IMP  2.1.0
The Integrative Modeling Platform
em/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 2.0.11
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 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_em.IMPSCOREFUNCTOR_SHOW_WARNINGS
284 import IMP.score_functor
285 IMP_STATISTICS_HAS_IMP_BASE = _IMP_em.IMP_STATISTICS_HAS_IMP_BASE
286 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_em.IMP_STATISTICS_HAS_IMP_CGAL
287 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
288 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
289 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_em.IMP_STATISTICS_HAS_BOOST_RANDOM
290 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_SYSTEM
291 IMP_STATISTICS_HAS_CGAL = _IMP_em.IMP_STATISTICS_HAS_CGAL
292 IMPSTATISTICS_SHOW_WARNINGS = _IMP_em.IMPSTATISTICS_SHOW_WARNINGS
293 import IMP.statistics
294 IMP_CORE_HAS_IMP_BASE = _IMP_em.IMP_CORE_HAS_IMP_BASE
295 IMP_CORE_HAS_IMP_CGAL = _IMP_em.IMP_CORE_HAS_IMP_CGAL
296 IMP_CORE_HAS_IMP_KERNEL = _IMP_em.IMP_CORE_HAS_IMP_KERNEL
297 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_FILESYSTEM
298 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
299 IMP_CORE_HAS_BOOST_RANDOM = _IMP_em.IMP_CORE_HAS_BOOST_RANDOM
300 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_SYSTEM
301 IMP_CORE_HAS_CGAL = _IMP_em.IMP_CORE_HAS_CGAL
302 IMPCORE_SHOW_WARNINGS = _IMP_em.IMPCORE_SHOW_WARNINGS
303 import IMP.core
304 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_em.IMP_CONTAINER_HAS_IMP_ALGEBRA
305 IMP_CONTAINER_HAS_IMP_BASE = _IMP_em.IMP_CONTAINER_HAS_IMP_BASE
306 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_em.IMP_CONTAINER_HAS_IMP_CGAL
307 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_em.IMP_CONTAINER_HAS_IMP_DISPLAY
308 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_em.IMP_CONTAINER_HAS_IMP_KERNEL
309 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
310 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
311 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
312 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_em.IMP_CONTAINER_HAS_BOOST_RANDOM
313 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_SYSTEM
314 IMP_CONTAINER_HAS_CGAL = _IMP_em.IMP_CONTAINER_HAS_CGAL
315 IMPCONTAINER_SHOW_WARNINGS = _IMP_em.IMPCONTAINER_SHOW_WARNINGS
316 import IMP.container
317 IMP_ATOM_HAS_IMP_BASE = _IMP_em.IMP_ATOM_HAS_IMP_BASE
318 IMP_ATOM_HAS_IMP_CGAL = _IMP_em.IMP_ATOM_HAS_IMP_CGAL
319 IMP_ATOM_HAS_IMP_KERNEL = _IMP_em.IMP_ATOM_HAS_IMP_KERNEL
320 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
321 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
322 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_em.IMP_ATOM_HAS_BOOST_RANDOM
323 IMP_ATOM_HAS_BOOST_REGEX = _IMP_em.IMP_ATOM_HAS_BOOST_REGEX
324 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_em.IMP_ATOM_HAS_BOOST_SYSTEM
325 IMP_ATOM_HAS_CGAL = _IMP_em.IMP_ATOM_HAS_CGAL
326 IMPATOM_SHOW_WARNINGS = _IMP_em.IMPATOM_SHOW_WARNINGS
327 IMP_ATOM_TYPE_INDEX = _IMP_em.IMP_ATOM_TYPE_INDEX
328 IMP_RESIDUE_TYPE_INDEX = _IMP_em.IMP_RESIDUE_TYPE_INDEX
329 IMP_HIERARCHY_TYPE_INDEX = _IMP_em.IMP_HIERARCHY_TYPE_INDEX
330 import IMP.atom
331 IMP_EM_HAS_IMP_CGAL = _IMP_em.IMP_EM_HAS_IMP_CGAL
332 IMP_EM_HAS_IMP_CONTAINER = _IMP_em.IMP_EM_HAS_IMP_CONTAINER
333 IMP_EM_HAS_IMP_DISPLAY = _IMP_em.IMP_EM_HAS_IMP_DISPLAY
334 IMP_EM_HAS_IMP_KERNEL = _IMP_em.IMP_EM_HAS_IMP_KERNEL
335 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_EM_HAS_IMP_SCORE_FUNCTOR
336 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_EM_HAS_BOOST_FILESYSTEM
337 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
338 IMP_EM_HAS_BOOST_RANDOM = _IMP_em.IMP_EM_HAS_BOOST_RANDOM
339 IMP_EM_HAS_BOOST_REGEX = _IMP_em.IMP_EM_HAS_BOOST_REGEX
340 IMP_EM_HAS_BOOST_SYSTEM = _IMP_em.IMP_EM_HAS_BOOST_SYSTEM
341 IMP_EM_HAS_CGAL = _IMP_em.IMP_EM_HAS_CGAL
342 IMPEM_SHOW_WARNINGS = _IMP_em.IMPEM_SHOW_WARNINGS
343 _object_types.append("DensityMap")
344 
345 
346 def _object_cast_to_DensityMap(*args):
347  """_object_cast_to_DensityMap(Object o) -> DensityMap"""
348  return _IMP_em._object_cast_to_DensityMap(*args)
349 _object_types.append("SampledDensityMap")
350 
351 
352 def _object_cast_to_SampledDensityMap(*args):
353  """_object_cast_to_SampledDensityMap(Object o) -> SampledDensityMap"""
354  return _IMP_em._object_cast_to_SampledDensityMap(*args)
355 _object_types.append("SurfaceShellDensityMap")
356 
357 
358 def _object_cast_to_SurfaceShellDensityMap(*args):
359  """_object_cast_to_SurfaceShellDensityMap(Object o) -> SurfaceShellDensityMap"""
360  return _IMP_em._object_cast_to_SurfaceShellDensityMap(*args)
361 _object_types.append("FitRestraint")
362 
363 
364 def _object_cast_to_FitRestraint(*args):
365  """_object_cast_to_FitRestraint(Object o) -> FitRestraint"""
366  return _IMP_em._object_cast_to_FitRestraint(*args)
367 _object_types.append("PCAFitRestraint")
368 
369 
370 def _object_cast_to_PCAFitRestraint(*args):
371  """_object_cast_to_PCAFitRestraint(Object o) -> PCAFitRestraint"""
372  return _IMP_em._object_cast_to_PCAFitRestraint(*args)
373 _object_types.append("EnvelopePenetrationRestraint")
374 
375 
376 def _object_cast_to_EnvelopePenetrationRestraint(*args):
377  """_object_cast_to_EnvelopePenetrationRestraint(Object o) -> EnvelopePenetrationRestraint"""
378  return _IMP_em._object_cast_to_EnvelopePenetrationRestraint(*args)
379 _object_types.append("EnvelopeFitRestraint")
380 
381 
382 def _object_cast_to_EnvelopeFitRestraint(*args):
383  """_object_cast_to_EnvelopeFitRestraint(Object o) -> EnvelopeFitRestraint"""
384  return _IMP_em._object_cast_to_EnvelopeFitRestraint(*args)
385 RadiusDependentKernelParametersList=list
386 _plural_types.append("RadiusDependentKernelParametersList")
387 _value_types.append("RadiusDependentKernelParameters")
388 
389 KernelParametersList=list
390 _plural_types.append("KernelParametersList")
391 _value_types.append("KernelParameters")
392 
393 _object_types.append("HighDensityEmbedding")
394 
395 
396 def _object_cast_to_HighDensityEmbedding(*args):
397  """_object_cast_to_HighDensityEmbedding(Object o) -> HighDensityEmbedding"""
398  return _IMP_em._object_cast_to_HighDensityEmbedding(*args)
399 _object_types.append("MapReaderWriter")
400 
401 
402 def _object_cast_to_MapReaderWriter(*args):
403  """_object_cast_to_MapReaderWriter(Object o) -> MapReaderWriter"""
404  return _IMP_em._object_cast_to_MapReaderWriter(*args)
405 _object_types.append("MRCReaderWriter")
406 
407 
408 def _object_cast_to_MRCReaderWriter(*args):
409  """_object_cast_to_MRCReaderWriter(Object o) -> MRCReaderWriter"""
410  return _IMP_em._object_cast_to_MRCReaderWriter(*args)
411 _object_types.append("SpiderMapReaderWriter")
412 
413 
414 def _object_cast_to_SpiderMapReaderWriter(*args):
415  """_object_cast_to_SpiderMapReaderWriter(Object o) -> SpiderMapReaderWriter"""
416  return _IMP_em._object_cast_to_SpiderMapReaderWriter(*args)
417 _object_types.append("EMReaderWriter")
418 
419 
420 def _object_cast_to_EMReaderWriter(*args):
421  """_object_cast_to_EMReaderWriter(Object o) -> EMReaderWriter"""
422  return _IMP_em._object_cast_to_EMReaderWriter(*args)
423 _object_types.append("XplorReaderWriter")
424 
425 
426 def _object_cast_to_XplorReaderWriter(*args):
427  """_object_cast_to_XplorReaderWriter(Object o) -> XplorReaderWriter"""
428  return _IMP_em._object_cast_to_XplorReaderWriter(*args)
429 _object_types.append("CoarseCC")
430 
431 
432 def _object_cast_to_CoarseCC(*args):
433  """_object_cast_to_CoarseCC(Object o) -> CoarseCC"""
434  return _IMP_em._object_cast_to_CoarseCC(*args)
435 _object_types.append("CoarseCCatIntervals")
436 
437 
438 def _object_cast_to_CoarseCCatIntervals(*args):
439  """_object_cast_to_CoarseCCatIntervals(Object o) -> CoarseCCatIntervals"""
440  return _IMP_em._object_cast_to_CoarseCCatIntervals(*args)
441 FittingSolutionsList=list
442 _plural_types.append("FittingSolutionsList")
443 _value_types.append("FittingSolutions")
444 
445 class MapReaderWriter(IMP.base.Object):
446  """Proxy of C++ IMP::em::MapReaderWriter class"""
447  __swig_setmethods__ = {}
448  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
449  __setattr__ = lambda self, name, value: _swig_setattr(self, MapReaderWriter, name, value)
450  __swig_getmethods__ = {}
451  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
452  __getattr__ = lambda self, name: _swig_getattr(self, MapReaderWriter, name)
453  def __init__(self):
454  """__init__(IMP::em::MapReaderWriter self) -> MapReaderWriter"""
455  this = _IMP_em.new_MapReaderWriter()
456  try: self.this.append(this)
457  except: self.this = this
458  def get_version_info(self):
459  """get_version_info(MapReaderWriter self) -> VersionInfo"""
460  return _IMP_em.MapReaderWriter_get_version_info(self)
461 
462  __swig_destroy__ = _IMP_em.delete_MapReaderWriter
463  __del__ = lambda self : None;
464  def __str__(self):
465  """__str__(MapReaderWriter self) -> std::string"""
466  return _IMP_em.MapReaderWriter___str__(self)
467 
468  def __repr__(self):
469  """__repr__(MapReaderWriter self) -> std::string"""
470  return _IMP_em.MapReaderWriter___repr__(self)
471 
472  def get_from(o):
473  return _object_cast_to_MapReaderWriter(o)
474  get_from = staticmethod(get_from)
475 
476 MapReaderWriter_swigregister = _IMP_em.MapReaderWriter_swigregister
477 MapReaderWriter_swigregister(MapReaderWriter)
478 cvar = _IMP_em.cvar
479 EPS = cvar.EPS
480 
481 class DensityHeader(_object):
482  """Proxy of C++ IMP::em::DensityHeader class"""
483  __swig_setmethods__ = {}
484  __setattr__ = lambda self, name, value: _swig_setattr(self, DensityHeader, name, value)
485  __swig_getmethods__ = {}
486  __getattr__ = lambda self, name: _swig_getattr(self, DensityHeader, name)
487  __repr__ = _swig_repr
488  def __init__(self):
489  """__init__(IMP::em::DensityHeader self) -> DensityHeader"""
490  this = _IMP_em.new_DensityHeader()
491  try: self.this.append(this)
492  except: self.this = this
493  def get_top(self, *args):
494  """get_top(DensityHeader self, int ind) -> IMP::em::emreal"""
495  return _IMP_em.DensityHeader_get_top(self, *args)
496 
497  def compute_xyz_top(self, force=False):
498  """
499  compute_xyz_top(DensityHeader self, bool force=False)
500  compute_xyz_top(DensityHeader self)
501  """
502  return _IMP_em.DensityHeader_compute_xyz_top(self, force)
503 
504  def update_map_dimensions(self, *args):
505  """update_map_dimensions(DensityHeader self, int nnx, int nny, int nnz)"""
506  return _IMP_em.DensityHeader_update_map_dimensions(self, *args)
507 
508  def update_cell_dimensions(self):
509  """update_cell_dimensions(DensityHeader self)"""
510  return _IMP_em.DensityHeader_update_cell_dimensions(self)
511 
512  def show(self, *args):
513  """
514  show(DensityHeader self, _ostream out=std::cout)
515  show(DensityHeader self)
516  """
517  return _IMP_em.DensityHeader_show(self, *args)
518 
519  MAP_FIELD_SIZE = _IMP_em.DensityHeader_MAP_FIELD_SIZE
520  USER_FIELD_SIZE = _IMP_em.DensityHeader_USER_FIELD_SIZE
521  COMMENT_FIELD_NUM_OF = _IMP_em.DensityHeader_COMMENT_FIELD_NUM_OF
522  COMMENT_FIELD_SINGLE_SIZE = _IMP_em.DensityHeader_COMMENT_FIELD_SINGLE_SIZE
523  __swig_setmethods__["nxstart"] = _IMP_em.DensityHeader_nxstart_set
524  __swig_getmethods__["nxstart"] = _IMP_em.DensityHeader_nxstart_get
525  if _newclass:nxstart = _swig_property(_IMP_em.DensityHeader_nxstart_get, _IMP_em.DensityHeader_nxstart_set)
526  __swig_setmethods__["nystart"] = _IMP_em.DensityHeader_nystart_set
527  __swig_getmethods__["nystart"] = _IMP_em.DensityHeader_nystart_get
528  if _newclass:nystart = _swig_property(_IMP_em.DensityHeader_nystart_get, _IMP_em.DensityHeader_nystart_set)
529  __swig_setmethods__["nzstart"] = _IMP_em.DensityHeader_nzstart_set
530  __swig_getmethods__["nzstart"] = _IMP_em.DensityHeader_nzstart_get
531  if _newclass:nzstart = _swig_property(_IMP_em.DensityHeader_nzstart_get, _IMP_em.DensityHeader_nzstart_set)
532  __swig_setmethods__["mx"] = _IMP_em.DensityHeader_mx_set
533  __swig_getmethods__["mx"] = _IMP_em.DensityHeader_mx_get
534  if _newclass:mx = _swig_property(_IMP_em.DensityHeader_mx_get, _IMP_em.DensityHeader_mx_set)
535  __swig_setmethods__["my"] = _IMP_em.DensityHeader_my_set
536  __swig_getmethods__["my"] = _IMP_em.DensityHeader_my_get
537  if _newclass:my = _swig_property(_IMP_em.DensityHeader_my_get, _IMP_em.DensityHeader_my_set)
538  __swig_setmethods__["mz"] = _IMP_em.DensityHeader_mz_set
539  __swig_getmethods__["mz"] = _IMP_em.DensityHeader_mz_get
540  if _newclass:mz = _swig_property(_IMP_em.DensityHeader_mz_get, _IMP_em.DensityHeader_mz_set)
541  __swig_setmethods__["xlen"] = _IMP_em.DensityHeader_xlen_set
542  __swig_getmethods__["xlen"] = _IMP_em.DensityHeader_xlen_get
543  if _newclass:xlen = _swig_property(_IMP_em.DensityHeader_xlen_get, _IMP_em.DensityHeader_xlen_set)
544  __swig_setmethods__["ylen"] = _IMP_em.DensityHeader_ylen_set
545  __swig_getmethods__["ylen"] = _IMP_em.DensityHeader_ylen_get
546  if _newclass:ylen = _swig_property(_IMP_em.DensityHeader_ylen_get, _IMP_em.DensityHeader_ylen_set)
547  __swig_setmethods__["zlen"] = _IMP_em.DensityHeader_zlen_set
548  __swig_getmethods__["zlen"] = _IMP_em.DensityHeader_zlen_get
549  if _newclass:zlen = _swig_property(_IMP_em.DensityHeader_zlen_get, _IMP_em.DensityHeader_zlen_set)
550  __swig_setmethods__["alpha"] = _IMP_em.DensityHeader_alpha_set
551  __swig_getmethods__["alpha"] = _IMP_em.DensityHeader_alpha_get
552  if _newclass:alpha = _swig_property(_IMP_em.DensityHeader_alpha_get, _IMP_em.DensityHeader_alpha_set)
553  __swig_setmethods__["beta"] = _IMP_em.DensityHeader_beta_set
554  __swig_getmethods__["beta"] = _IMP_em.DensityHeader_beta_get
555  if _newclass:beta = _swig_property(_IMP_em.DensityHeader_beta_get, _IMP_em.DensityHeader_beta_set)
556  __swig_setmethods__["gamma"] = _IMP_em.DensityHeader_gamma_set
557  __swig_getmethods__["gamma"] = _IMP_em.DensityHeader_gamma_get
558  if _newclass:gamma = _swig_property(_IMP_em.DensityHeader_gamma_get, _IMP_em.DensityHeader_gamma_set)
559  __swig_setmethods__["mapc"] = _IMP_em.DensityHeader_mapc_set
560  __swig_getmethods__["mapc"] = _IMP_em.DensityHeader_mapc_get
561  if _newclass:mapc = _swig_property(_IMP_em.DensityHeader_mapc_get, _IMP_em.DensityHeader_mapc_set)
562  __swig_setmethods__["mapr"] = _IMP_em.DensityHeader_mapr_set
563  __swig_getmethods__["mapr"] = _IMP_em.DensityHeader_mapr_get
564  if _newclass:mapr = _swig_property(_IMP_em.DensityHeader_mapr_get, _IMP_em.DensityHeader_mapr_set)
565  __swig_setmethods__["maps"] = _IMP_em.DensityHeader_maps_set
566  __swig_getmethods__["maps"] = _IMP_em.DensityHeader_maps_get
567  if _newclass:maps = _swig_property(_IMP_em.DensityHeader_maps_get, _IMP_em.DensityHeader_maps_set)
568  __swig_setmethods__["dmin"] = _IMP_em.DensityHeader_dmin_set
569  __swig_getmethods__["dmin"] = _IMP_em.DensityHeader_dmin_get
570  if _newclass:dmin = _swig_property(_IMP_em.DensityHeader_dmin_get, _IMP_em.DensityHeader_dmin_set)
571  __swig_setmethods__["dmax"] = _IMP_em.DensityHeader_dmax_set
572  __swig_getmethods__["dmax"] = _IMP_em.DensityHeader_dmax_get
573  if _newclass:dmax = _swig_property(_IMP_em.DensityHeader_dmax_get, _IMP_em.DensityHeader_dmax_set)
574  __swig_setmethods__["dmean"] = _IMP_em.DensityHeader_dmean_set
575  __swig_getmethods__["dmean"] = _IMP_em.DensityHeader_dmean_get
576  if _newclass:dmean = _swig_property(_IMP_em.DensityHeader_dmean_get, _IMP_em.DensityHeader_dmean_set)
577  __swig_setmethods__["ispg"] = _IMP_em.DensityHeader_ispg_set
578  __swig_getmethods__["ispg"] = _IMP_em.DensityHeader_ispg_get
579  if _newclass:ispg = _swig_property(_IMP_em.DensityHeader_ispg_get, _IMP_em.DensityHeader_ispg_set)
580  __swig_setmethods__["nsymbt"] = _IMP_em.DensityHeader_nsymbt_set
581  __swig_getmethods__["nsymbt"] = _IMP_em.DensityHeader_nsymbt_get
582  if _newclass:nsymbt = _swig_property(_IMP_em.DensityHeader_nsymbt_get, _IMP_em.DensityHeader_nsymbt_set)
583  __swig_setmethods__["user"] = _IMP_em.DensityHeader_user_set
584  __swig_getmethods__["user"] = _IMP_em.DensityHeader_user_get
585  if _newclass:user = _swig_property(_IMP_em.DensityHeader_user_get, _IMP_em.DensityHeader_user_set)
586  __swig_setmethods__["map"] = _IMP_em.DensityHeader_map_set
587  __swig_getmethods__["map"] = _IMP_em.DensityHeader_map_get
588  if _newclass:map = _swig_property(_IMP_em.DensityHeader_map_get, _IMP_em.DensityHeader_map_set)
589  __swig_setmethods__["machinestamp"] = _IMP_em.DensityHeader_machinestamp_set
590  __swig_getmethods__["machinestamp"] = _IMP_em.DensityHeader_machinestamp_get
591  if _newclass:machinestamp = _swig_property(_IMP_em.DensityHeader_machinestamp_get, _IMP_em.DensityHeader_machinestamp_set)
592  __swig_setmethods__["rms"] = _IMP_em.DensityHeader_rms_set
593  __swig_getmethods__["rms"] = _IMP_em.DensityHeader_rms_get
594  if _newclass:rms = _swig_property(_IMP_em.DensityHeader_rms_get, _IMP_em.DensityHeader_rms_set)
595  __swig_setmethods__["nlabl"] = _IMP_em.DensityHeader_nlabl_set
596  __swig_getmethods__["nlabl"] = _IMP_em.DensityHeader_nlabl_get
597  if _newclass:nlabl = _swig_property(_IMP_em.DensityHeader_nlabl_get, _IMP_em.DensityHeader_nlabl_set)
598  __swig_setmethods__["comments"] = _IMP_em.DensityHeader_comments_set
599  __swig_getmethods__["comments"] = _IMP_em.DensityHeader_comments_get
600  if _newclass:comments = _swig_property(_IMP_em.DensityHeader_comments_get, _IMP_em.DensityHeader_comments_set)
601  __swig_setmethods__["magic"] = _IMP_em.DensityHeader_magic_set
602  __swig_getmethods__["magic"] = _IMP_em.DensityHeader_magic_get
603  if _newclass:magic = _swig_property(_IMP_em.DensityHeader_magic_get, _IMP_em.DensityHeader_magic_set)
604  __swig_setmethods__["voltage"] = _IMP_em.DensityHeader_voltage_set
605  __swig_getmethods__["voltage"] = _IMP_em.DensityHeader_voltage_get
606  if _newclass:voltage = _swig_property(_IMP_em.DensityHeader_voltage_get, _IMP_em.DensityHeader_voltage_set)
607  __swig_setmethods__["Cs"] = _IMP_em.DensityHeader_Cs_set
608  __swig_getmethods__["Cs"] = _IMP_em.DensityHeader_Cs_get
609  if _newclass:Cs = _swig_property(_IMP_em.DensityHeader_Cs_get, _IMP_em.DensityHeader_Cs_set)
610  __swig_setmethods__["Aperture"] = _IMP_em.DensityHeader_Aperture_set
611  __swig_getmethods__["Aperture"] = _IMP_em.DensityHeader_Aperture_get
612  if _newclass:Aperture = _swig_property(_IMP_em.DensityHeader_Aperture_get, _IMP_em.DensityHeader_Aperture_set)
613  __swig_setmethods__["Magnification"] = _IMP_em.DensityHeader_Magnification_set
614  __swig_getmethods__["Magnification"] = _IMP_em.DensityHeader_Magnification_get
615  if _newclass:Magnification = _swig_property(_IMP_em.DensityHeader_Magnification_get, _IMP_em.DensityHeader_Magnification_set)
616  __swig_setmethods__["Postmagnification"] = _IMP_em.DensityHeader_Postmagnification_set
617  __swig_getmethods__["Postmagnification"] = _IMP_em.DensityHeader_Postmagnification_get
618  if _newclass:Postmagnification = _swig_property(_IMP_em.DensityHeader_Postmagnification_get, _IMP_em.DensityHeader_Postmagnification_set)
619  __swig_setmethods__["Exposuretime"] = _IMP_em.DensityHeader_Exposuretime_set
620  __swig_getmethods__["Exposuretime"] = _IMP_em.DensityHeader_Exposuretime_get
621  if _newclass:Exposuretime = _swig_property(_IMP_em.DensityHeader_Exposuretime_get, _IMP_em.DensityHeader_Exposuretime_set)
622  __swig_setmethods__["Microscope"] = _IMP_em.DensityHeader_Microscope_set
623  __swig_getmethods__["Microscope"] = _IMP_em.DensityHeader_Microscope_get
624  if _newclass:Microscope = _swig_property(_IMP_em.DensityHeader_Microscope_get, _IMP_em.DensityHeader_Microscope_set)
625  __swig_setmethods__["Pixelsize"] = _IMP_em.DensityHeader_Pixelsize_set
626  __swig_getmethods__["Pixelsize"] = _IMP_em.DensityHeader_Pixelsize_get
627  if _newclass:Pixelsize = _swig_property(_IMP_em.DensityHeader_Pixelsize_get, _IMP_em.DensityHeader_Pixelsize_set)
628  __swig_setmethods__["CCDArea"] = _IMP_em.DensityHeader_CCDArea_set
629  __swig_getmethods__["CCDArea"] = _IMP_em.DensityHeader_CCDArea_get
630  if _newclass:CCDArea = _swig_property(_IMP_em.DensityHeader_CCDArea_get, _IMP_em.DensityHeader_CCDArea_set)
631  __swig_setmethods__["Defocus"] = _IMP_em.DensityHeader_Defocus_set
632  __swig_getmethods__["Defocus"] = _IMP_em.DensityHeader_Defocus_get
633  if _newclass:Defocus = _swig_property(_IMP_em.DensityHeader_Defocus_get, _IMP_em.DensityHeader_Defocus_set)
634  __swig_setmethods__["Astigmatism"] = _IMP_em.DensityHeader_Astigmatism_set
635  __swig_getmethods__["Astigmatism"] = _IMP_em.DensityHeader_Astigmatism_get
636  if _newclass:Astigmatism = _swig_property(_IMP_em.DensityHeader_Astigmatism_get, _IMP_em.DensityHeader_Astigmatism_set)
637  __swig_setmethods__["AstigmatismAngle"] = _IMP_em.DensityHeader_AstigmatismAngle_set
638  __swig_getmethods__["AstigmatismAngle"] = _IMP_em.DensityHeader_AstigmatismAngle_get
639  if _newclass:AstigmatismAngle = _swig_property(_IMP_em.DensityHeader_AstigmatismAngle_get, _IMP_em.DensityHeader_AstigmatismAngle_set)
640  __swig_setmethods__["FocusIncrement"] = _IMP_em.DensityHeader_FocusIncrement_set
641  __swig_getmethods__["FocusIncrement"] = _IMP_em.DensityHeader_FocusIncrement_get
642  if _newclass:FocusIncrement = _swig_property(_IMP_em.DensityHeader_FocusIncrement_get, _IMP_em.DensityHeader_FocusIncrement_set)
643  __swig_setmethods__["CountsPerElectron"] = _IMP_em.DensityHeader_CountsPerElectron_set
644  __swig_getmethods__["CountsPerElectron"] = _IMP_em.DensityHeader_CountsPerElectron_get
645  if _newclass:CountsPerElectron = _swig_property(_IMP_em.DensityHeader_CountsPerElectron_get, _IMP_em.DensityHeader_CountsPerElectron_set)
646  __swig_setmethods__["Intensity"] = _IMP_em.DensityHeader_Intensity_set
647  __swig_getmethods__["Intensity"] = _IMP_em.DensityHeader_Intensity_get
648  if _newclass:Intensity = _swig_property(_IMP_em.DensityHeader_Intensity_get, _IMP_em.DensityHeader_Intensity_set)
649  __swig_setmethods__["EnergySlitwidth"] = _IMP_em.DensityHeader_EnergySlitwidth_set
650  __swig_getmethods__["EnergySlitwidth"] = _IMP_em.DensityHeader_EnergySlitwidth_get
651  if _newclass:EnergySlitwidth = _swig_property(_IMP_em.DensityHeader_EnergySlitwidth_get, _IMP_em.DensityHeader_EnergySlitwidth_set)
652  __swig_setmethods__["EnergyOffset"] = _IMP_em.DensityHeader_EnergyOffset_set
653  __swig_getmethods__["EnergyOffset"] = _IMP_em.DensityHeader_EnergyOffset_get
654  if _newclass:EnergyOffset = _swig_property(_IMP_em.DensityHeader_EnergyOffset_get, _IMP_em.DensityHeader_EnergyOffset_set)
655  __swig_setmethods__["Tiltangle"] = _IMP_em.DensityHeader_Tiltangle_set
656  __swig_getmethods__["Tiltangle"] = _IMP_em.DensityHeader_Tiltangle_get
657  if _newclass:Tiltangle = _swig_property(_IMP_em.DensityHeader_Tiltangle_get, _IMP_em.DensityHeader_Tiltangle_set)
658  __swig_setmethods__["Tiltaxis"] = _IMP_em.DensityHeader_Tiltaxis_set
659  __swig_getmethods__["Tiltaxis"] = _IMP_em.DensityHeader_Tiltaxis_get
660  if _newclass:Tiltaxis = _swig_property(_IMP_em.DensityHeader_Tiltaxis_get, _IMP_em.DensityHeader_Tiltaxis_set)
661  __swig_setmethods__["MarkerX"] = _IMP_em.DensityHeader_MarkerX_set
662  __swig_getmethods__["MarkerX"] = _IMP_em.DensityHeader_MarkerX_get
663  if _newclass:MarkerX = _swig_property(_IMP_em.DensityHeader_MarkerX_get, _IMP_em.DensityHeader_MarkerX_set)
664  __swig_setmethods__["MarkerY"] = _IMP_em.DensityHeader_MarkerY_set
665  __swig_getmethods__["MarkerY"] = _IMP_em.DensityHeader_MarkerY_get
666  if _newclass:MarkerY = _swig_property(_IMP_em.DensityHeader_MarkerY_get, _IMP_em.DensityHeader_MarkerY_set)
667  __swig_setmethods__["lswap"] = _IMP_em.DensityHeader_lswap_set
668  __swig_getmethods__["lswap"] = _IMP_em.DensityHeader_lswap_get
669  if _newclass:lswap = _swig_property(_IMP_em.DensityHeader_lswap_get, _IMP_em.DensityHeader_lswap_set)
670  def get_resolution(self):
671  """get_resolution(DensityHeader self) -> float"""
672  return _IMP_em.DensityHeader_get_resolution(self)
673 
674  def get_has_resolution(self):
675  """get_has_resolution(DensityHeader self) -> bool"""
676  return _IMP_em.DensityHeader_get_has_resolution(self)
677 
678  def set_resolution(self, *args):
679  """set_resolution(DensityHeader self, float resolution)"""
680  return _IMP_em.DensityHeader_set_resolution(self, *args)
681 
682  def get_spacing(self):
683  """get_spacing(DensityHeader self) -> float"""
684  return _IMP_em.DensityHeader_get_spacing(self)
685 
686  def get_xorigin(self):
687  """get_xorigin(DensityHeader self) -> float"""
688  return _IMP_em.DensityHeader_get_xorigin(self)
689 
690  def get_yorigin(self):
691  """get_yorigin(DensityHeader self) -> float"""
692  return _IMP_em.DensityHeader_get_yorigin(self)
693 
694  def get_zorigin(self):
695  """get_zorigin(DensityHeader self) -> float"""
696  return _IMP_em.DensityHeader_get_zorigin(self)
697 
698  def get_origin(self, *args):
699  """get_origin(DensityHeader self, int i) -> float"""
700  return _IMP_em.DensityHeader_get_origin(self, *args)
701 
702  def set_xorigin(self, *args):
703  """set_xorigin(DensityHeader self, float x)"""
704  return _IMP_em.DensityHeader_set_xorigin(self, *args)
705 
706  def set_yorigin(self, *args):
707  """set_yorigin(DensityHeader self, float y)"""
708  return _IMP_em.DensityHeader_set_yorigin(self, *args)
709 
710  def set_zorigin(self, *args):
711  """set_zorigin(DensityHeader self, float z)"""
712  return _IMP_em.DensityHeader_set_zorigin(self, *args)
713 
714  def is_top_calculated(self):
715  """is_top_calculated(DensityHeader self) -> bool"""
716  return _IMP_em.DensityHeader_is_top_calculated(self)
717 
718  __swig_setmethods__["Objectpixelsize_"] = _IMP_em.DensityHeader_Objectpixelsize__set
719  __swig_getmethods__["Objectpixelsize_"] = _IMP_em.DensityHeader_Objectpixelsize__get
720  if _newclass:Objectpixelsize_ = _swig_property(_IMP_em.DensityHeader_Objectpixelsize__get, _IMP_em.DensityHeader_Objectpixelsize__set)
721  def get_nx(self):
722  """get_nx(DensityHeader self) -> int"""
723  return _IMP_em.DensityHeader_get_nx(self)
724 
725  def get_ny(self):
726  """get_ny(DensityHeader self) -> int"""
727  return _IMP_em.DensityHeader_get_ny(self)
728 
729  def get_nz(self):
730  """get_nz(DensityHeader self) -> int"""
731  return _IMP_em.DensityHeader_get_nz(self)
732 
733  def get_number_of_voxels(self):
734  """get_number_of_voxels(DensityHeader self) -> int"""
735  return _IMP_em.DensityHeader_get_number_of_voxels(self)
736 
737  def get_data_type(self):
738  """get_data_type(DensityHeader self) -> int"""
739  return _IMP_em.DensityHeader_get_data_type(self)
740 
741  def set_data_type(self, *args):
742  """set_data_type(DensityHeader self, int data_type)"""
743  return _IMP_em.DensityHeader_set_data_type(self, *args)
744 
745  __swig_destroy__ = _IMP_em.delete_DensityHeader
746  __del__ = lambda self : None;
747 DensityHeader_swigregister = _IMP_em.DensityHeader_swigregister
748 DensityHeader_swigregister(DensityHeader)
749 
750 
751 def create_density_header(*args):
752  """create_density_header(BoundingBox3D bb, float spacing) -> DensityHeader"""
753  return _IMP_em.create_density_header(*args)
754 
755 def read_map(*args):
756  """
757  read_map(std::string filename, MapReaderWriter reader) -> DensityMap
758  read_map(std::string filename) -> DensityMap
759  """
760  return _IMP_em.read_map(*args)
761 
762 def write_map(*args):
763  """
764  write_map(DensityMap m, std::string filename, MapReaderWriter writer)
765  write_map(DensityMap m, std::string filename)
766  """
767  return _IMP_em.write_map(*args)
768 
769 def approximate_molecular_mass(*args):
770  """approximate_molecular_mass(DensityMap m, IMP::Float threshold) -> IMP::Float"""
771  return _IMP_em.approximate_molecular_mass(*args)
772 class DensityMap(IMP.base.Object):
773  """Proxy of C++ IMP::em::DensityMap class"""
774  __swig_setmethods__ = {}
775  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
776  __setattr__ = lambda self, name, value: _swig_setattr(self, DensityMap, name, value)
777  __swig_getmethods__ = {}
778  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
779  __getattr__ = lambda self, name: _swig_getattr(self, DensityMap, name)
780  def __init__(self, *args):
781  """
782  __init__(IMP::em::DensityMap self, std::string name="DensityMap%1%") -> DensityMap
783  __init__(IMP::em::DensityMap self) -> DensityMap
784  __init__(IMP::em::DensityMap self, DensityHeader header, std::string name="DensityMap%1%") -> DensityMap
785  __init__(IMP::em::DensityMap self, DensityHeader header) -> DensityMap
786  """
787  this = _IMP_em.new_DensityMap(*args)
788  try: self.this.append(this)
789  except: self.this = this
790  def release(self):
791  """release(DensityMap self)"""
792  return _IMP_em.DensityMap_release(self)
793 
794  def reset_data(self, value=0.0):
795  """
796  reset_data(DensityMap self, float value=0.0)
797  reset_data(DensityMap self)
798  """
799  return _IMP_em.DensityMap_reset_data(self, value)
800 
801  def calcRMS(self):
802  """calcRMS(DensityMap self) -> IMP::em::emreal"""
803  return _IMP_em.DensityMap_calcRMS(self)
804 
805  def std_normalize(self):
806  """std_normalize(DensityMap self)"""
807  return _IMP_em.DensityMap_std_normalize(self)
808 
809  def is_normalized(self):
810  """is_normalized(DensityMap self) -> bool"""
811  return _IMP_em.DensityMap_is_normalized(self)
812 
813  def get_location_in_dim_by_voxel(self, *args):
814  """get_location_in_dim_by_voxel(DensityMap self, long index, int dim) -> float"""
815  return _IMP_em.DensityMap_get_location_in_dim_by_voxel(self, *args)
816 
817  def xyz_ind2voxel(self, *args):
818  """xyz_ind2voxel(DensityMap self, int x, int y, int z) -> long"""
819  return _IMP_em.DensityMap_xyz_ind2voxel(self, *args)
820 
821  def get_voxel_by_location(self, *args):
822  """
823  get_voxel_by_location(DensityMap self, float x, float y, float z) -> long
824  get_voxel_by_location(DensityMap self, Vector3D v) -> long
825  """
826  return _IMP_em.DensityMap_get_voxel_by_location(self, *args)
827 
828  def get_location_by_voxel(self, *args):
829  """get_location_by_voxel(DensityMap self, long index) -> Vector3D"""
830  return _IMP_em.DensityMap_get_location_by_voxel(self, *args)
831 
832  def is_xyz_ind_part_of_volume(self, *args):
833  """is_xyz_ind_part_of_volume(DensityMap self, int ix, int iy, int iz) -> bool"""
834  return _IMP_em.DensityMap_is_xyz_ind_part_of_volume(self, *args)
835 
836  def is_part_of_volume(self, *args):
837  """
838  is_part_of_volume(DensityMap self, float x, float y, float z) -> bool
839  is_part_of_volume(DensityMap self, Vector3D v) -> bool
840  """
841  return _IMP_em.DensityMap_is_part_of_volume(self, *args)
842 
843  def get_value(self, *args):
844  """
845  get_value(DensityMap self, float x, float y, float z) -> IMP::em::emreal
846  get_value(DensityMap self, Vector3D point) -> IMP::em::emreal
847  get_value(DensityMap self, long index) -> IMP::em::emreal
848  """
849  return _IMP_em.DensityMap_get_value(self, *args)
850 
851  def set_value(self, *args):
852  """
853  set_value(DensityMap self, long index, IMP::em::emreal value)
854  set_value(DensityMap self, float x, float y, float z, IMP::em::emreal value)
855  """
856  return _IMP_em.DensityMap_set_value(self, *args)
857 
858  def set_origin(self, *args):
859  """
860  set_origin(DensityMap self, float x, float y, float z)
861  set_origin(DensityMap self, Vector3D v)
862  """
863  return _IMP_em.DensityMap_set_origin(self, *args)
864 
865  def get_origin(self):
866  """get_origin(DensityMap self) -> Vector3D"""
867  return _IMP_em.DensityMap_get_origin(self)
868 
869  def get_top(self):
870  """get_top(DensityMap self) -> Vector3D"""
871  return _IMP_em.DensityMap_get_top(self)
872 
873  def get_header(self):
874  h = _IMP_em.DensityMap_get_header(self)
875  h._owner = self
876  return h
877 
878 
879  def get_header_writable(self):
880  h = _IMP_em.DensityMap_get_header_writable(self)
881  h._owner = self
882  return h
883 
884 
885  def same_origin(self, *args):
886  """same_origin(DensityMap self, DensityMap other) -> bool"""
887  return _IMP_em.DensityMap_same_origin(self, *args)
888 
889  def same_dimensions(self, *args):
890  """same_dimensions(DensityMap self, DensityMap other) -> bool"""
891  return _IMP_em.DensityMap_same_dimensions(self, *args)
892 
893  def same_voxel_size(self, *args):
894  """same_voxel_size(DensityMap self, DensityMap other) -> bool"""
895  return _IMP_em.DensityMap_same_voxel_size(self, *args)
896 
897  def get_centroid(self, threshold=0.0):
898  """
899  get_centroid(DensityMap self, IMP::em::emreal threshold=0.0) -> Vector3D
900  get_centroid(DensityMap self) -> Vector3D
901  """
902  return _IMP_em.DensityMap_get_centroid(self, threshold)
903 
904  def get_max_value(self):
905  """get_max_value(DensityMap self) -> IMP::em::emreal"""
906  return _IMP_em.DensityMap_get_max_value(self)
907 
908  def get_min_value(self):
909  """get_min_value(DensityMap self) -> IMP::em::emreal"""
910  return _IMP_em.DensityMap_get_min_value(self)
911 
912  def add(self, *args):
913  """add(DensityMap self, DensityMap other)"""
914  return _IMP_em.DensityMap_add(self, *args)
915 
916  def pick_max(self, *args):
917  """pick_max(DensityMap self, DensityMap other)"""
918  return _IMP_em.DensityMap_pick_max(self, *args)
919 
920  def get_number_of_voxels(self):
921  """get_number_of_voxels(DensityMap self) -> long"""
922  return _IMP_em.DensityMap_get_number_of_voxels(self)
923 
924  def set_void_map(self, *args):
925  """set_void_map(DensityMap self, int nx, int ny, int nz)"""
926  return _IMP_em.DensityMap_set_void_map(self, *args)
927 
928  def pad(self, *args):
929  """
930  pad(DensityMap self, int nx, int ny, int nz, float val=0.0)
931  pad(DensityMap self, int nx, int ny, int nz)
932  """
933  return _IMP_em.DensityMap_pad(self, *args)
934 
935  def pad_margin(self, *args):
936  """
937  pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z, float val=0.0) -> DensityMap
938  pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z) -> DensityMap
939  """
940  return _IMP_em.DensityMap_pad_margin(self, *args)
941 
942  def get_cropped(self, *args):
943  """
944  get_cropped(DensityMap self, float threshold) -> DensityMap
945  get_cropped(DensityMap self, BoundingBox3D bb) -> DensityMap
946  """
947  return _IMP_em.DensityMap_get_cropped(self, *args)
948 
949  def get_maximum_value_in_xy_plane(self, *args):
950  """get_maximum_value_in_xy_plane(DensityMap self, int z_ind) -> float"""
951  return _IMP_em.DensityMap_get_maximum_value_in_xy_plane(self, *args)
952 
953  def get_maximum_value_in_xz_plane(self, *args):
954  """get_maximum_value_in_xz_plane(DensityMap self, int y_ind) -> float"""
955  return _IMP_em.DensityMap_get_maximum_value_in_xz_plane(self, *args)
956 
957  def get_maximum_value_in_yz_plane(self, *args):
958  """get_maximum_value_in_yz_plane(DensityMap self, int x_ind) -> float"""
959  return _IMP_em.DensityMap_get_maximum_value_in_yz_plane(self, *args)
960 
961  def multiply(self, *args):
962  """multiply(DensityMap self, float factor)"""
963  return _IMP_em.DensityMap_multiply(self, *args)
964 
965  def get_locations_string(self, *args):
966  """get_locations_string(DensityMap self, float t) -> std::string"""
967  return _IMP_em.DensityMap_get_locations_string(self, *args)
968 
969  def update_voxel_size(self, *args):
970  """update_voxel_size(DensityMap self, float new_apix)"""
971  return _IMP_em.DensityMap_update_voxel_size(self, *args)
972 
973  def get_spacing(self):
974  """get_spacing(DensityMap self) -> IMP::Float"""
975  return _IMP_em.DensityMap_get_spacing(self)
976 
977  def calc_all_voxel2loc(self):
978  """calc_all_voxel2loc(DensityMap self)"""
979  return _IMP_em.DensityMap_calc_all_voxel2loc(self)
980 
981  def copy_map(self, *args):
982  """copy_map(DensityMap self, DensityMap other)"""
983  return _IMP_em.DensityMap_copy_map(self, *args)
984 
985  def get_version_info(self):
986  """get_version_info(DensityMap self) -> VersionInfo"""
987  return _IMP_em.DensityMap_get_version_info(self)
988 
989  __swig_destroy__ = _IMP_em.delete_DensityMap
990  __del__ = lambda self : None;
991  def lower_voxel_shift(self, *args):
992  """lower_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
993  return _IMP_em.DensityMap_lower_voxel_shift(self, *args)
994 
995  def upper_voxel_shift(self, *args):
996  """upper_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
997  return _IMP_em.DensityMap_upper_voxel_shift(self, *args)
998 
999  def get_rms_calculated(self):
1000  """get_rms_calculated(DensityMap self) -> bool"""
1001  return _IMP_em.DensityMap_get_rms_calculated(self)
1002 
1003  def get_dim_index_by_location(self, *args):
1004  """
1005  get_dim_index_by_location(DensityMap self, Vector3D v, int ind) -> int
1006  get_dim_index_by_location(DensityMap self, float loc_val, int ind) -> int
1007  """
1008  return _IMP_em.DensityMap_get_dim_index_by_location(self, *args)
1009 
1010  def __str__(self):
1011  """__str__(DensityMap self) -> std::string"""
1012  return _IMP_em.DensityMap___str__(self)
1013 
1014  def __repr__(self):
1015  """__repr__(DensityMap self) -> std::string"""
1016  return _IMP_em.DensityMap___repr__(self)
1017 
1018  def get_from(o):
1019  return _object_cast_to_DensityMap(o)
1020  get_from = staticmethod(get_from)
1021 
1022 DensityMap_swigregister = _IMP_em.DensityMap_swigregister
1023 DensityMap_swigregister(DensityMap)
1024 
1025 
1026 def get_bounding_box(*args):
1027  """
1028  get_bounding_box(DensityMap m, IMP::Float threshold) -> BoundingBox3D
1029  get_bounding_box(DensityMap m) -> BoundingBox3D
1030  """
1031  return _IMP_em.get_bounding_box(*args)
1032 
1033 def get_density(*args):
1034  """get_density(DensityMap m, Vector3D v) -> double"""
1035  return _IMP_em.get_density(*args)
1036 
1037 def get_transformed(*args):
1038  """
1039  get_transformed(DensityMap input, Transformation3D tr, double threshold) -> DensityMap
1040  get_transformed(DensityMap input, Transformation3D tr) -> DensityMap
1041  """
1042  return _IMP_em.get_transformed(*args)
1043 
1044 def get_resampled(*args):
1045  """get_resampled(DensityMap input, double scaling) -> DensityMap"""
1046  return _IMP_em.get_resampled(*args)
1047 
1048 def get_transformed_into(*args):
1049  """
1050  get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into, bool calc_rms=True)
1051  get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into)
1052  """
1053  return _IMP_em.get_transformed_into(*args)
1054 
1055 def get_transformed_into2(*args):
1056  """get_transformed_into2(DensityMap source, Transformation3D tr, DensityMap into)"""
1057  return _IMP_em.get_transformed_into2(*args)
1058 
1059 def get_interiors_intersect(*args):
1060  """get_interiors_intersect(DensityMap d1, DensityMap d2) -> bool"""
1061  return _IMP_em.get_interiors_intersect(*args)
1062 
1063 def get_segment(*args):
1064  """
1065  get_segment(DensityMap map_to_segment, int nx_start, int nx_end, int ny_start, int ny_end, int nz_start,
1066  int nz_end) -> DensityMap
1067  get_segment(DensityMap map_to_segment, IMP::algebra::Vector3Ds vecs, float dist) -> DensityMap
1068  """
1069  return _IMP_em.get_segment(*args)
1070 
1071 def get_segment_by_masking(*args):
1072  """get_segment_by_masking(DensityMap map_to_segment, DensityMap mask, float mas_threshold) -> DensityMap"""
1073  return _IMP_em.get_segment_by_masking(*args)
1074 
1075 def binarize(*args):
1076  """
1077  binarize(DensityMap orig_map, float threshold, bool reverse=False) -> DensityMap
1078  binarize(DensityMap orig_map, float threshold) -> DensityMap
1079  """
1080  return _IMP_em.binarize(*args)
1081 
1082 def get_threshold_map(*args):
1083  """get_threshold_map(DensityMap orig_map, float threshold) -> DensityMap"""
1084  return _IMP_em.get_threshold_map(*args)
1085 
1086 def multiply(*args):
1087  """multiply(DensityMap m1, DensityMap m2) -> DensityMap"""
1088  return _IMP_em.multiply(*args)
1089 
1090 def convolute(*args):
1091  """convolute(DensityMap m1, DensityMap m2) -> double"""
1092  return _IMP_em.convolute(*args)
1093 
1094 def get_sum(*args):
1095  """get_sum(DensityMap m1) -> double"""
1096  return _IMP_em.get_sum(*args)
1097 
1098 def get_max_map(*args):
1099  """get_max_map(IMP::em::DensityMaps maps) -> DensityMap"""
1100  return _IMP_em.get_max_map(*args)
1101 
1102 def interpolate_map(*args):
1103  """interpolate_map(DensityMap in_map, double new_spacing) -> DensityMap"""
1104  return _IMP_em.interpolate_map(*args)
1105 
1106 def get_grid(*args):
1107  """get_grid(DensityMap in_map) -> DenseFloatGrid3D"""
1108  return _IMP_em.get_grid(*args)
1109 
1110 def create_density_map(*args):
1111  """
1112  create_density_map(DensityMap other) -> DensityMap
1113  create_density_map(BoundingBox3D bb, double spacing) -> DensityMap
1114  create_density_map(int nx, int ny, int nz, double spacing) -> DensityMap
1115  create_density_map(DenseFloatGrid3D grid) -> DensityMap
1116  """
1117  return _IMP_em.create_density_map(*args)
1118 
1119 def get_binarized_interior(*args):
1120  """get_binarized_interior(DensityMap dmap) -> DensityMap"""
1121  return _IMP_em.get_binarized_interior(*args)
1122 class RadiusDependentDistanceMask(_object):
1123  """Proxy of C++ IMP::em::RadiusDependentDistanceMask class"""
1124  __swig_setmethods__ = {}
1125  __setattr__ = lambda self, name, value: _swig_setattr(self, RadiusDependentDistanceMask, name, value)
1126  __swig_getmethods__ = {}
1127  __getattr__ = lambda self, name: _swig_getattr(self, RadiusDependentDistanceMask, name)
1128  __repr__ = _swig_repr
1129  def __init__(self, *args):
1130  """__init__(IMP::em::RadiusDependentDistanceMask self, float sampling_radius, DensityHeader header) -> RadiusDependentDistanceMask"""
1131  this = _IMP_em.new_RadiusDependentDistanceMask(*args)
1132  try: self.this.append(this)
1133  except: self.this = this
1134  def get_neighbor_shift(self):
1135  """get_neighbor_shift(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1136  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_shift(self)
1137 
1138  def get_neighbor_dist(self):
1139  """get_neighbor_dist(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1140  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist(self)
1141 
1142  def get_neighbor_dist_exp(self):
1143  """get_neighbor_dist_exp(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1144  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist_exp(self)
1145 
1146  def show(self, *args):
1147  """show(RadiusDependentDistanceMask self, _ostream out)"""
1148  return _IMP_em.RadiusDependentDistanceMask_show(self, *args)
1149 
1150  __swig_destroy__ = _IMP_em.delete_RadiusDependentDistanceMask
1151  __del__ = lambda self : None;
1152 RadiusDependentDistanceMask_swigregister = _IMP_em.RadiusDependentDistanceMask_swigregister
1153 RadiusDependentDistanceMask_swigregister(RadiusDependentDistanceMask)
1154 
1155 class DistanceMask(_object):
1156  """Proxy of C++ IMP::em::DistanceMask class"""
1157  __swig_setmethods__ = {}
1158  __setattr__ = lambda self, name, value: _swig_setattr(self, DistanceMask, name, value)
1159  __swig_getmethods__ = {}
1160  __getattr__ = lambda self, name: _swig_getattr(self, DistanceMask, name)
1161  __repr__ = _swig_repr
1162  def __init__(self, *args):
1163  """
1164  __init__(IMP::em::DistanceMask self) -> DistanceMask
1165  __init__(IMP::em::DistanceMask self, DensityHeader header) -> DistanceMask
1166  """
1167  this = _IMP_em.new_DistanceMask(*args)
1168  try: self.this.append(this)
1169  except: self.this = this
1170  def show(self, *args):
1171  """show(DistanceMask self, _ostream out)"""
1172  return _IMP_em.DistanceMask_show(self, *args)
1173 
1174  def is_mask_set(self, *args):
1175  """
1176  is_mask_set(DistanceMask self, float radius, float eps=0.001) -> bool
1177  is_mask_set(DistanceMask self, float radius) -> bool
1178  """
1179  return _IMP_em.DistanceMask_is_mask_set(self, *args)
1180 
1181  __swig_destroy__ = _IMP_em.delete_DistanceMask
1182  __del__ = lambda self : None;
1183 DistanceMask_swigregister = _IMP_em.DistanceMask_swigregister
1184 DistanceMask_swigregister(DistanceMask)
1185 
1186 class EMReaderWriter(MapReaderWriter):
1187  """Proxy of C++ IMP::em::EMReaderWriter class"""
1188  __swig_setmethods__ = {}
1189  for _s in [MapReaderWriter]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1190  __setattr__ = lambda self, name, value: _swig_setattr(self, EMReaderWriter, name, value)
1191  __swig_getmethods__ = {}
1192  for _s in [MapReaderWriter]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1193  __getattr__ = lambda self, name: _swig_getattr(self, EMReaderWriter, name)
1194  __swig_destroy__ = _IMP_em.delete_EMReaderWriter
1195  __del__ = lambda self : None;
1196  def __str__(self):
1197  """__str__(EMReaderWriter self) -> std::string"""
1198  return _IMP_em.EMReaderWriter___str__(self)
1199 
1200  def __repr__(self):
1201  """__repr__(EMReaderWriter self) -> std::string"""
1202  return _IMP_em.EMReaderWriter___repr__(self)
1203 
1204  def get_from(o):
1205  return _object_cast_to_EMReaderWriter(o)
1206  get_from = staticmethod(get_from)
1207 
1208  def __init__(self):
1209  """__init__(IMP::em::EMReaderWriter self) -> EMReaderWriter"""
1210  this = _IMP_em.new_EMReaderWriter()
1211  try: self.this.append(this)
1212  except: self.this = this
1213 EMReaderWriter_swigregister = _IMP_em.EMReaderWriter_swigregister
1214 EMReaderWriter_swigregister(EMReaderWriter)
1215 
1216 class XplorReaderWriter(MapReaderWriter):
1217  """Proxy of C++ IMP::em::XplorReaderWriter class"""
1218  __swig_setmethods__ = {}
1219  for _s in [MapReaderWriter]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1220  __setattr__ = lambda self, name, value: _swig_setattr(self, XplorReaderWriter, name, value)
1221  __swig_getmethods__ = {}
1222  for _s in [MapReaderWriter]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1223  __getattr__ = lambda self, name: _swig_getattr(self, XplorReaderWriter, name)
1224  __swig_destroy__ = _IMP_em.delete_XplorReaderWriter
1225  __del__ = lambda self : None;
1226  def __str__(self):
1227  """__str__(XplorReaderWriter self) -> std::string"""
1228  return _IMP_em.XplorReaderWriter___str__(self)
1229 
1230  def __repr__(self):
1231  """__repr__(XplorReaderWriter self) -> std::string"""
1232  return _IMP_em.XplorReaderWriter___repr__(self)
1233 
1234  def get_from(o):
1235  return _object_cast_to_XplorReaderWriter(o)
1236  get_from = staticmethod(get_from)
1237 
1238  def __init__(self):
1239  """__init__(IMP::em::XplorReaderWriter self) -> XplorReaderWriter"""
1240  this = _IMP_em.new_XplorReaderWriter()
1241  try: self.this.append(this)
1242  except: self.this = this
1243 XplorReaderWriter_swigregister = _IMP_em.XplorReaderWriter_swigregister
1244 XplorReaderWriter_swigregister(XplorReaderWriter)
1245 
1246 class MRCReaderWriter(MapReaderWriter):
1247  """Proxy of C++ IMP::em::MRCReaderWriter class"""
1248  __swig_setmethods__ = {}
1249  for _s in [MapReaderWriter]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1250  __setattr__ = lambda self, name, value: _swig_setattr(self, MRCReaderWriter, name, value)
1251  __swig_getmethods__ = {}
1252  for _s in [MapReaderWriter]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1253  __getattr__ = lambda self, name: _swig_getattr(self, MRCReaderWriter, name)
1254  def __init__(self, *args):
1255  """
1256  __init__(IMP::em::MRCReaderWriter self) -> MRCReaderWriter
1257  __init__(IMP::em::MRCReaderWriter self, std::string fn) -> MRCReaderWriter
1258  """
1259  this = _IMP_em.new_MRCReaderWriter(*args)
1260  try: self.this.append(this)
1261  except: self.this = this
1262  __swig_destroy__ = _IMP_em.delete_MRCReaderWriter
1263  __del__ = lambda self : None;
1264  def __str__(self):
1265  """__str__(MRCReaderWriter self) -> std::string"""
1266  return _IMP_em.MRCReaderWriter___str__(self)
1267 
1268  def __repr__(self):
1269  """__repr__(MRCReaderWriter self) -> std::string"""
1270  return _IMP_em.MRCReaderWriter___repr__(self)
1271 
1272  def get_from(o):
1273  return _object_cast_to_MRCReaderWriter(o)
1274  get_from = staticmethod(get_from)
1275 
1276 MRCReaderWriter_swigregister = _IMP_em.MRCReaderWriter_swigregister
1277 MRCReaderWriter_swigregister(MRCReaderWriter)
1278 
1279 class RadiusDependentKernelParameters(_object):
1280  """Proxy of C++ IMP::em::RadiusDependentKernelParameters class"""
1281  __swig_setmethods__ = {}
1282  __setattr__ = lambda self, name, value: _swig_setattr(self, RadiusDependentKernelParameters, name, value)
1283  __swig_getmethods__ = {}
1284  __getattr__ = lambda self, name: _swig_getattr(self, RadiusDependentKernelParameters, name)
1285  def __init__(self, *args):
1286  """
1287  __init__(IMP::em::RadiusDependentKernelParameters self, float radii, float rsigsq, float timessig, float sq2pi3, float inv_rsigsq, float rnormfac,
1288  float rkdist) -> RadiusDependentKernelParameters
1289  """
1290  this = _IMP_em.new_RadiusDependentKernelParameters(*args)
1291  try: self.this.append(this)
1292  except: self.this = this
1293  def show(self, *args):
1294  """
1295  show(RadiusDependentKernelParameters self, _ostream s=std::cout)
1296  show(RadiusDependentKernelParameters self)
1297  """
1298  return _IMP_em.RadiusDependentKernelParameters_show(self, *args)
1299 
1300  def get_vsig(self):
1301  """get_vsig(RadiusDependentKernelParameters self) -> float"""
1302  return _IMP_em.RadiusDependentKernelParameters_get_vsig(self)
1303 
1304  def get_vsigsq(self):
1305  """get_vsigsq(RadiusDependentKernelParameters self) -> float"""
1306  return _IMP_em.RadiusDependentKernelParameters_get_vsigsq(self)
1307 
1308  def get_inv_sigsq(self):
1309  """get_inv_sigsq(RadiusDependentKernelParameters self) -> float"""
1310  return _IMP_em.RadiusDependentKernelParameters_get_inv_sigsq(self)
1311 
1312  def get_sig(self):
1313  """get_sig(RadiusDependentKernelParameters self) -> float"""
1314  return _IMP_em.RadiusDependentKernelParameters_get_sig(self)
1315 
1316  def get_kdist(self):
1317  """get_kdist(RadiusDependentKernelParameters self) -> float"""
1318  return _IMP_em.RadiusDependentKernelParameters_get_kdist(self)
1319 
1320  def get_normfac(self):
1321  """get_normfac(RadiusDependentKernelParameters self) -> float"""
1322  return _IMP_em.RadiusDependentKernelParameters_get_normfac(self)
1323 
1324  __swig_destroy__ = _IMP_em.delete_RadiusDependentKernelParameters
1325  __del__ = lambda self : None;
1326  def __str__(self):
1327  """__str__(RadiusDependentKernelParameters self) -> std::string"""
1328  return _IMP_em.RadiusDependentKernelParameters___str__(self)
1329 
1330  def __repr__(self):
1331  """__repr__(RadiusDependentKernelParameters self) -> std::string"""
1332  return _IMP_em.RadiusDependentKernelParameters___repr__(self)
1333 
1334 RadiusDependentKernelParameters_swigregister = _IMP_em.RadiusDependentKernelParameters_swigregister
1335 RadiusDependentKernelParameters_swigregister(RadiusDependentKernelParameters)
1336 
1337 class KernelParameters(_object):
1338  """Proxy of C++ IMP::em::KernelParameters class"""
1339  __swig_setmethods__ = {}
1340  __setattr__ = lambda self, name, value: _swig_setattr(self, KernelParameters, name, value)
1341  __swig_getmethods__ = {}
1342  __getattr__ = lambda self, name: _swig_getattr(self, KernelParameters, name)
1343  def __init__(self, *args):
1344  """
1345  __init__(IMP::em::KernelParameters self) -> KernelParameters
1346  __init__(IMP::em::KernelParameters self, float resolution) -> KernelParameters
1347  """
1348  this = _IMP_em.new_KernelParameters(*args)
1349  try: self.this.append(this)
1350  except: self.this = this
1351  __swig_destroy__ = _IMP_em.delete_KernelParameters
1352  __del__ = lambda self : None;
1353  def set_params(self, *args):
1354  """set_params(KernelParameters self, float radius) -> RadiusDependentKernelParameters"""
1355  return _IMP_em.KernelParameters_set_params(self, *args)
1356 
1357  def get_params(self, *args):
1358  """
1359  get_params(KernelParameters self, float radius, float eps=0.001) -> RadiusDependentKernelParameters
1360  get_params(KernelParameters self, float radius) -> RadiusDependentKernelParameters
1361  """
1362  return _IMP_em.KernelParameters_get_params(self, *args)
1363 
1364  def get_rsig(self):
1365  """get_rsig(KernelParameters self) -> float"""
1366  return _IMP_em.KernelParameters_get_rsig(self)
1367 
1368  def get_rsigsq(self):
1369  """get_rsigsq(KernelParameters self) -> float"""
1370  return _IMP_em.KernelParameters_get_rsigsq(self)
1371 
1372  def get_inv_rsigsq(self):
1373  """get_inv_rsigsq(KernelParameters self) -> float"""
1374  return _IMP_em.KernelParameters_get_inv_rsigsq(self)
1375 
1376  def get_timessig(self):
1377  """get_timessig(KernelParameters self) -> float"""
1378  return _IMP_em.KernelParameters_get_timessig(self)
1379 
1380  def get_sq2pi3(self):
1381  """get_sq2pi3(KernelParameters self) -> float"""
1382  return _IMP_em.KernelParameters_get_sq2pi3(self)
1383 
1384  def get_rnormfac(self):
1385  """get_rnormfac(KernelParameters self) -> float"""
1386  return _IMP_em.KernelParameters_get_rnormfac(self)
1387 
1388  def get_rkdist(self):
1389  """get_rkdist(KernelParameters self) -> float"""
1390  return _IMP_em.KernelParameters_get_rkdist(self)
1391 
1392  def get_lim(self):
1393  """get_lim(KernelParameters self) -> float"""
1394  return _IMP_em.KernelParameters_get_lim(self)
1395 
1396  def show(self, *args):
1397  """
1398  show(KernelParameters self, _ostream out=std::cout)
1399  show(KernelParameters self)
1400  """
1401  return _IMP_em.KernelParameters_show(self, *args)
1402 
1403  def __str__(self):
1404  """__str__(KernelParameters self) -> std::string"""
1405  return _IMP_em.KernelParameters___str__(self)
1406 
1407  def __repr__(self):
1408  """__repr__(KernelParameters self) -> std::string"""
1409  return _IMP_em.KernelParameters___repr__(self)
1410 
1411 KernelParameters_swigregister = _IMP_em.KernelParameters_swigregister
1412 KernelParameters_swigregister(KernelParameters)
1413 
1414 GAUSSIAN = _IMP_em.GAUSSIAN
1415 BINARIZED_SPHERE = _IMP_em.BINARIZED_SPHERE
1416 SPHERE = _IMP_em.SPHERE
1417 class SampledDensityMap(DensityMap):
1418  """Proxy of C++ IMP::em::SampledDensityMap class"""
1419  __swig_setmethods__ = {}
1420  for _s in [DensityMap]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1421  __setattr__ = lambda self, name, value: _swig_setattr(self, SampledDensityMap, name, value)
1422  __swig_getmethods__ = {}
1423  for _s in [DensityMap]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1424  __getattr__ = lambda self, name: _swig_getattr(self, SampledDensityMap, name)
1425  def __init__(self, *args):
1426  """
1427  __init__(IMP::em::SampledDensityMap self, IMP::em::KernelType kt=GAUSSIAN) -> SampledDensityMap
1428  __init__(IMP::em::SampledDensityMap self) -> SampledDensityMap
1429  __init__(IMP::em::SampledDensityMap self, DensityHeader header, IMP::em::KernelType kt=GAUSSIAN) -> SampledDensityMap
1430  __init__(IMP::em::SampledDensityMap self, DensityHeader header) -> 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(), int sig_cuttoff=3,
1433  IMP::em::KernelType kt=GAUSSIAN) -> SampledDensityMap
1434  __init__(IMP::em::SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size,
1435  FloatKey mass_key=IMP::atom::Mass::get_mass_key(), int sig_cuttoff=3) -> SampledDensityMap
1436  __init__(IMP::em::SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size,
1437  FloatKey mass_key=IMP::atom::Mass::get_mass_key()) -> SampledDensityMap
1438  __init__(IMP::em::SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size) -> SampledDensityMap
1439  """
1440  this = _IMP_em.new_SampledDensityMap(*args)
1441  try: self.this.append(this)
1442  except: self.this = this
1443  def resample(self):
1444  """resample(SampledDensityMap self)"""
1445  return _IMP_em.SampledDensityMap_resample(self)
1446 
1447  def project(self, *args):
1448  """
1449  project(SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin,
1450  Vector3D shift=IMP::algebra::Vector3D(0.,0.,0.), FloatKey mass_key=IMP::atom::Mass::get_mass_key())
1451  project(SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin,
1452  Vector3D shift=IMP::algebra::Vector3D(0.,0.,0.))
1453  project(SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin)
1454  """
1455  return _IMP_em.SampledDensityMap_project(self, *args)
1456 
1457  def set_particles(self, *args):
1458  """
1459  set_particles(SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps, FloatKey mass_key=IMP::atom::Mass::get_mass_key())
1460  set_particles(SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps)
1461  """
1462  return _IMP_em.SampledDensityMap_set_particles(self, *args)
1463 
1464  def get_xyzr_particles(self):
1465  """get_xyzr_particles(SampledDensityMap self) -> IMP::core::XYZRs const &"""
1466  return _IMP_em.SampledDensityMap_get_xyzr_particles(self)
1467 
1468  def get_sampled_particles(self):
1469  """get_sampled_particles(SampledDensityMap self) -> IMP::kernel::Particles const &"""
1470  return _IMP_em.SampledDensityMap_get_sampled_particles(self)
1471 
1472  def get_weight_key(self):
1473  """get_weight_key(SampledDensityMap self) -> FloatKey"""
1474  return _IMP_em.SampledDensityMap_get_weight_key(self)
1475 
1476  def get_minimum_resampled_value(self):
1477  """get_minimum_resampled_value(SampledDensityMap self) -> float"""
1478  return _IMP_em.SampledDensityMap_get_minimum_resampled_value(self)
1479 
1480  __swig_destroy__ = _IMP_em.delete_SampledDensityMap
1481  __del__ = lambda self : None;
1482  def __str__(self):
1483  """__str__(SampledDensityMap self) -> std::string"""
1484  return _IMP_em.SampledDensityMap___str__(self)
1485 
1486  def __repr__(self):
1487  """__repr__(SampledDensityMap self) -> std::string"""
1488  return _IMP_em.SampledDensityMap___repr__(self)
1489 
1490  def get_from(o):
1491  return _object_cast_to_SampledDensityMap(o)
1492  get_from = staticmethod(get_from)
1493 
1494 SampledDensityMap_swigregister = _IMP_em.SampledDensityMap_swigregister
1495 SampledDensityMap_swigregister(SampledDensityMap)
1496 
1497 IMP_DEFAULT_NUM_SHELLS = _IMP_em.IMP_DEFAULT_NUM_SHELLS
1498 IMP_SIG_CUTOFF = _IMP_em.IMP_SIG_CUTOFF
1499 class SurfaceShellDensityMap(SampledDensityMap):
1500  """Proxy of C++ IMP::em::SurfaceShellDensityMap class"""
1501  __swig_setmethods__ = {}
1502  for _s in [SampledDensityMap]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1503  __setattr__ = lambda self, name, value: _swig_setattr(self, SurfaceShellDensityMap, name, value)
1504  __swig_getmethods__ = {}
1505  for _s in [SampledDensityMap]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1506  __getattr__ = lambda self, name: _swig_getattr(self, SurfaceShellDensityMap, name)
1507  def __init__(self, *args):
1508  """
1509  __init__(IMP::em::SurfaceShellDensityMap self) -> SurfaceShellDensityMap
1510  __init__(IMP::em::SurfaceShellDensityMap self, DensityHeader header) -> SurfaceShellDensityMap
1511  __init__(IMP::em::SurfaceShellDensityMap self, IMP::kernel::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key=IMP::atom::Mass::get_mass_key(),
1512  int num_shells=5) -> SurfaceShellDensityMap
1513  __init__(IMP::em::SurfaceShellDensityMap self, IMP::kernel::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key=IMP::atom::Mass::get_mass_key()) -> SurfaceShellDensityMap
1514  __init__(IMP::em::SurfaceShellDensityMap self, IMP::kernel::ParticlesTemp const & ps, float voxel_size) -> SurfaceShellDensityMap
1515  """
1516  this = _IMP_em.new_SurfaceShellDensityMap(*args)
1517  try: self.this.append(this)
1518  except: self.this = this
1519  def binaries(self, *args):
1520  """binaries(SurfaceShellDensityMap self, float scene_val)"""
1521  return _IMP_em.SurfaceShellDensityMap_binaries(self, *args)
1522 
1523  def has_background_neighbor(self, *args):
1524  """has_background_neighbor(SurfaceShellDensityMap self, long voxel_ind) -> bool"""
1525  return _IMP_em.SurfaceShellDensityMap_has_background_neighbor(self, *args)
1526 
1527  __swig_destroy__ = _IMP_em.delete_SurfaceShellDensityMap
1528  __del__ = lambda self : None;
1529  def __str__(self):
1530  """__str__(SurfaceShellDensityMap self) -> std::string"""
1531  return _IMP_em.SurfaceShellDensityMap___str__(self)
1532 
1533  def __repr__(self):
1534  """__repr__(SurfaceShellDensityMap self) -> std::string"""
1535  return _IMP_em.SurfaceShellDensityMap___repr__(self)
1536 
1537  def get_from(o):
1538  return _object_cast_to_SurfaceShellDensityMap(o)
1539  get_from = staticmethod(get_from)
1540 
1541 SurfaceShellDensityMap_swigregister = _IMP_em.SurfaceShellDensityMap_swigregister
1542 SurfaceShellDensityMap_swigregister(SurfaceShellDensityMap)
1543 
1544 class CoarseCC(IMP.base.Object):
1545  """Proxy of C++ IMP::em::CoarseCC class"""
1546  __swig_setmethods__ = {}
1547  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1548  __setattr__ = lambda self, name, value: _swig_setattr(self, CoarseCC, name, value)
1549  __swig_getmethods__ = {}
1550  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1551  __getattr__ = lambda self, name: _swig_getattr(self, CoarseCC, name)
1552  def __init__(self):
1553  """__init__(IMP::em::CoarseCC self) -> CoarseCC"""
1554  this = _IMP_em.new_CoarseCC()
1555  try: self.this.append(this)
1556  except: self.this = this
1557  def calc_score(*args):
1558  """
1559  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True,
1560  bool resample=True, IMP::FloatPair norm_factors=IMP::FloatPair(0.,0.)) -> float
1561  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True,
1562  bool resample=True) -> float
1563  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1564  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1565  """
1566  return _IMP_em.CoarseCC_calc_score(*args)
1567 
1568  if _newclass:calc_score = staticmethod(calc_score)
1569  __swig_getmethods__["calc_score"] = lambda x: calc_score
1570  def cross_correlation_coefficient(*args):
1571  """
1572  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False,
1573  IMP::FloatPair norm_factors=IMP::FloatPair(0.,0.)) -> double
1574  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1575  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1576  """
1577  return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1578 
1579  if _newclass:cross_correlation_coefficient = staticmethod(cross_correlation_coefficient)
1580  __swig_getmethods__["cross_correlation_coefficient"] = lambda x: cross_correlation_coefficient
1581  def local_cross_correlation_coefficient(*args):
1582  """local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1583  return _IMP_em.CoarseCC_local_cross_correlation_coefficient(*args)
1584 
1585  if _newclass:local_cross_correlation_coefficient = staticmethod(local_cross_correlation_coefficient)
1586  __swig_getmethods__["local_cross_correlation_coefficient"] = lambda x: local_cross_correlation_coefficient
1587  def get_version_info(self):
1588  """get_version_info(CoarseCC self) -> VersionInfo"""
1589  return _IMP_em.CoarseCC_get_version_info(self)
1590 
1591  __swig_destroy__ = _IMP_em.delete_CoarseCC
1592  __del__ = lambda self : None;
1593  def __str__(self):
1594  """__str__(CoarseCC self) -> std::string"""
1595  return _IMP_em.CoarseCC___str__(self)
1596 
1597  def __repr__(self):
1598  """__repr__(CoarseCC self) -> std::string"""
1599  return _IMP_em.CoarseCC___repr__(self)
1600 
1601  def get_from(o):
1602  return _object_cast_to_CoarseCC(o)
1603  get_from = staticmethod(get_from)
1604 
1605 CoarseCC_swigregister = _IMP_em.CoarseCC_swigregister
1606 CoarseCC_swigregister(CoarseCC)
1607 
1608 def CoarseCC_calc_score(*args):
1609  """
1610  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True,
1611  bool resample=True, IMP::FloatPair norm_factors=IMP::FloatPair(0.,0.)) -> float
1612  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True,
1613  bool resample=True) -> float
1614  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1615  CoarseCC_calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1616  """
1617  return _IMP_em.CoarseCC_calc_score(*args)
1618 
1619 def CoarseCC_cross_correlation_coefficient(*args):
1620  """
1621  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False,
1622  IMP::FloatPair norm_factors=IMP::FloatPair(0.,0.)) -> double
1623  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1624  CoarseCC_cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1625  """
1626  return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1627 
1628 def CoarseCC_local_cross_correlation_coefficient(*args):
1629  """CoarseCC_local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1630  return _IMP_em.CoarseCC_local_cross_correlation_coefficient(*args)
1631 
1632 class CoarseConvolution(_object):
1633  """Proxy of C++ IMP::em::CoarseConvolution class"""
1634  __swig_setmethods__ = {}
1635  __setattr__ = lambda self, name, value: _swig_setattr(self, CoarseConvolution, name, value)
1636  __swig_getmethods__ = {}
1637  __getattr__ = lambda self, name: _swig_getattr(self, CoarseConvolution, name)
1638  __repr__ = _swig_repr
1639  def convolution(*args):
1640  """
1641  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1642  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1643  """
1644  return _IMP_em.CoarseConvolution_convolution(*args)
1645 
1646  if _newclass:convolution = staticmethod(convolution)
1647  __swig_getmethods__["convolution"] = lambda x: convolution
1648  def __init__(self):
1649  """__init__(IMP::em::CoarseConvolution self) -> CoarseConvolution"""
1650  this = _IMP_em.new_CoarseConvolution()
1651  try: self.this.append(this)
1652  except: self.this = this
1653  __swig_destroy__ = _IMP_em.delete_CoarseConvolution
1654  __del__ = lambda self : None;
1655 CoarseConvolution_swigregister = _IMP_em.CoarseConvolution_swigregister
1656 CoarseConvolution_swigregister(CoarseConvolution)
1657 
1658 def CoarseConvolution_convolution(*args):
1659  """
1660  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1661  CoarseConvolution_convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1662  """
1663  return _IMP_em.CoarseConvolution_convolution(*args)
1664 
1665 class CoarseCCatIntervals(CoarseCC):
1666  """Proxy of C++ IMP::em::CoarseCCatIntervals class"""
1667  __swig_setmethods__ = {}
1668  for _s in [CoarseCC]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1669  __setattr__ = lambda self, name, value: _swig_setattr(self, CoarseCCatIntervals, name, value)
1670  __swig_getmethods__ = {}
1671  for _s in [CoarseCC]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1672  __getattr__ = lambda self, name: _swig_getattr(self, CoarseCCatIntervals, name)
1673  def __init__(self, *args):
1674  """
1675  __init__(IMP::em::CoarseCCatIntervals self, int const & ncd) -> CoarseCCatIntervals
1676  __init__(IMP::em::CoarseCCatIntervals self) -> CoarseCCatIntervals
1677  """
1678  this = _IMP_em.new_CoarseCCatIntervals(*args)
1679  try: self.this.append(this)
1680  except: self.this = this
1681  def evaluate(self, *args):
1682  """
1683  evaluate(CoarseCCatIntervals self, DensityMap em_map, SampledDensityMap model_map, IMP::algebra::Vector3Ds const & deriv,
1684  float scalefac, bool lderiv, unsigned long eval_interval) -> std::pair< double,IMP::algebra::Vector3Ds >
1685  """
1686  return _IMP_em.CoarseCCatIntervals_evaluate(self, *args)
1687 
1688  __swig_destroy__ = _IMP_em.delete_CoarseCCatIntervals
1689  __del__ = lambda self : None;
1690  def __str__(self):
1691  """__str__(CoarseCCatIntervals self) -> std::string"""
1692  return _IMP_em.CoarseCCatIntervals___str__(self)
1693 
1694  def __repr__(self):
1695  """__repr__(CoarseCCatIntervals self) -> std::string"""
1696  return _IMP_em.CoarseCCatIntervals___repr__(self)
1697 
1698  def get_from(o):
1699  return _object_cast_to_CoarseCCatIntervals(o)
1700  get_from = staticmethod(get_from)
1701 
1702 CoarseCCatIntervals_swigregister = _IMP_em.CoarseCCatIntervals_swigregister
1703 CoarseCCatIntervals_swigregister(CoarseCCatIntervals)
1704 
1705 class FitRestraint(IMP.kernel.Restraint):
1706  """Proxy of C++ IMP::em::FitRestraint class"""
1707  __swig_setmethods__ = {}
1708  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1709  __setattr__ = lambda self, name, value: _swig_setattr(self, FitRestraint, name, value)
1710  __swig_getmethods__ = {}
1711  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1712  __getattr__ = lambda self, name: _swig_getattr(self, FitRestraint, name)
1713  def __init__(self, *args):
1714  """
1715  __init__(IMP::em::FitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors=IMP::FloatPair(0.,0.),
1716  FloatKey weight_key=IMP::atom::Mass::get_mass_key(), float scale=1,
1717  bool use_rigid_bodies=True, IMP::em::KernelType kt=GAUSSIAN) -> FitRestraint
1718  __init__(IMP::em::FitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors=IMP::FloatPair(0.,0.),
1719  FloatKey weight_key=IMP::atom::Mass::get_mass_key(), float scale=1,
1720  bool use_rigid_bodies=True) -> FitRestraint
1721  __init__(IMP::em::FitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors=IMP::FloatPair(0.,0.),
1722  FloatKey weight_key=IMP::atom::Mass::get_mass_key(), float scale=1) -> FitRestraint
1723  __init__(IMP::em::FitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors=IMP::FloatPair(0.,0.),
1724  FloatKey weight_key=IMP::atom::Mass::get_mass_key()) -> FitRestraint
1725  __init__(IMP::em::FitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors=IMP::FloatPair(0.,0.)) -> FitRestraint
1726  __init__(IMP::em::FitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map) -> FitRestraint
1727  """
1728  this = _IMP_em.new_FitRestraint(*args)
1729  try: self.this.append(this)
1730  except: self.this = this
1731  def get_model_dens_map(self):
1732  """get_model_dens_map(FitRestraint self) -> SampledDensityMap"""
1733  return _IMP_em.FitRestraint_get_model_dens_map(self)
1734 
1735  def set_scale_factor(self, *args):
1736  """set_scale_factor(FitRestraint self, float scale)"""
1737  return _IMP_em.FitRestraint_set_scale_factor(self, *args)
1738 
1739  def get_scale_factor(self):
1740  """get_scale_factor(FitRestraint self) -> float"""
1741  return _IMP_em.FitRestraint_get_scale_factor(self)
1742 
1743  def do_get_inputs(self):
1744  """do_get_inputs(FitRestraint self) -> IMP::kernel::ModelObjectsTemp"""
1745  return _IMP_em.FitRestraint_do_get_inputs(self)
1746 
1747  def get_version_info(self):
1748  """get_version_info(FitRestraint self) -> VersionInfo"""
1749  return _IMP_em.FitRestraint_get_version_info(self)
1750 
1751  __swig_destroy__ = _IMP_em.delete_FitRestraint
1752  __del__ = lambda self : None;
1753  def __str__(self):
1754  """__str__(FitRestraint self) -> std::string"""
1755  return _IMP_em.FitRestraint___str__(self)
1756 
1757  def __repr__(self):
1758  """__repr__(FitRestraint self) -> std::string"""
1759  return _IMP_em.FitRestraint___repr__(self)
1760 
1761  def get_from(o):
1762  return _object_cast_to_FitRestraint(o)
1763  get_from = staticmethod(get_from)
1764 
1765  def cast(*args):
1766  """cast(Restraint r) -> FitRestraint"""
1767  return _IMP_em.FitRestraint_cast(*args)
1768 
1769  if _newclass:cast = staticmethod(cast)
1770  __swig_getmethods__["cast"] = lambda x: cast
1771 FitRestraint_swigregister = _IMP_em.FitRestraint_swigregister
1772 FitRestraint_swigregister(FitRestraint)
1773 
1774 def FitRestraint_cast(*args):
1775  """FitRestraint_cast(Restraint r) -> FitRestraint"""
1776  return _IMP_em.FitRestraint_cast(*args)
1777 
1778 
1779 def density2particles(*args):
1780  """
1781  density2particles(DensityMap dmap, IMP::Float threshold, Model m, int step=1) -> IMP::kernel::Particles
1782  density2particles(DensityMap dmap, IMP::Float threshold, Model m) -> IMP::kernel::Particles
1783  """
1784  return _IMP_em.density2particles(*args)
1785 
1786 def density2vectors(*args):
1787  """density2vectors(DensityMap dmap, IMP::Float threshold) -> IMP::algebra::Vector3Ds"""
1788  return _IMP_em.density2vectors(*args)
1789 
1790 def particles2density(*args):
1791  """
1792  particles2density(IMP::kernel::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3,
1793  FloatKey weight_key=IMP::atom::Mass::get_mass_key()) -> SampledDensityMap
1794  particles2density(IMP::kernel::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
1795  particles2density(IMP::kernel::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
1796  """
1797  return _IMP_em.particles2density(*args)
1798 
1799 def particles2binarized_density(*args):
1800  """
1801  particles2binarized_density(IMP::kernel::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3,
1802  FloatKey weight_key=IMP::atom::Mass::get_mass_key()) -> SampledDensityMap
1803  particles2binarized_density(IMP::kernel::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
1804  particles2binarized_density(IMP::kernel::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
1805  """
1806  return _IMP_em.particles2binarized_density(*args)
1807 
1808 def particles2surface(*args):
1809  """
1810  particles2surface(IMP::kernel::ParticlesTemp const & ps, IMP::Float apix, FloatKey weight_key=IMP::atom::Mass::get_mass_key()) -> SurfaceShellDensityMap
1811  particles2surface(IMP::kernel::ParticlesTemp const & ps, IMP::Float apix) -> SurfaceShellDensityMap
1812  """
1813  return _IMP_em.particles2surface(*args)
1814 
1815 def calculate_intersection_score(*args):
1816  """calculate_intersection_score(SurfaceShellDensityMap d1, SurfaceShellDensityMap d2) -> IMP::Float"""
1817  return _IMP_em.calculate_intersection_score(*args)
1818 class SpiderHeader(_object):
1819  """Proxy of C++ IMP::em::SpiderHeader class"""
1820  __swig_setmethods__ = {}
1821  __setattr__ = lambda self, name, value: _swig_setattr(self, SpiderHeader, name, value)
1822  __swig_getmethods__ = {}
1823  __getattr__ = lambda self, name: _swig_getattr(self, SpiderHeader, name)
1824  __repr__ = _swig_repr
1825  __swig_setmethods__["fNslice"] = _IMP_em.SpiderHeader_fNslice_set
1826  __swig_getmethods__["fNslice"] = _IMP_em.SpiderHeader_fNslice_get
1827  if _newclass:fNslice = _swig_property(_IMP_em.SpiderHeader_fNslice_get, _IMP_em.SpiderHeader_fNslice_set)
1828  __swig_setmethods__["fNrow"] = _IMP_em.SpiderHeader_fNrow_set
1829  __swig_getmethods__["fNrow"] = _IMP_em.SpiderHeader_fNrow_get
1830  if _newclass:fNrow = _swig_property(_IMP_em.SpiderHeader_fNrow_get, _IMP_em.SpiderHeader_fNrow_set)
1831  __swig_setmethods__["fNrec"] = _IMP_em.SpiderHeader_fNrec_set
1832  __swig_getmethods__["fNrec"] = _IMP_em.SpiderHeader_fNrec_get
1833  if _newclass:fNrec = _swig_property(_IMP_em.SpiderHeader_fNrec_get, _IMP_em.SpiderHeader_fNrec_set)
1834  __swig_setmethods__["fNlabel"] = _IMP_em.SpiderHeader_fNlabel_set
1835  __swig_getmethods__["fNlabel"] = _IMP_em.SpiderHeader_fNlabel_get
1836  if _newclass:fNlabel = _swig_property(_IMP_em.SpiderHeader_fNlabel_get, _IMP_em.SpiderHeader_fNlabel_set)
1837  __swig_setmethods__["fIform"] = _IMP_em.SpiderHeader_fIform_set
1838  __swig_getmethods__["fIform"] = _IMP_em.SpiderHeader_fIform_get
1839  if _newclass:fIform = _swig_property(_IMP_em.SpiderHeader_fIform_get, _IMP_em.SpiderHeader_fIform_set)
1840  __swig_setmethods__["fImami"] = _IMP_em.SpiderHeader_fImami_set
1841  __swig_getmethods__["fImami"] = _IMP_em.SpiderHeader_fImami_get
1842  if _newclass:fImami = _swig_property(_IMP_em.SpiderHeader_fImami_get, _IMP_em.SpiderHeader_fImami_set)
1843  __swig_setmethods__["fFmax"] = _IMP_em.SpiderHeader_fFmax_set
1844  __swig_getmethods__["fFmax"] = _IMP_em.SpiderHeader_fFmax_get
1845  if _newclass:fFmax = _swig_property(_IMP_em.SpiderHeader_fFmax_get, _IMP_em.SpiderHeader_fFmax_set)
1846  __swig_setmethods__["fFmin"] = _IMP_em.SpiderHeader_fFmin_set
1847  __swig_getmethods__["fFmin"] = _IMP_em.SpiderHeader_fFmin_get
1848  if _newclass:fFmin = _swig_property(_IMP_em.SpiderHeader_fFmin_get, _IMP_em.SpiderHeader_fFmin_set)
1849  __swig_setmethods__["fAv"] = _IMP_em.SpiderHeader_fAv_set
1850  __swig_getmethods__["fAv"] = _IMP_em.SpiderHeader_fAv_get
1851  if _newclass:fAv = _swig_property(_IMP_em.SpiderHeader_fAv_get, _IMP_em.SpiderHeader_fAv_set)
1852  __swig_setmethods__["fSig"] = _IMP_em.SpiderHeader_fSig_set
1853  __swig_getmethods__["fSig"] = _IMP_em.SpiderHeader_fSig_get
1854  if _newclass:fSig = _swig_property(_IMP_em.SpiderHeader_fSig_get, _IMP_em.SpiderHeader_fSig_set)
1855  __swig_setmethods__["fIhist"] = _IMP_em.SpiderHeader_fIhist_set
1856  __swig_getmethods__["fIhist"] = _IMP_em.SpiderHeader_fIhist_get
1857  if _newclass:fIhist = _swig_property(_IMP_em.SpiderHeader_fIhist_get, _IMP_em.SpiderHeader_fIhist_set)
1858  __swig_setmethods__["fNcol"] = _IMP_em.SpiderHeader_fNcol_set
1859  __swig_getmethods__["fNcol"] = _IMP_em.SpiderHeader_fNcol_get
1860  if _newclass:fNcol = _swig_property(_IMP_em.SpiderHeader_fNcol_get, _IMP_em.SpiderHeader_fNcol_set)
1861  __swig_setmethods__["fLabrec"] = _IMP_em.SpiderHeader_fLabrec_set
1862  __swig_getmethods__["fLabrec"] = _IMP_em.SpiderHeader_fLabrec_get
1863  if _newclass:fLabrec = _swig_property(_IMP_em.SpiderHeader_fLabrec_get, _IMP_em.SpiderHeader_fLabrec_set)
1864  __swig_setmethods__["fIangle"] = _IMP_em.SpiderHeader_fIangle_set
1865  __swig_getmethods__["fIangle"] = _IMP_em.SpiderHeader_fIangle_get
1866  if _newclass:fIangle = _swig_property(_IMP_em.SpiderHeader_fIangle_get, _IMP_em.SpiderHeader_fIangle_set)
1867  __swig_setmethods__["fPhi"] = _IMP_em.SpiderHeader_fPhi_set
1868  __swig_getmethods__["fPhi"] = _IMP_em.SpiderHeader_fPhi_get
1869  if _newclass:fPhi = _swig_property(_IMP_em.SpiderHeader_fPhi_get, _IMP_em.SpiderHeader_fPhi_set)
1870  __swig_setmethods__["fTheta"] = _IMP_em.SpiderHeader_fTheta_set
1871  __swig_getmethods__["fTheta"] = _IMP_em.SpiderHeader_fTheta_get
1872  if _newclass:fTheta = _swig_property(_IMP_em.SpiderHeader_fTheta_get, _IMP_em.SpiderHeader_fTheta_set)
1873  __swig_setmethods__["fPsi"] = _IMP_em.SpiderHeader_fPsi_set
1874  __swig_getmethods__["fPsi"] = _IMP_em.SpiderHeader_fPsi_get
1875  if _newclass:fPsi = _swig_property(_IMP_em.SpiderHeader_fPsi_get, _IMP_em.SpiderHeader_fPsi_set)
1876  __swig_setmethods__["fXoff"] = _IMP_em.SpiderHeader_fXoff_set
1877  __swig_getmethods__["fXoff"] = _IMP_em.SpiderHeader_fXoff_get
1878  if _newclass:fXoff = _swig_property(_IMP_em.SpiderHeader_fXoff_get, _IMP_em.SpiderHeader_fXoff_set)
1879  __swig_setmethods__["fYoff"] = _IMP_em.SpiderHeader_fYoff_set
1880  __swig_getmethods__["fYoff"] = _IMP_em.SpiderHeader_fYoff_get
1881  if _newclass:fYoff = _swig_property(_IMP_em.SpiderHeader_fYoff_get, _IMP_em.SpiderHeader_fYoff_set)
1882  __swig_setmethods__["fZoff"] = _IMP_em.SpiderHeader_fZoff_set
1883  __swig_getmethods__["fZoff"] = _IMP_em.SpiderHeader_fZoff_get
1884  if _newclass:fZoff = _swig_property(_IMP_em.SpiderHeader_fZoff_get, _IMP_em.SpiderHeader_fZoff_set)
1885  __swig_setmethods__["fScale"] = _IMP_em.SpiderHeader_fScale_set
1886  __swig_getmethods__["fScale"] = _IMP_em.SpiderHeader_fScale_get
1887  if _newclass:fScale = _swig_property(_IMP_em.SpiderHeader_fScale_get, _IMP_em.SpiderHeader_fScale_set)
1888  __swig_setmethods__["fLabbyt"] = _IMP_em.SpiderHeader_fLabbyt_set
1889  __swig_getmethods__["fLabbyt"] = _IMP_em.SpiderHeader_fLabbyt_get
1890  if _newclass:fLabbyt = _swig_property(_IMP_em.SpiderHeader_fLabbyt_get, _IMP_em.SpiderHeader_fLabbyt_set)
1891  __swig_setmethods__["fLenbyt"] = _IMP_em.SpiderHeader_fLenbyt_set
1892  __swig_getmethods__["fLenbyt"] = _IMP_em.SpiderHeader_fLenbyt_get
1893  if _newclass:fLenbyt = _swig_property(_IMP_em.SpiderHeader_fLenbyt_get, _IMP_em.SpiderHeader_fLenbyt_set)
1894  __swig_setmethods__["fNothing"] = _IMP_em.SpiderHeader_fNothing_set
1895  __swig_getmethods__["fNothing"] = _IMP_em.SpiderHeader_fNothing_get
1896  if _newclass:fNothing = _swig_property(_IMP_em.SpiderHeader_fNothing_get, _IMP_em.SpiderHeader_fNothing_set)
1897  __swig_setmethods__["fFlag"] = _IMP_em.SpiderHeader_fFlag_set
1898  __swig_getmethods__["fFlag"] = _IMP_em.SpiderHeader_fFlag_get
1899  if _newclass:fFlag = _swig_property(_IMP_em.SpiderHeader_fFlag_get, _IMP_em.SpiderHeader_fFlag_set)
1900  __swig_setmethods__["fPhi1"] = _IMP_em.SpiderHeader_fPhi1_set
1901  __swig_getmethods__["fPhi1"] = _IMP_em.SpiderHeader_fPhi1_get
1902  if _newclass:fPhi1 = _swig_property(_IMP_em.SpiderHeader_fPhi1_get, _IMP_em.SpiderHeader_fPhi1_set)
1903  __swig_setmethods__["fTheta1"] = _IMP_em.SpiderHeader_fTheta1_set
1904  __swig_getmethods__["fTheta1"] = _IMP_em.SpiderHeader_fTheta1_get
1905  if _newclass:fTheta1 = _swig_property(_IMP_em.SpiderHeader_fTheta1_get, _IMP_em.SpiderHeader_fTheta1_set)
1906  __swig_setmethods__["fPsi1"] = _IMP_em.SpiderHeader_fPsi1_set
1907  __swig_getmethods__["fPsi1"] = _IMP_em.SpiderHeader_fPsi1_get
1908  if _newclass:fPsi1 = _swig_property(_IMP_em.SpiderHeader_fPsi1_get, _IMP_em.SpiderHeader_fPsi1_set)
1909  __swig_setmethods__["fPhi2"] = _IMP_em.SpiderHeader_fPhi2_set
1910  __swig_getmethods__["fPhi2"] = _IMP_em.SpiderHeader_fPhi2_get
1911  if _newclass:fPhi2 = _swig_property(_IMP_em.SpiderHeader_fPhi2_get, _IMP_em.SpiderHeader_fPhi2_set)
1912  __swig_setmethods__["fTheta2"] = _IMP_em.SpiderHeader_fTheta2_set
1913  __swig_getmethods__["fTheta2"] = _IMP_em.SpiderHeader_fTheta2_get
1914  if _newclass:fTheta2 = _swig_property(_IMP_em.SpiderHeader_fTheta2_get, _IMP_em.SpiderHeader_fTheta2_set)
1915  __swig_setmethods__["fPsi2"] = _IMP_em.SpiderHeader_fPsi2_set
1916  __swig_getmethods__["fPsi2"] = _IMP_em.SpiderHeader_fPsi2_get
1917  if _newclass:fPsi2 = _swig_property(_IMP_em.SpiderHeader_fPsi2_get, _IMP_em.SpiderHeader_fPsi2_set)
1918  __swig_setmethods__["fGeo_matrix"] = _IMP_em.SpiderHeader_fGeo_matrix_set
1919  __swig_getmethods__["fGeo_matrix"] = _IMP_em.SpiderHeader_fGeo_matrix_get
1920  if _newclass:fGeo_matrix = _swig_property(_IMP_em.SpiderHeader_fGeo_matrix_get, _IMP_em.SpiderHeader_fGeo_matrix_set)
1921  __swig_setmethods__["fAngle1"] = _IMP_em.SpiderHeader_fAngle1_set
1922  __swig_getmethods__["fAngle1"] = _IMP_em.SpiderHeader_fAngle1_get
1923  if _newclass:fAngle1 = _swig_property(_IMP_em.SpiderHeader_fAngle1_get, _IMP_em.SpiderHeader_fAngle1_set)
1924  __swig_setmethods__["fr1"] = _IMP_em.SpiderHeader_fr1_set
1925  __swig_getmethods__["fr1"] = _IMP_em.SpiderHeader_fr1_get
1926  if _newclass:fr1 = _swig_property(_IMP_em.SpiderHeader_fr1_get, _IMP_em.SpiderHeader_fr1_set)
1927  __swig_setmethods__["fr2"] = _IMP_em.SpiderHeader_fr2_set
1928  __swig_getmethods__["fr2"] = _IMP_em.SpiderHeader_fr2_get
1929  if _newclass:fr2 = _swig_property(_IMP_em.SpiderHeader_fr2_get, _IMP_em.SpiderHeader_fr2_set)
1930  __swig_setmethods__["RTflag"] = _IMP_em.SpiderHeader_RTflag_set
1931  __swig_getmethods__["RTflag"] = _IMP_em.SpiderHeader_RTflag_get
1932  if _newclass:RTflag = _swig_property(_IMP_em.SpiderHeader_RTflag_get, _IMP_em.SpiderHeader_RTflag_set)
1933  __swig_setmethods__["Astart"] = _IMP_em.SpiderHeader_Astart_set
1934  __swig_getmethods__["Astart"] = _IMP_em.SpiderHeader_Astart_get
1935  if _newclass:Astart = _swig_property(_IMP_em.SpiderHeader_Astart_get, _IMP_em.SpiderHeader_Astart_set)
1936  __swig_setmethods__["Aend"] = _IMP_em.SpiderHeader_Aend_set
1937  __swig_getmethods__["Aend"] = _IMP_em.SpiderHeader_Aend_get
1938  if _newclass:Aend = _swig_property(_IMP_em.SpiderHeader_Aend_get, _IMP_em.SpiderHeader_Aend_set)
1939  __swig_setmethods__["Ainc"] = _IMP_em.SpiderHeader_Ainc_set
1940  __swig_getmethods__["Ainc"] = _IMP_em.SpiderHeader_Ainc_get
1941  if _newclass:Ainc = _swig_property(_IMP_em.SpiderHeader_Ainc_get, _IMP_em.SpiderHeader_Ainc_set)
1942  __swig_setmethods__["Rsigma"] = _IMP_em.SpiderHeader_Rsigma_set
1943  __swig_getmethods__["Rsigma"] = _IMP_em.SpiderHeader_Rsigma_get
1944  if _newclass:Rsigma = _swig_property(_IMP_em.SpiderHeader_Rsigma_get, _IMP_em.SpiderHeader_Rsigma_set)
1945  __swig_setmethods__["Tstart"] = _IMP_em.SpiderHeader_Tstart_set
1946  __swig_getmethods__["Tstart"] = _IMP_em.SpiderHeader_Tstart_get
1947  if _newclass:Tstart = _swig_property(_IMP_em.SpiderHeader_Tstart_get, _IMP_em.SpiderHeader_Tstart_set)
1948  __swig_setmethods__["Tend"] = _IMP_em.SpiderHeader_Tend_set
1949  __swig_getmethods__["Tend"] = _IMP_em.SpiderHeader_Tend_get
1950  if _newclass:Tend = _swig_property(_IMP_em.SpiderHeader_Tend_get, _IMP_em.SpiderHeader_Tend_set)
1951  __swig_setmethods__["Tinc"] = _IMP_em.SpiderHeader_Tinc_set
1952  __swig_getmethods__["Tinc"] = _IMP_em.SpiderHeader_Tinc_get
1953  if _newclass:Tinc = _swig_property(_IMP_em.SpiderHeader_Tinc_get, _IMP_em.SpiderHeader_Tinc_set)
1954  __swig_setmethods__["Weight"] = _IMP_em.SpiderHeader_Weight_set
1955  __swig_getmethods__["Weight"] = _IMP_em.SpiderHeader_Weight_get
1956  if _newclass:Weight = _swig_property(_IMP_em.SpiderHeader_Weight_get, _IMP_em.SpiderHeader_Weight_set)
1957  __swig_setmethods__["Flip"] = _IMP_em.SpiderHeader_Flip_set
1958  __swig_getmethods__["Flip"] = _IMP_em.SpiderHeader_Flip_get
1959  if _newclass:Flip = _swig_property(_IMP_em.SpiderHeader_Flip_get, _IMP_em.SpiderHeader_Flip_set)
1960  __swig_setmethods__["empty"] = _IMP_em.SpiderHeader_empty_set
1961  __swig_getmethods__["empty"] = _IMP_em.SpiderHeader_empty_get
1962  if _newclass:empty = _swig_property(_IMP_em.SpiderHeader_empty_get, _IMP_em.SpiderHeader_empty_set)
1963  __swig_setmethods__["szIDat"] = _IMP_em.SpiderHeader_szIDat_set
1964  __swig_getmethods__["szIDat"] = _IMP_em.SpiderHeader_szIDat_get
1965  if _newclass:szIDat = _swig_property(_IMP_em.SpiderHeader_szIDat_get, _IMP_em.SpiderHeader_szIDat_set)
1966  __swig_setmethods__["szITim"] = _IMP_em.SpiderHeader_szITim_set
1967  __swig_getmethods__["szITim"] = _IMP_em.SpiderHeader_szITim_get
1968  if _newclass:szITim = _swig_property(_IMP_em.SpiderHeader_szITim_get, _IMP_em.SpiderHeader_szITim_set)
1969  __swig_setmethods__["szITit"] = _IMP_em.SpiderHeader_szITit_set
1970  __swig_getmethods__["szITit"] = _IMP_em.SpiderHeader_szITit_get
1971  if _newclass:szITit = _swig_property(_IMP_em.SpiderHeader_szITit_get, _IMP_em.SpiderHeader_szITit_set)
1972  def show(self, *args):
1973  """show(SpiderHeader self, _ostream out)"""
1974  return _IMP_em.SpiderHeader_show(self, *args)
1975 
1976  def __init__(self):
1977  """__init__(IMP::em::SpiderHeader self) -> SpiderHeader"""
1978  this = _IMP_em.new_SpiderHeader()
1979  try: self.this.append(this)
1980  except: self.this = this
1981  __swig_destroy__ = _IMP_em.delete_SpiderHeader
1982  __del__ = lambda self : None;
1983 SpiderHeader_swigregister = _IMP_em.SpiderHeader_swigregister
1984 SpiderHeader_swigregister(SpiderHeader)
1985 
1986 class ImageHeader(_object):
1987  """Proxy of C++ IMP::em::ImageHeader class"""
1988  __swig_setmethods__ = {}
1989  __setattr__ = lambda self, name, value: _swig_setattr(self, ImageHeader, name, value)
1990  __swig_getmethods__ = {}
1991  __getattr__ = lambda self, name: _swig_getattr(self, ImageHeader, name)
1992  __repr__ = _swig_repr
1993  IMG_BYTE = _IMP_em.ImageHeader_IMG_BYTE
1994  IMG_IMPEM = _IMP_em.ImageHeader_IMG_IMPEM
1995  IMG_INT = _IMP_em.ImageHeader_IMG_INT
1996  VOL_BYTE = _IMP_em.ImageHeader_VOL_BYTE
1997  VOL_IMPEM = _IMP_em.ImageHeader_VOL_IMPEM
1998  VOL_INT = _IMP_em.ImageHeader_VOL_INT
1999  IMG_FOURIER = _IMP_em.ImageHeader_IMG_FOURIER
2000  VOL_FOURIER = _IMP_em.ImageHeader_VOL_FOURIER
2001  def __init__(self, *args):
2002  """
2003  __init__(IMP::em::ImageHeader self) -> ImageHeader
2004  __init__(IMP::em::ImageHeader self, IMP::em::ImageHeader::img_type im) -> ImageHeader
2005  __init__(IMP::em::ImageHeader self, float im) -> ImageHeader
2006  """
2007  this = _IMP_em.new_ImageHeader(*args)
2008  try: self.this.append(this)
2009  except: self.this = this
2010  def get_image_type(self):
2011  """get_image_type(ImageHeader self) -> float"""
2012  return _IMP_em.ImageHeader_get_image_type(self)
2013 
2014  def set_image_type(self, *args):
2015  """
2016  set_image_type(ImageHeader self, IMP::em::ImageHeader::img_type im)
2017  set_image_type(ImageHeader self, float im)
2018  """
2019  return _IMP_em.ImageHeader_set_image_type(self, *args)
2020 
2021  def do_show(self, *args):
2022  """do_show(ImageHeader self, _ostream out)"""
2023  return _IMP_em.ImageHeader_do_show(self, *args)
2024 
2025  def show(self, *args):
2026  """
2027  show(ImageHeader self, _ostream out=std::cout)
2028  show(ImageHeader self)
2029  """
2030  return _IMP_em.ImageHeader_show(self, *args)
2031 
2032  def print_hard(self, *args):
2033  """print_hard(ImageHeader self, _ostream out)"""
2034  return _IMP_em.ImageHeader_print_hard(self, *args)
2035 
2036  def show_projection_params(self, *args):
2037  """show_projection_params(ImageHeader self, _ostream out)"""
2038  return _IMP_em.ImageHeader_show_projection_params(self, *args)
2039 
2040  def read(self, *args):
2041  """
2042  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False,
2043  bool skip_extra_checkings=False) -> int
2044  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False) -> int
2045  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False) -> int
2046  read(ImageHeader self, IMP::String const filename) -> int
2047  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False, bool skip_extra_checkings=False) -> bool
2048  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False) -> bool
2049  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False) -> bool
2050  read(ImageHeader self, std::ifstream & f) -> bool
2051  """
2052  return _IMP_em.ImageHeader_read(self, *args)
2053 
2054  def write(self, *args):
2055  """
2056  write(ImageHeader self, IMP::String const & filename, bool force_reversed=False)
2057  write(ImageHeader self, IMP::String const & filename)
2058  write(ImageHeader self, std::ofstream & f, bool force_reversed=False)
2059  write(ImageHeader self, std::ofstream & f)
2060  """
2061  return _IMP_em.ImageHeader_write(self, *args)
2062 
2063  def clear(self):
2064  """clear(ImageHeader self)"""
2065  return _IMP_em.ImageHeader_clear(self)
2066 
2067  def set_header(self):
2068  """set_header(ImageHeader self)"""
2069  return _IMP_em.ImageHeader_set_header(self)
2070 
2071  def get_reversed(self):
2072  """get_reversed(ImageHeader self) -> bool"""
2073  return _IMP_em.ImageHeader_get_reversed(self)
2074 
2075  def set_reversed(self, *args):
2076  """set_reversed(ImageHeader self, bool value)"""
2077  return _IMP_em.ImageHeader_set_reversed(self, *args)
2078 
2079  def get_number_of_slices(self):
2080  """get_number_of_slices(ImageHeader self) -> unsigned int"""
2081  return _IMP_em.ImageHeader_get_number_of_slices(self)
2082 
2083  def set_number_of_slices(self, *args):
2084  """set_number_of_slices(ImageHeader self, unsigned int n)"""
2085  return _IMP_em.ImageHeader_set_number_of_slices(self, *args)
2086 
2087  def get_number_of_rows(self):
2088  """get_number_of_rows(ImageHeader self) -> unsigned int"""
2089  return _IMP_em.ImageHeader_get_number_of_rows(self)
2090 
2091  def set_number_of_rows(self, *args):
2092  """set_number_of_rows(ImageHeader self, unsigned int n)"""
2093  return _IMP_em.ImageHeader_set_number_of_rows(self, *args)
2094 
2095  def get_number_of_columns(self):
2096  """get_number_of_columns(ImageHeader self) -> unsigned int"""
2097  return _IMP_em.ImageHeader_get_number_of_columns(self)
2098 
2099  def set_number_of_columns(self, *args):
2100  """set_number_of_columns(ImageHeader self, unsigned int n)"""
2101  return _IMP_em.ImageHeader_set_number_of_columns(self, *args)
2102 
2103  def get_old_rot(self):
2104  """get_old_rot(ImageHeader self) -> float"""
2105  return _IMP_em.ImageHeader_get_old_rot(self)
2106 
2107  def set_old_rot(self, *args):
2108  """set_old_rot(ImageHeader self, float value)"""
2109  return _IMP_em.ImageHeader_set_old_rot(self, *args)
2110 
2111  def get_fAngle1(self):
2112  """get_fAngle1(ImageHeader self) -> float"""
2113  return _IMP_em.ImageHeader_get_fAngle1(self)
2114 
2115  def set_fAngle1(self, *args):
2116  """set_fAngle1(ImageHeader self, float value)"""
2117  return _IMP_em.ImageHeader_set_fAngle1(self, *args)
2118 
2119  def get_Scale(self):
2120  """get_Scale(ImageHeader self) -> float"""
2121  return _IMP_em.ImageHeader_get_Scale(self)
2122 
2123  def set_Scale(self, *args):
2124  """set_Scale(ImageHeader self, float value)"""
2125  return _IMP_em.ImageHeader_set_Scale(self, *args)
2126 
2127  def get_Flip(self):
2128  """get_Flip(ImageHeader self) -> float"""
2129  return _IMP_em.ImageHeader_get_Flip(self)
2130 
2131  def set_Flip(self, *args):
2132  """set_Flip(ImageHeader self, float value)"""
2133  return _IMP_em.ImageHeader_set_Flip(self, *args)
2134 
2135  def get_Weight(self):
2136  """get_Weight(ImageHeader self) -> float"""
2137  return _IMP_em.ImageHeader_get_Weight(self)
2138 
2139  def set_Weight(self, *args):
2140  """set_Weight(ImageHeader self, float value)"""
2141  return _IMP_em.ImageHeader_set_Weight(self, *args)
2142 
2143  def get_fNrec(self):
2144  """get_fNrec(ImageHeader self) -> float"""
2145  return _IMP_em.ImageHeader_get_fNrec(self)
2146 
2147  def set_fNrec(self, *args):
2148  """set_fNrec(ImageHeader self, float value)"""
2149  return _IMP_em.ImageHeader_set_fNrec(self, *args)
2150 
2151  def get_fNlabel(self):
2152  """get_fNlabel(ImageHeader self) -> float"""
2153  return _IMP_em.ImageHeader_get_fNlabel(self)
2154 
2155  def set_fNlabel(self, *args):
2156  """set_fNlabel(ImageHeader self, float value)"""
2157  return _IMP_em.ImageHeader_set_fNlabel(self, *args)
2158 
2159  def get_fIform(self):
2160  """get_fIform(ImageHeader self) -> float"""
2161  return _IMP_em.ImageHeader_get_fIform(self)
2162 
2163  def set_fIform(self, *args):
2164  """set_fIform(ImageHeader self, float value)"""
2165  return _IMP_em.ImageHeader_set_fIform(self, *args)
2166 
2167  def get_fImami(self):
2168  """get_fImami(ImageHeader self) -> float"""
2169  return _IMP_em.ImageHeader_get_fImami(self)
2170 
2171  def set_fImami(self, *args):
2172  """set_fImami(ImageHeader self, float value)"""
2173  return _IMP_em.ImageHeader_set_fImami(self, *args)
2174 
2175  def get_fFmax(self):
2176  """get_fFmax(ImageHeader self) -> float"""
2177  return _IMP_em.ImageHeader_get_fFmax(self)
2178 
2179  def set_fFmax(self, *args):
2180  """set_fFmax(ImageHeader self, float value)"""
2181  return _IMP_em.ImageHeader_set_fFmax(self, *args)
2182 
2183  def get_fFmin(self):
2184  """get_fFmin(ImageHeader self) -> float"""
2185  return _IMP_em.ImageHeader_get_fFmin(self)
2186 
2187  def set_fFmin(self, *args):
2188  """set_fFmin(ImageHeader self, float value)"""
2189  return _IMP_em.ImageHeader_set_fFmin(self, *args)
2190 
2191  def get_fAv(self):
2192  """get_fAv(ImageHeader self) -> float"""
2193  return _IMP_em.ImageHeader_get_fAv(self)
2194 
2195  def set_fAv(self, *args):
2196  """set_fAv(ImageHeader self, float value)"""
2197  return _IMP_em.ImageHeader_set_fAv(self, *args)
2198 
2199  def get_fSig(self):
2200  """get_fSig(ImageHeader self) -> float"""
2201  return _IMP_em.ImageHeader_get_fSig(self)
2202 
2203  def set_fSig(self, *args):
2204  """set_fSig(ImageHeader self, float value)"""
2205  return _IMP_em.ImageHeader_set_fSig(self, *args)
2206 
2207  def get_fIhist(self):
2208  """get_fIhist(ImageHeader self) -> float"""
2209  return _IMP_em.ImageHeader_get_fIhist(self)
2210 
2211  def set_fIhist(self, *args):
2212  """set_fIhist(ImageHeader self, float value)"""
2213  return _IMP_em.ImageHeader_set_fIhist(self, *args)
2214 
2215  def get_fLabrec(self):
2216  """get_fLabrec(ImageHeader self) -> float"""
2217  return _IMP_em.ImageHeader_get_fLabrec(self)
2218 
2219  def set_fLabrec(self, *args):
2220  """set_fLabrec(ImageHeader self, float value)"""
2221  return _IMP_em.ImageHeader_set_fLabrec(self, *args)
2222 
2223  def get_fIangle(self):
2224  """get_fIangle(ImageHeader self) -> float"""
2225  return _IMP_em.ImageHeader_get_fIangle(self)
2226 
2227  def set_fIangle(self, *args):
2228  """set_fIangle(ImageHeader self, float value)"""
2229  return _IMP_em.ImageHeader_set_fIangle(self, *args)
2230 
2231  def get_origin(self):
2232  """get_origin(ImageHeader self) -> Vector3D"""
2233  return _IMP_em.ImageHeader_get_origin(self)
2234 
2235  def set_origin(self, *args):
2236  """
2237  set_origin(ImageHeader self, Vector3D v)
2238  set_origin(ImageHeader self, Vector2D v)
2239  """
2240  return _IMP_em.ImageHeader_set_origin(self, *args)
2241 
2242  def get_object_pixel_size(self):
2243  """get_object_pixel_size(ImageHeader self) -> float"""
2244  return _IMP_em.ImageHeader_get_object_pixel_size(self)
2245 
2246  def set_object_pixel_size(self, *args):
2247  """set_object_pixel_size(ImageHeader self, float value)"""
2248  return _IMP_em.ImageHeader_set_object_pixel_size(self, *args)
2249 
2250  def get_fLabbyt(self):
2251  """get_fLabbyt(ImageHeader self) -> float"""
2252  return _IMP_em.ImageHeader_get_fLabbyt(self)
2253 
2254  def set_fLabbyt(self, *args):
2255  """set_fLabbyt(ImageHeader self, float value)"""
2256  return _IMP_em.ImageHeader_set_fLabbyt(self, *args)
2257 
2258  def get_fLenbyt(self):
2259  """get_fLenbyt(ImageHeader self) -> float"""
2260  return _IMP_em.ImageHeader_get_fLenbyt(self)
2261 
2262  def set_fLenbyt(self, *args):
2263  """set_fLenbyt(ImageHeader self, float value)"""
2264  return _IMP_em.ImageHeader_set_fLenbyt(self, *args)
2265 
2266  def get_fGeo_matrix(self, *args):
2267  """get_fGeo_matrix(ImageHeader self, unsigned int i, unsigned int j) -> double"""
2268  return _IMP_em.ImageHeader_get_fGeo_matrix(self, *args)
2269 
2270  def get_fFlag(self):
2271  """get_fFlag(ImageHeader self) -> float"""
2272  return _IMP_em.ImageHeader_get_fFlag(self)
2273 
2274  def set_fFlag(self, *args):
2275  """set_fFlag(ImageHeader self, float value)"""
2276  return _IMP_em.ImageHeader_set_fFlag(self, *args)
2277 
2278  def get_euler_angles(self):
2279  """get_euler_angles(ImageHeader self) -> Vector3D"""
2280  return _IMP_em.ImageHeader_get_euler_angles(self)
2281 
2282  def get_euler_angles1(self):
2283  """get_euler_angles1(ImageHeader self) -> Vector3D"""
2284  return _IMP_em.ImageHeader_get_euler_angles1(self)
2285 
2286  def get_euler_angles2(self):
2287  """get_euler_angles2(ImageHeader self) -> Vector3D"""
2288  return _IMP_em.ImageHeader_get_euler_angles2(self)
2289 
2290  def set_euler_angles(self, *args):
2291  """set_euler_angles(ImageHeader self, Vector3D euler)"""
2292  return _IMP_em.ImageHeader_set_euler_angles(self, *args)
2293 
2294  def set_euler_angles1(self, *args):
2295  """set_euler_angles1(ImageHeader self, Vector3D euler)"""
2296  return _IMP_em.ImageHeader_set_euler_angles1(self, *args)
2297 
2298  def set_euler_angles2(self, *args):
2299  """set_euler_angles2(ImageHeader self, Vector3D euler)"""
2300  return _IMP_em.ImageHeader_set_euler_angles2(self, *args)
2301 
2302  def is_normalized(self):
2303  """is_normalized(ImageHeader self) -> bool"""
2304  return _IMP_em.ImageHeader_is_normalized(self)
2305 
2306  def set_date(self):
2307  """set_date(ImageHeader self)"""
2308  return _IMP_em.ImageHeader_set_date(self)
2309 
2310  def set_time(self):
2311  """set_time(ImageHeader self)"""
2312  return _IMP_em.ImageHeader_set_time(self)
2313 
2314  def set_title(self, *args):
2315  """set_title(ImageHeader self, IMP::String newName)"""
2316  return _IMP_em.ImageHeader_set_title(self, *args)
2317 
2318  __swig_destroy__ = _IMP_em.delete_ImageHeader
2319  __del__ = lambda self : None;
2320 ImageHeader_swigregister = _IMP_em.ImageHeader_swigregister
2321 ImageHeader_swigregister(ImageHeader)
2322 
2323 class SpiderMapReaderWriter(MapReaderWriter):
2324  """Proxy of C++ IMP::em::SpiderMapReaderWriter class"""
2325  __swig_setmethods__ = {}
2326  for _s in [MapReaderWriter]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2327  __setattr__ = lambda self, name, value: _swig_setattr(self, SpiderMapReaderWriter, name, value)
2328  __swig_getmethods__ = {}
2329  for _s in [MapReaderWriter]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2330  __getattr__ = lambda self, name: _swig_getattr(self, SpiderMapReaderWriter, name)
2331  __swig_setmethods__["filename_"] = _IMP_em.SpiderMapReaderWriter_filename__set
2332  __swig_getmethods__["filename_"] = _IMP_em.SpiderMapReaderWriter_filename__get
2333  if _newclass:filename_ = _swig_property(_IMP_em.SpiderMapReaderWriter_filename__get, _IMP_em.SpiderMapReaderWriter_filename__set)
2334  __swig_setmethods__["skip_type_check_"] = _IMP_em.SpiderMapReaderWriter_skip_type_check__set
2335  __swig_getmethods__["skip_type_check_"] = _IMP_em.SpiderMapReaderWriter_skip_type_check__get
2336  if _newclass:skip_type_check_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_type_check__get, _IMP_em.SpiderMapReaderWriter_skip_type_check__set)
2337  __swig_setmethods__["force_reversed_"] = _IMP_em.SpiderMapReaderWriter_force_reversed__set
2338  __swig_getmethods__["force_reversed_"] = _IMP_em.SpiderMapReaderWriter_force_reversed__get
2339  if _newclass:force_reversed_ = _swig_property(_IMP_em.SpiderMapReaderWriter_force_reversed__get, _IMP_em.SpiderMapReaderWriter_force_reversed__set)
2340  __swig_setmethods__["skip_extra_checkings_"] = _IMP_em.SpiderMapReaderWriter_skip_extra_checkings__set
2341  __swig_getmethods__["skip_extra_checkings_"] = _IMP_em.SpiderMapReaderWriter_skip_extra_checkings__get
2342  if _newclass:skip_extra_checkings_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_extra_checkings__get, _IMP_em.SpiderMapReaderWriter_skip_extra_checkings__set)
2343  def __init__(self, *args):
2344  """
2345  __init__(IMP::em::SpiderMapReaderWriter self) -> SpiderMapReaderWriter
2346  __init__(IMP::em::SpiderMapReaderWriter self, IMP::String filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings) -> SpiderMapReaderWriter
2347  """
2348  this = _IMP_em.new_SpiderMapReaderWriter(*args)
2349  try: self.this.append(this)
2350  except: self.this = this
2351  __swig_destroy__ = _IMP_em.delete_SpiderMapReaderWriter
2352  __del__ = lambda self : None;
2353  def __str__(self):
2354  """__str__(SpiderMapReaderWriter self) -> std::string"""
2355  return _IMP_em.SpiderMapReaderWriter___str__(self)
2356 
2357  def __repr__(self):
2358  """__repr__(SpiderMapReaderWriter self) -> std::string"""
2359  return _IMP_em.SpiderMapReaderWriter___repr__(self)
2360 
2361  def get_from(o):
2362  return _object_cast_to_SpiderMapReaderWriter(o)
2363  get_from = staticmethod(get_from)
2364 
2365 SpiderMapReaderWriter_swigregister = _IMP_em.SpiderMapReaderWriter_swigregister
2366 SpiderMapReaderWriter_swigregister(SpiderMapReaderWriter)
2367 
2368 class FittingSolutions(_object):
2369  """Proxy of C++ IMP::em::FittingSolutions class"""
2370  __swig_setmethods__ = {}
2371  __setattr__ = lambda self, name, value: _swig_setattr(self, FittingSolutions, name, value)
2372  __swig_getmethods__ = {}
2373  __getattr__ = lambda self, name: _swig_getattr(self, FittingSolutions, name)
2374  def __init__(self):
2375  """__init__(IMP::em::FittingSolutions self) -> FittingSolutions"""
2376  this = _IMP_em.new_FittingSolutions()
2377  try: self.this.append(this)
2378  except: self.this = this
2379  def get_number_of_solutions(self):
2380  """get_number_of_solutions(FittingSolutions self) -> int"""
2381  return _IMP_em.FittingSolutions_get_number_of_solutions(self)
2382 
2383  def get_transformation(self, *args):
2384  """get_transformation(FittingSolutions self, unsigned int i) -> Transformation3D"""
2385  return _IMP_em.FittingSolutions_get_transformation(self, *args)
2386 
2387  def get_score(self, *args):
2388  """get_score(FittingSolutions self, unsigned int i) -> IMP::Float"""
2389  return _IMP_em.FittingSolutions_get_score(self, *args)
2390 
2391  def set_score(self, *args):
2392  """set_score(FittingSolutions self, unsigned int i, IMP::Float score)"""
2393  return _IMP_em.FittingSolutions_set_score(self, *args)
2394 
2395  def add_solution(self, *args):
2396  """add_solution(FittingSolutions self, Transformation3D t, IMP::Float score)"""
2397  return _IMP_em.FittingSolutions_add_solution(self, *args)
2398 
2399  def sort(self, reverse=False):
2400  """
2401  sort(FittingSolutions self, bool reverse=False)
2402  sort(FittingSolutions self)
2403  """
2404  return _IMP_em.FittingSolutions_sort(self, reverse)
2405 
2406  def multiply(self, *args):
2407  """multiply(FittingSolutions self, Transformation3D t)"""
2408  return _IMP_em.FittingSolutions_multiply(self, *args)
2409 
2410  def get_transformations(self):
2411  """get_transformations(FittingSolutions self) -> IMP::algebra::Transformation3Ds"""
2412  return _IMP_em.FittingSolutions_get_transformations(self)
2413 
2414  def show(self, *args):
2415  """
2416  show(FittingSolutions self, _ostream out=std::cout)
2417  show(FittingSolutions self)
2418  """
2419  return _IMP_em.FittingSolutions_show(self, *args)
2420 
2421  def __str__(self):
2422  """__str__(FittingSolutions self) -> std::string"""
2423  return _IMP_em.FittingSolutions___str__(self)
2424 
2425  def __repr__(self):
2426  """__repr__(FittingSolutions self) -> std::string"""
2427  return _IMP_em.FittingSolutions___repr__(self)
2428 
2429  __swig_destroy__ = _IMP_em.delete_FittingSolutions
2430  __del__ = lambda self : None;
2431 FittingSolutions_swigregister = _IMP_em.FittingSolutions_swigregister
2432 FittingSolutions_swigregister(FittingSolutions)
2433 
2434 
2436  """
2437  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid,
2438  IMP::kernel::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5,
2439  IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100,
2440  IMP::Float max_translation=2., IMP::Float max_rotation=.3, bool fast=False) -> FittingSolutions
2441  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid,
2442  IMP::kernel::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5,
2443  IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100,
2444  IMP::Float max_translation=2., IMP::Float max_rotation=.3) -> FittingSolutions
2445  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid,
2446  IMP::kernel::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5,
2447  IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100,
2448  IMP::Float max_translation=2.) -> FittingSolutions
2449  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid,
2450  IMP::kernel::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5,
2451  IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100) -> FittingSolutions
2452  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid,
2453  IMP::kernel::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5,
2454  IMP::Int number_of_mc_steps=10) -> FittingSolutions
2455  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid,
2456  IMP::kernel::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2457  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid,
2458  IMP::kernel::OptimizerStates display_log) -> FittingSolutions
2459  """
2460  return _IMP_em.local_rigid_fitting_around_point(*args)
2461 
2462 def local_rigid_fitting(*args):
2463  """
2464  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::kernel::OptimizerStates display_log,
2465  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10,
2466  IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2.,
2467  IMP::Float max_rotation=.3, bool fast=True) -> FittingSolutions
2468  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::kernel::OptimizerStates display_log,
2469  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10,
2470  IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2.,
2471  IMP::Float max_rotation=.3) -> FittingSolutions
2472  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::kernel::OptimizerStates display_log,
2473  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10,
2474  IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2.) -> FittingSolutions
2475  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::kernel::OptimizerStates display_log,
2476  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10,
2477  IMP::Int number_of_cg_steps=100) -> FittingSolutions
2478  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::kernel::OptimizerStates display_log,
2479  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10) -> FittingSolutions
2480  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::kernel::OptimizerStates display_log,
2481  IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2482  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::kernel::OptimizerStates display_log) -> FittingSolutions
2483  """
2484  return _IMP_em.local_rigid_fitting(*args)
2485 
2487  """
2488  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids,
2489  IMP::kernel::OptimizerStates display_log,
2490  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100,
2491  IMP::Float max_translation=2., IMP::Float max_rotation=.3) -> 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,
2494  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100,
2495  IMP::Float max_translation=2.) -> FittingSolutions
2496  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids,
2497  IMP::kernel::OptimizerStates display_log,
2498  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100) -> FittingSolutions
2499  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids,
2500  IMP::kernel::OptimizerStates display_log,
2501  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10) -> FittingSolutions
2502  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids,
2503  IMP::kernel::OptimizerStates display_log,
2504  IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2505  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids,
2506  IMP::kernel::OptimizerStates display_log) -> FittingSolutions
2507  """
2508  return _IMP_em.local_rigid_fitting_around_points(*args)
2509 
2511  """
2512  local_rigid_fitting_grid_search(IMP::kernel::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2,
2513  IMP::Int translation_step=1, IMP::Float max_angle_in_radians=0.174,
2514  IMP::Int number_of_rotations=100) -> FittingSolutions
2515  local_rigid_fitting_grid_search(IMP::kernel::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2,
2516  IMP::Int translation_step=1, IMP::Float max_angle_in_radians=0.174) -> FittingSolutions
2517  local_rigid_fitting_grid_search(IMP::kernel::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2,
2518  IMP::Int translation_step=1) -> FittingSolutions
2519  local_rigid_fitting_grid_search(IMP::kernel::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2) -> FittingSolutions
2520  local_rigid_fitting_grid_search(IMP::kernel::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap) -> FittingSolutions
2521  """
2522  return _IMP_em.local_rigid_fitting_grid_search(*args)
2523 
2524 def compute_fitting_scores(*args):
2525  """
2526  compute_fitting_scores(IMP::kernel::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations,
2527  bool fast_version=False, bool local_score=False,
2528  FloatKey wei_key=IMP::atom::Mass::get_mass_key()) -> FittingSolutions
2529  compute_fitting_scores(IMP::kernel::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations,
2530  bool fast_version=False, bool local_score=False) -> FittingSolutions
2531  compute_fitting_scores(IMP::kernel::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations,
2532  bool fast_version=False) -> FittingSolutions
2533  compute_fitting_scores(IMP::kernel::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2534  compute_fitting_scores(DensityMap em_map, RigidBody rb, Refiner refiner, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2535  """
2536  return _IMP_em.compute_fitting_scores(*args)
2537 
2538 def compute_fitting_score(*args):
2539  """
2540  compute_fitting_score(IMP::kernel::ParticlesTemp const & ps, DensityMap em_map, FloatKey wei_key=IMP::atom::Mass::get_mass_key()) -> IMP::Float
2541  compute_fitting_score(IMP::kernel::ParticlesTemp const & ps, DensityMap em_map) -> IMP::Float
2542  """
2543  return _IMP_em.compute_fitting_score(*args)
2544 
2546  """
2547  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::kernel::Particles const & ps, Transformation3D t=IMP::algebra::get_identity_transformation_3d(),
2548  float thr=0.0) -> long
2549  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::kernel::Particles const & ps, Transformation3D t=IMP::algebra::get_identity_transformation_3d()) -> long
2550  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::kernel::Particles const & ps) -> long
2551  """
2552  return _IMP_em.get_number_of_particles_outside_of_the_density(*args)
2553 
2555  """
2556  get_numbers_of_particles_outside_of_the_density(DensityMap dmap, IMP::kernel::Particles const & ps, IMP::algebra::Transformation3Ds const & transformations,
2557  float thr=0.0) -> IMP::Ints
2558  get_numbers_of_particles_outside_of_the_density(DensityMap dmap, IMP::kernel::Particles const & ps, IMP::algebra::Transformation3Ds const & transformations) -> IMP::Ints
2559  """
2560  return _IMP_em.get_numbers_of_particles_outside_of_the_density(*args)
2561 
2563  """
2564  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(),
2565  float thr=0.0) -> double
2566  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
2567  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::kernel::Particles const & ps, float smoothing_radius=3.) -> double
2568  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::kernel::Particles const & ps) -> double
2569  """
2570  return _IMP_em.get_percentage_of_voxels_covered_by_particles(*args)
2571 class HighDensityEmbedding(IMP.statistics.Embedding):
2572  """Proxy of C++ IMP::em::HighDensityEmbedding class"""
2573  __swig_setmethods__ = {}
2574  for _s in [IMP.statistics.Embedding]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2575  __setattr__ = lambda self, name, value: _swig_setattr(self, HighDensityEmbedding, name, value)
2576  __swig_getmethods__ = {}
2577  for _s in [IMP.statistics.Embedding]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2578  __getattr__ = lambda self, name: _swig_getattr(self, HighDensityEmbedding, name)
2579  def __init__(self, *args):
2580  """__init__(IMP::em::HighDensityEmbedding self, DensityMap dm, double threshold) -> HighDensityEmbedding"""
2581  this = _IMP_em.new_HighDensityEmbedding(*args)
2582  try: self.this.append(this)
2583  except: self.this = this
2584  def get_version_info(self):
2585  """get_version_info(HighDensityEmbedding self) -> VersionInfo"""
2586  return _IMP_em.HighDensityEmbedding_get_version_info(self)
2587 
2588  __swig_destroy__ = _IMP_em.delete_HighDensityEmbedding
2589  __del__ = lambda self : None;
2590  def __str__(self):
2591  """__str__(HighDensityEmbedding self) -> std::string"""
2592  return _IMP_em.HighDensityEmbedding___str__(self)
2593 
2594  def __repr__(self):
2595  """__repr__(HighDensityEmbedding self) -> std::string"""
2596  return _IMP_em.HighDensityEmbedding___repr__(self)
2597 
2598  def get_from(o):
2599  return _object_cast_to_HighDensityEmbedding(o)
2600  get_from = staticmethod(get_from)
2601 
2602 HighDensityEmbedding_swigregister = _IMP_em.HighDensityEmbedding_swigregister
2603 HighDensityEmbedding_swigregister(HighDensityEmbedding)
2604 
2605 
2606 def mask_and_norm(*args):
2607  """mask_and_norm(DensityMap dmap, DensityMap mask) -> DensityMap"""
2608  return _IMP_em.mask_and_norm(*args)
2609 
2610 def get_volume_at_threshold(*args):
2611  """get_volume_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float"""
2612  return _IMP_em.get_volume_at_threshold(*args)
2613 
2615  """
2616  get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold, IMP::atom::ProteinDensityReference ref=HARPAZ) -> IMP::Float
2617  get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float
2618  """
2619  return _IMP_em.get_molecular_mass_at_threshold(*args)
2620 
2622  """get_threshold_for_approximate_volume(DensityMap m, IMP::Float desired_volume) -> IMP::Float"""
2623  return _IMP_em.get_threshold_for_approximate_volume(*args)
2624 
2626  """
2627  get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass, IMP::atom::ProteinDensityReference ref=HARPAZ) -> IMP::Float
2628  get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass) -> IMP::Float
2629  """
2630  return _IMP_em.get_threshold_for_approximate_mass(*args)
2631 class EnvelopePenetrationRestraint(IMP.kernel.Restraint):
2632  """Proxy of C++ IMP::em::EnvelopePenetrationRestraint class"""
2633  __swig_setmethods__ = {}
2634  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2635  __setattr__ = lambda self, name, value: _swig_setattr(self, EnvelopePenetrationRestraint, name, value)
2636  __swig_getmethods__ = {}
2637  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2638  __getattr__ = lambda self, name: _swig_getattr(self, EnvelopePenetrationRestraint, name)
2639  def __init__(self, *args):
2640  """__init__(IMP::em::EnvelopePenetrationRestraint self, IMP::kernel::Particles ps, DensityMap em_map, IMP::Float threshold) -> EnvelopePenetrationRestraint"""
2641  this = _IMP_em.new_EnvelopePenetrationRestraint(*args)
2642  try: self.this.append(this)
2643  except: self.this = this
2644  def do_get_inputs(self):
2645  """do_get_inputs(EnvelopePenetrationRestraint self) -> IMP::kernel::ModelObjectsTemp"""
2646  return _IMP_em.EnvelopePenetrationRestraint_do_get_inputs(self)
2647 
2648  def get_version_info(self):
2649  """get_version_info(EnvelopePenetrationRestraint self) -> VersionInfo"""
2650  return _IMP_em.EnvelopePenetrationRestraint_get_version_info(self)
2651 
2652  __swig_destroy__ = _IMP_em.delete_EnvelopePenetrationRestraint
2653  __del__ = lambda self : None;
2654  def __str__(self):
2655  """__str__(EnvelopePenetrationRestraint self) -> std::string"""
2656  return _IMP_em.EnvelopePenetrationRestraint___str__(self)
2657 
2658  def __repr__(self):
2659  """__repr__(EnvelopePenetrationRestraint self) -> std::string"""
2660  return _IMP_em.EnvelopePenetrationRestraint___repr__(self)
2661 
2662  def get_from(o):
2663  return _object_cast_to_EnvelopePenetrationRestraint(o)
2664  get_from = staticmethod(get_from)
2665 
2666 EnvelopePenetrationRestraint_swigregister = _IMP_em.EnvelopePenetrationRestraint_swigregister
2667 EnvelopePenetrationRestraint_swigregister(EnvelopePenetrationRestraint)
2668 
2669 class PCAFitRestraint(IMP.kernel.Restraint):
2670  """Proxy of C++ IMP::em::PCAFitRestraint class"""
2671  __swig_setmethods__ = {}
2672  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2673  __setattr__ = lambda self, name, value: _swig_setattr(self, PCAFitRestraint, name, value)
2674  __swig_getmethods__ = {}
2675  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2676  __getattr__ = lambda self, name: _swig_getattr(self, PCAFitRestraint, name)
2677  def __init__(self, *args):
2678  """
2679  __init__(IMP::em::PCAFitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map, float threahold, float max_pca_size_diff,
2680  float max_angle_diff, float max_centroid_diff, FloatKey weight_key=IMP::atom::Mass::get_mass_key()) -> PCAFitRestraint
2681  __init__(IMP::em::PCAFitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map, float threahold, float max_pca_size_diff,
2682  float max_angle_diff, float max_centroid_diff) -> PCAFitRestraint
2683  """
2684  this = _IMP_em.new_PCAFitRestraint(*args)
2685  try: self.this.append(this)
2686  except: self.this = this
2687  def do_get_inputs(self):
2688  """do_get_inputs(PCAFitRestraint self) -> IMP::kernel::ModelObjectsTemp"""
2689  return _IMP_em.PCAFitRestraint_do_get_inputs(self)
2690 
2691  def get_version_info(self):
2692  """get_version_info(PCAFitRestraint self) -> VersionInfo"""
2693  return _IMP_em.PCAFitRestraint_get_version_info(self)
2694 
2695  __swig_destroy__ = _IMP_em.delete_PCAFitRestraint
2696  __del__ = lambda self : None;
2697  def __str__(self):
2698  """__str__(PCAFitRestraint self) -> std::string"""
2699  return _IMP_em.PCAFitRestraint___str__(self)
2700 
2701  def __repr__(self):
2702  """__repr__(PCAFitRestraint self) -> std::string"""
2703  return _IMP_em.PCAFitRestraint___repr__(self)
2704 
2705  def get_from(o):
2706  return _object_cast_to_PCAFitRestraint(o)
2707  get_from = staticmethod(get_from)
2708 
2709 PCAFitRestraint_swigregister = _IMP_em.PCAFitRestraint_swigregister
2710 PCAFitRestraint_swigregister(PCAFitRestraint)
2711 
2712 class EnvelopeFitRestraint(IMP.kernel.Restraint):
2713  """Proxy of C++ IMP::em::EnvelopeFitRestraint class"""
2714  __swig_setmethods__ = {}
2715  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2716  __setattr__ = lambda self, name, value: _swig_setattr(self, EnvelopeFitRestraint, name, value)
2717  __swig_getmethods__ = {}
2718  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2719  __getattr__ = lambda self, name: _swig_getattr(self, EnvelopeFitRestraint, name)
2720  def __init__(self, *args):
2721  """__init__(IMP::em::EnvelopeFitRestraint self, IMP::kernel::Particles particles, DensityMap em_map, double density_threshold, double penetration_threshold) -> EnvelopeFitRestraint"""
2722  this = _IMP_em.new_EnvelopeFitRestraint(*args)
2723  try: self.this.append(this)
2724  except: self.this = this
2725  def get_transformation(self):
2726  """get_transformation(EnvelopeFitRestraint self) -> Transformation3D"""
2727  return _IMP_em.EnvelopeFitRestraint_get_transformation(self)
2728 
2729  def apply_transformation(self):
2730  """apply_transformation(EnvelopeFitRestraint self)"""
2731  return _IMP_em.EnvelopeFitRestraint_apply_transformation(self)
2732 
2733  def do_get_inputs(self):
2734  """do_get_inputs(EnvelopeFitRestraint self) -> IMP::kernel::ModelObjectsTemp"""
2735  return _IMP_em.EnvelopeFitRestraint_do_get_inputs(self)
2736 
2737  def get_version_info(self):
2738  """get_version_info(EnvelopeFitRestraint self) -> VersionInfo"""
2739  return _IMP_em.EnvelopeFitRestraint_get_version_info(self)
2740 
2741  __swig_destroy__ = _IMP_em.delete_EnvelopeFitRestraint
2742  __del__ = lambda self : None;
2743  def __str__(self):
2744  """__str__(EnvelopeFitRestraint self) -> std::string"""
2745  return _IMP_em.EnvelopeFitRestraint___str__(self)
2746 
2747  def __repr__(self):
2748  """__repr__(EnvelopeFitRestraint self) -> std::string"""
2749  return _IMP_em.EnvelopeFitRestraint___repr__(self)
2750 
2751  def get_from(o):
2752  return _object_cast_to_EnvelopeFitRestraint(o)
2753  get_from = staticmethod(get_from)
2754 
2755 EnvelopeFitRestraint_swigregister = _IMP_em.EnvelopeFitRestraint_swigregister
2756 EnvelopeFitRestraint_swigregister(EnvelopeFitRestraint)
2757 
2758 import math
2759 
2760 def write_pca_cmm(pca, fh):
2761  """Write out principal components to a file in Chimera Marker format"""
2762  eigen_values = pca.get_principal_values()
2763  eigen_vecs = pca.get_principal_components()
2764  centroid = pca.get_centroid()
2765 
2766  print >> fh, "<marker_set>"
2767  print >> fh, "<!-- PCA with eigen values: (%g,%g,%g) and " \
2768  "centroid (%g,%g,%g) -->" \
2769  % (math.sqrt(eigen_values[0]),
2770  math.sqrt(eigen_values[1]),
2771  math.sqrt(eigen_values[2]),
2772  centroid[0], centroid[1], centroid[2])
2773 
2774  radius = 2.
2775 
2776  for i in range(3):
2777  val = math.sqrt(eigen_values[i])
2778  v1 = centroid - val * eigen_vecs[i]
2779  v2 = centroid + val * eigen_vecs[i]
2780  for markerid, v in ((i*2+1, v1), (i*2+2, v2)):
2781  print >> fh, "<marker id=\"%d\" x=\"%g\" y=\"%g\" z=\"%g\" " \
2782  "radius=\"%g\"/>" \
2783  % (markerid, v[0], v[1], v[2], radius)
2784 
2785  for i in range(1, 7, 2):
2786  print >> fh, "<link id1= \"%d\" id2=\"%d\" radius=\"%g\"/>" \
2787  % (i, i+1, radius)
2788  print >> fh, "</marker_set>"
2789 
2790 
2791 def get_module_version():
2792  """get_module_version() -> std::string const"""
2793  return _IMP_em.get_module_version()
2794 
2795 def get_example_path(*args):
2796  """get_example_path(std::string fname) -> std::string"""
2797  return _IMP_em.get_example_path(*args)
2798 
2799 def get_data_path(*args):
2800  """get_data_path(std::string fname) -> std::string"""
2801  return _IMP_em.get_data_path(*args)
2802 import _version_check
2803 _version_check.check_version(get_module_version())
2804 
2805 # This file is compatible with both classic and new-style classes.
2806 
2807 
void get_transformed_into(const DensityMap *source, const algebra::Transformation3D &tr, DensityMap *into, bool calc_rms=true)
Rotate a density map into another map.
DensityMap * get_threshold_map(DensityMap *orig_map, float threshold)
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.
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.
See IMP.container for more information.
DensityMap * binarize(DensityMap *orig_map, float threshold, bool reverse=false)
double get_sum(const DensityMap *m1)
Return the sum of all voxels.
See IMP.cgal for more information.
Definition: cgal_config.h:107
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.
DensityMap * mask_and_norm(em::DensityMap *dmap, em::DensityMap *mask)
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
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.
See IMP.base for more information.
Definition: base/Array.h:20
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.
See IMP.score_functor for more information.
Definition: AddScores.h:14
DensityMap * read_map(std::string filename, MapReaderWriter *reader)
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.
See IMP.statistics for more information.
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)
bool get_interiors_intersect(const BoundingBoxD< D > &a, const BoundingBoxD< D > &b)
Return true if they intersect.
Definition: BoundingBoxD.h:193
DensityMap * multiply(const DensityMap *m1, const DensityMap *m2)
void write_map(DensityMap *m, std::string filename, MapReaderWriter *writer)
DensityHeader create_density_header(const algebra::BoundingBoxD< 3 > &bb, float spacing)
Create a header from a bounding box 3D.
See IMP.kernel for more information.
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.
Float approximate_molecular_mass(DensityMap *m, Float threshold)
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.
See IMP.core for more information.
See IMP.algebra for more information.
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:82
See IMP.display for more information.
Definition: BildWriter.h:20
CheckLevel get_check_level()
Get the current audit mode.
See IMP.atom for more information.
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.
BoundingBoxD< D > get_bounding_box(const BoundingBoxD< D > &g)
Definition: BoundingBoxD.h:160
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.