMapReaderWriter(Object o) -> SpiderMapReaderWriter"""
476  return _IMP_em._object_cast_to_SpiderMapReaderWriter(o)
477 
478 _object_types.append("EMReaderWriter")
479 
480 
481 def _object_cast_to_EMReaderWriter(o):
482  """_object_cast_to_EMReaderWriter(Object o) -> EMReaderWriter"""
483  return _IMP_em._object_cast_to_EMReaderWriter(o)
484 
485 _object_types.append("XplorReaderWriter")
486 
487 
488 def _object_cast_to_XplorReaderWriter(o):
489  """_object_cast_to_XplorReaderWriter(Object o) -> XplorReaderWriter"""
490  return _IMP_em._object_cast_to_XplorReaderWriter(o)
491 
492 _object_types.append("CoarseCC")
493 
494 
495 def _object_cast_to_CoarseCC(o):
496  """_object_cast_to_CoarseCC(Object o) -> CoarseCC"""
497  return _IMP_em._object_cast_to_CoarseCC(o)
498 
499 _object_types.append("CoarseCCatIntervals")
500 
501 
502 def _object_cast_to_CoarseCCatIntervals(o):
503  """_object_cast_to_CoarseCCatIntervals(Object o) -> CoarseCCatIntervals"""
504  return _IMP_em._object_cast_to_CoarseCCatIntervals(o)
505 
506 FittingSolutionsList=list
507 _plural_types.append("FittingSolutionsList")
508 _value_types.append("FittingSolutions")
509 
510 
511 _object_types.append("MapDistanceTransform")
512 
513 
514 def _object_cast_to_MapDistanceTransform(o):
515  """_object_cast_to_MapDistanceTransform(Object o) -> MapDistanceTransform"""
516  return _IMP_em._object_cast_to_MapDistanceTransform(o)
517 
518 _object_types.append("EnvelopeScore")
519 
520 
521 def _object_cast_to_EnvelopeScore(o):
522  """_object_cast_to_EnvelopeScore(Object o) -> EnvelopeScore"""
523  return _IMP_em._object_cast_to_EnvelopeScore(o)
524 class MapReaderWriter(IMP.Object):
525  """Proxy of C++ IMP::em::MapReaderWriter class."""
526 
527  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
528 
529  def __init__(self):
530  """__init__(IMP::em::MapReaderWriter self) -> MapReaderWriter"""
531  this = _IMP_em.new_MapReaderWriter()
532  try:
533  self.this.append(this)
534  except __builtin__.Exception:
535  self.this = this
536 
537  def get_version_info(self):
538  """get_version_info(MapReaderWriter self) -> VersionInfo"""
539  return _IMP_em.MapReaderWriter_get_version_info(self)
540 
541 
542  def __str__(self):
543  """__str__(MapReaderWriter self) -> std::string"""
544  return _IMP_em.MapReaderWriter___str__(self)
545 
546 
547  def __repr__(self):
548  """__repr__(MapReaderWriter self) -> std::string"""
549  return _IMP_em.MapReaderWriter___repr__(self)
550 
551 
552  @staticmethod
553  def get_from(o):
554  return _object_cast_to_MapReaderWriter(o)
555 
556 MapReaderWriter_swigregister = _IMP_em.MapReaderWriter_swigregister
557 MapReaderWriter_swigregister(MapReaderWriter)
558 cvar = _IMP_em.cvar
559 EPS = cvar.EPS
560 
561 class DensityHeader(object):
562  """Proxy of C++ IMP::em::DensityHeader class."""
563 
564  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
565  __repr__ = _swig_repr
566 
567  def __init__(self):
568  """__init__(IMP::em::DensityHeader self) -> DensityHeader"""
569  this = _IMP_em.new_DensityHeader()
570  try:
571  self.this.append(this)
572  except __builtin__.Exception:
573  self.this = this
574 
575  def get_top(self, ind):
576  """get_top(DensityHeader self, int ind) -> IMP::em::emreal"""
577  return _IMP_em.DensityHeader_get_top(self, ind)
578 
579 
580  def compute_xyz_top(self, force=False):
581  """
582  compute_xyz_top(DensityHeader self, bool force=False)
583  compute_xyz_top(DensityHeader self)
584  """
585  return _IMP_em.DensityHeader_compute_xyz_top(self, force)
586 
587 
588  def update_map_dimensions(self, nnx, nny, nnz):
589  """update_map_dimensions(DensityHeader self, int nnx, int nny, int nnz)"""
590  return _IMP_em.DensityHeader_update_map_dimensions(self, nnx, nny, nnz)
591 
592 
593  def update_cell_dimensions(self):
594  """update_cell_dimensions(DensityHeader self)"""
595  return _IMP_em.DensityHeader_update_cell_dimensions(self)
596 
597 
598  def show(self, *args):
599  """
600  show(DensityHeader self, _ostream out)
601  show(DensityHeader self)
602  """
603  return _IMP_em.DensityHeader_show(self, *args)
604 
605  MAP_FIELD_SIZE = _IMP_em.DensityHeader_MAP_FIELD_SIZE
606  USER_FIELD_SIZE = _IMP_em.DensityHeader_USER_FIELD_SIZE
607  COMMENT_FIELD_NUM_OF = _IMP_em.DensityHeader_COMMENT_FIELD_NUM_OF
608  COMMENT_FIELD_SINGLE_SIZE = _IMP_em.DensityHeader_COMMENT_FIELD_SINGLE_SIZE
609  nxstart = _swig_property(_IMP_em.DensityHeader_nxstart_get, _IMP_em.DensityHeader_nxstart_set)
610  nystart = _swig_property(_IMP_em.DensityHeader_nystart_get, _IMP_em.DensityHeader_nystart_set)
611  nzstart = _swig_property(_IMP_em.DensityHeader_nzstart_get, _IMP_em.DensityHeader_nzstart_set)
612  mx = _swig_property(_IMP_em.DensityHeader_mx_get, _IMP_em.DensityHeader_mx_set)
613  my = _swig_property(_IMP_em.DensityHeader_my_get, _IMP_em.DensityHeader_my_set)
614  mz = _swig_property(_IMP_em.DensityHeader_mz_get, _IMP_em.DensityHeader_mz_set)
615  xlen = _swig_property(_IMP_em.DensityHeader_xlen_get, _IMP_em.DensityHeader_xlen_set)
616  ylen = _swig_property(_IMP_em.DensityHeader_ylen_get, _IMP_em.DensityHeader_ylen_set)
617  zlen = _swig_property(_IMP_em.DensityHeader_zlen_get, _IMP_em.DensityHeader_zlen_set)
618  alpha = _swig_property(_IMP_em.DensityHeader_alpha_get, _IMP_em.DensityHeader_alpha_set)
619  beta = _swig_property(_IMP_em.DensityHeader_beta_get, _IMP_em.DensityHeader_beta_set)
620  gamma = _swig_property(_IMP_em.DensityHeader_gamma_get, _IMP_em.DensityHeader_gamma_set)
621  mapc = _swig_property(_IMP_em.DensityHeader_mapc_get, _IMP_em.DensityHeader_mapc_set)
622  mapr = _swig_property(_IMP_em.DensityHeader_mapr_get, _IMP_em.DensityHeader_mapr_set)
623  maps = _swig_property(_IMP_em.DensityHeader_maps_get, _IMP_em.DensityHeader_maps_set)
624  dmin = _swig_property(_IMP_em.DensityHeader_dmin_get, _IMP_em.DensityHeader_dmin_set)
625  dmax = _swig_property(_IMP_em.DensityHeader_dmax_get, _IMP_em.DensityHeader_dmax_set)
626  dmean = _swig_property(_IMP_em.DensityHeader_dmean_get, _IMP_em.DensityHeader_dmean_set)
627  ispg = _swig_property(_IMP_em.DensityHeader_ispg_get, _IMP_em.DensityHeader_ispg_set)
628  nsymbt = _swig_property(_IMP_em.DensityHeader_nsymbt_get, _IMP_em.DensityHeader_nsymbt_set)
629  user = _swig_property(_IMP_em.DensityHeader_user_get, _IMP_em.DensityHeader_user_set)
630  map = _swig_property(_IMP_em.DensityHeader_map_get, _IMP_em.DensityHeader_map_set)
631  machinestamp = _swig_property(_IMP_em.DensityHeader_machinestamp_get, _IMP_em.DensityHeader_machinestamp_set)
632  rms = _swig_property(_IMP_em.DensityHeader_rms_get, _IMP_em.DensityHeader_rms_set)
633  nlabl = _swig_property(_IMP_em.DensityHeader_nlabl_get, _IMP_em.DensityHeader_nlabl_set)
634  comments = _swig_property(_IMP_em.DensityHeader_comments_get, _IMP_em.DensityHeader_comments_set)
635  magic = _swig_property(_IMP_em.DensityHeader_magic_get, _IMP_em.DensityHeader_magic_set)
636  voltage = _swig_property(_IMP_em.DensityHeader_voltage_get, _IMP_em.DensityHeader_voltage_set)
637  Cs = _swig_property(_IMP_em.DensityHeader_Cs_get, _IMP_em.DensityHeader_Cs_set)
638  Aperture = _swig_property(_IMP_em.DensityHeader_Aperture_get, _IMP_em.DensityHeader_Aperture_set)
639  Magnification = _swig_property(_IMP_em.DensityHeader_Magnification_get, _IMP_em.DensityHeader_Magnification_set)
640  Postmagnification = _swig_property(_IMP_em.DensityHeader_Postmagnification_get, _IMP_em.DensityHeader_Postmagnification_set)
641  Exposuretime = _swig_property(_IMP_em.DensityHeader_Exposuretime_get, _IMP_em.DensityHeader_Exposuretime_set)
642  Microscope = _swig_property(_IMP_em.DensityHeader_Microscope_get, _IMP_em.DensityHeader_Microscope_set)
643  Pixelsize = _swig_property(_IMP_em.DensityHeader_Pixelsize_get, _IMP_em.DensityHeader_Pixelsize_set)
644  CCDArea = _swig_property(_IMP_em.DensityHeader_CCDArea_get, _IMP_em.DensityHeader_CCDArea_set)
645  Defocus = _swig_property(_IMP_em.DensityHeader_Defocus_get, _IMP_em.DensityHeader_Defocus_set)
646  Astigmatism = _swig_property(_IMP_em.DensityHeader_Astigmatism_get, _IMP_em.DensityHeader_Astigmatism_set)
647  AstigmatismAngle = _swig_property(_IMP_em.DensityHeader_AstigmatismAngle_get, _IMP_em.DensityHeader_AstigmatismAngle_set)
648  FocusIncrement = _swig_property(_IMP_em.DensityHeader_FocusIncrement_get, _IMP_em.DensityHeader_FocusIncrement_set)
649  CountsPerElectron = _swig_property(_IMP_em.DensityHeader_CountsPerElectron_get, _IMP_em.DensityHeader_CountsPerElectron_set)
650  Intensity = _swig_property(_IMP_em.DensityHeader_Intensity_get, _IMP_em.DensityHeader_Intensity_set)
651  EnergySlitwidth = _swig_property(_IMP_em.DensityHeader_EnergySlitwidth_get, _IMP_em.DensityHeader_EnergySlitwidth_set)
652  EnergyOffset = _swig_property(_IMP_em.DensityHeader_EnergyOffset_get, _IMP_em.DensityHeader_EnergyOffset_set)
653  Tiltangle = _swig_property(_IMP_em.DensityHeader_Tiltangle_get, _IMP_em.DensityHeader_Tiltangle_set)
654  Tiltaxis = _swig_property(_IMP_em.DensityHeader_Tiltaxis_get, _IMP_em.DensityHeader_Tiltaxis_set)
655  MarkerX = _swig_property(_IMP_em.DensityHeader_MarkerX_get, _IMP_em.DensityHeader_MarkerX_set)
656  MarkerY = _swig_property(_IMP_em.DensityHeader_MarkerY_get, _IMP_em.DensityHeader_MarkerY_set)
657  lswap = _swig_property(_IMP_em.DensityHeader_lswap_get, _IMP_em.DensityHeader_lswap_set)
658 
659  def get_resolution(self):
660  """get_resolution(DensityHeader self) -> float"""
661  return _IMP_em.DensityHeader_get_resolution(self)
662 
663 
664  def get_has_resolution(self):
665  """get_has_resolution(DensityHeader self) -> bool"""
666  return _IMP_em.DensityHeader_get_has_resolution(self)
667 
668 
669  def set_resolution(self, resolution):
670  """set_resolution(DensityHeader self, float resolution)"""
671  return _IMP_em.DensityHeader_set_resolution(self, resolution)
672 
673 
674  def get_spacing(self):
675  """get_spacing(DensityHeader self) -> float"""
676  return _IMP_em.DensityHeader_get_spacing(self)
677 
678 
679  def get_xorigin(self):
680  """get_xorigin(DensityHeader self) -> float"""
681  return _IMP_em.DensityHeader_get_xorigin(self)
682 
683 
684  def get_yorigin(self):
685  """get_yorigin(DensityHeader self) -> float"""
686  return _IMP_em.DensityHeader_get_yorigin(self)
687 
688 
689  def get_zorigin(self):
690  """get_zorigin(DensityHeader self) -> float"""
691  return _IMP_em.DensityHeader_get_zorigin(self)
692 
693 
694  def get_origin(self, i):
695  """get_origin(DensityHeader self, int i) -> float"""
696  return _IMP_em.DensityHeader_get_origin(self, i)
697 
698 
699  def set_xorigin(self, x):
700  """set_xorigin(DensityHeader self, float x)"""
701  return _IMP_em.DensityHeader_set_xorigin(self, x)
702 
703 
704  def set_yorigin(self, y):
705  """set_yorigin(DensityHeader self, float y)"""
706  return _IMP_em.DensityHeader_set_yorigin(self, y)
707 
708 
709  def set_zorigin(self, z):
710  """set_zorigin(DensityHeader self, float z)"""
711  return _IMP_em.DensityHeader_set_zorigin(self, z)
712 
713 
714  def is_top_calculated(self):
715  """is_top_calculated(DensityHeader self) -> bool"""
716  return _IMP_em.DensityHeader_is_top_calculated(self)
717 
718  Objectpixelsize_ = _swig_property(_IMP_em.DensityHeader_Objectpixelsize__get, _IMP_em.DensityHeader_Objectpixelsize__set)
719 
720  def get_nx(self):
721  """get_nx(DensityHeader self) -> int"""
722  return _IMP_em.DensityHeader_get_nx(self)
723 
724 
725  def get_ny(self):
726  """get_ny(DensityHeader self) -> int"""
727  return _IMP_em.DensityHeader_get_ny(self)
728 
729 
730  def get_nz(self):
731  """get_nz(DensityHeader self) -> int"""
732  return _IMP_em.DensityHeader_get_nz(self)
733 
734 
735  def get_number_of_voxels(self):
736  """get_number_of_voxels(DensityHeader self) -> int"""
737  return _IMP_em.DensityHeader_get_number_of_voxels(self)
738 
739 
740  def get_data_type(self):
741  """get_data_type(DensityHeader self) -> int"""
742  return _IMP_em.DensityHeader_get_data_type(self)
743 
744 
745  def set_data_type(self, data_type):
746  """set_data_type(DensityHeader self, int data_type)"""
747  return _IMP_em.DensityHeader_set_data_type(self, data_type)
748 
749  __swig_destroy__ = _IMP_em.delete_DensityHeader
750  __del__ = lambda self: None
751 DensityHeader_swigregister = _IMP_em.DensityHeader_swigregister
752 DensityHeader_swigregister(DensityHeader)
753 
754 
755 def create_density_header(bb, spacing):
756  """create_density_header(BoundingBox3D bb, float spacing) -> DensityHeader"""
757  return _IMP_em.create_density_header(bb, spacing)
758 
759 def read_map(*args):
760  """
761  read_map(std::string filename, MapReaderWriter reader) -> DensityMap
762  read_map(std::string filename) -> DensityMap
763  """
764  return _IMP_em.read_map(*args)
765 
766 def write_map(*args):
767  """
768  write_map(DensityMap m, std::string filename, MapReaderWriter writer)
769  write_map(DensityMap m, std::string filename)
770  """
771  return _IMP_em.write_map(*args)
772 
773 def approximate_molecular_mass(m, threshold):
774  """approximate_molecular_mass(DensityMap m, IMP::Float threshold) -> IMP::Float"""
775  return _IMP_em.approximate_molecular_mass(m, threshold)
776 class DensityMap(IMP.Object):
777  """Proxy of C++ IMP::em::DensityMap class."""
778 
779  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
780 
781  def __init__(self, *args):
782  """
783  __init__(IMP::em::DensityMap self, std::string name) -> DensityMap
784  __init__(IMP::em::DensityMap self) -> DensityMap
785  __init__(IMP::em::DensityMap self, DensityHeader header, std::string name) -> DensityMap
786  __init__(IMP::em::DensityMap self, DensityHeader header) -> DensityMap
787  """
788  this = _IMP_em.new_DensityMap(*args)
789  try:
790  self.this.append(this)
791  except __builtin__.Exception:
792  self.this = this
793 
794  def reset_data(self, value=0.0):
795  """
796  reset_data(DensityMap self, float value=0.0)
797  reset_data(DensityMap self)
798  """
799  return _IMP_em.DensityMap_reset_data(self, value)
800 
801 
802  def calcRMS(self):
803  """calcRMS(DensityMap self) -> IMP::em::emreal"""
804  return _IMP_em.DensityMap_calcRMS(self)
805 
806 
807  def std_normalize(self):
808  """std_normalize(DensityMap self)"""
809  return _IMP_em.DensityMap_std_normalize(self)
810 
811 
812  def is_normalized(self):
813  """is_normalized(DensityMap self) -> bool"""
814  return _IMP_em.DensityMap_is_normalized(self)
815 
816 
817  def get_location_in_dim_by_voxel(self, index, dim):
818  """get_location_in_dim_by_voxel(DensityMap self, long index, int dim) -> float"""
819  return _IMP_em.DensityMap_get_location_in_dim_by_voxel(self, index, dim)
820 
821 
822  def xyz_ind2voxel(self, x, y, z):
823  """xyz_ind2voxel(DensityMap self, int x, int y, int z) -> long"""
824  return _IMP_em.DensityMap_xyz_ind2voxel(self, x, y, z)
825 
826 
827  def get_voxel_by_location(self, *args):
828  """
829  get_voxel_by_location(DensityMap self, float x, float y, float z) -> long
830  get_voxel_by_location(DensityMap self, Vector3D v) -> long
831  """
832  return _IMP_em.DensityMap_get_voxel_by_location(self, *args)
833 
834 
835  def get_location_by_voxel(self, index):
836  """get_location_by_voxel(DensityMap self, long index) -> Vector3D"""
837  return _IMP_em.DensityMap_get_location_by_voxel(self, index)
838 
839 
840  def is_xyz_ind_part_of_volume(self, ix, iy, iz):
841  """is_xyz_ind_part_of_volume(DensityMap self, int ix, int iy, int iz) -> bool"""
842  return _IMP_em.DensityMap_is_xyz_ind_part_of_volume(self, ix, iy, iz)
843 
844 
845  def is_part_of_volume(self, *args):
846  """
847  is_part_of_volume(DensityMap self, float x, float y, float z) -> bool
848  is_part_of_volume(DensityMap self, Vector3D v) -> bool
849  """
850  return _IMP_em.DensityMap_is_part_of_volume(self, *args)
851 
852 
853  def get_value(self, *args):
854  """
855  get_value(DensityMap self, float x, float y, float z) -> IMP::em::emreal
856  get_value(DensityMap self, Vector3D point) -> IMP::em::emreal
857  get_value(DensityMap self, long index) -> IMP::em::emreal
858  """
859  return _IMP_em.DensityMap_get_value(self, *args)
860 
861 
862  def set_value(self, *args):
863  """
864  set_value(DensityMap self, long index, IMP::em::emreal value)
865  set_value(DensityMap self, float x, float y, float z, IMP::em::emreal value)
866  """
867  return _IMP_em.DensityMap_set_value(self, *args)
868 
869 
870  def set_origin(self, *args):
871  """
872  set_origin(DensityMap self, float x, float y, float z)
873  set_origin(DensityMap self, Vector3D v)
874  """
875  return _IMP_em.DensityMap_set_origin(self, *args)
876 
877 
878  def get_origin(self):
879  """get_origin(DensityMap self) -> Vector3D"""
880  return _IMP_em.DensityMap_get_origin(self)
881 
882 
883  def get_top(self):
884  """get_top(DensityMap self) -> Vector3D"""
885  return _IMP_em.DensityMap_get_top(self)
886 
887 
888  def get_header(self):
889  h = _IMP_em.DensityMap_get_header(self)
890  h._owner = self
891  return h
892 
893 
894 
895  def get_header_writable(self):
896  h = _IMP_em.DensityMap_get_header_writable(self)
897  h._owner = self
898  return h
899 
900 
901 
902  def same_origin(self, other):
903  """same_origin(DensityMap self, DensityMap other) -> bool"""
904  return _IMP_em.DensityMap_same_origin(self, other)
905 
906 
907  def same_dimensions(self, other):
908  """same_dimensions(DensityMap self, DensityMap other) -> bool"""
909  return _IMP_em.DensityMap_same_dimensions(self, other)
910 
911 
912  def same_voxel_size(self, other):
913  """same_voxel_size(DensityMap self, DensityMap other) -> bool"""
914  return _IMP_em.DensityMap_same_voxel_size(self, other)
915 
916 
917  def get_centroid(self, threshold=0.0):
918  """
919  get_centroid(DensityMap self, IMP::em::emreal threshold=0.0) -> Vector3D
920  get_centroid(DensityMap self) -> Vector3D
921  """
922  return _IMP_em.DensityMap_get_centroid(self, threshold)
923 
924 
925  def get_max_value(self):
926  """get_max_value(DensityMap self) -> IMP::em::emreal"""
927  return _IMP_em.DensityMap_get_max_value(self)
928 
929 
930  def get_min_value(self):
931  """get_min_value(DensityMap self) -> IMP::em::emreal"""
932  return _IMP_em.DensityMap_get_min_value(self)
933 
934 
935  def add(self, *args):
936  """
937  add(DensityMap self, DensityMap other)
938  add(DensityMap self, IMP::Float d)
939  """
940  return _IMP_em.DensityMap_add(self, *args)
941 
942 
943  def pick_max(self, other):
944  """pick_max(DensityMap self, DensityMap other)"""
945  return _IMP_em.DensityMap_pick_max(self, other)
946 
947 
948  def get_number_of_voxels(self):
949  """get_number_of_voxels(DensityMap self) -> long"""
950  return _IMP_em.DensityMap_get_number_of_voxels(self)
951 
952 
953  def set_void_map(self, nx, ny, nz):
954  """set_void_map(DensityMap self, int nx, int ny, int nz)"""
955  return _IMP_em.DensityMap_set_void_map(self, nx, ny, nz)
956 
957 
958  def pad(self, nx, ny, nz, val=0.0):
959  """
960  pad(DensityMap self, int nx, int ny, int nz, float val=0.0)
961  pad(DensityMap self, int nx, int ny, int nz)
962  """
963  return _IMP_em.DensityMap_pad(self, nx, ny, nz, val)
964 
965 
966  def pad_margin(self, mrg_x, mrg_y, mrg_z, val=0.0):
967  """
968  pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z, float val=0.0) -> DensityMap
969  pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z) -> DensityMap
970  """
971  return _IMP_em.DensityMap_pad_margin(self, mrg_x, mrg_y, mrg_z, val)
972 
973 
974  def get_cropped(self, *args):
975  """
976  get_cropped(DensityMap self, float threshold) -> DensityMap
977  get_cropped(DensityMap self, BoundingBox3D bb) -> DensityMap
978  """
979  return _IMP_em.DensityMap_get_cropped(self, *args)
980 
981 
982  def get_maximum_value_in_xy_plane(self, z_ind):
983  """get_maximum_value_in_xy_plane(DensityMap self, int z_ind) -> float"""
984  return _IMP_em.DensityMap_get_maximum_value_in_xy_plane(self, z_ind)
985 
986 
987  def get_maximum_value_in_xz_plane(self, y_ind):
988  """get_maximum_value_in_xz_plane(DensityMap self, int y_ind) -> float"""
989  return _IMP_em.DensityMap_get_maximum_value_in_xz_plane(self, y_ind)
990 
991 
992  def get_maximum_value_in_yz_plane(self, x_ind):
993  """get_maximum_value_in_yz_plane(DensityMap self, int x_ind) -> float"""
994  return _IMP_em.DensityMap_get_maximum_value_in_yz_plane(self, x_ind)
995 
996 
997  def multiply(self, factor):
998  """multiply(DensityMap self, float factor)"""
999  return _IMP_em.DensityMap_multiply(self, factor)
1000 
1001 
1002  def get_locations_string(self, t):
1003  """get_locations_string(DensityMap self, float t) -> std::string"""
1004  return _IMP_em.DensityMap_get_locations_string(self, t)
1005 
1006 
1007  def update_voxel_size(self, new_apix):
1008  """update_voxel_size(DensityMap self, float new_apix)"""
1009  return _IMP_em.DensityMap_update_voxel_size(self, new_apix)
1010 
1011 
1012  def get_spacing(self):
1013  """get_spacing(DensityMap self) -> IMP::Float"""
1014  return _IMP_em.DensityMap_get_spacing(self)
1015 
1016 
1017  def calc_all_voxel2loc(self):
1018  """calc_all_voxel2loc(DensityMap self)"""
1019  return _IMP_em.DensityMap_calc_all_voxel2loc(self)
1020 
1021 
1022  def copy_map(self, other):
1023  """copy_map(DensityMap self, DensityMap other)"""
1024  return _IMP_em.DensityMap_copy_map(self, other)
1025 
1026 
1027  def get_version_info(self):
1028  """get_version_info(DensityMap self) -> VersionInfo"""
1029  return _IMP_em.DensityMap_get_version_info(self)
1030 
1031 
1032  def lower_voxel_shift(self, loc, kdist, orig, ndim):
1033  """lower_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
1034  return _IMP_em.DensityMap_lower_voxel_shift(self, loc, kdist, orig, ndim)
1035 
1036 
1037  def upper_voxel_shift(self, loc, kdist, orig, ndim):
1038  """upper_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
1039  return _IMP_em.DensityMap_upper_voxel_shift(self, loc, kdist, orig, ndim)
1040 
1041 
1042  def get_rms_calculated(self):
1043  """get_rms_calculated(DensityMap self) -> bool"""
1044  return _IMP_em.DensityMap_get_rms_calculated(self)
1045 
1046 
1047  def get_dim_index_by_location(self, *args):
1048  """
1049  get_dim_index_by_location(DensityMap self, Vector3D v, int ind) -> int
1050  get_dim_index_by_location(DensityMap self, float loc_val, int ind) -> int
1051  """
1052  return _IMP_em.DensityMap_get_dim_index_by_location(self, *args)
1053 
1054 
1055  def __str__(self):
1056  """__str__(DensityMap self) -> std::string"""
1057  return _IMP_em.DensityMap___str__(self)
1058 
1059 
1060  def __repr__(self):
1061  """__repr__(DensityMap self) -> std::string"""
1062  return _IMP_em.DensityMap___repr__(self)
1063 
1064 
1065  @staticmethod
1066  def get_from(o):
1067  return _object_cast_to_DensityMap(o)
1068 
1069 DensityMap_swigregister = _IMP_em.DensityMap_swigregister
1070 DensityMap_swigregister(DensityMap)
1071 
1072 
1073 def get_bounding_box(*args):
1074  """
1075  get_bounding_box(DensityMap m, IMP::Float threshold) -> BoundingBox3D
1076  get_bounding_box(DensityMap m) -> BoundingBox3D
1077  """
1078  return _IMP_em.get_bounding_box(*args)
1079 
1080 def get_density(m, v):
1081  """get_density(DensityMap m, Vector3D v) -> double"""
1082  return _IMP_em.get_density(m, v)
1083 
1084 def get_transformed(*args):
1085  """
1086  get_transformed(DensityMap input, Transformation3D tr, double threshold) -> DensityMap
1087  get_transformed(DensityMap input, Transformation3D tr) -> DensityMap
1088  """
1089  return _IMP_em.get_transformed(*args)
1090 
1091 def get_resampled(input, scaling):
1092  """get_resampled(DensityMap input, double scaling) -> DensityMap"""
1093  return _IMP_em.get_resampled(input, scaling)
1094 
1095 def get_transformed_into(source, tr, into, calc_rms=True):
1096  """
1097  get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into, bool calc_rms=True)
1098  get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into)
1099  """
1100  return _IMP_em.get_transformed_into(source, tr, into, calc_rms)
1101 
1102 def get_transformed_into2(source, tr, into):
1103  """get_transformed_into2(DensityMap source, Transformation3D tr, DensityMap into)"""
1104  return _IMP_em.get_transformed_into2(source, tr, into)
1105 
1106 def get_interiors_intersect(d1, d2):
1107  """get_interiors_intersect(DensityMap d1, DensityMap d2) -> bool"""
1108  return _IMP_em.get_interiors_intersect(d1, d2)
1109 
1110 def get_segment(*args):
1111  """
1112  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
1113  get_segment(DensityMap map_to_segment, IMP::algebra::Vector3Ds vecs, float dist) -> DensityMap
1114  """
1115  return _IMP_em.get_segment(*args)
1116 
1117 def get_segment_by_masking(map_to_segment, mask, mas_threshold):
1118  """get_segment_by_masking(DensityMap map_to_segment, DensityMap mask, float mas_threshold) -> DensityMap"""
1119  return _IMP_em.get_segment_by_masking(map_to_segment, mask, mas_threshold)
1120 
1121 def binarize(orig_map, threshold, reverse=False):
1122  """
1123  binarize(DensityMap orig_map, float threshold, bool reverse=False) -> DensityMap
1124  binarize(DensityMap orig_map, float threshold) -> DensityMap
1125  """
1126  return _IMP_em.binarize(orig_map, threshold, reverse)
1127 
1128 def get_threshold_map(orig_map, threshold):
1129  """get_threshold_map(DensityMap orig_map, float threshold) -> DensityMap"""
1130  return _IMP_em.get_threshold_map(orig_map, threshold)
1131 
1132 def multiply(m1, m2):
1133  """multiply(DensityMap m1, DensityMap m2) -> DensityMap"""
1134  return _IMP_em.multiply(m1, m2)
1135 
1136 def convolute(m1, m2):
1137  """convolute(DensityMap m1, DensityMap m2) -> double"""
1138  return _IMP_em.convolute(m1, m2)
1139 
1140 def get_sum(m1):
1141  """get_sum(DensityMap m1) -> double"""
1142  return _IMP_em.get_sum(m1)
1143 
1144 def get_max_map(maps):
1145  """get_max_map(IMP::em::DensityMaps maps) -> DensityMap"""
1146  return _IMP_em.get_max_map(maps)
1147 
1148 def interpolate_map(in_map, new_spacing):
1149  """interpolate_map(DensityMap in_map, double new_spacing) -> DensityMap"""
1150  return _IMP_em.interpolate_map(in_map, new_spacing)
1151 
1152 def get_grid(in_map):
1153  """get_grid(DensityMap in_map) -> IMP::algebra::GridD< 3,IMP::algebra::DenseGridStorageD< 3,float >,float,IMP::algebra::DefaultEmbeddingD< 3 > >"""
1154  return _IMP_em.get_grid(in_map)
1155 
1156 def create_density_map(*args):
1157  """
1158  create_density_map(DensityMap other) -> DensityMap
1159  create_density_map(BoundingBox3D bb, double spacing) -> DensityMap
1160  create_density_map(int nx, int ny, int nz, double spacing) -> DensityMap
1161  create_density_map(DenseFloatGrid3D grid) -> DensityMap
1162  create_density_map(DenseDoubleGrid3D grid) -> DensityMap
1163  """
1164  return _IMP_em.create_density_map(*args)
1165 
1166 def get_binarized_interior(dmap):
1167  """get_binarized_interior(DensityMap dmap) -> DensityMap"""
1168  return _IMP_em.get_binarized_interior(dmap)
1169 
1170 def add_to_map(dm, pis):
1171  """add_to_map(DensityMap dm, IMP::Particles const & pis)"""
1172  return _IMP_em.add_to_map(dm, pis)
1173 class RadiusDependentDistanceMask(object):
1174  """Proxy of C++ IMP::em::RadiusDependentDistanceMask class."""
1175 
1176  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1177  __repr__ = _swig_repr
1178 
1179  def __init__(self, sampling_radius, header):
1180  """__init__(IMP::em::RadiusDependentDistanceMask self, float sampling_radius, DensityHeader header) -> RadiusDependentDistanceMask"""
1181  this = _IMP_em.new_RadiusDependentDistanceMask(sampling_radius, header)
1182  try:
1183  self.this.append(this)
1184  except __builtin__.Exception:
1185  self.this = this
1186 
1187  def get_neighbor_shift(self):
1188  """get_neighbor_shift(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1189  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_shift(self)
1190 
1191 
1192  def get_neighbor_dist(self):
1193  """get_neighbor_dist(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1194  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist(self)
1195 
1196 
1197  def get_neighbor_dist_exp(self):
1198  """get_neighbor_dist_exp(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1199  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist_exp(self)
1200 
1201 
1202  def show(self, out):
1203  """show(RadiusDependentDistanceMask self, _ostream out)"""
1204  return _IMP_em.RadiusDependentDistanceMask_show(self, out)
1205 
1206  __swig_destroy__ = _IMP_em.delete_RadiusDependentDistanceMask
1207  __del__ = lambda self: None
1208 RadiusDependentDistanceMask_swigregister = _IMP_em.RadiusDependentDistanceMask_swigregister
1209 RadiusDependentDistanceMask_swigregister(RadiusDependentDistanceMask)
1210 
1211 class DistanceMask(object):
1212  """Proxy of C++ IMP::em::DistanceMask class."""
1213 
1214  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1215  __repr__ = _swig_repr
1216 
1217  def __init__(self, *args):
1218  """
1219  __init__(IMP::em::DistanceMask self) -> DistanceMask
1220  __init__(IMP::em::DistanceMask self, DensityHeader header) -> DistanceMask
1221  """
1222  this = _IMP_em.new_DistanceMask(*args)
1223  try:
1224  self.this.append(this)
1225  except __builtin__.Exception:
1226  self.this = this
1227 
1228  def show(self, out):
1229  """show(DistanceMask self, _ostream out)"""
1230  return _IMP_em.DistanceMask_show(self, out)
1231 
1232 
1233  def is_mask_set(self, radius, eps=0.001):
1234  """
1235  is_mask_set(DistanceMask self, float radius, float eps=0.001) -> bool
1236  is_mask_set(DistanceMask self, float radius) -> bool
1237  """
1238  return _IMP_em.DistanceMask_is_mask_set(self, radius, eps)
1239 
1240  __swig_destroy__ = _IMP_em.delete_DistanceMask
1241  __del__ = lambda self: None
1242 DistanceMask_swigregister = _IMP_em.DistanceMask_swigregister
1243 DistanceMask_swigregister(DistanceMask)
1244 
1245 class EMReaderWriter(MapReaderWriter):
1246  """Proxy of C++ IMP::em::EMReaderWriter class."""
1247 
1248  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1249 
1250  def __str__(self):
1251  """__str__(EMReaderWriter self) -> std::string"""
1252  return _IMP_em.EMReaderWriter___str__(self)
1253 
1254 
1255  def __repr__(self):
1256  """__repr__(EMReaderWriter self) -> std::string"""
1257  return _IMP_em.EMReaderWriter___repr__(self)
1258 
1259 
1260  @staticmethod
1261  def get_from(o):
1262  return _object_cast_to_EMReaderWriter(o)
1263 
1264 
1265  def __init__(self):
1266  """__init__(IMP::em::EMReaderWriter self) -> EMReaderWriter"""
1267  this = _IMP_em.new_EMReaderWriter()
1268  try:
1269  self.this.append(this)
1270  except __builtin__.Exception:
1271  self.this = this
1272 EMReaderWriter_swigregister = _IMP_em.EMReaderWriter_swigregister
1273 EMReaderWriter_swigregister(EMReaderWriter)
1274 
1275 class XplorReaderWriter(MapReaderWriter):
1276  """Proxy of C++ IMP::em::XplorReaderWriter class."""
1277 
1278  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1279 
1280  def __str__(self):
1281  """__str__(XplorReaderWriter self) -> std::string"""
1282  return _IMP_em.XplorReaderWriter___str__(self)
1283 
1284 
1285  def __repr__(self):
1286  """__repr__(XplorReaderWriter self) -> std::string"""
1287  return _IMP_em.XplorReaderWriter___repr__(self)
1288 
1289 
1290  @staticmethod
1291  def get_from(o):
1292  return _object_cast_to_XplorReaderWriter(o)
1293 
1294 
1295  def __init__(self):
1296  """__init__(IMP::em::XplorReaderWriter self) -> XplorReaderWriter"""
1297  this = _IMP_em.new_XplorReaderWriter()
1298  try:
1299  self.this.append(this)
1300  except __builtin__.Exception:
1301  self.this = this
1302 XplorReaderWriter_swigregister = _IMP_em.XplorReaderWriter_swigregister
1303 XplorReaderWriter_swigregister(XplorReaderWriter)
1304 
1305 class MRCReaderWriter(MapReaderWriter):
1306  """Proxy of C++ IMP::em::MRCReaderWriter class."""
1307 
1308  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1309 
1310  def __init__(self, *args):
1311  """
1312  __init__(IMP::em::MRCReaderWriter self) -> MRCReaderWriter
1313  __init__(IMP::em::MRCReaderWriter self, std::string fn) -> MRCReaderWriter
1314  """
1315  this = _IMP_em.new_MRCReaderWriter(*args)
1316  try:
1317  self.this.append(this)
1318  except __builtin__.Exception:
1319  self.this = this
1320 
1321  def __str__(self):
1322  """__str__(MRCReaderWriter self) -> std::string"""
1323  return _IMP_em.MRCReaderWriter___str__(self)
1324 
1325 
1326  def __repr__(self):
1327  """__repr__(MRCReaderWriter self) -> std::string"""
1328  return _IMP_em.MRCReaderWriter___repr__(self)
1329 
1330 
1331  @staticmethod
1332  def get_from(o):
1333  return _object_cast_to_MRCReaderWriter(o)
1334 
1335 MRCReaderWriter_swigregister = _IMP_em.MRCReaderWriter_swigregister
1336 MRCReaderWriter_swigregister(MRCReaderWriter)
1337 
1338 class KernelParameters(object):
1339  """Proxy of C++ IMP::em::KernelParameters class."""
1340 
1341  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1342 
1343  def __init__(self, *args):
1344  """
1345  __init__(IMP::em::KernelParameters self) -> KernelParameters
1346  __init__(IMP::em::KernelParameters self, float resolution) -> KernelParameters
1347  """
1348  this = _IMP_em.new_KernelParameters(*args)
1349  try:
1350  self.this.append(this)
1351  except __builtin__.Exception:
1352  self.this = this
1353  __swig_destroy__ = _IMP_em.delete_KernelParameters
1354  __del__ = lambda self: None
1355 
1356  def get_rsig(self):
1357  """get_rsig(KernelParameters self) -> float"""
1358  return _IMP_em.KernelParameters_get_rsig(self)
1359 
1360 
1361  def get_rsigsq(self):
1362  """get_rsigsq(KernelParameters self) -> float"""
1363  return _IMP_em.KernelParameters_get_rsigsq(self)
1364 
1365 
1366  def get_inv_rsigsq(self):
1367  """get_inv_rsigsq(KernelParameters self) -> float"""
1368  return _IMP_em.KernelParameters_get_inv_rsigsq(self)
1369 
1370 
1371  def get_timessig(self):
1372  """get_timessig(KernelParameters self) -> float"""
1373  return _IMP_em.KernelParameters_get_timessig(self)
1374 
1375 
1376  def get_sq2pi3(self):
1377  """get_sq2pi3(KernelParameters self) -> float"""
1378  return _IMP_em.KernelParameters_get_sq2pi3(self)
1379 
1380 
1381  def get_rnormfac(self):
1382  """get_rnormfac(KernelParameters self) -> float"""
1383  return _IMP_em.KernelParameters_get_rnormfac(self)
1384 
1385 
1386  def get_rkdist(self):
1387  """get_rkdist(KernelParameters self) -> float"""
1388  return _IMP_em.KernelParameters_get_rkdist(self)
1389 
1390 
1391  def get_rkdistsq(self):
1392  """get_rkdistsq(KernelParameters self) -> float"""
1393  return _IMP_em.KernelParameters_get_rkdistsq(self)
1394 
1395 
1396  def get_lim(self):
1397  """get_lim(KernelParameters self) -> float"""
1398  return _IMP_em.KernelParameters_get_lim(self)
1399 
1400 
1401  def show(self, *args):
1402  """
1403  show(KernelParameters self, _ostream out)
1404  show(KernelParameters self)
1405  """
1406  return _IMP_em.KernelParameters_show(self, *args)
1407 
1408 
1409  def __str__(self):
1410  """__str__(KernelParameters self) -> std::string"""
1411  return _IMP_em.KernelParameters___str__(self)
1412 
1413 
1414  def __repr__(self):
1415  """__repr__(KernelParameters self) -> std::string"""
1416  return _IMP_em.KernelParameters___repr__(self)
1417 
1418 KernelParameters_swigregister = _IMP_em.KernelParameters_swigregister
1419 KernelParameters_swigregister(KernelParameters)
1420 
1421 GAUSSIAN = _IMP_em.GAUSSIAN
1422 BINARIZED_SPHERE = _IMP_em.BINARIZED_SPHERE
1423 SPHERE = _IMP_em.SPHERE
1424 class SampledDensityMap(DensityMap):
1425  """Proxy of C++ IMP::em::SampledDensityMap class."""
1426 
1427  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1428 
1429  def __init__(self, *args):
1430  """
1431  __init__(IMP::em::SampledDensityMap self, IMP::em::KernelType kt) -> SampledDensityMap
1432  __init__(IMP::em::SampledDensityMap self) -> SampledDensityMap
1433  __init__(IMP::em::SampledDensityMap self, DensityHeader header, IMP::em::KernelType kt) -> SampledDensityMap
1434  __init__(IMP::em::SampledDensityMap self, DensityHeader header) -> SampledDensityMap
1435  __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
1436  __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
1437  __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size, FloatKey mass_key) -> SampledDensityMap
1438  __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size) -> SampledDensityMap
1439  """
1440  this = _IMP_em.new_SampledDensityMap(*args)
1441  try:
1442  self.this.append(this)
1443  except __builtin__.Exception:
1444  self.this = this
1445 
1446  def resample(self):
1447  """resample(SampledDensityMap self)"""
1448  return _IMP_em.SampledDensityMap_resample(self)
1449 
1450 
1451  def project(self, *args):
1452  """
1453  project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin, Vector3D shift, FloatKey mass_key)
1454  project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin, Vector3D shift)
1455  project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin)
1456  """
1457  return _IMP_em.SampledDensityMap_project(self, *args)
1458 
1459 
1460  def set_particles(self, *args):
1461  """
1462  set_particles(SampledDensityMap self, IMP::ParticlesTemp const & ps, FloatKey mass_key)
1463  set_particles(SampledDensityMap self, IMP::ParticlesTemp const & ps)
1464  """
1465  return _IMP_em.SampledDensityMap_set_particles(self, *args)
1466 
1467 
1468  def get_xyzr_particles(self):
1469  """get_xyzr_particles(SampledDensityMap self) -> IMP::core::XYZRs const &"""
1470  return _IMP_em.SampledDensityMap_get_xyzr_particles(self)
1471 
1472 
1473  def get_sampled_particles(self):
1474  """get_sampled_particles(SampledDensityMap self) -> IMP::Particles const &"""
1475  return _IMP_em.SampledDensityMap_get_sampled_particles(self)
1476 
1477 
1478  def get_weight_key(self):
1479  """get_weight_key(SampledDensityMap self) -> FloatKey"""
1480  return _IMP_em.SampledDensityMap_get_weight_key(self)
1481 
1482 
1483  def get_minimum_resampled_value(self):
1484  """get_minimum_resampled_value(SampledDensityMap self) -> float"""
1485  return _IMP_em.SampledDensityMap_get_minimum_resampled_value(self)
1486 
1487 
1488  def update_resolution(self, res):
1489  """update_resolution(SampledDensityMap self, IMP::Float res)"""
1490  return _IMP_em.SampledDensityMap_update_resolution(self, res)
1491 
1492  __swig_destroy__ = _IMP_em.delete_SampledDensityMap
1493  __del__ = lambda self: None
1494 
1495  def __str__(self):
1496  """__str__(SampledDensityMap self) -> std::string"""
1497  return _IMP_em.SampledDensityMap___str__(self)
1498 
1499 
1500  def __repr__(self):
1501  """__repr__(SampledDensityMap self) -> std::string"""
1502  return _IMP_em.SampledDensityMap___repr__(self)
1503 
1504 
1505  @staticmethod
1506  def get_from(o):
1507  return _object_cast_to_SampledDensityMap(o)
1508 
1509 SampledDensityMap_swigregister = _IMP_em.SampledDensityMap_swigregister
1510 SampledDensityMap_swigregister(SampledDensityMap)
1511 
1512 IMP_DEFAULT_NUM_SHELLS = _IMP_em.IMP_DEFAULT_NUM_SHELLS
1513 IMP_SIG_CUTOFF = _IMP_em.IMP_SIG_CUTOFF
1514 class SurfaceShellDensityMap(SampledDensityMap):
1515  """Proxy of C++ IMP::em::SurfaceShellDensityMap class."""
1516 
1517  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1518 
1519  def __init__(self, *args):
1520  """
1521  __init__(IMP::em::SurfaceShellDensityMap self) -> SurfaceShellDensityMap
1522  __init__(IMP::em::SurfaceShellDensityMap self, DensityHeader header) -> SurfaceShellDensityMap
1523  __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key, int num_shells=5) -> SurfaceShellDensityMap
1524  __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key) -> SurfaceShellDensityMap
1525  __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size) -> SurfaceShellDensityMap
1526  """
1527  this = _IMP_em.new_SurfaceShellDensityMap(*args)
1528  try:
1529  self.this.append(this)
1530  except __builtin__.Exception:
1531  self.this = this
1532 
1533  def binarize(self, scene_val):
1534  """binarize(SurfaceShellDensityMap self, float scene_val)"""
1535  return _IMP_em.SurfaceShellDensityMap_binarize(self, scene_val)
1536 
1537 
1538  def has_background_neighbor(self, voxel_ind):
1539  """has_background_neighbor(SurfaceShellDensityMap self, long voxel_ind) -> bool"""
1540  return _IMP_em.SurfaceShellDensityMap_has_background_neighbor(self, voxel_ind)
1541 
1542  __swig_destroy__ = _IMP_em.delete_SurfaceShellDensityMap
1543  __del__ = lambda self: None
1544 
1545  def __str__(self):
1546  """__str__(SurfaceShellDensityMap self) -> std::string"""
1547  return _IMP_em.SurfaceShellDensityMap___str__(self)
1548 
1549 
1550  def __repr__(self):
1551  """__repr__(SurfaceShellDensityMap self) -> std::string"""
1552  return _IMP_em.SurfaceShellDensityMap___repr__(self)
1553 
1554 
1555  @staticmethod
1556  def get_from(o):
1557  return _object_cast_to_SurfaceShellDensityMap(o)
1558 
1559 SurfaceShellDensityMap_swigregister = _IMP_em.SurfaceShellDensityMap_swigregister
1560 SurfaceShellDensityMap_swigregister(SurfaceShellDensityMap)
1561 
1562 class CoarseCC(IMP.Object):
1563  """Proxy of C++ IMP::em::CoarseCC class."""
1564 
1565  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1566 
1567  def __init__(self):
1568  """__init__(IMP::em::CoarseCC self) -> CoarseCC"""
1569  this = _IMP_em.new_CoarseCC()
1570  try:
1571  self.this.append(this)
1572  except __builtin__.Exception:
1573  self.this = this
1574 
1575  def calc_score(*args):
1576  """
1577  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True, IMP::FloatPair norm_factors) -> float
1578  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True) -> float
1579  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1580  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1581  """
1582  return _IMP_em.CoarseCC_calc_score(*args)
1583 
1584  calc_score = staticmethod(calc_score)
1585 
1586  def cross_correlation_coefficient(*args):
1587  """
1588  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False, IMP::FloatPair norm_factors) -> double
1589  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1590  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1591  """
1592  return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1593 
1594  cross_correlation_coefficient = staticmethod(cross_correlation_coefficient)
1595 
1596  def local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold):
1597  """local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1598  return _IMP_em.CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold)
1599 
1600  local_cross_correlation_coefficient = staticmethod(local_cross_correlation_coefficient)
1601 
1602  def get_version_info(self):
1603  """get_version_info(CoarseCC self) -> VersionInfo"""
1604  return _IMP_em.CoarseCC_get_version_info(self)
1605 
1606 
1607  def __str__(self):
1608  """__str__(CoarseCC self) -> std::string"""
1609  return _IMP_em.CoarseCC___str__(self)
1610 
1611 
1612  def __repr__(self):
1613  """__repr__(CoarseCC self) -> std::string"""
1614  return _IMP_em.CoarseCC___repr__(self)
1615 
1616 
1617  @staticmethod
1618  def get_from(o):
1619  return _object_cast_to_CoarseCC(o)
1620 
1621 CoarseCC_swigregister = _IMP_em.CoarseCC_swigregister
1622 CoarseCC_swigregister(CoarseCC)
1623 
1624 def CoarseCC_calc_score(*args):
1625  """
1626  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True, IMP::FloatPair norm_factors) -> float
1627  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True) -> float
1628  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1629  CoarseCC_calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1630  """
1631  return _IMP_em.CoarseCC_calc_score(*args)
1632 
1633 def CoarseCC_cross_correlation_coefficient(*args):
1634  """
1635  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False, IMP::FloatPair norm_factors) -> double
1636  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1637  CoarseCC_cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1638  """
1639  return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1640 
1641 def CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold):
1642  """CoarseCC_local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1643  return _IMP_em.CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold)
1644 
1645 class CoarseConvolution(object):
1646  """Proxy of C++ IMP::em::CoarseConvolution class."""
1647 
1648  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1649  __repr__ = _swig_repr
1650 
1651  def convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac=True):
1652  """
1653  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1654  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1655  """
1656  return _IMP_em.CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac)
1657 
1658  convolution = staticmethod(convolution)
1659 
1660  def __init__(self):
1661  """__init__(IMP::em::CoarseConvolution self) -> CoarseConvolution"""
1662  this = _IMP_em.new_CoarseConvolution()
1663  try:
1664  self.this.append(this)
1665  except __builtin__.Exception:
1666  self.this = this
1667  __swig_destroy__ = _IMP_em.delete_CoarseConvolution
1668  __del__ = lambda self: None
1669 CoarseConvolution_swigregister = _IMP_em.CoarseConvolution_swigregister
1670 CoarseConvolution_swigregister(CoarseConvolution)
1671 
1672 def CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac=True):
1673  """
1674  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1675  CoarseConvolution_convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1676  """
1677  return _IMP_em.CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac)
1678 
1679 class CoarseCCatIntervals(CoarseCC):
1680  """Proxy of C++ IMP::em::CoarseCCatIntervals class."""
1681 
1682  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1683 
1684  def __init__(self, *args):
1685  """
1686  __init__(IMP::em::CoarseCCatIntervals self, int const & ncd) -> CoarseCCatIntervals
1687  __init__(IMP::em::CoarseCCatIntervals self) -> CoarseCCatIntervals
1688  """
1689  this = _IMP_em.new_CoarseCCatIntervals(*args)
1690  try:
1691  self.this.append(this)
1692  except __builtin__.Exception:
1693  self.this = this
1694 
1695  def evaluate(self, em_map, model_map, deriv, scalefac, lderiv, eval_interval):
1696  """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 >"""
1697  return _IMP_em.CoarseCCatIntervals_evaluate(self, em_map, model_map, deriv, scalefac, lderiv, eval_interval)
1698 
1699 
1700  def __str__(self):
1701  """__str__(CoarseCCatIntervals self) -> std::string"""
1702  return _IMP_em.CoarseCCatIntervals___str__(self)
1703 
1704 
1705  def __repr__(self):
1706  """__repr__(CoarseCCatIntervals self) -> std::string"""
1707  return _IMP_em.CoarseCCatIntervals___repr__(self)
1708 
1709 
1710  @staticmethod
1711  def get_from(o):
1712  return _object_cast_to_CoarseCCatIntervals(o)
1713 
1714 CoarseCCatIntervals_swigregister = _IMP_em.CoarseCCatIntervals_swigregister
1715 CoarseCCatIntervals_swigregister(CoarseCCatIntervals)
1716 
1717 class FitRestraint(IMP.Restraint):
1718  """Proxy of C++ IMP::em::FitRestraint class."""
1719 
1720  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1721 
1722  def __init__(self, *args):
1723  """
1724  __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
1725  __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
1726  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key, float scale=1) -> FitRestraint
1727  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key) -> FitRestraint
1728  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors) -> FitRestraint
1729  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map) -> FitRestraint
1730  """
1731  this = _IMP_em.new_FitRestraint(*args)
1732  try:
1733  self.this.append(this)
1734  except __builtin__.Exception:
1735  self.this = this
1736 
1737  def get_model_dens_map(self):
1738  """get_model_dens_map(FitRestraint self) -> SampledDensityMap"""
1739  return _IMP_em.FitRestraint_get_model_dens_map(self)
1740 
1741 
1742  def set_scale_factor(self, scale):
1743  """set_scale_factor(FitRestraint self, float scale)"""
1744  return _IMP_em.FitRestraint_set_scale_factor(self, scale)
1745 
1746 
1747  def get_scale_factor(self):
1748  """get_scale_factor(FitRestraint self) -> float"""
1749  return _IMP_em.FitRestraint_get_scale_factor(self)
1750 
1751 
1752  def do_get_inputs(self):
1753  """do_get_inputs(FitRestraint self) -> IMP::ModelObjectsTemp"""
1754  return _IMP_em.FitRestraint_do_get_inputs(self)
1755 
1756 
1757  def get_version_info(self):
1758  """get_version_info(FitRestraint self) -> VersionInfo"""
1759  return _IMP_em.FitRestraint_get_version_info(self)
1760 
1761 
1762  def __str__(self):
1763  """__str__(FitRestraint self) -> std::string"""
1764  return _IMP_em.FitRestraint___str__(self)
1765 
1766 
1767  def __repr__(self):
1768  """__repr__(FitRestraint self) -> std::string"""
1769  return _IMP_em.FitRestraint___repr__(self)
1770 
1771 
1772  @staticmethod
1773  def get_from(o):
1774  return _object_cast_to_FitRestraint(o)
1775 
1776 
1777  def cast(r):
1778  """cast(Restraint r) -> FitRestraint"""
1779  return _IMP_em.FitRestraint_cast(r)
1780 
1781  cast = staticmethod(cast)
1782 FitRestraint_swigregister = _IMP_em.FitRestraint_swigregister
1783 FitRestraint_swigregister(FitRestraint)
1784 
1785 def FitRestraint_cast(r):
1786  """FitRestraint_cast(Restraint r) -> FitRestraint"""
1787  return _IMP_em.FitRestraint_cast(r)
1788 
1789 
1790 def density2particles(dmap, threshold, m, step=1):
1791  """
1792  density2particles(DensityMap dmap, IMP::Float threshold, Model m, int step=1) -> IMP::Particles
1793  density2particles(DensityMap dmap, IMP::Float threshold, Model m) -> IMP::Particles
1794  """
1795  return _IMP_em.density2particles(dmap, threshold, m, step)
1796 
1797 def density2vectors(dmap, threshold):
1798  """density2vectors(DensityMap dmap, IMP::Float threshold) -> IMP::algebra::Vector3Ds"""
1799  return _IMP_em.density2vectors(dmap, threshold)
1800 
1801 def particles2density(*args):
1802  """
1803  particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3, FloatKey weight_key) -> SampledDensityMap
1804  particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
1805  particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
1806  """
1807  return _IMP_em.particles2density(*args)
1808 
1809 def particles2binarized_density(*args):
1810  """
1811  particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3, FloatKey weight_key) -> SampledDensityMap
1812  particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
1813  particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
1814  """
1815  return _IMP_em.particles2binarized_density(*args)
1816 
1817 def particles2surface(*args):
1818  """
1819  particles2surface(IMP::ParticlesTemp const & ps, IMP::Float apix, FloatKey weight_key) -> SurfaceShellDensityMap
1820  particles2surface(IMP::ParticlesTemp const & ps, IMP::Float apix) -> SurfaceShellDensityMap
1821  """
1822  return _IMP_em.particles2surface(*args)
1823 
1824 def calculate_intersection_score(d1, d2):
1825  """calculate_intersection_score(SurfaceShellDensityMap d1, SurfaceShellDensityMap d2) -> IMP::Float"""
1826  return _IMP_em.calculate_intersection_score(d1, d2)
1827 class SpiderHeader(object):
1828  """Proxy of C++ IMP::em::SpiderHeader class."""
1829 
1830  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1831  __repr__ = _swig_repr
1832  fNslice = _swig_property(_IMP_em.SpiderHeader_fNslice_get, _IMP_em.SpiderHeader_fNslice_set)
1833  fNrow = _swig_property(_IMP_em.SpiderHeader_fNrow_get, _IMP_em.SpiderHeader_fNrow_set)
1834  fNrec = _swig_property(_IMP_em.SpiderHeader_fNrec_get, _IMP_em.SpiderHeader_fNrec_set)
1835  fNlabel = _swig_property(_IMP_em.SpiderHeader_fNlabel_get, _IMP_em.SpiderHeader_fNlabel_set)
1836  fIform = _swig_property(_IMP_em.SpiderHeader_fIform_get, _IMP_em.SpiderHeader_fIform_set)
1837  fImami = _swig_property(_IMP_em.SpiderHeader_fImami_get, _IMP_em.SpiderHeader_fImami_set)
1838  fFmax = _swig_property(_IMP_em.SpiderHeader_fFmax_get, _IMP_em.SpiderHeader_fFmax_set)
1839  fFmin = _swig_property(_IMP_em.SpiderHeader_fFmin_get, _IMP_em.SpiderHeader_fFmin_set)
1840  fAv = _swig_property(_IMP_em.SpiderHeader_fAv_get, _IMP_em.SpiderHeader_fAv_set)
1841  fSig = _swig_property(_IMP_em.SpiderHeader_fSig_get, _IMP_em.SpiderHeader_fSig_set)
1842  fIhist = _swig_property(_IMP_em.SpiderHeader_fIhist_get, _IMP_em.SpiderHeader_fIhist_set)
1843  fNcol = _swig_property(_IMP_em.SpiderHeader_fNcol_get, _IMP_em.SpiderHeader_fNcol_set)
1844  fLabrec = _swig_property(_IMP_em.SpiderHeader_fLabrec_get, _IMP_em.SpiderHeader_fLabrec_set)
1845  fIangle = _swig_property(_IMP_em.SpiderHeader_fIangle_get, _IMP_em.SpiderHeader_fIangle_set)
1846  fPhi = _swig_property(_IMP_em.SpiderHeader_fPhi_get, _IMP_em.SpiderHeader_fPhi_set)
1847  fTheta = _swig_property(_IMP_em.SpiderHeader_fTheta_get, _IMP_em.SpiderHeader_fTheta_set)
1848  fPsi = _swig_property(_IMP_em.SpiderHeader_fPsi_get, _IMP_em.SpiderHeader_fPsi_set)
1849  fXoff = _swig_property(_IMP_em.SpiderHeader_fXoff_get, _IMP_em.SpiderHeader_fXoff_set)
1850  fYoff = _swig_property(_IMP_em.SpiderHeader_fYoff_get, _IMP_em.SpiderHeader_fYoff_set)
1851  fZoff = _swig_property(_IMP_em.SpiderHeader_fZoff_get, _IMP_em.SpiderHeader_fZoff_set)
1852  fScale = _swig_property(_IMP_em.SpiderHeader_fScale_get, _IMP_em.SpiderHeader_fScale_set)
1853  fLabbyt = _swig_property(_IMP_em.SpiderHeader_fLabbyt_get, _IMP_em.SpiderHeader_fLabbyt_set)
1854  fLenbyt = _swig_property(_IMP_em.SpiderHeader_fLenbyt_get, _IMP_em.SpiderHeader_fLenbyt_set)
1855  fNothing = _swig_property(_IMP_em.SpiderHeader_fNothing_get, _IMP_em.SpiderHeader_fNothing_set)
1856  fFlag = _swig_property(_IMP_em.SpiderHeader_fFlag_get, _IMP_em.SpiderHeader_fFlag_set)
1857  fPhi1 = _swig_property(_IMP_em.SpiderHeader_fPhi1_get, _IMP_em.SpiderHeader_fPhi1_set)
1858  fTheta1 = _swig_property(_IMP_em.SpiderHeader_fTheta1_get, _IMP_em.SpiderHeader_fTheta1_set)
1859  fPsi1 = _swig_property(_IMP_em.SpiderHeader_fPsi1_get, _IMP_em.SpiderHeader_fPsi1_set)
1860  fPhi2 = _swig_property(_IMP_em.SpiderHeader_fPhi2_get, _IMP_em.SpiderHeader_fPhi2_set)
1861  fTheta2 = _swig_property(_IMP_em.SpiderHeader_fTheta2_get, _IMP_em.SpiderHeader_fTheta2_set)
1862  fPsi2 = _swig_property(_IMP_em.SpiderHeader_fPsi2_get, _IMP_em.SpiderHeader_fPsi2_set)
1863  fGeo_matrix = _swig_property(_IMP_em.SpiderHeader_fGeo_matrix_get, _IMP_em.SpiderHeader_fGeo_matrix_set)
1864  fAngle1 = _swig_property(_IMP_em.SpiderHeader_fAngle1_get, _IMP_em.SpiderHeader_fAngle1_set)
1865  fr1 = _swig_property(_IMP_em.SpiderHeader_fr1_get, _IMP_em.SpiderHeader_fr1_set)
1866  fr2 = _swig_property(_IMP_em.SpiderHeader_fr2_get, _IMP_em.SpiderHeader_fr2_set)
1867  RTflag = _swig_property(_IMP_em.SpiderHeader_RTflag_get, _IMP_em.SpiderHeader_RTflag_set)
1868  Astart = _swig_property(_IMP_em.SpiderHeader_Astart_get, _IMP_em.SpiderHeader_Astart_set)
1869  Aend = _swig_property(_IMP_em.SpiderHeader_Aend_get, _IMP_em.SpiderHeader_Aend_set)
1870  Ainc = _swig_property(_IMP_em.SpiderHeader_Ainc_get, _IMP_em.SpiderHeader_Ainc_set)
1871  Rsigma = _swig_property(_IMP_em.SpiderHeader_Rsigma_get, _IMP_em.SpiderHeader_Rsigma_set)
1872  Tstart = _swig_property(_IMP_em.SpiderHeader_Tstart_get, _IMP_em.SpiderHeader_Tstart_set)
1873  Tend = _swig_property(_IMP_em.SpiderHeader_Tend_get, _IMP_em.SpiderHeader_Tend_set)
1874  Tinc = _swig_property(_IMP_em.SpiderHeader_Tinc_get, _IMP_em.SpiderHeader_Tinc_set)
1875  Weight = _swig_property(_IMP_em.SpiderHeader_Weight_get, _IMP_em.SpiderHeader_Weight_set)
1876  Flip = _swig_property(_IMP_em.SpiderHeader_Flip_get, _IMP_em.SpiderHeader_Flip_set)
1877  empty = _swig_property(_IMP_em.SpiderHeader_empty_get, _IMP_em.SpiderHeader_empty_set)
1878  szIDat = _swig_property(_IMP_em.SpiderHeader_szIDat_get, _IMP_em.SpiderHeader_szIDat_set)
1879  szITim = _swig_property(_IMP_em.SpiderHeader_szITim_get, _IMP_em.SpiderHeader_szITim_set)
1880  szITit = _swig_property(_IMP_em.SpiderHeader_szITit_get, _IMP_em.SpiderHeader_szITit_set)
1881 
1882  def show(self, out):
1883  """show(SpiderHeader self, _ostream out)"""
1884  return _IMP_em.SpiderHeader_show(self, out)
1885 
1886 
1887  def __init__(self):
1888  """__init__(IMP::em::SpiderHeader self) -> SpiderHeader"""
1889  this = _IMP_em.new_SpiderHeader()
1890  try:
1891  self.this.append(this)
1892  except __builtin__.Exception:
1893  self.this = this
1894  __swig_destroy__ = _IMP_em.delete_SpiderHeader
1895  __del__ = lambda self: None
1896 SpiderHeader_swigregister = _IMP_em.SpiderHeader_swigregister
1897 SpiderHeader_swigregister(SpiderHeader)
1898 
1899 class ImageHeader(object):
1900  """Proxy of C++ IMP::em::ImageHeader class."""
1901 
1902  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1903  __repr__ = _swig_repr
1904  IMG_BYTE = _IMP_em.ImageHeader_IMG_BYTE
1905  IMG_IMPEM = _IMP_em.ImageHeader_IMG_IMPEM
1906  IMG_INT = _IMP_em.ImageHeader_IMG_INT
1907  VOL_BYTE = _IMP_em.ImageHeader_VOL_BYTE
1908  VOL_IMPEM = _IMP_em.ImageHeader_VOL_IMPEM
1909  VOL_INT = _IMP_em.ImageHeader_VOL_INT
1910  IMG_FOURIER = _IMP_em.ImageHeader_IMG_FOURIER
1911  VOL_FOURIER = _IMP_em.ImageHeader_VOL_FOURIER
1912 
1913  def __init__(self, *args):
1914  """
1915  __init__(IMP::em::ImageHeader self) -> ImageHeader
1916  __init__(IMP::em::ImageHeader self, IMP::em::ImageHeader::img_type im) -> ImageHeader
1917  __init__(IMP::em::ImageHeader self, float im) -> ImageHeader
1918  """
1919  this = _IMP_em.new_ImageHeader(*args)
1920  try:
1921  self.this.append(this)
1922  except __builtin__.Exception:
1923  self.this = this
1924 
1925  def get_image_type(self):
1926  """get_image_type(ImageHeader self) -> float"""
1927  return _IMP_em.ImageHeader_get_image_type(self)
1928 
1929 
1930  def set_image_type(self, *args):
1931  """
1932  set_image_type(ImageHeader self, IMP::em::ImageHeader::img_type im)
1933  set_image_type(ImageHeader self, float im)
1934  """
1935  return _IMP_em.ImageHeader_set_image_type(self, *args)
1936 
1937 
1938  def do_show(self, out):
1939  """do_show(ImageHeader self, _ostream out)"""
1940  return _IMP_em.ImageHeader_do_show(self, out)
1941 
1942 
1943  def show(self, *args):
1944  """
1945  show(ImageHeader self, _ostream out)
1946  show(ImageHeader self)
1947  """
1948  return _IMP_em.ImageHeader_show(self, *args)
1949 
1950 
1951  def print_hard(self, out):
1952  """print_hard(ImageHeader self, _ostream out)"""
1953  return _IMP_em.ImageHeader_print_hard(self, out)
1954 
1955 
1956  def show_projection_params(self, out):
1957  """show_projection_params(ImageHeader self, _ostream out)"""
1958  return _IMP_em.ImageHeader_show_projection_params(self, out)
1959 
1960 
1961  def read(self, *args):
1962  """
1963  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False, bool skip_extra_checkings=False) -> int
1964  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False) -> int
1965  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False) -> int
1966  read(ImageHeader self, IMP::String const filename) -> int
1967  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False, bool skip_extra_checkings=False) -> bool
1968  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False) -> bool
1969  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False) -> bool
1970  read(ImageHeader self, std::ifstream & f) -> bool
1971  """
1972  return _IMP_em.ImageHeader_read(self, *args)
1973 
1974 
1975  def write(self, *args):
1976  """
1977  write(ImageHeader self, IMP::String const & filename, bool force_reversed=False)
1978  write(ImageHeader self, IMP::String const & filename)
1979  write(ImageHeader self, std::ofstream & f, bool force_reversed=False)
1980  write(ImageHeader self, std::ofstream & f)
1981  """
1982  return _IMP_em.ImageHeader_write(self, *args)
1983 
1984 
1985  def clear(self):
1986  """clear(ImageHeader self)"""
1987  return _IMP_em.ImageHeader_clear(self)
1988 
1989 
1990  def set_header(self):
1991  """set_header(ImageHeader self)"""
1992  return _IMP_em.ImageHeader_set_header(self)
1993 
1994 
1995  def get_reversed(self):
1996  """get_reversed(ImageHeader self) -> bool"""
1997  return _IMP_em.ImageHeader_get_reversed(self)
1998 
1999 
2000  def set_reversed(self, value):
2001  """set_reversed(ImageHeader self, bool value)"""
2002  return _IMP_em.ImageHeader_set_reversed(self, value)
2003 
2004 
2005  def get_number_of_slices(self):
2006  """get_number_of_slices(ImageHeader self) -> unsigned int"""
2007  return _IMP_em.ImageHeader_get_number_of_slices(self)
2008 
2009 
2010  def set_number_of_slices(self, n):
2011  """set_number_of_slices(ImageHeader self, unsigned int n)"""
2012  return _IMP_em.ImageHeader_set_number_of_slices(self, n)
2013 
2014 
2015  def get_number_of_rows(self):
2016  """get_number_of_rows(ImageHeader self) -> unsigned int"""
2017  return _IMP_em.ImageHeader_get_number_of_rows(self)
2018 
2019 
2020  def set_number_of_rows(self, n):
2021  """set_number_of_rows(ImageHeader self, unsigned int n)"""
2022  return _IMP_em.ImageHeader_set_number_of_rows(self, n)
2023 
2024 
2025  def get_number_of_columns(self):
2026  """get_number_of_columns(ImageHeader self) -> unsigned int"""
2027  return _IMP_em.ImageHeader_get_number_of_columns(self)
2028 
2029 
2030  def set_number_of_columns(self, n):
2031  """set_number_of_columns(ImageHeader self, unsigned int n)"""
2032  return _IMP_em.ImageHeader_set_number_of_columns(self, n)
2033 
2034 
2035  def get_old_rot(self):
2036  """get_old_rot(ImageHeader self) -> float"""
2037  return _IMP_em.ImageHeader_get_old_rot(self)
2038 
2039 
2040  def set_old_rot(self, value):
2041  """set_old_rot(ImageHeader self, float value)"""
2042  return _IMP_em.ImageHeader_set_old_rot(self, value)
2043 
2044 
2045  def get_fAngle1(self):
2046  """get_fAngle1(ImageHeader self) -> float"""
2047  return _IMP_em.ImageHeader_get_fAngle1(self)
2048 
2049 
2050  def set_fAngle1(self, value):
2051  """set_fAngle1(ImageHeader self, float value)"""
2052  return _IMP_em.ImageHeader_set_fAngle1(self, value)
2053 
2054 
2055  def get_Scale(self):
2056  """get_Scale(ImageHeader self) -> float"""
2057  return _IMP_em.ImageHeader_get_Scale(self)
2058 
2059 
2060  def set_Scale(self, value):
2061  """set_Scale(ImageHeader self, float value)"""
2062  return _IMP_em.ImageHeader_set_Scale(self, value)
2063 
2064 
2065  def get_Flip(self):
2066  """get_Flip(ImageHeader self) -> float"""
2067  return _IMP_em.ImageHeader_get_Flip(self)
2068 
2069 
2070  def set_Flip(self, value):
2071  """set_Flip(ImageHeader self, float value)"""
2072  return _IMP_em.ImageHeader_set_Flip(self, value)
2073 
2074 
2075  def get_Weight(self):
2076  """get_Weight(ImageHeader self) -> float"""
2077  return _IMP_em.ImageHeader_get_Weight(self)
2078 
2079 
2080  def set_Weight(self, value):
2081  """set_Weight(ImageHeader self, float value)"""
2082  return _IMP_em.ImageHeader_set_Weight(self, value)
2083 
2084 
2085  def get_fNrec(self):
2086  """get_fNrec(ImageHeader self) -> float"""
2087  return _IMP_em.ImageHeader_get_fNrec(self)
2088 
2089 
2090  def set_fNrec(self, value):
2091  """set_fNrec(ImageHeader self, float value)"""
2092  return _IMP_em.ImageHeader_set_fNrec(self, value)
2093 
2094 
2095  def get_fNlabel(self):
2096  """get_fNlabel(ImageHeader self) -> float"""
2097  return _IMP_em.ImageHeader_get_fNlabel(self)
2098 
2099 
2100  def set_fNlabel(self, value):
2101  """set_fNlabel(ImageHeader self, float value)"""
2102  return _IMP_em.ImageHeader_set_fNlabel(self, value)
2103 
2104 
2105  def get_fIform(self):
2106  """get_fIform(ImageHeader self) -> float"""
2107  return _IMP_em.ImageHeader_get_fIform(self)
2108 
2109 
2110  def set_fIform(self, value):
2111  """set_fIform(ImageHeader self, float value)"""
2112  return _IMP_em.ImageHeader_set_fIform(self, value)
2113 
2114 
2115  def get_fImami(self):
2116  """get_fImami(ImageHeader self) -> float"""
2117  return _IMP_em.ImageHeader_get_fImami(self)
2118 
2119 
2120  def set_fImami(self, value):
2121  """set_fImami(ImageHeader self, float value)"""
2122  return _IMP_em.ImageHeader_set_fImami(self, value)
2123 
2124 
2125  def get_fFmax(self):
2126  """get_fFmax(ImageHeader self) -> float"""
2127  return _IMP_em.ImageHeader_get_fFmax(self)
2128 
2129 
2130  def set_fFmax(self, value):
2131  """set_fFmax(ImageHeader self, float value)"""
2132  return _IMP_em.ImageHeader_set_fFmax(self, value)
2133 
2134 
2135  def get_fFmin(self):
2136  """get_fFmin(ImageHeader self) -> float"""
2137  return _IMP_em.ImageHeader_get_fFmin(self)
2138 
2139 
2140  def set_fFmin(self, value):
2141  """set_fFmin(ImageHeader self, float value)"""
2142  return _IMP_em.ImageHeader_set_fFmin(self, value)
2143 
2144 
2145  def get_fAv(self):
2146  """get_fAv(ImageHeader self) -> float"""
2147  return _IMP_em.ImageHeader_get_fAv(self)
2148 
2149 
2150  def set_fAv(self, value):
2151  """set_fAv(ImageHeader self, float value)"""
2152  return _IMP_em.ImageHeader_set_fAv(self, value)
2153 
2154 
2155  def get_fSig(self):
2156  """get_fSig(ImageHeader self) -> float"""
2157  return _IMP_em.ImageHeader_get_fSig(self)
2158 
2159 
2160  def set_fSig(self, value):
2161  """set_fSig(ImageHeader self, float value)"""
2162  return _IMP_em.ImageHeader_set_fSig(self, value)
2163 
2164 
2165  def get_fIhist(self):
2166  """get_fIhist(ImageHeader self) -> float"""
2167  return _IMP_em.ImageHeader_get_fIhist(self)
2168 
2169 
2170  def set_fIhist(self, value):
2171  """set_fIhist(ImageHeader self, float value)"""
2172  return _IMP_em.ImageHeader_set_fIhist(self, value)
2173 
2174 
2175  def get_fLabrec(self):
2176  """get_fLabrec(ImageHeader self) -> float"""
2177  return _IMP_em.ImageHeader_get_fLabrec(self)
2178 
2179 
2180  def set_fLabrec(self, value):
2181  """set_fLabrec(ImageHeader self, float value)"""
2182  return _IMP_em.ImageHeader_set_fLabrec(self, value)
2183 
2184 
2185  def get_fIangle(self):
2186  """get_fIangle(ImageHeader self) -> float"""
2187  return _IMP_em.ImageHeader_get_fIangle(self)
2188 
2189 
2190  def set_fIangle(self, value):
2191  """set_fIangle(ImageHeader self, float value)"""
2192  return _IMP_em.ImageHeader_set_fIangle(self, value)
2193 
2194 
2195  def get_origin(self):
2196  """get_origin(ImageHeader self) -> Vector3D"""
2197  return _IMP_em.ImageHeader_get_origin(self)
2198 
2199 
2200  def set_origin(self, *args):
2201  """
2202  set_origin(ImageHeader self, Vector3D v)
2203  set_origin(ImageHeader self, Vector2D v)
2204  """
2205  return _IMP_em.ImageHeader_set_origin(self, *args)
2206 
2207 
2208  def get_object_pixel_size(self):
2209  """get_object_pixel_size(ImageHeader self) -> float"""
2210  return _IMP_em.ImageHeader_get_object_pixel_size(self)
2211 
2212 
2213  def set_object_pixel_size(self, value):
2214  """set_object_pixel_size(ImageHeader self, float value)"""
2215  return _IMP_em.ImageHeader_set_object_pixel_size(self, value)
2216 
2217 
2218  def get_fLabbyt(self):
2219  """get_fLabbyt(ImageHeader self) -> float"""
2220  return _IMP_em.ImageHeader_get_fLabbyt(self)
2221 
2222 
2223  def set_fLabbyt(self, value):
2224  """set_fLabbyt(ImageHeader self, float value)"""
2225  return _IMP_em.ImageHeader_set_fLabbyt(self, value)
2226 
2227 
2228  def get_fLenbyt(self):
2229  """get_fLenbyt(ImageHeader self) -> float"""
2230  return _IMP_em.ImageHeader_get_fLenbyt(self)
2231 
2232 
2233  def set_fLenbyt(self, value):
2234  """set_fLenbyt(ImageHeader self, float value)"""
2235  return _IMP_em.ImageHeader_set_fLenbyt(self, value)
2236 
2237 
2238  def get_fGeo_matrix(self, i, j):
2239  """get_fGeo_matrix(ImageHeader self, unsigned int i, unsigned int j) -> double"""
2240  return _IMP_em.ImageHeader_get_fGeo_matrix(self, i, j)
2241 
2242 
2243  def get_fFlag(self):
2244  """get_fFlag(ImageHeader self) -> float"""
2245  return _IMP_em.ImageHeader_get_fFlag(self)
2246 
2247 
2248  def set_fFlag(self, value):
2249  """set_fFlag(ImageHeader self, float value)"""
2250  return _IMP_em.ImageHeader_set_fFlag(self, value)
2251 
2252 
2253  def get_euler_angles(self):
2254  """get_euler_angles(ImageHeader self) -> Vector3D"""
2255  return _IMP_em.ImageHeader_get_euler_angles(self)
2256 
2257 
2258  def get_euler_angles1(self):
2259  """get_euler_angles1(ImageHeader self) -> Vector3D"""
2260  return _IMP_em.ImageHeader_get_euler_angles1(self)
2261 
2262 
2263  def get_euler_angles2(self):
2264  """get_euler_angles2(ImageHeader self) -> Vector3D"""
2265  return _IMP_em.ImageHeader_get_euler_angles2(self)
2266 
2267 
2268  def set_euler_angles(self, euler):
2269  """set_euler_angles(ImageHeader self, Vector3D euler)"""
2270  return _IMP_em.ImageHeader_set_euler_angles(self, euler)
2271 
2272 
2273  def set_euler_angles1(self, euler):
2274  """set_euler_angles1(ImageHeader self, Vector3D euler)"""
2275  return _IMP_em.ImageHeader_set_euler_angles1(self, euler)
2276 
2277 
2278  def set_euler_angles2(self, euler):
2279  """set_euler_angles2(ImageHeader self, Vector3D euler)"""
2280  return _IMP_em.ImageHeader_set_euler_angles2(self, euler)
2281 
2282 
2283  def is_normalized(self):
2284  """is_normalized(ImageHeader self) -> bool"""
2285  return _IMP_em.ImageHeader_is_normalized(self)
2286 
2287 
2288  def set_date(self):
2289  """set_date(ImageHeader self)"""
2290  return _IMP_em.ImageHeader_set_date(self)
2291 
2292 
2293  def set_time(self):
2294  """set_time(ImageHeader self)"""
2295  return _IMP_em.ImageHeader_set_time(self)
2296 
2297 
2298  def set_title(self, newName):
2299  """set_title(ImageHeader self, IMP::String newName)"""
2300  return _IMP_em.ImageHeader_set_title(self, newName)
2301 
2302  __swig_destroy__ = _IMP_em.delete_ImageHeader
2303  __del__ = lambda self: None
2304 ImageHeader_swigregister = _IMP_em.ImageHeader_swigregister
2305 ImageHeader_swigregister(ImageHeader)
2306 
2307 class SpiderMapReaderWriter(MapReaderWriter):
2308  """Proxy of C++ IMP::em::SpiderMapReaderWriter class."""
2309 
2310  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2311  filename_ = _swig_property(_IMP_em.SpiderMapReaderWriter_filename__get, _IMP_em.SpiderMapReaderWriter_filename__set)
2312  skip_type_check_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_type_check__get, _IMP_em.SpiderMapReaderWriter_skip_type_check__set)
2313  force_reversed_ = _swig_property(_IMP_em.SpiderMapReaderWriter_force_reversed__get, _IMP_em.SpiderMapReaderWriter_force_reversed__set)
2314  skip_extra_checkings_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_extra_checkings__get, _IMP_em.SpiderMapReaderWriter_skip_extra_checkings__set)
2315 
2316  def __init__(self, *args):
2317  """
2318  __init__(IMP::em::SpiderMapReaderWriter self) -> SpiderMapReaderWriter
2319  __init__(IMP::em::SpiderMapReaderWriter self, IMP::String filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings) -> SpiderMapReaderWriter
2320  """
2321  this = _IMP_em.new_SpiderMapReaderWriter(*args)
2322  try:
2323  self.this.append(this)
2324  except __builtin__.Exception:
2325  self.this = this
2326 
2327  def __str__(self):
2328  """__str__(SpiderMapReaderWriter self) -> std::string"""
2329  return _IMP_em.SpiderMapReaderWriter___str__(self)
2330 
2331 
2332  def __repr__(self):
2333  """__repr__(SpiderMapReaderWriter self) -> std::string"""
2334  return _IMP_em.SpiderMapReaderWriter___repr__(self)
2335 
2336 
2337  @staticmethod
2338  def get_from(o):
2339  return _object_cast_to_SpiderMapReaderWriter(o)
2340 
2341 SpiderMapReaderWriter_swigregister = _IMP_em.SpiderMapReaderWriter_swigregister
2342 SpiderMapReaderWriter_swigregister(SpiderMapReaderWriter)
2343 
2344 class FittingSolutions(object):
2345  """Proxy of C++ IMP::em::FittingSolutions class."""
2346 
2347  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2348 
2349  def __init__(self):
2350  """__init__(IMP::em::FittingSolutions self) -> FittingSolutions"""
2351  this = _IMP_em.new_FittingSolutions()
2352  try:
2353  self.this.append(this)
2354  except __builtin__.Exception:
2355  self.this = this
2356 
2357  def get_number_of_solutions(self):
2358  """get_number_of_solutions(FittingSolutions self) -> int"""
2359  return _IMP_em.FittingSolutions_get_number_of_solutions(self)
2360 
2361 
2362  def get_transformation(self, i):
2363  """get_transformation(FittingSolutions self, unsigned int i) -> Transformation3D"""
2364  return _IMP_em.FittingSolutions_get_transformation(self, i)
2365 
2366 
2367  def get_score(self, i):
2368  """get_score(FittingSolutions self, unsigned int i) -> IMP::Float"""
2369  return _IMP_em.FittingSolutions_get_score(self, i)
2370 
2371 
2372  def set_score(self, i, score):
2373  """set_score(FittingSolutions self, unsigned int i, IMP::Float score)"""
2374  return _IMP_em.FittingSolutions_set_score(self, i, score)
2375 
2376 
2377  def add_solution(self, t, score):
2378  """add_solution(FittingSolutions self, Transformation3D t, IMP::Float score)"""
2379  return _IMP_em.FittingSolutions_add_solution(self, t, score)
2380 
2381 
2382  def sort(self, reverse=False):
2383  """
2384  sort(FittingSolutions self, bool reverse=False)
2385  sort(FittingSolutions self)
2386  """
2387  return _IMP_em.FittingSolutions_sort(self, reverse)
2388 
2389 
2390  def multiply(self, t):
2391  """multiply(FittingSolutions self, Transformation3D t)"""
2392  return _IMP_em.FittingSolutions_multiply(self, t)
2393 
2394 
2395  def get_transformations(self):
2396  """get_transformations(FittingSolutions self) -> IMP::algebra::Transformation3Ds"""
2397  return _IMP_em.FittingSolutions_get_transformations(self)
2398 
2399 
2400  def show(self, *args):
2401  """
2402  show(FittingSolutions self, _ostream out)
2403  show(FittingSolutions self)
2404  """
2405  return _IMP_em.FittingSolutions_show(self, *args)
2406 
2407 
2408  def __str__(self):
2409  """__str__(FittingSolutions self) -> std::string"""
2410  return _IMP_em.FittingSolutions___str__(self)
2411 
2412 
2413  def __repr__(self):
2414  """__repr__(FittingSolutions self) -> std::string"""
2415  return _IMP_em.FittingSolutions___repr__(self)
2416 
2417  __swig_destroy__ = _IMP_em.delete_FittingSolutions
2418  __del__ = lambda self: None
2419 FittingSolutions_swigregister = _IMP_em.FittingSolutions_swigregister
2420 FittingSolutions_swigregister(FittingSolutions)
2421 
2422 
2423 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):
2424  """
2425  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
2426  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
2427  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
2428  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
2429  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
2430  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
2431  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log) -> FittingSolutions
2432  """
2433  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)
2434 
2435 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):
2436  """
2437  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
2438  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
2439  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
2440  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
2441  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
2442  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2443  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log) -> FittingSolutions
2444  """
2445  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)
2446 
2447 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):
2448  """
2449  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
2450  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
2451  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
2452  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
2453  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
2454  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
2455  """
2456  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)
2457 
2458 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):
2459  """
2460  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
2461  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
2462  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
2463  local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2) -> FittingSolutions
2464  local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap) -> FittingSolutions
2465  """
2466  return _IMP_em.local_rigid_fitting_grid_search(ps, wei_key, dmap, max_voxels_translation, translation_step, max_angle_in_radians, number_of_rotations)
2467 
2468 def compute_fitting_scores(*args):
2469  """
2470  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
2471  compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations, bool fast_version=False, bool local_score=False) -> FittingSolutions
2472  compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations, bool fast_version=False) -> FittingSolutions
2473  compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2474  compute_fitting_scores(DensityMap em_map, RigidBody rb, Refiner refiner, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2475  """
2476  return _IMP_em.compute_fitting_scores(*args)
2477 
2478 def compute_fitting_score(*args):
2479  """
2480  compute_fitting_score(IMP::ParticlesTemp const & ps, DensityMap em_map, FloatKey wei_key) -> IMP::Float
2481  compute_fitting_score(IMP::ParticlesTemp const & ps, DensityMap em_map) -> IMP::Float
2482  """
2483  return _IMP_em.compute_fitting_score(*args)
2484 
2486  """
2487  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, Transformation3D t, float thr=0.0) -> long
2488  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, Transformation3D t) -> long
2489  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps) -> long
2490  """
2491  return _IMP_em.get_number_of_particles_outside_of_the_density(*args)
2492 
2493 def get_numbers_of_particles_outside_of_the_density(dmap, ps, transformations, thr=0.0):
2494  """
2495  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
2496  get_numbers_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, IMP::algebra::Transformation3Ds const & transformations) -> IMP::Ints
2497  """
2498  return _IMP_em.get_numbers_of_particles_outside_of_the_density(dmap, ps, transformations, thr)
2499 
2501  """
2502  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3., Transformation3D t, float thr=0.0) -> double
2503  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3., Transformation3D t) -> double
2504  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3.) -> double
2505  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps) -> double
2506  """
2507  return _IMP_em.get_percentage_of_voxels_covered_by_particles(*args)
2508 class HighDensityEmbedding(IMP.statistics.Embedding):
2509  """Proxy of C++ IMP::em::HighDensityEmbedding class."""
2510 
2511  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2512 
2513  def __init__(self, dm, threshold):
2514  """__init__(IMP::em::HighDensityEmbedding self, DensityMap dm, double threshold) -> HighDensityEmbedding"""
2515  this = _IMP_em.new_HighDensityEmbedding(dm, threshold)
2516  try:
2517  self.this.append(this)
2518  except __builtin__.Exception:
2519  self.this = this
2520 
2521  def get_version_info(self):
2522  """get_version_info(HighDensityEmbedding self) -> VersionInfo"""
2523  return _IMP_em.HighDensityEmbedding_get_version_info(self)
2524 
2525 
2526  def __str__(self):
2527  """__str__(HighDensityEmbedding self) -> std::string"""
2528  return _IMP_em.HighDensityEmbedding___str__(self)
2529 
2530 
2531  def __repr__(self):
2532  """__repr__(HighDensityEmbedding self) -> std::string"""
2533  return _IMP_em.HighDensityEmbedding___repr__(self)
2534 
2535 
2536  @staticmethod
2537  def get_from(o):
2538  return _object_cast_to_HighDensityEmbedding(o)
2539 
2540 HighDensityEmbedding_swigregister = _IMP_em.HighDensityEmbedding_swigregister
2541 HighDensityEmbedding_swigregister(HighDensityEmbedding)
2542 
2543 
2544 def mask_and_norm(dmap, mask):
2545  """mask_and_norm(DensityMap dmap, DensityMap mask) -> DensityMap"""
2546  return _IMP_em.mask_and_norm(dmap, mask)
2547 
2548 def get_volume_at_threshold(m, threshold):
2549  """get_volume_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float"""
2550  return _IMP_em.get_volume_at_threshold(m, threshold)
2551 
2553  """
2554  get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold, IMP::atom::ProteinDensityReference ref) -> IMP::Float
2555  get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float
2556  """
2557  return _IMP_em.get_molecular_mass_at_threshold(*args)
2558 
2559 def get_threshold_for_approximate_volume(m, desired_volume):
2560  """get_threshold_for_approximate_volume(DensityMap m, IMP::Float desired_volume) -> IMP::Float"""
2561  return _IMP_em.get_threshold_for_approximate_volume(m, desired_volume)
2562 
2564  """
2565  get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass, IMP::atom::ProteinDensityReference ref) -> IMP::Float
2566  get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass) -> IMP::Float
2567  """
2568  return _IMP_em.get_threshold_for_approximate_mass(*args)
2569 class EnvelopePenetrationRestraint(IMP.Restraint):
2570  """Proxy of C++ IMP::em::EnvelopePenetrationRestraint class."""
2571 
2572  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2573 
2574  def __init__(self, ps, em_map, threshold):
2575  """__init__(IMP::em::EnvelopePenetrationRestraint self, IMP::Particles ps, DensityMap em_map, IMP::Float threshold) -> EnvelopePenetrationRestraint"""
2576  this = _IMP_em.new_EnvelopePenetrationRestraint(ps, em_map, threshold)
2577  try:
2578  self.this.append(this)
2579  except __builtin__.Exception:
2580  self.this = this
2581 
2582  def do_get_inputs(self):
2583  """do_get_inputs(EnvelopePenetrationRestraint self) -> IMP::ModelObjectsTemp"""
2584  return _IMP_em.EnvelopePenetrationRestraint_do_get_inputs(self)
2585 
2586 
2587  def get_version_info(self):
2588  """get_version_info(EnvelopePenetrationRestraint self) -> VersionInfo"""
2589  return _IMP_em.EnvelopePenetrationRestraint_get_version_info(self)
2590 
2591 
2592  def __str__(self):
2593  """__str__(EnvelopePenetrationRestraint self) -> std::string"""
2594  return _IMP_em.EnvelopePenetrationRestraint___str__(self)
2595 
2596 
2597  def __repr__(self):
2598  """__repr__(EnvelopePenetrationRestraint self) -> std::string"""
2599  return _IMP_em.EnvelopePenetrationRestraint___repr__(self)
2600 
2601 
2602  @staticmethod
2603  def get_from(o):
2604  return _object_cast_to_EnvelopePenetrationRestraint(o)
2605 
2606 EnvelopePenetrationRestraint_swigregister = _IMP_em.EnvelopePenetrationRestraint_swigregister
2607 EnvelopePenetrationRestraint_swigregister(EnvelopePenetrationRestraint)
2608 
2609 class PCAFitRestraint(IMP.Restraint):
2610  """Proxy of C++ IMP::em::PCAFitRestraint class."""
2611 
2612  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2613 
2614  def __init__(self, *args):
2615  """
2616  __init__(IMP::em::PCAFitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, float threshold, float max_pca_size_diff, float max_angle_diff, float max_centroid_diff, FloatKey weight_key) -> PCAFitRestraint
2617  __init__(IMP::em::PCAFitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, float threshold, float max_pca_size_diff, float max_angle_diff, float max_centroid_diff) -> PCAFitRestraint
2618  """
2619  this = _IMP_em.new_PCAFitRestraint(*args)
2620  try:
2621  self.this.append(this)
2622  except __builtin__.Exception:
2623  self.this = this
2624 
2625  def do_get_inputs(self):
2626  """do_get_inputs(PCAFitRestraint self) -> IMP::ModelObjectsTemp"""
2627  return _IMP_em.PCAFitRestraint_do_get_inputs(self)
2628 
2629 
2630  def get_version_info(self):
2631  """get_version_info(PCAFitRestraint self) -> VersionInfo"""
2632  return _IMP_em.PCAFitRestraint_get_version_info(self)
2633 
2634 
2635  def __str__(self):
2636  """__str__(PCAFitRestraint self) -> std::string"""
2637  return _IMP_em.PCAFitRestraint___str__(self)
2638 
2639 
2640  def __repr__(self):
2641  """__repr__(PCAFitRestraint self) -> std::string"""
2642  return _IMP_em.PCAFitRestraint___repr__(self)
2643 
2644 
2645  @staticmethod
2646  def get_from(o):
2647  return _object_cast_to_PCAFitRestraint(o)
2648 
2649 PCAFitRestraint_swigregister = _IMP_em.PCAFitRestraint_swigregister
2650 PCAFitRestraint_swigregister(PCAFitRestraint)
2651 
2652 class EnvelopeFitRestraint(IMP.Restraint):
2653  """Proxy of C++ IMP::em::EnvelopeFitRestraint class."""
2654 
2655  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2656 
2657  def __init__(self, particles, em_map, density_threshold, penetration_threshold):
2658  """__init__(IMP::em::EnvelopeFitRestraint self, IMP::Particles particles, DensityMap em_map, double density_threshold, double penetration_threshold) -> EnvelopeFitRestraint"""
2659  this = _IMP_em.new_EnvelopeFitRestraint(particles, em_map, density_threshold, penetration_threshold)
2660  try:
2661  self.this.append(this)
2662  except __builtin__.Exception:
2663  self.this = this
2664 
2665  def get_transformation(self):
2666  """get_transformation(EnvelopeFitRestraint self) -> Transformation3D"""
2667  return _IMP_em.EnvelopeFitRestraint_get_transformation(self)
2668 
2669 
2670  def apply_transformation(self):
2671  """apply_transformation(EnvelopeFitRestraint self)"""
2672  return _IMP_em.EnvelopeFitRestraint_apply_transformation(self)
2673 
2674 
2675  def do_get_inputs(self):
2676  """do_get_inputs(EnvelopeFitRestraint self) -> IMP::ModelObjectsTemp"""
2677  return _IMP_em.EnvelopeFitRestraint_do_get_inputs(self)
2678 
2679 
2680  def get_version_info(self):
2681  """get_version_info(EnvelopeFitRestraint self) -> VersionInfo"""
2682  return _IMP_em.EnvelopeFitRestraint_get_version_info(self)
2683 
2684 
2685  def __str__(self):
2686  """__str__(EnvelopeFitRestraint self) -> std::string"""
2687  return _IMP_em.EnvelopeFitRestraint___str__(self)
2688 
2689 
2690  def __repr__(self):
2691  """__repr__(EnvelopeFitRestraint self) -> std::string"""
2692  return _IMP_em.EnvelopeFitRestraint___repr__(self)
2693 
2694 
2695  @staticmethod
2696  def get_from(o):
2697  return _object_cast_to_EnvelopeFitRestraint(o)
2698 
2699 EnvelopeFitRestraint_swigregister = _IMP_em.EnvelopeFitRestraint_swigregister
2700 EnvelopeFitRestraint_swigregister(EnvelopeFitRestraint)
2701 
2702 class MapDistanceTransform(DensityMap):
2703  """Proxy of C++ IMP::em::MapDistanceTransform class."""
2704 
2705  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2706 
2707  def __init__(self, map, density_threshold, max_distance):
2708  """__init__(IMP::em::MapDistanceTransform self, DensityMap map, float density_threshold, float max_distance) -> MapDistanceTransform"""
2709  this = _IMP_em.new_MapDistanceTransform(map, density_threshold, max_distance)
2710  try:
2711  self.this.append(this)
2712  except __builtin__.Exception:
2713  self.this = this
2714 
2715  def get_distance_from_envelope(self, v):
2716  """get_distance_from_envelope(MapDistanceTransform self, Vector3D v) -> float"""
2717  return _IMP_em.MapDistanceTransform_get_distance_from_envelope(self, v)
2718 
2719 
2720  def __str__(self):
2721  """__str__(MapDistanceTransform self) -> std::string"""
2722  return _IMP_em.MapDistanceTransform___str__(self)
2723 
2724 
2725  def __repr__(self):
2726  """__repr__(MapDistanceTransform self) -> std::string"""
2727  return _IMP_em.MapDistanceTransform___repr__(self)
2728 
2729 
2730  @staticmethod
2731  def get_from(o):
2732  return _object_cast_to_MapDistanceTransform(o)
2733 
2734  __swig_destroy__ = _IMP_em.delete_MapDistanceTransform
2735  __del__ = lambda self: None
2736 MapDistanceTransform_swigregister = _IMP_em.MapDistanceTransform_swigregister
2737 MapDistanceTransform_swigregister(MapDistanceTransform)
2738 
2739 class EnvelopeScore(IMP.Object):
2740  """Proxy of C++ IMP::em::EnvelopeScore class."""
2741 
2742  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2743 
2744  def __init__(self, mdt):
2745  """__init__(IMP::em::EnvelopeScore self, MapDistanceTransform mdt) -> EnvelopeScore"""
2746  this = _IMP_em.new_EnvelopeScore(mdt)
2747  try:
2748  self.this.append(this)
2749  except __builtin__.Exception:
2750  self.this = this
2751 
2752  def is_penetrating(self, *args):
2753  """
2754  is_penetrating(EnvelopeScore self, IMP::algebra::Vector3Ds const & points, float penetration_thr) -> bool
2755  is_penetrating(EnvelopeScore self, IMP::algebra::Vector3Ds const & points, Transformation3D trans, float penetration_thr) -> bool
2756  """
2757  return _IMP_em.EnvelopeScore_is_penetrating(self, *args)
2758 
2759 
2760  def score(self, *args):
2761  """
2762  score(EnvelopeScore self, IMP::algebra::Vector3Ds const & points) -> double
2763  score(EnvelopeScore self, IMP::algebra::Vector3Ds const & points, Transformation3D trans) -> double
2764  """
2765  return _IMP_em.EnvelopeScore_score(self, *args)
2766 
2767  __swig_destroy__ = _IMP_em.delete_EnvelopeScore
2768  __del__ = lambda self: None
2769 
2770  def __str__(self):
2771  """__str__(EnvelopeScore self) -> std::string"""
2772  return _IMP_em.EnvelopeScore___str__(self)
2773 
2774 
2775  def __repr__(self):
2776  """__repr__(EnvelopeScore self) -> std::string"""
2777  return _IMP_em.EnvelopeScore___repr__(self)
2778 
2779 
2780  @staticmethod
2781  def get_from(o):
2782  return _object_cast_to_EnvelopeScore(o)
2783 
2784 EnvelopeScore_swigregister = _IMP_em.EnvelopeScore_swigregister
2785 EnvelopeScore_swigregister(EnvelopeScore)
2786 
2787 
2788 import math
2789 
2790 def write_pca_cmm(pca, fh):
2791  """Write out principal components to a file in Chimera Marker format"""
2792  eigen_values = pca.get_principal_values()
2793  eigen_vecs = pca.get_principal_components()
2794  centroid = pca.get_centroid()
2795 
2796  fh.write("<marker_set>\n")
2797  fh.write("<!-- PCA with eigen values: (%g,%g,%g) and "
2798  "centroid (%g,%g,%g) -->\n"
2799  % (math.sqrt(eigen_values[0]),
2800  math.sqrt(eigen_values[1]),
2801  math.sqrt(eigen_values[2]),
2802  centroid[0], centroid[1], centroid[2]))
2803 
2804  radius = 2.
2805 
2806  for i in range(3):
2807  val = math.sqrt(eigen_values[i])
2808  v1 = centroid - val * eigen_vecs[i]
2809  v2 = centroid + val * eigen_vecs[i]
2810  for markerid, v in ((i*2+1, v1), (i*2+2, v2)):
2811  fh.write("<marker id=\"%d\" x=\"%g\" y=\"%g\" z=\"%g\" "
2812  "radius=\"%g\"/>\n"
2813  % (markerid, v[0], v[1], v[2], radius))
2814 
2815  for i in range(1, 7, 2):
2816  fh.write("<link id1= \"%d\" id2=\"%d\" radius=\"%g\"/>\n"
2817  % (i, i+1, radius))
2818  fh.write("</marker_set>\n")
2819 
2820 
2821 def get_module_version():
2822  """get_module_version() -> std::string const"""
2823  return _IMP_em.get_module_version()
2824 
2825 def get_example_path(fname):
2826  """get_example_path(std::string fname) -> std::string"""
2827  return _IMP_em.get_example_path(fname)
2828 
2829 def get_data_path(fname):
2830  """get_data_path(std::string fname) -> std::string"""
2831  return _IMP_em.get_data_path(fname)
2832 
2833 from . import _version_check
2834 _version_check.check_version(get_module_version())
2835 __version__ = get_module_version()
2836 
2837 
2838 
Float get_threshold_for_approximate_mass(DensityMap *m, Float desired_mass, atom::ProteinDensityReference ref=atom::HARPAZ)
Computes the threshold to consider in an EM map to get a desired mass.
DensityMap * interpolate_map(DensityMap *in_map, double new_spacing)
Return a new map with an updated spacing.
Particles density2particles(DensityMap *dmap, Float threshold, Model *m, int step=1)
Convert a density grid to a set of particles.
algebra::Vector3Ds density2vectors(DensityMap *dmap, Float threshold)
Convert a density grid to a set of vectors.
algebra::BoundingBoxD< 3 > get_bounding_box(const DensityMap *m, Float threshold)
Get the bounding box for a map.
std::string get_module_version()
Return the version of this module, as a string.
Ints get_numbers_of_particles_outside_of_the_density(DensityMap *dmap, const Particles &ps, const IMP::algebra::Transformation3Ds &transformations, float thr=0.0)
Get numbers of particles (mult transforms) that are outside the density.
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