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IMP Reference Guide  2.8.0
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 2007-2017 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_GPERFTOOLS = _IMP_cnmultifit.IMP_KERNEL_HAS_GPERFTOOLS
239 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_cnmultifit.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
240 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_cnmultifit.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
241 IMPKERNEL_SHOW_WARNINGS = _IMP_cnmultifit.IMPKERNEL_SHOW_WARNINGS
242 
243 import sys
244 class _DirectorObjects(object):
245  """@internal Simple class to keep references to director objects
246  to prevent premature deletion."""
247  def __init__(self):
248  self._objects = []
249  def register(self, obj):
250  """Take a reference to a director object; will only work for
251  refcounted C++ classes"""
252  if hasattr(obj, 'get_ref_count'):
253  self._objects.append(obj)
254  def cleanup(self):
255  """Only drop our reference and allow cleanup by Python if no other
256  Python references exist (we hold 3 references: one in self._objects,
257  one in x, and one in the argument list for getrefcount) *and* no
258  other C++ references exist (the Python object always holds one)"""
259  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
260  or x.get_ref_count() > 1]
261 # Do in two steps so the references are kept until the end of the
262 # function (deleting references may trigger a fresh call to this method)
263  self._objects = objs
264  def get_object_count(self):
265  """Get number of director objects (useful for testing only)"""
266  return len(self._objects)
267 _director_objects = _DirectorObjects()
268 
269 class _ostream(object):
270  """Proxy of C++ std::ostream class."""
271 
272  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
273 
274  def __init__(self, *args, **kwargs):
275  raise AttributeError("No constructor defined")
276  __repr__ = _swig_repr
277 
278  def write(self, osa_buf):
279  """write(_ostream self, char const * osa_buf)"""
280  return _IMP_cnmultifit._ostream_write(self, osa_buf)
281 
282 _ostream_swigregister = _IMP_cnmultifit._ostream_swigregister
283 _ostream_swigregister(_ostream)
284 
285 IMP_COMPILER_HAS_OVERRIDE = _IMP_cnmultifit.IMP_COMPILER_HAS_OVERRIDE
286 IMP_COMPILER_HAS_FINAL = _IMP_cnmultifit.IMP_COMPILER_HAS_FINAL
287 IMP_HAS_NOEXCEPT = _IMP_cnmultifit.IMP_HAS_NOEXCEPT
288 import IMP
289 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_CGAL_HAS_BOOST_FILESYSTEM
290 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
291 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_CGAL_HAS_BOOST_RANDOM
292 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_CGAL_HAS_BOOST_SYSTEM
293 IMPCGAL_SHOW_WARNINGS = _IMP_cnmultifit.IMPCGAL_SHOW_WARNINGS
294 import IMP.cgal
295 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_ALGEBRA_HAS_IMP_CGAL
296 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
297 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
298 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_ALGEBRA_HAS_BOOST_RANDOM
299 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_ALGEBRA_HAS_BOOST_SYSTEM
300 IMP_ALGEBRA_HAS_CGAL = _IMP_cnmultifit.IMP_ALGEBRA_HAS_CGAL
301 IMP_ALGEBRA_HAS_ANN = _IMP_cnmultifit.IMP_ALGEBRA_HAS_ANN
302 IMPALGEBRA_SHOW_WARNINGS = _IMP_cnmultifit.IMPALGEBRA_SHOW_WARNINGS
303 import IMP.algebra
304 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_DISPLAY_HAS_IMP_CGAL
305 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
306 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
307 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_DISPLAY_HAS_BOOST_RANDOM
308 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_DISPLAY_HAS_BOOST_SYSTEM
309 IMP_DISPLAY_HAS_CGAL = _IMP_cnmultifit.IMP_DISPLAY_HAS_CGAL
310 IMPDISPLAY_SHOW_WARNINGS = _IMP_cnmultifit.IMPDISPLAY_SHOW_WARNINGS
311 import IMP.display
312 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
313 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
314 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
315 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
316 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
317 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_CGAL
318 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_HDF5
319 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_cnmultifit.IMPSCOREFUNCTOR_SHOW_WARNINGS
320 import IMP.score_functor
321 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_STATISTICS_HAS_IMP_CGAL
322 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
323 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
324 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_STATISTICS_HAS_BOOST_RANDOM
325 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_STATISTICS_HAS_BOOST_SYSTEM
326 IMP_STATISTICS_HAS_CGAL = _IMP_cnmultifit.IMP_STATISTICS_HAS_CGAL
327 IMPSTATISTICS_SHOW_WARNINGS = _IMP_cnmultifit.IMPSTATISTICS_SHOW_WARNINGS
328 import IMP.statistics
329 IMP_CORE_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_CORE_HAS_IMP_CGAL
330 IMP_CORE_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_CORE_HAS_IMP_KERNEL
331 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_CORE_HAS_BOOST_FILESYSTEM
332 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
333 IMP_CORE_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_CORE_HAS_BOOST_RANDOM
334 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_CORE_HAS_BOOST_SYSTEM
335 IMP_CORE_HAS_CGAL = _IMP_cnmultifit.IMP_CORE_HAS_CGAL
336 IMP_CORE_HAS_HDF5 = _IMP_cnmultifit.IMP_CORE_HAS_HDF5
337 IMPCORE_SHOW_WARNINGS = _IMP_cnmultifit.IMPCORE_SHOW_WARNINGS
338 import IMP.core
339 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_ALGEBRA
340 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_CGAL
341 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_DISPLAY
342 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_KERNEL
343 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
344 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
345 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
346 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_CONTAINER_HAS_BOOST_RANDOM
347 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_CONTAINER_HAS_BOOST_SYSTEM
348 IMP_CONTAINER_HAS_CGAL = _IMP_cnmultifit.IMP_CONTAINER_HAS_CGAL
349 IMP_CONTAINER_HAS_HDF5 = _IMP_cnmultifit.IMP_CONTAINER_HAS_HDF5
350 IMPCONTAINER_SHOW_WARNINGS = _IMP_cnmultifit.IMPCONTAINER_SHOW_WARNINGS
351 import IMP.container
352 IMP_ATOM_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_ATOM_HAS_IMP_CGAL
353 IMP_ATOM_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_ATOM_HAS_IMP_KERNEL
354 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
355 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
356 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_ATOM_HAS_BOOST_RANDOM
357 IMP_ATOM_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_ATOM_HAS_BOOST_REGEX
358 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_ATOM_HAS_BOOST_SYSTEM
359 IMP_ATOM_HAS_CGAL = _IMP_cnmultifit.IMP_ATOM_HAS_CGAL
360 IMP_ATOM_HAS_HDF5 = _IMP_cnmultifit.IMP_ATOM_HAS_HDF5
361 IMPATOM_SHOW_WARNINGS = _IMP_cnmultifit.IMPATOM_SHOW_WARNINGS
362 IMP_ATOM_TYPE_INDEX = _IMP_cnmultifit.IMP_ATOM_TYPE_INDEX
363 IMP_RESIDUE_TYPE_INDEX = _IMP_cnmultifit.IMP_RESIDUE_TYPE_INDEX
364 IMP_HIERARCHY_TYPE_INDEX = _IMP_cnmultifit.IMP_HIERARCHY_TYPE_INDEX
365 import IMP.atom
366 IMP_EM_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_EM_HAS_IMP_CGAL
367 IMP_EM_HAS_IMP_CONTAINER = _IMP_cnmultifit.IMP_EM_HAS_IMP_CONTAINER
368 IMP_EM_HAS_IMP_DISPLAY = _IMP_cnmultifit.IMP_EM_HAS_IMP_DISPLAY
369 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_EM_HAS_IMP_SCORE_FUNCTOR
370 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_EM_HAS_BOOST_FILESYSTEM
371 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
372 IMP_EM_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_EM_HAS_BOOST_RANDOM
373 IMP_EM_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_EM_HAS_BOOST_REGEX
374 IMP_EM_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_EM_HAS_BOOST_SYSTEM
375 IMP_EM_HAS_CGAL = _IMP_cnmultifit.IMP_EM_HAS_CGAL
376 IMP_EM_HAS_HDF5 = _IMP_cnmultifit.IMP_EM_HAS_HDF5
377 IMPEM_SHOW_WARNINGS = _IMP_cnmultifit.IMPEM_SHOW_WARNINGS
378 import IMP.em
379 IMP_RMF_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_RMF_HAS_IMP_CGAL
380 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
381 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_FILESYSTEM
382 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
383 IMP_RMF_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_RANDOM
384 IMP_RMF_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_REGEX
385 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_SYSTEM
386 IMP_RMF_HAS_CGAL = _IMP_cnmultifit.IMP_RMF_HAS_CGAL
387 IMP_RMF_HAS_HDF5 = _IMP_cnmultifit.IMP_RMF_HAS_HDF5
388 IMPRMF_SHOW_WARNINGS = _IMP_cnmultifit.IMPRMF_SHOW_WARNINGS
389 import IMP.rmf
390 import RMF
391 IMP_DOMINO_HAS_IMP_ATOM = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_ATOM
392 IMP_DOMINO_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_CGAL
393 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_KERNEL
394 IMP_DOMINO_HAS_IMP_RMF = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_RMF
395 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
396 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_FILESYSTEM
397 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
398 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_RANDOM
399 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_REGEX
400 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_SYSTEM
401 IMP_DOMINO_HAS_CGAL = _IMP_cnmultifit.IMP_DOMINO_HAS_CGAL
402 IMP_DOMINO_HAS_HDF5 = _IMP_cnmultifit.IMP_DOMINO_HAS_HDF5
403 IMP_DOMINO_HAS_RMF = _IMP_cnmultifit.IMP_DOMINO_HAS_RMF
404 IMPDOMINO_SHOW_WARNINGS = _IMP_cnmultifit.IMPDOMINO_SHOW_WARNINGS
405 import RMF_HDF5
406 import IMP.domino
407 IMP_MULTIFIT_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_CGAL
408 IMP_MULTIFIT_HAS_IMP_CONTAINER = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_CONTAINER
409 IMP_MULTIFIT_HAS_IMP_DISPLAY = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_DISPLAY
410 IMP_MULTIFIT_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_KERNEL
411 IMP_MULTIFIT_HAS_IMP_RMF = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_RMF
412 IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR
413 IMP_MULTIFIT_HAS_BOOST_GRAPH = _IMP_cnmultifit.IMP_MULTIFIT_HAS_BOOST_GRAPH
414 IMP_MULTIFIT_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_MULTIFIT_HAS_BOOST_RANDOM
415 IMP_MULTIFIT_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_MULTIFIT_HAS_BOOST_REGEX
416 IMP_MULTIFIT_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_MULTIFIT_HAS_BOOST_SYSTEM
417 IMP_MULTIFIT_HAS_CGAL = _IMP_cnmultifit.IMP_MULTIFIT_HAS_CGAL
418 IMP_MULTIFIT_HAS_HDF5 = _IMP_cnmultifit.IMP_MULTIFIT_HAS_HDF5
419 IMP_MULTIFIT_HAS_RMF = _IMP_cnmultifit.IMP_MULTIFIT_HAS_RMF
420 IMPMULTIFIT_SHOW_WARNINGS = _IMP_cnmultifit.IMPMULTIFIT_SHOW_WARNINGS
421 import IMP.multifit
422 IMP_CNMULTIFIT_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_CGAL
423 IMP_CNMULTIFIT_HAS_IMP_CONTAINER = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_CONTAINER
424 IMP_CNMULTIFIT_HAS_IMP_DISPLAY = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_DISPLAY
425 IMP_CNMULTIFIT_HAS_IMP_DOMINO = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_DOMINO
426 IMP_CNMULTIFIT_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_KERNEL
427 IMP_CNMULTIFIT_HAS_IMP_RMF = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_RMF
428 IMP_CNMULTIFIT_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_SCORE_FUNCTOR
429 IMP_CNMULTIFIT_HAS_BOOST_GRAPH = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_BOOST_GRAPH
430 IMP_CNMULTIFIT_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_BOOST_RANDOM
431 IMP_CNMULTIFIT_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_BOOST_REGEX
432 IMP_CNMULTIFIT_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_BOOST_SYSTEM
433 IMP_CNMULTIFIT_HAS_CGAL = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_CGAL
434 IMP_CNMULTIFIT_HAS_FFTW3 = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_FFTW3
435 IMP_CNMULTIFIT_HAS_HDF5 = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_HDF5
436 IMP_CNMULTIFIT_HAS_RMF = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_RMF
437 IMPCNMULTIFIT_SHOW_WARNINGS = _IMP_cnmultifit.IMPCNMULTIFIT_SHOW_WARNINGS
438 
439 AlignSymmetrics=list
440 _plural_types.append("AlignSymmetrics")
441 _value_types.append("AlignSymmetric")
442 
443 
444 CnSymmAxisDetectors=list
445 _plural_types.append("CnSymmAxisDetectors")
446 _value_types.append("CnSymmAxisDetector")
447 
448 
449 MolCnSymmAxisDetectors=list
450 _plural_types.append("MolCnSymmAxisDetectors")
451 _value_types.append("MolCnSymmAxisDetector")
452 
453 class CnSymmAxisDetector(object):
454  """Proxy of C++ IMP::cnmultifit::CnSymmAxisDetector class."""
455 
456  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
457 
458  def __init__(self, *args):
459  """
460  __init__(IMP::cnmultifit::CnSymmAxisDetector self, int symm_deg, DensityMap dmap, float density_threshold, float top_p=0.8) -> CnSymmAxisDetector
461  __init__(IMP::cnmultifit::CnSymmAxisDetector self, int symm_deg, DensityMap dmap, float density_threshold) -> CnSymmAxisDetector
462  __init__(IMP::cnmultifit::CnSymmAxisDetector self, int symm_deg, IMP::atom::Hierarchies const & mhs) -> CnSymmAxisDetector
463  """
464  this = _IMP_cnmultifit.new_CnSymmAxisDetector(*args)
465  try:
466  self.this.append(this)
467  except __builtin__.Exception:
468  self.this = this
469 
470  def get_pca(self):
471  """get_pca(CnSymmAxisDetector self) -> PrincipalComponentAnalysis3D"""
472  return _IMP_cnmultifit.CnSymmAxisDetector_get_pca(self)
473 
474 
475  def calc_symm_score(self, symm_axis_ind):
476  """calc_symm_score(CnSymmAxisDetector self, int symm_axis_ind) -> float"""
477  return _IMP_cnmultifit.CnSymmAxisDetector_calc_symm_score(self, symm_axis_ind)
478 
479 
480  def get_symmetry_axis(self):
481  """get_symmetry_axis(CnSymmAxisDetector self) -> Vector3D"""
482  return _IMP_cnmultifit.CnSymmAxisDetector_get_symmetry_axis(self)
483 
484 
485  def get_symmetry_axis_index(self):
486  """get_symmetry_axis_index(CnSymmAxisDetector self) -> int"""
487  return _IMP_cnmultifit.CnSymmAxisDetector_get_symmetry_axis_index(self)
488 
489 
490  def get_non_symmetry_axis_length(self):
491  """get_non_symmetry_axis_length(CnSymmAxisDetector self) -> int"""
492  return _IMP_cnmultifit.CnSymmAxisDetector_get_non_symmetry_axis_length(self)
493 
494 
495  def show(self, *args):
496  """
497  show(CnSymmAxisDetector self, _ostream out)
498  show(CnSymmAxisDetector self)
499  """
500  return _IMP_cnmultifit.CnSymmAxisDetector_show(self, *args)
501 
502 
503  def __str__(self):
504  """__str__(CnSymmAxisDetector self) -> std::string"""
505  return _IMP_cnmultifit.CnSymmAxisDetector___str__(self)
506 
507 
508  def __repr__(self):
509  """__repr__(CnSymmAxisDetector self) -> std::string"""
510  return _IMP_cnmultifit.CnSymmAxisDetector___repr__(self)
511 
512  __swig_destroy__ = _IMP_cnmultifit.delete_CnSymmAxisDetector
513  __del__ = lambda self: None
514 CnSymmAxisDetector_swigregister = _IMP_cnmultifit.CnSymmAxisDetector_swigregister
515 CnSymmAxisDetector_swigregister(CnSymmAxisDetector)
516 
517 class MolCnSymmAxisDetector(object):
518  """Proxy of C++ IMP::cnmultifit::MolCnSymmAxisDetector class."""
519 
520  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
521 
522  def __init__(self, symm_deg, mhs):
523  """__init__(IMP::cnmultifit::MolCnSymmAxisDetector self, int symm_deg, IMP::atom::Hierarchies const & mhs) -> MolCnSymmAxisDetector"""
524  this = _IMP_cnmultifit.new_MolCnSymmAxisDetector(symm_deg, mhs)
525  try:
526  self.this.append(this)
527  except __builtin__.Exception:
528  self.this = this
529 
530  def get_pca(self):
531  """get_pca(MolCnSymmAxisDetector self) -> PrincipalComponentAnalysis3D"""
532  return _IMP_cnmultifit.MolCnSymmAxisDetector_get_pca(self)
533 
534 
535  def get_symmetry_axis(self):
536  """get_symmetry_axis(MolCnSymmAxisDetector self) -> Vector3D"""
537  return _IMP_cnmultifit.MolCnSymmAxisDetector_get_symmetry_axis(self)
538 
539 
540  def get_symmetry_axis_index(self):
541  """get_symmetry_axis_index(MolCnSymmAxisDetector self) -> int"""
542  return _IMP_cnmultifit.MolCnSymmAxisDetector_get_symmetry_axis_index(self)
543 
544 
545  def show(self, *args):
546  """
547  show(MolCnSymmAxisDetector self, _ostream out)
548  show(MolCnSymmAxisDetector self)
549  """
550  return _IMP_cnmultifit.MolCnSymmAxisDetector_show(self, *args)
551 
552 
553  def calc_symm_score(self, symm_axis_ind):
554  """calc_symm_score(MolCnSymmAxisDetector self, int symm_axis_ind) -> float"""
555  return _IMP_cnmultifit.MolCnSymmAxisDetector_calc_symm_score(self, symm_axis_ind)
556 
557 
558  def __str__(self):
559  """__str__(MolCnSymmAxisDetector self) -> std::string"""
560  return _IMP_cnmultifit.MolCnSymmAxisDetector___str__(self)
561 
562 
563  def __repr__(self):
564  """__repr__(MolCnSymmAxisDetector self) -> std::string"""
565  return _IMP_cnmultifit.MolCnSymmAxisDetector___repr__(self)
566 
567  __swig_destroy__ = _IMP_cnmultifit.delete_MolCnSymmAxisDetector
568  __del__ = lambda self: None
569 MolCnSymmAxisDetector_swigregister = _IMP_cnmultifit.MolCnSymmAxisDetector_swigregister
570 MolCnSymmAxisDetector_swigregister(MolCnSymmAxisDetector)
571 
572 class AlignSymmetric(object):
573  """Proxy of C++ IMP::cnmultifit::AlignSymmetric class."""
574 
575  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
576 
577  def __init__(self, dmap, threshold, cn_symm_deg):
578  """__init__(IMP::cnmultifit::AlignSymmetric self, DensityMap dmap, float threshold, int cn_symm_deg) -> AlignSymmetric"""
579  this = _IMP_cnmultifit.new_AlignSymmetric(dmap, threshold, cn_symm_deg)
580  try:
581  self.this.append(this)
582  except __builtin__.Exception:
583  self.this = this
584 
585  def get_sorted_principal_values(self):
586  """get_sorted_principal_values(AlignSymmetric self) -> IMP::Floats"""
587  return _IMP_cnmultifit.AlignSymmetric_get_sorted_principal_values(self)
588 
589 
590  def score_alignment(self, mhs, max_allowed_diff):
591  """score_alignment(AlignSymmetric self, IMP::atom::Hierarchies mhs, float max_allowed_diff) -> int"""
592  return _IMP_cnmultifit.AlignSymmetric_score_alignment(self, mhs, max_allowed_diff)
593 
594 
595  def get_symm_axis_alignments_from_model_to_density(self, mhs, sample_translation, fine_rotation_sampling=True):
596  """
597  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
598  get_symm_axis_alignments_from_model_to_density(AlignSymmetric self, IMP::atom::Hierarchies mhs, bool sample_translation) -> IMP::algebra::Transformation3Ds
599  """
600  return _IMP_cnmultifit.AlignSymmetric_get_symm_axis_alignments_from_model_to_density(self, mhs, sample_translation, fine_rotation_sampling)
601 
602 
603  def show(self, *args):
604  """
605  show(AlignSymmetric self, _ostream out)
606  show(AlignSymmetric self)
607  """
608  return _IMP_cnmultifit.AlignSymmetric_show(self, *args)
609 
610 
611  def __str__(self):
612  """__str__(AlignSymmetric self) -> std::string"""
613  return _IMP_cnmultifit.AlignSymmetric___str__(self)
614 
615 
616  def __repr__(self):
617  """__repr__(AlignSymmetric self) -> std::string"""
618  return _IMP_cnmultifit.AlignSymmetric___repr__(self)
619 
620  __swig_destroy__ = _IMP_cnmultifit.delete_AlignSymmetric
621  __del__ = lambda self: None
622 AlignSymmetric_swigregister = _IMP_cnmultifit.AlignSymmetric_swigregister
623 AlignSymmetric_swigregister(AlignSymmetric)
624 
625 
626 def generate_cn_transformations(mhs, symm_deg):
627  """generate_cn_transformations(IMP::atom::Hierarchies mhs, int symm_deg) -> IMP::algebra::Transformation3Ds"""
628  return _IMP_cnmultifit.generate_cn_transformations(mhs, symm_deg)
629 
630 def generate_translations_along_symm_axis(mhs, symm_deg):
631  """generate_translations_along_symm_axis(IMP::atom::Hierarchies mhs, int symm_deg) -> IMP::algebra::Transformation3Ds"""
632  return _IMP_cnmultifit.generate_translations_along_symm_axis(mhs, symm_deg)
633 
634 def symmetry_local_fitting(mhs, cn_symm_deg, dn_symm_deg, dmap, num_of_trans_to_consider):
635  """symmetry_local_fitting(IMP::atom::Hierarchies mhs, int cn_symm_deg, int dn_symm_deg, DensityMap dmap, int num_of_trans_to_consider) -> FittingSolutions"""
636  return _IMP_cnmultifit.symmetry_local_fitting(mhs, cn_symm_deg, dn_symm_deg, dmap, num_of_trans_to_consider)
637 
638 def build_cn_dens_assembly(subunit_dens, asmb_dens_header, monomer_t, symm_deg):
639  """build_cn_dens_assembly(DensityMap subunit_dens, DensityHeader asmb_dens_header, Transformation3D monomer_t, int symm_deg) -> DensityMap"""
640  return _IMP_cnmultifit.build_cn_dens_assembly(subunit_dens, asmb_dens_header, monomer_t, symm_deg)
641 
642 def transform_cn_assembly(mhs, monomer_t):
643  """transform_cn_assembly(IMP::atom::Hierarchies mhs, Transformation3D monomer_t)"""
644  return _IMP_cnmultifit.transform_cn_assembly(mhs, monomer_t)
645 
646 def fit_cn_assembly(*args):
647  """
648  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
649  fit_cn_assembly(IMP::atom::Hierarchies mhs, int dn_symm_deg, DensityMap dmap, float threshold, AlignSymmetric aligner, bool sample_translation=False) -> FittingSolutions
650  fit_cn_assembly(IMP::atom::Hierarchies mhs, int dn_symm_deg, DensityMap dmap, float threshold, AlignSymmetric aligner) -> FittingSolutions
651  fit_cn_assembly(DensityMap asmb_map, MolCnSymmAxisDetector symm_mol, DensityMap dmap, CnSymmAxisDetector symm_map, int symm_deg, float threshold) -> FittingSolutions
652  """
653  return _IMP_cnmultifit.fit_cn_assembly(*args)
654 
655 def pca_matching(pca1, pca2, resolution):
656  """pca_matching(PrincipalComponentAnalysis3D pca1, PrincipalComponentAnalysis3D pca2, float resolution) -> bool"""
657  return _IMP_cnmultifit.pca_matching(pca1, pca2, resolution)
658 
659 def cn_symm_score(mhs, center, direction, symm_deg):
660  """cn_symm_score(IMP::atom::Hierarchies mhs, Vector3D center, Vector3D direction, int symm_deg) -> float"""
661  return _IMP_cnmultifit.cn_symm_score(mhs, center, direction, symm_deg)
662 
663 def prune_by_pca(param_fn, sols, dn=1):
664  """
665  prune_by_pca(std::string const & param_fn, IMP::multifit::FittingSolutionRecords const & sols, int dn=1) -> IMP::multifit::FittingSolutionRecords
666  prune_by_pca(std::string const & param_fn, IMP::multifit::FittingSolutionRecords const & sols) -> IMP::multifit::FittingSolutionRecords
667  """
668  return _IMP_cnmultifit.prune_by_pca(param_fn, sols, dn)
669 
670 def calc_transformation_around_axis(a, b, angle_rad):
671  """calc_transformation_around_axis(Vector3D a, Vector3D b, float angle_rad) -> Transformation3D"""
672  return _IMP_cnmultifit.calc_transformation_around_axis(a, b, angle_rad)
673 
674 def get_cn_rmsd(mh1, mh2):
675  """get_cn_rmsd(IMP::atom::Hierarchies mh1, IMP::atom::Hierarchies mh2) -> float"""
676  return _IMP_cnmultifit.get_cn_rmsd(mh1, mh2)
677 
678 def do_all_fitting(*args):
679  """
680  do_all_fitting(std::string const param_filename, std::string const chimera_filename)
681  do_all_fitting(std::string const param_filename)
682  """
683  return _IMP_cnmultifit.do_all_fitting(*args)
684 
685 def get_rmsd_for_models(param_filename, trans_filename, ref_filename, start_model=0, end_model=-1):
686  """
687  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
688  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
689  get_rmsd_for_models(std::string const param_filename, std::string const trans_filename, std::string const ref_filename) -> IMP::Floats
690  """
691  return _IMP_cnmultifit.get_rmsd_for_models(param_filename, trans_filename, ref_filename, start_model, end_model)
692 
693 _all_commands = ["build", "rmsd", "surface",
694  "param", "chimera_models"]
695 
696 
697 def get_module_version():
698  """get_module_version() -> std::string const"""
699  return _IMP_cnmultifit.get_module_version()
700 
701 def get_example_path(fname):
702  """get_example_path(std::string fname) -> std::string"""
703  return _IMP_cnmultifit.get_example_path(fname)
704 
705 def get_data_path(fname):
706  """get_data_path(std::string fname) -> std::string"""
707  return _IMP_cnmultifit.get_data_path(fname)
708 
709 from . import _version_check
710 _version_check.check_version(get_module_version())
711 __version__ = get_module_version()
712 
713 
714 
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.