IMP  2.0.1
The Integrative Modeling Platform
em/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 2.0.8
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 from sys import version_info
10 if version_info >= (2,6,0):
11  def swig_import_helper():
12  from os.path import dirname
13  import imp
14  fp = None
15  try:
16  fp, pathname, description = imp.find_module('_IMP_em', [dirname(__file__)])
17  except ImportError:
18  import _IMP_em
19  return _IMP_em
20  if fp is not None:
21  try:
22  _mod = imp.load_module('_IMP_em', fp, pathname, description)
23  finally:
24  fp.close()
25  return _mod
26  _IMP_em = swig_import_helper()
27  del swig_import_helper
28 else:
29  import _IMP_em
30 del version_info
31 try:
32  _swig_property = property
33 except NameError:
34  pass # Python < 2.2 doesn't have 'property'.
35 def _swig_setattr_nondynamic(self,class_type,name,value,static=1):
36  if (name == "thisown"): return self.this.own(value)
37  if (name == "this"):
38  if type(value).__name__ == 'SwigPyObject':
39  self.__dict__[name] = value
40  return
41  method = class_type.__swig_setmethods__.get(name,None)
42  if method: return method(self,value)
43  if (not static):
44  self.__dict__[name] = value
45  else:
46  raise AttributeError("You cannot add attributes to %s" % self)
47 
48 def _swig_setattr(self,class_type,name,value):
49  return _swig_setattr_nondynamic(self,class_type,name,value,0)
50 
51 def _swig_getattr(self,class_type,name):
52  if (name == "thisown"): return self.this.own()
53  method = class_type.__swig_getmethods__.get(name,None)
54  if method: return method(self)
55  raise AttributeError(name)
56 
57 def _swig_repr(self):
58  try: strthis = "proxy of " + self.this.__repr__()
59  except: strthis = ""
60  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
61 
62 try:
63  _object = object
64  _newclass = 1
65 except AttributeError:
66  class _object : pass
67  _newclass = 0
68 
69 
70 try:
71  import weakref
72  weakref_proxy = weakref.proxy
73 except:
74  weakref_proxy = lambda x: x
75 
76 
77 class IMP_EM_SwigPyIterator(_object):
78  """Proxy of C++ swig::IMP_EM_SwigPyIterator class"""
79  __swig_setmethods__ = {}
80  __setattr__ = lambda self, name, value: _swig_setattr(self, IMP_EM_SwigPyIterator, name, value)
81  __swig_getmethods__ = {}
82  __getattr__ = lambda self, name: _swig_getattr(self, IMP_EM_SwigPyIterator, name)
83  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
84  __repr__ = _swig_repr
85  __swig_destroy__ = _IMP_em.delete_IMP_EM_SwigPyIterator
86  __del__ = lambda self : None;
87  def value(self):
88  """value(IMP_EM_SwigPyIterator self) -> PyObject *"""
89  return _IMP_em.IMP_EM_SwigPyIterator_value(self)
90 
91  def incr(self, n=1):
92  """
93  incr(IMP_EM_SwigPyIterator self, size_t n=1) -> IMP_EM_SwigPyIterator
94  incr(IMP_EM_SwigPyIterator self) -> IMP_EM_SwigPyIterator
95  """
96  return _IMP_em.IMP_EM_SwigPyIterator_incr(self, n)
97 
98  def decr(self, n=1):
99  """
100  decr(IMP_EM_SwigPyIterator self, size_t n=1) -> IMP_EM_SwigPyIterator
101  decr(IMP_EM_SwigPyIterator self) -> IMP_EM_SwigPyIterator
102  """
103  return _IMP_em.IMP_EM_SwigPyIterator_decr(self, n)
104 
105  def distance(self, *args):
106  """distance(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> ptrdiff_t"""
107  return _IMP_em.IMP_EM_SwigPyIterator_distance(self, *args)
108 
109  def equal(self, *args):
110  """equal(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> bool"""
111  return _IMP_em.IMP_EM_SwigPyIterator_equal(self, *args)
112 
113  def copy(self):
114  """copy(IMP_EM_SwigPyIterator self) -> IMP_EM_SwigPyIterator"""
115  return _IMP_em.IMP_EM_SwigPyIterator_copy(self)
116 
117  def next(self):
118  """next(IMP_EM_SwigPyIterator self) -> PyObject *"""
119  return _IMP_em.IMP_EM_SwigPyIterator_next(self)
120 
121  def __next__(self):
122  """__next__(IMP_EM_SwigPyIterator self) -> PyObject *"""
123  return _IMP_em.IMP_EM_SwigPyIterator___next__(self)
124 
125  def previous(self):
126  """previous(IMP_EM_SwigPyIterator self) -> PyObject *"""
127  return _IMP_em.IMP_EM_SwigPyIterator_previous(self)
128 
129  def advance(self, *args):
130  """advance(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator"""
131  return _IMP_em.IMP_EM_SwigPyIterator_advance(self, *args)
132 
133  def __eq__(self, *args):
134  """__eq__(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> bool"""
135  return _IMP_em.IMP_EM_SwigPyIterator___eq__(self, *args)
136 
137  def __ne__(self, *args):
138  """__ne__(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> bool"""
139  return _IMP_em.IMP_EM_SwigPyIterator___ne__(self, *args)
140 
141  def __iadd__(self, *args):
142  """__iadd__(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator"""
143  return _IMP_em.IMP_EM_SwigPyIterator___iadd__(self, *args)
144 
145  def __isub__(self, *args):
146  """__isub__(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator"""
147  return _IMP_em.IMP_EM_SwigPyIterator___isub__(self, *args)
148 
149  def __add__(self, *args):
150  """__add__(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator"""
151  return _IMP_em.IMP_EM_SwigPyIterator___add__(self, *args)
152 
153  def __sub__(self, *args):
154  """
155  __sub__(IMP_EM_SwigPyIterator self, ptrdiff_t n) -> IMP_EM_SwigPyIterator
156  __sub__(IMP_EM_SwigPyIterator self, IMP_EM_SwigPyIterator x) -> ptrdiff_t
157  """
158  return _IMP_em.IMP_EM_SwigPyIterator___sub__(self, *args)
159 
160  def __iter__(self): return self
161 IMP_EM_SwigPyIterator_swigregister = _IMP_em.IMP_EM_SwigPyIterator_swigregister
162 IMP_EM_SwigPyIterator_swigregister(IMP_EM_SwigPyIterator)
163 
164 _value_types=[]
165 _object_types=[]
166 _raii_types=[]
167 _plural_types=[]
168 
169 IMP_HAS_DEPRECATED = _IMP_em.IMP_HAS_DEPRECATED
170 IMP_DEBUG = _IMP_em.IMP_DEBUG
171 IMP_RELEASE = _IMP_em.IMP_RELEASE
172 IMP_SILENT = _IMP_em.IMP_SILENT
173 IMP_PROGRESS = _IMP_em.IMP_PROGRESS
174 IMP_TERSE = _IMP_em.IMP_TERSE
175 IMP_VERBOSE = _IMP_em.IMP_VERBOSE
176 IMP_NONE = _IMP_em.IMP_NONE
177 IMP_USAGE = _IMP_em.IMP_USAGE
178 IMP_INTERNAL = _IMP_em.IMP_INTERNAL
179 IMP_COMPILER_HAS_AUTO = _IMP_em.IMP_COMPILER_HAS_AUTO
180 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_em.IMP_COMPILER_HAS_DEBUG_VECTOR
181 IMP_COMPILER_HAS_NULLPTR = _IMP_em.IMP_COMPILER_HAS_NULLPTR
182 IMP_BASE_HAS_BOOST_RANDOM = _IMP_em.IMP_BASE_HAS_BOOST_RANDOM
183 IMP_BASE_HAS_GPERFTOOLS = _IMP_em.IMP_BASE_HAS_GPERFTOOLS
184 IMP_BASE_HAS_LOG4CXX = _IMP_em.IMP_BASE_HAS_LOG4CXX
185 IMP_BASE_HAS_TCMALLOC_HEAPCHECKER = _IMP_em.IMP_BASE_HAS_TCMALLOC_HEAPCHECKER
186 IMP_BASE_HAS_TCMALLOC_HEAPPROFILER = _IMP_em.IMP_BASE_HAS_TCMALLOC_HEAPPROFILER
187 import sys
188 class _DirectorObjects(object):
189  """@internal Simple class to keep references to director objects
190  to prevent premature deletion."""
191  def __init__(self):
192  self._objects = []
193  def register(self, obj):
194  """Take a reference to a director object; will only work for
195  refcounted C++ classes"""
196  if hasattr(obj, 'get_ref_count'):
197  self._objects.append(obj)
198  def cleanup(self):
199  """Only drop our reference and allow cleanup by Python if no other
200  Python references exist (we hold 3 references: one in self._objects,
201  one in x, and one in the argument list for getrefcount) *and* no
202  other C++ references exist (the Python object always holds one)"""
203  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
204  or x.get_ref_count() > 1]
205 
206 
207  self._objects = objs
208  def get_object_count(self):
209  """Get number of director objects (useful for testing only)"""
210  return len(self._objects)
211 _director_objects = _DirectorObjects()
212 
213 DEFAULT_CHECK = _IMP_em.DEFAULT_CHECK
214 NONE = _IMP_em.NONE
215 USAGE = _IMP_em.USAGE
216 USAGE_AND_INTERNAL = _IMP_em.USAGE_AND_INTERNAL
217 
218 def set_check_level(*args):
219  """set_check_level(IMP::base::CheckLevel tf)"""
220  return _IMP_em.set_check_level(*args)
221 
222 def get_check_level():
223  """get_check_level() -> IMP::base::CheckLevel"""
224  return _IMP_em.get_check_level()
225 class _ostream(_object):
226  """Proxy of C++ std::ostream class"""
227  __swig_setmethods__ = {}
228  __setattr__ = lambda self, name, value: _swig_setattr(self, _ostream, name, value)
229  __swig_getmethods__ = {}
230  __getattr__ = lambda self, name: _swig_getattr(self, _ostream, name)
231  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined")
232  __repr__ = _swig_repr
233  def write(self, *args):
234  """write(_ostream self, char const * osa_buf)"""
235  return _IMP_em._ostream_write(self, *args)
236 
237 _ostream_swigregister = _IMP_em._ostream_swigregister
238 _ostream_swigregister(_ostream)
239 
240 IMP_COMPILER_HAS_OVERRIDE = _IMP_em.IMP_COMPILER_HAS_OVERRIDE
241 IMP_COMPILER_HAS_FINAL = _IMP_em.IMP_COMPILER_HAS_FINAL
242 import IMP.base
243 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CGAL_HAS_BOOST_FILESYSTEM
244 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
245 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_em.IMP_CGAL_HAS_BOOST_RANDOM
246 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_em.IMP_CGAL_HAS_BOOST_SYSTEM
247 import IMP.cgal
248 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_em.IMP_ALGEBRA_HAS_IMP_CGAL
249 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
250 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
251 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_RANDOM
252 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_em.IMP_ALGEBRA_HAS_BOOST_SYSTEM
253 IMP_ALGEBRA_HAS_CGAL = _IMP_em.IMP_ALGEBRA_HAS_CGAL
254 IMP_ALGEBRA_HAS_ANN = _IMP_em.IMP_ALGEBRA_HAS_ANN
255 import IMP.algebra
256 IMP_KERNEL_HAS_IMP_CGAL = _IMP_em.IMP_KERNEL_HAS_IMP_CGAL
257 IMP_KERNEL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_KERNEL_HAS_BOOST_PROGRAMOPTIONS
258 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_em.IMP_KERNEL_HAS_BOOST_RANDOM
259 IMP_KERNEL_HAS_BOOST_SYSTEM = _IMP_em.IMP_KERNEL_HAS_BOOST_SYSTEM
260 IMP_KERNEL_HAS_CGAL = _IMP_em.IMP_KERNEL_HAS_CGAL
261 import IMP.kernel
262 IMP_DISPLAY_HAS_IMP_BASE = _IMP_em.IMP_DISPLAY_HAS_IMP_BASE
263 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_em.IMP_DISPLAY_HAS_IMP_CGAL
264 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
265 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
266 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_em.IMP_DISPLAY_HAS_BOOST_RANDOM
267 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_em.IMP_DISPLAY_HAS_BOOST_SYSTEM
268 IMP_DISPLAY_HAS_CGAL = _IMP_em.IMP_DISPLAY_HAS_CGAL
269 import IMP.display
270 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_em.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
271 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
272 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
273 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
274 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_em.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
275 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_em.IMP_SCORE_FUNCTOR_HAS_CGAL
276 import IMP.score_functor
277 IMP_STATISTICS_HAS_IMP_BASE = _IMP_em.IMP_STATISTICS_HAS_IMP_BASE
278 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_em.IMP_STATISTICS_HAS_IMP_CGAL
279 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
280 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
281 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_em.IMP_STATISTICS_HAS_BOOST_RANDOM
282 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_em.IMP_STATISTICS_HAS_BOOST_SYSTEM
283 IMP_STATISTICS_HAS_CGAL = _IMP_em.IMP_STATISTICS_HAS_CGAL
284 import IMP.statistics
285 IMP_CORE_HAS_IMP_BASE = _IMP_em.IMP_CORE_HAS_IMP_BASE
286 IMP_CORE_HAS_IMP_CGAL = _IMP_em.IMP_CORE_HAS_IMP_CGAL
287 IMP_CORE_HAS_IMP_KERNEL = _IMP_em.IMP_CORE_HAS_IMP_KERNEL
288 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_FILESYSTEM
289 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
290 IMP_CORE_HAS_BOOST_RANDOM = _IMP_em.IMP_CORE_HAS_BOOST_RANDOM
291 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_em.IMP_CORE_HAS_BOOST_SYSTEM
292 IMP_CORE_HAS_CGAL = _IMP_em.IMP_CORE_HAS_CGAL
293 import IMP.core
294 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_em.IMP_CONTAINER_HAS_IMP_ALGEBRA
295 IMP_CONTAINER_HAS_IMP_BASE = _IMP_em.IMP_CONTAINER_HAS_IMP_BASE
296 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_em.IMP_CONTAINER_HAS_IMP_CGAL
297 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_em.IMP_CONTAINER_HAS_IMP_DISPLAY
298 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_em.IMP_CONTAINER_HAS_IMP_KERNEL
299 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
300 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
301 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
302 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_em.IMP_CONTAINER_HAS_BOOST_RANDOM
303 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_em.IMP_CONTAINER_HAS_BOOST_SYSTEM
304 IMP_CONTAINER_HAS_CGAL = _IMP_em.IMP_CONTAINER_HAS_CGAL
305 import IMP.container
306 IMP_ATOM_HAS_IMP_BASE = _IMP_em.IMP_ATOM_HAS_IMP_BASE
307 IMP_ATOM_HAS_IMP_CGAL = _IMP_em.IMP_ATOM_HAS_IMP_CGAL
308 IMP_ATOM_HAS_IMP_KERNEL = _IMP_em.IMP_ATOM_HAS_IMP_KERNEL
309 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
310 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
311 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_em.IMP_ATOM_HAS_BOOST_RANDOM
312 IMP_ATOM_HAS_BOOST_REGEX = _IMP_em.IMP_ATOM_HAS_BOOST_REGEX
313 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_em.IMP_ATOM_HAS_BOOST_SYSTEM
314 IMP_ATOM_HAS_CGAL = _IMP_em.IMP_ATOM_HAS_CGAL
315 IMP_ATOM_TYPE_INDEX = _IMP_em.IMP_ATOM_TYPE_INDEX
316 IMP_RESIDUE_TYPE_INDEX = _IMP_em.IMP_RESIDUE_TYPE_INDEX
317 IMP_HIERARCHY_TYPE_INDEX = _IMP_em.IMP_HIERARCHY_TYPE_INDEX
318 import IMP.atom
319 IMP_EM_HAS_IMP_CGAL = _IMP_em.IMP_EM_HAS_IMP_CGAL
320 IMP_EM_HAS_IMP_CONTAINER = _IMP_em.IMP_EM_HAS_IMP_CONTAINER
321 IMP_EM_HAS_IMP_DISPLAY = _IMP_em.IMP_EM_HAS_IMP_DISPLAY
322 IMP_EM_HAS_IMP_KERNEL = _IMP_em.IMP_EM_HAS_IMP_KERNEL
323 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_em.IMP_EM_HAS_IMP_SCORE_FUNCTOR
324 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_em.IMP_EM_HAS_BOOST_FILESYSTEM
325 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
326 IMP_EM_HAS_BOOST_RANDOM = _IMP_em.IMP_EM_HAS_BOOST_RANDOM
327 IMP_EM_HAS_BOOST_REGEX = _IMP_em.IMP_EM_HAS_BOOST_REGEX
328 IMP_EM_HAS_BOOST_SYSTEM = _IMP_em.IMP_EM_HAS_BOOST_SYSTEM
329 IMP_EM_HAS_CGAL = _IMP_em.IMP_EM_HAS_CGAL
330 _object_types.append("DensityMap")
331 
332 
333 def _object_cast_to_DensityMap(*args):
334  """_object_cast_to_DensityMap(Object o) -> DensityMap"""
335  return _IMP_em._object_cast_to_DensityMap(*args)
336 _object_types.append("SampledDensityMap")
337 
338 
339 def _object_cast_to_SampledDensityMap(*args):
340  """_object_cast_to_SampledDensityMap(Object o) -> SampledDensityMap"""
341  return _IMP_em._object_cast_to_SampledDensityMap(*args)
342 _object_types.append("SurfaceShellDensityMap")
343 
344 
345 def _object_cast_to_SurfaceShellDensityMap(*args):
346  """_object_cast_to_SurfaceShellDensityMap(Object o) -> SurfaceShellDensityMap"""
347  return _IMP_em._object_cast_to_SurfaceShellDensityMap(*args)
348 _object_types.append("FitRestraint")
349 
350 
351 def _object_cast_to_FitRestraint(*args):
352  """_object_cast_to_FitRestraint(Object o) -> FitRestraint"""
353  return _IMP_em._object_cast_to_FitRestraint(*args)
354 _object_types.append("PCAFitRestraint")
355 
356 
357 def _object_cast_to_PCAFitRestraint(*args):
358  """_object_cast_to_PCAFitRestraint(Object o) -> PCAFitRestraint"""
359  return _IMP_em._object_cast_to_PCAFitRestraint(*args)
360 _object_types.append("EnvelopePenetrationRestraint")
361 
362 
363 def _object_cast_to_EnvelopePenetrationRestraint(*args):
364  """_object_cast_to_EnvelopePenetrationRestraint(Object o) -> EnvelopePenetrationRestraint"""
365  return _IMP_em._object_cast_to_EnvelopePenetrationRestraint(*args)
366 _object_types.append("EnvelopeFitRestraint")
367 
368 
369 def _object_cast_to_EnvelopeFitRestraint(*args):
370  """_object_cast_to_EnvelopeFitRestraint(Object o) -> EnvelopeFitRestraint"""
371  return _IMP_em._object_cast_to_EnvelopeFitRestraint(*args)
372 RadiusDependentKernelParametersList=list
373 _plural_types.append("RadiusDependentKernelParametersList")
374 _value_types.append("RadiusDependentKernelParameters")
375 
376 KernelParametersList=list
377 _plural_types.append("KernelParametersList")
378 _value_types.append("KernelParameters")
379 
380 _object_types.append("HighDensityEmbedding")
381 
382 
383 def _object_cast_to_HighDensityEmbedding(*args):
384  """_object_cast_to_HighDensityEmbedding(Object o) -> HighDensityEmbedding"""
385  return _IMP_em._object_cast_to_HighDensityEmbedding(*args)
386 _object_types.append("MapReaderWriter")
387 
388 
389 def _object_cast_to_MapReaderWriter(*args):
390  """_object_cast_to_MapReaderWriter(Object o) -> MapReaderWriter"""
391  return _IMP_em._object_cast_to_MapReaderWriter(*args)
392 _object_types.append("MRCReaderWriter")
393 
394 
395 def _object_cast_to_MRCReaderWriter(*args):
396  """_object_cast_to_MRCReaderWriter(Object o) -> MRCReaderWriter"""
397  return _IMP_em._object_cast_to_MRCReaderWriter(*args)
398 _object_types.append("SpiderMapReaderWriter")
399 
400 
401 def _object_cast_to_SpiderMapReaderWriter(*args):
402  """_object_cast_to_SpiderMapReaderWriter(Object o) -> SpiderMapReaderWriter"""
403  return _IMP_em._object_cast_to_SpiderMapReaderWriter(*args)
404 _object_types.append("EMReaderWriter")
405 
406 
407 def _object_cast_to_EMReaderWriter(*args):
408  """_object_cast_to_EMReaderWriter(Object o) -> EMReaderWriter"""
409  return _IMP_em._object_cast_to_EMReaderWriter(*args)
410 _object_types.append("XplorReaderWriter")
411 
412 
413 def _object_cast_to_XplorReaderWriter(*args):
414  """_object_cast_to_XplorReaderWriter(Object o) -> XplorReaderWriter"""
415  return _IMP_em._object_cast_to_XplorReaderWriter(*args)
416 _object_types.append("CoarseCC")
417 
418 
419 def _object_cast_to_CoarseCC(*args):
420  """_object_cast_to_CoarseCC(Object o) -> CoarseCC"""
421  return _IMP_em._object_cast_to_CoarseCC(*args)
422 _object_types.append("CoarseCCatIntervals")
423 
424 
425 def _object_cast_to_CoarseCCatIntervals(*args):
426  """_object_cast_to_CoarseCCatIntervals(Object o) -> CoarseCCatIntervals"""
427  return _IMP_em._object_cast_to_CoarseCCatIntervals(*args)
428 FittingSolutionsList=list
429 _plural_types.append("FittingSolutionsList")
430 _value_types.append("FittingSolutions")
431 
432 class MapReaderWriter(IMP.base.Object):
433  """Proxy of C++ IMP::em::MapReaderWriter class"""
434  __swig_setmethods__ = {}
435  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
436  __setattr__ = lambda self, name, value: _swig_setattr(self, MapReaderWriter, name, value)
437  __swig_getmethods__ = {}
438  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
439  __getattr__ = lambda self, name: _swig_getattr(self, MapReaderWriter, name)
440  def __init__(self):
441  """__init__(IMP::em::MapReaderWriter self) -> MapReaderWriter"""
442  this = _IMP_em.new_MapReaderWriter()
443  try: self.this.append(this)
444  except: self.this = this
445  def get_version_info(self):
446  """get_version_info(MapReaderWriter self) -> VersionInfo"""
447  return _IMP_em.MapReaderWriter_get_version_info(self)
448 
449  __swig_destroy__ = _IMP_em.delete_MapReaderWriter
450  __del__ = lambda self : None;
451  def __str__(self):
452  """__str__(MapReaderWriter self) -> std::string"""
453  return _IMP_em.MapReaderWriter___str__(self)
454 
455  def __repr__(self):
456  """__repr__(MapReaderWriter self) -> std::string"""
457  return _IMP_em.MapReaderWriter___repr__(self)
458 
459  def get_from(o):
460  return _object_cast_to_MapReaderWriter(o)
461  get_from = staticmethod(get_from)
462 
463 MapReaderWriter_swigregister = _IMP_em.MapReaderWriter_swigregister
464 MapReaderWriter_swigregister(MapReaderWriter)
465 cvar = _IMP_em.cvar
466 EPS = cvar.EPS
467 
468 class DensityHeader(_object):
469  """Proxy of C++ IMP::em::DensityHeader class"""
470  __swig_setmethods__ = {}
471  __setattr__ = lambda self, name, value: _swig_setattr(self, DensityHeader, name, value)
472  __swig_getmethods__ = {}
473  __getattr__ = lambda self, name: _swig_getattr(self, DensityHeader, name)
474  __repr__ = _swig_repr
475  def __init__(self):
476  """__init__(IMP::em::DensityHeader self) -> DensityHeader"""
477  this = _IMP_em.new_DensityHeader()
478  try: self.this.append(this)
479  except: self.this = this
480  def get_top(self, *args):
481  """get_top(DensityHeader self, int ind) -> IMP::em::emreal"""
482  return _IMP_em.DensityHeader_get_top(self, *args)
483 
484  def compute_xyz_top(self, force=False):
485  """
486  compute_xyz_top(DensityHeader self, bool force=False)
487  compute_xyz_top(DensityHeader self)
488  """
489  return _IMP_em.DensityHeader_compute_xyz_top(self, force)
490 
491  def update_map_dimensions(self, *args):
492  """update_map_dimensions(DensityHeader self, int nnx, int nny, int nnz)"""
493  return _IMP_em.DensityHeader_update_map_dimensions(self, *args)
494 
495  def update_cell_dimensions(self):
496  """update_cell_dimensions(DensityHeader self)"""
497  return _IMP_em.DensityHeader_update_cell_dimensions(self)
498 
499  def show(self, *args):
500  """
501  show(DensityHeader self, _ostream out=std::cout)
502  show(DensityHeader self)
503  """
504  return _IMP_em.DensityHeader_show(self, *args)
505 
506  MAP_FIELD_SIZE = _IMP_em.DensityHeader_MAP_FIELD_SIZE
507  USER_FIELD_SIZE = _IMP_em.DensityHeader_USER_FIELD_SIZE
508  COMMENT_FIELD_NUM_OF = _IMP_em.DensityHeader_COMMENT_FIELD_NUM_OF
509  COMMENT_FIELD_SINGLE_SIZE = _IMP_em.DensityHeader_COMMENT_FIELD_SINGLE_SIZE
510  __swig_setmethods__["nxstart"] = _IMP_em.DensityHeader_nxstart_set
511  __swig_getmethods__["nxstart"] = _IMP_em.DensityHeader_nxstart_get
512  if _newclass:nxstart = _swig_property(_IMP_em.DensityHeader_nxstart_get, _IMP_em.DensityHeader_nxstart_set)
513  __swig_setmethods__["nystart"] = _IMP_em.DensityHeader_nystart_set
514  __swig_getmethods__["nystart"] = _IMP_em.DensityHeader_nystart_get
515  if _newclass:nystart = _swig_property(_IMP_em.DensityHeader_nystart_get, _IMP_em.DensityHeader_nystart_set)
516  __swig_setmethods__["nzstart"] = _IMP_em.DensityHeader_nzstart_set
517  __swig_getmethods__["nzstart"] = _IMP_em.DensityHeader_nzstart_get
518  if _newclass:nzstart = _swig_property(_IMP_em.DensityHeader_nzstart_get, _IMP_em.DensityHeader_nzstart_set)
519  __swig_setmethods__["mx"] = _IMP_em.DensityHeader_mx_set
520  __swig_getmethods__["mx"] = _IMP_em.DensityHeader_mx_get
521  if _newclass:mx = _swig_property(_IMP_em.DensityHeader_mx_get, _IMP_em.DensityHeader_mx_set)
522  __swig_setmethods__["my"] = _IMP_em.DensityHeader_my_set
523  __swig_getmethods__["my"] = _IMP_em.DensityHeader_my_get
524  if _newclass:my = _swig_property(_IMP_em.DensityHeader_my_get, _IMP_em.DensityHeader_my_set)
525  __swig_setmethods__["mz"] = _IMP_em.DensityHeader_mz_set
526  __swig_getmethods__["mz"] = _IMP_em.DensityHeader_mz_get
527  if _newclass:mz = _swig_property(_IMP_em.DensityHeader_mz_get, _IMP_em.DensityHeader_mz_set)
528  __swig_setmethods__["xlen"] = _IMP_em.DensityHeader_xlen_set
529  __swig_getmethods__["xlen"] = _IMP_em.DensityHeader_xlen_get
530  if _newclass:xlen = _swig_property(_IMP_em.DensityHeader_xlen_get, _IMP_em.DensityHeader_xlen_set)
531  __swig_setmethods__["ylen"] = _IMP_em.DensityHeader_ylen_set
532  __swig_getmethods__["ylen"] = _IMP_em.DensityHeader_ylen_get
533  if _newclass:ylen = _swig_property(_IMP_em.DensityHeader_ylen_get, _IMP_em.DensityHeader_ylen_set)
534  __swig_setmethods__["zlen"] = _IMP_em.DensityHeader_zlen_set
535  __swig_getmethods__["zlen"] = _IMP_em.DensityHeader_zlen_get
536  if _newclass:zlen = _swig_property(_IMP_em.DensityHeader_zlen_get, _IMP_em.DensityHeader_zlen_set)
537  __swig_setmethods__["alpha"] = _IMP_em.DensityHeader_alpha_set
538  __swig_getmethods__["alpha"] = _IMP_em.DensityHeader_alpha_get
539  if _newclass:alpha = _swig_property(_IMP_em.DensityHeader_alpha_get, _IMP_em.DensityHeader_alpha_set)
540  __swig_setmethods__["beta"] = _IMP_em.DensityHeader_beta_set
541  __swig_getmethods__["beta"] = _IMP_em.DensityHeader_beta_get
542  if _newclass:beta = _swig_property(_IMP_em.DensityHeader_beta_get, _IMP_em.DensityHeader_beta_set)
543  __swig_setmethods__["gamma"] = _IMP_em.DensityHeader_gamma_set
544  __swig_getmethods__["gamma"] = _IMP_em.DensityHeader_gamma_get
545  if _newclass:gamma = _swig_property(_IMP_em.DensityHeader_gamma_get, _IMP_em.DensityHeader_gamma_set)
546  __swig_setmethods__["mapc"] = _IMP_em.DensityHeader_mapc_set
547  __swig_getmethods__["mapc"] = _IMP_em.DensityHeader_mapc_get
548  if _newclass:mapc = _swig_property(_IMP_em.DensityHeader_mapc_get, _IMP_em.DensityHeader_mapc_set)
549  __swig_setmethods__["mapr"] = _IMP_em.DensityHeader_mapr_set
550  __swig_getmethods__["mapr"] = _IMP_em.DensityHeader_mapr_get
551  if _newclass:mapr = _swig_property(_IMP_em.DensityHeader_mapr_get, _IMP_em.DensityHeader_mapr_set)
552  __swig_setmethods__["maps"] = _IMP_em.DensityHeader_maps_set
553  __swig_getmethods__["maps"] = _IMP_em.DensityHeader_maps_get
554  if _newclass:maps = _swig_property(_IMP_em.DensityHeader_maps_get, _IMP_em.DensityHeader_maps_set)
555  __swig_setmethods__["dmin"] = _IMP_em.DensityHeader_dmin_set
556  __swig_getmethods__["dmin"] = _IMP_em.DensityHeader_dmin_get
557  if _newclass:dmin = _swig_property(_IMP_em.DensityHeader_dmin_get, _IMP_em.DensityHeader_dmin_set)
558  __swig_setmethods__["dmax"] = _IMP_em.DensityHeader_dmax_set
559  __swig_getmethods__["dmax"] = _IMP_em.DensityHeader_dmax_get
560  if _newclass:dmax = _swig_property(_IMP_em.DensityHeader_dmax_get, _IMP_em.DensityHeader_dmax_set)
561  __swig_setmethods__["dmean"] = _IMP_em.DensityHeader_dmean_set
562  __swig_getmethods__["dmean"] = _IMP_em.DensityHeader_dmean_get
563  if _newclass:dmean = _swig_property(_IMP_em.DensityHeader_dmean_get, _IMP_em.DensityHeader_dmean_set)
564  __swig_setmethods__["ispg"] = _IMP_em.DensityHeader_ispg_set
565  __swig_getmethods__["ispg"] = _IMP_em.DensityHeader_ispg_get
566  if _newclass:ispg = _swig_property(_IMP_em.DensityHeader_ispg_get, _IMP_em.DensityHeader_ispg_set)
567  __swig_setmethods__["nsymbt"] = _IMP_em.DensityHeader_nsymbt_set
568  __swig_getmethods__["nsymbt"] = _IMP_em.DensityHeader_nsymbt_get
569  if _newclass:nsymbt = _swig_property(_IMP_em.DensityHeader_nsymbt_get, _IMP_em.DensityHeader_nsymbt_set)
570  __swig_setmethods__["user"] = _IMP_em.DensityHeader_user_set
571  __swig_getmethods__["user"] = _IMP_em.DensityHeader_user_get
572  if _newclass:user = _swig_property(_IMP_em.DensityHeader_user_get, _IMP_em.DensityHeader_user_set)
573  __swig_setmethods__["map"] = _IMP_em.DensityHeader_map_set
574  __swig_getmethods__["map"] = _IMP_em.DensityHeader_map_get
575  if _newclass:map = _swig_property(_IMP_em.DensityHeader_map_get, _IMP_em.DensityHeader_map_set)
576  __swig_setmethods__["machinestamp"] = _IMP_em.DensityHeader_machinestamp_set
577  __swig_getmethods__["machinestamp"] = _IMP_em.DensityHeader_machinestamp_get
578  if _newclass:machinestamp = _swig_property(_IMP_em.DensityHeader_machinestamp_get, _IMP_em.DensityHeader_machinestamp_set)
579  __swig_setmethods__["rms"] = _IMP_em.DensityHeader_rms_set
580  __swig_getmethods__["rms"] = _IMP_em.DensityHeader_rms_get
581  if _newclass:rms = _swig_property(_IMP_em.DensityHeader_rms_get, _IMP_em.DensityHeader_rms_set)
582  __swig_setmethods__["nlabl"] = _IMP_em.DensityHeader_nlabl_set
583  __swig_getmethods__["nlabl"] = _IMP_em.DensityHeader_nlabl_get
584  if _newclass:nlabl = _swig_property(_IMP_em.DensityHeader_nlabl_get, _IMP_em.DensityHeader_nlabl_set)
585  __swig_setmethods__["comments"] = _IMP_em.DensityHeader_comments_set
586  __swig_getmethods__["comments"] = _IMP_em.DensityHeader_comments_get
587  if _newclass:comments = _swig_property(_IMP_em.DensityHeader_comments_get, _IMP_em.DensityHeader_comments_set)
588  __swig_setmethods__["magic"] = _IMP_em.DensityHeader_magic_set
589  __swig_getmethods__["magic"] = _IMP_em.DensityHeader_magic_get
590  if _newclass:magic = _swig_property(_IMP_em.DensityHeader_magic_get, _IMP_em.DensityHeader_magic_set)
591  __swig_setmethods__["voltage"] = _IMP_em.DensityHeader_voltage_set
592  __swig_getmethods__["voltage"] = _IMP_em.DensityHeader_voltage_get
593  if _newclass:voltage = _swig_property(_IMP_em.DensityHeader_voltage_get, _IMP_em.DensityHeader_voltage_set)
594  __swig_setmethods__["Cs"] = _IMP_em.DensityHeader_Cs_set
595  __swig_getmethods__["Cs"] = _IMP_em.DensityHeader_Cs_get
596  if _newclass:Cs = _swig_property(_IMP_em.DensityHeader_Cs_get, _IMP_em.DensityHeader_Cs_set)
597  __swig_setmethods__["Aperture"] = _IMP_em.DensityHeader_Aperture_set
598  __swig_getmethods__["Aperture"] = _IMP_em.DensityHeader_Aperture_get
599  if _newclass:Aperture = _swig_property(_IMP_em.DensityHeader_Aperture_get, _IMP_em.DensityHeader_Aperture_set)
600  __swig_setmethods__["Magnification"] = _IMP_em.DensityHeader_Magnification_set
601  __swig_getmethods__["Magnification"] = _IMP_em.DensityHeader_Magnification_get
602  if _newclass:Magnification = _swig_property(_IMP_em.DensityHeader_Magnification_get, _IMP_em.DensityHeader_Magnification_set)
603  __swig_setmethods__["Postmagnification"] = _IMP_em.DensityHeader_Postmagnification_set
604  __swig_getmethods__["Postmagnification"] = _IMP_em.DensityHeader_Postmagnification_get
605  if _newclass:Postmagnification = _swig_property(_IMP_em.DensityHeader_Postmagnification_get, _IMP_em.DensityHeader_Postmagnification_set)
606  __swig_setmethods__["Exposuretime"] = _IMP_em.DensityHeader_Exposuretime_set
607  __swig_getmethods__["Exposuretime"] = _IMP_em.DensityHeader_Exposuretime_get
608  if _newclass:Exposuretime = _swig_property(_IMP_em.DensityHeader_Exposuretime_get, _IMP_em.DensityHeader_Exposuretime_set)
609  __swig_setmethods__["Microscope"] = _IMP_em.DensityHeader_Microscope_set
610  __swig_getmethods__["Microscope"] = _IMP_em.DensityHeader_Microscope_get
611  if _newclass:Microscope = _swig_property(_IMP_em.DensityHeader_Microscope_get, _IMP_em.DensityHeader_Microscope_set)
612  __swig_setmethods__["Pixelsize"] = _IMP_em.DensityHeader_Pixelsize_set
613  __swig_getmethods__["Pixelsize"] = _IMP_em.DensityHeader_Pixelsize_get
614  if _newclass:Pixelsize = _swig_property(_IMP_em.DensityHeader_Pixelsize_get, _IMP_em.DensityHeader_Pixelsize_set)
615  __swig_setmethods__["CCDArea"] = _IMP_em.DensityHeader_CCDArea_set
616  __swig_getmethods__["CCDArea"] = _IMP_em.DensityHeader_CCDArea_get
617  if _newclass:CCDArea = _swig_property(_IMP_em.DensityHeader_CCDArea_get, _IMP_em.DensityHeader_CCDArea_set)
618  __swig_setmethods__["Defocus"] = _IMP_em.DensityHeader_Defocus_set
619  __swig_getmethods__["Defocus"] = _IMP_em.DensityHeader_Defocus_get
620  if _newclass:Defocus = _swig_property(_IMP_em.DensityHeader_Defocus_get, _IMP_em.DensityHeader_Defocus_set)
621  __swig_setmethods__["Astigmatism"] = _IMP_em.DensityHeader_Astigmatism_set
622  __swig_getmethods__["Astigmatism"] = _IMP_em.DensityHeader_Astigmatism_get
623  if _newclass:Astigmatism = _swig_property(_IMP_em.DensityHeader_Astigmatism_get, _IMP_em.DensityHeader_Astigmatism_set)
624  __swig_setmethods__["AstigmatismAngle"] = _IMP_em.DensityHeader_AstigmatismAngle_set
625  __swig_getmethods__["AstigmatismAngle"] = _IMP_em.DensityHeader_AstigmatismAngle_get
626  if _newclass:AstigmatismAngle = _swig_property(_IMP_em.DensityHeader_AstigmatismAngle_get, _IMP_em.DensityHeader_AstigmatismAngle_set)
627  __swig_setmethods__["FocusIncrement"] = _IMP_em.DensityHeader_FocusIncrement_set
628  __swig_getmethods__["FocusIncrement"] = _IMP_em.DensityHeader_FocusIncrement_get
629  if _newclass:FocusIncrement = _swig_property(_IMP_em.DensityHeader_FocusIncrement_get, _IMP_em.DensityHeader_FocusIncrement_set)
630  __swig_setmethods__["CountsPerElectron"] = _IMP_em.DensityHeader_CountsPerElectron_set
631  __swig_getmethods__["CountsPerElectron"] = _IMP_em.DensityHeader_CountsPerElectron_get
632  if _newclass:CountsPerElectron = _swig_property(_IMP_em.DensityHeader_CountsPerElectron_get, _IMP_em.DensityHeader_CountsPerElectron_set)
633  __swig_setmethods__["Intensity"] = _IMP_em.DensityHeader_Intensity_set
634  __swig_getmethods__["Intensity"] = _IMP_em.DensityHeader_Intensity_get
635  if _newclass:Intensity = _swig_property(_IMP_em.DensityHeader_Intensity_get, _IMP_em.DensityHeader_Intensity_set)
636  __swig_setmethods__["EnergySlitwidth"] = _IMP_em.DensityHeader_EnergySlitwidth_set
637  __swig_getmethods__["EnergySlitwidth"] = _IMP_em.DensityHeader_EnergySlitwidth_get
638  if _newclass:EnergySlitwidth = _swig_property(_IMP_em.DensityHeader_EnergySlitwidth_get, _IMP_em.DensityHeader_EnergySlitwidth_set)
639  __swig_setmethods__["EnergyOffset"] = _IMP_em.DensityHeader_EnergyOffset_set
640  __swig_getmethods__["EnergyOffset"] = _IMP_em.DensityHeader_EnergyOffset_get
641  if _newclass:EnergyOffset = _swig_property(_IMP_em.DensityHeader_EnergyOffset_get, _IMP_em.DensityHeader_EnergyOffset_set)
642  __swig_setmethods__["Tiltangle"] = _IMP_em.DensityHeader_Tiltangle_set
643  __swig_getmethods__["Tiltangle"] = _IMP_em.DensityHeader_Tiltangle_get
644  if _newclass:Tiltangle = _swig_property(_IMP_em.DensityHeader_Tiltangle_get, _IMP_em.DensityHeader_Tiltangle_set)
645  __swig_setmethods__["Tiltaxis"] = _IMP_em.DensityHeader_Tiltaxis_set
646  __swig_getmethods__["Tiltaxis"] = _IMP_em.DensityHeader_Tiltaxis_get
647  if _newclass:Tiltaxis = _swig_property(_IMP_em.DensityHeader_Tiltaxis_get, _IMP_em.DensityHeader_Tiltaxis_set)
648  __swig_setmethods__["MarkerX"] = _IMP_em.DensityHeader_MarkerX_set
649  __swig_getmethods__["MarkerX"] = _IMP_em.DensityHeader_MarkerX_get
650  if _newclass:MarkerX = _swig_property(_IMP_em.DensityHeader_MarkerX_get, _IMP_em.DensityHeader_MarkerX_set)
651  __swig_setmethods__["MarkerY"] = _IMP_em.DensityHeader_MarkerY_set
652  __swig_getmethods__["MarkerY"] = _IMP_em.DensityHeader_MarkerY_get
653  if _newclass:MarkerY = _swig_property(_IMP_em.DensityHeader_MarkerY_get, _IMP_em.DensityHeader_MarkerY_set)
654  __swig_setmethods__["lswap"] = _IMP_em.DensityHeader_lswap_set
655  __swig_getmethods__["lswap"] = _IMP_em.DensityHeader_lswap_get
656  if _newclass:lswap = _swig_property(_IMP_em.DensityHeader_lswap_get, _IMP_em.DensityHeader_lswap_set)
657  def get_resolution(self):
658  """get_resolution(DensityHeader self) -> float"""
659  return _IMP_em.DensityHeader_get_resolution(self)
660 
661  def get_has_resolution(self):
662  """get_has_resolution(DensityHeader self) -> bool"""
663  return _IMP_em.DensityHeader_get_has_resolution(self)
664 
665  def set_resolution(self, *args):
666  """set_resolution(DensityHeader self, float resolution)"""
667  return _IMP_em.DensityHeader_set_resolution(self, *args)
668 
669  def get_spacing(self):
670  """get_spacing(DensityHeader self) -> float"""
671  return _IMP_em.DensityHeader_get_spacing(self)
672 
673  def get_xorigin(self):
674  """get_xorigin(DensityHeader self) -> float"""
675  return _IMP_em.DensityHeader_get_xorigin(self)
676 
677  def get_yorigin(self):
678  """get_yorigin(DensityHeader self) -> float"""
679  return _IMP_em.DensityHeader_get_yorigin(self)
680 
681  def get_zorigin(self):
682  """get_zorigin(DensityHeader self) -> float"""
683  return _IMP_em.DensityHeader_get_zorigin(self)
684 
685  def get_origin(self, *args):
686  """get_origin(DensityHeader self, int i) -> float"""
687  return _IMP_em.DensityHeader_get_origin(self, *args)
688 
689  def set_xorigin(self, *args):
690  """set_xorigin(DensityHeader self, float x)"""
691  return _IMP_em.DensityHeader_set_xorigin(self, *args)
692 
693  def set_yorigin(self, *args):
694  """set_yorigin(DensityHeader self, float y)"""
695  return _IMP_em.DensityHeader_set_yorigin(self, *args)
696 
697  def set_zorigin(self, *args):
698  """set_zorigin(DensityHeader self, float z)"""
699  return _IMP_em.DensityHeader_set_zorigin(self, *args)
700 
701  def is_top_calculated(self):
702  """is_top_calculated(DensityHeader self) -> bool"""
703  return _IMP_em.DensityHeader_is_top_calculated(self)
704 
705  __swig_setmethods__["Objectpixelsize_"] = _IMP_em.DensityHeader_Objectpixelsize__set
706  __swig_getmethods__["Objectpixelsize_"] = _IMP_em.DensityHeader_Objectpixelsize__get
707  if _newclass:Objectpixelsize_ = _swig_property(_IMP_em.DensityHeader_Objectpixelsize__get, _IMP_em.DensityHeader_Objectpixelsize__set)
708  def get_nx(self):
709  """get_nx(DensityHeader self) -> int"""
710  return _IMP_em.DensityHeader_get_nx(self)
711 
712  def get_ny(self):
713  """get_ny(DensityHeader self) -> int"""
714  return _IMP_em.DensityHeader_get_ny(self)
715 
716  def get_nz(self):
717  """get_nz(DensityHeader self) -> int"""
718  return _IMP_em.DensityHeader_get_nz(self)
719 
720  def get_number_of_voxels(self):
721  """get_number_of_voxels(DensityHeader self) -> int"""
722  return _IMP_em.DensityHeader_get_number_of_voxels(self)
723 
724  def get_data_type(self):
725  """get_data_type(DensityHeader self) -> int"""
726  return _IMP_em.DensityHeader_get_data_type(self)
727 
728  def set_data_type(self, *args):
729  """set_data_type(DensityHeader self, int data_type)"""
730  return _IMP_em.DensityHeader_set_data_type(self, *args)
731 
732  __swig_destroy__ = _IMP_em.delete_DensityHeader
733  __del__ = lambda self : None;
734 DensityHeader_swigregister = _IMP_em.DensityHeader_swigregister
735 DensityHeader_swigregister(DensityHeader)
736 
737 
738 def create_density_header(*args):
739  """create_density_header(BoundingBox3D bb, float spacing) -> DensityHeader"""
740  return _IMP_em.create_density_header(*args)
741 
742 def read_map(*args):
743  """
744  read_map(std::string filename, MapReaderWriter reader) -> DensityMap
745  read_map(std::string filename) -> DensityMap
746  """
747  return _IMP_em.read_map(*args)
748 
749 def write_map(*args):
750  """
751  write_map(DensityMap m, std::string filename, MapReaderWriter writer)
752  write_map(DensityMap m, std::string filename)
753  """
754  return _IMP_em.write_map(*args)
755 
756 def approximate_molecular_mass(*args):
757  """approximate_molecular_mass(DensityMap m, IMP::Float threshold) -> IMP::Float"""
758  return _IMP_em.approximate_molecular_mass(*args)
759 class DensityMap(IMP.base.Object):
760  """Proxy of C++ IMP::em::DensityMap class"""
761  __swig_setmethods__ = {}
762  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
763  __setattr__ = lambda self, name, value: _swig_setattr(self, DensityMap, name, value)
764  __swig_getmethods__ = {}
765  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
766  __getattr__ = lambda self, name: _swig_getattr(self, DensityMap, name)
767  def __init__(self, *args):
768  """
769  __init__(IMP::em::DensityMap self, std::string name="DensityMap%1%") -> DensityMap
770  __init__(IMP::em::DensityMap self) -> DensityMap
771  __init__(IMP::em::DensityMap self, DensityHeader header, std::string name="DensityMap%1%") -> DensityMap
772  __init__(IMP::em::DensityMap self, DensityHeader header) -> DensityMap
773  """
774  this = _IMP_em.new_DensityMap(*args)
775  try: self.this.append(this)
776  except: self.this = this
777  def release(self):
778  """release(DensityMap self)"""
779  return _IMP_em.DensityMap_release(self)
780 
781  def reset_data(self, value=0.0):
782  """
783  reset_data(DensityMap self, float value=0.0)
784  reset_data(DensityMap self)
785  """
786  return _IMP_em.DensityMap_reset_data(self, value)
787 
788  def calcRMS(self):
789  """calcRMS(DensityMap self) -> IMP::em::emreal"""
790  return _IMP_em.DensityMap_calcRMS(self)
791 
792  def std_normalize(self):
793  """std_normalize(DensityMap self)"""
794  return _IMP_em.DensityMap_std_normalize(self)
795 
796  def is_normalized(self):
797  """is_normalized(DensityMap self) -> bool"""
798  return _IMP_em.DensityMap_is_normalized(self)
799 
800  def get_location_in_dim_by_voxel(self, *args):
801  """get_location_in_dim_by_voxel(DensityMap self, long index, int dim) -> float"""
802  return _IMP_em.DensityMap_get_location_in_dim_by_voxel(self, *args)
803 
804  def xyz_ind2voxel(self, *args):
805  """xyz_ind2voxel(DensityMap self, int x, int y, int z) -> long"""
806  return _IMP_em.DensityMap_xyz_ind2voxel(self, *args)
807 
808  def get_voxel_by_location(self, *args):
809  """
810  get_voxel_by_location(DensityMap self, float x, float y, float z) -> long
811  get_voxel_by_location(DensityMap self, Vector3D v) -> long
812  """
813  return _IMP_em.DensityMap_get_voxel_by_location(self, *args)
814 
815  def get_location_by_voxel(self, *args):
816  """get_location_by_voxel(DensityMap self, long index) -> Vector3D"""
817  return _IMP_em.DensityMap_get_location_by_voxel(self, *args)
818 
819  def is_xyz_ind_part_of_volume(self, *args):
820  """is_xyz_ind_part_of_volume(DensityMap self, int ix, int iy, int iz) -> bool"""
821  return _IMP_em.DensityMap_is_xyz_ind_part_of_volume(self, *args)
822 
823  def is_part_of_volume(self, *args):
824  """
825  is_part_of_volume(DensityMap self, float x, float y, float z) -> bool
826  is_part_of_volume(DensityMap self, Vector3D v) -> bool
827  """
828  return _IMP_em.DensityMap_is_part_of_volume(self, *args)
829 
830  def get_value(self, *args):
831  """
832  get_value(DensityMap self, float x, float y, float z) -> IMP::em::emreal
833  get_value(DensityMap self, Vector3D point) -> IMP::em::emreal
834  get_value(DensityMap self, long index) -> IMP::em::emreal
835  """
836  return _IMP_em.DensityMap_get_value(self, *args)
837 
838  def set_value(self, *args):
839  """
840  set_value(DensityMap self, long index, IMP::em::emreal value)
841  set_value(DensityMap self, float x, float y, float z, IMP::em::emreal value)
842  """
843  return _IMP_em.DensityMap_set_value(self, *args)
844 
845  def set_origin(self, *args):
846  """
847  set_origin(DensityMap self, float x, float y, float z)
848  set_origin(DensityMap self, Vector3D v)
849  """
850  return _IMP_em.DensityMap_set_origin(self, *args)
851 
852  def get_origin(self):
853  """get_origin(DensityMap self) -> Vector3D"""
854  return _IMP_em.DensityMap_get_origin(self)
855 
856  def get_top(self):
857  """get_top(DensityMap self) -> Vector3D"""
858  return _IMP_em.DensityMap_get_top(self)
859 
860  def get_header(self):
861  h = _IMP_em.DensityMap_get_header(self)
862  h._owner = self
863  return h
864 
865 
866  def get_header_writable(self):
867  h = _IMP_em.DensityMap_get_header_writable(self)
868  h._owner = self
869  return h
870 
871 
872  def same_origin(self, *args):
873  """same_origin(DensityMap self, DensityMap other) -> bool"""
874  return _IMP_em.DensityMap_same_origin(self, *args)
875 
876  def same_dimensions(self, *args):
877  """same_dimensions(DensityMap self, DensityMap other) -> bool"""
878  return _IMP_em.DensityMap_same_dimensions(self, *args)
879 
880  def same_voxel_size(self, *args):
881  """same_voxel_size(DensityMap self, DensityMap other) -> bool"""
882  return _IMP_em.DensityMap_same_voxel_size(self, *args)
883 
884  def get_centroid(self, threshold=0.0):
885  """
886  get_centroid(DensityMap self, IMP::em::emreal threshold=0.0) -> Vector3D
887  get_centroid(DensityMap self) -> Vector3D
888  """
889  return _IMP_em.DensityMap_get_centroid(self, threshold)
890 
891  def get_max_value(self):
892  """get_max_value(DensityMap self) -> IMP::em::emreal"""
893  return _IMP_em.DensityMap_get_max_value(self)
894 
895  def get_min_value(self):
896  """get_min_value(DensityMap self) -> IMP::em::emreal"""
897  return _IMP_em.DensityMap_get_min_value(self)
898 
899  def add(self, *args):
900  """add(DensityMap self, DensityMap other)"""
901  return _IMP_em.DensityMap_add(self, *args)
902 
903  def pick_max(self, *args):
904  """pick_max(DensityMap self, DensityMap other)"""
905  return _IMP_em.DensityMap_pick_max(self, *args)
906 
907  def get_number_of_voxels(self):
908  """get_number_of_voxels(DensityMap self) -> long"""
909  return _IMP_em.DensityMap_get_number_of_voxels(self)
910 
911  def set_void_map(self, *args):
912  """set_void_map(DensityMap self, int nx, int ny, int nz)"""
913  return _IMP_em.DensityMap_set_void_map(self, *args)
914 
915  def pad(self, *args):
916  """
917  pad(DensityMap self, int nx, int ny, int nz, float val=0.0)
918  pad(DensityMap self, int nx, int ny, int nz)
919  """
920  return _IMP_em.DensityMap_pad(self, *args)
921 
922  def pad_margin(self, *args):
923  """
924  pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z, float val=0.0) -> DensityMap
925  pad_margin(DensityMap self, int mrg_x, int mrg_y, int mrg_z) -> DensityMap
926  """
927  return _IMP_em.DensityMap_pad_margin(self, *args)
928 
929  def get_cropped(self, *args):
930  """
931  get_cropped(DensityMap self, float threshold) -> DensityMap
932  get_cropped(DensityMap self, BoundingBox3D bb) -> DensityMap
933  """
934  return _IMP_em.DensityMap_get_cropped(self, *args)
935 
936  def get_maximum_value_in_xy_plane(self, *args):
937  """get_maximum_value_in_xy_plane(DensityMap self, int z_ind) -> float"""
938  return _IMP_em.DensityMap_get_maximum_value_in_xy_plane(self, *args)
939 
940  def get_maximum_value_in_xz_plane(self, *args):
941  """get_maximum_value_in_xz_plane(DensityMap self, int y_ind) -> float"""
942  return _IMP_em.DensityMap_get_maximum_value_in_xz_plane(self, *args)
943 
944  def get_maximum_value_in_yz_plane(self, *args):
945  """get_maximum_value_in_yz_plane(DensityMap self, int x_ind) -> float"""
946  return _IMP_em.DensityMap_get_maximum_value_in_yz_plane(self, *args)
947 
948  def multiply(self, *args):
949  """multiply(DensityMap self, float factor)"""
950  return _IMP_em.DensityMap_multiply(self, *args)
951 
952  def get_locations_string(self, *args):
953  """get_locations_string(DensityMap self, float t) -> std::string"""
954  return _IMP_em.DensityMap_get_locations_string(self, *args)
955 
956  def update_voxel_size(self, *args):
957  """update_voxel_size(DensityMap self, float new_apix)"""
958  return _IMP_em.DensityMap_update_voxel_size(self, *args)
959 
960  def get_spacing(self):
961  """get_spacing(DensityMap self) -> IMP::Float"""
962  return _IMP_em.DensityMap_get_spacing(self)
963 
964  def calc_all_voxel2loc(self):
965  """calc_all_voxel2loc(DensityMap self)"""
966  return _IMP_em.DensityMap_calc_all_voxel2loc(self)
967 
968  def copy_map(self, *args):
969  """copy_map(DensityMap self, DensityMap other)"""
970  return _IMP_em.DensityMap_copy_map(self, *args)
971 
972  def get_version_info(self):
973  """get_version_info(DensityMap self) -> VersionInfo"""
974  return _IMP_em.DensityMap_get_version_info(self)
975 
976  __swig_destroy__ = _IMP_em.delete_DensityMap
977  __del__ = lambda self : None;
978  def lower_voxel_shift(self, *args):
979  """lower_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
980  return _IMP_em.DensityMap_lower_voxel_shift(self, *args)
981 
982  def upper_voxel_shift(self, *args):
983  """upper_voxel_shift(DensityMap self, IMP::em::emreal loc, IMP::em::emreal kdist, IMP::em::emreal orig, int ndim) -> int"""
984  return _IMP_em.DensityMap_upper_voxel_shift(self, *args)
985 
986  def get_rms_calculated(self):
987  """get_rms_calculated(DensityMap self) -> bool"""
988  return _IMP_em.DensityMap_get_rms_calculated(self)
989 
990  def get_dim_index_by_location(self, *args):
991  """
992  get_dim_index_by_location(DensityMap self, Vector3D v, int ind) -> int
993  get_dim_index_by_location(DensityMap self, float loc_val, int ind) -> int
994  """
995  return _IMP_em.DensityMap_get_dim_index_by_location(self, *args)
996 
997  def __str__(self):
998  """__str__(DensityMap self) -> std::string"""
999  return _IMP_em.DensityMap___str__(self)
1000 
1001  def __repr__(self):
1002  """__repr__(DensityMap self) -> std::string"""
1003  return _IMP_em.DensityMap___repr__(self)
1004 
1005  def get_from(o):
1006  return _object_cast_to_DensityMap(o)
1007  get_from = staticmethod(get_from)
1008 
1009 DensityMap_swigregister = _IMP_em.DensityMap_swigregister
1010 DensityMap_swigregister(DensityMap)
1011 
1012 
1013 def get_bounding_box(*args):
1014  """
1015  get_bounding_box(DensityMap m, IMP::Float threshold) -> BoundingBox3D
1016  get_bounding_box(DensityMap m) -> BoundingBox3D
1017  """
1018  return _IMP_em.get_bounding_box(*args)
1019 
1020 def get_density(*args):
1021  """get_density(DensityMap m, Vector3D v) -> double"""
1022  return _IMP_em.get_density(*args)
1023 
1024 def get_transformed(*args):
1025  """
1026  get_transformed(DensityMap input, Transformation3D tr, double threshold) -> DensityMap
1027  get_transformed(DensityMap input, Transformation3D tr) -> DensityMap
1028  """
1029  return _IMP_em.get_transformed(*args)
1030 
1031 def get_resampled(*args):
1032  """get_resampled(DensityMap input, double scaling) -> DensityMap"""
1033  return _IMP_em.get_resampled(*args)
1034 
1035 def get_transformed_into(*args):
1036  """
1037  get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into, bool calc_rms=True)
1038  get_transformed_into(DensityMap source, Transformation3D tr, DensityMap into)
1039  """
1040  return _IMP_em.get_transformed_into(*args)
1041 
1042 def get_transformed_into2(*args):
1043  """get_transformed_into2(DensityMap source, Transformation3D tr, DensityMap into)"""
1044  return _IMP_em.get_transformed_into2(*args)
1045 
1046 def get_interiors_intersect(*args):
1047  """get_interiors_intersect(DensityMap d1, DensityMap d2) -> bool"""
1048  return _IMP_em.get_interiors_intersect(*args)
1049 
1050 def get_segment(*args):
1051  """
1052  get_segment(DensityMap map_to_segment, int nx_start, int nx_end, int ny_start, int ny_end, int nz_start,
1053  int nz_end) -> DensityMap
1054  get_segment(DensityMap map_to_segment, IMP::algebra::Vector3Ds vecs, float dist) -> DensityMap
1055  """
1056  return _IMP_em.get_segment(*args)
1057 
1058 def get_segment_by_masking(*args):
1059  """get_segment_by_masking(DensityMap map_to_segment, DensityMap mask, float mas_threshold) -> DensityMap"""
1060  return _IMP_em.get_segment_by_masking(*args)
1061 
1062 def binarize(*args):
1063  """
1064  binarize(DensityMap orig_map, float threshold, bool reverse=False) -> DensityMap
1065  binarize(DensityMap orig_map, float threshold) -> DensityMap
1066  """
1067  return _IMP_em.binarize(*args)
1068 
1069 def get_threshold_map(*args):
1070  """get_threshold_map(DensityMap orig_map, float threshold) -> DensityMap"""
1071  return _IMP_em.get_threshold_map(*args)
1072 
1073 def multiply(*args):
1074  """multiply(DensityMap m1, DensityMap m2) -> DensityMap"""
1075  return _IMP_em.multiply(*args)
1076 
1077 def convolute(*args):
1078  """convolute(DensityMap m1, DensityMap m2) -> double"""
1079  return _IMP_em.convolute(*args)
1080 
1081 def get_sum(*args):
1082  """get_sum(DensityMap m1) -> double"""
1083  return _IMP_em.get_sum(*args)
1084 
1085 def get_max_map(*args):
1086  """get_max_map(IMP::em::DensityMaps maps) -> DensityMap"""
1087  return _IMP_em.get_max_map(*args)
1088 
1089 def interpolate_map(*args):
1090  """interpolate_map(DensityMap in_map, double new_spacing) -> DensityMap"""
1091  return _IMP_em.interpolate_map(*args)
1092 
1093 def get_grid(*args):
1094  """get_grid(DensityMap in_map) -> DenseFloatGrid3D"""
1095  return _IMP_em.get_grid(*args)
1096 
1097 def create_density_map(*args):
1098  """
1099  create_density_map(DensityMap other) -> DensityMap
1100  create_density_map(BoundingBox3D bb, double spacing) -> DensityMap
1101  create_density_map(int nx, int ny, int nz, double spacing) -> DensityMap
1102  create_density_map(DenseFloatGrid3D grid) -> DensityMap
1103  """
1104  return _IMP_em.create_density_map(*args)
1105 
1106 def get_binarized_interior(*args):
1107  """get_binarized_interior(DensityMap dmap) -> DensityMap"""
1108  return _IMP_em.get_binarized_interior(*args)
1109 class RadiusDependentDistanceMask(_object):
1110  """Proxy of C++ IMP::em::RadiusDependentDistanceMask class"""
1111  __swig_setmethods__ = {}
1112  __setattr__ = lambda self, name, value: _swig_setattr(self, RadiusDependentDistanceMask, name, value)
1113  __swig_getmethods__ = {}
1114  __getattr__ = lambda self, name: _swig_getattr(self, RadiusDependentDistanceMask, name)
1115  __repr__ = _swig_repr
1116  def __init__(self, *args):
1117  """__init__(IMP::em::RadiusDependentDistanceMask self, float sampling_radius, DensityHeader header) -> RadiusDependentDistanceMask"""
1118  this = _IMP_em.new_RadiusDependentDistanceMask(*args)
1119  try: self.this.append(this)
1120  except: self.this = this
1121  def get_neighbor_shift(self):
1122  """get_neighbor_shift(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1123  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_shift(self)
1124 
1125  def get_neighbor_dist(self):
1126  """get_neighbor_dist(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1127  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist(self)
1128 
1129  def get_neighbor_dist_exp(self):
1130  """get_neighbor_dist_exp(RadiusDependentDistanceMask self) -> std::vector< double,std::allocator< double > > const *"""
1131  return _IMP_em.RadiusDependentDistanceMask_get_neighbor_dist_exp(self)
1132 
1133  def show(self, *args):
1134  """show(RadiusDependentDistanceMask self, _ostream out)"""
1135  return _IMP_em.RadiusDependentDistanceMask_show(self, *args)
1136 
1137  __swig_destroy__ = _IMP_em.delete_RadiusDependentDistanceMask
1138  __del__ = lambda self : None;
1139 RadiusDependentDistanceMask_swigregister = _IMP_em.RadiusDependentDistanceMask_swigregister
1140 RadiusDependentDistanceMask_swigregister(RadiusDependentDistanceMask)
1141 
1142 class DistanceMask(_object):
1143  """Proxy of C++ IMP::em::DistanceMask class"""
1144  __swig_setmethods__ = {}
1145  __setattr__ = lambda self, name, value: _swig_setattr(self, DistanceMask, name, value)
1146  __swig_getmethods__ = {}
1147  __getattr__ = lambda self, name: _swig_getattr(self, DistanceMask, name)
1148  __repr__ = _swig_repr
1149  def __init__(self, *args):
1150  """
1151  __init__(IMP::em::DistanceMask self) -> DistanceMask
1152  __init__(IMP::em::DistanceMask self, DensityHeader header) -> DistanceMask
1153  """
1154  this = _IMP_em.new_DistanceMask(*args)
1155  try: self.this.append(this)
1156  except: self.this = this
1157  def show(self, *args):
1158  """show(DistanceMask self, _ostream out)"""
1159  return _IMP_em.DistanceMask_show(self, *args)
1160 
1161  def is_mask_set(self, *args):
1162  """
1163  is_mask_set(DistanceMask self, float radius, float eps=0.001) -> bool
1164  is_mask_set(DistanceMask self, float radius) -> bool
1165  """
1166  return _IMP_em.DistanceMask_is_mask_set(self, *args)
1167 
1168  __swig_destroy__ = _IMP_em.delete_DistanceMask
1169  __del__ = lambda self : None;
1170 DistanceMask_swigregister = _IMP_em.DistanceMask_swigregister
1171 DistanceMask_swigregister(DistanceMask)
1172 
1173 class EMReaderWriter(MapReaderWriter):
1174  """Proxy of C++ IMP::em::EMReaderWriter class"""
1175  __swig_setmethods__ = {}
1176  for _s in [MapReaderWriter]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1177  __setattr__ = lambda self, name, value: _swig_setattr(self, EMReaderWriter, name, value)
1178  __swig_getmethods__ = {}
1179  for _s in [MapReaderWriter]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1180  __getattr__ = lambda self, name: _swig_getattr(self, EMReaderWriter, name)
1181  __swig_destroy__ = _IMP_em.delete_EMReaderWriter
1182  __del__ = lambda self : None;
1183  def __str__(self):
1184  """__str__(EMReaderWriter self) -> std::string"""
1185  return _IMP_em.EMReaderWriter___str__(self)
1186 
1187  def __repr__(self):
1188  """__repr__(EMReaderWriter self) -> std::string"""
1189  return _IMP_em.EMReaderWriter___repr__(self)
1190 
1191  def get_from(o):
1192  return _object_cast_to_EMReaderWriter(o)
1193  get_from = staticmethod(get_from)
1194 
1195  def __init__(self):
1196  """__init__(IMP::em::EMReaderWriter self) -> EMReaderWriter"""
1197  this = _IMP_em.new_EMReaderWriter()
1198  try: self.this.append(this)
1199  except: self.this = this
1200 EMReaderWriter_swigregister = _IMP_em.EMReaderWriter_swigregister
1201 EMReaderWriter_swigregister(EMReaderWriter)
1202 
1203 class XplorReaderWriter(MapReaderWriter):
1204  """Proxy of C++ IMP::em::XplorReaderWriter class"""
1205  __swig_setmethods__ = {}
1206  for _s in [MapReaderWriter]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1207  __setattr__ = lambda self, name, value: _swig_setattr(self, XplorReaderWriter, name, value)
1208  __swig_getmethods__ = {}
1209  for _s in [MapReaderWriter]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1210  __getattr__ = lambda self, name: _swig_getattr(self, XplorReaderWriter, name)
1211  __swig_destroy__ = _IMP_em.delete_XplorReaderWriter
1212  __del__ = lambda self : None;
1213  def __str__(self):
1214  """__str__(XplorReaderWriter self) -> std::string"""
1215  return _IMP_em.XplorReaderWriter___str__(self)
1216 
1217  def __repr__(self):
1218  """__repr__(XplorReaderWriter self) -> std::string"""
1219  return _IMP_em.XplorReaderWriter___repr__(self)
1220 
1221  def get_from(o):
1222  return _object_cast_to_XplorReaderWriter(o)
1223  get_from = staticmethod(get_from)
1224 
1225  def __init__(self):
1226  """__init__(IMP::em::XplorReaderWriter self) -> XplorReaderWriter"""
1227  this = _IMP_em.new_XplorReaderWriter()
1228  try: self.this.append(this)
1229  except: self.this = this
1230 XplorReaderWriter_swigregister = _IMP_em.XplorReaderWriter_swigregister
1231 XplorReaderWriter_swigregister(XplorReaderWriter)
1232 
1233 class MRCReaderWriter(MapReaderWriter):
1234  """Proxy of C++ IMP::em::MRCReaderWriter class"""
1235  __swig_setmethods__ = {}
1236  for _s in [MapReaderWriter]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1237  __setattr__ = lambda self, name, value: _swig_setattr(self, MRCReaderWriter, name, value)
1238  __swig_getmethods__ = {}
1239  for _s in [MapReaderWriter]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1240  __getattr__ = lambda self, name: _swig_getattr(self, MRCReaderWriter, name)
1241  def __init__(self, *args):
1242  """
1243  __init__(IMP::em::MRCReaderWriter self) -> MRCReaderWriter
1244  __init__(IMP::em::MRCReaderWriter self, std::string fn) -> MRCReaderWriter
1245  """
1246  this = _IMP_em.new_MRCReaderWriter(*args)
1247  try: self.this.append(this)
1248  except: self.this = this
1249  __swig_destroy__ = _IMP_em.delete_MRCReaderWriter
1250  __del__ = lambda self : None;
1251  def __str__(self):
1252  """__str__(MRCReaderWriter self) -> std::string"""
1253  return _IMP_em.MRCReaderWriter___str__(self)
1254 
1255  def __repr__(self):
1256  """__repr__(MRCReaderWriter self) -> std::string"""
1257  return _IMP_em.MRCReaderWriter___repr__(self)
1258 
1259  def get_from(o):
1260  return _object_cast_to_MRCReaderWriter(o)
1261  get_from = staticmethod(get_from)
1262 
1263 MRCReaderWriter_swigregister = _IMP_em.MRCReaderWriter_swigregister
1264 MRCReaderWriter_swigregister(MRCReaderWriter)
1265 
1266 class RadiusDependentKernelParameters(_object):
1267  """Proxy of C++ IMP::em::RadiusDependentKernelParameters class"""
1268  __swig_setmethods__ = {}
1269  __setattr__ = lambda self, name, value: _swig_setattr(self, RadiusDependentKernelParameters, name, value)
1270  __swig_getmethods__ = {}
1271  __getattr__ = lambda self, name: _swig_getattr(self, RadiusDependentKernelParameters, name)
1272  def __init__(self, *args):
1273  """
1274  __init__(IMP::em::RadiusDependentKernelParameters self, float radii, float rsigsq, float timessig, float sq2pi3, float inv_rsigsq, float rnormfac,
1275  float rkdist) -> RadiusDependentKernelParameters
1276  """
1277  this = _IMP_em.new_RadiusDependentKernelParameters(*args)
1278  try: self.this.append(this)
1279  except: self.this = this
1280  def show(self, *args):
1281  """
1282  show(RadiusDependentKernelParameters self, _ostream s=std::cout)
1283  show(RadiusDependentKernelParameters self)
1284  """
1285  return _IMP_em.RadiusDependentKernelParameters_show(self, *args)
1286 
1287  def get_vsig(self):
1288  """get_vsig(RadiusDependentKernelParameters self) -> float"""
1289  return _IMP_em.RadiusDependentKernelParameters_get_vsig(self)
1290 
1291  def get_vsigsq(self):
1292  """get_vsigsq(RadiusDependentKernelParameters self) -> float"""
1293  return _IMP_em.RadiusDependentKernelParameters_get_vsigsq(self)
1294 
1295  def get_inv_sigsq(self):
1296  """get_inv_sigsq(RadiusDependentKernelParameters self) -> float"""
1297  return _IMP_em.RadiusDependentKernelParameters_get_inv_sigsq(self)
1298 
1299  def get_sig(self):
1300  """get_sig(RadiusDependentKernelParameters self) -> float"""
1301  return _IMP_em.RadiusDependentKernelParameters_get_sig(self)
1302 
1303  def get_kdist(self):
1304  """get_kdist(RadiusDependentKernelParameters self) -> float"""
1305  return _IMP_em.RadiusDependentKernelParameters_get_kdist(self)
1306 
1307  def get_normfac(self):
1308  """get_normfac(RadiusDependentKernelParameters self) -> float"""
1309  return _IMP_em.RadiusDependentKernelParameters_get_normfac(self)
1310 
1311  __swig_destroy__ = _IMP_em.delete_RadiusDependentKernelParameters
1312  __del__ = lambda self : None;
1313  def __str__(self):
1314  """__str__(RadiusDependentKernelParameters self) -> std::string"""
1315  return _IMP_em.RadiusDependentKernelParameters___str__(self)
1316 
1317  def __repr__(self):
1318  """__repr__(RadiusDependentKernelParameters self) -> std::string"""
1319  return _IMP_em.RadiusDependentKernelParameters___repr__(self)
1320 
1321 RadiusDependentKernelParameters_swigregister = _IMP_em.RadiusDependentKernelParameters_swigregister
1322 RadiusDependentKernelParameters_swigregister(RadiusDependentKernelParameters)
1323 
1324 class KernelParameters(_object):
1325  """Proxy of C++ IMP::em::KernelParameters class"""
1326  __swig_setmethods__ = {}
1327  __setattr__ = lambda self, name, value: _swig_setattr(self, KernelParameters, name, value)
1328  __swig_getmethods__ = {}
1329  __getattr__ = lambda self, name: _swig_getattr(self, KernelParameters, name)
1330  def __init__(self, *args):
1331  """
1332  __init__(IMP::em::KernelParameters self) -> KernelParameters
1333  __init__(IMP::em::KernelParameters self, float resolution) -> KernelParameters
1334  """
1335  this = _IMP_em.new_KernelParameters(*args)
1336  try: self.this.append(this)
1337  except: self.this = this
1338  __swig_destroy__ = _IMP_em.delete_KernelParameters
1339  __del__ = lambda self : None;
1340  def set_params(self, *args):
1341  """set_params(KernelParameters self, float radius) -> RadiusDependentKernelParameters"""
1342  return _IMP_em.KernelParameters_set_params(self, *args)
1343 
1344  def get_params(self, *args):
1345  """
1346  get_params(KernelParameters self, float radius, float eps=0.001) -> RadiusDependentKernelParameters
1347  get_params(KernelParameters self, float radius) -> RadiusDependentKernelParameters
1348  """
1349  return _IMP_em.KernelParameters_get_params(self, *args)
1350 
1351  def get_rsig(self):
1352  """get_rsig(KernelParameters self) -> float"""
1353  return _IMP_em.KernelParameters_get_rsig(self)
1354 
1355  def get_rsigsq(self):
1356  """get_rsigsq(KernelParameters self) -> float"""
1357  return _IMP_em.KernelParameters_get_rsigsq(self)
1358 
1359  def get_inv_rsigsq(self):
1360  """get_inv_rsigsq(KernelParameters self) -> float"""
1361  return _IMP_em.KernelParameters_get_inv_rsigsq(self)
1362 
1363  def get_timessig(self):
1364  """get_timessig(KernelParameters self) -> float"""
1365  return _IMP_em.KernelParameters_get_timessig(self)
1366 
1367  def get_sq2pi3(self):
1368  """get_sq2pi3(KernelParameters self) -> float"""
1369  return _IMP_em.KernelParameters_get_sq2pi3(self)
1370 
1371  def get_rnormfac(self):
1372  """get_rnormfac(KernelParameters self) -> float"""
1373  return _IMP_em.KernelParameters_get_rnormfac(self)
1374 
1375  def get_rkdist(self):
1376  """get_rkdist(KernelParameters self) -> float"""
1377  return _IMP_em.KernelParameters_get_rkdist(self)
1378 
1379  def get_lim(self):
1380  """get_lim(KernelParameters self) -> float"""
1381  return _IMP_em.KernelParameters_get_lim(self)
1382 
1383  def show(self, *args):
1384  """
1385  show(KernelParameters self, _ostream out=std::cout)
1386  show(KernelParameters self)
1387  """
1388  return _IMP_em.KernelParameters_show(self, *args)
1389 
1390  def __str__(self):
1391  """__str__(KernelParameters self) -> std::string"""
1392  return _IMP_em.KernelParameters___str__(self)
1393 
1394  def __repr__(self):
1395  """__repr__(KernelParameters self) -> std::string"""
1396  return _IMP_em.KernelParameters___repr__(self)
1397 
1398 KernelParameters_swigregister = _IMP_em.KernelParameters_swigregister
1399 KernelParameters_swigregister(KernelParameters)
1400 
1401 GAUSSIAN = _IMP_em.GAUSSIAN
1402 BINARIZED_SPHERE = _IMP_em.BINARIZED_SPHERE
1403 SPHERE = _IMP_em.SPHERE
1404 class SampledDensityMap(DensityMap):
1405  """Proxy of C++ IMP::em::SampledDensityMap class"""
1406  __swig_setmethods__ = {}
1407  for _s in [DensityMap]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1408  __setattr__ = lambda self, name, value: _swig_setattr(self, SampledDensityMap, name, value)
1409  __swig_getmethods__ = {}
1410  for _s in [DensityMap]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1411  __getattr__ = lambda self, name: _swig_getattr(self, SampledDensityMap, name)
1412  def __init__(self, *args):
1413  """
1414  __init__(IMP::em::SampledDensityMap self, IMP::em::KernelType kt=GAUSSIAN) -> SampledDensityMap
1415  __init__(IMP::em::SampledDensityMap self) -> SampledDensityMap
1416  __init__(IMP::em::SampledDensityMap self, DensityHeader header, IMP::em::KernelType kt=GAUSSIAN) -> SampledDensityMap
1417  __init__(IMP::em::SampledDensityMap self, DensityHeader header) -> SampledDensityMap
1418  __init__(IMP::em::SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size,
1419  FloatKey mass_key=IMP::atom::Mass::get_mass_key(), int sig_cuttoff=3,
1420  IMP::em::KernelType kt=GAUSSIAN) -> SampledDensityMap
1421  __init__(IMP::em::SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size,
1422  FloatKey mass_key=IMP::atom::Mass::get_mass_key(), int sig_cuttoff=3) -> SampledDensityMap
1423  __init__(IMP::em::SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size,
1424  FloatKey mass_key=IMP::atom::Mass::get_mass_key()) -> SampledDensityMap
1425  __init__(IMP::em::SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps, IMP::em::emreal resolution, IMP::em::emreal voxel_size) -> SampledDensityMap
1426  """
1427  this = _IMP_em.new_SampledDensityMap(*args)
1428  try: self.this.append(this)
1429  except: self.this = this
1430  def resample(self):
1431  """resample(SampledDensityMap self)"""
1432  return _IMP_em.SampledDensityMap_resample(self)
1433 
1434  def project(self, *args):
1435  """
1436  project(SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin,
1437  Vector3D shift=IMP::algebra::Vector3D(0.,0.,0.), FloatKey mass_key=IMP::atom::Mass::get_mass_key())
1438  project(SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin,
1439  Vector3D shift=IMP::algebra::Vector3D(0.,0.,0.))
1440  project(SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps, int x_margin, int y_margin, int z_margin)
1441  """
1442  return _IMP_em.SampledDensityMap_project(self, *args)
1443 
1444  def set_particles(self, *args):
1445  """
1446  set_particles(SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps, FloatKey mass_key=IMP::atom::Mass::get_mass_key())
1447  set_particles(SampledDensityMap self, IMP::kernel::ParticlesTemp const & ps)
1448  """
1449  return _IMP_em.SampledDensityMap_set_particles(self, *args)
1450 
1451  def get_xyzr_particles(self):
1452  """get_xyzr_particles(SampledDensityMap self) -> IMP::core::XYZRs const &"""
1453  return _IMP_em.SampledDensityMap_get_xyzr_particles(self)
1454 
1455  def get_sampled_particles(self):
1456  """get_sampled_particles(SampledDensityMap self) -> IMP::kernel::Particles const &"""
1457  return _IMP_em.SampledDensityMap_get_sampled_particles(self)
1458 
1459  def get_weight_key(self):
1460  """get_weight_key(SampledDensityMap self) -> FloatKey"""
1461  return _IMP_em.SampledDensityMap_get_weight_key(self)
1462 
1463  def get_minimum_resampled_value(self):
1464  """get_minimum_resampled_value(SampledDensityMap self) -> float"""
1465  return _IMP_em.SampledDensityMap_get_minimum_resampled_value(self)
1466 
1467  __swig_destroy__ = _IMP_em.delete_SampledDensityMap
1468  __del__ = lambda self : None;
1469  def __str__(self):
1470  """__str__(SampledDensityMap self) -> std::string"""
1471  return _IMP_em.SampledDensityMap___str__(self)
1472 
1473  def __repr__(self):
1474  """__repr__(SampledDensityMap self) -> std::string"""
1475  return _IMP_em.SampledDensityMap___repr__(self)
1476 
1477  def get_from(o):
1478  return _object_cast_to_SampledDensityMap(o)
1479  get_from = staticmethod(get_from)
1480 
1481 SampledDensityMap_swigregister = _IMP_em.SampledDensityMap_swigregister
1482 SampledDensityMap_swigregister(SampledDensityMap)
1483 
1484 IMP_DEFAULT_NUM_SHELLS = _IMP_em.IMP_DEFAULT_NUM_SHELLS
1485 IMP_SIG_CUTOFF = _IMP_em.IMP_SIG_CUTOFF
1486 class SurfaceShellDensityMap(SampledDensityMap):
1487  """Proxy of C++ IMP::em::SurfaceShellDensityMap class"""
1488  __swig_setmethods__ = {}
1489  for _s in [SampledDensityMap]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1490  __setattr__ = lambda self, name, value: _swig_setattr(self, SurfaceShellDensityMap, name, value)
1491  __swig_getmethods__ = {}
1492  for _s in [SampledDensityMap]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1493  __getattr__ = lambda self, name: _swig_getattr(self, SurfaceShellDensityMap, name)
1494  def __init__(self, *args):
1495  """
1496  __init__(IMP::em::SurfaceShellDensityMap self) -> SurfaceShellDensityMap
1497  __init__(IMP::em::SurfaceShellDensityMap self, DensityHeader header) -> SurfaceShellDensityMap
1498  __init__(IMP::em::SurfaceShellDensityMap self, IMP::kernel::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key=IMP::atom::Mass::get_mass_key(),
1499  int num_shells=5) -> SurfaceShellDensityMap
1500  __init__(IMP::em::SurfaceShellDensityMap self, IMP::kernel::ParticlesTemp const & ps, float voxel_size, FloatKey mass_key=IMP::atom::Mass::get_mass_key()) -> SurfaceShellDensityMap
1501  __init__(IMP::em::SurfaceShellDensityMap self, IMP::kernel::ParticlesTemp const & ps, float voxel_size) -> SurfaceShellDensityMap
1502  """
1503  this = _IMP_em.new_SurfaceShellDensityMap(*args)
1504  try: self.this.append(this)
1505  except: self.this = this
1506  def binaries(self, *args):
1507  """binaries(SurfaceShellDensityMap self, float scene_val)"""
1508  return _IMP_em.SurfaceShellDensityMap_binaries(self, *args)
1509 
1510  def has_background_neighbor(self, *args):
1511  """has_background_neighbor(SurfaceShellDensityMap self, long voxel_ind) -> bool"""
1512  return _IMP_em.SurfaceShellDensityMap_has_background_neighbor(self, *args)
1513 
1514  __swig_destroy__ = _IMP_em.delete_SurfaceShellDensityMap
1515  __del__ = lambda self : None;
1516  def __str__(self):
1517  """__str__(SurfaceShellDensityMap self) -> std::string"""
1518  return _IMP_em.SurfaceShellDensityMap___str__(self)
1519 
1520  def __repr__(self):
1521  """__repr__(SurfaceShellDensityMap self) -> std::string"""
1522  return _IMP_em.SurfaceShellDensityMap___repr__(self)
1523 
1524  def get_from(o):
1525  return _object_cast_to_SurfaceShellDensityMap(o)
1526  get_from = staticmethod(get_from)
1527 
1528 SurfaceShellDensityMap_swigregister = _IMP_em.SurfaceShellDensityMap_swigregister
1529 SurfaceShellDensityMap_swigregister(SurfaceShellDensityMap)
1530 
1531 class CoarseCC(IMP.base.Object):
1532  """Proxy of C++ IMP::em::CoarseCC class"""
1533  __swig_setmethods__ = {}
1534  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1535  __setattr__ = lambda self, name, value: _swig_setattr(self, CoarseCC, name, value)
1536  __swig_getmethods__ = {}
1537  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1538  __getattr__ = lambda self, name: _swig_getattr(self, CoarseCC, name)
1539  def __init__(self):
1540  """__init__(IMP::em::CoarseCC self) -> CoarseCC"""
1541  this = _IMP_em.new_CoarseCC()
1542  try: self.this.append(this)
1543  except: self.this = this
1544  def calc_score(*args):
1545  """
1546  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True,
1547  bool resample=True, IMP::FloatPair norm_factors=IMP::FloatPair(0.,0.)) -> float
1548  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True,
1549  bool resample=True) -> float
1550  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1551  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1552  """
1553  return _IMP_em.CoarseCC_calc_score(*args)
1554 
1555  if _newclass:calc_score = staticmethod(calc_score)
1556  __swig_getmethods__["calc_score"] = lambda x: calc_score
1557  def cross_correlation_coefficient(*args):
1558  """
1559  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False,
1560  IMP::FloatPair norm_factors=IMP::FloatPair(0.,0.)) -> double
1561  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1562  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1563  """
1564  return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1565 
1566  if _newclass:cross_correlation_coefficient = staticmethod(cross_correlation_coefficient)
1567  __swig_getmethods__["cross_correlation_coefficient"] = lambda x: cross_correlation_coefficient
1568  def local_cross_correlation_coefficient(*args):
1569  """local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1570  return _IMP_em.CoarseCC_local_cross_correlation_coefficient(*args)
1571 
1572  if _newclass:local_cross_correlation_coefficient = staticmethod(local_cross_correlation_coefficient)
1573  __swig_getmethods__["local_cross_correlation_coefficient"] = lambda x: local_cross_correlation_coefficient
1574  def get_version_info(self):
1575  """get_version_info(CoarseCC self) -> VersionInfo"""
1576  return _IMP_em.CoarseCC_get_version_info(self)
1577 
1578  __swig_destroy__ = _IMP_em.delete_CoarseCC
1579  __del__ = lambda self : None;
1580  def __str__(self):
1581  """__str__(CoarseCC self) -> std::string"""
1582  return _IMP_em.CoarseCC___str__(self)
1583 
1584  def __repr__(self):
1585  """__repr__(CoarseCC self) -> std::string"""
1586  return _IMP_em.CoarseCC___repr__(self)
1587 
1588  def get_from(o):
1589  return _object_cast_to_CoarseCC(o)
1590  get_from = staticmethod(get_from)
1591 
1592 CoarseCC_swigregister = _IMP_em.CoarseCC_swigregister
1593 CoarseCC_swigregister(CoarseCC)
1594 
1595 def CoarseCC_calc_score(*args):
1596  """
1597  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True,
1598  bool resample=True, IMP::FloatPair norm_factors=IMP::FloatPair(0.,0.)) -> float
1599  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True,
1600  bool resample=True) -> float
1601  calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=True) -> float
1602  CoarseCC_calc_score(DensityMap data, SampledDensityMap model_map, float scalefactor) -> float
1603  """
1604  return _IMP_em.CoarseCC_calc_score(*args)
1605 
1606 def CoarseCC_cross_correlation_coefficient(*args):
1607  """
1608  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False,
1609  IMP::FloatPair norm_factors=IMP::FloatPair(0.,0.)) -> double
1610  cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=False) -> double
1611  CoarseCC_cross_correlation_coefficient(DensityMap grid1, DensityMap grid2, float grid2_voxel_data_threshold) -> double
1612  """
1613  return _IMP_em.CoarseCC_cross_correlation_coefficient(*args)
1614 
1615 def CoarseCC_local_cross_correlation_coefficient(*args):
1616  """CoarseCC_local_cross_correlation_coefficient(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float"""
1617  return _IMP_em.CoarseCC_local_cross_correlation_coefficient(*args)
1618 
1619 class CoarseConvolution(_object):
1620  """Proxy of C++ IMP::em::CoarseConvolution class"""
1621  __swig_setmethods__ = {}
1622  __setattr__ = lambda self, name, value: _swig_setattr(self, CoarseConvolution, name, value)
1623  __swig_getmethods__ = {}
1624  __getattr__ = lambda self, name: _swig_getattr(self, CoarseConvolution, name)
1625  __repr__ = _swig_repr
1626  def convolution(*args):
1627  """
1628  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1629  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1630  """
1631  return _IMP_em.CoarseConvolution_convolution(*args)
1632 
1633  if _newclass:convolution = staticmethod(convolution)
1634  __swig_getmethods__["convolution"] = lambda x: convolution
1635  def __init__(self):
1636  """__init__(IMP::em::CoarseConvolution self) -> CoarseConvolution"""
1637  this = _IMP_em.new_CoarseConvolution()
1638  try: self.this.append(this)
1639  except: self.this = this
1640  __swig_destroy__ = _IMP_em.delete_CoarseConvolution
1641  __del__ = lambda self : None;
1642 CoarseConvolution_swigregister = _IMP_em.CoarseConvolution_swigregister
1643 CoarseConvolution_swigregister(CoarseConvolution)
1644 
1645 def CoarseConvolution_convolution(*args):
1646  """
1647  convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold, bool recalc_ccnormfac=True) -> float
1648  CoarseConvolution_convolution(DensityMap em_map, DensityMap model_map, float voxel_data_threshold) -> float
1649  """
1650  return _IMP_em.CoarseConvolution_convolution(*args)
1651 
1652 class CoarseCCatIntervals(CoarseCC):
1653  """Proxy of C++ IMP::em::CoarseCCatIntervals class"""
1654  __swig_setmethods__ = {}
1655  for _s in [CoarseCC]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1656  __setattr__ = lambda self, name, value: _swig_setattr(self, CoarseCCatIntervals, name, value)
1657  __swig_getmethods__ = {}
1658  for _s in [CoarseCC]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1659  __getattr__ = lambda self, name: _swig_getattr(self, CoarseCCatIntervals, name)
1660  def __init__(self, *args):
1661  """
1662  __init__(IMP::em::CoarseCCatIntervals self, int const & ncd) -> CoarseCCatIntervals
1663  __init__(IMP::em::CoarseCCatIntervals self) -> CoarseCCatIntervals
1664  """
1665  this = _IMP_em.new_CoarseCCatIntervals(*args)
1666  try: self.this.append(this)
1667  except: self.this = this
1668  def evaluate(self, *args):
1669  """
1670  evaluate(CoarseCCatIntervals self, DensityMap em_map, SampledDensityMap model_map, IMP::algebra::Vector3Ds const & deriv,
1671  float scalefac, bool lderiv, unsigned long eval_interval) -> std::pair< double,IMP::algebra::Vector3Ds >
1672  """
1673  return _IMP_em.CoarseCCatIntervals_evaluate(self, *args)
1674 
1675  __swig_destroy__ = _IMP_em.delete_CoarseCCatIntervals
1676  __del__ = lambda self : None;
1677  def __str__(self):
1678  """__str__(CoarseCCatIntervals self) -> std::string"""
1679  return _IMP_em.CoarseCCatIntervals___str__(self)
1680 
1681  def __repr__(self):
1682  """__repr__(CoarseCCatIntervals self) -> std::string"""
1683  return _IMP_em.CoarseCCatIntervals___repr__(self)
1684 
1685  def get_from(o):
1686  return _object_cast_to_CoarseCCatIntervals(o)
1687  get_from = staticmethod(get_from)
1688 
1689 CoarseCCatIntervals_swigregister = _IMP_em.CoarseCCatIntervals_swigregister
1690 CoarseCCatIntervals_swigregister(CoarseCCatIntervals)
1691 
1692 class FitRestraint(IMP.kernel.Restraint):
1693  """Proxy of C++ IMP::em::FitRestraint class"""
1694  __swig_setmethods__ = {}
1695  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1696  __setattr__ = lambda self, name, value: _swig_setattr(self, FitRestraint, name, value)
1697  __swig_getmethods__ = {}
1698  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1699  __getattr__ = lambda self, name: _swig_getattr(self, FitRestraint, name)
1700  def __init__(self, *args):
1701  """
1702  __init__(IMP::em::FitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors=IMP::FloatPair(0.,0.),
1703  FloatKey weight_key=IMP::atom::Mass::get_mass_key(), float scale=1,
1704  bool use_rigid_bodies=True, IMP::em::KernelType kt=GAUSSIAN) -> FitRestraint
1705  __init__(IMP::em::FitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors=IMP::FloatPair(0.,0.),
1706  FloatKey weight_key=IMP::atom::Mass::get_mass_key(), float scale=1,
1707  bool use_rigid_bodies=True) -> FitRestraint
1708  __init__(IMP::em::FitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors=IMP::FloatPair(0.,0.),
1709  FloatKey weight_key=IMP::atom::Mass::get_mass_key(), float scale=1) -> FitRestraint
1710  __init__(IMP::em::FitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors=IMP::FloatPair(0.,0.),
1711  FloatKey weight_key=IMP::atom::Mass::get_mass_key()) -> FitRestraint
1712  __init__(IMP::em::FitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map, IMP::FloatPair norm_factors=IMP::FloatPair(0.,0.)) -> FitRestraint
1713  __init__(IMP::em::FitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map) -> FitRestraint
1714  """
1715  this = _IMP_em.new_FitRestraint(*args)
1716  try: self.this.append(this)
1717  except: self.this = this
1718  def get_model_dens_map(self):
1719  """get_model_dens_map(FitRestraint self) -> SampledDensityMap"""
1720  return _IMP_em.FitRestraint_get_model_dens_map(self)
1721 
1722  def set_scale_factor(self, *args):
1723  """set_scale_factor(FitRestraint self, float scale)"""
1724  return _IMP_em.FitRestraint_set_scale_factor(self, *args)
1725 
1726  def get_scale_factor(self):
1727  """get_scale_factor(FitRestraint self) -> float"""
1728  return _IMP_em.FitRestraint_get_scale_factor(self)
1729 
1730  def get_input_particles(self):
1731  """get_input_particles(FitRestraint self) -> IMP::kernel::ParticlesTemp"""
1732  return _IMP_em.FitRestraint_get_input_particles(self)
1733 
1734  def get_input_containers(self):
1735  """get_input_containers(FitRestraint self) -> IMP::kernel::ContainersTemp"""
1736  return _IMP_em.FitRestraint_get_input_containers(self)
1737 
1738  def do_get_inputs(self):
1739  """do_get_inputs(FitRestraint self) -> IMP::kernel::ModelObjectsTemp"""
1740  return _IMP_em.FitRestraint_do_get_inputs(self)
1741 
1742  def get_version_info(self):
1743  """get_version_info(FitRestraint self) -> VersionInfo"""
1744  return _IMP_em.FitRestraint_get_version_info(self)
1745 
1746  def do_show(self, *args):
1747  """do_show(FitRestraint self, _ostream out)"""
1748  return _IMP_em.FitRestraint_do_show(self, *args)
1749 
1750  __swig_destroy__ = _IMP_em.delete_FitRestraint
1751  __del__ = lambda self : None;
1752  def __str__(self):
1753  """__str__(FitRestraint self) -> std::string"""
1754  return _IMP_em.FitRestraint___str__(self)
1755 
1756  def __repr__(self):
1757  """__repr__(FitRestraint self) -> std::string"""
1758  return _IMP_em.FitRestraint___repr__(self)
1759 
1760  def get_from(o):
1761  return _object_cast_to_FitRestraint(o)
1762  get_from = staticmethod(get_from)
1763 
1764  def cast(*args):
1765  """cast(Restraint r) -> FitRestraint"""
1766  return _IMP_em.FitRestraint_cast(*args)
1767 
1768  if _newclass:cast = staticmethod(cast)
1769  __swig_getmethods__["cast"] = lambda x: cast
1770 FitRestraint_swigregister = _IMP_em.FitRestraint_swigregister
1771 FitRestraint_swigregister(FitRestraint)
1772 
1773 def FitRestraint_cast(*args):
1774  """FitRestraint_cast(Restraint r) -> FitRestraint"""
1775  return _IMP_em.FitRestraint_cast(*args)
1776 
1777 
1778 def density2particles(*args):
1779  """
1780  density2particles(DensityMap dmap, IMP::Float threshold, Model m, int step=1) -> IMP::kernel::Particles
1781  density2particles(DensityMap dmap, IMP::Float threshold, Model m) -> IMP::kernel::Particles
1782  """
1783  return _IMP_em.density2particles(*args)
1784 
1785 def density2vectors(*args):
1786  """density2vectors(DensityMap dmap, IMP::Float threshold) -> IMP::algebra::Vector3Ds"""
1787  return _IMP_em.density2vectors(*args)
1788 
1789 def particles2density(*args):
1790  """
1791  particles2density(IMP::kernel::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3,
1792  FloatKey weight_key=IMP::atom::Mass::get_mass_key()) -> SampledDensityMap
1793  particles2density(IMP::kernel::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
1794  particles2density(IMP::kernel::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
1795  """
1796  return _IMP_em.particles2density(*args)
1797 
1798 def particles2binarized_density(*args):
1799  """
1800  particles2binarized_density(IMP::kernel::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3,
1801  FloatKey weight_key=IMP::atom::Mass::get_mass_key()) -> SampledDensityMap
1802  particles2binarized_density(IMP::kernel::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix, int sig_cutoff=3) -> SampledDensityMap
1803  particles2binarized_density(IMP::kernel::ParticlesTemp const & ps, IMP::Float resolution, IMP::Float apix) -> SampledDensityMap
1804  """
1805  return _IMP_em.particles2binarized_density(*args)
1806 
1807 def particles2surface(*args):
1808  """
1809  particles2surface(IMP::kernel::ParticlesTemp const & ps, IMP::Float apix, FloatKey weight_key=IMP::atom::Mass::get_mass_key()) -> SurfaceShellDensityMap
1810  particles2surface(IMP::kernel::ParticlesTemp const & ps, IMP::Float apix) -> SurfaceShellDensityMap
1811  """
1812  return _IMP_em.particles2surface(*args)
1813 
1814 def calculate_intersection_score(*args):
1815  """calculate_intersection_score(SurfaceShellDensityMap d1, SurfaceShellDensityMap d2) -> IMP::Float"""
1816  return _IMP_em.calculate_intersection_score(*args)
1817 class SpiderHeader(_object):
1818  """Proxy of C++ IMP::em::SpiderHeader class"""
1819  __swig_setmethods__ = {}
1820  __setattr__ = lambda self, name, value: _swig_setattr(self, SpiderHeader, name, value)
1821  __swig_getmethods__ = {}
1822  __getattr__ = lambda self, name: _swig_getattr(self, SpiderHeader, name)
1823  __repr__ = _swig_repr
1824  __swig_setmethods__["fNslice"] = _IMP_em.SpiderHeader_fNslice_set
1825  __swig_getmethods__["fNslice"] = _IMP_em.SpiderHeader_fNslice_get
1826  if _newclass:fNslice = _swig_property(_IMP_em.SpiderHeader_fNslice_get, _IMP_em.SpiderHeader_fNslice_set)
1827  __swig_setmethods__["fNrow"] = _IMP_em.SpiderHeader_fNrow_set
1828  __swig_getmethods__["fNrow"] = _IMP_em.SpiderHeader_fNrow_get
1829  if _newclass:fNrow = _swig_property(_IMP_em.SpiderHeader_fNrow_get, _IMP_em.SpiderHeader_fNrow_set)
1830  __swig_setmethods__["fNrec"] = _IMP_em.SpiderHeader_fNrec_set
1831  __swig_getmethods__["fNrec"] = _IMP_em.SpiderHeader_fNrec_get
1832  if _newclass:fNrec = _swig_property(_IMP_em.SpiderHeader_fNrec_get, _IMP_em.SpiderHeader_fNrec_set)
1833  __swig_setmethods__["fNlabel"] = _IMP_em.SpiderHeader_fNlabel_set
1834  __swig_getmethods__["fNlabel"] = _IMP_em.SpiderHeader_fNlabel_get
1835  if _newclass:fNlabel = _swig_property(_IMP_em.SpiderHeader_fNlabel_get, _IMP_em.SpiderHeader_fNlabel_set)
1836  __swig_setmethods__["fIform"] = _IMP_em.SpiderHeader_fIform_set
1837  __swig_getmethods__["fIform"] = _IMP_em.SpiderHeader_fIform_get
1838  if _newclass:fIform = _swig_property(_IMP_em.SpiderHeader_fIform_get, _IMP_em.SpiderHeader_fIform_set)
1839  __swig_setmethods__["fImami"] = _IMP_em.SpiderHeader_fImami_set
1840  __swig_getmethods__["fImami"] = _IMP_em.SpiderHeader_fImami_get
1841  if _newclass:fImami = _swig_property(_IMP_em.SpiderHeader_fImami_get, _IMP_em.SpiderHeader_fImami_set)
1842  __swig_setmethods__["fFmax"] = _IMP_em.SpiderHeader_fFmax_set
1843  __swig_getmethods__["fFmax"] = _IMP_em.SpiderHeader_fFmax_get
1844  if _newclass:fFmax = _swig_property(_IMP_em.SpiderHeader_fFmax_get, _IMP_em.SpiderHeader_fFmax_set)
1845  __swig_setmethods__["fFmin"] = _IMP_em.SpiderHeader_fFmin_set
1846  __swig_getmethods__["fFmin"] = _IMP_em.SpiderHeader_fFmin_get
1847  if _newclass:fFmin = _swig_property(_IMP_em.SpiderHeader_fFmin_get, _IMP_em.SpiderHeader_fFmin_set)
1848  __swig_setmethods__["fAv"] = _IMP_em.SpiderHeader_fAv_set
1849  __swig_getmethods__["fAv"] = _IMP_em.SpiderHeader_fAv_get
1850  if _newclass:fAv = _swig_property(_IMP_em.SpiderHeader_fAv_get, _IMP_em.SpiderHeader_fAv_set)
1851  __swig_setmethods__["fSig"] = _IMP_em.SpiderHeader_fSig_set
1852  __swig_getmethods__["fSig"] = _IMP_em.SpiderHeader_fSig_get
1853  if _newclass:fSig = _swig_property(_IMP_em.SpiderHeader_fSig_get, _IMP_em.SpiderHeader_fSig_set)
1854  __swig_setmethods__["fIhist"] = _IMP_em.SpiderHeader_fIhist_set
1855  __swig_getmethods__["fIhist"] = _IMP_em.SpiderHeader_fIhist_get
1856  if _newclass:fIhist = _swig_property(_IMP_em.SpiderHeader_fIhist_get, _IMP_em.SpiderHeader_fIhist_set)
1857  __swig_setmethods__["fNcol"] = _IMP_em.SpiderHeader_fNcol_set
1858  __swig_getmethods__["fNcol"] = _IMP_em.SpiderHeader_fNcol_get
1859  if _newclass:fNcol = _swig_property(_IMP_em.SpiderHeader_fNcol_get, _IMP_em.SpiderHeader_fNcol_set)
1860  __swig_setmethods__["fLabrec"] = _IMP_em.SpiderHeader_fLabrec_set
1861  __swig_getmethods__["fLabrec"] = _IMP_em.SpiderHeader_fLabrec_get
1862  if _newclass:fLabrec = _swig_property(_IMP_em.SpiderHeader_fLabrec_get, _IMP_em.SpiderHeader_fLabrec_set)
1863  __swig_setmethods__["fIangle"] = _IMP_em.SpiderHeader_fIangle_set
1864  __swig_getmethods__["fIangle"] = _IMP_em.SpiderHeader_fIangle_get
1865  if _newclass:fIangle = _swig_property(_IMP_em.SpiderHeader_fIangle_get, _IMP_em.SpiderHeader_fIangle_set)
1866  __swig_setmethods__["fPhi"] = _IMP_em.SpiderHeader_fPhi_set
1867  __swig_getmethods__["fPhi"] = _IMP_em.SpiderHeader_fPhi_get
1868  if _newclass:fPhi = _swig_property(_IMP_em.SpiderHeader_fPhi_get, _IMP_em.SpiderHeader_fPhi_set)
1869  __swig_setmethods__["fTheta"] = _IMP_em.SpiderHeader_fTheta_set
1870  __swig_getmethods__["fTheta"] = _IMP_em.SpiderHeader_fTheta_get
1871  if _newclass:fTheta = _swig_property(_IMP_em.SpiderHeader_fTheta_get, _IMP_em.SpiderHeader_fTheta_set)
1872  __swig_setmethods__["fPsi"] = _IMP_em.SpiderHeader_fPsi_set
1873  __swig_getmethods__["fPsi"] = _IMP_em.SpiderHeader_fPsi_get
1874  if _newclass:fPsi = _swig_property(_IMP_em.SpiderHeader_fPsi_get, _IMP_em.SpiderHeader_fPsi_set)
1875  __swig_setmethods__["fXoff"] = _IMP_em.SpiderHeader_fXoff_set
1876  __swig_getmethods__["fXoff"] = _IMP_em.SpiderHeader_fXoff_get
1877  if _newclass:fXoff = _swig_property(_IMP_em.SpiderHeader_fXoff_get, _IMP_em.SpiderHeader_fXoff_set)
1878  __swig_setmethods__["fYoff"] = _IMP_em.SpiderHeader_fYoff_set
1879  __swig_getmethods__["fYoff"] = _IMP_em.SpiderHeader_fYoff_get
1880  if _newclass:fYoff = _swig_property(_IMP_em.SpiderHeader_fYoff_get, _IMP_em.SpiderHeader_fYoff_set)
1881  __swig_setmethods__["fZoff"] = _IMP_em.SpiderHeader_fZoff_set
1882  __swig_getmethods__["fZoff"] = _IMP_em.SpiderHeader_fZoff_get
1883  if _newclass:fZoff = _swig_property(_IMP_em.SpiderHeader_fZoff_get, _IMP_em.SpiderHeader_fZoff_set)
1884  __swig_setmethods__["fScale"] = _IMP_em.SpiderHeader_fScale_set
1885  __swig_getmethods__["fScale"] = _IMP_em.SpiderHeader_fScale_get
1886  if _newclass:fScale = _swig_property(_IMP_em.SpiderHeader_fScale_get, _IMP_em.SpiderHeader_fScale_set)
1887  __swig_setmethods__["fLabbyt"] = _IMP_em.SpiderHeader_fLabbyt_set
1888  __swig_getmethods__["fLabbyt"] = _IMP_em.SpiderHeader_fLabbyt_get
1889  if _newclass:fLabbyt = _swig_property(_IMP_em.SpiderHeader_fLabbyt_get, _IMP_em.SpiderHeader_fLabbyt_set)
1890  __swig_setmethods__["fLenbyt"] = _IMP_em.SpiderHeader_fLenbyt_set
1891  __swig_getmethods__["fLenbyt"] = _IMP_em.SpiderHeader_fLenbyt_get
1892  if _newclass:fLenbyt = _swig_property(_IMP_em.SpiderHeader_fLenbyt_get, _IMP_em.SpiderHeader_fLenbyt_set)
1893  __swig_setmethods__["fNothing"] = _IMP_em.SpiderHeader_fNothing_set
1894  __swig_getmethods__["fNothing"] = _IMP_em.SpiderHeader_fNothing_get
1895  if _newclass:fNothing = _swig_property(_IMP_em.SpiderHeader_fNothing_get, _IMP_em.SpiderHeader_fNothing_set)
1896  __swig_setmethods__["fFlag"] = _IMP_em.SpiderHeader_fFlag_set
1897  __swig_getmethods__["fFlag"] = _IMP_em.SpiderHeader_fFlag_get
1898  if _newclass:fFlag = _swig_property(_IMP_em.SpiderHeader_fFlag_get, _IMP_em.SpiderHeader_fFlag_set)
1899  __swig_setmethods__["fPhi1"] = _IMP_em.SpiderHeader_fPhi1_set
1900  __swig_getmethods__["fPhi1"] = _IMP_em.SpiderHeader_fPhi1_get
1901  if _newclass:fPhi1 = _swig_property(_IMP_em.SpiderHeader_fPhi1_get, _IMP_em.SpiderHeader_fPhi1_set)
1902  __swig_setmethods__["fTheta1"] = _IMP_em.SpiderHeader_fTheta1_set
1903  __swig_getmethods__["fTheta1"] = _IMP_em.SpiderHeader_fTheta1_get
1904  if _newclass:fTheta1 = _swig_property(_IMP_em.SpiderHeader_fTheta1_get, _IMP_em.SpiderHeader_fTheta1_set)
1905  __swig_setmethods__["fPsi1"] = _IMP_em.SpiderHeader_fPsi1_set
1906  __swig_getmethods__["fPsi1"] = _IMP_em.SpiderHeader_fPsi1_get
1907  if _newclass:fPsi1 = _swig_property(_IMP_em.SpiderHeader_fPsi1_get, _IMP_em.SpiderHeader_fPsi1_set)
1908  __swig_setmethods__["fPhi2"] = _IMP_em.SpiderHeader_fPhi2_set
1909  __swig_getmethods__["fPhi2"] = _IMP_em.SpiderHeader_fPhi2_get
1910  if _newclass:fPhi2 = _swig_property(_IMP_em.SpiderHeader_fPhi2_get, _IMP_em.SpiderHeader_fPhi2_set)
1911  __swig_setmethods__["fTheta2"] = _IMP_em.SpiderHeader_fTheta2_set
1912  __swig_getmethods__["fTheta2"] = _IMP_em.SpiderHeader_fTheta2_get
1913  if _newclass:fTheta2 = _swig_property(_IMP_em.SpiderHeader_fTheta2_get, _IMP_em.SpiderHeader_fTheta2_set)
1914  __swig_setmethods__["fPsi2"] = _IMP_em.SpiderHeader_fPsi2_set
1915  __swig_getmethods__["fPsi2"] = _IMP_em.SpiderHeader_fPsi2_get
1916  if _newclass:fPsi2 = _swig_property(_IMP_em.SpiderHeader_fPsi2_get, _IMP_em.SpiderHeader_fPsi2_set)
1917  __swig_setmethods__["fGeo_matrix"] = _IMP_em.SpiderHeader_fGeo_matrix_set
1918  __swig_getmethods__["fGeo_matrix"] = _IMP_em.SpiderHeader_fGeo_matrix_get
1919  if _newclass:fGeo_matrix = _swig_property(_IMP_em.SpiderHeader_fGeo_matrix_get, _IMP_em.SpiderHeader_fGeo_matrix_set)
1920  __swig_setmethods__["fAngle1"] = _IMP_em.SpiderHeader_fAngle1_set
1921  __swig_getmethods__["fAngle1"] = _IMP_em.SpiderHeader_fAngle1_get
1922  if _newclass:fAngle1 = _swig_property(_IMP_em.SpiderHeader_fAngle1_get, _IMP_em.SpiderHeader_fAngle1_set)
1923  __swig_setmethods__["fr1"] = _IMP_em.SpiderHeader_fr1_set
1924  __swig_getmethods__["fr1"] = _IMP_em.SpiderHeader_fr1_get
1925  if _newclass:fr1 = _swig_property(_IMP_em.SpiderHeader_fr1_get, _IMP_em.SpiderHeader_fr1_set)
1926  __swig_setmethods__["fr2"] = _IMP_em.SpiderHeader_fr2_set
1927  __swig_getmethods__["fr2"] = _IMP_em.SpiderHeader_fr2_get
1928  if _newclass:fr2 = _swig_property(_IMP_em.SpiderHeader_fr2_get, _IMP_em.SpiderHeader_fr2_set)
1929  __swig_setmethods__["RTflag"] = _IMP_em.SpiderHeader_RTflag_set
1930  __swig_getmethods__["RTflag"] = _IMP_em.SpiderHeader_RTflag_get
1931  if _newclass:RTflag = _swig_property(_IMP_em.SpiderHeader_RTflag_get, _IMP_em.SpiderHeader_RTflag_set)
1932  __swig_setmethods__["Astart"] = _IMP_em.SpiderHeader_Astart_set
1933  __swig_getmethods__["Astart"] = _IMP_em.SpiderHeader_Astart_get
1934  if _newclass:Astart = _swig_property(_IMP_em.SpiderHeader_Astart_get, _IMP_em.SpiderHeader_Astart_set)
1935  __swig_setmethods__["Aend"] = _IMP_em.SpiderHeader_Aend_set
1936  __swig_getmethods__["Aend"] = _IMP_em.SpiderHeader_Aend_get
1937  if _newclass:Aend = _swig_property(_IMP_em.SpiderHeader_Aend_get, _IMP_em.SpiderHeader_Aend_set)
1938  __swig_setmethods__["Ainc"] = _IMP_em.SpiderHeader_Ainc_set
1939  __swig_getmethods__["Ainc"] = _IMP_em.SpiderHeader_Ainc_get
1940  if _newclass:Ainc = _swig_property(_IMP_em.SpiderHeader_Ainc_get, _IMP_em.SpiderHeader_Ainc_set)
1941  __swig_setmethods__["Rsigma"] = _IMP_em.SpiderHeader_Rsigma_set
1942  __swig_getmethods__["Rsigma"] = _IMP_em.SpiderHeader_Rsigma_get
1943  if _newclass:Rsigma = _swig_property(_IMP_em.SpiderHeader_Rsigma_get, _IMP_em.SpiderHeader_Rsigma_set)
1944  __swig_setmethods__["Tstart"] = _IMP_em.SpiderHeader_Tstart_set
1945  __swig_getmethods__["Tstart"] = _IMP_em.SpiderHeader_Tstart_get
1946  if _newclass:Tstart = _swig_property(_IMP_em.SpiderHeader_Tstart_get, _IMP_em.SpiderHeader_Tstart_set)
1947  __swig_setmethods__["Tend"] = _IMP_em.SpiderHeader_Tend_set
1948  __swig_getmethods__["Tend"] = _IMP_em.SpiderHeader_Tend_get
1949  if _newclass:Tend = _swig_property(_IMP_em.SpiderHeader_Tend_get, _IMP_em.SpiderHeader_Tend_set)
1950  __swig_setmethods__["Tinc"] = _IMP_em.SpiderHeader_Tinc_set
1951  __swig_getmethods__["Tinc"] = _IMP_em.SpiderHeader_Tinc_get
1952  if _newclass:Tinc = _swig_property(_IMP_em.SpiderHeader_Tinc_get, _IMP_em.SpiderHeader_Tinc_set)
1953  __swig_setmethods__["Weight"] = _IMP_em.SpiderHeader_Weight_set
1954  __swig_getmethods__["Weight"] = _IMP_em.SpiderHeader_Weight_get
1955  if _newclass:Weight = _swig_property(_IMP_em.SpiderHeader_Weight_get, _IMP_em.SpiderHeader_Weight_set)
1956  __swig_setmethods__["Flip"] = _IMP_em.SpiderHeader_Flip_set
1957  __swig_getmethods__["Flip"] = _IMP_em.SpiderHeader_Flip_get
1958  if _newclass:Flip = _swig_property(_IMP_em.SpiderHeader_Flip_get, _IMP_em.SpiderHeader_Flip_set)
1959  __swig_setmethods__["empty"] = _IMP_em.SpiderHeader_empty_set
1960  __swig_getmethods__["empty"] = _IMP_em.SpiderHeader_empty_get
1961  if _newclass:empty = _swig_property(_IMP_em.SpiderHeader_empty_get, _IMP_em.SpiderHeader_empty_set)
1962  __swig_setmethods__["szIDat"] = _IMP_em.SpiderHeader_szIDat_set
1963  __swig_getmethods__["szIDat"] = _IMP_em.SpiderHeader_szIDat_get
1964  if _newclass:szIDat = _swig_property(_IMP_em.SpiderHeader_szIDat_get, _IMP_em.SpiderHeader_szIDat_set)
1965  __swig_setmethods__["szITim"] = _IMP_em.SpiderHeader_szITim_set
1966  __swig_getmethods__["szITim"] = _IMP_em.SpiderHeader_szITim_get
1967  if _newclass:szITim = _swig_property(_IMP_em.SpiderHeader_szITim_get, _IMP_em.SpiderHeader_szITim_set)
1968  __swig_setmethods__["szITit"] = _IMP_em.SpiderHeader_szITit_set
1969  __swig_getmethods__["szITit"] = _IMP_em.SpiderHeader_szITit_get
1970  if _newclass:szITit = _swig_property(_IMP_em.SpiderHeader_szITit_get, _IMP_em.SpiderHeader_szITit_set)
1971  def show(self, *args):
1972  """show(SpiderHeader self, _ostream out)"""
1973  return _IMP_em.SpiderHeader_show(self, *args)
1974 
1975  def __init__(self):
1976  """__init__(IMP::em::SpiderHeader self) -> SpiderHeader"""
1977  this = _IMP_em.new_SpiderHeader()
1978  try: self.this.append(this)
1979  except: self.this = this
1980  __swig_destroy__ = _IMP_em.delete_SpiderHeader
1981  __del__ = lambda self : None;
1982 SpiderHeader_swigregister = _IMP_em.SpiderHeader_swigregister
1983 SpiderHeader_swigregister(SpiderHeader)
1984 
1985 class ImageHeader(_object):
1986  """Proxy of C++ IMP::em::ImageHeader class"""
1987  __swig_setmethods__ = {}
1988  __setattr__ = lambda self, name, value: _swig_setattr(self, ImageHeader, name, value)
1989  __swig_getmethods__ = {}
1990  __getattr__ = lambda self, name: _swig_getattr(self, ImageHeader, name)
1991  __repr__ = _swig_repr
1992  IMG_BYTE = _IMP_em.ImageHeader_IMG_BYTE
1993  IMG_IMPEM = _IMP_em.ImageHeader_IMG_IMPEM
1994  IMG_INT = _IMP_em.ImageHeader_IMG_INT
1995  VOL_BYTE = _IMP_em.ImageHeader_VOL_BYTE
1996  VOL_IMPEM = _IMP_em.ImageHeader_VOL_IMPEM
1997  VOL_INT = _IMP_em.ImageHeader_VOL_INT
1998  IMG_FOURIER = _IMP_em.ImageHeader_IMG_FOURIER
1999  VOL_FOURIER = _IMP_em.ImageHeader_VOL_FOURIER
2000  def __init__(self, *args):
2001  """
2002  __init__(IMP::em::ImageHeader self) -> ImageHeader
2003  __init__(IMP::em::ImageHeader self, IMP::em::ImageHeader::img_type im) -> ImageHeader
2004  __init__(IMP::em::ImageHeader self, float im) -> ImageHeader
2005  """
2006  this = _IMP_em.new_ImageHeader(*args)
2007  try: self.this.append(this)
2008  except: self.this = this
2009  def get_image_type(self):
2010  """get_image_type(ImageHeader self) -> float"""
2011  return _IMP_em.ImageHeader_get_image_type(self)
2012 
2013  def set_image_type(self, *args):
2014  """
2015  set_image_type(ImageHeader self, IMP::em::ImageHeader::img_type im)
2016  set_image_type(ImageHeader self, float im)
2017  """
2018  return _IMP_em.ImageHeader_set_image_type(self, *args)
2019 
2020  def do_show(self, *args):
2021  """do_show(ImageHeader self, _ostream out)"""
2022  return _IMP_em.ImageHeader_do_show(self, *args)
2023 
2024  def show(self, *args):
2025  """
2026  show(ImageHeader self, _ostream out=std::cout)
2027  show(ImageHeader self)
2028  """
2029  return _IMP_em.ImageHeader_show(self, *args)
2030 
2031  def print_hard(self, *args):
2032  """print_hard(ImageHeader self, _ostream out)"""
2033  return _IMP_em.ImageHeader_print_hard(self, *args)
2034 
2035  def show_projection_params(self, *args):
2036  """show_projection_params(ImageHeader self, _ostream out)"""
2037  return _IMP_em.ImageHeader_show_projection_params(self, *args)
2038 
2039  def read(self, *args):
2040  """
2041  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False,
2042  bool skip_extra_checkings=False) -> int
2043  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False, bool force_reversed=False) -> int
2044  read(ImageHeader self, IMP::String const filename, bool skip_type_check=False) -> int
2045  read(ImageHeader self, IMP::String const filename) -> int
2046  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False, bool skip_extra_checkings=False) -> bool
2047  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False, bool force_reversed=False) -> bool
2048  read(ImageHeader self, std::ifstream & f, bool skip_type_check=False) -> bool
2049  read(ImageHeader self, std::ifstream & f) -> bool
2050  """
2051  return _IMP_em.ImageHeader_read(self, *args)
2052 
2053  def write(self, *args):
2054  """
2055  write(ImageHeader self, IMP::String const & filename, bool force_reversed=False)
2056  write(ImageHeader self, IMP::String const & filename)
2057  write(ImageHeader self, std::ofstream & f, bool force_reversed=False)
2058  write(ImageHeader self, std::ofstream & f)
2059  """
2060  return _IMP_em.ImageHeader_write(self, *args)
2061 
2062  def clear(self):
2063  """clear(ImageHeader self)"""
2064  return _IMP_em.ImageHeader_clear(self)
2065 
2066  def set_header(self):
2067  """set_header(ImageHeader self)"""
2068  return _IMP_em.ImageHeader_set_header(self)
2069 
2070  def get_reversed(self):
2071  """get_reversed(ImageHeader self) -> bool"""
2072  return _IMP_em.ImageHeader_get_reversed(self)
2073 
2074  def set_reversed(self, *args):
2075  """set_reversed(ImageHeader self, bool value)"""
2076  return _IMP_em.ImageHeader_set_reversed(self, *args)
2077 
2078  def get_number_of_slices(self):
2079  """get_number_of_slices(ImageHeader self) -> unsigned int"""
2080  return _IMP_em.ImageHeader_get_number_of_slices(self)
2081 
2082  def set_number_of_slices(self, *args):
2083  """set_number_of_slices(ImageHeader self, unsigned int n)"""
2084  return _IMP_em.ImageHeader_set_number_of_slices(self, *args)
2085 
2086  def get_number_of_rows(self):
2087  """get_number_of_rows(ImageHeader self) -> unsigned int"""
2088  return _IMP_em.ImageHeader_get_number_of_rows(self)
2089 
2090  def set_number_of_rows(self, *args):
2091  """set_number_of_rows(ImageHeader self, unsigned int n)"""
2092  return _IMP_em.ImageHeader_set_number_of_rows(self, *args)
2093 
2094  def get_number_of_columns(self):
2095  """get_number_of_columns(ImageHeader self) -> unsigned int"""
2096  return _IMP_em.ImageHeader_get_number_of_columns(self)
2097 
2098  def set_number_of_columns(self, *args):
2099  """set_number_of_columns(ImageHeader self, unsigned int n)"""
2100  return _IMP_em.ImageHeader_set_number_of_columns(self, *args)
2101 
2102  def get_old_rot(self):
2103  """get_old_rot(ImageHeader self) -> float"""
2104  return _IMP_em.ImageHeader_get_old_rot(self)
2105 
2106  def set_old_rot(self, *args):
2107  """set_old_rot(ImageHeader self, float value)"""
2108  return _IMP_em.ImageHeader_set_old_rot(self, *args)
2109 
2110  def get_fAngle1(self):
2111  """get_fAngle1(ImageHeader self) -> float"""
2112  return _IMP_em.ImageHeader_get_fAngle1(self)
2113 
2114  def set_fAngle1(self, *args):
2115  """set_fAngle1(ImageHeader self, float value)"""
2116  return _IMP_em.ImageHeader_set_fAngle1(self, *args)
2117 
2118  def get_Scale(self):
2119  """get_Scale(ImageHeader self) -> float"""
2120  return _IMP_em.ImageHeader_get_Scale(self)
2121 
2122  def set_Scale(self, *args):
2123  """set_Scale(ImageHeader self, float value)"""
2124  return _IMP_em.ImageHeader_set_Scale(self, *args)
2125 
2126  def get_Flip(self):
2127  """get_Flip(ImageHeader self) -> float"""
2128  return _IMP_em.ImageHeader_get_Flip(self)
2129 
2130  def set_Flip(self, *args):
2131  """set_Flip(ImageHeader self, float value)"""
2132  return _IMP_em.ImageHeader_set_Flip(self, *args)
2133 
2134  def get_Weight(self):
2135  """get_Weight(ImageHeader self) -> float"""
2136  return _IMP_em.ImageHeader_get_Weight(self)
2137 
2138  def set_Weight(self, *args):
2139  """set_Weight(ImageHeader self, float value)"""
2140  return _IMP_em.ImageHeader_set_Weight(self, *args)
2141 
2142  def get_fNrec(self):
2143  """get_fNrec(ImageHeader self) -> float"""
2144  return _IMP_em.ImageHeader_get_fNrec(self)
2145 
2146  def set_fNrec(self, *args):
2147  """set_fNrec(ImageHeader self, float value)"""
2148  return _IMP_em.ImageHeader_set_fNrec(self, *args)
2149 
2150  def get_fNlabel(self):
2151  """get_fNlabel(ImageHeader self) -> float"""
2152  return _IMP_em.ImageHeader_get_fNlabel(self)
2153 
2154  def set_fNlabel(self, *args):
2155  """set_fNlabel(ImageHeader self, float value)"""
2156  return _IMP_em.ImageHeader_set_fNlabel(self, *args)
2157 
2158  def get_fIform(self):
2159  """get_fIform(ImageHeader self) -> float"""
2160  return _IMP_em.ImageHeader_get_fIform(self)
2161 
2162  def set_fIform(self, *args):
2163  """set_fIform(ImageHeader self, float value)"""
2164  return _IMP_em.ImageHeader_set_fIform(self, *args)
2165 
2166  def get_fImami(self):
2167  """get_fImami(ImageHeader self) -> float"""
2168  return _IMP_em.ImageHeader_get_fImami(self)
2169 
2170  def set_fImami(self, *args):
2171  """set_fImami(ImageHeader self, float value)"""
2172  return _IMP_em.ImageHeader_set_fImami(self, *args)
2173 
2174  def get_fFmax(self):
2175  """get_fFmax(ImageHeader self) -> float"""
2176  return _IMP_em.ImageHeader_get_fFmax(self)
2177 
2178  def set_fFmax(self, *args):
2179  """set_fFmax(ImageHeader self, float value)"""
2180  return _IMP_em.ImageHeader_set_fFmax(self, *args)
2181 
2182  def get_fFmin(self):
2183  """get_fFmin(ImageHeader self) -> float"""
2184  return _IMP_em.ImageHeader_get_fFmin(self)
2185 
2186  def set_fFmin(self, *args):
2187  """set_fFmin(ImageHeader self, float value)"""
2188  return _IMP_em.ImageHeader_set_fFmin(self, *args)
2189 
2190  def get_fAv(self):
2191  """get_fAv(ImageHeader self) -> float"""
2192  return _IMP_em.ImageHeader_get_fAv(self)
2193 
2194  def set_fAv(self, *args):
2195  """set_fAv(ImageHeader self, float value)"""
2196  return _IMP_em.ImageHeader_set_fAv(self, *args)
2197 
2198  def get_fSig(self):
2199  """get_fSig(ImageHeader self) -> float"""
2200  return _IMP_em.ImageHeader_get_fSig(self)
2201 
2202  def set_fSig(self, *args):
2203  """set_fSig(ImageHeader self, float value)"""
2204  return _IMP_em.ImageHeader_set_fSig(self, *args)
2205 
2206  def get_fIhist(self):
2207  """get_fIhist(ImageHeader self) -> float"""
2208  return _IMP_em.ImageHeader_get_fIhist(self)
2209 
2210  def set_fIhist(self, *args):
2211  """set_fIhist(ImageHeader self, float value)"""
2212  return _IMP_em.ImageHeader_set_fIhist(self, *args)
2213 
2214  def get_fLabrec(self):
2215  """get_fLabrec(ImageHeader self) -> float"""
2216  return _IMP_em.ImageHeader_get_fLabrec(self)
2217 
2218  def set_fLabrec(self, *args):
2219  """set_fLabrec(ImageHeader self, float value)"""
2220  return _IMP_em.ImageHeader_set_fLabrec(self, *args)
2221 
2222  def get_fIangle(self):
2223  """get_fIangle(ImageHeader self) -> float"""
2224  return _IMP_em.ImageHeader_get_fIangle(self)
2225 
2226  def set_fIangle(self, *args):
2227  """set_fIangle(ImageHeader self, float value)"""
2228  return _IMP_em.ImageHeader_set_fIangle(self, *args)
2229 
2230  def get_origin(self):
2231  """get_origin(ImageHeader self) -> Vector3D"""
2232  return _IMP_em.ImageHeader_get_origin(self)
2233 
2234  def set_origin(self, *args):
2235  """
2236  set_origin(ImageHeader self, Vector3D v)
2237  set_origin(ImageHeader self, Vector2D v)
2238  """
2239  return _IMP_em.ImageHeader_set_origin(self, *args)
2240 
2241  def get_object_pixel_size(self):
2242  """get_object_pixel_size(ImageHeader self) -> float"""
2243  return _IMP_em.ImageHeader_get_object_pixel_size(self)
2244 
2245  def set_object_pixel_size(self, *args):
2246  """set_object_pixel_size(ImageHeader self, float value)"""
2247  return _IMP_em.ImageHeader_set_object_pixel_size(self, *args)
2248 
2249  def get_fLabbyt(self):
2250  """get_fLabbyt(ImageHeader self) -> float"""
2251  return _IMP_em.ImageHeader_get_fLabbyt(self)
2252 
2253  def set_fLabbyt(self, *args):
2254  """set_fLabbyt(ImageHeader self, float value)"""
2255  return _IMP_em.ImageHeader_set_fLabbyt(self, *args)
2256 
2257  def get_fLenbyt(self):
2258  """get_fLenbyt(ImageHeader self) -> float"""
2259  return _IMP_em.ImageHeader_get_fLenbyt(self)
2260 
2261  def set_fLenbyt(self, *args):
2262  """set_fLenbyt(ImageHeader self, float value)"""
2263  return _IMP_em.ImageHeader_set_fLenbyt(self, *args)
2264 
2265  def get_fGeo_matrix(self, *args):
2266  """get_fGeo_matrix(ImageHeader self, unsigned int i, unsigned int j) -> double"""
2267  return _IMP_em.ImageHeader_get_fGeo_matrix(self, *args)
2268 
2269  def get_fFlag(self):
2270  """get_fFlag(ImageHeader self) -> float"""
2271  return _IMP_em.ImageHeader_get_fFlag(self)
2272 
2273  def set_fFlag(self, *args):
2274  """set_fFlag(ImageHeader self, float value)"""
2275  return _IMP_em.ImageHeader_set_fFlag(self, *args)
2276 
2277  def get_euler_angles(self):
2278  """get_euler_angles(ImageHeader self) -> Vector3D"""
2279  return _IMP_em.ImageHeader_get_euler_angles(self)
2280 
2281  def get_euler_angles1(self):
2282  """get_euler_angles1(ImageHeader self) -> Vector3D"""
2283  return _IMP_em.ImageHeader_get_euler_angles1(self)
2284 
2285  def get_euler_angles2(self):
2286  """get_euler_angles2(ImageHeader self) -> Vector3D"""
2287  return _IMP_em.ImageHeader_get_euler_angles2(self)
2288 
2289  def set_euler_angles(self, *args):
2290  """set_euler_angles(ImageHeader self, Vector3D euler)"""
2291  return _IMP_em.ImageHeader_set_euler_angles(self, *args)
2292 
2293  def set_euler_angles1(self, *args):
2294  """set_euler_angles1(ImageHeader self, Vector3D euler)"""
2295  return _IMP_em.ImageHeader_set_euler_angles1(self, *args)
2296 
2297  def set_euler_angles2(self, *args):
2298  """set_euler_angles2(ImageHeader self, Vector3D euler)"""
2299  return _IMP_em.ImageHeader_set_euler_angles2(self, *args)
2300 
2301  def is_normalized(self):
2302  """is_normalized(ImageHeader self) -> bool"""
2303  return _IMP_em.ImageHeader_is_normalized(self)
2304 
2305  def set_date(self):
2306  """set_date(ImageHeader self)"""
2307  return _IMP_em.ImageHeader_set_date(self)
2308 
2309  def set_time(self):
2310  """set_time(ImageHeader self)"""
2311  return _IMP_em.ImageHeader_set_time(self)
2312 
2313  def set_title(self, *args):
2314  """set_title(ImageHeader self, IMP::String newName)"""
2315  return _IMP_em.ImageHeader_set_title(self, *args)
2316 
2317  __swig_destroy__ = _IMP_em.delete_ImageHeader
2318  __del__ = lambda self : None;
2319 ImageHeader_swigregister = _IMP_em.ImageHeader_swigregister
2320 ImageHeader_swigregister(ImageHeader)
2321 
2322 class SpiderMapReaderWriter(MapReaderWriter):
2323  """Proxy of C++ IMP::em::SpiderMapReaderWriter class"""
2324  __swig_setmethods__ = {}
2325  for _s in [MapReaderWriter]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2326  __setattr__ = lambda self, name, value: _swig_setattr(self, SpiderMapReaderWriter, name, value)
2327  __swig_getmethods__ = {}
2328  for _s in [MapReaderWriter]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2329  __getattr__ = lambda self, name: _swig_getattr(self, SpiderMapReaderWriter, name)
2330  __swig_setmethods__["filename_"] = _IMP_em.SpiderMapReaderWriter_filename__set
2331  __swig_getmethods__["filename_"] = _IMP_em.SpiderMapReaderWriter_filename__get
2332  if _newclass:filename_ = _swig_property(_IMP_em.SpiderMapReaderWriter_filename__get, _IMP_em.SpiderMapReaderWriter_filename__set)
2333  __swig_setmethods__["skip_type_check_"] = _IMP_em.SpiderMapReaderWriter_skip_type_check__set
2334  __swig_getmethods__["skip_type_check_"] = _IMP_em.SpiderMapReaderWriter_skip_type_check__get
2335  if _newclass:skip_type_check_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_type_check__get, _IMP_em.SpiderMapReaderWriter_skip_type_check__set)
2336  __swig_setmethods__["force_reversed_"] = _IMP_em.SpiderMapReaderWriter_force_reversed__set
2337  __swig_getmethods__["force_reversed_"] = _IMP_em.SpiderMapReaderWriter_force_reversed__get
2338  if _newclass:force_reversed_ = _swig_property(_IMP_em.SpiderMapReaderWriter_force_reversed__get, _IMP_em.SpiderMapReaderWriter_force_reversed__set)
2339  __swig_setmethods__["skip_extra_checkings_"] = _IMP_em.SpiderMapReaderWriter_skip_extra_checkings__set
2340  __swig_getmethods__["skip_extra_checkings_"] = _IMP_em.SpiderMapReaderWriter_skip_extra_checkings__get
2341  if _newclass:skip_extra_checkings_ = _swig_property(_IMP_em.SpiderMapReaderWriter_skip_extra_checkings__get, _IMP_em.SpiderMapReaderWriter_skip_extra_checkings__set)
2342  def __init__(self, *args):
2343  """
2344  __init__(IMP::em::SpiderMapReaderWriter self) -> SpiderMapReaderWriter
2345  __init__(IMP::em::SpiderMapReaderWriter self, IMP::String filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings) -> SpiderMapReaderWriter
2346  """
2347  this = _IMP_em.new_SpiderMapReaderWriter(*args)
2348  try: self.this.append(this)
2349  except: self.this = this
2350  __swig_destroy__ = _IMP_em.delete_SpiderMapReaderWriter
2351  __del__ = lambda self : None;
2352  def __str__(self):
2353  """__str__(SpiderMapReaderWriter self) -> std::string"""
2354  return _IMP_em.SpiderMapReaderWriter___str__(self)
2355 
2356  def __repr__(self):
2357  """__repr__(SpiderMapReaderWriter self) -> std::string"""
2358  return _IMP_em.SpiderMapReaderWriter___repr__(self)
2359 
2360  def get_from(o):
2361  return _object_cast_to_SpiderMapReaderWriter(o)
2362  get_from = staticmethod(get_from)
2363 
2364 SpiderMapReaderWriter_swigregister = _IMP_em.SpiderMapReaderWriter_swigregister
2365 SpiderMapReaderWriter_swigregister(SpiderMapReaderWriter)
2366 
2367 class FittingSolutions(_object):
2368  """Proxy of C++ IMP::em::FittingSolutions class"""
2369  __swig_setmethods__ = {}
2370  __setattr__ = lambda self, name, value: _swig_setattr(self, FittingSolutions, name, value)
2371  __swig_getmethods__ = {}
2372  __getattr__ = lambda self, name: _swig_getattr(self, FittingSolutions, name)
2373  def __init__(self):
2374  """__init__(IMP::em::FittingSolutions self) -> FittingSolutions"""
2375  this = _IMP_em.new_FittingSolutions()
2376  try: self.this.append(this)
2377  except: self.this = this
2378  def get_number_of_solutions(self):
2379  """get_number_of_solutions(FittingSolutions self) -> int"""
2380  return _IMP_em.FittingSolutions_get_number_of_solutions(self)
2381 
2382  def get_transformation(self, *args):
2383  """get_transformation(FittingSolutions self, unsigned int i) -> Transformation3D"""
2384  return _IMP_em.FittingSolutions_get_transformation(self, *args)
2385 
2386  def get_score(self, *args):
2387  """get_score(FittingSolutions self, unsigned int i) -> IMP::Float"""
2388  return _IMP_em.FittingSolutions_get_score(self, *args)
2389 
2390  def set_score(self, *args):
2391  """set_score(FittingSolutions self, unsigned int i, IMP::Float score)"""
2392  return _IMP_em.FittingSolutions_set_score(self, *args)
2393 
2394  def add_solution(self, *args):
2395  """add_solution(FittingSolutions self, Transformation3D t, IMP::Float score)"""
2396  return _IMP_em.FittingSolutions_add_solution(self, *args)
2397 
2398  def sort(self, reverse=False):
2399  """
2400  sort(FittingSolutions self, bool reverse=False)
2401  sort(FittingSolutions self)
2402  """
2403  return _IMP_em.FittingSolutions_sort(self, reverse)
2404 
2405  def multiply(self, *args):
2406  """multiply(FittingSolutions self, Transformation3D t)"""
2407  return _IMP_em.FittingSolutions_multiply(self, *args)
2408 
2409  def get_transformations(self):
2410  """get_transformations(FittingSolutions self) -> IMP::algebra::Transformation3Ds"""
2411  return _IMP_em.FittingSolutions_get_transformations(self)
2412 
2413  def show(self, *args):
2414  """
2415  show(FittingSolutions self, _ostream out=std::cout)
2416  show(FittingSolutions self)
2417  """
2418  return _IMP_em.FittingSolutions_show(self, *args)
2419 
2420  def __str__(self):
2421  """__str__(FittingSolutions self) -> std::string"""
2422  return _IMP_em.FittingSolutions___str__(self)
2423 
2424  def __repr__(self):
2425  """__repr__(FittingSolutions self) -> std::string"""
2426  return _IMP_em.FittingSolutions___repr__(self)
2427 
2428  __swig_destroy__ = _IMP_em.delete_FittingSolutions
2429  __del__ = lambda self : None;
2430 FittingSolutions_swigregister = _IMP_em.FittingSolutions_swigregister
2431 FittingSolutions_swigregister(FittingSolutions)
2432 
2433 
2434 def local_rigid_fitting_around_point(*args):
2435  """
2436  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid,
2437  IMP::kernel::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5,
2438  IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100,
2439  IMP::Float max_translation=2., IMP::Float max_rotation=.3, bool fast=False) -> FittingSolutions
2440  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid,
2441  IMP::kernel::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5,
2442  IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100,
2443  IMP::Float max_translation=2., IMP::Float max_rotation=.3) -> FittingSolutions
2444  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid,
2445  IMP::kernel::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5,
2446  IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100,
2447  IMP::Float max_translation=2.) -> FittingSolutions
2448  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid,
2449  IMP::kernel::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5,
2450  IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100) -> FittingSolutions
2451  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid,
2452  IMP::kernel::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5,
2453  IMP::Int number_of_mc_steps=10) -> FittingSolutions
2454  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid,
2455  IMP::kernel::OptimizerStates display_log, IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2456  local_rigid_fitting_around_point(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, Vector3D anchor_centroid,
2457  IMP::kernel::OptimizerStates display_log) -> FittingSolutions
2458  """
2459  return _IMP_em.local_rigid_fitting_around_point(*args)
2460 
2461 def local_rigid_fitting(*args):
2462  """
2463  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::kernel::OptimizerStates display_log,
2464  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10,
2465  IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2.,
2466  IMP::Float max_rotation=.3, bool fast=True) -> FittingSolutions
2467  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::kernel::OptimizerStates display_log,
2468  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10,
2469  IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2.,
2470  IMP::Float max_rotation=.3) -> FittingSolutions
2471  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::kernel::OptimizerStates display_log,
2472  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10,
2473  IMP::Int number_of_cg_steps=100, IMP::Float max_translation=2.) -> FittingSolutions
2474  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::kernel::OptimizerStates display_log,
2475  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10,
2476  IMP::Int number_of_cg_steps=100) -> FittingSolutions
2477  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::kernel::OptimizerStates display_log,
2478  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10) -> FittingSolutions
2479  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::kernel::OptimizerStates display_log,
2480  IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2481  local_rigid_fitting(Particle p, Refiner refiner, FloatKey weight_key, DensityMap dmap, IMP::kernel::OptimizerStates display_log) -> FittingSolutions
2482  """
2483  return _IMP_em.local_rigid_fitting(*args)
2484 
2485 def local_rigid_fitting_around_points(*args):
2486  """
2487  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids,
2488  IMP::kernel::OptimizerStates display_log,
2489  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100,
2490  IMP::Float max_translation=2., IMP::Float max_rotation=.3) -> FittingSolutions
2491  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids,
2492  IMP::kernel::OptimizerStates display_log,
2493  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100,
2494  IMP::Float max_translation=2.) -> FittingSolutions
2495  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids,
2496  IMP::kernel::OptimizerStates display_log,
2497  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10, IMP::Int number_of_cg_steps=100) -> FittingSolutions
2498  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids,
2499  IMP::kernel::OptimizerStates display_log,
2500  IMP::Int number_of_optimization_runs=5, IMP::Int number_of_mc_steps=10) -> FittingSolutions
2501  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids,
2502  IMP::kernel::OptimizerStates display_log,
2503  IMP::Int number_of_optimization_runs=5) -> FittingSolutions
2504  local_rigid_fitting_around_points(Particle p, Refiner refiner, FloatKey wei_key, DensityMap dmap, IMP::algebra::Vector3Ds const & anchor_centroids,
2505  IMP::kernel::OptimizerStates display_log) -> FittingSolutions
2506  """
2507  return _IMP_em.local_rigid_fitting_around_points(*args)
2508 
2509 def local_rigid_fitting_grid_search(*args):
2510  """
2511  local_rigid_fitting_grid_search(IMP::kernel::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2,
2512  IMP::Int translation_step=1, IMP::Float max_angle_in_radians=0.174,
2513  IMP::Int number_of_rotations=100) -> FittingSolutions
2514  local_rigid_fitting_grid_search(IMP::kernel::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2,
2515  IMP::Int translation_step=1, IMP::Float max_angle_in_radians=0.174) -> FittingSolutions
2516  local_rigid_fitting_grid_search(IMP::kernel::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2,
2517  IMP::Int translation_step=1) -> FittingSolutions
2518  local_rigid_fitting_grid_search(IMP::kernel::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap, IMP::Int max_voxels_translation=2) -> FittingSolutions
2519  local_rigid_fitting_grid_search(IMP::kernel::ParticlesTemp const & ps, FloatKey wei_key, DensityMap dmap) -> FittingSolutions
2520  """
2521  return _IMP_em.local_rigid_fitting_grid_search(*args)
2522 
2523 def compute_fitting_scores(*args):
2524  """
2525  compute_fitting_scores(IMP::kernel::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations,
2526  bool fast_version=False, bool local_score=False,
2527  FloatKey wei_key=IMP::atom::Mass::get_mass_key()) -> FittingSolutions
2528  compute_fitting_scores(IMP::kernel::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations,
2529  bool fast_version=False, bool local_score=False) -> FittingSolutions
2530  compute_fitting_scores(IMP::kernel::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations,
2531  bool fast_version=False) -> FittingSolutions
2532  compute_fitting_scores(IMP::kernel::ParticlesTemp const & ps, DensityMap em_map, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2533  compute_fitting_scores(DensityMap em_map, RigidBody rb, Refiner refiner, IMP::algebra::Transformation3Ds const & transformations) -> FittingSolutions
2534  """
2535  return _IMP_em.compute_fitting_scores(*args)
2536 
2537 def compute_fitting_score(*args):
2538  """
2539  compute_fitting_score(IMP::kernel::ParticlesTemp const & ps, DensityMap em_map, FloatKey wei_key=IMP::atom::Mass::get_mass_key()) -> IMP::Float
2540  compute_fitting_score(IMP::kernel::ParticlesTemp const & ps, DensityMap em_map) -> IMP::Float
2541  """
2542  return _IMP_em.compute_fitting_score(*args)
2543 
2544 def get_number_of_particles_outside_of_the_density(*args):
2545  """
2546  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::kernel::Particles const & ps, Transformation3D t=IMP::algebra::get_identity_transformation_3d(),
2547  float thr=0.0) -> long
2548  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::kernel::Particles const & ps, Transformation3D t=IMP::algebra::get_identity_transformation_3d()) -> long
2549  get_number_of_particles_outside_of_the_density(DensityMap dmap, IMP::kernel::Particles const & ps) -> long
2550  """
2551  return _IMP_em.get_number_of_particles_outside_of_the_density(*args)
2552 
2553 def get_numbers_of_particles_outside_of_the_density(*args):
2554  """
2555  get_numbers_of_particles_outside_of_the_density(DensityMap dmap, IMP::kernel::Particles const & ps, IMP::algebra::Transformation3Ds const & transformations,
2556  float thr=0.0) -> IMP::Ints
2557  get_numbers_of_particles_outside_of_the_density(DensityMap dmap, IMP::kernel::Particles const & ps, IMP::algebra::Transformation3Ds const & transformations) -> IMP::Ints
2558  """
2559  return _IMP_em.get_numbers_of_particles_outside_of_the_density(*args)
2560 
2561 def get_percentage_of_voxels_covered_by_particles(*args):
2562  """
2563  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(),
2564  float thr=0.0) -> double
2565  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
2566  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::kernel::Particles const & ps, float smoothing_radius=3.) -> double
2567  get_percentage_of_voxels_covered_by_particles(DensityMap dmap, IMP::kernel::Particles const & ps) -> double
2568  """
2569  return _IMP_em.get_percentage_of_voxels_covered_by_particles(*args)
2570 class HighDensityEmbedding(IMP.statistics.Embedding):
2571  """Proxy of C++ IMP::em::HighDensityEmbedding class"""
2572  __swig_setmethods__ = {}
2573  for _s in [IMP.statistics.Embedding]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2574  __setattr__ = lambda self, name, value: _swig_setattr(self, HighDensityEmbedding, name, value)
2575  __swig_getmethods__ = {}
2576  for _s in [IMP.statistics.Embedding]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2577  __getattr__ = lambda self, name: _swig_getattr(self, HighDensityEmbedding, name)
2578  def __init__(self, *args):
2579  """__init__(IMP::em::HighDensityEmbedding self, DensityMap dm, double threshold) -> HighDensityEmbedding"""
2580  this = _IMP_em.new_HighDensityEmbedding(*args)
2581  try: self.this.append(this)
2582  except: self.this = this
2583  def get_version_info(self):
2584  """get_version_info(HighDensityEmbedding self) -> VersionInfo"""
2585  return _IMP_em.HighDensityEmbedding_get_version_info(self)
2586 
2587  def do_show(self, *args):
2588  """do_show(HighDensityEmbedding self, _ostream out)"""
2589  return _IMP_em.HighDensityEmbedding_do_show(self, *args)
2590 
2591  __swig_destroy__ = _IMP_em.delete_HighDensityEmbedding
2592  __del__ = lambda self : None;
2593  def __str__(self):
2594  """__str__(HighDensityEmbedding self) -> std::string"""
2595  return _IMP_em.HighDensityEmbedding___str__(self)
2596 
2597  def __repr__(self):
2598  """__repr__(HighDensityEmbedding self) -> std::string"""
2599  return _IMP_em.HighDensityEmbedding___repr__(self)
2600 
2601  def get_from(o):
2602  return _object_cast_to_HighDensityEmbedding(o)
2603  get_from = staticmethod(get_from)
2604 
2605 HighDensityEmbedding_swigregister = _IMP_em.HighDensityEmbedding_swigregister
2606 HighDensityEmbedding_swigregister(HighDensityEmbedding)
2607 
2608 
2609 def mask_and_norm(*args):
2610  """mask_and_norm(DensityMap dmap, DensityMap mask) -> DensityMap"""
2611  return _IMP_em.mask_and_norm(*args)
2612 
2613 def get_volume_at_threshold(*args):
2614  """get_volume_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float"""
2615  return _IMP_em.get_volume_at_threshold(*args)
2616 
2617 def get_molecular_mass_at_threshold(*args):
2618  """
2619  get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold, IMP::atom::ProteinDensityReference ref=HARPAZ) -> IMP::Float
2620  get_molecular_mass_at_threshold(DensityMap m, IMP::Float threshold) -> IMP::Float
2621  """
2622  return _IMP_em.get_molecular_mass_at_threshold(*args)
2623 
2624 def get_threshold_for_approximate_volume(*args):
2625  """get_threshold_for_approximate_volume(DensityMap m, IMP::Float desired_volume) -> IMP::Float"""
2626  return _IMP_em.get_threshold_for_approximate_volume(*args)
2627 
2628 def get_threshold_for_approximate_mass(*args):
2629  """
2630  get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass, IMP::atom::ProteinDensityReference ref=HARPAZ) -> IMP::Float
2631  get_threshold_for_approximate_mass(DensityMap m, IMP::Float desired_mass) -> IMP::Float
2632  """
2633  return _IMP_em.get_threshold_for_approximate_mass(*args)
2634 class EnvelopePenetrationRestraint(IMP.kernel.Restraint):
2635  """Proxy of C++ IMP::em::EnvelopePenetrationRestraint class"""
2636  __swig_setmethods__ = {}
2637  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2638  __setattr__ = lambda self, name, value: _swig_setattr(self, EnvelopePenetrationRestraint, name, value)
2639  __swig_getmethods__ = {}
2640  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2641  __getattr__ = lambda self, name: _swig_getattr(self, EnvelopePenetrationRestraint, name)
2642  def __init__(self, *args):
2643  """__init__(IMP::em::EnvelopePenetrationRestraint self, IMP::kernel::Particles ps, DensityMap em_map, IMP::Float threshold) -> EnvelopePenetrationRestraint"""
2644  this = _IMP_em.new_EnvelopePenetrationRestraint(*args)
2645  try: self.this.append(this)
2646  except: self.this = this
2647  def get_input_particles(self):
2648  """get_input_particles(EnvelopePenetrationRestraint self) -> IMP::kernel::ParticlesTemp"""
2649  return _IMP_em.EnvelopePenetrationRestraint_get_input_particles(self)
2650 
2651  def get_input_containers(self):
2652  """get_input_containers(EnvelopePenetrationRestraint self) -> IMP::kernel::ContainersTemp"""
2653  return _IMP_em.EnvelopePenetrationRestraint_get_input_containers(self)
2654 
2655  def do_get_inputs(self):
2656  """do_get_inputs(EnvelopePenetrationRestraint self) -> IMP::kernel::ModelObjectsTemp"""
2657  return _IMP_em.EnvelopePenetrationRestraint_do_get_inputs(self)
2658 
2659  def get_version_info(self):
2660  """get_version_info(EnvelopePenetrationRestraint self) -> VersionInfo"""
2661  return _IMP_em.EnvelopePenetrationRestraint_get_version_info(self)
2662 
2663  def do_show(self, *args):
2664  """do_show(EnvelopePenetrationRestraint self, _ostream out)"""
2665  return _IMP_em.EnvelopePenetrationRestraint_do_show(self, *args)
2666 
2667  __swig_destroy__ = _IMP_em.delete_EnvelopePenetrationRestraint
2668  __del__ = lambda self : None;
2669  def __str__(self):
2670  """__str__(EnvelopePenetrationRestraint self) -> std::string"""
2671  return _IMP_em.EnvelopePenetrationRestraint___str__(self)
2672 
2673  def __repr__(self):
2674  """__repr__(EnvelopePenetrationRestraint self) -> std::string"""
2675  return _IMP_em.EnvelopePenetrationRestraint___repr__(self)
2676 
2677  def get_from(o):
2678  return _object_cast_to_EnvelopePenetrationRestraint(o)
2679  get_from = staticmethod(get_from)
2680 
2681 EnvelopePenetrationRestraint_swigregister = _IMP_em.EnvelopePenetrationRestraint_swigregister
2682 EnvelopePenetrationRestraint_swigregister(EnvelopePenetrationRestraint)
2683 
2684 class PCAFitRestraint(IMP.kernel.Restraint):
2685  """Proxy of C++ IMP::em::PCAFitRestraint class"""
2686  __swig_setmethods__ = {}
2687  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2688  __setattr__ = lambda self, name, value: _swig_setattr(self, PCAFitRestraint, name, value)
2689  __swig_getmethods__ = {}
2690  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2691  __getattr__ = lambda self, name: _swig_getattr(self, PCAFitRestraint, name)
2692  def __init__(self, *args):
2693  """
2694  __init__(IMP::em::PCAFitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map, float threahold, float max_pca_size_diff,
2695  float max_angle_diff, float max_centroid_diff, FloatKey weight_key=IMP::atom::Mass::get_mass_key()) -> PCAFitRestraint
2696  __init__(IMP::em::PCAFitRestraint self, IMP::kernel::ParticlesTemp ps, DensityMap em_map, float threahold, float max_pca_size_diff,
2697  float max_angle_diff, float max_centroid_diff) -> PCAFitRestraint
2698  """
2699  this = _IMP_em.new_PCAFitRestraint(*args)
2700  try: self.this.append(this)
2701  except: self.this = this
2702  def get_input_particles(self):
2703  """get_input_particles(PCAFitRestraint self) -> IMP::kernel::ParticlesTemp"""
2704  return _IMP_em.PCAFitRestraint_get_input_particles(self)
2705 
2706  def get_input_containers(self):
2707  """get_input_containers(PCAFitRestraint self) -> IMP::kernel::ContainersTemp"""
2708  return _IMP_em.PCAFitRestraint_get_input_containers(self)
2709 
2710  def do_get_inputs(self):
2711  """do_get_inputs(PCAFitRestraint self) -> IMP::kernel::ModelObjectsTemp"""
2712  return _IMP_em.PCAFitRestraint_do_get_inputs(self)
2713 
2714  def get_version_info(self):
2715  """get_version_info(PCAFitRestraint self) -> VersionInfo"""
2716  return _IMP_em.PCAFitRestraint_get_version_info(self)
2717 
2718  def do_show(self, *args):
2719  """do_show(PCAFitRestraint self, _ostream out)"""
2720  return _IMP_em.PCAFitRestraint_do_show(self, *args)
2721 
2722  __swig_destroy__ = _IMP_em.delete_PCAFitRestraint
2723  __del__ = lambda self : None;
2724  def __str__(self):
2725  """__str__(PCAFitRestraint self) -> std::string"""
2726  return _IMP_em.PCAFitRestraint___str__(self)
2727 
2728  def __repr__(self):
2729  """__repr__(PCAFitRestraint self) -> std::string"""
2730  return _IMP_em.PCAFitRestraint___repr__(self)
2731 
2732  def get_from(o):
2733  return _object_cast_to_PCAFitRestraint(o)
2734  get_from = staticmethod(get_from)
2735 
2736 PCAFitRestraint_swigregister = _IMP_em.PCAFitRestraint_swigregister
2737 PCAFitRestraint_swigregister(PCAFitRestraint)
2738 
2739 class EnvelopeFitRestraint(IMP.kernel.Restraint):
2740  """Proxy of C++ IMP::em::EnvelopeFitRestraint class"""
2741  __swig_setmethods__ = {}
2742  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2743  __setattr__ = lambda self, name, value: _swig_setattr(self, EnvelopeFitRestraint, name, value)
2744  __swig_getmethods__ = {}
2745  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2746  __getattr__ = lambda self, name: _swig_getattr(self, EnvelopeFitRestraint, name)
2747  def __init__(self, *args):
2748  """__init__(IMP::em::EnvelopeFitRestraint self, IMP::kernel::Particles particles, DensityMap em_map, double density_threshold, double penetration_threshold) -> EnvelopeFitRestraint"""
2749  this = _IMP_em.new_EnvelopeFitRestraint(*args)
2750  try: self.this.append(this)
2751  except: self.this = this
2752  def get_transformation(self):
2753  """get_transformation(EnvelopeFitRestraint self) -> Transformation3D"""
2754  return _IMP_em.EnvelopeFitRestraint_get_transformation(self)
2755 
2756  def apply_transformation(self):
2757  """apply_transformation(EnvelopeFitRestraint self)"""
2758  return _IMP_em.EnvelopeFitRestraint_apply_transformation(self)
2759 
2760  def do_get_inputs(self):
2761  """do_get_inputs(EnvelopeFitRestraint self) -> IMP::ModelObjectsTemp"""
2762  return _IMP_em.EnvelopeFitRestraint_do_get_inputs(self)
2763 
2764  def get_version_info(self):
2765  """get_version_info(EnvelopeFitRestraint self) -> VersionInfo"""
2766  return _IMP_em.EnvelopeFitRestraint_get_version_info(self)
2767 
2768  __swig_destroy__ = _IMP_em.delete_EnvelopeFitRestraint
2769  __del__ = lambda self : None;
2770  def __str__(self):
2771  """__str__(EnvelopeFitRestraint self) -> std::string"""
2772  return _IMP_em.EnvelopeFitRestraint___str__(self)
2773 
2774  def __repr__(self):
2775  """__repr__(EnvelopeFitRestraint self) -> std::string"""
2776  return _IMP_em.EnvelopeFitRestraint___repr__(self)
2777 
2778  def get_from(o):
2779  return _object_cast_to_EnvelopeFitRestraint(o)
2780  get_from = staticmethod(get_from)
2781 
2782 EnvelopeFitRestraint_swigregister = _IMP_em.EnvelopeFitRestraint_swigregister
2783 EnvelopeFitRestraint_swigregister(EnvelopeFitRestraint)
2784 
2785 import math
2786 
2787 def write_pca_cmm(pca, fh):
2788  """Write out principal components to a file in Chimera Marker format"""
2789  eigen_values = pca.get_principal_values()
2790  eigen_vecs = pca.get_principal_components()
2791  centroid = pca.get_centroid()
2792 
2793  print >> fh, "<marker_set>"
2794  print >> fh, "<!-- PCA with eigen values: (%g,%g,%g) and " \
2795  "centroid (%g,%g,%g) -->" \
2796  % (math.sqrt(eigen_values[0]),
2797  math.sqrt(eigen_values[1]),
2798  math.sqrt(eigen_values[2]),
2799  centroid[0], centroid[1], centroid[2])
2800 
2801  radius = 2.
2802 
2803  for i in range(3):
2804  val = math.sqrt(eigen_values[i])
2805  v1 = centroid - val * eigen_vecs[i]
2806  v2 = centroid + val * eigen_vecs[i]
2807  for markerid, v in ((i*2+1, v1), (i*2+2, v2)):
2808  print >> fh, "<marker id=\"%d\" x=\"%g\" y=\"%g\" z=\"%g\" " \
2809  "radius=\"%g\"/>" \
2810  % (markerid, v[0], v[1], v[2], radius)
2811 
2812  for i in range(1, 7, 2):
2813  print >> fh, "<link id1= \"%d\" id2=\"%d\" radius=\"%g\"/>" \
2814  % (i, i+1, radius)
2815  print >> fh, "</marker_set>"
2816 
2817 
2818 def get_module_version():
2819  """get_module_version() -> std::string const"""
2820  return _IMP_em.get_module_version()
2821 
2822 def get_example_path(*args):
2823  """get_example_path(std::string fname) -> std::string"""
2824  return _IMP_em.get_example_path(*args)
2825 
2826 def get_data_path(*args):
2827  """get_data_path(std::string fname) -> std::string"""
2828  return _IMP_em.get_data_path(*args)
2829 import _version_check
2830 _version_check.check_version(get_module_version())
2831 
2832 # This file is compatible with both classic and new-style classes.
2833 
2834