IMP  2.3.0
The Integrative Modeling Platform
em/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.2
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 
8 
9 
10 
11 from sys import version_info
12 if version_info >= (2,6,0):
13  def swig_import_helper():
14  from os.path import dirname
15  import imp
16  fp = None
17  try:
18  fp, pathname, description = imp.find_module('_IMP_em', [dirname(__file__)])
19  except ImportError:
20  import _IMP_em
21  return _IMP_em
22  if fp is not None:
23  try:
24  _mod = imp.load_module('_IMP_em', fp, pathname, description)
25  finally:
26  fp.close()
27  return _mod
28  _IMP_em = swig_import_helper()
29  del swig_import_helper
30 else:
31  import _IMP_em
32 del version_info
33 try:
34  _swig_property = property
35 except NameError:
36  pass # Python < 2.2 doesn't have 'property'.
37 def _swig_setattr_nondynamic(self,class_type,name,value,static=1):
38  if (name == "thisown"): return self.this.own(value)
39  if (name == "this"):
40  if type(value).__name__ == 'SwigPyObject':
41  self.__dict__[name] = value
42  return
43  method = class_type.__swig_setmethods__.get(name,None)
44  if method: return method(self,value)
45  if (not static):
46  self.__dict__[name] = value
47  else:
48  raise AttributeError("You cannot add attributes to %s" % self)
49 
50 def _swig_setattr(self,class_type,name,value):
51  return _swig_setattr_nondynamic(self,class_type,name,value,0)
52 
53 def _swig_getattr(self,class_type,name):
54  if (name == "thisown"): return self.this.own()
55  method = class_type.__swig_getmethods__.get(name,None)
56  if method: return method(self)
57  raise AttributeError(name)
58 
59 def _swig_repr(self):
60  try: strthis = "proxy of " + self.this.__repr__()
61  except: strthis = ""
62  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
63 
64 try:
65  _object = object
66  _newclass = 1
67 except AttributeError:
68  class _object : pass
69  _newclass = 0
70 
71 
72 try:
73  import weakref
74  weakref_proxy = weakref.proxy
75 except:
76  weakref_proxy = lambda x: x
77 
78 
79 class IMP_EM_SwigPyIterator(_object):
80  """Proxy of C++ swig::IMP_EM_SwigPyIterator class"""
81  __swig_setmethods__ = {}
82  __setattr__ = lambda self, name, value: _swig_setattr(self, IMP_EM_SwigPyIterator, name, value)
83  __swig_getmethods__ = {}
84  __getattr__ = lambda self, name: _swig_getattr(self, IMP_EM_SwigPyIterator, name)
85  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
86  __repr__ = _swig_repr
87  __swig_destroy__ = _IMP_em.delete_IMP_EM_SwigPyIterator
88  __del__ = lambda self : None;
89  def value(self):
90  """value(IMP_EM_SwigPyIterator self) -> PyObject *"""
91  return _IMP_em.IMP_EM_SwigPyIterator_value(self)
92 
93  def incr(self, n=1):
94  """
95  incr(IMP_EM_SwigPyIterator self, size_t n=1) -> IMP_EM_SwigPyIterator
96  incr(IMP_EM_SwigPyIterator self) -> IMP_EM_SwigPyIterator
97  """
98  return _IMP_em.IMP_EM_SwigPyIterator_incr(self, n)
99 
100  def decr(self, n=1):
101  """
102  decr(IMP_EM_SwigPyIterator self, size_t n=1) -> IMP_EM_SwigPyIterator
103  decr(IMP_EM_SwigPyIterator self) -> IMP_EM_SwigPyIterator
104  """
105  return _IMP_em.IMP_EM_SwigPyIterator_decr(self, n)
106 
107  def distance(self, *args):
108  """distance(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> ptrdiff_t"""
109  return _IMP_em.IMP_EM_SwigPyIterator_distance(self, *args)
110 
111  def equal(self, *args):
112  """equal(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> bool"""
113  return _IMP_em.IMP_EM_SwigPyIterator_equal(self, *args)
114 
115  def copy(self):
116  """copy(IMP_EM_SwigPyIterator self) -> IMP_EM_SwigPyIterator"""
117  return _IMP_em.IMP_EM_SwigPyIterator_copy(self)
118 
119  def next(self):
120  """next(IMP_EM_SwigPyIterator self) -> PyObject *"""
121  return _IMP_em.IMP_EM_SwigPyIterator_next(self)
122 
123  def __next__(self):
124  """__next__(IMP_EM_SwigPyIterator self) -> PyObject *"""
125  return _IMP_em.IMP_EM_SwigPyIterator___next__(self)
126 
127  def previous(self):
128  """previous(IMP_EM_SwigPyIterator self) -> PyObject *"""
129  return _IMP_em.IMP_EM_SwigPyIterator_previous(self)
130 
131  def advance(self, *args):
132  """advance(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator"""
133  return _IMP_em.IMP_EM_SwigPyIterator_advance(self, *args)
134 
135  def __eq__(self, *args):
136  """__eq__(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> bool"""
137  return _IMP_em.IMP_EM_SwigPyIterator___eq__(self, *args)
138 
139  def __ne__(self, *args):
140  """__ne__(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> bool"""
141  return _IMP_em.IMP_EM_SwigPyIterator___ne__(self, *args)
142 
143  def __iadd__(self, *args):
144  """__iadd__(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator"""
145  return _IMP_em.IMP_EM_SwigPyIterator___iadd__(self, *args)
146 
147  def __isub__(self, *args):
148  """__isub__(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator"""
149  return _IMP_em.IMP_EM_SwigPyIterator___isub__(self, *args)
150 
151  def __add__(self, *args):
152  """__add__(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator"""
153  return _IMP_em.IMP_EM_SwigPyIterator___add__(self, *args)
154 
155  def __sub__(self, *args):
156  """
157  __sub__(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator
158  __sub__(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> ptrdiff_t
159  """
160  return _IMP_em.IMP_EM_SwigPyIterator___sub__(self, *args)
161 
162  def __iter__(self): return self
163 IMP_EM_SwigPyIterator_swigregister = _IMP_em.IMP_EM_SwigPyIterator_swigregister
164 IMP_EM_SwigPyIterator_swigregister(IMP_EM_SwigPyIterator)
165 
166 _value_types=[]
167 _object_types=[]
168 _raii_types=[]
169 _plural_types=[]
170 
171 IMP_DEBUG = _IMP_em.IMP_DEBUG
172 IMP_RELEASE = _IMP_em.IMP_RELEASE
173 IMP_SILENT = _IMP_em.IMP_SILENT
174 IMP_PROGRESS = _IMP_em.IMP_PROGRESS
175 IMP_TERSE = _IMP_em.IMP_TERSE
176 IMP_VERBOSE = _IMP_em.IMP_VERBOSE
177 IMP_MEMORY = _IMP_em.IMP_MEMORY
178 IMP_NONE = _IMP_em.IMP_NONE
179 IMP_USAGE = _IMP_em.IMP_USAGE
180 IMP_INTERNAL = _IMP_em.IMP_INTERNAL
181 IMP_BASE_HAS_LOG4CXX = _IMP_em.IMP_BASE_HAS_LOG4CXX
182 IMP_COMPILER_HAS_AUTO = _IMP_em.IMP_COMPILER_HAS_AUTO
183 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_em.IMP_COMPILER_HAS_DEBUG_VECTOR
184 IMP_BASE_HAS_BOOST_RANDOM = _IMP_em.IMP_BASE_HAS_BOOST_RANDOM
185 IMP_BASE_HAS_GPERFTOOLS = _IMP_em.IMP_BASE_HAS_GPERFTOOLS
186 IMP_BASE_HAS_TCMALLOC_HEAPCHECKER = _IMP_em.IMP_BASE_HAS_TCMALLOC_HEAPCHECKER
187 IMP_BASE_HAS_TCMALLOC_HEAPPROFILER = _IMP_em.IMP_BASE_HAS_TCMALLOC_HEAPPROFILER
188 IMPBASE_SHOW_WARNINGS = _IMP_em.IMPBASE_SHOW_WARNINGS
189 import sys
190 class _DirectorObjects(object):
191  """@internal Simple class to keep references to director objects
192  to prevent premature deletion."""
193  def __init__(self):
194  self._objects = []
195  def register(self, obj):
196  """Take a reference to a director object; will only work for
197  refcounted C++ classes"""
198  if hasattr(obj, 'get_ref_count'):
199  self._objects.append(obj)
200  def cleanup(self):
201  """Only drop our reference and allow cleanup by Python if no other
202  Python references exist (we hold 3 references: one in self._objects,
203  one in x, and one in the argument list for getrefcount) *and* no
204  other C++ references exist (the Python object always holds one)"""
205  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
206  or x.get_ref_count() > 1]
207 
208 
209  self._objects = objs
210  def get_object_count(self):
211  """Get number of director objects (useful for testing only)"""
212  return len(self._objects)
213 _director_objects = _DirectorObjects()
214 
215 DEFAULT_CHECK = _IMP_em.DEFAULT_CHECK
216 NONE = _IMP_em.NONE
217 USAGE = _IMP_em.USAGE
218 USAGE_AND_INTERNAL = _IMP_em.USAGE_AND_INTERNAL
219 
220 def set_check_level(*args):
221  """set_check_level(IMP::base::CheckLevel tf)"""
222  return _IMP_em.set_check_level(*args)
223 
224 def get_check_level():
225  """get_check_level() -> IMP::base::CheckLevel"""
226  return _IMP_em.get_check_level()
227 class _ostream(_object):
228  """Proxy of C++ std::ostream class"""
229  __swig_setmethods__ = {}
230  __setattr__ = lambda self, name, value: _swig_setattr(self, _ostream, name, value)
231  __swig_getmethods__ = {}
232  __getattr__ = lambda self, name: _swig_getattr(self, _ostream, name)
233  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined")
234  __repr__ = _swig_repr
235  def write(self, *args):
236  """write(_ostream self, char const * osa_buf)"""
237  return _IMP_em._ostream_write(self, *args)
238 
239 _ostream_swigregister = _IMP_em._ostream_swigregister
240 _ostream_swigregister(_ostream)
241 
242 IMP_COMPILER_HAS_OVERRIDE = _IMP_em.IMP_COMPILER_HAS_OVERRIDE
243 IMP_COMPILER_HAS_FINAL = _IMP_em.IMP_COMPILER_HAS_FINAL
244 IMP_HAS_NOEXCEPT = _IMP_em.IMP_HAS_NOEXCEPT
245 import IMP.base
246 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CGAL_HAS_BOOST_FILESYSTEM
247 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
248 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_em.IMP_CGAL_HAS_BOOST_RANDOM
249 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_em.IMP_CGAL_HAS_BOOST_SYSTEM
250 IMPCGAL_SHOW_WARNINGS = _IMP_em.IMPCGAL_SHOW_WARNINGS
251 import IMP.cgal
252 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_em.IMP_ALGEBRA_HAS_IMP_CGAL
253 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
254 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
255 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_RANDOM
256 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_SYSTEM
257 IMP_ALGEBRA_HAS_CGAL = _IMP_em.IMP_ALGEBRA_HAS_CGAL
258 IMP_ALGEBRA_HAS_ANN = _IMP_em.IMP_ALGEBRA_HAS_ANN
259 IMPALGEBRA_SHOW_WARNINGS = _IMP_em.IMPALGEBRA_SHOW_WARNINGS
260 import IMP.algebra
261 IMP_KERNEL_HAS_IMP_CGAL = _IMP_em.IMP_KERNEL_HAS_IMP_CGAL
262 IMP_KERNEL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_KERNEL_HAS_BOOST_PROGRAMOPTIONS
263 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_em.IMP_KERNEL_HAS_BOOST_RANDOM
264 IMP_KERNEL_HAS_BOOST_SYSTEM = _IMP_em.IMP_KERNEL_HAS_BOOST_SYSTEM
265 IMP_KERNEL_HAS_CGAL = _IMP_em.IMP_KERNEL_HAS_CGAL
266 IMPKERNEL_SHOW_WARNINGS = _IMP_em.IMPKERNEL_SHOW_WARNINGS
267 import IMP.kernel
268 IMP_DISPLAY_HAS_IMP_BASE = _IMP_em.IMP_DISPLAY_HAS_IMP_BASE
269 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_em.IMP_DISPLAY_HAS_IMP_CGAL
270 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
271 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
272 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_em.IMP_DISPLAY_HAS_BOOST_RANDOM
273 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_em.IMP_DISPLAY_HAS_BOOST_SYSTEM
274 IMP_DISPLAY_HAS_CGAL = _IMP_em.IMP_DISPLAY_HAS_CGAL
275 IMPDISPLAY_SHOW_WARNINGS = _IMP_em.IMPDISPLAY_SHOW_WARNINGS
276 import IMP.display
277 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_em.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
278 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
279 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
280 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
281 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
282 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_em.IMP_SCORE_FUNCTOR_HAS_CGAL
283 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_em.IMP_SCORE_FUNCTOR_HAS_HDF5
284 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_em.IMPSCOREFUNCTOR_SHOW_WARNINGS
285 import IMP.score_functor
286 IMP_STATISTICS_HAS_IMP_BASE = _IMP_em.IMP_STATISTICS_HAS_IMP_BASE
287 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_em.IMP_STATISTICS_HAS_IMP_CGAL
288 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
289 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
290 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_em.IMP_STATISTICS_HAS_BOOST_RANDOM
291 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_SYSTEM
292 IMP_STATISTICS_HAS_CGAL = _IMP_em.IMP_STATISTICS_HAS_CGAL
293 IMPSTATISTICS_SHOW_WARNINGS = _IMP_em.IMPSTATISTICS_SHOW_WARNINGS
294 import IMP.statistics
295 IMP_CORE_HAS_IMP_BASE = _IMP_em.IMP_CORE_HAS_IMP_BASE
296 IMP_CORE_HAS_IMP_CGAL = _IMP_em.IMP_CORE_HAS_IMP_CGAL
297 IMP_CORE_HAS_IMP_KERNEL = _IMP_em.IMP_CORE_HAS_IMP_KERNEL
298 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_FILESYSTEM
299 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
300 IMP_CORE_HAS_BOOST_RANDOM = _IMP_em.IMP_CORE_HAS_BOOST_RANDOM
301 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_SYSTEM
302 IMP_CORE_HAS_CGAL = _IMP_em.IMP_CORE_HAS_CGAL
303 IMP_CORE_HAS_HDF5 = _IMP_em.IMP_CORE_HAS_HDF5
304 IMPCORE_SHOW_WARNINGS = _IMP_em.IMPCORE_SHOW_WARNINGS
305 import IMP.core
306 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_em.IMP_CONTAINER_HAS_IMP_ALGEBRA
307 IMP_CONTAINER_HAS_IMP_BASE = _IMP_em.IMP_CONTAINER_HAS_IMP_BASE
308 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_em.IMP_CONTAINER_HAS_IMP_CGAL
309 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_em.IMP_CONTAINER_HAS_IMP_DISPLAY
310 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_em.IMP_CONTAINER_HAS_IMP_KERNEL
311 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
312 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
313 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
314 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_em.IMP_CONTAINER_HAS_BOOST_RANDOM
315 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_SYSTEM
316 IMP_CONTAINER_HAS_CGAL = _IMP_em.IMP_CONTAINER_HAS_CGAL
317 IMP_CONTAINER_HAS_HDF5 = _IMP_em.IMP_CONTAINER_HAS_HDF5
318 IMPCONTAINER_SHOW_WARNINGS = _IMP_em.IMPCONTAINER_SHOW_WARNINGS
319 import IMP.container
320 IMP_ATOM_HAS_IMP_BASE = _IMP_em.IMP_ATOM_HAS_IMP_BASE
321 IMP_ATOM_HAS_IMP_CGAL = _IMP_em.IMP_ATOM_HAS_IMP_CGAL
322 IMP_ATOM_HAS_IMP_KERNEL = _IMP_em.IMP_ATOM_HAS_IMP_KERNEL
323 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
324 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
325 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_em.IMP_ATOM_HAS_BOOST_RANDOM
326 IMP_ATOM_HAS_BOOST_REGEX = _IMP_em.IMP_ATOM_HAS_BOOST_REGEX
327 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_em.IMP_ATOM_HAS_BOOST_SYSTEM
328 IMP_ATOM_HAS_CGAL = _IMP_em.IMP_ATOM_HAS_CGAL
329 IMP_ATOM_HAS_HDF5 = _IMP_em.IMP_ATOM_HAS_HDF5
330 IMPATOM_SHOW_WARNINGS = _IMP_em.IMPATOM_SHOW_WARNINGS
331 IMP_ATOM_TYPE_INDEX = _IMP_em.IMP_ATOM_TYPE_INDEX
332 IMP_RESIDUE_TYPE_INDEX = _IMP_em.IMP_RESIDUE_TYPE_INDEX
333 IMP_HIERARCHY_TYPE_INDEX = _IMP_em.IMP_HIERARCHY_TYPE_INDEX
334 import IMP.atom
335 IMP_EM_HAS_IMP_CGAL = _IMP_em.IMP_EM_HAS_IMP_CGAL
336 IMP_EM_HAS_IMP_CONTAINER = _IMP_em.IMP_EM_HAS_IMP_CONTAINER
337 IMP_EM_HAS_IMP_DISPLAY = _IMP_em.IMP_EM_HAS_IMP_DISPLAY
338 IMP_EM_HAS_IMP_KERNEL = _IMP_em.IMP_EM_HAS_IMP_KERNEL
339 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_EM_HAS_IMP_SCORE_FUNCTOR
340 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_EM_HAS_BOOST_FILESYSTEM
341 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
342 IMP_EM_HAS_BOOST_RANDOM = _IMP_em.IMP_EM_HAS_BOOST_RANDOM
343 IMP_EM_HAS_BOOST_REGEX = _IMP_em.IMP_EM_HAS_BOOST_REGEX
344 IMP_EM_HAS_BOOST_SYSTEM = _IMP_em.IMP_EM_HAS_BOOST_SYSTEM
345 IMP_EM_HAS_CGAL = _IMP_em.IMP_EM_HAS_CGAL
346 IMP_EM_HAS_HDF5 = _IMP_em.IMP_EM_HAS_HDF5
347 IMPEM_SHOW_WARNINGS = _IMP_em.IMPEM_SHOW_WARNINGS
348 _object_types.append("DensityMap")
349 
350 
351 def _object_cast_to_DensityMap(*args):
352  """_object_cast_to_DensityMap(Object o) -> DensityMap"""
353  return _IMP_em._object_cast_to_DensityMap(*args)
354 _object_types.append("SampledDensityMap")
355 
356 
357 def _object_cast_to_SampledDensityMap(*args):
358  """_object_cast_to_SampledDensityMap(Object o) -> SampledDensityMap"""
359  return _IMP_em._object_cast_to_SampledDensityMap(*args)
360 _object_types.append("SurfaceShellDensityMap")
361 
362 
363 def _object_cast_to_SurfaceShellDensityMap(*args):
364  """_object_cast_to_SurfaceShellDensityMap(Object o) -> SurfaceShellDensityMap"""
365  return _IMP_em._object_cast_to_SurfaceShellDensityMap(*args)
366 _object_types.append("FitRestraint")
367 
368 
369 def _object_cast_to_FitRestraint(*args):
370  """_object_cast_to_FitRestraint(Object o) -> FitRestraint"""
371  return _IMP_em._object_cast_to_FitRestraint(*args)
372 _object_types.append("PCAFitRestraint")
373 
374 
375 def _object_cast_to_PCAFitRestraint(*args):
376  """_object_cast_to_PCAFitRestraint(Object o) -> PCAFitRestraint"""
377  return _IMP_em._object_cast_to_PCAFitRestraint(*args)
378 _object_types.append("EnvelopePenetrationRestraint")
379 
380 
381 def _object_cast_to_EnvelopePenetrationRestraint(*args):
382  """_object_cast_to_EnvelopePenetrationRestraint(Object o) -> EnvelopePenetrationRestraint"""
383  return _IMP_em._object_cast_to_EnvelopePenetrationRestraint(*args)
384 _object_types.append("EnvelopeFitRestraint")
385 
386 
387 def _object_cast_to_EnvelopeFitRestraint(*args):
388  """_object_cast_to_EnvelopeFitRestraint(Object o) -> EnvelopeFitRestraint"""
389  return _IMP_em._object_cast_to_EnvelopeFitRestraint(*args)
390 RadiusDependentKernelParametersList=list
391 _plural_types.append("RadiusDependentKernelParametersList")
392 _value_types.append("RadiusDependentKernelParameters")
393 
394 KernelParametersList=list
395 _plural_types.append("KernelParametersList")
396 _value_types.append("KernelParameters")
397 
398 _object_types.append("HighDensityEmbedding")
399 
400 
401 def _object_cast_to_HighDensityEmbedding(*args):
402  """_object_cast_to_HighDensityEmbedding(Object o) -> HighDensityEmbedding"""
403  return _IMP_em._object_cast_to_HighDensityEmbedding(*args)
404 _object_types.append("MapReaderWriter")
405 
406 
407 def _object_cast_to_MapReaderWriter(*args):
408  """_object_cast_to_MapReaderWriter(Object o) -> MapReaderWriter"""
409  return _IMP_em._object_cast_to_MapReaderWriter(*args)
410 _object_types.append("MRCReaderWriter")
411 
412 
413 def _object_cast_to_MRCReaderWriter(*args):
414  """_object_cast_to_MRCReaderWriter(Object o) -> MRCReaderWriter"""
415  return _IMP_em._object_cast_to_MRCReaderWriter(*args)
416 _object_types.append("SpiderMapReaderWriter")
417 
418 
419 def _object_cast_to_SpiderMapReaderWriter(*args):
420  """_object_cast_to_SpiderMapReaderWriter(Object o) -> SpiderMapReaderWriter"""
421  return _IMP_em._object_cast_to_SpiderMapReaderWriter(*args)
422 _object_types.append("EMReaderWriter")
423 
424 
425 def _object_cast_to_EMReaderWriter(*args):
426  """_object_cast_to_EMReaderWriter(Object o) -> EMReaderWriter"""
427  return _IMP_em._object_cast_to_EMReaderWriter(*args)
428 _object_types.append("XplorReaderWriter")
429 
430 
431 def _object_cast_to_XplorReaderWriter(*args):
432  """_object_cast_to_XplorReaderWriter(Object o) -> XplorReaderWriter"""
433  return _IMP_em._object_cast_to_XplorReaderWriter(*args)
434 _object_types.append("CoarseCC")
435 
436 
437 def _object_cast_to_CoarseCC(*args):
438  """_object_cast_to_CoarseCC(Object o) -> CoarseCC"""
439  return _IMP_em._object_cast_to_CoarseCC(*args)
440 _object_types.append("CoarseCCatIntervals")
441 
442 
443 def _object_cast_to_CoarseCCatIntervals(*args):
444  """_object_cast_to_CoarseCCatIntervals(Object o) -> CoarseCCatIntervals"""
445  return _IMP_em._object_cast_to_CoarseCCatIntervals(*args)
446 FittingSolutionsList=list
447 _plural_types.append("FittingSolutionsList")
448 _value_types.append("FittingSolutions")
449 
450 class MapReaderWriter(IMP.base.Object):
451  """Proxy of C++ IMP::em::MapReaderWriter class"""
452  __swig_setmethods__ = {}
453  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
454  __setattr__ = lambda self, name, value: _swig_setattr(self, MapReaderWriter, name, value)
455  __swig_getmethods__ = {}
456  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
457  __getattr__ = lambda self, name: _swig_getattr(self, MapReaderWriter, name)
458  def __init__(self):
459  """__init__(IMP::em::MapReaderWriter self) -> MapReaderWriter"""
460  this = _IMP_em.new_MapReaderWriter()
461  try: self.this.append(this)
462  except: self.this = this
463  def get_version_info(self):
464  """get_version_info(MapReaderWriter self) -> VersionInfo"""
465  return _IMP_em.MapReaderWriter_get_version_info(self)
466 
467  def __str__(self):
468  """__str__(MapReaderWriter self) -> std::string"""
469  return _IMP_em.MapReaderWriter___str__(self)
470 
471  def __repr__(self):
472  """__repr__(MapReaderWriter self) -> std::string"""
473  return _IMP_em.MapReaderWriter___repr__(self)
474 
475  def get_from(o):
476  return _object_cast_to_MapReaderWriter(o)
477  get_from = staticmethod(get_from)
478 
479 MapReaderWriter_swigregister = _IMP_em.MapReaderWriter_swigregister
480 MapReaderWriter_swigregister(MapReaderWriter)
481 cvar = _IMP_em.cvar
482 EPS = cvar.EPS
483 
484 class DensityHeader(_object):
485  """Proxy of C++ IMP::em::DensityHeader class"""
486  __swig_setmethods__ = {}
487  __setattr__ = lambda self, name, value: _swig_setattr(self, DensityHeader, name, value)
488  __swig_getmethods__ = {}
489  __getattr__ = lambda self, name: _swig_getattr(self, DensityHeader, name)
490  __repr__ = _swig_repr
491  def __init__(self):
492  """__init__(IMP::em::DensityHeader self) -> DensityHeader"""
493  this = _IMP_em.new_DensityHeader()
494  try: self.this.append(this)
495  except: self.this = this
496  def get_top(self, *args):
497  """get_top(DensityHeader self, int ind) -> IMP::em::emreal"""
498  return _IMP_em.DensityHeader_get_top(self, *args)
499 
500  def compute_xyz_top(self, force=False):
501  """
502  compute_xyz_top(DensityHeader self, bool force=False)
503  compute_xyz_top(DensityHeader self)
504  """
505  return _IMP_em.DensityHeader_compute_xyz_top(self, force)
506 
507  def update_map_dimensions(self, *args):
508  """update_map_dimensions(DensityHeader self, int nnx, int nny, int nnz)"""
509  return _IMP_em.DensityHeader_update_map_dimensions(self, *args)
510 
511  def update_cell_dimensions(self):
512  """update_cell_dimensions(DensityHeader self)"""
513  return _IMP_em.DensityHeader_update_cell_dimensions(self)
514 
515  def show(self, *args):
516  """
517  show(DensityHeader self, _ostream out=std::cout)
518  show(DensityHeader self)
519  """
520  return _IMP_em.DensityHeader_show(self, *args)
521 
522  MAP_FIELD_SIZE = _IMP_em.DensityHeader_MAP_FIELD_SIZE
523  USER_FIELD_SIZE = _IMP_em.DensityHeader_USER_FIELD_SIZE
524  COMMENT_FIELD_NUM_OF = _IMP_em.DensityHeader_COMMENT_FIELD_NUM_OF
525  COMMENT_FIELD_SINGLE_SIZE = _IMP_em.DensityHeader_COMMENT_FIELD_SINGLE_SIZE
526  __swig_setmethods__["nxstart"] = _IMP_em.DensityHeader_nxstart_set
527  __swig_getmethods__["nxstart"] = _IMP_em.DensityHeader_nxstart_get
528  if _newclass:nxstart = _swig_property(_IMP_em.DensityHeader_nxstart_get, _IMP_em.DensityHeader_nxstart_set)
529  __swig_setmethods__["nystart"] = _IMP_em.DensityHeader_nystart_set
530  __swig_getmethods__["nystart"] = _IMP_em.DensityHeader_nystart_get
531  if _newclass:nystart = _swig_property(_IMP_em.DensityHeader_nystart_get, _IMP_em.DensityHeader_nystart_set)
532  __swig_setmethods__["nzstart"] = _IMP_em.DensityHeader_nzstart_set
533  __swig_getmethods__["nzstart"] = _IMP_em.DensityHeader_nzstart_get
534  if _newclass:nzstart = _swig_property(_IMP_em.DensityHeader_nzstart_get, _IMP_em.DensityHeader_nzstart_set)
535  __swig_setmethods__["mx"] = _IMP_em.DensityHeader_mx_set
536  __swig_getmethods__["mx"] = _IMP_em.DensityHeader_mx_get
537  if _newclass:mx = _swig_property(_IMP_em.DensityHeader_mx_get, _IMP_em.DensityHeader_mx_set)
538  __swig_setmethods__["my"] = _IMP_em.DensityHeader_my_set
539  __swig_getmethods__["my"] = _IMP_em.DensityHeader_my_get
540  if _newclass:my = _swig_property(_IMP_em.DensityHeader_my_get, _IMP_em.DensityHeader_my_set)
541  __swig_setmethods__["mz"] = _IMP_em.DensityHeader_mz_set
542  __swig_getmethods__["mz"] = _IMP_em.DensityHeader_mz_get
543  if _newclass:mz = _swig_property(_IMP_em.DensityHeader_mz_get, _IMP_em.DensityHeader_mz_set)
544  __swig_setmethods__["xlen"] = _IMP_em.DensityHeader_xlen_set
545  __swig_getmethods__["xlen"] = _IMP_em.DensityHeader_xlen_get
546  if _newclass:xlen = _swig_property(_IMP_em.DensityHeader_xlen_get, _IMP_em.DensityHeader_xlen_set)
547  __swig_setmethods__["ylen"] = _IMP_em.DensityHeader_ylen_set
548  __swig_getmethods__["ylen"] = _IMP_em.DensityHeader_ylen_get
549  if _newclass:ylen = _swig_property(_IMP_em.DensityHeader_ylen_get, _IMP_em.DensityHeader_ylen_set)
550  __swig_setmethods__["zlen"] = _IMP_em.DensityHeader_zlen_set
551  __swig_getmethods__["zlen"] = _IMP_em.DensityHeader_zlen_get
552  if _newclass:zlen = _swig_property(_IMP_em.DensityHeader_zlen_get, _IMP_em.DensityHeader_zlen_set)
553  __swig_setmethods__["alpha"] = _IMP_em.DensityHeader_alpha_set
554  __swig_getmethods__["alpha"] = _IMP_em.DensityHeader_alpha_get
555  if _newclass:alpha = _swig_property(_IMP_em.DensityHeader_alpha_get, _IMP_em.DensityHeader_alpha_set)
556  __swig_setmethods__["beta"] = _IMP_em.DensityHeader_beta_set
557  __swig_getmethods__["beta"] = _IMP_em.DensityHeader_beta_get
558  if _newclass:beta = _swig_property(_IMP_em.DensityHeader_beta_get, _IMP_em.DensityHeader_beta_set)
559  __swig_setmethods__["gamma"] = _IMP_em.DensityHeader_gamma_set
560  __swig_getmethods__["gamma"] = _IMP_em.DensityHeader_gamma_get
561  if _newclass:gamma = _swig_property(_IMP_em.DensityHeader_gamma_get, _IMP_em.DensityHeader_gamma_set)
562  __swig_setmethods__["mapc"] = _IMP_em.DensityHeader_mapc_set
563  __swig_getmethods__["mapc"] = _IMP_em.DensityHeader_mapc_get
564  if _newclass:mapc = _swig_property(_IMP_em.DensityHeader_mapc_get, _IMP_em.DensityHeader_mapc_set)
565  __swig_setmethods__["mapr"] = _IMP_em.DensityHeader_mapr_set
566  __swig_getmethods__["mapr"] = _IMP_em.DensityHeader_mapr_get
567  if _newclass:mapr = _swig_property(_IMP_em.DensityHeader_mapr_get, _IMP_em.DensityHeader_mapr_set)
568  __swig_setmethods__["maps"] = _IMP_em.DensityHeader_maps_set
569  __swig_getmethods__["maps"] = _IMP_em.DensityHeader_maps_get
570  if _newclass:maps = _swig_property(_IMP_em.DensityHeader_maps_get, _IMP_em.DensityHeader_maps_set)
571  __swig_setmethods__["dmin"] = _IMP_em.DensityHeader_dmin_set
572  __swig_getmethods__["dmin"] = _IMP_em.DensityHeader_dmin_get
573  if _newclass:dmin = _swig_property(_IMP_em.DensityHeader_dmin_get, _IMP_em.DensityHeader_dmin_set)
574  __swig_setmethods__["dmax"] = _IMP_em.DensityHeader_dmax_set
575  __swig_getmethods__["dmax"] = _IMP_em.DensityHeader_dmax_get
576  if _newclass:dmax = _swig_property(_IMP_em.DensityHeader_dmax_get, _IMP_em.DensityHeader_dmax_set)
577  __swig_setmethods__["dmean"] = _IMP_em.DensityHeader_dmean_set
578  __swig_getmethods__["dmean"] = _IMP_em.DensityHeader_dmean_get
579  if _newclass:dmean = _swig_property(_IMP_em.DensityHeader_dmean_get, _IMP_em.DensityHeader_dmean_set)
580  __swig_setmethods__["ispg"] = _IMP_em.DensityHeader_ispg_set
581  __swig_getmethods__["ispg"] = _IMP_em.DensityHeader_ispg_get
582  if _newclass:ispg = _swig_property(_IMP_em.DensityHeader_ispg_get, _IMP_em.DensityHeader_ispg_set)
583  __swig_setmethods__["nsymbt"] = _IMP_em.DensityHeader_nsymbt_set
584  __swig_getmethods__["nsymbt"] = _IMP_em.DensityHeader_nsymbt_get
585  if _newclass:nsymbt = _swig_property(_IMP_em.DensityHeader_nsymbt_get, _IMP_em.DensityHeader_nsymbt_set)
586  __swig_setmethods__["user"] = _IMP_em.DensityHeader_user_set
587  __swig_getmethods__["user"] = _IMP_em.DensityHeader_user_get
588  if _newclass:user = _swig_property(_IMP_em.DensityHeader_user_get, _IMP_em.DensityHeader_user_set)
589  __swig_setmethods__["map"] = _IMP_em.DensityHeader_map_set
590  __swig_getmethods__["map"] = _IMP_em.DensityHeader_map_get
591  if _newclass:map = _swig_property(_IMP_em.DensityHeader_map_get, _IMP_em.DensityHeader_map_set)
592  __swig_setmethods__["machinestamp"] = _IMP_em.DensityHeader_machinestamp_set
593  __swig_getmethods__["machinestamp"] = _IMP_em.DensityHeader_machinestamp_get
594  if _newclass:machinestamp = _swig_property(_IMP_em.DensityHeader_machinestamp_get, _IMP_em.DensityHeader_machinestamp_set)
595  __swig_setmethods__["rms"] = _IMP_em.DensityHeader_rms_set
596  __swig_getmethods__["rms"] = _IMP_em.DensityHeader_rms_get
597  if _newclass:rms = _swig_property(_IMP_em.DensityHeader_rms_get, _IMP_em.DensityHeader_rms_set)
598  __swig_setmethods__["nlabl"] = _IMP_em.DensityHeader_nlabl_set
599  __swig_getmethods__["nlabl"] = _IMP_em.DensityHeader_nlabl_get
600  if _newclass:nlabl = _swig_property(_IMP_em.DensityHeader_nlabl_get, _IMP_em.DensityHeader_nlabl_set)
601  __swig_setmethods__["comments"] = _IMP_em.DensityHeader_comments_set
602  __swig_getmethods__["comments"] = _IMP_em.DensityHeader_comments_get
603  if _newclass:comments = _swig_property(_IMP_em.DensityHeader_comments_get, _IMP_em.DensityHeader_comments_set)
604  __swig_setmethods__["magic"] = _IMP_em.DensityHeader_magic_set
605  __swig_getmethods__["magic"] = _IMP_em.DensityHeader_magic_get
606  if _newclass:magic = _swig_property(_IMP_em.DensityHeader_magic_get, _IMP_em.DensityHeader_magic_set)
607  __swig_setmethods__["voltage"] = _IMP_em.DensityHeader_voltage_set
608  __swig_getmethods__["voltage"] = _IMP_em.DensityHeader_voltage_get
609  if _newclass:voltage = _swig_property(_IMP_em.DensityHeader_voltage_get, _IMP_em.DensityHeader_voltage_set)
610  __swig_setmethods__["Cs"] = _IMP_em.DensityHeader_Cs_set
611  __swig_getmethods__["Cs"] = _IMP_em.DensityHeader_Cs_get
612  if _newclass:Cs = _swig_property(_IMP_em.DensityHeader_Cs_get, _IMP_em.DensityHeader_Cs_set)
613  __swig_setmethods__["Aperture"] = _IMP_em.DensityHeader_Aperture_set
614  __swig_getmethods__["Aperture"] = _IMP_em.DensityHeader_Aperture_get
615  if _newclass:Aperture = _swig_property(_IMP_em.DensityHeader_Aperture_get, _IMP_em.DensityHeader_Aperture_set)
616  __swig_setmethods__["Magnification"] = _IMP_em.DensityHeader_Magnification_set
617  __swig_getmethods__["Magnification"] = _IMP_em.DensityHeader_Magnification_get
618  if _newclass:Magnification = _swig_property(_IMP_em.DensityHeader_Magnification_get, _IMP_em.DensityHeader_Magnification_set)
619  __swig_setmethods__["Postmagnification"] = _IMP_em.DensityHeader_Postmagnification_set
620  __swig_getmethods__["Postmagnification"] = _IMP_em.DensityHeader_Postmagnification_get
621  if _newclass:Postmagnification = _swig_property(_IMP_em.DensityHeader_Postmagnification_get, _IMP_em.DensityHeader_Postmagnification_set)
622  __swig_setmethods__["Exposuretime"] = _IMP_em.DensityHeader_Exposuretime_set
623  __swig_getmethods__["Exposuretime"] = _IMP_em.DensityHeader_Exposuretime_get
624  if _newclass:Exposuretime = _swig_property(_IMP_em.DensityHeader_Exposuretime_get, _IMP_em.DensityHeader_Exposuretime_set)
625  __swig_setmethods__["Microscope"] = _IMP_em.DensityHeader_Microscope_set
626  __swig_getmethods__["Microscope"] = _IMP_em.DensityHeader_Microscope_get
627  if _newclass:Microscope = _swig_property(_IMP_em.DensityHeader_Microscope_get, _IMP_em.DensityHeader_Microscope_set)
628  __swig_setmethods__["Pixelsize"] = _IMP_em.DensityHeader_Pixelsize_set
629  __swig_getmethods__["Pixelsize"] = _IMP_em.DensityHeader_Pixelsize_get
630  if _newclass:Pixelsize = _swig_property(_IMP_em.DensityHeader_Pixelsize_get, _IMP_em.DensityHeader_Pixelsize_set)
631  __swig_setmethods__["CCDArea"] = _IMP_em.DensityHeader_CCDArea_set
632  __swig_getmethods__["CCDArea"] = _IMP_em.DensityHeader_CCDArea_get
633  if _newclass:CCDArea = _swig_property(_IMP_em.DensityHeader_CCDArea_get, _IMP_em.DensityHeader_CCDArea_set)
634  __swig_setmethods__["Defocus"] = _IMP_em.DensityHeader_Defocus_set
635  __swig_getmethods__["Defocus"] = _IMP_em.DensityHeader_Defocus_get
636  if _newclass:Defocus = _swig_property(_IMP_em.DensityHeader_Defocus_get, _IMP_em.DensityHeader_Defocus_set)
637  __swig_setmethods__["Astigmatism"] = _IMP_em.DensityHeader_Astigmatism_set
638  __swig_getmethods__["Astigmatism"] = _IMP_em.DensityHeader_Astigmatism_get
639  if _newclass:Astigmatism = _swig_property(_IMP_em.DensityHeader_Astigmatism_get, _IMP_em.DensityHeader_Astigmatism_set)
640  __swig_setmethods__["AstigmatismAngle"] = _IMP_em.DensityHeader_AstigmatismAngle_set
641  __swig_getmethods__["AstigmatismAngle"] = _IMP_em.DensityHeader_AstigmatismAngle_get
642  if _newclass:AstigmatismAngle = _swig_property(_IMP_em.DensityHeader_AstigmatismAngle_get, _IMP_em.DensityHeader_AstigmatismAngle_set)
643  __swig_setmethods__["FocusIncrement"] = _IMP_em.DensityHeader_FocusIncrement_set
644  __swig_getmethods__["FocusIncrement"] = _IMP_em.DensityHeader_FocusIncrement_get
645  if _newclass:FocusIncrement = _swig_property(_IMP_em.DensityHeader_FocusIncrement_get, _IMP_em.DensityHeader_FocusIncrement_set)
646  __swig_setmethods__["CountsPerElectron"] = _IMP_em.DensityHeader_CountsPerElectron_set
647  __swig_getmethods__["CountsPerElectron"] = _IMP_em.DensityHeader_CountsPerElectron_get
648  if _newclass:CountsPerElectron = _swig_property(_IMP_em.DensityHeader_CountsPerElectron_get, _IMP_em.DensityHeader_CountsPerElectron_set)
649  __swig_setmethods__["Intensity"] = _IMP_em.DensityHeader_Intensity_set
650  __swig_getmethods__["Intensity"] = _IMP_em.DensityHeader_Intensity_get
651  if _newclass:Intensity = _swig_property(_IMP_em.DensityHeader_Intensity_get, _IMP_em.DensityHeader_Intensity_set)
652  __swig_setmethods__["EnergySlitwidth"] = _IMP_em.DensityHeader_EnergySlitwidth_set
653  __swig_getmethods__["EnergySlitwidth"] = _IMP_em.DensityHeader_EnergySlitwidth_get
654  if _newclass:EnergySlitwidth = _swig_property(_IMP_em.DensityHeader_EnergySlitwidth_get, _IMP_em.DensityHeader_EnergySlitwidth_set)
655  __swig_setmethods__["EnergyOffset"] = _IMP_em.DensityHeader_EnergyOffset_set
656  __swig_getmethods__["EnergyOffset"] = _IMP_em.DensityHeader_EnergyOffset_get
657  if _newclass:EnergyOffset = _swig_property(_IMP_em.DensityHeader_EnergyOffset_get, _IMP_em.DensityHeader_EnergyOffset_set)
658  __swig_setmethods__["Tiltangle"] = _IMP_em.DensityHeader_Tiltangle_set
659  __swig_getmethods__["Tiltangle"] = _IMP_em.DensityHeader_Tiltangle_get
660  if _newclass:Tiltangle = _swig_property(_IMP_em.DensityHeader_Tiltangle_get, _IMP_em.DensityHeader_Tiltangle_set)
661  __swig_setmethods__["Tiltaxis"] = _IMP_em.DensityHeader_Tiltaxis_set
662  __swig_getmethods__["Tiltaxis"] = _IMP_em.DensityHeader_Tiltaxis_get
663  if _newclass:Tiltaxis = _swig_property(_IMP_em.DensityHeader_Tiltaxis_get, _IMP_em.DensityHeader_Tiltaxis_set)
664  __swig_setmethods__["MarkerX"] = _IMP_em.DensityHeader_MarkerX_set
665  __swig_getmethods__["MarkerX"] = _IMP_em.DensityHeader_MarkerX_get
666  if _newclass:MarkerX = _swig_property(_IMP_em.DensityHeader_MarkerX_get, _IMP_em.DensityHeader_MarkerX_set)
667  __swig_setmethods__["MarkerY"] = _IMP_em.DensityHeader_MarkerY_set
668  __swig_getmethods__["MarkerY"] = _IMP_em.DensityHeader_MarkerY_get
669  if _newclass:MarkerY = _swig_property(_IMP_em.DensityHeader_MarkerY_get, _IMP_em.DensityHeader_MarkerY_set)
670  __swig_setmethods__["lswap"] = _IMP_em.DensityHeader_lswap_set
671  __swig_getmethods__["lswap"] = _IMP_em.DensityHeader_lswap_get
672  if _newclass:lswap = _swig_property(_IMP_em.DensityHeader_lswap_get, _IMP_em.DensityHeader_lswap_set)
673  def get_resolution(self):
674  """get_resolution(DensityHeader self) -> float"""
675  return _IMP_em.DensityHeader_get_resolution(self)
676 
677  def get_has_resolution(self):
678  """get_has_resolution(DensityHeader self) -> bool"""
679  return _IMP_em.DensityHeader_get_has_resolution(self)
680 
681  def set_resolution(self, *args):
682  """set_resolution(DensityHeader self, float resolution)"""
683  return _IMP_em.DensityHeader_set_resolution(self, *args)
684 
685  def get_spacing(self):
686  """get_spacing(DensityHeader self) -> float"""
687  return _IMP_em.DensityHeader_get_spacing(self)
688 
689  def get_xorigin(self):
690  """get_xorigin(DensityHeader self) -> float"""
691  return _IMP_em.DensityHeader_get_xorigin(self)
692 
693  def get_yorigin(self):
694  """get_yorigin(DensityHeader self) -> float"""
695  return _IMP_em.DensityHeader_get_yorigin(self)
696 
697  def get_zorigin(self):
698  """get_zorigin(DensityHeader self) -> float"""
699  return _IMP_em.DensityHeader_get_zorigin(self)
700 
701  def get_origin(self, *args):
702  """get_origin(DensityHeader self, int i) -> float"""
703  return _IMP_em.DensityHeader_get_origin(self, *args)
704 
705  def set_xorigin(self, *args):
706  """set_xorigin(DensityHeader self, float x)"""
707  return _IMP_em.DensityHeader_set_xorigin(self, *args)
708 
709  def set_yorigin(self, *args):
710  """set_yorigin(DensityHeader self, float y)"""
711  return _IMP_em.DensityHeader_set_yorigin(self, *args)
712 
713  def set_zorigin(self, *args):
714  """set_zorigin(DensityHeader self, float z)"""
715  return _IMP_em.DensityHeader_set_zorigin(self, *args)
716 
717  def is_top_calculated(self):
718  """is_top_calculated(DensityHeader self) -> bool"""
719  return _IMP_em.DensityHeader_is_top_calculated(self)
720 
721  __swig_setmethods__["Objectpixelsize_"] = _IMP_em.DensityHeader_Objectpixelsize__set
722  __swig_getmethods__["Objectpixelsize_"] = _IMP_em.DensityHeader_Objectpixelsize__get
723  if _newclass:Objectpixelsize_ = _swig_property(_IMP_em.DensityHeader_Objectpixelsize__get, _IMP_em.DensityHeader_Objectpixelsize__set)
724  def get_nx(self):
725  """get_nx(DensityHeader self) -> int"""
726  return _IMP_em.DensityHeader_get_nx(self)
727 
728  def get_ny(self):
729  """get_ny(DensityHeader self) -> int"""
730  return _IMP_em.DensityHeader_get_ny(self)
731 
732  def get_nz(self):
733  """get_nz(DensityHeader self) -> int"""
734  return _IMP_em.DensityHeader_get_nz(self)
735 
736  def get_number_of_voxels(self):
737  """get_number_of_voxels(DensityHeader self) -> int"""
738  return _IMP_em.DensityHeader_get_number_of_voxels(self)
739 
740  def get_data_type(self):
741  """get_data_type(DensityHeader self) -> int"""
742  return _IMP_em.DensityHeader_get_data_type(self)
743 
744  def set_data_type(self, *args):
745  """set_data_type(DensityHeader self, int data_type)"""
746  return _IMP_em.DensityHeader_set_data_type(self, *args)
747 
748  __swig_destroy__ = _IMP_em.delete_DensityHeader
749  __del__ = lambda self : None;
750 DensityHeader_swigregister = _IMP_em.DensityHeader_swigregister
751 DensityHeader_swigregister(DensityHeader)
752 
753 
754 def create_density_header(*args):
755  """create_density_header(BoundingBox3D bb, float spacing) -> DensityHeader"""
756  return _IMP_em.create_density_header(*args)
757 
758 def read_map(*args):
759  """
760  read_map(std::string filename, MapReaderWriter reader) -> DensityMap
761  read_map(std::string filename) -> DensityMap
762  """
763  return _IMP_em.read_map(*args)
764 
765 def write_map(*args):
766  """
767  write_map(DensityMap m, std::string filename, MapReaderWriter writer)
768  write_map(DensityMap m, std::string filename)
769  """
770  return _IMP_em.write_map(*args)
771 
772 def approximate_molecular_mass(*args):
773  """approximate_molecular_mass(DensityMap m, IMP::Float threshold) -> IMP::Float"""
774  return _IMP_em.approximate_molecular_mass(*args)
775 class DensityMap(IMP.base.Object):
776  """Proxy of C++ IMP::em::DensityMap class"""
777  __swig_setmethods__ = {}
778  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
779  __setattr__ = lambda self, name, value: _swig_setattr(self, DensityMap, name, value)
780  __swig_getmethods__ = {}
781  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
782  __getattr__ = lambda self, name: _swig_getattr(self, DensityMap, name)
783  def __init__(self, *args):
784  """
785  __init__(IMP::em::DensityMap self, std::string name="DensityMap%1%") -> DensityMap
786  __init__(IMP::em::DensityMap self) -> DensityMap
787  __init__(IMP::em::DensityMap self, DensityHeader header, std::string name="DensityMap%1%") -> DensityMap
788  __init__(IMP::em::DensityMap self, DensityHeader header) -> DensityMap
789  """
790  this = _IMP_em.new_DensityMap(*args)
791  try: self.this.append(this)
792  except: self.this = this
793  def reset_data(self, value=0.0):
794  """
795  reset_data(DensityMap self, float value=0.0)
796  reset_data(DensityMap self)
797  """
798  return _IMP_em.DensityMap_reset_data(self, value)
799 
800  def calcRMS(self):
801  """calcRMS(DensityMap self) -> IMP::em::emreal"""
802  return _IMP_em.DensityMap_calcRMS(self)
803 
804  def std_normalize(self):
805  """std_normalize(DensityMap self)"""
806  return _IMP_em.DensityMap_std_normalize(self)
807 
808  def is_normalized(self):
809  """is_normalized(DensityMap self) -> bool"""
810  return _IMP_em.DensityMap_is_normalized(self)
811 
812  def get_location_in_dim_by_voxel(self, *args):
813  """get_location_in_dim_by_voxel(DensityMap self, long index, int dim) -> float"""
814  return _IMP_em.DensityMap_get_location_in_dim_by_voxel(self, *args)
815 
816  def xyz_ind2voxel(self, *args):
817  """xyz_ind2voxel(DensityMap self, int x, int y, int z) -> long"""
818  return _IMP_em.DensityMap_xyz_ind2voxel(self, *args)
819 
820  def get_voxel_by_location(self, *args):
821  """
822  get_voxel_by_location(DensityMap self, float x, float y, float z) -> long
823  get_voxel_by_location(DensityMap self, Vector3D v) -> long
824  """
825  return _IMP_em.DensityMap_get_voxel_by_location(self, *args)
826 
827  def get_location_by_voxel(self, *args):
828  """get_location_by_voxel(DensityMap self, long index) -> Vector3D"""
829  return _IMP_em.DensityMap_get_location_by_voxel(self, *args)
830 
831  def is_xyz_ind_part_of_volume(self, *args):
832  """is_xyz_ind_part_of_volume(DensityMap self, int ix, int iy, int iz) -> bool"""
833  return _IMP_em.DensityMap_is_xyz_ind_part_of_volume(self, *args)
834 
835  def is_part_of_volume(self, *args):
836  """
837  is_part_of_volume(DensityMap self, float x, float y, float z) -> bool
838  is_part_of_volume(DensityMap self, Vector3D v) -> bool
839  """
840  return _IMP_em.DensityMap_is_part_of_volume(self, *args)
841 
842  def get_value(self, *args):
843  """
844  get_value(DensityMap self, float x, float y, float z) -> IMP::em::emreal
845  get_value(DensityMap self, Vector3D point) -> IMP::em::emreal
846  get_value(DensityMap self, long index) -> IMP::em::emreal
847  """
848  return _IMP_em.DensityMap_get_value(self, *args)
849 
850  def set_value(self, *args):
851  """
852  set_value(DensityMap self, long index, IMP::em::emreal value)
853  set_value(DensityMap self, float x, float y, float z, IMP::em::emreal value)
854  """
855  return _IMP_em.DensityMap_set_value(self, *args)
856 
857  def set_origin(self, *args):
858  """
859  set_origin(DensityMap self, float x, float y, float z)
860  set_origin(DensityMap self, Vector3D v)
861  """
862  return _IMP_em.DensityMap_set_origin(self, *args)
863 
864  def get_origin(self):
865  """get_origin(DensityMap self) -> Vector3D"""
866  return _IMP_em.DensityMap_get_origin(self)
867 
868  def get_top(self):
869  """get_top(DensityMap self) -> Vector3D"""
870  return _IMP_em.DensityMap_get_top(self)
871 
872  def get_header(self):
873  h = _IMP_em.DensityMap_get_header(self)
874  h._owner = self
875  return h
876 
877 
878  def get_header_writable(self):
879  h = _IMP_em.DensityMap_get_header_writable(self)
880  h._owner = self
881  return h
882 
883 
884  def same_origin(self, *args):
885  """same_origin(DensityMap self, DensityMap other) -> bool"""
886  return _IMP_em.DensityMap_same_origin(self, *args)
887 
888  def same_dimensions(self, *args):
889  """same_dimensions(DensityMap self, DensityMap other) -> bool"""
890  return _IMP_em.DensityMap_same_dimensions(self, *args)
891 
892  def same_voxel_size(self, *args):
893  """same_voxel_size(DensityMap self, DensityMap other) -> bool"""
894  return _IMP_em.DensityMap_same_voxel_size(self, *args)
895 
896  def get_centroid(self, threshold=0.0):
897  """
898  get_centroid(DensityMap self, IMP::em::emreal threshold=0.0) -> Vector3D
899  get_centroid(DensityMap self) -> Vector3D
900  """
901  return _IMP_em.DensityMap_get_centroid(self, threshold)
902 
903  def get_max_value(self):
904  """get_max_value(DensityMap self) -> IMP::em::emreal"""
905  return _IMP_em.DensityMap_get_max_value(self)
906 
907  def get_min_value(self):
908  """get_min_value(DensityMap self) -> IMP::em::emreal"""
909  return _IMP_em.DensityMap_get_min_value(self)
910 
911  def add(self, *args):
912  """add(DensityMap self, DensityMap other)"""
913  return _IMP_em.DensityMap_add(self, *args)
914 
915  def pick_max(self, *args):
916  """pick_max(DensityMap self, DensityMap other)"""
917  return _IMP_em.DensityMap_pick_max(self, *args)
918 
919  def get_number_of_voxels(self):
920  """get_number_of_voxels(DensityMap self) -> long"""
921  return _IMP_em.DensityMap_get_number_of_voxels(self)
922 
923  def set_void_map(self, *args):
924  """set_void_map(DensityMap self, int nx, int ny, int nz)"""
925  return _IMP_em.DensityMap_set_void_map(self, *args)
926 
927  def pad(self, *args):
928  """
929  pad(DensityMap self, int nx, int ny, int nz, float val=0.0)
930  pad(DensityMap self, int nx, int ny, int nz)
931  """
932  return _IMP_em.DensityMap_pad(self, *args)
933 
934  def pad_margin(self, *args):
935  """
936  pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z, float val=0.0) -> DensityMap
937  pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z) -> DensityMap
938  """
939  return _IMP_em.DensityMap_pad_margin(self, *args)
940 
941  def get_cropped(self, *args):
942  """
943  get_cropped(DensityMap self, float threshold) -> DensityMap
944  get_cropped(DensityMap self, BoundingBox3D bb) -> DensityMap
945  """
946  return _IMP_em.DensityMap_get_cropped(self, *args)
947 
948  def get_maximum_value_in_xy_plane(self, *args):
949  """get_maximum_value_in_xy_plane(DensityMap self, int z_ind) -> float"""
950  return _IMP_em.DensityMap_get_maximum_value_in_xy_plane(self, *args)
951 
952  def get_maximum_value_in_xz_plane(self, *args):
953  """get_maximum_value_in_xz_plane(DensityMap self, int y_ind) -> float"""
954  return _IMP_em.DensityMap_get_maximum_value_in_xz_plane(self, *args)
955 
956  def get_maximum_value_in_yz_plane(self, *args):
957  """get_maximum_value_in_yz_plane(DensityMap self, int x_ind) -> float"""
958  return _IMP_em.DensityMap_get_maximum_value_in_yz_plane(self, *args)
959 
960  def multiply(self, *args):
961  """multiply(DensityMap self, float factor)"""
962  return _IMP_em.DensityMap_multiply(self, *args)
963 
964  def get_locations_string(self, *args):
965  """get_locations_string(DensityMap self, float t) -> std::string"""
966  return _IMP_em.DensityMap_get_locations_string(self, *args)
967 
968  def update_voxel_size(self, *args):
969  """update_voxel_size(DensityMap self, float new_apix)"""
970  return _IMP_em.DensityMap_update_voxel_size(self, *args)
971 
972  def get_spacing(self):
973  """get_spacing(DensityMap self) -> IMP::Float"""
974  return _IMP_em.DensityMap_get_spacing(self)
975 
976  def calc_all_voxel2loc(self):
977  """calc_all_voxel2loc(DensityMap self)"""
978  return _IMP_em.DensityMap_calc_all_voxel2loc(self)
979 
980  def copy_map(self, *args):
981  """copy_map(DensityMap self, DensityMap other)"""
982  return _IMP_em.DensityMap_copy_map(self, *args)
983 
984  def get_version_info(self):
985  """get_version_info(DensityMap self) -> VersionInfo"""
986  return _IMP_em.DensityMap_get_version_info(self)
987 
988  def lower_voxel_shift(self, *args):
989  """lower_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
990  return _IMP_em.DensityMap_lower_voxel_shift(self, *args)
991 
992  def upper_voxel_shift(self, *args):
993  """upper_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
994  return _IMP_em.DensityMap_upper_voxel_shift(self, *args)
995 
996  def get_rms_calculated(self):
997  """get_rms_calculated(DensityMap self) -> bool"""
998  return _IMP_em.DensityMap_get_rms_calculated(self)
999 
1000  def get_dim_index_by_location(self, *args):
1001  """
1002  get_dim_index_by_location(DensityMap self, Vector3D v, int ind) -> int
1003  get_dim_index_by_location(DensityMap self, float loc_val, int ind) -> int
1004  """
1005  return _IMP_em.DensityMap_get_dim_index_by_location(self, *args)
1006 
1007  def __str__(self):
1008  """__str__(DensityMap self) -> std::string"""
1009  return _IMP_em.DensityMap___str__(self)
1010 
1011  def __repr__(self):
1012  """__repr__(DensityMap self) -> std::string"""
1013  return _IMP_em.DensityMap___repr__(self)
1014 
1015  def get_from(o):
1016  return _object_cast_to_DensityMap(o)
1017  get_from = staticmethod(get_from)
1018 
1019 DensityMap_swigregister = _IMP_em.DensityMap_swigregister
1020 DensityMap_swigregister(DensityMap)
1021 
1022 
1023 def get_bounding_box(*args):
1024  """
1025  get_bounding_box(DensityMap m, IMP::Float threshold) -> BoundingBox3D
1026  get_bounding_box(DensityMap m) -> BoundingBox3D
1027  """
1028  return _IMP_em.get_bounding_box(*args)
1029 
1030 def get_density(*args):
1031  """get_density(DensityMap m, Vector3D v) -> double"""
1032  return _IMP_em.get_density(*args)
1033 
1034 def get_transformed(*args):
1035  """
1036  get_transformed(DensityMap input, Transformation3D tr, double threshold) -> DensityMap
1037  get_transformed(DensityMap input, Transformation3D tr) -> DensityMap
1038  """
1039  return _IMP_em.get_transformed(*args)
1040 
1041 def get_resampled(*args):
1042  """get_resampled(DensityMap input, double scaling) -> DensityMap"""
1043  return _IMP_em.get_resampled(*args)
1044 
1045 def get_transformed_into(*args):
1046  """
1047  get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into, bool calc_rms=True)
1048  get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into)
1049  """
1050  return _IMP_em.get_transformed_into(*args)
1051 
1052 def get_transformed_into2(*args):
1053  """get_transformed_into2(DensityMap source, Transformation3D tr, DensityMap into)"""
1054  return _IMP_em.get_transformed_into2(*args)
1055 
1056 def get_interiors_intersect(*args):
1057  """get_interiors_intersect(DensityMap d1, DensityMap d2) -> bool"""
1058  return _IMP_em.get_interiors_intersect(*args)
1059 
1060 def get_segment(*args):
1061  """
1062  get_segment(DensityMap map_to_segment, int nx_start, int nx_end, int ny_start, int ny_end, int nz_start,
1063  int nz_end) -> DensityMap
1064  get_segment(DensityMap map_to_segment, IMP::algebra::Vector3Ds vecs, float dist) -> DensityMap
1065  """
1066  return _IMP_em.get_segment(*args)
1067 
1068 def get_segment_by_masking(*args):
1069  """get_segment_by_masking(DensityMap map_to_segment, DensityMap mask, float mas_threshold) -> DensityMap"""
1070  return _IMP_em.get_segment_by_masking(*args)
1071 
1072 def binarize(*args):
1073  """
1074  binarize(DensityMap orig_map, float threshold, bool reverse=False) -> DensityMap
1075  binarize(DensityMap orig_map, float threshold) -> DensityMap
1076  """
1077  return _IMP_em.binarize(*args)
1078 
1079 def get_threshold_map(*args):
1080  """get_threshold_map(DensityMap orig_map, float threshold) -> DensityMap"""
1081  return _IMP_em.get_threshold_map(*args)
1082 
1083 def multiply(*args):
1084  """multiply(DensityMap m1, DensityMap m2) -> DensityMap"""
1085  return _IMP_em.multiply(*args)
1086 
1087 def convolute(*args):
1088  """convolute(DensityMap m1, DensityMap m2) -> double"""
1089  return _IMP_em.convolute(*args)
1090 
1091 def get_sum(*args):
1092  """get_sum(DensityMap m1) -> double"""
1093  return _IMP_em.get_sum(*args)
1094 
1095 def get_max_map(*args):
1096  """get_max_map(IMP::em::DensityMaps maps) -> DensityMap"""
1097  return _IMP_em.get_max_map(*args)
1098 
1099 def interpolate_map(*args):
1100  """interpolate_map(DensityMap in_map, double new_spacing) -> DensityMap"""
1101  return _IMP_em.interpolate_map(*args)
1102 
1103 def get_grid(*args):
1104  """get_grid(DensityMap in_map) -> IMP::algebra::GridD< 3,IMP::algebra::DenseGridStorageD< 3,float >,float,IMP::algebra::DefaultEmbeddingD< 3 > >"""
1105  return _IMP_em.get_grid(*args)
1106 
1107 def create_density_map(*args):
1108  """
1109  create_density_map(DensityMap other) -> DensityMap
1110  create_density_map(BoundingBox3D bb, double spacing) -> DensityMap
1111  create_density_map(int nx, int ny, int nz, double spacing) -> DensityMap
1112  create_density_map(IMP::algebra::GridD< 3,IMP::algebra::DenseGridStorageD< 3,float >,float,IMP::algebra::DefaultEmbeddingD< 3 > > const & grid) -> DensityMap
1113  """
1114  return _IMP_em.create_density_map(*args)
1115 
1116 def get_binarized_interior(*args):
1117  """get_binarized_interior(DensityMap dmap) -> DensityMap"""
1118  return _IMP_em.get_binarized_interior(*args)
1119 
1120 def add_to_map(*args):
1121  """add_to_map(DensityMap dm, IMP::kernel::Particles const & pis)"""
1122  return _IMP_em.add_to_map(*args)
1123 class RadiusDependentDistanceMask(_object):
1124  """Proxy of C++ IMP::em::RadiusDependentDistanceMask class"""
1125  __swig_setmethods__ = {}
1126  __setattr__ = lambda self, name, value: _swig_setattr(self, RadiusDependentDistanceMask, name, value)
1127  __swig_getmethods__ = {}
1128  __getattr__ = lambda self, name: _swig_getattr(self, RadiusDependentDistanceMask, name)
1129  __repr__ = _swig_repr
1130  def __init__(self, *args):
1131  """__init__(IMP::em::RadiusDependentDistanceMask self, float sampling_radius, DensityHeader header) -> RadiusDependentDistanceMask"""
1132  this = _IMP_em.new_RadiusDependentDistanceMask(*args)
1133  try: self.this.append(this)
1134  except: self.this = this
1135  def get_neighbor_shift(self):
1136  """get_neighbor_shift(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1137  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_shift(self)
1138 
1139  def get_neighbor_dist(self):
1140  """get_neighbor_dist(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1141  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist(self)
1142 
1143  def get_neighbor_dist_exp(self):
1144  """get_neighbor_dist_exp(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1145  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist_exp(self)
1146 
1147  def show(self, *args):
1148  """show(RadiusDependentDistanceMask self, _ostream out)"""
1149  return _IMP_em.RadiusDependentDistanceMask_show(self, *args)
1150 
1151  __swig_destroy__ = _IMP_em.delete_RadiusDependentDistanceMask
1152  __del__ = lambda self : None;
1153 RadiusDependentDistanceMask_swigregister = _IMP_em.RadiusDependentDistanceMask_swigregister
1154 RadiusDependentDistanceMask_swigregister(RadiusDependentDistanceMask)
1155 
1156 class DistanceMask(_object):
1157  """Proxy of C++ IMP::em::DistanceMask class"""
1158  __swig_setmethods__ = {}
1159  __setattr__ = lambda self, name, value: _swig_setattr(self, DistanceMask, name, value)
1160  __swig_getmethods__ = {}
1161  __getattr__ = lambda self, name: _swig_getattr(self, DistanceMask, name)
1162  __repr__ = _swig_repr
1163  def __init__(self, *args):
1164  """
1165  __init__(IMP::em::DistanceMask self) -> DistanceMask
1166  __init__(IMP::em::DistanceMask self, DensityHeader header) -> DistanceMask
1167  """
1168  this = _IMP_em.new_DistanceMask(*args)
1169  try: self.this.append(this)
1170  except: self.this = this
1171  def show(self, *args):
1172  """show(DistanceMask self, _ostream out)"""
1173  return _IMP_em.DistanceMask_show(self, *args)
1174 
1175  def is_mask_set(self, *args):
1176  """
1177  is_mask_set(DistanceMask self, float radius, float eps=0.001) -> bool
1178  is_mask_set(DistanceMask self, float radius) -> bool
1179  """
1180  return _IMP_em.DistanceMask_is_mask_set(self, *args)
1181 
1182  __swig_destroy__ = _IMP_em.delete_DistanceMask
1183  __del__ = lambda self : None;
1184 DistanceMask_swigregister = _IMP_em.DistanceMask_swigregister
1185 DistanceMask_swigregister(DistanceMask)
1186 
1187 class EMReaderWriter(MapReaderWriter):
1188  """Proxy of C++ IMP::em::EMReaderWriter class"""
1189  __swig_setmethods__ = {}
1190  for _s in [MapReaderWriter]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1191  __setattr__ = lambda self, name, value: _swig_setattr(self, EMReaderWriter, name, value)
1192  __swig_getmethods__ = {}
1193  for _s in [MapReaderWriter]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1194  __getattr__ = lambda self, name: _swig_getattr(self, EMReaderWriter, name)
1195  def __str__(self):
1196  """__str__(EMReaderWriter self) -> std::string"""
1197  return _IMP_em.EMReaderWriter___str__(self)
1198 
1199  def __repr__(self):
1200  """__repr__(EMReaderWriter self) -> std::string"""
1201  return _IMP_em.EMReaderWriter___repr__(self)
1202 
1203  def get_from(o):
1204  return _object_cast_to_EMReaderWriter(o)
1205  get_from = staticmethod(get_from)
1206 
1207  def __init__(self):
1208  """__init__(IMP::em::EMReaderWriter self) -> EMReaderWriter"""
1209  this = _IMP_em.new_EMReaderWriter()
1210  try: self.this.append(this)
1211  except: self.this = this
1212 EMReaderWriter_swigregister = _IMP_em.EMReaderWriter_swigregister
1213 EMReaderWriter_swigregister(EMReaderWriter)
1214 
1215 class XplorReaderWriter(MapReaderWriter):
1216  """Proxy of C++ IMP::em::XplorReaderWriter class"""
1217  __swig_setmethods__ = {}
1218  for _s in [MapReaderWriter]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1219  __setattr__ = lambda self, name, value: _swig_setattr(self, XplorReaderWriter, name, value)
1220  __swig_getmethods__ = {}
1221  for _s in [MapReaderWriter]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1222  __getattr__ = lambda self, name: _swig_getattr(self, XplorReaderWriter, name)
1223  def __str__(self):
1224  """__str__(XplorReaderWriter self) -> std::string"""
1225  return _IMP_em.XplorReaderWriter___str__(self)
1226 
1227  def __repr__(self):
1228  """__repr__(XplorReaderWriter self) -> std::string"""
1229  return _IMP_em.XplorReaderWriter___repr__(self)
1230 
1231  def get_from(o):
1232  return _object_cast_to_XplorReaderWriter(o)
1233  get_from = staticmethod(get_from)
1234 
1235  def __init__(self):
1236  """__init__(IMP::em::XplorReaderWriter self) -> XplorReaderWriter"""
1237  this = _IMP_em.new_XplorReaderWriter()
1238  try: self.this.append(this)
1239  except: self.this = this
1240 XplorReaderWriter_swigregister = _IMP_em.XplorReaderWriter_swigregister
1241 XplorReaderWriter_swigregister(XplorReaderWriter)
1242 
1243 class MRCReaderWriter(MapReaderWriter):
1244  """Proxy of C++ IMP::em::MRCReaderWriter class"""
1245  __swig_setmethods__ = {}
1246  for _s in [MapReaderWriter]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1247  __setattr__ = lambda self, name, value: _swig_setattr(self, MRCReaderWriter, name, value)
1248  __swig_getmethods__ = {}
1249  for _s in [MapReaderWriter]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1250  __getattr__ = lambda self, name: _swig_getattr(self, MRCReaderWriter, name)
1251  def __init__(self, *args):
1252  """
1253  __init__(IMP::em::MRCReaderWriter self) -> MRCReaderWriter
1254  __init__(IMP::em::MRCReaderWriter self, std::string fn) -> MRCReaderWriter
1255  """
1256  this = _IMP_em.new_MRCReaderWriter(*args)
1257  try: self.this.append(this)
1258  except: self.this = this
1259  def __str__(self):
1260  """__str__(MRCReaderWriter self) -> std::string"""
1261  return _IMP_em.MRCReaderWriter___str__(self)
1262 
1263  def __repr__(self):
1264  """__repr__(MRCReaderWriter self) -> std::string"""
1265  return _IMP_em.MRCReaderWriter___repr__(self)
1266 
1267  def get_from(o):
1268  return _object_cast_to_MRCReaderWriter(o)
1269  get_from = staticmethod(get_from)
1270 
1271 MRCReaderWriter_swigregister = _IMP_em.MRCReaderWriter_swigregister
1272 MRCReaderWriter_swigregister(MRCReaderWriter)
1273 
1274 class RadiusDependentKernelParameters(_object):
1275  """Proxy of C++ IMP::em::RadiusDependentKernelParameters class"""
1276  __swig_setmethods__ = {}
1277  __setattr__ = lambda self, name, value: _swig_setattr(self, RadiusDependentKernelParameters, name, value)
1278  __swig_getmethods__ = {}
1279  __getattr__ = lambda self, name: _swig_getattr(self, RadiusDependentKernelParameters, name)
1280  def __init__(self, *args):
1281  """
1282  __init__(IMP::em::RadiusDependentKernelParameters self, float radii, float rsigsq, float timessig, float sq2pi3, float inv_rsigsq, float rnormfac,
1283  float rkdist) -> RadiusDependentKernelParameters
1284  """
1285  this = _IMP_em.new_RadiusDependentKernelParameters(*args)
1286  try: self.this.append(this)
1287  except: self.this = this
1288  def show(self, *args):
1289  """
1290  show(RadiusDependentKernelParameters self, _ostream s=std::cout)
1291  show(RadiusDependentKernelParameters self)
1292  """
1293  return _IMP_em.RadiusDependentKernelParameters_show(self, *args)
1294 
1295  def get_vsig(self):
1296  """get_vsig(RadiusDependentKernelParameters self) -> float"""
1297  return _IMP_em.RadiusDependentKernelParameters_get_vsig(self)
1298 
1299  def get_vsigsq(self):
1300  """get_vsigsq(RadiusDependentKernelParameters self) -> float"""
1301  return _IMP_em.RadiusDependentKernelParameters_get_vsigsq(self)
1302 
1303  def get_inv_sigsq(self):
1304  """get_inv_sigsq(RadiusDependentKernelParameters self) -> float"""
1305  return _IMP_em.RadiusDependentKernelParameters_get_inv_sigsq(self)
1306 
1307  def get_sig(self):
1308  """get_sig(RadiusDependentKernelParameters self) -> float"""
1309  return _IMP_em.RadiusDependentKernelParameters_get_sig(self)
1310 
1311  def get_kdist(self):
1312  """get_kdist(RadiusDependentKernelParameters self) -> float"""
1313  return _IMP_em.RadiusDependentKernelParameters_get_kdist(self)
1314 
1315  def get_normfac(self):
1316  """get_normfac(RadiusDependentKernelParameters self) -> float"""
1317  return _IMP_em.RadiusDependentKernelParameters_get_normfac(self)
1318 
1319  __swig_destroy__ = _IMP_em.delete_RadiusDependentKernelParameters
1320  __del__ = lambda self : None;
1321  def __str__(self):
1322  """__str__(RadiusDependentKernelParameters self) -> std::string"""
1323  return _IMP_em.RadiusDependentKernelParameters___str__(self)
1324 
1325  def __repr__(self):
1326  """__repr__(RadiusDependentKernelParameters self) -> std::string"""
1327  return _IMP_em.RadiusDependentKernelParameters___repr__(self)
1328 
1329 RadiusDependentKernelParameters_swigregister = _IMP_em.RadiusDependentKernelParameters_swigregister
1330 RadiusDependentKernelParameters_swigregister(RadiusDependentKernelParameters)
1331 
1332 class KernelParameters(_object):
1333  """Proxy of C++ IMP::em::KernelParameters class"""
1334  __swig_setmethods__ = {}
1335  __setattr__ = lambda self, name, value: _swig_setattr(self, KernelParameters, name, value)
1336  __swig_getmethods__ = {}
1337  __getattr__ = lambda self, name: _swig_getattr(self, KernelParameters, name)
1338  def __init__(self, *args):
1339  """
1340  __init__(IMP::em::KernelParameters self) -> KernelParameters
1341  __init__(IMP::em::KernelParameters self, float resolution) -> KernelParameters
1342  """
1343  this = _IMP_em.new_KernelParameters(*args)
1344  try: self.this.append(this)
1345  except: self.this = this
1346  __swig_destroy__ = _IMP_em.delete_KernelParameters
1347  __del__ = lambda self : None;
1348  def set_params(self, *args):
1349  """set_params(KernelParameters self, float radius) -> RadiusDependentKernelParameters"""
1350  return _IMP_em.KernelParameters_set_params(self, *args)
1351 
1352  def get_params(self, *args):
1353  """
1354  get_params(KernelParameters self, float radius, float eps=0.001) -> RadiusDependentKernelParameters
1355  get_params(KernelParameters self, float radius) -> RadiusDependentKernelParameters
1356  """
1357  return _IMP_em.KernelParameters_get_params(self, *args)
1358 
1359  def get_rsig(self):
1360  """get_rsig(KernelParameters self) -> float"""
1361  return _IMP_em.KernelParameters_get_rsig(self)
1362 
1363  def get_rsigsq(self):
1364  """get_rsigsq(KernelParameters self) -> float"""
1365  return _IMP_em.KernelParameters_get_rsigsq(self)
1366 
1367  def get_inv_rsigsq(self):
1368  """get_inv_rsigsq(KernelParameters self) -> float"""
1369  return _IMP_em.KernelParameters_get_inv_rsigsq(self)
1370 
1371  def get_timessig(self):
1372  """get_timessig(KernelParameters self) -> float"""
1373  return _IMP_em.KernelParameters_get_timessig(self)
1374 
1375  def get_sq2pi3(self):
1376  """get_sq2pi3(KernelParameters self) -> float"""
1377  return _IMP_em.KernelParameters_get_sq2pi3(self)
1378 
1379  def get_rnormfac(self):
1380  """get_rnormfac(KernelParameters self) -> float"""
1381  return _IMP_em.KernelParameters_get_rnormfac(self)
1382 
1383  def get_rkdist(self):
1384  """get_rkdist(KernelParameters self) -> float"""
1385  return _IMP_em.KernelParameters_get_rkdist(self)
1386 
1387  def get_lim(self):
1388  """get_lim(KernelParameters self) -> float"""
1389  return _IMP_em.KernelParameters_get_lim(self)
1390 
1391  def show(self, *args):
1392  """
1393  show(KernelParameters self, _ostream out=std::cout)
1394  show(KernelParameters self)
1395  """
1396  return _IMP_em.KernelParameters_show(self, *args)
1397 
1398  def __str__(self):
1399  """__str__(KernelParameters self) -> std::string"""
1400  return _IMP_em.KernelParameters___str__(self)
1401 
1402  def __repr__(self):
1403  """__repr__(KernelParameters self) -> std::string"""
1404  return _IMP_em.KernelParameters___repr__(self)
1405 
1406 KernelParameters_swigregister = _IMP_em.KernelParameters_swigregister
1407 KernelParameters_swigregister(KernelParameters)
1408 
1409 GAUSSIAN = _IMP_em.GAUSSIAN
1410 BINARIZED_SPHERE = _IMP_em.BINARIZED_SPHERE
1411 SPHERE = _IMP_em.SPHERE
1412 class SampledDensityMap(DensityMap):
1413  """Proxy of C++ IMP::em::SampledDensityMap class"""
1414  __swig_setmethods__ = {}
1415  for _s in [DensityMap]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1416  __setattr__ = lambda self, name, value: _swig_setattr(self, SampledDensityMap, name, value)
1417  __swig_getmethods__ = {}
1418  for _s in [DensityMap]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1419  __getattr__ = lambda self, name: _swig_getattr(self, SampledDensityMap, name)
1420  def __init__(self, *args):
1421  """
1422  __init__(IMP::em::SampledDensityMap self, IMP::em::KernelType kt=GAUSSIAN) -> SampledDensityMap
1423  __init__(IMP::em::SampledDensityMap self) -> SampledDensityMap
1424  __init__(IMP::em::SampledDensityMap self, DensityHeader header, IMP::em::KernelType kt=GAUSSIAN) -> SampledDensityMap
1425  __init__(IMP::em::SampledDensityMap self, DensityHeader header) -> SampledDensityMap
1426  __init__(IMP::em::SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size,
1427  FloatKey mass_key=IMP::atom::Mass::get_mass_key(), int sig_cuttoff=3,
1428  IMP::em::KernelType kt=GAUSSIAN) -> SampledDensityMap
1429  __init__(IMP::em::SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size,
1430  FloatKey mass_key=IMP::atom::Mass::get_mass_key(), int sig_cuttoff=3) -> SampledDensityMap
1431  __init__(IMP::em::SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size,
1432  FloatKey mass_key=IMP::atom::Mass::get_mass_key()) -> SampledDensityMap
1433  __init__(IMP::em::SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size) -> SampledDensityMap
1434  """
1435  this = _IMP_em.new_SampledDensityMap(*args)
1436  try: self.this.append(this)
1437  except: self.this = this
1438  def resample(self):
1439  """resample(SampledDensityMap self)"""
1440  return _IMP_em.SampledDensityMap_resample(self)
1441 
1442  def project(self, *args):
1443  """
1444  project(SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin,
1445  Vector3D shift=IMP::algebra::Vector3D(0., 0., 0.), FloatKey mass_key=IMP::atom::Mass::get_mass_key())
1446  project(SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin,
1447  Vector3D shift=IMP::algebra::Vector3D(0., 0., 0.))
1448  project(SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin)
1449  """
1450  return _IMP_em.SampledDensityMap_project(self, *args)
1451 
1452  def set_particles(self, *args):
1453  """
1454  set_particles(SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps, FloatKey mass_key=IMP::atom::Mass::get_mass_key())
1455  set_particles(SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps)
1456  """
1457  return _IMP_em.SampledDensityMap_set_particles(self, *args)
1458 
1459  def get_xyzr_particles(self):
1460  """get_xyzr_particles(SampledDensityMap self) -> IMP::core::XYZRs const &"""
1461  return _IMP_em.SampledDensityMap_get_xyzr_particles(self)
1462 
1463  def get_sampled_particles(self):
1464  """get_sampled_particles(SampledDensityMap self) -> IMP::kernel::Particles const &"""
1465  return _IMP_em.SampledDensityMap_get_sampled_particles(self)
1466 
1467  def get_weight_key(self):
1468  """get_weight_key(SampledDensityMap self) -> FloatKey"""
1469  return _IMP_em.SampledDensityMap_get_weight_key(self)
1470 
1471  def get_minimum_resampled_value(self):
1472  """get_minimum_resampled_value(SampledDensityMap self) -> float"""
1473  return _IMP_em.SampledDensityMap_get_minimum_resampled_value(self)
1474 
1475  __swig_destroy__ = _IMP_em.delete_SampledDensityMap
1476  __del__ = lambda self : None;
1477  def __str__(self):
1478  """__str__(SampledDensityMap self) -> std::string"""
1479  return _IMP_em.SampledDensityMap___str__(self)
1480 
1481  def __repr__(self):
1482  """__repr__(SampledDensityMap self) -> std::string"""
1483  return _IMP_em.SampledDensityMap___repr__(self)
1484 
1485  def get_from(o):
1486  return _object_cast_to_SampledDensityMap(o)
1487  get_from = staticmethod(get_from)
1488 
1489 SampledDensityMap_swigregister = _IMP_em.SampledDensityMap_swigregister
1490 SampledDensityMap_swigregister(SampledDensityMap)
1491 
1492 IMP_DEFAULT_NUM_SHELLS = _IMP_em.IMP_DEFAULT_NUM_SHELLS
1493 IMP_SIG_CUTOFF = _IMP_em.IMP_SIG_CUTOFF
1494 class SurfaceShellDensityMap(SampledDensityMap):
1495  """Proxy of C++ IMP::em::SurfaceShellDensityMap class"""
1496  __swig_setmethods__ = {}
1497  for _s in [SampledDensityMap]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1498  __setattr__ = lambda self, name, value: _swig_setattr(self, SurfaceShellDensityMap, name, value)
1499  __swig_getmethods__ = {}
1500  for _s in [SampledDensityMap]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1501  __getattr__ = lambda self, name: _swig_getattr(self, SurfaceShellDensityMap, name)
1502  def __init__(self, *args):
1503  """
1504  __init__(IMP::em::SurfaceShellDensityMap self) -> SurfaceShellDensityMap
1505  __init__(IMP::em::SurfaceShellDensityMap self, DensityHeader header) -> SurfaceShellDensityMap
1506  __init__(IMP::em::SurfaceShellDensityMap self, IMP::kernel::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key=IMP::atom::Mass::get_mass_key(),
1507  int num_shells=5) -> SurfaceShellDensityMap
1508  __init__(IMP::em::SurfaceShellDensityMap self, IMP::kernel::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key=IMP::atom::Mass::get_mass_key()) -> SurfaceShellDensityMap
1509  __init__(IMP::em::SurfaceShellDensityMap self, IMP::kernel::ParticlesTemp const & ps, float voxel_size) -> SurfaceShellDensityMap
1510  """
1511  this = _IMP_em.new_SurfaceShellDensityMap(*args)
1512  try: self.this.append(this)
1513  except: self.this = this
1514  def binaries(self, *args):
1515  """binaries(SurfaceShellDensityMap self, float scene_val)"""
1516  return _IMP_em.SurfaceShellDensityMap_binaries(self, *args)
1517 
1518  def has_background_neighbor(self, *args):
1519  """has_background_neighbor(SurfaceShellDensityMap self, long voxel_ind) -> bool"""
1520  return _IMP_em.SurfaceShellDensityMap_has_background_neighbor(self, *args)
1521 
1522  __swig_destroy__ = _IMP_em.delete_SurfaceShellDensityMap
1523  __del__ = lambda self : None;
1524  def __str__(self):
1525  """__str__(SurfaceShellDensityMap self) -> std::string"""
1526  return _IMP_em.SurfaceShellDensityMap___str__(self)
1527 
1528  def __repr__(self):
1529  """__repr__(SurfaceShellDensityMap self) -> std::string"""
1530  return _IMP_em.SurfaceShellDensityMap___repr__(self)
1531 
1532  def get_from(o):
1533  return _object_cast_to_SurfaceShellDensityMap(o)
1534  get_from = staticmethod(get_from)
1535 
1536 SurfaceShellDensityMap_swigregister = _IMP_em.SurfaceShellDensityMap_swigregister
1537 SurfaceShellDensityMap_swigregister(SurfaceShellDensityMap)
1538 
1539 class CoarseCC(IMP.base.Object):
1540  """Proxy of C++ IMP::em::CoarseCC class"""
1541  __swig_setmethods__ = {}
1542  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1543  __setattr__ = lambda self, name, value: _swig_setattr(self, CoarseCC, name, value)
1544  __swig_getmethods__ = {}
1545  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1546  __getattr__ = lambda self, name: _swig_getattr(self, CoarseCC, name)
1547  def __init__(self):
1548  """__init__(IMP::em::CoarseCC self) -> CoarseCC"""
1549  this = _IMP_em.new_CoarseCC()
1550  try: self.this.append(this)
1551  except: self.this = this
1552  def calc_score(*args):
1553  """
1554  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True,
1555  bool resample=True, IMP::FloatPair norm_factors=IMP::FloatPair(0., 0.)) -> float
1556  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True,
1557  bool resample=True) -> float
1558  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1559  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1560  """
1561  return _IMP_em.CoarseCC_calc_score(*args)
1562 
1563  if _newclass:calc_score = staticmethod(calc_score)
1564  __swig_getmethods__["calc_score"] = lambda x: calc_score
1565  def cross_correlation_coefficient(*args):
1566  """
1567  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False,
1568  IMP::FloatPair norm_factors=IMP::FloatPair(0., 0.)) -> double
1569  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1570  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1571  """
1572  return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1573 
1574  if _newclass:cross_correlation_coefficient = staticmethod(cross_correlation_coefficient)
1575  __swig_getmethods__["cross_correlation_coefficient"] = lambda x: cross_correlation_coefficient
1576  def local_cross_correlation_coefficient(*args):
1577  """local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1578  return _IMP_em.CoarseCC_local_cross_correlation_coefficient(*args)
1579 
1580  if _newclass:local_cross_correlation_coefficient = staticmethod(local_cross_correlation_coefficient)
1581  __swig_getmethods__["local_cross_correlation_coefficient"] = lambda x: local_cross_correlation_coefficient
1582  def get_version_info(self):
1583  """get_version_info(CoarseCC self) -> VersionInfo"""
1584  return _IMP_em.CoarseCC_get_version_info(self)
1585 
1586  def __str__(self):
1587  """__str__(CoarseCC self) -> std::string"""
1588  return _IMP_em.CoarseCC___str__(self)
1589 
1590  def __repr__(self):
1591  """__repr__(CoarseCC self) -> std::string"""
1592  return _IMP_em.CoarseCC___repr__(self)
1593 
1594  def get_from(o):
1595  return _object_cast_to_CoarseCC(o)
1596  get_from = staticmethod(get_from)
1597 
1598 CoarseCC_swigregister = _IMP_em.CoarseCC_swigregister
1599 CoarseCC_swigregister(CoarseCC)
1600 
1601 def CoarseCC_calc_score(*args):
1602  """
1603  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True,
1604  bool resample=True, IMP::FloatPair norm_factors=IMP::FloatPair(0., 0.)) -> float
1605  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True,
1606  bool resample=True) -> float
1607  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1608  CoarseCC_calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1609  """
1610  return _IMP_em.CoarseCC_calc_score(*args)
1611 
1612 def CoarseCC_cross_correlation_coefficient(*args):
1613  """
1614  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False,
1615  IMP::FloatPair norm_factors=IMP::FloatPair(0., 0.)) -> double
1616  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1617  CoarseCC_cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1618  """
1619  return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1620 
1621 def CoarseCC_local_cross_correlation_coefficient(*args):
1622  """CoarseCC_local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1623  return _IMP_em.CoarseCC_local_cross_correlation_coefficient(*args)
1624 
1625 class CoarseConvolution(_object):
1626  """Proxy of C++ IMP::em::CoarseConvolution class"""
1627  __swig_setmethods__ = {}
1628  __setattr__ = lambda self, name, value: _swig_setattr(self, CoarseConvolution, name, value)
1629  __swig_getmethods__ = {}
1630  __getattr__ = lambda self, name: _swig_getattr(self, CoarseConvolution, name)
1631  __repr__ = _swig_repr
1632  def convolution(*args):
1633  """
1634  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1635  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1636  """
1637  return _IMP_em.CoarseConvolution_convolution(*args)
1638 
1639  if _newclass:convolution = staticmethod(convolution)
1640  __swig_getmethods__["convolution"] = lambda x: convolution
1641  def __init__(self):
1642  """__init__(IMP::em::CoarseConvolution self) -> CoarseConvolution"""
1643  this = _IMP_em.new_CoarseConvolution()
1644  try: self.this.append(this)
1645  except: self.this = this
1646  __swig_destroy__ = _IMP_em.delete_CoarseConvolution
1647  __del__ = lambda self : None;
1648 CoarseConvolution_swigregister = _IMP_em.CoarseConvolution_swigregister
1649 CoarseConvolution_swigregister(CoarseConvolution)
1650 
1651 def CoarseConvolution_convolution(*args):
1652  """
1653  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1654  CoarseConvolution_convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1655  """
1656  return _IMP_em.CoarseConvolution_convolution(*args)
1657 
1658 class CoarseCCatIntervals(CoarseCC):
1659  """Proxy of C++ IMP::em::CoarseCCatIntervals class"""
1660  __swig_setmethods__ = {}
1661  for _s in [CoarseCC]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1662  __setattr__ = lambda self, name, value: _swig_setattr(self, CoarseCCatIntervals, name, value)
1663  __swig_getmethods__ = {}
1664  for _s in [CoarseCC]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1665  __getattr__ = lambda self, name: _swig_getattr(self, CoarseCCatIntervals, name)
1666  def __init__(self, *args):
1667  """
1668  __init__(IMP::em::CoarseCCatIntervals self, int const & ncd) -> CoarseCCatIntervals
1669  __init__(IMP::em::CoarseCCatIntervals self) -> CoarseCCatIntervals
1670  """
1671  this = _IMP_em.new_CoarseCCatIntervals(*args)
1672  try: self.this.append(this)
1673  except: self.this = this
1674  def evaluate(self, *args):
1675  """
1676  evaluate(CoarseCCatIntervals self, DensityMap em_map, SampledDensityMap model_map, IMP::algebra::Vector3Ds const & deriv,
1677  float scalefac, bool lderiv, unsigned long eval_interval) -> std::pair< double,IMP::algebra::Vector3Ds >
1678  """
1679  return _IMP_em.CoarseCCatIntervals_evaluate(self, *args)
1680 
1681  def __str__(self):
1682  """__str__(CoarseCCatIntervals self) -> std::string"""
1683  return _IMP_em.CoarseCCatIntervals___str__(self)
1684 
1685  def __repr__(self):
1686  """__repr__(CoarseCCatIntervals self) -> std::string"""
1687  return _IMP_em.CoarseCCatIntervals___repr__(self)
1688 
1689  def get_from(o):
1690  return _object_cast_to_CoarseCCatIntervals(o)
1691  get_from = staticmethod(get_from)
1692 
1693 CoarseCCatIntervals_swigregister = _IMP_em.CoarseCCatIntervals_swigregister
1694 CoarseCCatIntervals_swigregister(CoarseCCatIntervals)
1695 
1696 class FitRestraint(IMP.kernel.Restraint):
1697  """Proxy of C++ IMP::em::FitRestraint class"""
1698  __swig_setmethods__ = {}
1699  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1700  __setattr__ = lambda self, name, value: _swig_setattr(self, FitRestraint, name, value)
1701  __swig_getmethods__ = {}
1702  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1703  __getattr__ = lambda self, name: _swig_getattr(self, FitRestraint, name)
1704  def __init__(self, *args):
1705  """
1706  __init__(IMP::em::FitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors=IMP::FloatPair(0., 0.),
1707  FloatKey weight_key=IMP::atom::Mass::get_mass_key(), float scale=1,
1708  bool use_rigid_bodies=True, IMP::em::KernelType kt=GAUSSIAN) -> FitRestraint
1709  __init__(IMP::em::FitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors=IMP::FloatPair(0., 0.),
1710  FloatKey weight_key=IMP::atom::Mass::get_mass_key(), float scale=1,
1711  bool use_rigid_bodies=True) -> FitRestraint
1712  __init__(IMP::em::FitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors=IMP::FloatPair(0., 0.),
1713  FloatKey weight_key=IMP::atom::Mass::get_mass_key(), float scale=1) -> FitRestraint
1714  __init__(IMP::em::FitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors=IMP::FloatPair(0., 0.),
1715  FloatKey weight_key=IMP::atom::Mass::get_mass_key()) -> FitRestraint
1716  __init__(IMP::em::FitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors=IMP::FloatPair(0., 0.)) -> FitRestraint
1717  __init__(IMP::em::FitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map) -> FitRestraint
1718  """
1719  this = _IMP_em.new_FitRestraint(*args)
1720  try: self.this.append(this)
1721  except: self.this = this
1722  def get_model_dens_map(self):
1723  """get_model_dens_map(FitRestraint self) -> SampledDensityMap"""
1724  return _IMP_em.FitRestraint_get_model_dens_map(self)
1725 
1726  def set_scale_factor(self, *args):
1727  """set_scale_factor(FitRestraint self, float scale)"""
1728  return _IMP_em.FitRestraint_set_scale_factor(self, *args)
1729 
1730  def get_scale_factor(self):
1731  """get_scale_factor(FitRestraint self) -> float"""
1732  return _IMP_em.FitRestraint_get_scale_factor(self)
1733 
1734  def do_get_inputs(self):
1735  """do_get_inputs(FitRestraint self) -> IMP::kernel::ModelObjectsTemp"""
1736  return _IMP_em.FitRestraint_do_get_inputs(self)
1737 
1738  def get_version_info(self):
1739  """get_version_info(FitRestraint self) -> VersionInfo"""
1740  return _IMP_em.FitRestraint_get_version_info(self)
1741 
1742  def __str__(self):
1743  """__str__(FitRestraint self) -> std::string"""
1744  return _IMP_em.FitRestraint___str__(self)
1745 
1746  def __repr__(self):
1747  """__repr__(FitRestraint self) -> std::string"""
1748  return _IMP_em.FitRestraint___repr__(self)
1749 
1750  def get_from(o):
1751  return _object_cast_to_FitRestraint(o)
1752  get_from = staticmethod(get_from)
1753 
1754  def cast(*args):
1755  """cast(Restraint r) -> FitRestraint"""
1756  return _IMP_em.FitRestraint_cast(*args)
1757 
1758  if _newclass:cast = staticmethod(cast)
1759  __swig_getmethods__["cast"] = lambda x: cast
1760 FitRestraint_swigregister = _IMP_em.FitRestraint_swigregister
1761 FitRestraint_swigregister(FitRestraint)
1762 
1763 def FitRestraint_cast(*args):
1764  """FitRestraint_cast(Restraint r) -> FitRestraint"""
1765  return _IMP_em.FitRestraint_cast(*args)
1766 
1767 
1768 def density2particles(*args):
1769  """
1770  density2particles(DensityMap dmap, IMP::Float threshold, Model m, int step=1) -> IMP::kernel::Particles
1771  density2particles(DensityMap dmap, IMP::Float threshold, Model m) -> IMP::kernel::Particles
1772  """
1773  return _IMP_em.density2particles(*args)
1774 
1775 def density2vectors(*args):
1776  """density2vectors(DensityMap dmap, IMP::Float threshold) -> IMP::algebra::Vector3Ds"""
1777  return _IMP_em.density2vectors(*args)
1778 
1779 def particles2density(*args):
1780  """
1781  particles2density(IMP::kernel::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3,
1782  FloatKey weight_key=IMP::atom::Mass::get_mass_key()) -> SampledDensityMap
1783  particles2density(IMP::kernel::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
1784  particles2density(IMP::kernel::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
1785  """
1786  return _IMP_em.particles2density(*args)
1787 
1788 def particles2binarized_density(*args):
1789  """
1790  particles2binarized_density(IMP::kernel::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3,
1791  FloatKey weight_key=IMP::atom::Mass::get_mass_key()) -> SampledDensityMap
1792  particles2binarized_density(IMP::kernel::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
1793  particles2binarized_density(IMP::kernel::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
1794  """
1795  return _IMP_em.particles2binarized_density(*args)
1796 
1797 def particles2surface(*args):
1798  """
1799  particles2surface(IMP::kernel::ParticlesTemp const & ps, IMP::Float apix, FloatKey weight_key=IMP::atom::Mass::get_mass_key()) -> SurfaceShellDensityMap
1800  particles2surface(IMP::kernel::ParticlesTemp const & ps, IMP::Float apix) -> SurfaceShellDensityMap
1801  """
1802  return _IMP_em.particles2surface(*args)
1803 
1804 def calculate_intersection_score(*args):
1805  """calculate_intersection_score(SurfaceShellDensityMap d1, SurfaceShellDensityMap d2) -> IMP::Float"""
1806  return _IMP_em.calculate_intersection_score(*args)
1807 class SpiderHeader(_object):
1808  """Proxy of C++ IMP::em::SpiderHeader class"""
1809  __swig_setmethods__ = {}
1810  __setattr__ = lambda self, name, value: _swig_setattr(self, SpiderHeader, name, value)
1811  __swig_getmethods__ = {}
1812  __getattr__ = lambda self, name: _swig_getattr(self, SpiderHeader, name)
1813  __repr__ = _swig_repr
1814  __swig_setmethods__["fNslice"] = _IMP_em.SpiderHeader_fNslice_set
1815  __swig_getmethods__["fNslice"] = _IMP_em.SpiderHeader_fNslice_get
1816  if _newclass:fNslice = _swig_property(_IMP_em.SpiderHeader_fNslice_get, _IMP_em.SpiderHeader_fNslice_set)
1817  __swig_setmethods__["fNrow"] = _IMP_em.SpiderHeader_fNrow_set
1818  __swig_getmethods__["fNrow"] = _IMP_em.SpiderHeader_fNrow_get
1819  if _newclass:fNrow = _swig_property(_IMP_em.SpiderHeader_fNrow_get, _IMP_em.SpiderHeader_fNrow_set)
1820  __swig_setmethods__["fNrec"] = _IMP_em.SpiderHeader_fNrec_set
1821  __swig_getmethods__["fNrec"] = _IMP_em.SpiderHeader_fNrec_get
1822  if _newclass:fNrec = _swig_property(_IMP_em.SpiderHeader_fNrec_get, _IMP_em.SpiderHeader_fNrec_set)
1823  __swig_setmethods__["fNlabel"] = _IMP_em.SpiderHeader_fNlabel_set
1824  __swig_getmethods__["fNlabel"] = _IMP_em.SpiderHeader_fNlabel_get
1825  if _newclass:fNlabel = _swig_property(_IMP_em.SpiderHeader_fNlabel_get, _IMP_em.SpiderHeader_fNlabel_set)
1826  __swig_setmethods__["fIform"] = _IMP_em.SpiderHeader_fIform_set
1827  __swig_getmethods__["fIform"] = _IMP_em.SpiderHeader_fIform_get
1828  if _newclass:fIform = _swig_property(_IMP_em.SpiderHeader_fIform_get, _IMP_em.SpiderHeader_fIform_set)
1829  __swig_setmethods__["fImami"] = _IMP_em.SpiderHeader_fImami_set
1830  __swig_getmethods__["fImami"] = _IMP_em.SpiderHeader_fImami_get
1831  if _newclass:fImami = _swig_property(_IMP_em.SpiderHeader_fImami_get, _IMP_em.SpiderHeader_fImami_set)
1832  __swig_setmethods__["fFmax"] = _IMP_em.SpiderHeader_fFmax_set
1833  __swig_getmethods__["fFmax"] = _IMP_em.SpiderHeader_fFmax_get
1834  if _newclass:fFmax = _swig_property(_IMP_em.SpiderHeader_fFmax_get, _IMP_em.SpiderHeader_fFmax_set)
1835  __swig_setmethods__["fFmin"] = _IMP_em.SpiderHeader_fFmin_set
1836  __swig_getmethods__["fFmin"] = _IMP_em.SpiderHeader_fFmin_get
1837  if _newclass:fFmin = _swig_property(_IMP_em.SpiderHeader_fFmin_get, _IMP_em.SpiderHeader_fFmin_set)
1838  __swig_setmethods__["fAv"] = _IMP_em.SpiderHeader_fAv_set
1839  __swig_getmethods__["fAv"] = _IMP_em.SpiderHeader_fAv_get
1840  if _newclass:fAv = _swig_property(_IMP_em.SpiderHeader_fAv_get, _IMP_em.SpiderHeader_fAv_set)
1841  __swig_setmethods__["fSig"] = _IMP_em.SpiderHeader_fSig_set
1842  __swig_getmethods__["fSig"] = _IMP_em.SpiderHeader_fSig_get
1843  if _newclass:fSig = _swig_property(_IMP_em.SpiderHeader_fSig_get, _IMP_em.SpiderHeader_fSig_set)
1844  __swig_setmethods__["fIhist"] = _IMP_em.SpiderHeader_fIhist_set
1845  __swig_getmethods__["fIhist"] = _IMP_em.SpiderHeader_fIhist_get
1846  if _newclass:fIhist = _swig_property(_IMP_em.SpiderHeader_fIhist_get, _IMP_em.SpiderHeader_fIhist_set)
1847  __swig_setmethods__["fNcol"] = _IMP_em.SpiderHeader_fNcol_set
1848  __swig_getmethods__["fNcol"] = _IMP_em.SpiderHeader_fNcol_get
1849  if _newclass:fNcol = _swig_property(_IMP_em.SpiderHeader_fNcol_get, _IMP_em.SpiderHeader_fNcol_set)
1850  __swig_setmethods__["fLabrec"] = _IMP_em.SpiderHeader_fLabrec_set
1851  __swig_getmethods__["fLabrec"] = _IMP_em.SpiderHeader_fLabrec_get
1852  if _newclass:fLabrec = _swig_property(_IMP_em.SpiderHeader_fLabrec_get, _IMP_em.SpiderHeader_fLabrec_set)
1853  __swig_setmethods__["fIangle"] = _IMP_em.SpiderHeader_fIangle_set
1854  __swig_getmethods__["fIangle"] = _IMP_em.SpiderHeader_fIangle_get
1855  if _newclass:fIangle = _swig_property(_IMP_em.SpiderHeader_fIangle_get, _IMP_em.SpiderHeader_fIangle_set)
1856  __swig_setmethods__["fPhi"] = _IMP_em.SpiderHeader_fPhi_set
1857  __swig_getmethods__["fPhi"] = _IMP_em.SpiderHeader_fPhi_get
1858  if _newclass:fPhi = _swig_property(_IMP_em.SpiderHeader_fPhi_get, _IMP_em.SpiderHeader_fPhi_set)
1859  __swig_setmethods__["fTheta"] = _IMP_em.SpiderHeader_fTheta_set
1860  __swig_getmethods__["fTheta"] = _IMP_em.SpiderHeader_fTheta_get
1861  if _newclass:fTheta = _swig_property(_IMP_em.SpiderHeader_fTheta_get, _IMP_em.SpiderHeader_fTheta_set)
1862  __swig_setmethods__["fPsi"] = _IMP_em.SpiderHeader_fPsi_set
1863  __swig_getmethods__["fPsi"] = _IMP_em.SpiderHeader_fPsi_get
1864  if _newclass:fPsi = _swig_property(_IMP_em.SpiderHeader_fPsi_get, _IMP_em.SpiderHeader_fPsi_set)
1865  __swig_setmethods__["fXoff"] = _IMP_em.SpiderHeader_fXoff_set
1866  __swig_getmethods__["fXoff"] = _IMP_em.SpiderHeader_fXoff_get
1867  if _newclass:fXoff = _swig_property(_IMP_em.SpiderHeader_fXoff_get, _IMP_em.SpiderHeader_fXoff_set)
1868  __swig_setmethods__["fYoff"] = _IMP_em.SpiderHeader_fYoff_set
1869  __swig_getmethods__["fYoff"] = _IMP_em.SpiderHeader_fYoff_get
1870  if _newclass:fYoff = _swig_property(_IMP_em.SpiderHeader_fYoff_get, _IMP_em.SpiderHeader_fYoff_set)
1871  __swig_setmethods__["fZoff"] = _IMP_em.SpiderHeader_fZoff_set
1872  __swig_getmethods__["fZoff"] = _IMP_em.SpiderHeader_fZoff_get
1873  if _newclass:fZoff = _swig_property(_IMP_em.SpiderHeader_fZoff_get, _IMP_em.SpiderHeader_fZoff_set)
1874  __swig_setmethods__["fScale"] = _IMP_em.SpiderHeader_fScale_set
1875  __swig_getmethods__["fScale"] = _IMP_em.SpiderHeader_fScale_get
1876  if _newclass:fScale = _swig_property(_IMP_em.SpiderHeader_fScale_get, _IMP_em.SpiderHeader_fScale_set)
1877  __swig_setmethods__["fLabbyt"] = _IMP_em.SpiderHeader_fLabbyt_set
1878  __swig_getmethods__["fLabbyt"] = _IMP_em.SpiderHeader_fLabbyt_get
1879  if _newclass:fLabbyt = _swig_property(_IMP_em.SpiderHeader_fLabbyt_get, _IMP_em.SpiderHeader_fLabbyt_set)
1880  __swig_setmethods__["fLenbyt"] = _IMP_em.SpiderHeader_fLenbyt_set
1881  __swig_getmethods__["fLenbyt"] = _IMP_em.SpiderHeader_fLenbyt_get
1882  if _newclass:fLenbyt = _swig_property(_IMP_em.SpiderHeader_fLenbyt_get, _IMP_em.SpiderHeader_fLenbyt_set)
1883  __swig_setmethods__["fNothing"] = _IMP_em.SpiderHeader_fNothing_set
1884  __swig_getmethods__["fNothing"] = _IMP_em.SpiderHeader_fNothing_get
1885  if _newclass:fNothing = _swig_property(_IMP_em.SpiderHeader_fNothing_get, _IMP_em.SpiderHeader_fNothing_set)
1886  __swig_setmethods__["fFlag"] = _IMP_em.SpiderHeader_fFlag_set
1887  __swig_getmethods__["fFlag"] = _IMP_em.SpiderHeader_fFlag_get
1888  if _newclass:fFlag = _swig_property(_IMP_em.SpiderHeader_fFlag_get, _IMP_em.SpiderHeader_fFlag_set)
1889  __swig_setmethods__["fPhi1"] = _IMP_em.SpiderHeader_fPhi1_set
1890  __swig_getmethods__["fPhi1"] = _IMP_em.SpiderHeader_fPhi1_get
1891  if _newclass:fPhi1 = _swig_property(_IMP_em.SpiderHeader_fPhi1_get, _IMP_em.SpiderHeader_fPhi1_set)
1892  __swig_setmethods__["fTheta1"] = _IMP_em.SpiderHeader_fTheta1_set
1893  __swig_getmethods__["fTheta1"] = _IMP_em.SpiderHeader_fTheta1_get
1894  if _newclass:fTheta1 = _swig_property(_IMP_em.SpiderHeader_fTheta1_get, _IMP_em.SpiderHeader_fTheta1_set)
1895  __swig_setmethods__["fPsi1"] = _IMP_em.SpiderHeader_fPsi1_set
1896  __swig_getmethods__["fPsi1"] = _IMP_em.SpiderHeader_fPsi1_get
1897  if _newclass:fPsi1 = _swig_property(_IMP_em.SpiderHeader_fPsi1_get, _IMP_em.SpiderHeader_fPsi1_set)
1898  __swig_setmethods__["fPhi2"] = _IMP_em.SpiderHeader_fPhi2_set
1899  __swig_getmethods__["fPhi2"] = _IMP_em.SpiderHeader_fPhi2_get
1900  if _newclass:fPhi2 = _swig_property(_IMP_em.SpiderHeader_fPhi2_get, _IMP_em.SpiderHeader_fPhi2_set)
1901  __swig_setmethods__["fTheta2"] = _IMP_em.SpiderHeader_fTheta2_set
1902  __swig_getmethods__["fTheta2"] = _IMP_em.SpiderHeader_fTheta2_get
1903  if _newclass:fTheta2 = _swig_property(_IMP_em.SpiderHeader_fTheta2_get, _IMP_em.SpiderHeader_fTheta2_set)
1904  __swig_setmethods__["fPsi2"] = _IMP_em.SpiderHeader_fPsi2_set
1905  __swig_getmethods__["fPsi2"] = _IMP_em.SpiderHeader_fPsi2_get
1906  if _newclass:fPsi2 = _swig_property(_IMP_em.SpiderHeader_fPsi2_get, _IMP_em.SpiderHeader_fPsi2_set)
1907  __swig_setmethods__["fGeo_matrix"] = _IMP_em.SpiderHeader_fGeo_matrix_set
1908  __swig_getmethods__["fGeo_matrix"] = _IMP_em.SpiderHeader_fGeo_matrix_get
1909  if _newclass:fGeo_matrix = _swig_property(_IMP_em.SpiderHeader_fGeo_matrix_get, _IMP_em.SpiderHeader_fGeo_matrix_set)
1910  __swig_setmethods__["fAngle1"] = _IMP_em.SpiderHeader_fAngle1_set
1911  __swig_getmethods__["fAngle1"] = _IMP_em.SpiderHeader_fAngle1_get
1912  if _newclass:fAngle1 = _swig_property(_IMP_em.SpiderHeader_fAngle1_get, _IMP_em.SpiderHeader_fAngle1_set)
1913  __swig_setmethods__["fr1"] = _IMP_em.SpiderHeader_fr1_set
1914  __swig_getmethods__["fr1"] = _IMP_em.SpiderHeader_fr1_get
1915  if _newclass:fr1 = _swig_property(_IMP_em.SpiderHeader_fr1_get, _IMP_em.SpiderHeader_fr1_set)
1916  __swig_setmethods__["fr2"] = _IMP_em.SpiderHeader_fr2_set
1917  __swig_getmethods__["fr2"] = _IMP_em.SpiderHeader_fr2_get
1918  if _newclass:fr2 = _swig_property(_IMP_em.SpiderHeader_fr2_get, _IMP_em.SpiderHeader_fr2_set)
1919  __swig_setmethods__["RTflag"] = _IMP_em.SpiderHeader_RTflag_set
1920  __swig_getmethods__["RTflag"] = _IMP_em.SpiderHeader_RTflag_get
1921  if _newclass:RTflag = _swig_property(_IMP_em.SpiderHeader_RTflag_get, _IMP_em.SpiderHeader_RTflag_set)
1922  __swig_setmethods__["Astart"] = _IMP_em.SpiderHeader_Astart_set
1923  __swig_getmethods__["Astart"] = _IMP_em.SpiderHeader_Astart_get
1924  if _newclass:Astart = _swig_property(_IMP_em.SpiderHeader_Astart_get, _IMP_em.SpiderHeader_Astart_set)
1925  __swig_setmethods__["Aend"] = _IMP_em.SpiderHeader_Aend_set
1926  __swig_getmethods__["Aend"] = _IMP_em.SpiderHeader_Aend_get
1927  if _newclass:Aend = _swig_property(_IMP_em.SpiderHeader_Aend_get, _IMP_em.SpiderHeader_Aend_set)
1928  __swig_setmethods__["Ainc"] = _IMP_em.SpiderHeader_Ainc_set
1929  __swig_getmethods__["Ainc"] = _IMP_em.SpiderHeader_Ainc_get
1930  if _newclass:Ainc = _swig_property(_IMP_em.SpiderHeader_Ainc_get, _IMP_em.SpiderHeader_Ainc_set)
1931  __swig_setmethods__["Rsigma"] = _IMP_em.SpiderHeader_Rsigma_set
1932  __swig_getmethods__["Rsigma"] = _IMP_em.SpiderHeader_Rsigma_get
1933  if _newclass:Rsigma = _swig_property(_IMP_em.SpiderHeader_Rsigma_get, _IMP_em.SpiderHeader_Rsigma_set)
1934  __swig_setmethods__["Tstart"] = _IMP_em.SpiderHeader_Tstart_set
1935  __swig_getmethods__["Tstart"] = _IMP_em.SpiderHeader_Tstart_get
1936  if _newclass:Tstart = _swig_property(_IMP_em.SpiderHeader_Tstart_get, _IMP_em.SpiderHeader_Tstart_set)
1937  __swig_setmethods__["Tend"] = _IMP_em.SpiderHeader_Tend_set
1938  __swig_getmethods__["Tend"] = _IMP_em.SpiderHeader_Tend_get
1939  if _newclass:Tend = _swig_property(_IMP_em.SpiderHeader_Tend_get, _IMP_em.SpiderHeader_Tend_set)
1940  __swig_setmethods__["Tinc"] = _IMP_em.SpiderHeader_Tinc_set
1941  __swig_getmethods__["Tinc"] = _IMP_em.SpiderHeader_Tinc_get
1942  if _newclass:Tinc = _swig_property(_IMP_em.SpiderHeader_Tinc_get, _IMP_em.SpiderHeader_Tinc_set)
1943  __swig_setmethods__["Weight"] = _IMP_em.SpiderHeader_Weight_set
1944  __swig_getmethods__["Weight"] = _IMP_em.SpiderHeader_Weight_get
1945  if _newclass:Weight = _swig_property(_IMP_em.SpiderHeader_Weight_get, _IMP_em.SpiderHeader_Weight_set)
1946  __swig_setmethods__["Flip"] = _IMP_em.SpiderHeader_Flip_set
1947  __swig_getmethods__["Flip"] = _IMP_em.SpiderHeader_Flip_get
1948  if _newclass:Flip = _swig_property(_IMP_em.SpiderHeader_Flip_get, _IMP_em.SpiderHeader_Flip_set)
1949  __swig_setmethods__["empty"] = _IMP_em.SpiderHeader_empty_set
1950  __swig_getmethods__["empty"] = _IMP_em.SpiderHeader_empty_get
1951  if _newclass:empty = _swig_property(_IMP_em.SpiderHeader_empty_get, _IMP_em.SpiderHeader_empty_set)
1952  __swig_setmethods__["szIDat"] = _IMP_em.SpiderHeader_szIDat_set
1953  __swig_getmethods__["szIDat"] = _IMP_em.SpiderHeader_szIDat_get
1954  if _newclass:szIDat = _swig_property(_IMP_em.SpiderHeader_szIDat_get, _IMP_em.SpiderHeader_szIDat_set)
1955  __swig_setmethods__["szITim"] = _IMP_em.SpiderHeader_szITim_set
1956  __swig_getmethods__["szITim"] = _IMP_em.SpiderHeader_szITim_get
1957  if _newclass:szITim = _swig_property(_IMP_em.SpiderHeader_szITim_get, _IMP_em.SpiderHeader_szITim_set)
1958  __swig_setmethods__["szITit"] = _IMP_em.SpiderHeader_szITit_set
1959  __swig_getmethods__["szITit"] = _IMP_em.SpiderHeader_szITit_get
1960  if _newclass:szITit = _swig_property(_IMP_em.SpiderHeader_szITit_get, _IMP_em.SpiderHeader_szITit_set)
1961  def show(self, *args):
1962  """show(SpiderHeader self, _ostream out)"""
1963  return _IMP_em.SpiderHeader_show(self, *args)
1964 
1965  def __init__(self):
1966  """__init__(IMP::em::SpiderHeader self) -> SpiderHeader"""
1967  this = _IMP_em.new_SpiderHeader()
1968  try: self.this.append(this)
1969  except: self.this = this
1970  __swig_destroy__ = _IMP_em.delete_SpiderHeader
1971  __del__ = lambda self : None;
1972 SpiderHeader_swigregister = _IMP_em.SpiderHeader_swigregister
1973 SpiderHeader_swigregister(SpiderHeader)
1974 
1975 class ImageHeader(_object):
1976  """Proxy of C++ IMP::em::ImageHeader class"""
1977  __swig_setmethods__ = {}
1978  __setattr__ = lambda self, name, value: _swig_setattr(self, ImageHeader, name, value)
1979  __swig_getmethods__ = {}
1980  __getattr__ = lambda self, name: _swig_getattr(self, ImageHeader, name)
1981  __repr__ = _swig_repr
1982  IMG_BYTE = _IMP_em.ImageHeader_IMG_BYTE
1983  IMG_IMPEM = _IMP_em.ImageHeader_IMG_IMPEM
1984  IMG_INT = _IMP_em.ImageHeader_IMG_INT
1985  VOL_BYTE = _IMP_em.ImageHeader_VOL_BYTE
1986  VOL_IMPEM = _IMP_em.ImageHeader_VOL_IMPEM
1987  VOL_INT = _IMP_em.ImageHeader_VOL_INT
1988  IMG_FOURIER = _IMP_em.ImageHeader_IMG_FOURIER
1989  VOL_FOURIER = _IMP_em.ImageHeader_VOL_FOURIER
1990  def __init__(self, *args):
1991  """
1992  __init__(IMP::em::ImageHeader self) -> ImageHeader
1993  __init__(IMP::em::ImageHeader self, IMP::em::ImageHeader::img_type im) -> ImageHeader
1994  __init__(IMP::em::ImageHeader self, float im) -> ImageHeader
1995  """
1996  this = _IMP_em.new_ImageHeader(*args)
1997  try: self.this.append(this)
1998  except: self.this = this
1999  def get_image_type(self):
2000  """get_image_type(ImageHeader self) -> float"""
2001  return _IMP_em.ImageHeader_get_image_type(self)
2002 
2003  def set_image_type(self, *args):
2004  """
2005  set_image_type(ImageHeader self, IMP::em::ImageHeader::img_type im)
2006  set_image_type(ImageHeader self, float im)
2007  """
2008  return _IMP_em.ImageHeader_set_image_type(self, *args)
2009 
2010  def do_show(self, *args):
2011  """do_show(ImageHeader self, _ostream out)"""
2012  return _IMP_em.ImageHeader_do_show(self, *args)
2013 
2014  def show(self, *args):
2015  """
2016  show(ImageHeader self, _ostream out=std::cout)
2017  show(ImageHeader self)
2018  """
2019  return _IMP_em.ImageHeader_show(self, *args)
2020 
2021  def print_hard(self, *args):
2022  """print_hard(ImageHeader self, _ostream out)"""
2023  return _IMP_em.ImageHeader_print_hard(self, *args)
2024 
2025  def show_projection_params(self, *args):
2026  """show_projection_params(ImageHeader self, _ostream out)"""
2027  return _IMP_em.ImageHeader_show_projection_params(self, *args)
2028 
2029  def read(self, *args):
2030  """
2031  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False,
2032  bool skip_extra_checkings=False) -> int
2033  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False) -> int
2034  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False) -> int
2035  read(ImageHeader self, IMP::String const filename) -> int
2036  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False, bool skip_extra_checkings=False) -> bool
2037  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False) -> bool
2038  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False) -> bool
2039  read(ImageHeader self, std::ifstream & f) -> bool
2040  """
2041  return _IMP_em.ImageHeader_read(self, *args)
2042 
2043  def write(self, *args):
2044  """
2045  write(ImageHeader self, IMP::String const & filename, bool force_reversed=False)
2046  write(ImageHeader self, IMP::String const & filename)
2047  write(ImageHeader self, std::ofstream & f, bool force_reversed=False)
2048  write(ImageHeader self, std::ofstream & f)
2049  """
2050  return _IMP_em.ImageHeader_write(self, *args)
2051 
2052  def clear(self):
2053  """clear(ImageHeader self)"""
2054  return _IMP_em.ImageHeader_clear(self)
2055 
2056  def set_header(self):
2057  """set_header(ImageHeader self)"""
2058  return _IMP_em.ImageHeader_set_header(self)
2059 
2060  def get_reversed(self):
2061  """get_reversed(ImageHeader self) -> bool"""
2062  return _IMP_em.ImageHeader_get_reversed(self)
2063 
2064  def set_reversed(self, *args):
2065  """set_reversed(ImageHeader self, bool value)"""
2066  return _IMP_em.ImageHeader_set_reversed(self, *args)
2067 
2068  def get_number_of_slices(self):
2069  """get_number_of_slices(ImageHeader self) -> unsigned int"""
2070  return _IMP_em.ImageHeader_get_number_of_slices(self)
2071 
2072  def set_number_of_slices(self, *args):
2073  """set_number_of_slices(ImageHeader self, unsigned int n)"""
2074  return _IMP_em.ImageHeader_set_number_of_slices(self, *args)
2075 
2076  def get_number_of_rows(self):
2077  """get_number_of_rows(ImageHeader self) -> unsigned int"""
2078  return _IMP_em.ImageHeader_get_number_of_rows(self)
2079 
2080  def set_number_of_rows(self, *args):
2081  """set_number_of_rows(ImageHeader self, unsigned int n)"""
2082  return _IMP_em.ImageHeader_set_number_of_rows(self, *args)
2083 
2084  def get_number_of_columns(self):
2085  """get_number_of_columns(ImageHeader self) -> unsigned int"""
2086  return _IMP_em.ImageHeader_get_number_of_columns(self)
2087 
2088  def set_number_of_columns(self, *args):
2089  """set_number_of_columns(ImageHeader self, unsigned int n)"""
2090  return _IMP_em.ImageHeader_set_number_of_columns(self, *args)
2091 
2092  def get_old_rot(self):
2093  """get_old_rot(ImageHeader self) -> float"""
2094  return _IMP_em.ImageHeader_get_old_rot(self)
2095 
2096  def set_old_rot(self, *args):
2097  """set_old_rot(ImageHeader self, float value)"""
2098  return _IMP_em.ImageHeader_set_old_rot(self, *args)
2099 
2100  def get_fAngle1(self):
2101  """get_fAngle1(ImageHeader self) -> float"""
2102  return _IMP_em.ImageHeader_get_fAngle1(self)
2103 
2104  def set_fAngle1(self, *args):
2105  """set_fAngle1(ImageHeader self, float value)"""
2106  return _IMP_em.ImageHeader_set_fAngle1(self, *args)
2107 
2108  def get_Scale(self):
2109  """get_Scale(ImageHeader self) -> float"""
2110  return _IMP_em.ImageHeader_get_Scale(self)
2111 
2112  def set_Scale(self, *args):
2113  """set_Scale(ImageHeader self, float value)"""
2114  return _IMP_em.ImageHeader_set_Scale(self, *args)
2115 
2116  def get_Flip(self):
2117  """get_Flip(ImageHeader self) -> float"""
2118  return _IMP_em.ImageHeader_get_Flip(self)
2119 
2120  def set_Flip(self, *args):
2121  """set_Flip(ImageHeader self, float value)"""
2122  return _IMP_em.ImageHeader_set_Flip(self, *args)
2123 
2124  def get_Weight(self):
2125  """get_Weight(ImageHeader self) -> float"""
2126  return _IMP_em.ImageHeader_get_Weight(self)
2127 
2128  def set_Weight(self, *args):
2129  """set_Weight(ImageHeader self, float value)"""
2130  return _IMP_em.ImageHeader_set_Weight(self, *args)
2131 
2132  def get_fNrec(self):
2133  """get_fNrec(ImageHeader self) -> float"""
2134  return _IMP_em.ImageHeader_get_fNrec(self)
2135 
2136  def set_fNrec(self, *args):
2137  """set_fNrec(ImageHeader self, float value)"""
2138  return _IMP_em.ImageHeader_set_fNrec(self, *args)
2139 
2140  def get_fNlabel(self):
2141  """get_fNlabel(ImageHeader self) -> float"""
2142  return _IMP_em.ImageHeader_get_fNlabel(self)
2143 
2144  def set_fNlabel(self, *args):
2145  """set_fNlabel(ImageHeader self, float value)"""
2146  return _IMP_em.ImageHeader_set_fNlabel(self, *args)
2147 
2148  def get_fIform(self):
2149  """get_fIform(ImageHeader self) -> float"""
2150  return _IMP_em.ImageHeader_get_fIform(self)
2151 
2152  def set_fIform(self, *args):
2153  """set_fIform(ImageHeader self, float value)"""
2154  return _IMP_em.ImageHeader_set_fIform(self, *args)
2155 
2156  def get_fImami(self):
2157  """get_fImami(ImageHeader self) -> float"""
2158  return _IMP_em.ImageHeader_get_fImami(self)
2159 
2160  def set_fImami(self, *args):
2161  """set_fImami(ImageHeader self, float value)"""
2162  return _IMP_em.ImageHeader_set_fImami(self, *args)
2163 
2164  def get_fFmax(self):
2165  """get_fFmax(ImageHeader self) -> float"""
2166  return _IMP_em.ImageHeader_get_fFmax(self)
2167 
2168  def set_fFmax(self, *args):
2169  """set_fFmax(ImageHeader self, float value)"""
2170  return _IMP_em.ImageHeader_set_fFmax(self, *args)
2171 
2172  def get_fFmin(self):
2173  """get_fFmin(ImageHeader self) -> float"""
2174  return _IMP_em.ImageHeader_get_fFmin(self)
2175 
2176  def set_fFmin(self, *args):
2177  """set_fFmin(ImageHeader self, float value)"""
2178  return _IMP_em.ImageHeader_set_fFmin(self, *args)
2179 
2180  def get_fAv(self):
2181  """get_fAv(ImageHeader self) -> float"""
2182  return _IMP_em.ImageHeader_get_fAv(self)
2183 
2184  def set_fAv(self, *args):
2185  """set_fAv(ImageHeader self, float value)"""
2186  return _IMP_em.ImageHeader_set_fAv(self, *args)
2187 
2188  def get_fSig(self):
2189  """get_fSig(ImageHeader self) -> float"""
2190  return _IMP_em.ImageHeader_get_fSig(self)
2191 
2192  def set_fSig(self, *args):
2193  """set_fSig(ImageHeader self, float value)"""
2194  return _IMP_em.ImageHeader_set_fSig(self, *args)
2195 
2196  def get_fIhist(self):
2197  """get_fIhist(ImageHeader self) -> float"""
2198  return _IMP_em.ImageHeader_get_fIhist(self)
2199 
2200  def set_fIhist(self, *args):
2201  """set_fIhist(ImageHeader self, float value)"""
2202  return _IMP_em.ImageHeader_set_fIhist(self, *args)
2203 
2204  def get_fLabrec(self):
2205  """get_fLabrec(ImageHeader self) -> float"""
2206  return _IMP_em.ImageHeader_get_fLabrec(self)
2207 
2208  def set_fLabrec(self, *args):
2209  """set_fLabrec(ImageHeader self, float value)"""
2210  return _IMP_em.ImageHeader_set_fLabrec(self, *args)
2211 
2212  def get_fIangle(self):
2213  """get_fIangle(ImageHeader self) -> float"""
2214  return _IMP_em.ImageHeader_get_fIangle(self)
2215 
2216  def set_fIangle(self, *args):
2217  """set_fIangle(ImageHeader self, float value)"""
2218  return _IMP_em.ImageHeader_set_fIangle(self, *args)
2219 
2220  def get_origin(self):
2221  """get_origin(ImageHeader self) -> Vector3D"""
2222  return _IMP_em.ImageHeader_get_origin(self)
2223 
2224  def set_origin(self, *args):
2225  """
2226  set_origin(ImageHeader self, Vector3D v)
2227  set_origin(ImageHeader self, Vector2D v)
2228  """
2229  return _IMP_em.ImageHeader_set_origin(self, *args)
2230 
2231  def get_object_pixel_size(self):
2232  """get_object_pixel_size(ImageHeader self) -> float"""
2233  return _IMP_em.ImageHeader_get_object_pixel_size(self)
2234 
2235  def set_object_pixel_size(self, *args):
2236  """set_object_pixel_size(ImageHeader self, float value)"""
2237  return _IMP_em.ImageHeader_set_object_pixel_size(self, *args)
2238 
2239  def get_fLabbyt(self):
2240  """get_fLabbyt(ImageHeader self) -> float"""
2241  return _IMP_em.ImageHeader_get_fLabbyt(self)
2242 
2243  def set_fLabbyt(self, *args):
2244  """set_fLabbyt(ImageHeader self, float value)"""
2245  return _IMP_em.ImageHeader_set_fLabbyt(self, *args)
2246 
2247  def get_fLenbyt(self):
2248  """get_fLenbyt(ImageHeader self) -> float"""
2249  return _IMP_em.ImageHeader_get_fLenbyt(self)
2250 
2251  def set_fLenbyt(self, *args):
2252  """set_fLenbyt(ImageHeader self, float value)"""
2253  return _IMP_em.ImageHeader_set_fLenbyt(self, *args)
2254 
2255  def get_fGeo_matrix(self, *args):
2256  """get_fGeo_matrix(ImageHeader self, unsigned int i, unsigned int j) -> double"""
2257  return _IMP_em.ImageHeader_get_fGeo_matrix(self, *args)
2258 
2259  def get_fFlag(self):
2260  """get_fFlag(ImageHeader self) -> float"""
2261  return _IMP_em.ImageHeader_get_fFlag(self)
2262 
2263  def set_fFlag(self, *args):
2264  """set_fFlag(ImageHeader self, float value)"""
2265  return _IMP_em.ImageHeader_set_fFlag(self, *args)
2266 
2267  def get_euler_angles(self):
2268  """get_euler_angles(ImageHeader self) -> Vector3D"""
2269  return _IMP_em.ImageHeader_get_euler_angles(self)
2270 
2271  def get_euler_angles1(self):
2272  """get_euler_angles1(ImageHeader self) -> Vector3D"""
2273  return _IMP_em.ImageHeader_get_euler_angles1(self)
2274 
2275  def get_euler_angles2(self):
2276  """get_euler_angles2(ImageHeader self) -> Vector3D"""
2277  return _IMP_em.ImageHeader_get_euler_angles2(self)
2278 
2279  def set_euler_angles(self, *args):
2280  """set_euler_angles(ImageHeader self, Vector3D euler)"""
2281  return _IMP_em.ImageHeader_set_euler_angles(self, *args)
2282 
2283  def set_euler_angles1(self, *args):
2284  """set_euler_angles1(ImageHeader self, Vector3D euler)"""
2285  return _IMP_em.ImageHeader_set_euler_angles1(self, *args)
2286 
2287  def set_euler_angles2(self, *args):
2288  """set_euler_angles2(ImageHeader self, Vector3D euler)"""
2289  return _IMP_em.ImageHeader_set_euler_angles2(self, *args)
2290 
2291  def is_normalized(self):
2292  """is_normalized(ImageHeader self) -> bool"""
2293  return _IMP_em.ImageHeader_is_normalized(self)
2294 
2295  def set_date(self):
2296  """set_date(ImageHeader self)"""
2297  return _IMP_em.ImageHeader_set_date(self)
2298 
2299  def set_time(self):
2300  """set_time(ImageHeader self)"""
2301  return _IMP_em.ImageHeader_set_time(self)
2302 
2303  def set_title(self, *args):
2304  """set_title(ImageHeader self, IMP::String newName)"""
2305  return _IMP_em.ImageHeader_set_title(self, *args)
2306 
2307  __swig_destroy__ = _IMP_em.delete_ImageHeader
2308  __del__ = lambda self : None;
2309 ImageHeader_swigregister = _IMP_em.ImageHeader_swigregister
2310 ImageHeader_swigregister(ImageHeader)
2311 
2312 class SpiderMapReaderWriter(MapReaderWriter):
2313  """Proxy of C++ IMP::em::SpiderMapReaderWriter class"""
2314  __swig_setmethods__ = {}
2315  for _s in [MapReaderWriter]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2316  __setattr__ = lambda self, name, value: _swig_setattr(self, SpiderMapReaderWriter, name, value)
2317  __swig_getmethods__ = {}
2318  for _s in [MapReaderWriter]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2319  __getattr__ = lambda self, name: _swig_getattr(self, SpiderMapReaderWriter, name)
2320  __swig_setmethods__["filename_"] = _IMP_em.SpiderMapReaderWriter_filename__set
2321  __swig_getmethods__["filename_"] = _IMP_em.SpiderMapReaderWriter_filename__get
2322  if _newclass:filename_ = _swig_property(_IMP_em.SpiderMapReaderWriter_filename__get, _IMP_em.SpiderMapReaderWriter_filename__set)
2323  __swig_setmethods__["skip_type_check_"] = _IMP_em.SpiderMapReaderWriter_skip_type_check__set
2324  __swig_getmethods__["skip_type_check_"] = _IMP_em.SpiderMapReaderWriter_skip_type_check__get
2325  if _newclass:skip_type_check_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_type_check__get, _IMP_em.SpiderMapReaderWriter_skip_type_check__set)
2326  __swig_setmethods__["force_reversed_"] = _IMP_em.SpiderMapReaderWriter_force_reversed__set
2327  __swig_getmethods__["force_reversed_"] = _IMP_em.SpiderMapReaderWriter_force_reversed__get
2328  if _newclass:force_reversed_ = _swig_property(_IMP_em.SpiderMapReaderWriter_force_reversed__get, _IMP_em.SpiderMapReaderWriter_force_reversed__set)
2329  __swig_setmethods__["skip_extra_checkings_"] = _IMP_em.SpiderMapReaderWriter_skip_extra_checkings__set
2330  __swig_getmethods__["skip_extra_checkings_"] = _IMP_em.SpiderMapReaderWriter_skip_extra_checkings__get
2331  if _newclass:skip_extra_checkings_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_extra_checkings__get, _IMP_em.SpiderMapReaderWriter_skip_extra_checkings__set)
2332  def __init__(self, *args):
2333  """
2334  __init__(IMP::em::SpiderMapReaderWriter self) -> SpiderMapReaderWriter
2335  __init__(IMP::em::SpiderMapReaderWriter self, IMP::String filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings) -> SpiderMapReaderWriter
2336  """
2337  this = _IMP_em.new_SpiderMapReaderWriter(*args)
2338  try: self.this.append(this)
2339  except: self.this = this
2340  def __str__(self):
2341  """__str__(SpiderMapReaderWriter self) -> std::string"""
2342  return _IMP_em.SpiderMapReaderWriter___str__(self)
2343 
2344  def __repr__(self):
2345  """__repr__(SpiderMapReaderWriter self) -> std::string"""
2346  return _IMP_em.SpiderMapReaderWriter___repr__(self)
2347 
2348  def get_from(o):
2349  return _object_cast_to_SpiderMapReaderWriter(o)
2350  get_from = staticmethod(get_from)
2351 
2352 SpiderMapReaderWriter_swigregister = _IMP_em.SpiderMapReaderWriter_swigregister
2353 SpiderMapReaderWriter_swigregister(SpiderMapReaderWriter)
2354 
2355 class FittingSolutions(_object):
2356  """Proxy of C++ IMP::em::FittingSolutions class"""
2357  __swig_setmethods__ = {}
2358  __setattr__ = lambda self, name, value: _swig_setattr(self, FittingSolutions, name, value)
2359  __swig_getmethods__ = {}
2360  __getattr__ = lambda self, name: _swig_getattr(self, FittingSolutions, name)
2361  def __init__(self):
2362  """__init__(IMP::em::FittingSolutions self) -> FittingSolutions"""
2363  this = _IMP_em.new_FittingSolutions()
2364  try: self.this.append(this)
2365  except: self.this = this
2366  def get_number_of_solutions(self):
2367  """get_number_of_solutions(FittingSolutions self) -> int"""
2368  return _IMP_em.FittingSolutions_get_number_of_solutions(self)
2369 
2370  def get_transformation(self, *args):
2371  """get_transformation(FittingSolutions self, unsigned int i) -> Transformation3D"""
2372  return _IMP_em.FittingSolutions_get_transformation(self, *args)
2373 
2374  def get_score(self, *args):
2375  """get_score(FittingSolutions self, unsigned int i) -> IMP::Float"""
2376  return _IMP_em.FittingSolutions_get_score(self, *args)
2377 
2378  def set_score(self, *args):
2379  """set_score(FittingSolutions self, unsigned int i, IMP::Float score)"""
2380  return _IMP_em.FittingSolutions_set_score(self, *args)
2381 
2382  def add_solution(self, *args):
2383  """add_solution(FittingSolutions self, Transformation3D t, IMP::Float score)"""
2384  return _IMP_em.FittingSolutions_add_solution(self, *args)
2385 
2386  def sort(self, reverse=False):
2387  """
2388  sort(FittingSolutions self, bool reverse=False)
2389  sort(FittingSolutions self)
2390  """
2391  return _IMP_em.FittingSolutions_sort(self, reverse)
2392 
2393  def multiply(self, *args):
2394  """multiply(FittingSolutions self, Transformation3D t)"""
2395  return _IMP_em.FittingSolutions_multiply(self, *args)
2396 
2397  def get_transformations(self):
2398  """get_transformations(FittingSolutions self) -> IMP::algebra::Transformation3Ds"""
2399  return _IMP_em.FittingSolutions_get_transformations(self)
2400 
2401  def show(self, *args):
2402  """
2403  show(FittingSolutions self, _ostream out=std::cout)
2404  show(FittingSolutions self)
2405  """
2406  return _IMP_em.FittingSolutions_show(self, *args)
2407 
2408  def __str__(self):
2409  """__str__(FittingSolutions self) -> std::string"""
2410  return _IMP_em.FittingSolutions___str__(self)
2411 
2412  def __repr__(self):
2413  """__repr__(FittingSolutions self) -> std::string"""
2414  return _IMP_em.FittingSolutions___repr__(self)
2415 
2416  __swig_destroy__ = _IMP_em.delete_FittingSolutions
2417  __del__ = lambda self : None;
2418 FittingSolutions_swigregister = _IMP_em.FittingSolutions_swigregister
2419 FittingSolutions_swigregister(FittingSolutions)
2420 
2421 
2423  """
2424  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid,
2425  IMP::kernel::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5,
2426  IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100,
2427  IMP::Float max_translation=2., IMP::Float max_rotation=.3, bool fast=False) -> FittingSolutions
2428  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid,
2429  IMP::kernel::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5,
2430  IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100,
2431  IMP::Float max_translation=2., IMP::Float max_rotation=.3) -> FittingSolutions
2432  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid,
2433  IMP::kernel::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5,
2434  IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100,
2435  IMP::Float max_translation=2.) -> FittingSolutions
2436  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid,
2437  IMP::kernel::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5,
2438  IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100) -> FittingSolutions
2439  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid,
2440  IMP::kernel::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5,
2441  IMP::Int number_of_mc_steps=10) -> FittingSolutions
2442  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid,
2443  IMP::kernel::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2444  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid,
2445  IMP::kernel::OptimizerStates display_log) -> FittingSolutions
2446  """
2447  return _IMP_em.local_rigid_fitting_around_point(*args)
2448 
2449 def local_rigid_fitting(*args):
2450  """
2451  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::kernel::OptimizerStates display_log,
2452  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10,
2453  IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2.,
2454  IMP::Float max_rotation=.3, bool fast=True) -> FittingSolutions
2455  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::kernel::OptimizerStates display_log,
2456  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10,
2457  IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2.,
2458  IMP::Float max_rotation=.3) -> FittingSolutions
2459  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::kernel::OptimizerStates display_log,
2460  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10,
2461  IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2.) -> FittingSolutions
2462  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::kernel::OptimizerStates display_log,
2463  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10,
2464  IMP::Int number_of_cg_steps=100) -> FittingSolutions
2465  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::kernel::OptimizerStates display_log,
2466  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10) -> FittingSolutions
2467  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::kernel::OptimizerStates display_log,
2468  IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2469  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::kernel::OptimizerStates display_log) -> FittingSolutions
2470  """
2471  return _IMP_em.local_rigid_fitting(*args)
2472 
2474  """
2475  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids,
2476  IMP::kernel::OptimizerStates display_log,
2477  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100,
2478  IMP::Float max_translation=2., IMP::Float max_rotation=.3) -> FittingSolutions
2479  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids,
2480  IMP::kernel::OptimizerStates display_log,
2481  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100,
2482  IMP::Float max_translation=2.) -> FittingSolutions
2483  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids,
2484  IMP::kernel::OptimizerStates display_log,
2485  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100) -> FittingSolutions
2486  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids,
2487  IMP::kernel::OptimizerStates display_log,
2488  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10) -> FittingSolutions
2489  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids,
2490  IMP::kernel::OptimizerStates display_log,
2491  IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2492  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids,
2493  IMP::kernel::OptimizerStates display_log) -> FittingSolutions
2494  """
2495  return _IMP_em.local_rigid_fitting_around_points(*args)
2496 
2498  """
2499  local_rigid_fitting_grid_search(IMP::kernel::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2,
2500  IMP::Int translation_step=1, IMP::Float max_angle_in_radians=0.174,
2501  IMP::Int number_of_rotations=100) -> FittingSolutions
2502  local_rigid_fitting_grid_search(IMP::kernel::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2,
2503  IMP::Int translation_step=1, IMP::Float max_angle_in_radians=0.174) -> FittingSolutions
2504  local_rigid_fitting_grid_search(IMP::kernel::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2,
2505  IMP::Int translation_step=1) -> FittingSolutions
2506  local_rigid_fitting_grid_search(IMP::kernel::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2) -> FittingSolutions
2507  local_rigid_fitting_grid_search(IMP::kernel::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap) -> FittingSolutions
2508  """
2509  return _IMP_em.local_rigid_fitting_grid_search(*args)
2510 
2511 def compute_fitting_scores(*args):
2512  """
2513  compute_fitting_scores(IMP::kernel::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations,
2514  bool fast_version=False, bool local_score=False,
2515  FloatKey wei_key=IMP::atom::Mass::get_mass_key()) -> FittingSolutions
2516  compute_fitting_scores(IMP::kernel::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations,
2517  bool fast_version=False, bool local_score=False) -> FittingSolutions
2518  compute_fitting_scores(IMP::kernel::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations,
2519  bool fast_version=False) -> FittingSolutions
2520  compute_fitting_scores(IMP::kernel::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2521  compute_fitting_scores(DensityMap em_map, RigidBody rb, Refiner refiner, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2522  """
2523  return _IMP_em.compute_fitting_scores(*args)
2524 
2525 def compute_fitting_score(*args):
2526  """
2527  compute_fitting_score(IMP::kernel::ParticlesTemp const & ps, DensityMap em_map, FloatKey wei_key=IMP::atom::Mass::get_mass_key()) -> IMP::Float
2528  compute_fitting_score(IMP::kernel::ParticlesTemp const & ps, DensityMap em_map) -> IMP::Float
2529  """
2530  return _IMP_em.compute_fitting_score(*args)
2531 
2533  """
2534  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::kernel::Particles const & ps, Transformation3D t=IMP::algebra::get_identity_transformation_3d(),
2535  float thr=0.0) -> long
2536  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::kernel::Particles const & ps, Transformation3D t=IMP::algebra::get_identity_transformation_3d()) -> long
2537  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::kernel::Particles const & ps) -> long
2538  """
2539  return _IMP_em.get_number_of_particles_outside_of_the_density(*args)
2540 
2542  """
2543  get_numbers_of_particles_outside_of_the_density(DensityMap dmap, IMP::kernel::Particles const & ps, IMP::algebra::Transformation3Ds const & transformations,
2544  float thr=0.0) -> IMP::Ints
2545  get_numbers_of_particles_outside_of_the_density(DensityMap dmap, IMP::kernel::Particles const & ps, IMP::algebra::Transformation3Ds const & transformations) -> IMP::Ints
2546  """
2547  return _IMP_em.get_numbers_of_particles_outside_of_the_density(*args)
2548 
2550  """
2551  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::kernel::Particles const & ps, float smoothing_radius=3., Transformation3D t=IMP::algebra::get_identity_transformation_3d(),
2552  float thr=0.0) -> double
2553  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::kernel::Particles const & ps, float smoothing_radius=3., Transformation3D t=IMP::algebra::get_identity_transformation_3d()) -> double
2554  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::kernel::Particles const & ps, float smoothing_radius=3.) -> double
2555  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::kernel::Particles const & ps) -> double
2556  """
2557  return _IMP_em.get_percentage_of_voxels_covered_by_particles(*args)
2558 class HighDensityEmbedding(IMP.statistics.Embedding):
2559  """Proxy of C++ IMP::em::HighDensityEmbedding class"""
2560  __swig_setmethods__ = {}
2561  for _s in [IMP.statistics.Embedding]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2562  __setattr__ = lambda self, name, value: _swig_setattr(self, HighDensityEmbedding, name, value)
2563  __swig_getmethods__ = {}
2564  for _s in [IMP.statistics.Embedding]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2565  __getattr__ = lambda self, name: _swig_getattr(self, HighDensityEmbedding, name)
2566  def __init__(self, *args):
2567  """__init__(IMP::em::HighDensityEmbedding self, DensityMap dm, double threshold) -> HighDensityEmbedding"""
2568  this = _IMP_em.new_HighDensityEmbedding(*args)
2569  try: self.this.append(this)
2570  except: self.this = this
2571  def get_version_info(self):
2572  """get_version_info(HighDensityEmbedding self) -> VersionInfo"""
2573  return _IMP_em.HighDensityEmbedding_get_version_info(self)
2574 
2575  def __str__(self):
2576  """__str__(HighDensityEmbedding self) -> std::string"""
2577  return _IMP_em.HighDensityEmbedding___str__(self)
2578 
2579  def __repr__(self):
2580  """__repr__(HighDensityEmbedding self) -> std::string"""
2581  return _IMP_em.HighDensityEmbedding___repr__(self)
2582 
2583  def get_from(o):
2584  return _object_cast_to_HighDensityEmbedding(o)
2585  get_from = staticmethod(get_from)
2586 
2587 HighDensityEmbedding_swigregister = _IMP_em.HighDensityEmbedding_swigregister
2588 HighDensityEmbedding_swigregister(HighDensityEmbedding)
2589 
2590 
2591 def mask_and_norm(*args):
2592  """mask_and_norm(DensityMap dmap, DensityMap mask) -> DensityMap"""
2593  return _IMP_em.mask_and_norm(*args)
2594 
2595 def get_volume_at_threshold(*args):
2596  """get_volume_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float"""
2597  return _IMP_em.get_volume_at_threshold(*args)
2598 
2600  """
2601  get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold, IMP::atom::ProteinDensityReference ref=HARPAZ) -> IMP::Float
2602  get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float
2603  """
2604  return _IMP_em.get_molecular_mass_at_threshold(*args)
2605 
2607  """get_threshold_for_approximate_volume(DensityMap m, IMP::Float desired_volume) -> IMP::Float"""
2608  return _IMP_em.get_threshold_for_approximate_volume(*args)
2609 
2611  """
2612  get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass, IMP::atom::ProteinDensityReference ref=HARPAZ) -> IMP::Float
2613  get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass) -> IMP::Float
2614  """
2615  return _IMP_em.get_threshold_for_approximate_mass(*args)
2616 class EnvelopePenetrationRestraint(IMP.kernel.Restraint):
2617  """Proxy of C++ IMP::em::EnvelopePenetrationRestraint class"""
2618  __swig_setmethods__ = {}
2619  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2620  __setattr__ = lambda self, name, value: _swig_setattr(self, EnvelopePenetrationRestraint, name, value)
2621  __swig_getmethods__ = {}
2622  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2623  __getattr__ = lambda self, name: _swig_getattr(self, EnvelopePenetrationRestraint, name)
2624  def __init__(self, *args):
2625  """__init__(IMP::em::EnvelopePenetrationRestraint self, IMP::kernel::Particles ps, DensityMap em_map, IMP::Float threshold) -> EnvelopePenetrationRestraint"""
2626  this = _IMP_em.new_EnvelopePenetrationRestraint(*args)
2627  try: self.this.append(this)
2628  except: self.this = this
2629  def do_get_inputs(self):
2630  """do_get_inputs(EnvelopePenetrationRestraint self) -> IMP::kernel::ModelObjectsTemp"""
2631  return _IMP_em.EnvelopePenetrationRestraint_do_get_inputs(self)
2632 
2633  def get_version_info(self):
2634  """get_version_info(EnvelopePenetrationRestraint self) -> VersionInfo"""
2635  return _IMP_em.EnvelopePenetrationRestraint_get_version_info(self)
2636 
2637  def __str__(self):
2638  """__str__(EnvelopePenetrationRestraint self) -> std::string"""
2639  return _IMP_em.EnvelopePenetrationRestraint___str__(self)
2640 
2641  def __repr__(self):
2642  """__repr__(EnvelopePenetrationRestraint self) -> std::string"""
2643  return _IMP_em.EnvelopePenetrationRestraint___repr__(self)
2644 
2645  def get_from(o):
2646  return _object_cast_to_EnvelopePenetrationRestraint(o)
2647  get_from = staticmethod(get_from)
2648 
2649 EnvelopePenetrationRestraint_swigregister = _IMP_em.EnvelopePenetrationRestraint_swigregister
2650 EnvelopePenetrationRestraint_swigregister(EnvelopePenetrationRestraint)
2651 
2652 class PCAFitRestraint(IMP.kernel.Restraint):
2653  """Proxy of C++ IMP::em::PCAFitRestraint class"""
2654  __swig_setmethods__ = {}
2655  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2656  __setattr__ = lambda self, name, value: _swig_setattr(self, PCAFitRestraint, name, value)
2657  __swig_getmethods__ = {}
2658  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2659  __getattr__ = lambda self, name: _swig_getattr(self, PCAFitRestraint, name)
2660  def __init__(self, *args):
2661  """
2662  __init__(IMP::em::PCAFitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map, float threahold, float max_pca_size_diff,
2663  float max_angle_diff, float max_centroid_diff, FloatKey weight_key=IMP::atom::Mass::get_mass_key()) -> PCAFitRestraint
2664  __init__(IMP::em::PCAFitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map, float threahold, float max_pca_size_diff,
2665  float max_angle_diff, float max_centroid_diff) -> PCAFitRestraint
2666  """
2667  this = _IMP_em.new_PCAFitRestraint(*args)
2668  try: self.this.append(this)
2669  except: self.this = this
2670  def do_get_inputs(self):
2671  """do_get_inputs(PCAFitRestraint self) -> IMP::kernel::ModelObjectsTemp"""
2672  return _IMP_em.PCAFitRestraint_do_get_inputs(self)
2673 
2674  def get_version_info(self):
2675  """get_version_info(PCAFitRestraint self) -> VersionInfo"""
2676  return _IMP_em.PCAFitRestraint_get_version_info(self)
2677 
2678  def __str__(self):
2679  """__str__(PCAFitRestraint self) -> std::string"""
2680  return _IMP_em.PCAFitRestraint___str__(self)
2681 
2682  def __repr__(self):
2683  """__repr__(PCAFitRestraint self) -> std::string"""
2684  return _IMP_em.PCAFitRestraint___repr__(self)
2685 
2686  def get_from(o):
2687  return _object_cast_to_PCAFitRestraint(o)
2688  get_from = staticmethod(get_from)
2689 
2690 PCAFitRestraint_swigregister = _IMP_em.PCAFitRestraint_swigregister
2691 PCAFitRestraint_swigregister(PCAFitRestraint)
2692 
2693 class EnvelopeFitRestraint(IMP.kernel.Restraint):
2694  """Proxy of C++ IMP::em::EnvelopeFitRestraint class"""
2695  __swig_setmethods__ = {}
2696  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2697  __setattr__ = lambda self, name, value: _swig_setattr(self, EnvelopeFitRestraint, name, value)
2698  __swig_getmethods__ = {}
2699  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2700  __getattr__ = lambda self, name: _swig_getattr(self, EnvelopeFitRestraint, name)
2701  def __init__(self, *args):
2702  """__init__(IMP::em::EnvelopeFitRestraint self, IMP::kernel::Particles particles, DensityMap em_map, double density_threshold, double penetration_threshold) -> EnvelopeFitRestraint"""
2703  this = _IMP_em.new_EnvelopeFitRestraint(*args)
2704  try: self.this.append(this)
2705  except: self.this = this
2706  def get_transformation(self):
2707  """get_transformation(EnvelopeFitRestraint self) -> Transformation3D"""
2708  return _IMP_em.EnvelopeFitRestraint_get_transformation(self)
2709 
2710  def apply_transformation(self):
2711  """apply_transformation(EnvelopeFitRestraint self)"""
2712  return _IMP_em.EnvelopeFitRestraint_apply_transformation(self)
2713 
2714  def do_get_inputs(self):
2715  """do_get_inputs(EnvelopeFitRestraint self) -> IMP::kernel::ModelObjectsTemp"""
2716  return _IMP_em.EnvelopeFitRestraint_do_get_inputs(self)
2717 
2718  def get_version_info(self):
2719  """get_version_info(EnvelopeFitRestraint self) -> VersionInfo"""
2720  return _IMP_em.EnvelopeFitRestraint_get_version_info(self)
2721 
2722  def __str__(self):
2723  """__str__(EnvelopeFitRestraint self) -> std::string"""
2724  return _IMP_em.EnvelopeFitRestraint___str__(self)
2725 
2726  def __repr__(self):
2727  """__repr__(EnvelopeFitRestraint self) -> std::string"""
2728  return _IMP_em.EnvelopeFitRestraint___repr__(self)
2729 
2730  def get_from(o):
2731  return _object_cast_to_EnvelopeFitRestraint(o)
2732  get_from = staticmethod(get_from)
2733 
2734 EnvelopeFitRestraint_swigregister = _IMP_em.EnvelopeFitRestraint_swigregister
2735 EnvelopeFitRestraint_swigregister(EnvelopeFitRestraint)
2736 
2737 import math
2738 
2739 def write_pca_cmm(pca, fh):
2740  """Write out principal components to a file in Chimera Marker format"""
2741  eigen_values = pca.get_principal_values()
2742  eigen_vecs = pca.get_principal_components()
2743  centroid = pca.get_centroid()
2744 
2745  print >> fh, "<marker_set>"
2746  print >> fh, "<!-- PCA with eigen values: (%g,%g,%g) and " \
2747  "centroid (%g,%g,%g) -->" \
2748  % (math.sqrt(eigen_values[0]),
2749  math.sqrt(eigen_values[1]),
2750  math.sqrt(eigen_values[2]),
2751  centroid[0], centroid[1], centroid[2])
2752 
2753  radius = 2.
2754 
2755  for i in range(3):
2756  val = math.sqrt(eigen_values[i])
2757  v1 = centroid - val * eigen_vecs[i]
2758  v2 = centroid + val * eigen_vecs[i]
2759  for markerid, v in ((i*2+1, v1), (i*2+2, v2)):
2760  print >> fh, "<marker id=\"%d\" x=\"%g\" y=\"%g\" z=\"%g\" " \
2761  "radius=\"%g\"/>" \
2762  % (markerid, v[0], v[1], v[2], radius)
2763 
2764  for i in range(1, 7, 2):
2765  print >> fh, "<link id1= \"%d\" id2=\"%d\" radius=\"%g\"/>" \
2766  % (i, i+1, radius)
2767  print >> fh, "</marker_set>"
2768 
2769 
2770 def get_module_version():
2771  """get_module_version() -> std::string const"""
2772  return _IMP_em.get_module_version()
2773 
2774 def get_example_path(*args):
2775  """get_example_path(std::string fname) -> std::string"""
2776  return _IMP_em.get_example_path(*args)
2777 
2778 def get_data_path(*args):
2779  """get_data_path(std::string fname) -> std::string"""
2780  return _IMP_em.get_data_path(*args)
2781 import _version_check
2782 _version_check.check_version(get_module_version())
2783 
2784 # This file is compatible with both classic and new-style classes.
2785 
2786 
void get_transformed_into(const DensityMap *source, const algebra::Transformation3D &tr, DensityMap *into, bool calc_rms=true)
Rotate a density map into another map.
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)
algebra::Vector3Ds density2vectors(DensityMap *dmap, Float threshold)
Converts a density grid to a set of paritlces.
algebra::BoundingBoxD< 3 > get_bounding_box(const DensityMap *m, Float threshold)
SurfaceShellDensityMap * particles2surface(const kernel::ParticlesTemp &ps, Float apix, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
Resample a set of particles into a density grid.
SampledDensityMap * particles2density(const kernel::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.
Various classes to hold sets of particles.
DensityMap * binarize(DensityMap *orig_map, float threshold, bool reverse=false)
double get_sum(const DensityMap *m1)
Return the sum of all voxels.
void add_to_map(DensityMap *dm, const kernel::Particles &pis)
Make CGAL functionality available to IMP.
FittingSolutions local_rigid_fitting_grid_search(const kernel::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(kernel::Model *m, kernel::ParticleIndex pi)
DensityMap * mask_and_norm(em::DensityMap *dmap, em::DensityMap *mask)
Return a masked density, and normalize the output map within the mask region.
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
Definition: exception.h:73
Ints get_numbers_of_particles_outside_of_the_density(DensityMap *dmap, const kernel::Particles &ps, const IMP::algebra::Transformation3Ds &transformations, float thr=0.0)
Get numbers of particles (mult transforms) that are outside the density.
Low level functionality (logging, error handling, profiling, command line flags etc) that is used by ...
DensityMap * get_threshold_map(const DensityMap *orig_map, float 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 installed data.
Composable functors to implement scores via compile-time composition.
DensityMap * read_map(std::string filename, MapReaderWriter *reader)
Read a density map from a file and return it.
double get_percentage_of_voxels_covered_by_particles(DensityMap *dmap, const kernel::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.
FittingSolutions compute_fitting_scores(const kernel::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.
Code to compute statistical measures.
algebra::GridD< 3, algebra::DenseGridStorageD< 3, float >, float > get_grid(DensityMap *in_map)
def write_pca_cmm
Write out principal components to a file in Chimera Marker format.
double convolute(const DensityMap *m1, const DensityMap *m2)
DensityMap * multiply(const DensityMap *m1, const DensityMap *m2)
void write_map(DensityMap *m, std::string filename, MapReaderWriter *writer)
Write a density map to a file.
DensityHeader create_density_header(const algebra::BoundingBoxD< 3 > &bb, float spacing)
Create a header from a bounding box in 3D.
Base functionality and abstract base classes for representation, scoring and sampling.
DensityMap * get_binarized_interior(DensityMap *dmap)
Return a binaries density map with 1 for voxels that are internal.
A restraint is a term in an IMP ScoringFunction.
Float compute_fitting_score(const kernel::ParticlesTemp &ps, DensityMap *em_map, FloatKey wei_key=atom::Mass::get_mass_key())
Compute fitting scores for a given set of rigid transformations.
double get_density(const DensityMap *m, const algebra::Vector3D &v)
DensityMap * get_max_map(DensityMaps maps)
DensityMap * create_density_map(const DensityMap *other)
create a copy of another map
Store data to be clustered for embedding based algorithms.
Common base class for heavy weight IMP objects.
Definition: Object.h:106
Float approximate_molecular_mass(DensityMap *m, Float threshold)
DensityMap * get_transformed(const DensityMap *input, const algebra::Transformation3D &tr, double threshold)
Return a new density map containing a rotated version of the old one.
Vector3D get_centroid(const Vector3Ds &ps)
Returns the centroid of a set of vectors.
Definition: Vector3D.h:56
std::string get_example_path(std::string file_name)
Return the path to installed example data for this module.
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...
void show(Hierarchy h, std::ostream &out=std::cout)
Print out a molecular hierarchy.
FittingSolutions local_rigid_fitting_around_points(kernel::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.
kernel::Particles density2particles(DensityMap *dmap, Float threshold, kernel::Model *m, int step=1)
Converts a density grid to a set of paritlces.
FittingSolutions local_rigid_fitting_around_point(kernel::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.
SampledDensityMap * particles2binarized_density(const kernel::ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
Definition: converters.h:80
Output IMP model data in various file formats.
CheckLevel get_check_level()
Get the current audit mode.
Definition: exception.h:81
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.
long get_number_of_particles_outside_of_the_density(DensityMap *dmap, const kernel::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_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.
DensityMap * get_resampled(DensityMap *input, double scaling)
Get a resampled version of the map.
FittingSolutions local_rigid_fitting(kernel::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.
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.