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IMP Reference Guide  2.12.0
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 2007-2019 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 class MapReaderWriter(IMP.Object):
511  """Proxy of C++ IMP::em::MapReaderWriter class."""
512 
513  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
514 
515  def __init__(self):
516  """__init__(IMP::em::MapReaderWriter self) -> MapReaderWriter"""
517  this = _IMP_em.new_MapReaderWriter()
518  try:
519  self.this.append(this)
520  except __builtin__.Exception:
521  self.this = this
522 
523  def get_version_info(self):
524  """get_version_info(MapReaderWriter self) -> VersionInfo"""
525  return _IMP_em.MapReaderWriter_get_version_info(self)
526 
527 
528  def __str__(self):
529  """__str__(MapReaderWriter self) -> std::string"""
530  return _IMP_em.MapReaderWriter___str__(self)
531 
532 
533  def __repr__(self):
534  """__repr__(MapReaderWriter self) -> std::string"""
535  return _IMP_em.MapReaderWriter___repr__(self)
536 
537 
538  @staticmethod
539  def get_from(o):
540  return _object_cast_to_MapReaderWriter(o)
541 
542 MapReaderWriter_swigregister = _IMP_em.MapReaderWriter_swigregister
543 MapReaderWriter_swigregister(MapReaderWriter)
544 cvar = _IMP_em.cvar
545 EPS = cvar.EPS
546 
547 class DensityHeader(object):
548  """Proxy of C++ IMP::em::DensityHeader class."""
549 
550  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
551  __repr__ = _swig_repr
552 
553  def __init__(self):
554  """__init__(IMP::em::DensityHeader self) -> DensityHeader"""
555  this = _IMP_em.new_DensityHeader()
556  try:
557  self.this.append(this)
558  except __builtin__.Exception:
559  self.this = this
560 
561  def get_top(self, ind):
562  """get_top(DensityHeader self, int ind) -> IMP::em::emreal"""
563  return _IMP_em.DensityHeader_get_top(self, ind)
564 
565 
566  def compute_xyz_top(self, force=False):
567  """
568  compute_xyz_top(DensityHeader self, bool force=False)
569  compute_xyz_top(DensityHeader self)
570  """
571  return _IMP_em.DensityHeader_compute_xyz_top(self, force)
572 
573 
574  def update_map_dimensions(self, nnx, nny, nnz):
575  """update_map_dimensions(DensityHeader self, int nnx, int nny, int nnz)"""
576  return _IMP_em.DensityHeader_update_map_dimensions(self, nnx, nny, nnz)
577 
578 
579  def update_cell_dimensions(self):
580  """update_cell_dimensions(DensityHeader self)"""
581  return _IMP_em.DensityHeader_update_cell_dimensions(self)
582 
583 
584  def show(self, *args):
585  """
586  show(DensityHeader self, _ostream out)
587  show(DensityHeader self)
588  """
589  return _IMP_em.DensityHeader_show(self, *args)
590 
591  MAP_FIELD_SIZE = _IMP_em.DensityHeader_MAP_FIELD_SIZE
592  USER_FIELD_SIZE = _IMP_em.DensityHeader_USER_FIELD_SIZE
593  COMMENT_FIELD_NUM_OF = _IMP_em.DensityHeader_COMMENT_FIELD_NUM_OF
594  COMMENT_FIELD_SINGLE_SIZE = _IMP_em.DensityHeader_COMMENT_FIELD_SINGLE_SIZE
595  nxstart = _swig_property(_IMP_em.DensityHeader_nxstart_get, _IMP_em.DensityHeader_nxstart_set)
596  nystart = _swig_property(_IMP_em.DensityHeader_nystart_get, _IMP_em.DensityHeader_nystart_set)
597  nzstart = _swig_property(_IMP_em.DensityHeader_nzstart_get, _IMP_em.DensityHeader_nzstart_set)
598  mx = _swig_property(_IMP_em.DensityHeader_mx_get, _IMP_em.DensityHeader_mx_set)
599  my = _swig_property(_IMP_em.DensityHeader_my_get, _IMP_em.DensityHeader_my_set)
600  mz = _swig_property(_IMP_em.DensityHeader_mz_get, _IMP_em.DensityHeader_mz_set)
601  xlen = _swig_property(_IMP_em.DensityHeader_xlen_get, _IMP_em.DensityHeader_xlen_set)
602  ylen = _swig_property(_IMP_em.DensityHeader_ylen_get, _IMP_em.DensityHeader_ylen_set)
603  zlen = _swig_property(_IMP_em.DensityHeader_zlen_get, _IMP_em.DensityHeader_zlen_set)
604  alpha = _swig_property(_IMP_em.DensityHeader_alpha_get, _IMP_em.DensityHeader_alpha_set)
605  beta = _swig_property(_IMP_em.DensityHeader_beta_get, _IMP_em.DensityHeader_beta_set)
606  gamma = _swig_property(_IMP_em.DensityHeader_gamma_get, _IMP_em.DensityHeader_gamma_set)
607  mapc = _swig_property(_IMP_em.DensityHeader_mapc_get, _IMP_em.DensityHeader_mapc_set)
608  mapr = _swig_property(_IMP_em.DensityHeader_mapr_get, _IMP_em.DensityHeader_mapr_set)
609  maps = _swig_property(_IMP_em.DensityHeader_maps_get, _IMP_em.DensityHeader_maps_set)
610  dmin = _swig_property(_IMP_em.DensityHeader_dmin_get, _IMP_em.DensityHeader_dmin_set)
611  dmax = _swig_property(_IMP_em.DensityHeader_dmax_get, _IMP_em.DensityHeader_dmax_set)
612  dmean = _swig_property(_IMP_em.DensityHeader_dmean_get, _IMP_em.DensityHeader_dmean_set)
613  ispg = _swig_property(_IMP_em.DensityHeader_ispg_get, _IMP_em.DensityHeader_ispg_set)
614  nsymbt = _swig_property(_IMP_em.DensityHeader_nsymbt_get, _IMP_em.DensityHeader_nsymbt_set)
615  user = _swig_property(_IMP_em.DensityHeader_user_get, _IMP_em.DensityHeader_user_set)
616  map = _swig_property(_IMP_em.DensityHeader_map_get, _IMP_em.DensityHeader_map_set)
617  machinestamp = _swig_property(_IMP_em.DensityHeader_machinestamp_get, _IMP_em.DensityHeader_machinestamp_set)
618  rms = _swig_property(_IMP_em.DensityHeader_rms_get, _IMP_em.DensityHeader_rms_set)
619  nlabl = _swig_property(_IMP_em.DensityHeader_nlabl_get, _IMP_em.DensityHeader_nlabl_set)
620  comments = _swig_property(_IMP_em.DensityHeader_comments_get, _IMP_em.DensityHeader_comments_set)
621  magic = _swig_property(_IMP_em.DensityHeader_magic_get, _IMP_em.DensityHeader_magic_set)
622  voltage = _swig_property(_IMP_em.DensityHeader_voltage_get, _IMP_em.DensityHeader_voltage_set)
623  Cs = _swig_property(_IMP_em.DensityHeader_Cs_get, _IMP_em.DensityHeader_Cs_set)
624  Aperture = _swig_property(_IMP_em.DensityHeader_Aperture_get, _IMP_em.DensityHeader_Aperture_set)
625  Magnification = _swig_property(_IMP_em.DensityHeader_Magnification_get, _IMP_em.DensityHeader_Magnification_set)
626  Postmagnification = _swig_property(_IMP_em.DensityHeader_Postmagnification_get, _IMP_em.DensityHeader_Postmagnification_set)
627  Exposuretime = _swig_property(_IMP_em.DensityHeader_Exposuretime_get, _IMP_em.DensityHeader_Exposuretime_set)
628  Microscope = _swig_property(_IMP_em.DensityHeader_Microscope_get, _IMP_em.DensityHeader_Microscope_set)
629  Pixelsize = _swig_property(_IMP_em.DensityHeader_Pixelsize_get, _IMP_em.DensityHeader_Pixelsize_set)
630  CCDArea = _swig_property(_IMP_em.DensityHeader_CCDArea_get, _IMP_em.DensityHeader_CCDArea_set)
631  Defocus = _swig_property(_IMP_em.DensityHeader_Defocus_get, _IMP_em.DensityHeader_Defocus_set)
632  Astigmatism = _swig_property(_IMP_em.DensityHeader_Astigmatism_get, _IMP_em.DensityHeader_Astigmatism_set)
633  AstigmatismAngle = _swig_property(_IMP_em.DensityHeader_AstigmatismAngle_get, _IMP_em.DensityHeader_AstigmatismAngle_set)
634  FocusIncrement = _swig_property(_IMP_em.DensityHeader_FocusIncrement_get, _IMP_em.DensityHeader_FocusIncrement_set)
635  CountsPerElectron = _swig_property(_IMP_em.DensityHeader_CountsPerElectron_get, _IMP_em.DensityHeader_CountsPerElectron_set)
636  Intensity = _swig_property(_IMP_em.DensityHeader_Intensity_get, _IMP_em.DensityHeader_Intensity_set)
637  EnergySlitwidth = _swig_property(_IMP_em.DensityHeader_EnergySlitwidth_get, _IMP_em.DensityHeader_EnergySlitwidth_set)
638  EnergyOffset = _swig_property(_IMP_em.DensityHeader_EnergyOffset_get, _IMP_em.DensityHeader_EnergyOffset_set)
639  Tiltangle = _swig_property(_IMP_em.DensityHeader_Tiltangle_get, _IMP_em.DensityHeader_Tiltangle_set)
640  Tiltaxis = _swig_property(_IMP_em.DensityHeader_Tiltaxis_get, _IMP_em.DensityHeader_Tiltaxis_set)
641  MarkerX = _swig_property(_IMP_em.DensityHeader_MarkerX_get, _IMP_em.DensityHeader_MarkerX_set)
642  MarkerY = _swig_property(_IMP_em.DensityHeader_MarkerY_get, _IMP_em.DensityHeader_MarkerY_set)
643  lswap = _swig_property(_IMP_em.DensityHeader_lswap_get, _IMP_em.DensityHeader_lswap_set)
644 
645  def get_resolution(self):
646  """get_resolution(DensityHeader self) -> float"""
647  return _IMP_em.DensityHeader_get_resolution(self)
648 
649 
650  def get_has_resolution(self):
651  """get_has_resolution(DensityHeader self) -> bool"""
652  return _IMP_em.DensityHeader_get_has_resolution(self)
653 
654 
655  def set_resolution(self, resolution):
656  """set_resolution(DensityHeader self, float resolution)"""
657  return _IMP_em.DensityHeader_set_resolution(self, resolution)
658 
659 
660  def get_spacing(self):
661  """get_spacing(DensityHeader self) -> float"""
662  return _IMP_em.DensityHeader_get_spacing(self)
663 
664 
665  def get_xorigin(self):
666  """get_xorigin(DensityHeader self) -> float"""
667  return _IMP_em.DensityHeader_get_xorigin(self)
668 
669 
670  def get_yorigin(self):
671  """get_yorigin(DensityHeader self) -> float"""
672  return _IMP_em.DensityHeader_get_yorigin(self)
673 
674 
675  def get_zorigin(self):
676  """get_zorigin(DensityHeader self) -> float"""
677  return _IMP_em.DensityHeader_get_zorigin(self)
678 
679 
680  def get_origin(self, i):
681  """get_origin(DensityHeader self, int i) -> float"""
682  return _IMP_em.DensityHeader_get_origin(self, i)
683 
684 
685  def set_xorigin(self, x):
686  """set_xorigin(DensityHeader self, float x)"""
687  return _IMP_em.DensityHeader_set_xorigin(self, x)
688 
689 
690  def set_yorigin(self, y):
691  """set_yorigin(DensityHeader self, float y)"""
692  return _IMP_em.DensityHeader_set_yorigin(self, y)
693 
694 
695  def set_zorigin(self, z):
696  """set_zorigin(DensityHeader self, float z)"""
697  return _IMP_em.DensityHeader_set_zorigin(self, z)
698 
699 
700  def is_top_calculated(self):
701  """is_top_calculated(DensityHeader self) -> bool"""
702  return _IMP_em.DensityHeader_is_top_calculated(self)
703 
704  Objectpixelsize_ = _swig_property(_IMP_em.DensityHeader_Objectpixelsize__get, _IMP_em.DensityHeader_Objectpixelsize__set)
705 
706  def get_nx(self):
707  """get_nx(DensityHeader self) -> int"""
708  return _IMP_em.DensityHeader_get_nx(self)
709 
710 
711  def get_ny(self):
712  """get_ny(DensityHeader self) -> int"""
713  return _IMP_em.DensityHeader_get_ny(self)
714 
715 
716  def get_nz(self):
717  """get_nz(DensityHeader self) -> int"""
718  return _IMP_em.DensityHeader_get_nz(self)
719 
720 
721  def get_number_of_voxels(self):
722  """get_number_of_voxels(DensityHeader self) -> int"""
723  return _IMP_em.DensityHeader_get_number_of_voxels(self)
724 
725 
726  def get_data_type(self):
727  """get_data_type(DensityHeader self) -> int"""
728  return _IMP_em.DensityHeader_get_data_type(self)
729 
730 
731  def set_data_type(self, data_type):
732  """set_data_type(DensityHeader self, int data_type)"""
733  return _IMP_em.DensityHeader_set_data_type(self, data_type)
734 
735  __swig_destroy__ = _IMP_em.delete_DensityHeader
736  __del__ = lambda self: None
737 DensityHeader_swigregister = _IMP_em.DensityHeader_swigregister
738 DensityHeader_swigregister(DensityHeader)
739 
740 
741 def create_density_header(bb, spacing):
742  """create_density_header(BoundingBox3D bb, float spacing) -> DensityHeader"""
743  return _IMP_em.create_density_header(bb, spacing)
744 
745 def read_map(*args):
746  """
747  read_map(std::string filename, MapReaderWriter reader) -> DensityMap
748  read_map(std::string filename) -> DensityMap
749  """
750  return _IMP_em.read_map(*args)
751 
752 def write_map(*args):
753  """
754  write_map(DensityMap m, std::string filename, MapReaderWriter writer)
755  write_map(DensityMap m, std::string filename)
756  """
757  return _IMP_em.write_map(*args)
758 
759 def approximate_molecular_mass(m, threshold):
760  """approximate_molecular_mass(DensityMap m, IMP::Float threshold) -> IMP::Float"""
761  return _IMP_em.approximate_molecular_mass(m, threshold)
762 class DensityMap(IMP.Object):
763  """Proxy of C++ IMP::em::DensityMap class."""
764 
765  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
766 
767  def __init__(self, *args):
768  """
769  __init__(IMP::em::DensityMap self, std::string name) -> DensityMap
770  __init__(IMP::em::DensityMap self) -> DensityMap
771  __init__(IMP::em::DensityMap self, DensityHeader header, std::string name) -> DensityMap
772  __init__(IMP::em::DensityMap self, DensityHeader header) -> DensityMap
773  """
774  this = _IMP_em.new_DensityMap(*args)
775  try:
776  self.this.append(this)
777  except __builtin__.Exception:
778  self.this = this
779 
780  def reset_data(self, value=0.0):
781  """
782  reset_data(DensityMap self, float value=0.0)
783  reset_data(DensityMap self)
784  """
785  return _IMP_em.DensityMap_reset_data(self, value)
786 
787 
788  def calcRMS(self):
789  """calcRMS(DensityMap self) -> IMP::em::emreal"""
790  return _IMP_em.DensityMap_calcRMS(self)
791 
792 
793  def std_normalize(self):
794  """std_normalize(DensityMap self)"""
795  return _IMP_em.DensityMap_std_normalize(self)
796 
797 
798  def is_normalized(self):
799  """is_normalized(DensityMap self) -> bool"""
800  return _IMP_em.DensityMap_is_normalized(self)
801 
802 
803  def get_location_in_dim_by_voxel(self, index, dim):
804  """get_location_in_dim_by_voxel(DensityMap self, long index, int dim) -> float"""
805  return _IMP_em.DensityMap_get_location_in_dim_by_voxel(self, index, dim)
806 
807 
808  def xyz_ind2voxel(self, x, y, z):
809  """xyz_ind2voxel(DensityMap self, int x, int y, int z) -> long"""
810  return _IMP_em.DensityMap_xyz_ind2voxel(self, x, y, z)
811 
812 
813  def get_voxel_by_location(self, *args):
814  """
815  get_voxel_by_location(DensityMap self, float x, float y, float z) -> long
816  get_voxel_by_location(DensityMap self, Vector3D v) -> long
817  """
818  return _IMP_em.DensityMap_get_voxel_by_location(self, *args)
819 
820 
821  def get_location_by_voxel(self, index):
822  """get_location_by_voxel(DensityMap self, long index) -> Vector3D"""
823  return _IMP_em.DensityMap_get_location_by_voxel(self, index)
824 
825 
826  def is_xyz_ind_part_of_volume(self, ix, iy, iz):
827  """is_xyz_ind_part_of_volume(DensityMap self, int ix, int iy, int iz) -> bool"""
828  return _IMP_em.DensityMap_is_xyz_ind_part_of_volume(self, ix, iy, iz)
829 
830 
831  def is_part_of_volume(self, *args):
832  """
833  is_part_of_volume(DensityMap self, float x, float y, float z) -> bool
834  is_part_of_volume(DensityMap self, Vector3D v) -> bool
835  """
836  return _IMP_em.DensityMap_is_part_of_volume(self, *args)
837 
838 
839  def get_value(self, *args):
840  """
841  get_value(DensityMap self, float x, float y, float z) -> IMP::em::emreal
842  get_value(DensityMap self, Vector3D point) -> IMP::em::emreal
843  get_value(DensityMap self, long index) -> IMP::em::emreal
844  """
845  return _IMP_em.DensityMap_get_value(self, *args)
846 
847 
848  def set_value(self, *args):
849  """
850  set_value(DensityMap self, long index, IMP::em::emreal value)
851  set_value(DensityMap self, float x, float y, float z, IMP::em::emreal value)
852  """
853  return _IMP_em.DensityMap_set_value(self, *args)
854 
855 
856  def set_origin(self, *args):
857  """
858  set_origin(DensityMap self, float x, float y, float z)
859  set_origin(DensityMap self, Vector3D v)
860  """
861  return _IMP_em.DensityMap_set_origin(self, *args)
862 
863 
864  def get_origin(self):
865  """get_origin(DensityMap self) -> Vector3D"""
866  return _IMP_em.DensityMap_get_origin(self)
867 
868 
869  def get_top(self):
870  """get_top(DensityMap self) -> Vector3D"""
871  return _IMP_em.DensityMap_get_top(self)
872 
873 
874  def get_header(self):
875  h = _IMP_em.DensityMap_get_header(self)
876  h._owner = self
877  return h
878 
879 
880 
881  def get_header_writable(self):
882  h = _IMP_em.DensityMap_get_header_writable(self)
883  h._owner = self
884  return h
885 
886 
887 
888  def same_origin(self, other):
889  """same_origin(DensityMap self, DensityMap other) -> bool"""
890  return _IMP_em.DensityMap_same_origin(self, other)
891 
892 
893  def same_dimensions(self, other):
894  """same_dimensions(DensityMap self, DensityMap other) -> bool"""
895  return _IMP_em.DensityMap_same_dimensions(self, other)
896 
897 
898  def same_voxel_size(self, other):
899  """same_voxel_size(DensityMap self, DensityMap other) -> bool"""
900  return _IMP_em.DensityMap_same_voxel_size(self, other)
901 
902 
903  def get_centroid(self, threshold=0.0):
904  """
905  get_centroid(DensityMap self, IMP::em::emreal threshold=0.0) -> Vector3D
906  get_centroid(DensityMap self) -> Vector3D
907  """
908  return _IMP_em.DensityMap_get_centroid(self, threshold)
909 
910 
911  def get_max_value(self):
912  """get_max_value(DensityMap self) -> IMP::em::emreal"""
913  return _IMP_em.DensityMap_get_max_value(self)
914 
915 
916  def get_min_value(self):
917  """get_min_value(DensityMap self) -> IMP::em::emreal"""
918  return _IMP_em.DensityMap_get_min_value(self)
919 
920 
921  def add(self, *args):
922  """
923  add(DensityMap self, DensityMap other)
924  add(DensityMap self, IMP::Float d)
925  """
926  return _IMP_em.DensityMap_add(self, *args)
927 
928 
929  def pick_max(self, other):
930  """pick_max(DensityMap self, DensityMap other)"""
931  return _IMP_em.DensityMap_pick_max(self, other)
932 
933 
934  def get_number_of_voxels(self):
935  """get_number_of_voxels(DensityMap self) -> long"""
936  return _IMP_em.DensityMap_get_number_of_voxels(self)
937 
938 
939  def set_void_map(self, nx, ny, nz):
940  """set_void_map(DensityMap self, int nx, int ny, int nz)"""
941  return _IMP_em.DensityMap_set_void_map(self, nx, ny, nz)
942 
943 
944  def pad(self, nx, ny, nz, val=0.0):
945  """
946  pad(DensityMap self, int nx, int ny, int nz, float val=0.0)
947  pad(DensityMap self, int nx, int ny, int nz)
948  """
949  return _IMP_em.DensityMap_pad(self, nx, ny, nz, val)
950 
951 
952  def pad_margin(self, mrg_x, mrg_y, mrg_z, val=0.0):
953  """
954  pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z, float val=0.0) -> DensityMap
955  pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z) -> DensityMap
956  """
957  return _IMP_em.DensityMap_pad_margin(self, mrg_x, mrg_y, mrg_z, val)
958 
959 
960  def get_cropped(self, *args):
961  """
962  get_cropped(DensityMap self, float threshold) -> DensityMap
963  get_cropped(DensityMap self, BoundingBox3D bb) -> DensityMap
964  """
965  return _IMP_em.DensityMap_get_cropped(self, *args)
966 
967 
968  def get_maximum_value_in_xy_plane(self, z_ind):
969  """get_maximum_value_in_xy_plane(DensityMap self, int z_ind) -> float"""
970  return _IMP_em.DensityMap_get_maximum_value_in_xy_plane(self, z_ind)
971 
972 
973  def get_maximum_value_in_xz_plane(self, y_ind):
974  """get_maximum_value_in_xz_plane(DensityMap self, int y_ind) -> float"""
975  return _IMP_em.DensityMap_get_maximum_value_in_xz_plane(self, y_ind)
976 
977 
978  def get_maximum_value_in_yz_plane(self, x_ind):
979  """get_maximum_value_in_yz_plane(DensityMap self, int x_ind) -> float"""
980  return _IMP_em.DensityMap_get_maximum_value_in_yz_plane(self, x_ind)
981 
982 
983  def multiply(self, factor):
984  """multiply(DensityMap self, float factor)"""
985  return _IMP_em.DensityMap_multiply(self, factor)
986 
987 
988  def get_locations_string(self, t):
989  """get_locations_string(DensityMap self, float t) -> std::string"""
990  return _IMP_em.DensityMap_get_locations_string(self, t)
991 
992 
993  def update_voxel_size(self, new_apix):
994  """update_voxel_size(DensityMap self, float new_apix)"""
995  return _IMP_em.DensityMap_update_voxel_size(self, new_apix)
996 
997 
998  def get_spacing(self):
999  """get_spacing(DensityMap self) -> IMP::Float"""
1000  return _IMP_em.DensityMap_get_spacing(self)
1001 
1002 
1003  def calc_all_voxel2loc(self):
1004  """calc_all_voxel2loc(DensityMap self)"""
1005  return _IMP_em.DensityMap_calc_all_voxel2loc(self)
1006 
1007 
1008  def copy_map(self, other):
1009  """copy_map(DensityMap self, DensityMap other)"""
1010  return _IMP_em.DensityMap_copy_map(self, other)
1011 
1012 
1013  def get_version_info(self):
1014  """get_version_info(DensityMap self) -> VersionInfo"""
1015  return _IMP_em.DensityMap_get_version_info(self)
1016 
1017 
1018  def lower_voxel_shift(self, loc, kdist, orig, ndim):
1019  """lower_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
1020  return _IMP_em.DensityMap_lower_voxel_shift(self, loc, kdist, orig, ndim)
1021 
1022 
1023  def upper_voxel_shift(self, loc, kdist, orig, ndim):
1024  """upper_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
1025  return _IMP_em.DensityMap_upper_voxel_shift(self, loc, kdist, orig, ndim)
1026 
1027 
1028  def get_rms_calculated(self):
1029  """get_rms_calculated(DensityMap self) -> bool"""
1030  return _IMP_em.DensityMap_get_rms_calculated(self)
1031 
1032 
1033  def get_dim_index_by_location(self, *args):
1034  """
1035  get_dim_index_by_location(DensityMap self, Vector3D v, int ind) -> int
1036  get_dim_index_by_location(DensityMap self, float loc_val, int ind) -> int
1037  """
1038  return _IMP_em.DensityMap_get_dim_index_by_location(self, *args)
1039 
1040 
1041  def __str__(self):
1042  """__str__(DensityMap self) -> std::string"""
1043  return _IMP_em.DensityMap___str__(self)
1044 
1045 
1046  def __repr__(self):
1047  """__repr__(DensityMap self) -> std::string"""
1048  return _IMP_em.DensityMap___repr__(self)
1049 
1050 
1051  @staticmethod
1052  def get_from(o):
1053  return _object_cast_to_DensityMap(o)
1054 
1055 DensityMap_swigregister = _IMP_em.DensityMap_swigregister
1056 DensityMap_swigregister(DensityMap)
1057 
1058 
1059 def get_bounding_box(*args):
1060  """
1061  get_bounding_box(DensityMap m, IMP::Float threshold) -> BoundingBox3D
1062  get_bounding_box(DensityMap m) -> BoundingBox3D
1063  """
1064  return _IMP_em.get_bounding_box(*args)
1065 
1066 def get_density(m, v):
1067  """get_density(DensityMap m, Vector3D v) -> double"""
1068  return _IMP_em.get_density(m, v)
1069 
1070 def get_transformed(*args):
1071  """
1072  get_transformed(DensityMap input, Transformation3D tr, double threshold) -> DensityMap
1073  get_transformed(DensityMap input, Transformation3D tr) -> DensityMap
1074  """
1075  return _IMP_em.get_transformed(*args)
1076 
1077 def get_resampled(input, scaling):
1078  """get_resampled(DensityMap input, double scaling) -> DensityMap"""
1079  return _IMP_em.get_resampled(input, scaling)
1080 
1081 def get_transformed_into(source, tr, into, calc_rms=True):
1082  """
1083  get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into, bool calc_rms=True)
1084  get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into)
1085  """
1086  return _IMP_em.get_transformed_into(source, tr, into, calc_rms)
1087 
1088 def get_transformed_into2(source, tr, into):
1089  """get_transformed_into2(DensityMap source, Transformation3D tr, DensityMap into)"""
1090  return _IMP_em.get_transformed_into2(source, tr, into)
1091 
1092 def get_interiors_intersect(d1, d2):
1093  """get_interiors_intersect(DensityMap d1, DensityMap d2) -> bool"""
1094  return _IMP_em.get_interiors_intersect(d1, d2)
1095 
1096 def get_segment(*args):
1097  """
1098  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
1099  get_segment(DensityMap map_to_segment, IMP::algebra::Vector3Ds vecs, float dist) -> DensityMap
1100  """
1101  return _IMP_em.get_segment(*args)
1102 
1103 def get_segment_by_masking(map_to_segment, mask, mas_threshold):
1104  """get_segment_by_masking(DensityMap map_to_segment, DensityMap mask, float mas_threshold) -> DensityMap"""
1105  return _IMP_em.get_segment_by_masking(map_to_segment, mask, mas_threshold)
1106 
1107 def binarize(orig_map, threshold, reverse=False):
1108  """
1109  binarize(DensityMap orig_map, float threshold, bool reverse=False) -> DensityMap
1110  binarize(DensityMap orig_map, float threshold) -> DensityMap
1111  """
1112  return _IMP_em.binarize(orig_map, threshold, reverse)
1113 
1114 def get_threshold_map(orig_map, threshold):
1115  """get_threshold_map(DensityMap orig_map, float threshold) -> DensityMap"""
1116  return _IMP_em.get_threshold_map(orig_map, threshold)
1117 
1118 def multiply(m1, m2):
1119  """multiply(DensityMap m1, DensityMap m2) -> DensityMap"""
1120  return _IMP_em.multiply(m1, m2)
1121 
1122 def convolute(m1, m2):
1123  """convolute(DensityMap m1, DensityMap m2) -> double"""
1124  return _IMP_em.convolute(m1, m2)
1125 
1126 def get_sum(m1):
1127  """get_sum(DensityMap m1) -> double"""
1128  return _IMP_em.get_sum(m1)
1129 
1130 def get_max_map(maps):
1131  """get_max_map(IMP::em::DensityMaps maps) -> DensityMap"""
1132  return _IMP_em.get_max_map(maps)
1133 
1134 def interpolate_map(in_map, new_spacing):
1135  """interpolate_map(DensityMap in_map, double new_spacing) -> DensityMap"""
1136  return _IMP_em.interpolate_map(in_map, new_spacing)
1137 
1138 def get_grid(in_map):
1139  """get_grid(DensityMap in_map) -> IMP::algebra::GridD< 3,IMP::algebra::DenseGridStorageD< 3,float >,float,IMP::algebra::DefaultEmbeddingD< 3 > >"""
1140  return _IMP_em.get_grid(in_map)
1141 
1142 def create_density_map(*args):
1143  """
1144  create_density_map(DensityMap other) -> DensityMap
1145  create_density_map(BoundingBox3D bb, double spacing) -> DensityMap
1146  create_density_map(int nx, int ny, int nz, double spacing) -> DensityMap
1147  create_density_map(DenseFloatGrid3D grid) -> DensityMap
1148  create_density_map(DenseDoubleGrid3D grid) -> DensityMap
1149  """
1150  return _IMP_em.create_density_map(*args)
1151 
1152 def get_binarized_interior(dmap):
1153  """get_binarized_interior(DensityMap dmap) -> DensityMap"""
1154  return _IMP_em.get_binarized_interior(dmap)
1155 
1156 def add_to_map(dm, pis):
1157  """add_to_map(DensityMap dm, IMP::Particles const & pis)"""
1158  return _IMP_em.add_to_map(dm, pis)
1159 class RadiusDependentDistanceMask(object):
1160  """Proxy of C++ IMP::em::RadiusDependentDistanceMask class."""
1161 
1162  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1163  __repr__ = _swig_repr
1164 
1165  def __init__(self, sampling_radius, header):
1166  """__init__(IMP::em::RadiusDependentDistanceMask self, float sampling_radius, DensityHeader header) -> RadiusDependentDistanceMask"""
1167  this = _IMP_em.new_RadiusDependentDistanceMask(sampling_radius, header)
1168  try:
1169  self.this.append(this)
1170  except __builtin__.Exception:
1171  self.this = this
1172 
1173  def get_neighbor_shift(self):
1174  """get_neighbor_shift(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1175  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_shift(self)
1176 
1177 
1178  def get_neighbor_dist(self):
1179  """get_neighbor_dist(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1180  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist(self)
1181 
1182 
1183  def get_neighbor_dist_exp(self):
1184  """get_neighbor_dist_exp(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1185  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist_exp(self)
1186 
1187 
1188  def show(self, out):
1189  """show(RadiusDependentDistanceMask self, _ostream out)"""
1190  return _IMP_em.RadiusDependentDistanceMask_show(self, out)
1191 
1192  __swig_destroy__ = _IMP_em.delete_RadiusDependentDistanceMask
1193  __del__ = lambda self: None
1194 RadiusDependentDistanceMask_swigregister = _IMP_em.RadiusDependentDistanceMask_swigregister
1195 RadiusDependentDistanceMask_swigregister(RadiusDependentDistanceMask)
1196 
1197 class DistanceMask(object):
1198  """Proxy of C++ IMP::em::DistanceMask class."""
1199 
1200  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1201  __repr__ = _swig_repr
1202 
1203  def __init__(self, *args):
1204  """
1205  __init__(IMP::em::DistanceMask self) -> DistanceMask
1206  __init__(IMP::em::DistanceMask self, DensityHeader header) -> DistanceMask
1207  """
1208  this = _IMP_em.new_DistanceMask(*args)
1209  try:
1210  self.this.append(this)
1211  except __builtin__.Exception:
1212  self.this = this
1213 
1214  def show(self, out):
1215  """show(DistanceMask self, _ostream out)"""
1216  return _IMP_em.DistanceMask_show(self, out)
1217 
1218 
1219  def is_mask_set(self, radius, eps=0.001):
1220  """
1221  is_mask_set(DistanceMask self, float radius, float eps=0.001) -> bool
1222  is_mask_set(DistanceMask self, float radius) -> bool
1223  """
1224  return _IMP_em.DistanceMask_is_mask_set(self, radius, eps)
1225 
1226  __swig_destroy__ = _IMP_em.delete_DistanceMask
1227  __del__ = lambda self: None
1228 DistanceMask_swigregister = _IMP_em.DistanceMask_swigregister
1229 DistanceMask_swigregister(DistanceMask)
1230 
1231 class EMReaderWriter(MapReaderWriter):
1232  """Proxy of C++ IMP::em::EMReaderWriter class."""
1233 
1234  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1235 
1236  def __str__(self):
1237  """__str__(EMReaderWriter self) -> std::string"""
1238  return _IMP_em.EMReaderWriter___str__(self)
1239 
1240 
1241  def __repr__(self):
1242  """__repr__(EMReaderWriter self) -> std::string"""
1243  return _IMP_em.EMReaderWriter___repr__(self)
1244 
1245 
1246  @staticmethod
1247  def get_from(o):
1248  return _object_cast_to_EMReaderWriter(o)
1249 
1250 
1251  def __init__(self):
1252  """__init__(IMP::em::EMReaderWriter self) -> EMReaderWriter"""
1253  this = _IMP_em.new_EMReaderWriter()
1254  try:
1255  self.this.append(this)
1256  except __builtin__.Exception:
1257  self.this = this
1258 EMReaderWriter_swigregister = _IMP_em.EMReaderWriter_swigregister
1259 EMReaderWriter_swigregister(EMReaderWriter)
1260 
1261 class XplorReaderWriter(MapReaderWriter):
1262  """Proxy of C++ IMP::em::XplorReaderWriter class."""
1263 
1264  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1265 
1266  def __str__(self):
1267  """__str__(XplorReaderWriter self) -> std::string"""
1268  return _IMP_em.XplorReaderWriter___str__(self)
1269 
1270 
1271  def __repr__(self):
1272  """__repr__(XplorReaderWriter self) -> std::string"""
1273  return _IMP_em.XplorReaderWriter___repr__(self)
1274 
1275 
1276  @staticmethod
1277  def get_from(o):
1278  return _object_cast_to_XplorReaderWriter(o)
1279 
1280 
1281  def __init__(self):
1282  """__init__(IMP::em::XplorReaderWriter self) -> XplorReaderWriter"""
1283  this = _IMP_em.new_XplorReaderWriter()
1284  try:
1285  self.this.append(this)
1286  except __builtin__.Exception:
1287  self.this = this
1288 XplorReaderWriter_swigregister = _IMP_em.XplorReaderWriter_swigregister
1289 XplorReaderWriter_swigregister(XplorReaderWriter)
1290 
1291 class MRCReaderWriter(MapReaderWriter):
1292  """Proxy of C++ IMP::em::MRCReaderWriter class."""
1293 
1294  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1295 
1296  def __init__(self, *args):
1297  """
1298  __init__(IMP::em::MRCReaderWriter self) -> MRCReaderWriter
1299  __init__(IMP::em::MRCReaderWriter self, std::string fn) -> MRCReaderWriter
1300  """
1301  this = _IMP_em.new_MRCReaderWriter(*args)
1302  try:
1303  self.this.append(this)
1304  except __builtin__.Exception:
1305  self.this = this
1306 
1307  def __str__(self):
1308  """__str__(MRCReaderWriter self) -> std::string"""
1309  return _IMP_em.MRCReaderWriter___str__(self)
1310 
1311 
1312  def __repr__(self):
1313  """__repr__(MRCReaderWriter self) -> std::string"""
1314  return _IMP_em.MRCReaderWriter___repr__(self)
1315 
1316 
1317  @staticmethod
1318  def get_from(o):
1319  return _object_cast_to_MRCReaderWriter(o)
1320 
1321 MRCReaderWriter_swigregister = _IMP_em.MRCReaderWriter_swigregister
1322 MRCReaderWriter_swigregister(MRCReaderWriter)
1323 
1324 class KernelParameters(object):
1325  """Proxy of C++ IMP::em::KernelParameters class."""
1326 
1327  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1328 
1329  def __init__(self, *args):
1330  """
1331  __init__(IMP::em::KernelParameters self) -> KernelParameters
1332  __init__(IMP::em::KernelParameters self, float resolution) -> KernelParameters
1333  """
1334  this = _IMP_em.new_KernelParameters(*args)
1335  try:
1336  self.this.append(this)
1337  except __builtin__.Exception:
1338  self.this = this
1339  __swig_destroy__ = _IMP_em.delete_KernelParameters
1340  __del__ = lambda self: None
1341 
1342  def get_rsig(self):
1343  """get_rsig(KernelParameters self) -> float"""
1344  return _IMP_em.KernelParameters_get_rsig(self)
1345 
1346 
1347  def get_rsigsq(self):
1348  """get_rsigsq(KernelParameters self) -> float"""
1349  return _IMP_em.KernelParameters_get_rsigsq(self)
1350 
1351 
1352  def get_inv_rsigsq(self):
1353  """get_inv_rsigsq(KernelParameters self) -> float"""
1354  return _IMP_em.KernelParameters_get_inv_rsigsq(self)
1355 
1356 
1357  def get_timessig(self):
1358  """get_timessig(KernelParameters self) -> float"""
1359  return _IMP_em.KernelParameters_get_timessig(self)
1360 
1361 
1362  def get_sq2pi3(self):
1363  """get_sq2pi3(KernelParameters self) -> float"""
1364  return _IMP_em.KernelParameters_get_sq2pi3(self)
1365 
1366 
1367  def get_rnormfac(self):
1368  """get_rnormfac(KernelParameters self) -> float"""
1369  return _IMP_em.KernelParameters_get_rnormfac(self)
1370 
1371 
1372  def get_rkdist(self):
1373  """get_rkdist(KernelParameters self) -> float"""
1374  return _IMP_em.KernelParameters_get_rkdist(self)
1375 
1376 
1377  def get_rkdistsq(self):
1378  """get_rkdistsq(KernelParameters self) -> float"""
1379  return _IMP_em.KernelParameters_get_rkdistsq(self)
1380 
1381 
1382  def get_lim(self):
1383  """get_lim(KernelParameters self) -> float"""
1384  return _IMP_em.KernelParameters_get_lim(self)
1385 
1386 
1387  def show(self, *args):
1388  """
1389  show(KernelParameters self, _ostream out)
1390  show(KernelParameters self)
1391  """
1392  return _IMP_em.KernelParameters_show(self, *args)
1393 
1394 
1395  def __str__(self):
1396  """__str__(KernelParameters self) -> std::string"""
1397  return _IMP_em.KernelParameters___str__(self)
1398 
1399 
1400  def __repr__(self):
1401  """__repr__(KernelParameters self) -> std::string"""
1402  return _IMP_em.KernelParameters___repr__(self)
1403 
1404 KernelParameters_swigregister = _IMP_em.KernelParameters_swigregister
1405 KernelParameters_swigregister(KernelParameters)
1406 
1407 GAUSSIAN = _IMP_em.GAUSSIAN
1408 BINARIZED_SPHERE = _IMP_em.BINARIZED_SPHERE
1409 SPHERE = _IMP_em.SPHERE
1410 class SampledDensityMap(DensityMap):
1411  """Proxy of C++ IMP::em::SampledDensityMap class."""
1412 
1413  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1414 
1415  def __init__(self, *args):
1416  """
1417  __init__(IMP::em::SampledDensityMap self, IMP::em::KernelType kt) -> SampledDensityMap
1418  __init__(IMP::em::SampledDensityMap self) -> SampledDensityMap
1419  __init__(IMP::em::SampledDensityMap self, DensityHeader header, IMP::em::KernelType kt) -> SampledDensityMap
1420  __init__(IMP::em::SampledDensityMap self, DensityHeader header) -> SampledDensityMap
1421  __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
1422  __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
1423  __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size, FloatKey mass_key) -> SampledDensityMap
1424  __init__(IMP::em::SampledDensityMap self, IMP::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size) -> SampledDensityMap
1425  """
1426  this = _IMP_em.new_SampledDensityMap(*args)
1427  try:
1428  self.this.append(this)
1429  except __builtin__.Exception:
1430  self.this = this
1431 
1432  def resample(self):
1433  """resample(SampledDensityMap self)"""
1434  return _IMP_em.SampledDensityMap_resample(self)
1435 
1436 
1437  def project(self, *args):
1438  """
1439  project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin, Vector3D shift, FloatKey mass_key)
1440  project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin, Vector3D shift)
1441  project(SampledDensityMap self, IMP::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin)
1442  """
1443  return _IMP_em.SampledDensityMap_project(self, *args)
1444 
1445 
1446  def set_particles(self, *args):
1447  """
1448  set_particles(SampledDensityMap self, IMP::ParticlesTemp const & ps, FloatKey mass_key)
1449  set_particles(SampledDensityMap self, IMP::ParticlesTemp const & ps)
1450  """
1451  return _IMP_em.SampledDensityMap_set_particles(self, *args)
1452 
1453 
1454  def get_xyzr_particles(self):
1455  """get_xyzr_particles(SampledDensityMap self) -> IMP::core::XYZRs const &"""
1456  return _IMP_em.SampledDensityMap_get_xyzr_particles(self)
1457 
1458 
1459  def get_sampled_particles(self):
1460  """get_sampled_particles(SampledDensityMap self) -> IMP::Particles const &"""
1461  return _IMP_em.SampledDensityMap_get_sampled_particles(self)
1462 
1463 
1464  def get_weight_key(self):
1465  """get_weight_key(SampledDensityMap self) -> FloatKey"""
1466  return _IMP_em.SampledDensityMap_get_weight_key(self)
1467 
1468 
1469  def get_minimum_resampled_value(self):
1470  """get_minimum_resampled_value(SampledDensityMap self) -> float"""
1471  return _IMP_em.SampledDensityMap_get_minimum_resampled_value(self)
1472 
1473 
1474  def update_resolution(self, res):
1475  """update_resolution(SampledDensityMap self, IMP::Float res)"""
1476  return _IMP_em.SampledDensityMap_update_resolution(self, res)
1477 
1478  __swig_destroy__ = _IMP_em.delete_SampledDensityMap
1479  __del__ = lambda self: None
1480 
1481  def __str__(self):
1482  """__str__(SampledDensityMap self) -> std::string"""
1483  return _IMP_em.SampledDensityMap___str__(self)
1484 
1485 
1486  def __repr__(self):
1487  """__repr__(SampledDensityMap self) -> std::string"""
1488  return _IMP_em.SampledDensityMap___repr__(self)
1489 
1490 
1491  @staticmethod
1492  def get_from(o):
1493  return _object_cast_to_SampledDensityMap(o)
1494 
1495 SampledDensityMap_swigregister = _IMP_em.SampledDensityMap_swigregister
1496 SampledDensityMap_swigregister(SampledDensityMap)
1497 
1498 IMP_DEFAULT_NUM_SHELLS = _IMP_em.IMP_DEFAULT_NUM_SHELLS
1499 IMP_SIG_CUTOFF = _IMP_em.IMP_SIG_CUTOFF
1500 class SurfaceShellDensityMap(SampledDensityMap):
1501  """Proxy of C++ IMP::em::SurfaceShellDensityMap class."""
1502 
1503  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1504 
1505  def __init__(self, *args):
1506  """
1507  __init__(IMP::em::SurfaceShellDensityMap self) -> SurfaceShellDensityMap
1508  __init__(IMP::em::SurfaceShellDensityMap self, DensityHeader header) -> SurfaceShellDensityMap
1509  __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key, int num_shells=5) -> SurfaceShellDensityMap
1510  __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key) -> SurfaceShellDensityMap
1511  __init__(IMP::em::SurfaceShellDensityMap self, IMP::ParticlesTemp const & ps, float voxel_size) -> SurfaceShellDensityMap
1512  """
1513  this = _IMP_em.new_SurfaceShellDensityMap(*args)
1514  try:
1515  self.this.append(this)
1516  except __builtin__.Exception:
1517  self.this = this
1518 
1519  def binarize(self, scene_val):
1520  """binarize(SurfaceShellDensityMap self, float scene_val)"""
1521  return _IMP_em.SurfaceShellDensityMap_binarize(self, scene_val)
1522 
1523 
1524  def has_background_neighbor(self, voxel_ind):
1525  """has_background_neighbor(SurfaceShellDensityMap self, long voxel_ind) -> bool"""
1526  return _IMP_em.SurfaceShellDensityMap_has_background_neighbor(self, voxel_ind)
1527 
1528  __swig_destroy__ = _IMP_em.delete_SurfaceShellDensityMap
1529  __del__ = lambda self: None
1530 
1531  def __str__(self):
1532  """__str__(SurfaceShellDensityMap self) -> std::string"""
1533  return _IMP_em.SurfaceShellDensityMap___str__(self)
1534 
1535 
1536  def __repr__(self):
1537  """__repr__(SurfaceShellDensityMap self) -> std::string"""
1538  return _IMP_em.SurfaceShellDensityMap___repr__(self)
1539 
1540 
1541  @staticmethod
1542  def get_from(o):
1543  return _object_cast_to_SurfaceShellDensityMap(o)
1544 
1545 SurfaceShellDensityMap_swigregister = _IMP_em.SurfaceShellDensityMap_swigregister
1546 SurfaceShellDensityMap_swigregister(SurfaceShellDensityMap)
1547 
1548 class CoarseCC(IMP.Object):
1549  """Proxy of C++ IMP::em::CoarseCC class."""
1550 
1551  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1552 
1553  def __init__(self):
1554  """__init__(IMP::em::CoarseCC self) -> CoarseCC"""
1555  this = _IMP_em.new_CoarseCC()
1556  try:
1557  self.this.append(this)
1558  except __builtin__.Exception:
1559  self.this = this
1560 
1561  def calc_score(*args):
1562  """
1563  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True, IMP::FloatPair norm_factors) -> float
1564  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True) -> float
1565  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1566  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1567  """
1568  return _IMP_em.CoarseCC_calc_score(*args)
1569 
1570  calc_score = staticmethod(calc_score)
1571 
1572  def cross_correlation_coefficient(*args):
1573  """
1574  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False, IMP::FloatPair norm_factors) -> double
1575  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1576  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1577  """
1578  return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1579 
1580  cross_correlation_coefficient = staticmethod(cross_correlation_coefficient)
1581 
1582  def local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold):
1583  """local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1584  return _IMP_em.CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold)
1585 
1586  local_cross_correlation_coefficient = staticmethod(local_cross_correlation_coefficient)
1587 
1588  def get_version_info(self):
1589  """get_version_info(CoarseCC self) -> VersionInfo"""
1590  return _IMP_em.CoarseCC_get_version_info(self)
1591 
1592 
1593  def __str__(self):
1594  """__str__(CoarseCC self) -> std::string"""
1595  return _IMP_em.CoarseCC___str__(self)
1596 
1597 
1598  def __repr__(self):
1599  """__repr__(CoarseCC self) -> std::string"""
1600  return _IMP_em.CoarseCC___repr__(self)
1601 
1602 
1603  @staticmethod
1604  def get_from(o):
1605  return _object_cast_to_CoarseCC(o)
1606 
1607 CoarseCC_swigregister = _IMP_em.CoarseCC_swigregister
1608 CoarseCC_swigregister(CoarseCC)
1609 
1610 def CoarseCC_calc_score(*args):
1611  """
1612  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True, IMP::FloatPair norm_factors) -> float
1613  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True, bool resample=True) -> float
1614  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1615  CoarseCC_calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1616  """
1617  return _IMP_em.CoarseCC_calc_score(*args)
1618 
1619 def CoarseCC_cross_correlation_coefficient(*args):
1620  """
1621  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False, IMP::FloatPair norm_factors) -> double
1622  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1623  CoarseCC_cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1624  """
1625  return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1626 
1627 def CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold):
1628  """CoarseCC_local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1629  return _IMP_em.CoarseCC_local_cross_correlation_coefficient(em_map, model_map, voxel_data_threshold)
1630 
1631 class CoarseConvolution(object):
1632  """Proxy of C++ IMP::em::CoarseConvolution class."""
1633 
1634  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1635  __repr__ = _swig_repr
1636 
1637  def convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac=True):
1638  """
1639  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1640  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1641  """
1642  return _IMP_em.CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac)
1643 
1644  convolution = staticmethod(convolution)
1645 
1646  def __init__(self):
1647  """__init__(IMP::em::CoarseConvolution self) -> CoarseConvolution"""
1648  this = _IMP_em.new_CoarseConvolution()
1649  try:
1650  self.this.append(this)
1651  except __builtin__.Exception:
1652  self.this = this
1653  __swig_destroy__ = _IMP_em.delete_CoarseConvolution
1654  __del__ = lambda self: None
1655 CoarseConvolution_swigregister = _IMP_em.CoarseConvolution_swigregister
1656 CoarseConvolution_swigregister(CoarseConvolution)
1657 
1658 def CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac=True):
1659  """
1660  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1661  CoarseConvolution_convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1662  """
1663  return _IMP_em.CoarseConvolution_convolution(em_map, model_map, voxel_data_threshold, recalc_ccnormfac)
1664 
1665 class CoarseCCatIntervals(CoarseCC):
1666  """Proxy of C++ IMP::em::CoarseCCatIntervals class."""
1667 
1668  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1669 
1670  def __init__(self, *args):
1671  """
1672  __init__(IMP::em::CoarseCCatIntervals self, int const & ncd) -> CoarseCCatIntervals
1673  __init__(IMP::em::CoarseCCatIntervals self) -> CoarseCCatIntervals
1674  """
1675  this = _IMP_em.new_CoarseCCatIntervals(*args)
1676  try:
1677  self.this.append(this)
1678  except __builtin__.Exception:
1679  self.this = this
1680 
1681  def evaluate(self, em_map, model_map, deriv, scalefac, lderiv, eval_interval):
1682  """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 >"""
1683  return _IMP_em.CoarseCCatIntervals_evaluate(self, em_map, model_map, deriv, scalefac, lderiv, eval_interval)
1684 
1685 
1686  def __str__(self):
1687  """__str__(CoarseCCatIntervals self) -> std::string"""
1688  return _IMP_em.CoarseCCatIntervals___str__(self)
1689 
1690 
1691  def __repr__(self):
1692  """__repr__(CoarseCCatIntervals self) -> std::string"""
1693  return _IMP_em.CoarseCCatIntervals___repr__(self)
1694 
1695 
1696  @staticmethod
1697  def get_from(o):
1698  return _object_cast_to_CoarseCCatIntervals(o)
1699 
1700 CoarseCCatIntervals_swigregister = _IMP_em.CoarseCCatIntervals_swigregister
1701 CoarseCCatIntervals_swigregister(CoarseCCatIntervals)
1702 
1703 class FitRestraint(IMP.Restraint):
1704  """Proxy of C++ IMP::em::FitRestraint class."""
1705 
1706  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1707 
1708  def __init__(self, *args):
1709  """
1710  __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
1711  __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
1712  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key, float scale=1) -> FitRestraint
1713  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors, FloatKey weight_key) -> FitRestraint
1714  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors) -> FitRestraint
1715  __init__(IMP::em::FitRestraint self, IMP::ParticlesTemp ps, DensityMap em_map) -> FitRestraint
1716  """
1717  this = _IMP_em.new_FitRestraint(*args)
1718  try:
1719  self.this.append(this)
1720  except __builtin__.Exception:
1721  self.this = this
1722 
1723  def get_model_dens_map(self):
1724  """get_model_dens_map(FitRestraint self) -> SampledDensityMap"""
1725  return _IMP_em.FitRestraint_get_model_dens_map(self)
1726 
1727 
1728  def set_scale_factor(self, scale):
1729  """set_scale_factor(FitRestraint self, float scale)"""
1730  return _IMP_em.FitRestraint_set_scale_factor(self, scale)
1731 
1732 
1733  def get_scale_factor(self):
1734  """get_scale_factor(FitRestraint self) -> float"""
1735  return _IMP_em.FitRestraint_get_scale_factor(self)
1736 
1737 
1738  def do_get_inputs(self):
1739  """do_get_inputs(FitRestraint self) -> IMP::ModelObjectsTemp"""
1740  return _IMP_em.FitRestraint_do_get_inputs(self)
1741 
1742 
1743  def get_version_info(self):
1744  """get_version_info(FitRestraint self) -> VersionInfo"""
1745  return _IMP_em.FitRestraint_get_version_info(self)
1746 
1747 
1748  def __str__(self):
1749  """__str__(FitRestraint self) -> std::string"""
1750  return _IMP_em.FitRestraint___str__(self)
1751 
1752 
1753  def __repr__(self):
1754  """__repr__(FitRestraint self) -> std::string"""
1755  return _IMP_em.FitRestraint___repr__(self)
1756 
1757 
1758  @staticmethod
1759  def get_from(o):
1760  return _object_cast_to_FitRestraint(o)
1761 
1762 
1763  def cast(r):
1764  """cast(Restraint r) -> FitRestraint"""
1765  return _IMP_em.FitRestraint_cast(r)
1766 
1767  cast = staticmethod(cast)
1768 FitRestraint_swigregister = _IMP_em.FitRestraint_swigregister
1769 FitRestraint_swigregister(FitRestraint)
1770 
1771 def FitRestraint_cast(r):
1772  """FitRestraint_cast(Restraint r) -> FitRestraint"""
1773  return _IMP_em.FitRestraint_cast(r)
1774 
1775 
1776 def density2particles(dmap, threshold, m, step=1):
1777  """
1778  density2particles(DensityMap dmap, IMP::Float threshold, Model m, int step=1) -> IMP::Particles
1779  density2particles(DensityMap dmap, IMP::Float threshold, Model m) -> IMP::Particles
1780  """
1781  return _IMP_em.density2particles(dmap, threshold, m, step)
1782 
1783 def density2vectors(dmap, threshold):
1784  """density2vectors(DensityMap dmap, IMP::Float threshold) -> IMP::algebra::Vector3Ds"""
1785  return _IMP_em.density2vectors(dmap, threshold)
1786 
1787 def particles2density(*args):
1788  """
1789  particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3, FloatKey weight_key) -> SampledDensityMap
1790  particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
1791  particles2density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
1792  """
1793  return _IMP_em.particles2density(*args)
1794 
1795 def particles2binarized_density(*args):
1796  """
1797  particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3, FloatKey weight_key) -> SampledDensityMap
1798  particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
1799  particles2binarized_density(IMP::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
1800  """
1801  return _IMP_em.particles2binarized_density(*args)
1802 
1803 def particles2surface(*args):
1804  """
1805  particles2surface(IMP::ParticlesTemp const & ps, IMP::Float apix, FloatKey weight_key) -> SurfaceShellDensityMap
1806  particles2surface(IMP::ParticlesTemp const & ps, IMP::Float apix) -> SurfaceShellDensityMap
1807  """
1808  return _IMP_em.particles2surface(*args)
1809 
1810 def calculate_intersection_score(d1, d2):
1811  """calculate_intersection_score(SurfaceShellDensityMap d1, SurfaceShellDensityMap d2) -> IMP::Float"""
1812  return _IMP_em.calculate_intersection_score(d1, d2)
1813 class SpiderHeader(object):
1814  """Proxy of C++ IMP::em::SpiderHeader class."""
1815 
1816  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1817  __repr__ = _swig_repr
1818  fNslice = _swig_property(_IMP_em.SpiderHeader_fNslice_get, _IMP_em.SpiderHeader_fNslice_set)
1819  fNrow = _swig_property(_IMP_em.SpiderHeader_fNrow_get, _IMP_em.SpiderHeader_fNrow_set)
1820  fNrec = _swig_property(_IMP_em.SpiderHeader_fNrec_get, _IMP_em.SpiderHeader_fNrec_set)
1821  fNlabel = _swig_property(_IMP_em.SpiderHeader_fNlabel_get, _IMP_em.SpiderHeader_fNlabel_set)
1822  fIform = _swig_property(_IMP_em.SpiderHeader_fIform_get, _IMP_em.SpiderHeader_fIform_set)
1823  fImami = _swig_property(_IMP_em.SpiderHeader_fImami_get, _IMP_em.SpiderHeader_fImami_set)
1824  fFmax = _swig_property(_IMP_em.SpiderHeader_fFmax_get, _IMP_em.SpiderHeader_fFmax_set)
1825  fFmin = _swig_property(_IMP_em.SpiderHeader_fFmin_get, _IMP_em.SpiderHeader_fFmin_set)
1826  fAv = _swig_property(_IMP_em.SpiderHeader_fAv_get, _IMP_em.SpiderHeader_fAv_set)
1827  fSig = _swig_property(_IMP_em.SpiderHeader_fSig_get, _IMP_em.SpiderHeader_fSig_set)
1828  fIhist = _swig_property(_IMP_em.SpiderHeader_fIhist_get, _IMP_em.SpiderHeader_fIhist_set)
1829  fNcol = _swig_property(_IMP_em.SpiderHeader_fNcol_get, _IMP_em.SpiderHeader_fNcol_set)
1830  fLabrec = _swig_property(_IMP_em.SpiderHeader_fLabrec_get, _IMP_em.SpiderHeader_fLabrec_set)
1831  fIangle = _swig_property(_IMP_em.SpiderHeader_fIangle_get, _IMP_em.SpiderHeader_fIangle_set)
1832  fPhi = _swig_property(_IMP_em.SpiderHeader_fPhi_get, _IMP_em.SpiderHeader_fPhi_set)
1833  fTheta = _swig_property(_IMP_em.SpiderHeader_fTheta_get, _IMP_em.SpiderHeader_fTheta_set)
1834  fPsi = _swig_property(_IMP_em.SpiderHeader_fPsi_get, _IMP_em.SpiderHeader_fPsi_set)
1835  fXoff = _swig_property(_IMP_em.SpiderHeader_fXoff_get, _IMP_em.SpiderHeader_fXoff_set)
1836  fYoff = _swig_property(_IMP_em.SpiderHeader_fYoff_get, _IMP_em.SpiderHeader_fYoff_set)
1837  fZoff = _swig_property(_IMP_em.SpiderHeader_fZoff_get, _IMP_em.SpiderHeader_fZoff_set)
1838  fScale = _swig_property(_IMP_em.SpiderHeader_fScale_get, _IMP_em.SpiderHeader_fScale_set)
1839  fLabbyt = _swig_property(_IMP_em.SpiderHeader_fLabbyt_get, _IMP_em.SpiderHeader_fLabbyt_set)
1840  fLenbyt = _swig_property(_IMP_em.SpiderHeader_fLenbyt_get, _IMP_em.SpiderHeader_fLenbyt_set)
1841  fNothing = _swig_property(_IMP_em.SpiderHeader_fNothing_get, _IMP_em.SpiderHeader_fNothing_set)
1842  fFlag = _swig_property(_IMP_em.SpiderHeader_fFlag_get, _IMP_em.SpiderHeader_fFlag_set)
1843  fPhi1 = _swig_property(_IMP_em.SpiderHeader_fPhi1_get, _IMP_em.SpiderHeader_fPhi1_set)
1844  fTheta1 = _swig_property(_IMP_em.SpiderHeader_fTheta1_get, _IMP_em.SpiderHeader_fTheta1_set)
1845  fPsi1 = _swig_property(_IMP_em.SpiderHeader_fPsi1_get, _IMP_em.SpiderHeader_fPsi1_set)
1846  fPhi2 = _swig_property(_IMP_em.SpiderHeader_fPhi2_get, _IMP_em.SpiderHeader_fPhi2_set)
1847  fTheta2 = _swig_property(_IMP_em.SpiderHeader_fTheta2_get, _IMP_em.SpiderHeader_fTheta2_set)
1848  fPsi2 = _swig_property(_IMP_em.SpiderHeader_fPsi2_get, _IMP_em.SpiderHeader_fPsi2_set)
1849  fGeo_matrix = _swig_property(_IMP_em.SpiderHeader_fGeo_matrix_get, _IMP_em.SpiderHeader_fGeo_matrix_set)
1850  fAngle1 = _swig_property(_IMP_em.SpiderHeader_fAngle1_get, _IMP_em.SpiderHeader_fAngle1_set)
1851  fr1 = _swig_property(_IMP_em.SpiderHeader_fr1_get, _IMP_em.SpiderHeader_fr1_set)
1852  fr2 = _swig_property(_IMP_em.SpiderHeader_fr2_get, _IMP_em.SpiderHeader_fr2_set)
1853  RTflag = _swig_property(_IMP_em.SpiderHeader_RTflag_get, _IMP_em.SpiderHeader_RTflag_set)
1854  Astart = _swig_property(_IMP_em.SpiderHeader_Astart_get, _IMP_em.SpiderHeader_Astart_set)
1855  Aend = _swig_property(_IMP_em.SpiderHeader_Aend_get, _IMP_em.SpiderHeader_Aend_set)
1856  Ainc = _swig_property(_IMP_em.SpiderHeader_Ainc_get, _IMP_em.SpiderHeader_Ainc_set)
1857  Rsigma = _swig_property(_IMP_em.SpiderHeader_Rsigma_get, _IMP_em.SpiderHeader_Rsigma_set)
1858  Tstart = _swig_property(_IMP_em.SpiderHeader_Tstart_get, _IMP_em.SpiderHeader_Tstart_set)
1859  Tend = _swig_property(_IMP_em.SpiderHeader_Tend_get, _IMP_em.SpiderHeader_Tend_set)
1860  Tinc = _swig_property(_IMP_em.SpiderHeader_Tinc_get, _IMP_em.SpiderHeader_Tinc_set)
1861  Weight = _swig_property(_IMP_em.SpiderHeader_Weight_get, _IMP_em.SpiderHeader_Weight_set)
1862  Flip = _swig_property(_IMP_em.SpiderHeader_Flip_get, _IMP_em.SpiderHeader_Flip_set)
1863  empty = _swig_property(_IMP_em.SpiderHeader_empty_get, _IMP_em.SpiderHeader_empty_set)
1864  szIDat = _swig_property(_IMP_em.SpiderHeader_szIDat_get, _IMP_em.SpiderHeader_szIDat_set)
1865  szITim = _swig_property(_IMP_em.SpiderHeader_szITim_get, _IMP_em.SpiderHeader_szITim_set)
1866  szITit = _swig_property(_IMP_em.SpiderHeader_szITit_get, _IMP_em.SpiderHeader_szITit_set)
1867 
1868  def show(self, out):
1869  """show(SpiderHeader self, _ostream out)"""
1870  return _IMP_em.SpiderHeader_show(self, out)
1871 
1872 
1873  def __init__(self):
1874  """__init__(IMP::em::SpiderHeader self) -> SpiderHeader"""
1875  this = _IMP_em.new_SpiderHeader()
1876  try:
1877  self.this.append(this)
1878  except __builtin__.Exception:
1879  self.this = this
1880  __swig_destroy__ = _IMP_em.delete_SpiderHeader
1881  __del__ = lambda self: None
1882 SpiderHeader_swigregister = _IMP_em.SpiderHeader_swigregister
1883 SpiderHeader_swigregister(SpiderHeader)
1884 
1885 class ImageHeader(object):
1886  """Proxy of C++ IMP::em::ImageHeader class."""
1887 
1888  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1889  __repr__ = _swig_repr
1890  IMG_BYTE = _IMP_em.ImageHeader_IMG_BYTE
1891  IMG_IMPEM = _IMP_em.ImageHeader_IMG_IMPEM
1892  IMG_INT = _IMP_em.ImageHeader_IMG_INT
1893  VOL_BYTE = _IMP_em.ImageHeader_VOL_BYTE
1894  VOL_IMPEM = _IMP_em.ImageHeader_VOL_IMPEM
1895  VOL_INT = _IMP_em.ImageHeader_VOL_INT
1896  IMG_FOURIER = _IMP_em.ImageHeader_IMG_FOURIER
1897  VOL_FOURIER = _IMP_em.ImageHeader_VOL_FOURIER
1898 
1899  def __init__(self, *args):
1900  """
1901  __init__(IMP::em::ImageHeader self) -> ImageHeader
1902  __init__(IMP::em::ImageHeader self, IMP::em::ImageHeader::img_type im) -> ImageHeader
1903  __init__(IMP::em::ImageHeader self, float im) -> ImageHeader
1904  """
1905  this = _IMP_em.new_ImageHeader(*args)
1906  try:
1907  self.this.append(this)
1908  except __builtin__.Exception:
1909  self.this = this
1910 
1911  def get_image_type(self):
1912  """get_image_type(ImageHeader self) -> float"""
1913  return _IMP_em.ImageHeader_get_image_type(self)
1914 
1915 
1916  def set_image_type(self, *args):
1917  """
1918  set_image_type(ImageHeader self, IMP::em::ImageHeader::img_type im)
1919  set_image_type(ImageHeader self, float im)
1920  """
1921  return _IMP_em.ImageHeader_set_image_type(self, *args)
1922 
1923 
1924  def do_show(self, out):
1925  """do_show(ImageHeader self, _ostream out)"""
1926  return _IMP_em.ImageHeader_do_show(self, out)
1927 
1928 
1929  def show(self, *args):
1930  """
1931  show(ImageHeader self, _ostream out)
1932  show(ImageHeader self)
1933  """
1934  return _IMP_em.ImageHeader_show(self, *args)
1935 
1936 
1937  def print_hard(self, out):
1938  """print_hard(ImageHeader self, _ostream out)"""
1939  return _IMP_em.ImageHeader_print_hard(self, out)
1940 
1941 
1942  def show_projection_params(self, out):
1943  """show_projection_params(ImageHeader self, _ostream out)"""
1944  return _IMP_em.ImageHeader_show_projection_params(self, out)
1945 
1946 
1947  def read(self, *args):
1948  """
1949  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False, bool skip_extra_checkings=False) -> int
1950  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False) -> int
1951  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False) -> int
1952  read(ImageHeader self, IMP::String const filename) -> int
1953  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False, bool skip_extra_checkings=False) -> bool
1954  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False) -> bool
1955  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False) -> bool
1956  read(ImageHeader self, std::ifstream & f) -> bool
1957  """
1958  return _IMP_em.ImageHeader_read(self, *args)
1959 
1960 
1961  def write(self, *args):
1962  """
1963  write(ImageHeader self, IMP::String const & filename, bool force_reversed=False)
1964  write(ImageHeader self, IMP::String const & filename)
1965  write(ImageHeader self, std::ofstream & f, bool force_reversed=False)
1966  write(ImageHeader self, std::ofstream & f)
1967  """
1968  return _IMP_em.ImageHeader_write(self, *args)
1969 
1970 
1971  def clear(self):
1972  """clear(ImageHeader self)"""
1973  return _IMP_em.ImageHeader_clear(self)
1974 
1975 
1976  def set_header(self):
1977  """set_header(ImageHeader self)"""
1978  return _IMP_em.ImageHeader_set_header(self)
1979 
1980 
1981  def get_reversed(self):
1982  """get_reversed(ImageHeader self) -> bool"""
1983  return _IMP_em.ImageHeader_get_reversed(self)
1984 
1985 
1986  def set_reversed(self, value):
1987  """set_reversed(ImageHeader self, bool value)"""
1988  return _IMP_em.ImageHeader_set_reversed(self, value)
1989 
1990 
1991  def get_number_of_slices(self):
1992  """get_number_of_slices(ImageHeader self) -> unsigned int"""
1993  return _IMP_em.ImageHeader_get_number_of_slices(self)
1994 
1995 
1996  def set_number_of_slices(self, n):
1997  """set_number_of_slices(ImageHeader self, unsigned int n)"""
1998  return _IMP_em.ImageHeader_set_number_of_slices(self, n)
1999 
2000 
2001  def get_number_of_rows(self):
2002  """get_number_of_rows(ImageHeader self) -> unsigned int"""
2003  return _IMP_em.ImageHeader_get_number_of_rows(self)
2004 
2005 
2006  def set_number_of_rows(self, n):
2007  """set_number_of_rows(ImageHeader self, unsigned int n)"""
2008  return _IMP_em.ImageHeader_set_number_of_rows(self, n)
2009 
2010 
2011  def get_number_of_columns(self):
2012  """get_number_of_columns(ImageHeader self) -> unsigned int"""
2013  return _IMP_em.ImageHeader_get_number_of_columns(self)
2014 
2015 
2016  def set_number_of_columns(self, n):
2017  """set_number_of_columns(ImageHeader self, unsigned int n)"""
2018  return _IMP_em.ImageHeader_set_number_of_columns(self, n)
2019 
2020 
2021  def get_old_rot(self):
2022  """get_old_rot(ImageHeader self) -> float"""
2023  return _IMP_em.ImageHeader_get_old_rot(self)
2024 
2025 
2026  def set_old_rot(self, value):
2027  """set_old_rot(ImageHeader self, float value)"""
2028  return _IMP_em.ImageHeader_set_old_rot(self, value)
2029 
2030 
2031  def get_fAngle1(self):
2032  """get_fAngle1(ImageHeader self) -> float"""
2033  return _IMP_em.ImageHeader_get_fAngle1(self)
2034 
2035 
2036  def set_fAngle1(self, value):
2037  """set_fAngle1(ImageHeader self, float value)"""
2038  return _IMP_em.ImageHeader_set_fAngle1(self, value)
2039 
2040 
2041  def get_Scale(self):
2042  """get_Scale(ImageHeader self) -> float"""
2043  return _IMP_em.ImageHeader_get_Scale(self)
2044 
2045 
2046  def set_Scale(self, value):
2047  """set_Scale(ImageHeader self, float value)"""
2048  return _IMP_em.ImageHeader_set_Scale(self, value)
2049 
2050 
2051  def get_Flip(self):
2052  """get_Flip(ImageHeader self) -> float"""
2053  return _IMP_em.ImageHeader_get_Flip(self)
2054 
2055 
2056  def set_Flip(self, value):
2057  """set_Flip(ImageHeader self, float value)"""
2058  return _IMP_em.ImageHeader_set_Flip(self, value)
2059 
2060 
2061  def get_Weight(self):
2062  """get_Weight(ImageHeader self) -> float"""
2063  return _IMP_em.ImageHeader_get_Weight(self)
2064 
2065 
2066  def set_Weight(self, value):
2067  """set_Weight(ImageHeader self, float value)"""
2068  return _IMP_em.ImageHeader_set_Weight(self, value)
2069 
2070 
2071  def get_fNrec(self):
2072  """get_fNrec(ImageHeader self) -> float"""
2073  return _IMP_em.ImageHeader_get_fNrec(self)
2074 
2075 
2076  def set_fNrec(self, value):
2077  """set_fNrec(ImageHeader self, float value)"""
2078  return _IMP_em.ImageHeader_set_fNrec(self, value)
2079 
2080 
2081  def get_fNlabel(self):
2082  """get_fNlabel(ImageHeader self) -> float"""
2083  return _IMP_em.ImageHeader_get_fNlabel(self)
2084 
2085 
2086  def set_fNlabel(self, value):
2087  """set_fNlabel(ImageHeader self, float value)"""
2088  return _IMP_em.ImageHeader_set_fNlabel(self, value)
2089 
2090 
2091  def get_fIform(self):
2092  """get_fIform(ImageHeader self) -> float"""
2093  return _IMP_em.ImageHeader_get_fIform(self)
2094 
2095 
2096  def set_fIform(self, value):
2097  """set_fIform(ImageHeader self, float value)"""
2098  return _IMP_em.ImageHeader_set_fIform(self, value)
2099 
2100 
2101  def get_fImami(self):
2102  """get_fImami(ImageHeader self) -> float"""
2103  return _IMP_em.ImageHeader_get_fImami(self)
2104 
2105 
2106  def set_fImami(self, value):
2107  """set_fImami(ImageHeader self, float value)"""
2108  return _IMP_em.ImageHeader_set_fImami(self, value)
2109 
2110 
2111  def get_fFmax(self):
2112  """get_fFmax(ImageHeader self) -> float"""
2113  return _IMP_em.ImageHeader_get_fFmax(self)
2114 
2115 
2116  def set_fFmax(self, value):
2117  """set_fFmax(ImageHeader self, float value)"""
2118  return _IMP_em.ImageHeader_set_fFmax(self, value)
2119 
2120 
2121  def get_fFmin(self):
2122  """get_fFmin(ImageHeader self) -> float"""
2123  return _IMP_em.ImageHeader_get_fFmin(self)
2124 
2125 
2126  def set_fFmin(self, value):
2127  """set_fFmin(ImageHeader self, float value)"""
2128  return _IMP_em.ImageHeader_set_fFmin(self, value)
2129 
2130 
2131  def get_fAv(self):
2132  """get_fAv(ImageHeader self) -> float"""
2133  return _IMP_em.ImageHeader_get_fAv(self)
2134 
2135 
2136  def set_fAv(self, value):
2137  """set_fAv(ImageHeader self, float value)"""
2138  return _IMP_em.ImageHeader_set_fAv(self, value)
2139 
2140 
2141  def get_fSig(self):
2142  """get_fSig(ImageHeader self) -> float"""
2143  return _IMP_em.ImageHeader_get_fSig(self)
2144 
2145 
2146  def set_fSig(self, value):
2147  """set_fSig(ImageHeader self, float value)"""
2148  return _IMP_em.ImageHeader_set_fSig(self, value)
2149 
2150 
2151  def get_fIhist(self):
2152  """get_fIhist(ImageHeader self) -> float"""
2153  return _IMP_em.ImageHeader_get_fIhist(self)
2154 
2155 
2156  def set_fIhist(self, value):
2157  """set_fIhist(ImageHeader self, float value)"""
2158  return _IMP_em.ImageHeader_set_fIhist(self, value)
2159 
2160 
2161  def get_fLabrec(self):
2162  """get_fLabrec(ImageHeader self) -> float"""
2163  return _IMP_em.ImageHeader_get_fLabrec(self)
2164 
2165 
2166  def set_fLabrec(self, value):
2167  """set_fLabrec(ImageHeader self, float value)"""
2168  return _IMP_em.ImageHeader_set_fLabrec(self, value)
2169 
2170 
2171  def get_fIangle(self):
2172  """get_fIangle(ImageHeader self) -> float"""
2173  return _IMP_em.ImageHeader_get_fIangle(self)
2174 
2175 
2176  def set_fIangle(self, value):
2177  """set_fIangle(ImageHeader self, float value)"""
2178  return _IMP_em.ImageHeader_set_fIangle(self, value)
2179 
2180 
2181  def get_origin(self):
2182  """get_origin(ImageHeader self) -> Vector3D"""
2183  return _IMP_em.ImageHeader_get_origin(self)
2184 
2185 
2186  def set_origin(self, *args):
2187  """
2188  set_origin(ImageHeader self, Vector3D v)
2189  set_origin(ImageHeader self, Vector2D v)
2190  """
2191  return _IMP_em.ImageHeader_set_origin(self, *args)
2192 
2193 
2194  def get_object_pixel_size(self):
2195  """get_object_pixel_size(ImageHeader self) -> float"""
2196  return _IMP_em.ImageHeader_get_object_pixel_size(self)
2197 
2198 
2199  def set_object_pixel_size(self, value):
2200  """set_object_pixel_size(ImageHeader self, float value)"""
2201  return _IMP_em.ImageHeader_set_object_pixel_size(self, value)
2202 
2203 
2204  def get_fLabbyt(self):
2205  """get_fLabbyt(ImageHeader self) -> float"""
2206  return _IMP_em.ImageHeader_get_fLabbyt(self)
2207 
2208 
2209  def set_fLabbyt(self, value):
2210  """set_fLabbyt(ImageHeader self, float value)"""
2211  return _IMP_em.ImageHeader_set_fLabbyt(self, value)
2212 
2213 
2214  def get_fLenbyt(self):
2215  """get_fLenbyt(ImageHeader self) -> float"""
2216  return _IMP_em.ImageHeader_get_fLenbyt(self)
2217 
2218 
2219  def set_fLenbyt(self, value):
2220  """set_fLenbyt(ImageHeader self, float value)"""
2221  return _IMP_em.ImageHeader_set_fLenbyt(self, value)
2222 
2223 
2224  def get_fGeo_matrix(self, i, j):
2225  """get_fGeo_matrix(ImageHeader self, unsigned int i, unsigned int j) -> double"""
2226  return _IMP_em.ImageHeader_get_fGeo_matrix(self, i, j)
2227 
2228 
2229  def get_fFlag(self):
2230  """get_fFlag(ImageHeader self) -> float"""
2231  return _IMP_em.ImageHeader_get_fFlag(self)
2232 
2233 
2234  def set_fFlag(self, value):
2235  """set_fFlag(ImageHeader self, float value)"""
2236  return _IMP_em.ImageHeader_set_fFlag(self, value)
2237 
2238 
2239  def get_euler_angles(self):
2240  """get_euler_angles(ImageHeader self) -> Vector3D"""
2241  return _IMP_em.ImageHeader_get_euler_angles(self)
2242 
2243 
2244  def get_euler_angles1(self):
2245  """get_euler_angles1(ImageHeader self) -> Vector3D"""
2246  return _IMP_em.ImageHeader_get_euler_angles1(self)
2247 
2248 
2249  def get_euler_angles2(self):
2250  """get_euler_angles2(ImageHeader self) -> Vector3D"""
2251  return _IMP_em.ImageHeader_get_euler_angles2(self)
2252 
2253 
2254  def set_euler_angles(self, euler):
2255  """set_euler_angles(ImageHeader self, Vector3D euler)"""
2256  return _IMP_em.ImageHeader_set_euler_angles(self, euler)
2257 
2258 
2259  def set_euler_angles1(self, euler):
2260  """set_euler_angles1(ImageHeader self, Vector3D euler)"""
2261  return _IMP_em.ImageHeader_set_euler_angles1(self, euler)
2262 
2263 
2264  def set_euler_angles2(self, euler):
2265  """set_euler_angles2(ImageHeader self, Vector3D euler)"""
2266  return _IMP_em.ImageHeader_set_euler_angles2(self, euler)
2267 
2268 
2269  def is_normalized(self):
2270  """is_normalized(ImageHeader self) -> bool"""
2271  return _IMP_em.ImageHeader_is_normalized(self)
2272 
2273 
2274  def set_date(self):
2275  """set_date(ImageHeader self)"""
2276  return _IMP_em.ImageHeader_set_date(self)
2277 
2278 
2279  def set_time(self):
2280  """set_time(ImageHeader self)"""
2281  return _IMP_em.ImageHeader_set_time(self)
2282 
2283 
2284  def set_title(self, newName):
2285  """set_title(ImageHeader self, IMP::String newName)"""
2286  return _IMP_em.ImageHeader_set_title(self, newName)
2287 
2288  __swig_destroy__ = _IMP_em.delete_ImageHeader
2289  __del__ = lambda self: None
2290 ImageHeader_swigregister = _IMP_em.ImageHeader_swigregister
2291 ImageHeader_swigregister(ImageHeader)
2292 
2293 class SpiderMapReaderWriter(MapReaderWriter):
2294  """Proxy of C++ IMP::em::SpiderMapReaderWriter class."""
2295 
2296  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2297  filename_ = _swig_property(_IMP_em.SpiderMapReaderWriter_filename__get, _IMP_em.SpiderMapReaderWriter_filename__set)
2298  skip_type_check_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_type_check__get, _IMP_em.SpiderMapReaderWriter_skip_type_check__set)
2299  force_reversed_ = _swig_property(_IMP_em.SpiderMapReaderWriter_force_reversed__get, _IMP_em.SpiderMapReaderWriter_force_reversed__set)
2300  skip_extra_checkings_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_extra_checkings__get, _IMP_em.SpiderMapReaderWriter_skip_extra_checkings__set)
2301 
2302  def __init__(self, *args):
2303  """
2304  __init__(IMP::em::SpiderMapReaderWriter self) -> SpiderMapReaderWriter
2305  __init__(IMP::em::SpiderMapReaderWriter self, IMP::String filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings) -> SpiderMapReaderWriter
2306  """
2307  this = _IMP_em.new_SpiderMapReaderWriter(*args)
2308  try:
2309  self.this.append(this)
2310  except __builtin__.Exception:
2311  self.this = this
2312 
2313  def __str__(self):
2314  """__str__(SpiderMapReaderWriter self) -> std::string"""
2315  return _IMP_em.SpiderMapReaderWriter___str__(self)
2316 
2317 
2318  def __repr__(self):
2319  """__repr__(SpiderMapReaderWriter self) -> std::string"""
2320  return _IMP_em.SpiderMapReaderWriter___repr__(self)
2321 
2322 
2323  @staticmethod
2324  def get_from(o):
2325  return _object_cast_to_SpiderMapReaderWriter(o)
2326 
2327 SpiderMapReaderWriter_swigregister = _IMP_em.SpiderMapReaderWriter_swigregister
2328 SpiderMapReaderWriter_swigregister(SpiderMapReaderWriter)
2329 
2330 class FittingSolutions(object):
2331  """Proxy of C++ IMP::em::FittingSolutions class."""
2332 
2333  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2334 
2335  def __init__(self):
2336  """__init__(IMP::em::FittingSolutions self) -> FittingSolutions"""
2337  this = _IMP_em.new_FittingSolutions()
2338  try:
2339  self.this.append(this)
2340  except __builtin__.Exception:
2341  self.this = this
2342 
2343  def get_number_of_solutions(self):
2344  """get_number_of_solutions(FittingSolutions self) -> int"""
2345  return _IMP_em.FittingSolutions_get_number_of_solutions(self)
2346 
2347 
2348  def get_transformation(self, i):
2349  """get_transformation(FittingSolutions self, unsigned int i) -> Transformation3D"""
2350  return _IMP_em.FittingSolutions_get_transformation(self, i)
2351 
2352 
2353  def get_score(self, i):
2354  """get_score(FittingSolutions self, unsigned int i) -> IMP::Float"""
2355  return _IMP_em.FittingSolutions_get_score(self, i)
2356 
2357 
2358  def set_score(self, i, score):
2359  """set_score(FittingSolutions self, unsigned int i, IMP::Float score)"""
2360  return _IMP_em.FittingSolutions_set_score(self, i, score)
2361 
2362 
2363  def add_solution(self, t, score):
2364  """add_solution(FittingSolutions self, Transformation3D t, IMP::Float score)"""
2365  return _IMP_em.FittingSolutions_add_solution(self, t, score)
2366 
2367 
2368  def sort(self, reverse=False):
2369  """
2370  sort(FittingSolutions self, bool reverse=False)
2371  sort(FittingSolutions self)
2372  """
2373  return _IMP_em.FittingSolutions_sort(self, reverse)
2374 
2375 
2376  def multiply(self, t):
2377  """multiply(FittingSolutions self, Transformation3D t)"""
2378  return _IMP_em.FittingSolutions_multiply(self, t)
2379 
2380 
2381  def get_transformations(self):
2382  """get_transformations(FittingSolutions self) -> IMP::algebra::Transformation3Ds"""
2383  return _IMP_em.FittingSolutions_get_transformations(self)
2384 
2385 
2386  def show(self, *args):
2387  """
2388  show(FittingSolutions self, _ostream out)
2389  show(FittingSolutions self)
2390  """
2391  return _IMP_em.FittingSolutions_show(self, *args)
2392 
2393 
2394  def __str__(self):
2395  """__str__(FittingSolutions self) -> std::string"""
2396  return _IMP_em.FittingSolutions___str__(self)
2397 
2398 
2399  def __repr__(self):
2400  """__repr__(FittingSolutions self) -> std::string"""
2401  return _IMP_em.FittingSolutions___repr__(self)
2402 
2403  __swig_destroy__ = _IMP_em.delete_FittingSolutions
2404  __del__ = lambda self: None
2405 FittingSolutions_swigregister = _IMP_em.FittingSolutions_swigregister
2406 FittingSolutions_swigregister(FittingSolutions)
2407 
2408 
2409 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):
2410  """
2411  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
2412  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
2413  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
2414  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
2415  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
2416  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
2417  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid, IMP::OptimizerStates display_log) -> FittingSolutions
2418  """
2419  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)
2420 
2421 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):
2422  """
2423  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
2424  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
2425  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
2426  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
2427  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
2428  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2429  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::OptimizerStates display_log) -> FittingSolutions
2430  """
2431  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)
2432 
2433 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):
2434  """
2435  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
2436  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
2437  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
2438  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
2439  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
2440  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
2441  """
2442  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)
2443 
2444 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):
2445  """
2446  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
2447  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
2448  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
2449  local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2) -> FittingSolutions
2450  local_rigid_fitting_grid_search(IMP::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap) -> FittingSolutions
2451  """
2452  return _IMP_em.local_rigid_fitting_grid_search(ps, wei_key, dmap, max_voxels_translation, translation_step, max_angle_in_radians, number_of_rotations)
2453 
2454 def compute_fitting_scores(*args):
2455  """
2456  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
2457  compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations, bool fast_version=False, bool local_score=False) -> FittingSolutions
2458  compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations, bool fast_version=False) -> FittingSolutions
2459  compute_fitting_scores(IMP::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2460  compute_fitting_scores(DensityMap em_map, RigidBody rb, Refiner refiner, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2461  """
2462  return _IMP_em.compute_fitting_scores(*args)
2463 
2464 def compute_fitting_score(*args):
2465  """
2466  compute_fitting_score(IMP::ParticlesTemp const & ps, DensityMap em_map, FloatKey wei_key) -> IMP::Float
2467  compute_fitting_score(IMP::ParticlesTemp const & ps, DensityMap em_map) -> IMP::Float
2468  """
2469  return _IMP_em.compute_fitting_score(*args)
2470 
2472  """
2473  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, Transformation3D t, float thr=0.0) -> long
2474  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, Transformation3D t) -> long
2475  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps) -> long
2476  """
2477  return _IMP_em.get_number_of_particles_outside_of_the_density(*args)
2478 
2479 def get_numbers_of_particles_outside_of_the_density(dmap, ps, transformations, thr=0.0):
2480  """
2481  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
2482  get_numbers_of_particles_outside_of_the_density(DensityMap dmap, IMP::Particles const & ps, IMP::algebra::Transformation3Ds const & transformations) -> IMP::Ints
2483  """
2484  return _IMP_em.get_numbers_of_particles_outside_of_the_density(dmap, ps, transformations, thr)
2485 
2487  """
2488  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3., Transformation3D t, float thr=0.0) -> double
2489  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3., Transformation3D t) -> double
2490  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps, float smoothing_radius=3.) -> double
2491  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::Particles const & ps) -> double
2492  """
2493  return _IMP_em.get_percentage_of_voxels_covered_by_particles(*args)
2494 class HighDensityEmbedding(IMP.statistics.Embedding):
2495  """Proxy of C++ IMP::em::HighDensityEmbedding class."""
2496 
2497  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2498 
2499  def __init__(self, dm, threshold):
2500  """__init__(IMP::em::HighDensityEmbedding self, DensityMap dm, double threshold) -> HighDensityEmbedding"""
2501  this = _IMP_em.new_HighDensityEmbedding(dm, threshold)
2502  try:
2503  self.this.append(this)
2504  except __builtin__.Exception:
2505  self.this = this
2506 
2507  def get_version_info(self):
2508  """get_version_info(HighDensityEmbedding self) -> VersionInfo"""
2509  return _IMP_em.HighDensityEmbedding_get_version_info(self)
2510 
2511 
2512  def __str__(self):
2513  """__str__(HighDensityEmbedding self) -> std::string"""
2514  return _IMP_em.HighDensityEmbedding___str__(self)
2515 
2516 
2517  def __repr__(self):
2518  """__repr__(HighDensityEmbedding self) -> std::string"""
2519  return _IMP_em.HighDensityEmbedding___repr__(self)
2520 
2521 
2522  @staticmethod
2523  def get_from(o):
2524  return _object_cast_to_HighDensityEmbedding(o)
2525 
2526 HighDensityEmbedding_swigregister = _IMP_em.HighDensityEmbedding_swigregister
2527 HighDensityEmbedding_swigregister(HighDensityEmbedding)
2528 
2529 
2530 def mask_and_norm(dmap, mask):
2531  """mask_and_norm(DensityMap dmap, DensityMap mask) -> DensityMap"""
2532  return _IMP_em.mask_and_norm(dmap, mask)
2533 
2534 def get_volume_at_threshold(m, threshold):
2535  """get_volume_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float"""
2536  return _IMP_em.get_volume_at_threshold(m, threshold)
2537 
2539  """
2540  get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold, IMP::atom::ProteinDensityReference ref) -> IMP::Float
2541  get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float
2542  """
2543  return _IMP_em.get_molecular_mass_at_threshold(*args)
2544 
2545 def get_threshold_for_approximate_volume(m, desired_volume):
2546  """get_threshold_for_approximate_volume(DensityMap m, IMP::Float desired_volume) -> IMP::Float"""
2547  return _IMP_em.get_threshold_for_approximate_volume(m, desired_volume)
2548 
2550  """
2551  get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass, IMP::atom::ProteinDensityReference ref) -> IMP::Float
2552  get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass) -> IMP::Float
2553  """
2554  return _IMP_em.get_threshold_for_approximate_mass(*args)
2555 class EnvelopePenetrationRestraint(IMP.Restraint):
2556  """Proxy of C++ IMP::em::EnvelopePenetrationRestraint class."""
2557 
2558  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2559 
2560  def __init__(self, ps, em_map, threshold):
2561  """__init__(IMP::em::EnvelopePenetrationRestraint self, IMP::Particles ps, DensityMap em_map, IMP::Float threshold) -> EnvelopePenetrationRestraint"""
2562  this = _IMP_em.new_EnvelopePenetrationRestraint(ps, em_map, threshold)
2563  try:
2564  self.this.append(this)
2565  except __builtin__.Exception:
2566  self.this = this
2567 
2568  def do_get_inputs(self):
2569  """do_get_inputs(EnvelopePenetrationRestraint self) -> IMP::ModelObjectsTemp"""
2570  return _IMP_em.EnvelopePenetrationRestraint_do_get_inputs(self)
2571 
2572 
2573  def get_version_info(self):
2574  """get_version_info(EnvelopePenetrationRestraint self) -> VersionInfo"""
2575  return _IMP_em.EnvelopePenetrationRestraint_get_version_info(self)
2576 
2577 
2578  def __str__(self):
2579  """__str__(EnvelopePenetrationRestraint self) -> std::string"""
2580  return _IMP_em.EnvelopePenetrationRestraint___str__(self)
2581 
2582 
2583  def __repr__(self):
2584  """__repr__(EnvelopePenetrationRestraint self) -> std::string"""
2585  return _IMP_em.EnvelopePenetrationRestraint___repr__(self)
2586 
2587 
2588  @staticmethod
2589  def get_from(o):
2590  return _object_cast_to_EnvelopePenetrationRestraint(o)
2591 
2592 EnvelopePenetrationRestraint_swigregister = _IMP_em.EnvelopePenetrationRestraint_swigregister
2593 EnvelopePenetrationRestraint_swigregister(EnvelopePenetrationRestraint)
2594 
2595 class PCAFitRestraint(IMP.Restraint):
2596  """Proxy of C++ IMP::em::PCAFitRestraint class."""
2597 
2598  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2599 
2600  def __init__(self, *args):
2601  """
2602  __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
2603  __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
2604  """
2605  this = _IMP_em.new_PCAFitRestraint(*args)
2606  try:
2607  self.this.append(this)
2608  except __builtin__.Exception:
2609  self.this = this
2610 
2611  def do_get_inputs(self):
2612  """do_get_inputs(PCAFitRestraint self) -> IMP::ModelObjectsTemp"""
2613  return _IMP_em.PCAFitRestraint_do_get_inputs(self)
2614 
2615 
2616  def get_version_info(self):
2617  """get_version_info(PCAFitRestraint self) -> VersionInfo"""
2618  return _IMP_em.PCAFitRestraint_get_version_info(self)
2619 
2620 
2621  def __str__(self):
2622  """__str__(PCAFitRestraint self) -> std::string"""
2623  return _IMP_em.PCAFitRestraint___str__(self)
2624 
2625 
2626  def __repr__(self):
2627  """__repr__(PCAFitRestraint self) -> std::string"""
2628  return _IMP_em.PCAFitRestraint___repr__(self)
2629 
2630 
2631  @staticmethod
2632  def get_from(o):
2633  return _object_cast_to_PCAFitRestraint(o)
2634 
2635 PCAFitRestraint_swigregister = _IMP_em.PCAFitRestraint_swigregister
2636 PCAFitRestraint_swigregister(PCAFitRestraint)
2637 
2638 class EnvelopeFitRestraint(IMP.Restraint):
2639  """Proxy of C++ IMP::em::EnvelopeFitRestraint class."""
2640 
2641  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2642 
2643  def __init__(self, particles, em_map, density_threshold, penetration_threshold):
2644  """__init__(IMP::em::EnvelopeFitRestraint self, IMP::Particles particles, DensityMap em_map, double density_threshold, double penetration_threshold) -> EnvelopeFitRestraint"""
2645  this = _IMP_em.new_EnvelopeFitRestraint(particles, em_map, density_threshold, penetration_threshold)
2646  try:
2647  self.this.append(this)
2648  except __builtin__.Exception:
2649  self.this = this
2650 
2651  def get_transformation(self):
2652  """get_transformation(EnvelopeFitRestraint self) -> Transformation3D"""
2653  return _IMP_em.EnvelopeFitRestraint_get_transformation(self)
2654 
2655 
2656  def apply_transformation(self):
2657  """apply_transformation(EnvelopeFitRestraint self)"""
2658  return _IMP_em.EnvelopeFitRestraint_apply_transformation(self)
2659 
2660 
2661  def do_get_inputs(self):
2662  """do_get_inputs(EnvelopeFitRestraint self) -> IMP::ModelObjectsTemp"""
2663  return _IMP_em.EnvelopeFitRestraint_do_get_inputs(self)
2664 
2665 
2666  def get_version_info(self):
2667  """get_version_info(EnvelopeFitRestraint self) -> VersionInfo"""
2668  return _IMP_em.EnvelopeFitRestraint_get_version_info(self)
2669 
2670 
2671  def __str__(self):
2672  """__str__(EnvelopeFitRestraint self) -> std::string"""
2673  return _IMP_em.EnvelopeFitRestraint___str__(self)
2674 
2675 
2676  def __repr__(self):
2677  """__repr__(EnvelopeFitRestraint self) -> std::string"""
2678  return _IMP_em.EnvelopeFitRestraint___repr__(self)
2679 
2680 
2681  @staticmethod
2682  def get_from(o):
2683  return _object_cast_to_EnvelopeFitRestraint(o)
2684 
2685 EnvelopeFitRestraint_swigregister = _IMP_em.EnvelopeFitRestraint_swigregister
2686 EnvelopeFitRestraint_swigregister(EnvelopeFitRestraint)
2687 
2688 
2689 import math
2690 
2691 def write_pca_cmm(pca, fh):
2692  """Write out principal components to a file in Chimera Marker format"""
2693  eigen_values = pca.get_principal_values()
2694  eigen_vecs = pca.get_principal_components()
2695  centroid = pca.get_centroid()
2696 
2697  fh.write("<marker_set>\n")
2698  fh.write("<!-- PCA with eigen values: (%g,%g,%g) and "
2699  "centroid (%g,%g,%g) -->\n"
2700  % (math.sqrt(eigen_values[0]),
2701  math.sqrt(eigen_values[1]),
2702  math.sqrt(eigen_values[2]),
2703  centroid[0], centroid[1], centroid[2]))
2704 
2705  radius = 2.
2706 
2707  for i in range(3):
2708  val = math.sqrt(eigen_values[i])
2709  v1 = centroid - val * eigen_vecs[i]
2710  v2 = centroid + val * eigen_vecs[i]
2711  for markerid, v in ((i*2+1, v1), (i*2+2, v2)):
2712  fh.write("<marker id=\"%d\" x=\"%g\" y=\"%g\" z=\"%g\" "
2713  "radius=\"%g\"/>\n"
2714  % (markerid, v[0], v[1], v[2], radius))
2715 
2716  for i in range(1, 7, 2):
2717  fh.write("<link id1= \"%d\" id2=\"%d\" radius=\"%g\"/>\n"
2718  % (i, i+1, radius))
2719  fh.write("</marker_set>\n")
2720 
2721 
2722 def get_module_version():
2723  """get_module_version() -> std::string const"""
2724  return _IMP_em.get_module_version()
2725 
2726 def get_example_path(fname):
2727  """get_example_path(std::string fname) -> std::string"""
2728  return _IMP_em.get_example_path(fname)
2729 
2730 def get_data_path(fname):
2731  """get_data_path(std::string fname) -> std::string"""
2732  return _IMP_em.get_data_path(fname)
2733 
2734 from . import _version_check
2735 _version_check.check_version(get_module_version())
2736 __version__ = get_module_version()
2737 
2738 
2739 
Float get_threshold_for_approximate_mass(DensityMap *m, Float desired_mass, atom::ProteinDensityReference ref=atom::HARPAZ)
Computes the threshold to consider in an EM map to get a desired mass.
DensityMap * interpolate_map(DensityMap *in_map, double new_spacing)
Return a new map with an updated spacing.
Particles density2particles(DensityMap *dmap, Float threshold, Model *m, int step=1)
Convert a density grid to a set of particles.
algebra::Vector3Ds density2vectors(DensityMap *dmap, Float threshold)
Convert a density grid to a set of vectors.
algebra::BoundingBoxD< 3 > get_bounding_box(const DensityMap *m, Float threshold)
Get the bounding box for a map.
Ints get_numbers_of_particles_outside_of_the_density(DensityMap *dmap, const Particles &ps, const IMP::algebra::Transformation3Ds &transformations, float thr=0.0)
Get numbers of particles (mult transforms) that are outside the density.
Various classes to hold sets of particles.
DensityMap * binarize(DensityMap *orig_map, float threshold, bool reverse=false)
Return a map with 0 for all voxels below the threshold and 1 for those above.
double get_sum(const DensityMap *m1)
Return the sum of all voxels.
SampledDensityMap * particles2binarized_density(const ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
Definition: converters.h:76
Make CGAL functionality available to IMP.
DensityMap * mask_and_norm(em::DensityMap *dmap, em::DensityMap *mask)
Return a masked density, and normalize the output map within the mask region.
FittingSolutions compute_fitting_scores(const ParticlesTemp &ps, DensityMap *em_map, const algebra::Transformation3Ds &transformations, bool fast_version=false, bool local_score=false, const FloatKey &wei_key=atom::Mass::get_mass_key())
Compute fitting scores for a given set of rigid transformations.
DensityMap * get_threshold_map(const DensityMap *orig_map, float threshold)
Return a map with 0 for all voxels below the threshold.
DensityMap * get_segment_by_masking(DensityMap *map_to_segment, DensityMap *mask, float mas_threshold)
Get a segment of the map covered by another map.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
SampledDensityMap * particles2density(const ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
Resample a set of particles into a density grid.
Composable functors to implement scores via compile-time composition.
Code to compute statistical measures.
algebra::GridD< 3, algebra::DenseGridStorageD< 3, float >, float > get_grid(DensityMap *in_map)
Return a dense grid containing the voxels of the passed density map.
def write_pca_cmm
Write out principal components to a file in Chimera Marker format.
double convolute(const DensityMap *m1, const DensityMap *m2)
Return a convolution between density maps m1 and m2.
Common base class for heavy weight IMP objects.
Definition: Object.h:106
DensityMap * multiply(const DensityMap *m1, const DensityMap *m2)
Return a density map for which voxel i contains the result of m1[i]*m2[i].
DensityHeader create_density_header(const algebra::BoundingBoxD< 3 > &bb, float spacing)
Create a header from a bounding box in 3D.
Float compute_fitting_score(const ParticlesTemp &ps, DensityMap *em_map, FloatKey wei_key=atom::Mass::get_mass_key())
Compute fitting scores for a given set of rigid transformations.
FittingSolutions local_rigid_fitting_around_point(Particle *p, Refiner *refiner, const FloatKey &weight_key, DensityMap *dmap, const algebra::Vector3D &anchor_centroid, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3, bool fast=false)
Local rigid fitting of a rigid body around a center point.
long get_number_of_particles_outside_of_the_density(DensityMap *dmap, const Particles &ps, const IMP::algebra::Transformation3D &t=IMP::algebra::get_identity_transformation_3d(), float thr=0.0)
Get the number of particles that are outside of the density.
DensityMap * get_max_map(DensityMaps maps)
Return a map where each voxel is the maximum value from the input maps.
DensityMap * create_density_map(const DensityMap *other)
Create a copy of another map.
Store data to be clustered for embedding based algorithms.
Float approximate_molecular_mass(DensityMap *m, Float threshold)
Estimate the molecular mass from a map.
double get_percentage_of_voxels_covered_by_particles(DensityMap *dmap, const Particles &ps, float smoothing_radius=3., const IMP::algebra::Transformation3D &t=IMP::algebra::get_identity_transformation_3d(), float thr=0.0)
Get the number of density voxels that are not covered by particles.
Vector3D get_centroid(const Vector3Ds &ps)
Return the centroid of a set of vectors.
Definition: Vector3D.h:68
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
FittingSolutions local_rigid_fitting(Particle *p, Refiner *refiner, const FloatKey &weight_key, DensityMap *dmap, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3, bool fast=true)
Local rigid fitting of a rigid body.
Basic functionality that is expected to be used by a wide variety of IMP users.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
SurfaceShellDensityMap * particles2surface(const ParticlesTemp &ps, Float apix, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
Resample a set of particles into a density grid.
FittingSolutions local_rigid_fitting_around_points(Particle *p, Refiner *refiner, const FloatKey &wei_key, DensityMap *dmap, const algebra::Vector3Ds &anchor_centroids, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3)
Local rigid fitting of a rigid body around a set of center points.
FittingSolutions local_rigid_fitting_grid_search(const ParticlesTemp &ps, const FloatKey &wei_key, DensityMap *dmap, Int max_voxels_translation=2, Int translation_step=1, Float max_angle_in_radians=0.174, Int number_of_rotations=100)
Local grid search rigid fitting.
double get_resolution(Model *m, ParticleIndex pi)
Estimate the resolution of the hierarchy as used by Representation.
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
Float get_molecular_mass_at_threshold(DensityMap *m, Float threshold, atom::ProteinDensityReference ref=atom::HARPAZ)
Compute an approximate molecular mass.
DensityMap * get_segment(DensityMap *map_to_segment, int nx_start, int nx_end, int ny_start, int ny_end, int nz_start, int nz_end)
Get a segment of the map according to xyz indexes.
Float get_threshold_for_approximate_volume(DensityMap *m, Float desired_volume)
Computes the threshold consider in an EM map to get a desired volume.
Float get_volume_at_threshold(DensityMap *m, Float threshold)
Compute an approximate volume.
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:54