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IMP Reference Guide  2.13.0
The Integrative Modeling Platform
cnmultifit/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.10
3 #
4 # Do not make changes to this file unless you know what you are doing--modify
5 # the SWIG interface file instead.
6 
7 # This wrapper is part of IMP,
8 # Copyright 2007-2020 IMP Inventors. All rights reserved.
9 
10 from __future__ import print_function, division, absolute_import
11 
12 
13 
14 
15 from sys import version_info as _swig_python_version_info
16 if _swig_python_version_info >= (2, 7, 0):
17  def swig_import_helper():
18  import importlib
19  pkg = __name__.rpartition('.')[0]
20  mname = '.'.join((pkg, '_IMP_cnmultifit')).lstrip('.')
21  try:
22  return importlib.import_module(mname)
23  except ImportError:
24  return importlib.import_module('_IMP_cnmultifit')
25  _IMP_cnmultifit = swig_import_helper()
26  del swig_import_helper
27 elif _swig_python_version_info >= (2, 6, 0):
28  def swig_import_helper():
29  from os.path import dirname
30  import imp
31  fp = None
32  try:
33  fp, pathname, description = imp.find_module('_IMP_cnmultifit', [dirname(__file__)])
34  except ImportError:
35  import _IMP_cnmultifit
36  return _IMP_cnmultifit
37  if fp is not None:
38  try:
39  _mod = imp.load_module('_IMP_cnmultifit', fp, pathname, description)
40  finally:
41  fp.close()
42  return _mod
43  _IMP_cnmultifit = swig_import_helper()
44  del swig_import_helper
45 else:
46  import _IMP_cnmultifit
47 del _swig_python_version_info
48 try:
49  _swig_property = property
50 except NameError:
51  pass # Python < 2.2 doesn't have 'property'.
52 
53 try:
54  import builtins as __builtin__
55 except ImportError:
56  import __builtin__
57 
58 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
59  if (name == "thisown"):
60  return self.this.own(value)
61  if (name == "this"):
62  if type(value).__name__ == 'SwigPyObject':
63  self.__dict__[name] = value
64  return
65  method = class_type.__swig_setmethods__.get(name, None)
66  if method:
67  return method(self, value)
68  if (not static):
69  object.__setattr__(self, name, value)
70  else:
71  raise AttributeError("You cannot add attributes to %s" % self)
72 
73 
74 def _swig_setattr(self, class_type, name, value):
75  return _swig_setattr_nondynamic(self, class_type, name, value, 0)
76 
77 
78 def _swig_getattr(self, class_type, name):
79  if (name == "thisown"):
80  return self.this.own()
81  method = class_type.__swig_getmethods__.get(name, None)
82  if method:
83  return method(self)
84  raise AttributeError("'%s' object has no attribute '%s'" % (class_type.__name__, name))
85 
86 
87 def _swig_repr(self):
88  try:
89  strthis = "proxy of " + self.this.__repr__()
90  except __builtin__.Exception:
91  strthis = ""
92  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
93 
94 
95 def _swig_setattr_nondynamic_method(set):
96  def set_attr(self, name, value):
97  if (name == "thisown"):
98  return self.this.own(value)
99  if hasattr(self, name) or (name == "this"):
100  set(self, name, value)
101  else:
102  raise AttributeError("You cannot add attributes to %s" % self)
103  return set_attr
104 
105 
106 try:
107  import weakref
108  weakref_proxy = weakref.proxy
109 except __builtin__.Exception:
110  weakref_proxy = lambda x: x
111 
112 
113 class IMP_CNMULTIFIT_SwigPyIterator(object):
114  """Proxy of C++ swig::IMP_CNMULTIFIT_SwigPyIterator class."""
115 
116  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
117 
118  def __init__(self, *args, **kwargs):
119  raise AttributeError("No constructor defined - class is abstract")
120  __repr__ = _swig_repr
121  __swig_destroy__ = _IMP_cnmultifit.delete_IMP_CNMULTIFIT_SwigPyIterator
122  __del__ = lambda self: None
123 
124  def value(self):
125  """value(IMP_CNMULTIFIT_SwigPyIterator self) -> PyObject *"""
126  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_value(self)
127 
128 
129  def incr(self, n=1):
130  """
131  incr(IMP_CNMULTIFIT_SwigPyIterator self, size_t n=1) -> IMP_CNMULTIFIT_SwigPyIterator
132  incr(IMP_CNMULTIFIT_SwigPyIterator self) -> IMP_CNMULTIFIT_SwigPyIterator
133  """
134  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_incr(self, n)
135 
136 
137  def decr(self, n=1):
138  """
139  decr(IMP_CNMULTIFIT_SwigPyIterator self, size_t n=1) -> IMP_CNMULTIFIT_SwigPyIterator
140  decr(IMP_CNMULTIFIT_SwigPyIterator self) -> IMP_CNMULTIFIT_SwigPyIterator
141  """
142  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_decr(self, n)
143 
144 
145  def distance(self, x):
146  """distance(IMP_CNMULTIFIT_SwigPyIterator self, IMP_CNMULTIFIT_SwigPyIterator x) -> ptrdiff_t"""
147  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_distance(self, x)
148 
149 
150  def equal(self, x):
151  """equal(IMP_CNMULTIFIT_SwigPyIterator self, IMP_CNMULTIFIT_SwigPyIterator x) -> bool"""
152  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_equal(self, x)
153 
154 
155  def copy(self):
156  """copy(IMP_CNMULTIFIT_SwigPyIterator self) -> IMP_CNMULTIFIT_SwigPyIterator"""
157  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_copy(self)
158 
159 
160  def next(self):
161  """next(IMP_CNMULTIFIT_SwigPyIterator self) -> PyObject *"""
162  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_next(self)
163 
164 
165  def __next__(self):
166  """__next__(IMP_CNMULTIFIT_SwigPyIterator self) -> PyObject *"""
167  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___next__(self)
168 
169 
170  def previous(self):
171  """previous(IMP_CNMULTIFIT_SwigPyIterator self) -> PyObject *"""
172  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_previous(self)
173 
174 
175  def advance(self, n):
176  """advance(IMP_CNMULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_CNMULTIFIT_SwigPyIterator"""
177  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_advance(self, n)
178 
179 
180  def __eq__(self, x):
181  """__eq__(IMP_CNMULTIFIT_SwigPyIterator self, IMP_CNMULTIFIT_SwigPyIterator x) -> bool"""
182  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___eq__(self, x)
183 
184 
185  def __ne__(self, x):
186  """__ne__(IMP_CNMULTIFIT_SwigPyIterator self, IMP_CNMULTIFIT_SwigPyIterator x) -> bool"""
187  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___ne__(self, x)
188 
189 
190  def __iadd__(self, n):
191  """__iadd__(IMP_CNMULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_CNMULTIFIT_SwigPyIterator"""
192  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___iadd__(self, n)
193 
194 
195  def __isub__(self, n):
196  """__isub__(IMP_CNMULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_CNMULTIFIT_SwigPyIterator"""
197  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___isub__(self, n)
198 
199 
200  def __add__(self, n):
201  """__add__(IMP_CNMULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_CNMULTIFIT_SwigPyIterator"""
202  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___add__(self, n)
203 
204 
205  def __sub__(self, *args):
206  """
207  __sub__(IMP_CNMULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_CNMULTIFIT_SwigPyIterator
208  __sub__(IMP_CNMULTIFIT_SwigPyIterator self, IMP_CNMULTIFIT_SwigPyIterator x) -> ptrdiff_t
209  """
210  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___sub__(self, *args)
211 
212  def __iter__(self):
213  return self
214 IMP_CNMULTIFIT_SwigPyIterator_swigregister = _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_swigregister
215 IMP_CNMULTIFIT_SwigPyIterator_swigregister(IMP_CNMULTIFIT_SwigPyIterator)
216 
217 
218 _value_types=[]
219 _object_types=[]
220 _raii_types=[]
221 _plural_types=[]
222 
223 IMP_DEBUG = _IMP_cnmultifit.IMP_DEBUG
224 IMP_RELEASE = _IMP_cnmultifit.IMP_RELEASE
225 IMP_SILENT = _IMP_cnmultifit.IMP_SILENT
226 IMP_PROGRESS = _IMP_cnmultifit.IMP_PROGRESS
227 IMP_TERSE = _IMP_cnmultifit.IMP_TERSE
228 IMP_VERBOSE = _IMP_cnmultifit.IMP_VERBOSE
229 IMP_MEMORY = _IMP_cnmultifit.IMP_MEMORY
230 IMP_NONE = _IMP_cnmultifit.IMP_NONE
231 IMP_USAGE = _IMP_cnmultifit.IMP_USAGE
232 IMP_INTERNAL = _IMP_cnmultifit.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_cnmultifit.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_cnmultifit.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_cnmultifit.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_cnmultifit.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_NUMPY = _IMP_cnmultifit.IMP_KERNEL_HAS_NUMPY
239 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_cnmultifit.IMP_KERNEL_HAS_GPERFTOOLS
240 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_cnmultifit.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
241 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_cnmultifit.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
242 IMPKERNEL_SHOW_WARNINGS = _IMP_cnmultifit.IMPKERNEL_SHOW_WARNINGS
243 
244 import sys
245 class _DirectorObjects(object):
246  """@internal Simple class to keep references to director objects
247  to prevent premature deletion."""
248  def __init__(self):
249  self._objects = []
250  def register(self, obj):
251  """Take a reference to a director object; will only work for
252  refcounted C++ classes"""
253  if hasattr(obj, 'get_ref_count'):
254  self._objects.append(obj)
255  def cleanup(self):
256  """Only drop our reference and allow cleanup by Python if no other
257  Python references exist (we hold 3 references: one in self._objects,
258  one in x, and one in the argument list for getrefcount) *and* no
259  other C++ references exist (the Python object always holds one)"""
260  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
261  or x.get_ref_count() > 1]
262 # Do in two steps so the references are kept until the end of the
263 # function (deleting references may trigger a fresh call to this method)
264  self._objects = objs
265  def get_object_count(self):
266  """Get number of director objects (useful for testing only)"""
267  return len(self._objects)
268 _director_objects = _DirectorObjects()
269 
270 class _ostream(object):
271  """Proxy of C++ std::ostream class."""
272 
273  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
274 
275  def __init__(self, *args, **kwargs):
276  raise AttributeError("No constructor defined")
277  __repr__ = _swig_repr
278 
279  def write(self, osa_buf):
280  """write(_ostream self, char const * osa_buf)"""
281  return _IMP_cnmultifit._ostream_write(self, osa_buf)
282 
283 _ostream_swigregister = _IMP_cnmultifit._ostream_swigregister
284 _ostream_swigregister(_ostream)
285 
286 IMP_COMPILER_HAS_OVERRIDE = _IMP_cnmultifit.IMP_COMPILER_HAS_OVERRIDE
287 IMP_COMPILER_HAS_FINAL = _IMP_cnmultifit.IMP_COMPILER_HAS_FINAL
288 IMP_HAS_NOEXCEPT = _IMP_cnmultifit.IMP_HAS_NOEXCEPT
289 IMP_C_OPEN_BINARY = _IMP_cnmultifit.IMP_C_OPEN_BINARY
290 import IMP
291 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_CGAL_HAS_BOOST_FILESYSTEM
292 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
293 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_CGAL_HAS_BOOST_RANDOM
294 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_CGAL_HAS_BOOST_SYSTEM
295 IMP_CGAL_HAS_NUMPY = _IMP_cnmultifit.IMP_CGAL_HAS_NUMPY
296 IMPCGAL_SHOW_WARNINGS = _IMP_cnmultifit.IMPCGAL_SHOW_WARNINGS
297 import IMP.cgal
298 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_ALGEBRA_HAS_IMP_CGAL
299 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
300 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
301 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_ALGEBRA_HAS_BOOST_RANDOM
302 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_ALGEBRA_HAS_BOOST_SYSTEM
303 IMP_ALGEBRA_HAS_CGAL = _IMP_cnmultifit.IMP_ALGEBRA_HAS_CGAL
304 IMP_ALGEBRA_HAS_NUMPY = _IMP_cnmultifit.IMP_ALGEBRA_HAS_NUMPY
305 IMP_ALGEBRA_HAS_ANN = _IMP_cnmultifit.IMP_ALGEBRA_HAS_ANN
306 IMPALGEBRA_SHOW_WARNINGS = _IMP_cnmultifit.IMPALGEBRA_SHOW_WARNINGS
307 import IMP.algebra
308 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_DISPLAY_HAS_IMP_CGAL
309 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
310 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
311 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_DISPLAY_HAS_BOOST_RANDOM
312 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_DISPLAY_HAS_BOOST_SYSTEM
313 IMP_DISPLAY_HAS_CGAL = _IMP_cnmultifit.IMP_DISPLAY_HAS_CGAL
314 IMP_DISPLAY_HAS_NUMPY = _IMP_cnmultifit.IMP_DISPLAY_HAS_NUMPY
315 IMPDISPLAY_SHOW_WARNINGS = _IMP_cnmultifit.IMPDISPLAY_SHOW_WARNINGS
316 import IMP.display
317 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
318 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
319 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
320 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
321 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
322 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_CGAL
323 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_HDF5
324 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_NUMPY
325 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_cnmultifit.IMPSCOREFUNCTOR_SHOW_WARNINGS
326 import IMP.score_functor
327 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_STATISTICS_HAS_IMP_CGAL
328 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
329 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
330 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_STATISTICS_HAS_BOOST_RANDOM
331 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_STATISTICS_HAS_BOOST_SYSTEM
332 IMP_STATISTICS_HAS_CGAL = _IMP_cnmultifit.IMP_STATISTICS_HAS_CGAL
333 IMP_STATISTICS_HAS_NUMPY = _IMP_cnmultifit.IMP_STATISTICS_HAS_NUMPY
334 IMPSTATISTICS_SHOW_WARNINGS = _IMP_cnmultifit.IMPSTATISTICS_SHOW_WARNINGS
335 import IMP.statistics
336 IMP_CORE_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_CORE_HAS_IMP_CGAL
337 IMP_CORE_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_CORE_HAS_IMP_KERNEL
338 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_CORE_HAS_BOOST_FILESYSTEM
339 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
340 IMP_CORE_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_CORE_HAS_BOOST_RANDOM
341 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_CORE_HAS_BOOST_SYSTEM
342 IMP_CORE_HAS_CGAL = _IMP_cnmultifit.IMP_CORE_HAS_CGAL
343 IMP_CORE_HAS_HDF5 = _IMP_cnmultifit.IMP_CORE_HAS_HDF5
344 IMP_CORE_HAS_NUMPY = _IMP_cnmultifit.IMP_CORE_HAS_NUMPY
345 IMPCORE_SHOW_WARNINGS = _IMP_cnmultifit.IMPCORE_SHOW_WARNINGS
346 import IMP.core
347 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_ALGEBRA
348 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_CGAL
349 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_DISPLAY
350 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_KERNEL
351 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
352 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
353 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
354 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_CONTAINER_HAS_BOOST_RANDOM
355 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_CONTAINER_HAS_BOOST_SYSTEM
356 IMP_CONTAINER_HAS_CGAL = _IMP_cnmultifit.IMP_CONTAINER_HAS_CGAL
357 IMP_CONTAINER_HAS_HDF5 = _IMP_cnmultifit.IMP_CONTAINER_HAS_HDF5
358 IMP_CONTAINER_HAS_NUMPY = _IMP_cnmultifit.IMP_CONTAINER_HAS_NUMPY
359 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_cnmultifit.IMP_CONTAINER_HAS_PYTHON_IHM
360 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_cnmultifit.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
361 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_cnmultifit.IMP_CONTAINER_HAS_ROBIN_MAP
362 IMPCONTAINER_SHOW_WARNINGS = _IMP_cnmultifit.IMPCONTAINER_SHOW_WARNINGS
363 import IMP.container
364 IMP_ATOM_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_ATOM_HAS_IMP_CGAL
365 IMP_ATOM_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_ATOM_HAS_IMP_KERNEL
366 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
367 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
368 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_ATOM_HAS_BOOST_RANDOM
369 IMP_ATOM_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_ATOM_HAS_BOOST_REGEX
370 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_ATOM_HAS_BOOST_SYSTEM
371 IMP_ATOM_HAS_CGAL = _IMP_cnmultifit.IMP_ATOM_HAS_CGAL
372 IMP_ATOM_HAS_HDF5 = _IMP_cnmultifit.IMP_ATOM_HAS_HDF5
373 IMP_ATOM_HAS_NUMPY = _IMP_cnmultifit.IMP_ATOM_HAS_NUMPY
374 IMP_ATOM_HAS_PYTHON_IHM = _IMP_cnmultifit.IMP_ATOM_HAS_PYTHON_IHM
375 IMPATOM_SHOW_WARNINGS = _IMP_cnmultifit.IMPATOM_SHOW_WARNINGS
376 IMP_ATOM_TYPE_INDEX = _IMP_cnmultifit.IMP_ATOM_TYPE_INDEX
377 IMP_RESIDUE_TYPE_INDEX = _IMP_cnmultifit.IMP_RESIDUE_TYPE_INDEX
378 IMP_HIERARCHY_TYPE_INDEX = _IMP_cnmultifit.IMP_HIERARCHY_TYPE_INDEX
379 IMP_CHAIN_TYPE_INDEX = _IMP_cnmultifit.IMP_CHAIN_TYPE_INDEX
380 import IMP.atom
381 IMP_EM_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_EM_HAS_IMP_CGAL
382 IMP_EM_HAS_IMP_CONTAINER = _IMP_cnmultifit.IMP_EM_HAS_IMP_CONTAINER
383 IMP_EM_HAS_IMP_DISPLAY = _IMP_cnmultifit.IMP_EM_HAS_IMP_DISPLAY
384 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_EM_HAS_IMP_SCORE_FUNCTOR
385 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_EM_HAS_BOOST_FILESYSTEM
386 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
387 IMP_EM_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_EM_HAS_BOOST_RANDOM
388 IMP_EM_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_EM_HAS_BOOST_REGEX
389 IMP_EM_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_EM_HAS_BOOST_SYSTEM
390 IMP_EM_HAS_CGAL = _IMP_cnmultifit.IMP_EM_HAS_CGAL
391 IMP_EM_HAS_HDF5 = _IMP_cnmultifit.IMP_EM_HAS_HDF5
392 IMP_EM_HAS_NUMPY = _IMP_cnmultifit.IMP_EM_HAS_NUMPY
393 IMP_EM_HAS_PYTHON_IHM = _IMP_cnmultifit.IMP_EM_HAS_PYTHON_IHM
394 IMPEM_SHOW_WARNINGS = _IMP_cnmultifit.IMPEM_SHOW_WARNINGS
395 import IMP.em
396 IMP_SAXS_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_SAXS_HAS_IMP_CGAL
397 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_cnmultifit.IMP_SAXS_HAS_IMP_CONTAINER
398 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_cnmultifit.IMP_SAXS_HAS_IMP_DISPLAY
399 IMP_SAXS_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_SAXS_HAS_IMP_KERNEL
400 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
401 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_SAXS_HAS_BOOST_FILESYSTEM
402 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
403 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_SAXS_HAS_BOOST_RANDOM
404 IMP_SAXS_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_SAXS_HAS_BOOST_REGEX
405 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_SAXS_HAS_BOOST_SYSTEM
406 IMP_SAXS_HAS_CGAL = _IMP_cnmultifit.IMP_SAXS_HAS_CGAL
407 IMP_SAXS_HAS_HDF5 = _IMP_cnmultifit.IMP_SAXS_HAS_HDF5
408 IMP_SAXS_HAS_NUMPY = _IMP_cnmultifit.IMP_SAXS_HAS_NUMPY
409 IMP_SAXS_HAS_PYTHON_IHM = _IMP_cnmultifit.IMP_SAXS_HAS_PYTHON_IHM
410 IMPSAXS_SHOW_WARNINGS = _IMP_cnmultifit.IMPSAXS_SHOW_WARNINGS
411 import IMP.saxs
412 IMP_ISD_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_ISD_HAS_IMP_CGAL
413 IMP_ISD_HAS_IMP_DISPLAY = _IMP_cnmultifit.IMP_ISD_HAS_IMP_DISPLAY
414 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
415 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_ISD_HAS_BOOST_FILESYSTEM
416 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
417 IMP_ISD_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_ISD_HAS_BOOST_RANDOM
418 IMP_ISD_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_ISD_HAS_BOOST_REGEX
419 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_ISD_HAS_BOOST_SYSTEM
420 IMP_ISD_HAS_CGAL = _IMP_cnmultifit.IMP_ISD_HAS_CGAL
421 IMP_ISD_HAS_HDF5 = _IMP_cnmultifit.IMP_ISD_HAS_HDF5
422 IMP_ISD_HAS_NUMPY = _IMP_cnmultifit.IMP_ISD_HAS_NUMPY
423 IMP_ISD_HAS_PYTHON_IHM = _IMP_cnmultifit.IMP_ISD_HAS_PYTHON_IHM
424 IMPISD_SHOW_WARNINGS = _IMP_cnmultifit.IMPISD_SHOW_WARNINGS
425 import IMP.isd
426 IMP_RMF_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_RMF_HAS_IMP_CGAL
427 IMP_RMF_HAS_IMP_EM = _IMP_cnmultifit.IMP_RMF_HAS_IMP_EM
428 IMP_RMF_HAS_IMP_SAXS = _IMP_cnmultifit.IMP_RMF_HAS_IMP_SAXS
429 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
430 IMP_RMF_HAS_IMP_STATISTICS = _IMP_cnmultifit.IMP_RMF_HAS_IMP_STATISTICS
431 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_FILESYSTEM
432 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
433 IMP_RMF_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_RANDOM
434 IMP_RMF_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_REGEX
435 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_SYSTEM
436 IMP_RMF_HAS_CGAL = _IMP_cnmultifit.IMP_RMF_HAS_CGAL
437 IMP_RMF_HAS_HDF5 = _IMP_cnmultifit.IMP_RMF_HAS_HDF5
438 IMP_RMF_HAS_NUMPY = _IMP_cnmultifit.IMP_RMF_HAS_NUMPY
439 IMP_RMF_HAS_PYTHON_IHM = _IMP_cnmultifit.IMP_RMF_HAS_PYTHON_IHM
440 IMPRMF_SHOW_WARNINGS = _IMP_cnmultifit.IMPRMF_SHOW_WARNINGS
441 import IMP.rmf
442 import RMF
443 IMP_DOMINO_HAS_IMP_ATOM = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_ATOM
444 IMP_DOMINO_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_CGAL
445 IMP_DOMINO_HAS_IMP_EM = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_EM
446 IMP_DOMINO_HAS_IMP_ISD = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_ISD
447 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_KERNEL
448 IMP_DOMINO_HAS_IMP_RMF = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_RMF
449 IMP_DOMINO_HAS_IMP_SAXS = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_SAXS
450 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
451 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_FILESYSTEM
452 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
453 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_RANDOM
454 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_REGEX
455 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_SYSTEM
456 IMP_DOMINO_HAS_CGAL = _IMP_cnmultifit.IMP_DOMINO_HAS_CGAL
457 IMP_DOMINO_HAS_HDF5 = _IMP_cnmultifit.IMP_DOMINO_HAS_HDF5
458 IMP_DOMINO_HAS_NUMPY = _IMP_cnmultifit.IMP_DOMINO_HAS_NUMPY
459 IMP_DOMINO_HAS_RMF = _IMP_cnmultifit.IMP_DOMINO_HAS_RMF
460 IMP_DOMINO_HAS_PYTHON_IHM = _IMP_cnmultifit.IMP_DOMINO_HAS_PYTHON_IHM
461 IMPDOMINO_SHOW_WARNINGS = _IMP_cnmultifit.IMPDOMINO_SHOW_WARNINGS
462 import RMF_HDF5
463 import IMP.domino
464 IMP_MULTIFIT_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_CGAL
465 IMP_MULTIFIT_HAS_IMP_CONTAINER = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_CONTAINER
466 IMP_MULTIFIT_HAS_IMP_DISPLAY = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_DISPLAY
467 IMP_MULTIFIT_HAS_IMP_ISD = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_ISD
468 IMP_MULTIFIT_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_KERNEL
469 IMP_MULTIFIT_HAS_IMP_RMF = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_RMF
470 IMP_MULTIFIT_HAS_IMP_SAXS = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_SAXS
471 IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR
472 IMP_MULTIFIT_HAS_BOOST_GRAPH = _IMP_cnmultifit.IMP_MULTIFIT_HAS_BOOST_GRAPH
473 IMP_MULTIFIT_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_MULTIFIT_HAS_BOOST_RANDOM
474 IMP_MULTIFIT_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_MULTIFIT_HAS_BOOST_REGEX
475 IMP_MULTIFIT_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_MULTIFIT_HAS_BOOST_SYSTEM
476 IMP_MULTIFIT_HAS_CGAL = _IMP_cnmultifit.IMP_MULTIFIT_HAS_CGAL
477 IMP_MULTIFIT_HAS_HDF5 = _IMP_cnmultifit.IMP_MULTIFIT_HAS_HDF5
478 IMP_MULTIFIT_HAS_NUMPY = _IMP_cnmultifit.IMP_MULTIFIT_HAS_NUMPY
479 IMP_MULTIFIT_HAS_RMF = _IMP_cnmultifit.IMP_MULTIFIT_HAS_RMF
480 IMP_MULTIFIT_HAS_PYTHON_IHM = _IMP_cnmultifit.IMP_MULTIFIT_HAS_PYTHON_IHM
481 IMPMULTIFIT_SHOW_WARNINGS = _IMP_cnmultifit.IMPMULTIFIT_SHOW_WARNINGS
482 import IMP.multifit
483 IMP_CNMULTIFIT_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_CGAL
484 IMP_CNMULTIFIT_HAS_IMP_CONTAINER = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_CONTAINER
485 IMP_CNMULTIFIT_HAS_IMP_DISPLAY = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_DISPLAY
486 IMP_CNMULTIFIT_HAS_IMP_DOMINO = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_DOMINO
487 IMP_CNMULTIFIT_HAS_IMP_ISD = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_ISD
488 IMP_CNMULTIFIT_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_KERNEL
489 IMP_CNMULTIFIT_HAS_IMP_RMF = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_RMF
490 IMP_CNMULTIFIT_HAS_IMP_SAXS = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_SAXS
491 IMP_CNMULTIFIT_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_SCORE_FUNCTOR
492 IMP_CNMULTIFIT_HAS_BOOST_GRAPH = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_BOOST_GRAPH
493 IMP_CNMULTIFIT_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_BOOST_RANDOM
494 IMP_CNMULTIFIT_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_BOOST_REGEX
495 IMP_CNMULTIFIT_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_BOOST_SYSTEM
496 IMP_CNMULTIFIT_HAS_CGAL = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_CGAL
497 IMP_CNMULTIFIT_HAS_FFTW3 = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_FFTW3
498 IMP_CNMULTIFIT_HAS_HDF5 = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_HDF5
499 IMP_CNMULTIFIT_HAS_NUMPY = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_NUMPY
500 IMP_CNMULTIFIT_HAS_RMF = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_RMF
501 IMP_CNMULTIFIT_HAS_PYTHON_IHM = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_PYTHON_IHM
502 IMPCNMULTIFIT_SHOW_WARNINGS = _IMP_cnmultifit.IMPCNMULTIFIT_SHOW_WARNINGS
503 
504 AlignSymmetrics=list
505 _plural_types.append("AlignSymmetrics")
506 _value_types.append("AlignSymmetric")
507 
508 
509 CnSymmAxisDetectors=list
510 _plural_types.append("CnSymmAxisDetectors")
511 _value_types.append("CnSymmAxisDetector")
512 
513 
514 MolCnSymmAxisDetectors=list
515 _plural_types.append("MolCnSymmAxisDetectors")
516 _value_types.append("MolCnSymmAxisDetector")
517 
518 class CnSymmAxisDetector(object):
519  """Proxy of C++ IMP::cnmultifit::CnSymmAxisDetector class."""
520 
521  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
522 
523  def __init__(self, *args):
524  """
525  __init__(IMP::cnmultifit::CnSymmAxisDetector self, int symm_deg, DensityMap dmap, float density_threshold, float top_p=0.8) -> CnSymmAxisDetector
526  __init__(IMP::cnmultifit::CnSymmAxisDetector self, int symm_deg, DensityMap dmap, float density_threshold) -> CnSymmAxisDetector
527  __init__(IMP::cnmultifit::CnSymmAxisDetector self, int symm_deg, IMP::atom::Hierarchies const & mhs) -> CnSymmAxisDetector
528  """
529  this = _IMP_cnmultifit.new_CnSymmAxisDetector(*args)
530  try:
531  self.this.append(this)
532  except __builtin__.Exception:
533  self.this = this
534 
535  def get_pca(self):
536  """get_pca(CnSymmAxisDetector self) -> PrincipalComponentAnalysis3D"""
537  return _IMP_cnmultifit.CnSymmAxisDetector_get_pca(self)
538 
539 
540  def calc_symm_score(self, symm_axis_ind):
541  """calc_symm_score(CnSymmAxisDetector self, int symm_axis_ind) -> float"""
542  return _IMP_cnmultifit.CnSymmAxisDetector_calc_symm_score(self, symm_axis_ind)
543 
544 
545  def get_symmetry_axis(self):
546  """get_symmetry_axis(CnSymmAxisDetector self) -> Vector3D"""
547  return _IMP_cnmultifit.CnSymmAxisDetector_get_symmetry_axis(self)
548 
549 
550  def get_symmetry_axis_index(self):
551  """get_symmetry_axis_index(CnSymmAxisDetector self) -> int"""
552  return _IMP_cnmultifit.CnSymmAxisDetector_get_symmetry_axis_index(self)
553 
554 
555  def get_non_symmetry_axis_length(self):
556  """get_non_symmetry_axis_length(CnSymmAxisDetector self) -> int"""
557  return _IMP_cnmultifit.CnSymmAxisDetector_get_non_symmetry_axis_length(self)
558 
559 
560  def show(self, *args):
561  """
562  show(CnSymmAxisDetector self, _ostream out)
563  show(CnSymmAxisDetector self)
564  """
565  return _IMP_cnmultifit.CnSymmAxisDetector_show(self, *args)
566 
567 
568  def __str__(self):
569  """__str__(CnSymmAxisDetector self) -> std::string"""
570  return _IMP_cnmultifit.CnSymmAxisDetector___str__(self)
571 
572 
573  def __repr__(self):
574  """__repr__(CnSymmAxisDetector self) -> std::string"""
575  return _IMP_cnmultifit.CnSymmAxisDetector___repr__(self)
576 
577  __swig_destroy__ = _IMP_cnmultifit.delete_CnSymmAxisDetector
578  __del__ = lambda self: None
579 CnSymmAxisDetector_swigregister = _IMP_cnmultifit.CnSymmAxisDetector_swigregister
580 CnSymmAxisDetector_swigregister(CnSymmAxisDetector)
581 
582 class MolCnSymmAxisDetector(object):
583  """Proxy of C++ IMP::cnmultifit::MolCnSymmAxisDetector class."""
584 
585  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
586 
587  def __init__(self, symm_deg, mhs):
588  """__init__(IMP::cnmultifit::MolCnSymmAxisDetector self, int symm_deg, IMP::atom::Hierarchies const & mhs) -> MolCnSymmAxisDetector"""
589  this = _IMP_cnmultifit.new_MolCnSymmAxisDetector(symm_deg, mhs)
590  try:
591  self.this.append(this)
592  except __builtin__.Exception:
593  self.this = this
594 
595  def get_pca(self):
596  """get_pca(MolCnSymmAxisDetector self) -> PrincipalComponentAnalysis3D"""
597  return _IMP_cnmultifit.MolCnSymmAxisDetector_get_pca(self)
598 
599 
600  def get_symmetry_axis(self):
601  """get_symmetry_axis(MolCnSymmAxisDetector self) -> Vector3D"""
602  return _IMP_cnmultifit.MolCnSymmAxisDetector_get_symmetry_axis(self)
603 
604 
605  def get_symmetry_axis_index(self):
606  """get_symmetry_axis_index(MolCnSymmAxisDetector self) -> int"""
607  return _IMP_cnmultifit.MolCnSymmAxisDetector_get_symmetry_axis_index(self)
608 
609 
610  def show(self, *args):
611  """
612  show(MolCnSymmAxisDetector self, _ostream out)
613  show(MolCnSymmAxisDetector self)
614  """
615  return _IMP_cnmultifit.MolCnSymmAxisDetector_show(self, *args)
616 
617 
618  def calc_symm_score(self, symm_axis_ind):
619  """calc_symm_score(MolCnSymmAxisDetector self, int symm_axis_ind) -> float"""
620  return _IMP_cnmultifit.MolCnSymmAxisDetector_calc_symm_score(self, symm_axis_ind)
621 
622 
623  def __str__(self):
624  """__str__(MolCnSymmAxisDetector self) -> std::string"""
625  return _IMP_cnmultifit.MolCnSymmAxisDetector___str__(self)
626 
627 
628  def __repr__(self):
629  """__repr__(MolCnSymmAxisDetector self) -> std::string"""
630  return _IMP_cnmultifit.MolCnSymmAxisDetector___repr__(self)
631 
632  __swig_destroy__ = _IMP_cnmultifit.delete_MolCnSymmAxisDetector
633  __del__ = lambda self: None
634 MolCnSymmAxisDetector_swigregister = _IMP_cnmultifit.MolCnSymmAxisDetector_swigregister
635 MolCnSymmAxisDetector_swigregister(MolCnSymmAxisDetector)
636 
637 class AlignSymmetric(object):
638  """Proxy of C++ IMP::cnmultifit::AlignSymmetric class."""
639 
640  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
641 
642  def __init__(self, dmap, threshold, cn_symm_deg):
643  """__init__(IMP::cnmultifit::AlignSymmetric self, DensityMap dmap, float threshold, int cn_symm_deg) -> AlignSymmetric"""
644  this = _IMP_cnmultifit.new_AlignSymmetric(dmap, threshold, cn_symm_deg)
645  try:
646  self.this.append(this)
647  except __builtin__.Exception:
648  self.this = this
649 
650  def get_sorted_principal_values(self):
651  """get_sorted_principal_values(AlignSymmetric self) -> IMP::Floats"""
652  return _IMP_cnmultifit.AlignSymmetric_get_sorted_principal_values(self)
653 
654 
655  def score_alignment(self, mhs, max_allowed_diff):
656  """score_alignment(AlignSymmetric self, IMP::atom::Hierarchies mhs, float max_allowed_diff) -> int"""
657  return _IMP_cnmultifit.AlignSymmetric_score_alignment(self, mhs, max_allowed_diff)
658 
659 
660  def get_symm_axis_alignments_from_model_to_density(self, mhs, sample_translation, fine_rotation_sampling=True):
661  """
662  get_symm_axis_alignments_from_model_to_density(AlignSymmetric self, IMP::atom::Hierarchies mhs, bool sample_translation, bool fine_rotation_sampling=True) -> IMP::algebra::Transformation3Ds
663  get_symm_axis_alignments_from_model_to_density(AlignSymmetric self, IMP::atom::Hierarchies mhs, bool sample_translation) -> IMP::algebra::Transformation3Ds
664  """
665  return _IMP_cnmultifit.AlignSymmetric_get_symm_axis_alignments_from_model_to_density(self, mhs, sample_translation, fine_rotation_sampling)
666 
667 
668  def show(self, *args):
669  """
670  show(AlignSymmetric self, _ostream out)
671  show(AlignSymmetric self)
672  """
673  return _IMP_cnmultifit.AlignSymmetric_show(self, *args)
674 
675 
676  def __str__(self):
677  """__str__(AlignSymmetric self) -> std::string"""
678  return _IMP_cnmultifit.AlignSymmetric___str__(self)
679 
680 
681  def __repr__(self):
682  """__repr__(AlignSymmetric self) -> std::string"""
683  return _IMP_cnmultifit.AlignSymmetric___repr__(self)
684 
685  __swig_destroy__ = _IMP_cnmultifit.delete_AlignSymmetric
686  __del__ = lambda self: None
687 AlignSymmetric_swigregister = _IMP_cnmultifit.AlignSymmetric_swigregister
688 AlignSymmetric_swigregister(AlignSymmetric)
689 
690 
691 def generate_cn_transformations(mhs, symm_deg):
692  """generate_cn_transformations(IMP::atom::Hierarchies mhs, int symm_deg) -> IMP::algebra::Transformation3Ds"""
693  return _IMP_cnmultifit.generate_cn_transformations(mhs, symm_deg)
694 
695 def generate_translations_along_symm_axis(mhs, symm_deg):
696  """generate_translations_along_symm_axis(IMP::atom::Hierarchies mhs, int symm_deg) -> IMP::algebra::Transformation3Ds"""
697  return _IMP_cnmultifit.generate_translations_along_symm_axis(mhs, symm_deg)
698 
699 def symmetry_local_fitting(mhs, cn_symm_deg, dn_symm_deg, dmap, num_of_trans_to_consider):
700  """symmetry_local_fitting(IMP::atom::Hierarchies mhs, int cn_symm_deg, int dn_symm_deg, DensityMap dmap, int num_of_trans_to_consider) -> FittingSolutions"""
701  return _IMP_cnmultifit.symmetry_local_fitting(mhs, cn_symm_deg, dn_symm_deg, dmap, num_of_trans_to_consider)
702 
703 def build_cn_dens_assembly(subunit_dens, asmb_dens_header, monomer_t, symm_deg):
704  """build_cn_dens_assembly(DensityMap subunit_dens, DensityHeader asmb_dens_header, Transformation3D monomer_t, int symm_deg) -> DensityMap"""
705  return _IMP_cnmultifit.build_cn_dens_assembly(subunit_dens, asmb_dens_header, monomer_t, symm_deg)
706 
707 def transform_cn_assembly(mhs, monomer_t):
708  """transform_cn_assembly(IMP::atom::Hierarchies mhs, Transformation3D monomer_t)"""
709  return _IMP_cnmultifit.transform_cn_assembly(mhs, monomer_t)
710 
711 def fit_cn_assembly(*args):
712  """
713  fit_cn_assembly(IMP::atom::Hierarchies mhs, int dn_symm_deg, DensityMap dmap, float threshold, AlignSymmetric aligner, bool sample_translation=False, bool fine_rotational_sampling=True) -> FittingSolutions
714  fit_cn_assembly(IMP::atom::Hierarchies mhs, int dn_symm_deg, DensityMap dmap, float threshold, AlignSymmetric aligner, bool sample_translation=False) -> FittingSolutions
715  fit_cn_assembly(IMP::atom::Hierarchies mhs, int dn_symm_deg, DensityMap dmap, float threshold, AlignSymmetric aligner) -> FittingSolutions
716  fit_cn_assembly(DensityMap asmb_map, MolCnSymmAxisDetector symm_mol, DensityMap dmap, CnSymmAxisDetector symm_map, int symm_deg, float threshold) -> FittingSolutions
717  """
718  return _IMP_cnmultifit.fit_cn_assembly(*args)
719 
720 def pca_matching(pca1, pca2, resolution):
721  """pca_matching(PrincipalComponentAnalysis3D pca1, PrincipalComponentAnalysis3D pca2, float resolution) -> bool"""
722  return _IMP_cnmultifit.pca_matching(pca1, pca2, resolution)
723 
724 def cn_symm_score(mhs, center, direction, symm_deg):
725  """cn_symm_score(IMP::atom::Hierarchies mhs, Vector3D center, Vector3D direction, int symm_deg) -> float"""
726  return _IMP_cnmultifit.cn_symm_score(mhs, center, direction, symm_deg)
727 
728 def prune_by_pca(param_fn, sols, dn=1):
729  """
730  prune_by_pca(std::string const & param_fn, IMP::multifit::FittingSolutionRecords const & sols, int dn=1) -> IMP::multifit::FittingSolutionRecords
731  prune_by_pca(std::string const & param_fn, IMP::multifit::FittingSolutionRecords const & sols) -> IMP::multifit::FittingSolutionRecords
732  """
733  return _IMP_cnmultifit.prune_by_pca(param_fn, sols, dn)
734 
735 def calc_transformation_around_axis(a, b, angle_rad):
736  """calc_transformation_around_axis(Vector3D a, Vector3D b, float angle_rad) -> Transformation3D"""
737  return _IMP_cnmultifit.calc_transformation_around_axis(a, b, angle_rad)
738 
739 def get_cn_rmsd(mh1, mh2):
740  """get_cn_rmsd(IMP::atom::Hierarchies mh1, IMP::atom::Hierarchies mh2) -> float"""
741  return _IMP_cnmultifit.get_cn_rmsd(mh1, mh2)
742 
743 def do_all_fitting(*args):
744  """
745  do_all_fitting(std::string const param_filename, std::string const chimera_filename)
746  do_all_fitting(std::string const param_filename)
747  """
748  return _IMP_cnmultifit.do_all_fitting(*args)
749 
750 def get_rmsd_for_models(param_filename, trans_filename, ref_filename, start_model=0, end_model=-1):
751  """
752  get_rmsd_for_models(std::string const param_filename, std::string const trans_filename, std::string const ref_filename, int start_model=0, int end_model=-1) -> IMP::Floats
753  get_rmsd_for_models(std::string const param_filename, std::string const trans_filename, std::string const ref_filename, int start_model=0) -> IMP::Floats
754  get_rmsd_for_models(std::string const param_filename, std::string const trans_filename, std::string const ref_filename) -> IMP::Floats
755  """
756  return _IMP_cnmultifit.get_rmsd_for_models(param_filename, trans_filename, ref_filename, start_model, end_model)
757 
758 _all_commands = ["build", "rmsd", "surface",
759  "param", "chimera_models"]
760 
761 
762 def get_module_version():
763  """get_module_version() -> std::string const"""
764  return _IMP_cnmultifit.get_module_version()
765 
766 def get_example_path(fname):
767  """get_example_path(std::string fname) -> std::string"""
768  return _IMP_cnmultifit.get_example_path(fname)
769 
770 def get_data_path(fname):
771  """get_data_path(std::string fname) -> std::string"""
772  return _IMP_cnmultifit.get_data_path(fname)
773 
774 from . import _version_check
775 _version_check.check_version(get_module_version())
776 __version__ = get_module_version()
777 
778 
779 
Various classes to hold sets of particles.
void do_all_fitting(const std::string param_filename, const std::string chimera_filename="")
High level interface to build cyclic symmetric complexes.
Make CGAL functionality available to IMP.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
Composable functors to implement scores via compile-time composition.
Code to compute statistical measures.
float cn_symm_score(atom::Hierarchies mhs, const algebra::Vector3D &center, const algebra::Vector3D &direction, int symm_deg)
scores an input vector as a symmetry axis
Fitting atomic structures into a cryo-electron microscopy density map.
Basic utilities for handling cryo-electron microscopy 3D density maps.
float get_cn_rmsd(atom::Hierarchies mh1, atom::Hierarchies mh2)
Find correspondence between the two rings and calculate rmsd.
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
Basic functionality that is expected to be used by a wide variety of IMP users.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
em::FittingSolutions fit_cn_assembly(atom::Hierarchies mhs, int dn_symm_deg, em::DensityMap *dmap, float threshold, const AlignSymmetric &aligner, bool sample_translation=false, bool fine_rotational_sampling=true)
Fit a symmetric model to its density.
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for the RMF file format for storing hierarchical molecular data and markup.
Divide-and-conquer inferential optimization in discrete space.
Support for small angle X-ray scattering (SAXS) data.
std::string get_module_version()
Return the version of this module, as a string.
Inferential scoring building on methods developed as part of the Inferential Structure Determination ...