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IMP Reference Guide  2.8.0
The Integrative Modeling Platform
multifit/__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_multifit')).lstrip('.')
21  try:
22  return importlib.import_module(mname)
23  except ImportError:
24  return importlib.import_module('_IMP_multifit')
25  _IMP_multifit = 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_multifit', [dirname(__file__)])
34  except ImportError:
35  import _IMP_multifit
36  return _IMP_multifit
37  if fp is not None:
38  try:
39  _mod = imp.load_module('_IMP_multifit', fp, pathname, description)
40  finally:
41  fp.close()
42  return _mod
43  _IMP_multifit = swig_import_helper()
44  del swig_import_helper
45 else:
46  import _IMP_multifit
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_MULTIFIT_SwigPyIterator(object):
114  """Proxy of C++ swig::IMP_MULTIFIT_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_multifit.delete_IMP_MULTIFIT_SwigPyIterator
122  __del__ = lambda self: None
123 
124  def value(self):
125  """value(IMP_MULTIFIT_SwigPyIterator self) -> PyObject *"""
126  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_value(self)
127 
128 
129  def incr(self, n=1):
130  """
131  incr(IMP_MULTIFIT_SwigPyIterator self, size_t n=1) -> IMP_MULTIFIT_SwigPyIterator
132  incr(IMP_MULTIFIT_SwigPyIterator self) -> IMP_MULTIFIT_SwigPyIterator
133  """
134  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_incr(self, n)
135 
136 
137  def decr(self, n=1):
138  """
139  decr(IMP_MULTIFIT_SwigPyIterator self, size_t n=1) -> IMP_MULTIFIT_SwigPyIterator
140  decr(IMP_MULTIFIT_SwigPyIterator self) -> IMP_MULTIFIT_SwigPyIterator
141  """
142  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_decr(self, n)
143 
144 
145  def distance(self, x):
146  """distance(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> ptrdiff_t"""
147  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_distance(self, x)
148 
149 
150  def equal(self, x):
151  """equal(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> bool"""
152  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_equal(self, x)
153 
154 
155  def copy(self):
156  """copy(IMP_MULTIFIT_SwigPyIterator self) -> IMP_MULTIFIT_SwigPyIterator"""
157  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_copy(self)
158 
159 
160  def next(self):
161  """next(IMP_MULTIFIT_SwigPyIterator self) -> PyObject *"""
162  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_next(self)
163 
164 
165  def __next__(self):
166  """__next__(IMP_MULTIFIT_SwigPyIterator self) -> PyObject *"""
167  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___next__(self)
168 
169 
170  def previous(self):
171  """previous(IMP_MULTIFIT_SwigPyIterator self) -> PyObject *"""
172  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_previous(self)
173 
174 
175  def advance(self, n):
176  """advance(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator"""
177  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_advance(self, n)
178 
179 
180  def __eq__(self, x):
181  """__eq__(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> bool"""
182  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___eq__(self, x)
183 
184 
185  def __ne__(self, x):
186  """__ne__(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> bool"""
187  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___ne__(self, x)
188 
189 
190  def __iadd__(self, n):
191  """__iadd__(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator"""
192  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___iadd__(self, n)
193 
194 
195  def __isub__(self, n):
196  """__isub__(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator"""
197  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___isub__(self, n)
198 
199 
200  def __add__(self, n):
201  """__add__(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator"""
202  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___add__(self, n)
203 
204 
205  def __sub__(self, *args):
206  """
207  __sub__(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator
208  __sub__(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> ptrdiff_t
209  """
210  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___sub__(self, *args)
211 
212  def __iter__(self):
213  return self
214 IMP_MULTIFIT_SwigPyIterator_swigregister = _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_swigregister
215 IMP_MULTIFIT_SwigPyIterator_swigregister(IMP_MULTIFIT_SwigPyIterator)
216 
217 
218 _value_types=[]
219 _object_types=[]
220 _raii_types=[]
221 _plural_types=[]
222 
223 IMP_DEBUG = _IMP_multifit.IMP_DEBUG
224 IMP_RELEASE = _IMP_multifit.IMP_RELEASE
225 IMP_SILENT = _IMP_multifit.IMP_SILENT
226 IMP_PROGRESS = _IMP_multifit.IMP_PROGRESS
227 IMP_TERSE = _IMP_multifit.IMP_TERSE
228 IMP_VERBOSE = _IMP_multifit.IMP_VERBOSE
229 IMP_MEMORY = _IMP_multifit.IMP_MEMORY
230 IMP_NONE = _IMP_multifit.IMP_NONE
231 IMP_USAGE = _IMP_multifit.IMP_USAGE
232 IMP_INTERNAL = _IMP_multifit.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_multifit.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_multifit.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_multifit.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_multifit.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_multifit.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_multifit.IMP_KERNEL_HAS_GPERFTOOLS
239 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_multifit.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
240 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_multifit.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
241 IMPKERNEL_SHOW_WARNINGS = _IMP_multifit.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_multifit._ostream_write(self, osa_buf)
281 
282 _ostream_swigregister = _IMP_multifit._ostream_swigregister
283 _ostream_swigregister(_ostream)
284 
285 IMP_COMPILER_HAS_OVERRIDE = _IMP_multifit.IMP_COMPILER_HAS_OVERRIDE
286 IMP_COMPILER_HAS_FINAL = _IMP_multifit.IMP_COMPILER_HAS_FINAL
287 IMP_HAS_NOEXCEPT = _IMP_multifit.IMP_HAS_NOEXCEPT
288 import IMP
289 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CGAL_HAS_BOOST_FILESYSTEM
290 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
291 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CGAL_HAS_BOOST_RANDOM
292 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CGAL_HAS_BOOST_SYSTEM
293 IMPCGAL_SHOW_WARNINGS = _IMP_multifit.IMPCGAL_SHOW_WARNINGS
294 import IMP.cgal
295 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_multifit.IMP_ALGEBRA_HAS_IMP_CGAL
296 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
297 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
298 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_RANDOM
299 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_SYSTEM
300 IMP_ALGEBRA_HAS_CGAL = _IMP_multifit.IMP_ALGEBRA_HAS_CGAL
301 IMP_ALGEBRA_HAS_ANN = _IMP_multifit.IMP_ALGEBRA_HAS_ANN
302 IMPALGEBRA_SHOW_WARNINGS = _IMP_multifit.IMPALGEBRA_SHOW_WARNINGS
303 import IMP.algebra
304 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_multifit.IMP_DISPLAY_HAS_IMP_CGAL
305 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
306 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
307 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_RANDOM
308 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_SYSTEM
309 IMP_DISPLAY_HAS_CGAL = _IMP_multifit.IMP_DISPLAY_HAS_CGAL
310 IMPDISPLAY_SHOW_WARNINGS = _IMP_multifit.IMPDISPLAY_SHOW_WARNINGS
311 import IMP.display
312 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
313 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
314 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
315 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
316 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
317 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_CGAL
318 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_HDF5
319 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_multifit.IMPSCOREFUNCTOR_SHOW_WARNINGS
320 import IMP.score_functor
321 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_multifit.IMP_STATISTICS_HAS_IMP_CGAL
322 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
323 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
324 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_RANDOM
325 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_SYSTEM
326 IMP_STATISTICS_HAS_CGAL = _IMP_multifit.IMP_STATISTICS_HAS_CGAL
327 IMPSTATISTICS_SHOW_WARNINGS = _IMP_multifit.IMPSTATISTICS_SHOW_WARNINGS
328 import IMP.statistics
329 IMP_CORE_HAS_IMP_CGAL = _IMP_multifit.IMP_CORE_HAS_IMP_CGAL
330 IMP_CORE_HAS_IMP_KERNEL = _IMP_multifit.IMP_CORE_HAS_IMP_KERNEL
331 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CORE_HAS_BOOST_FILESYSTEM
332 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
333 IMP_CORE_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CORE_HAS_BOOST_RANDOM
334 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CORE_HAS_BOOST_SYSTEM
335 IMP_CORE_HAS_CGAL = _IMP_multifit.IMP_CORE_HAS_CGAL
336 IMP_CORE_HAS_HDF5 = _IMP_multifit.IMP_CORE_HAS_HDF5
337 IMPCORE_SHOW_WARNINGS = _IMP_multifit.IMPCORE_SHOW_WARNINGS
338 import IMP.core
339 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_multifit.IMP_CONTAINER_HAS_IMP_ALGEBRA
340 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_multifit.IMP_CONTAINER_HAS_IMP_CGAL
341 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_multifit.IMP_CONTAINER_HAS_IMP_DISPLAY
342 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_multifit.IMP_CONTAINER_HAS_IMP_KERNEL
343 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
344 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
345 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
346 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_RANDOM
347 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_SYSTEM
348 IMP_CONTAINER_HAS_CGAL = _IMP_multifit.IMP_CONTAINER_HAS_CGAL
349 IMP_CONTAINER_HAS_HDF5 = _IMP_multifit.IMP_CONTAINER_HAS_HDF5
350 IMPCONTAINER_SHOW_WARNINGS = _IMP_multifit.IMPCONTAINER_SHOW_WARNINGS
351 import IMP.container
352 IMP_ATOM_HAS_IMP_CGAL = _IMP_multifit.IMP_ATOM_HAS_IMP_CGAL
353 IMP_ATOM_HAS_IMP_KERNEL = _IMP_multifit.IMP_ATOM_HAS_IMP_KERNEL
354 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
355 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
356 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_multifit.IMP_ATOM_HAS_BOOST_RANDOM
357 IMP_ATOM_HAS_BOOST_REGEX = _IMP_multifit.IMP_ATOM_HAS_BOOST_REGEX
358 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_ATOM_HAS_BOOST_SYSTEM
359 IMP_ATOM_HAS_CGAL = _IMP_multifit.IMP_ATOM_HAS_CGAL
360 IMP_ATOM_HAS_HDF5 = _IMP_multifit.IMP_ATOM_HAS_HDF5
361 IMPATOM_SHOW_WARNINGS = _IMP_multifit.IMPATOM_SHOW_WARNINGS
362 IMP_ATOM_TYPE_INDEX = _IMP_multifit.IMP_ATOM_TYPE_INDEX
363 IMP_RESIDUE_TYPE_INDEX = _IMP_multifit.IMP_RESIDUE_TYPE_INDEX
364 IMP_HIERARCHY_TYPE_INDEX = _IMP_multifit.IMP_HIERARCHY_TYPE_INDEX
365 import IMP.atom
366 IMP_EM_HAS_IMP_CGAL = _IMP_multifit.IMP_EM_HAS_IMP_CGAL
367 IMP_EM_HAS_IMP_CONTAINER = _IMP_multifit.IMP_EM_HAS_IMP_CONTAINER
368 IMP_EM_HAS_IMP_DISPLAY = _IMP_multifit.IMP_EM_HAS_IMP_DISPLAY
369 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_EM_HAS_IMP_SCORE_FUNCTOR
370 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_EM_HAS_BOOST_FILESYSTEM
371 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
372 IMP_EM_HAS_BOOST_RANDOM = _IMP_multifit.IMP_EM_HAS_BOOST_RANDOM
373 IMP_EM_HAS_BOOST_REGEX = _IMP_multifit.IMP_EM_HAS_BOOST_REGEX
374 IMP_EM_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_EM_HAS_BOOST_SYSTEM
375 IMP_EM_HAS_CGAL = _IMP_multifit.IMP_EM_HAS_CGAL
376 IMP_EM_HAS_HDF5 = _IMP_multifit.IMP_EM_HAS_HDF5
377 IMPEM_SHOW_WARNINGS = _IMP_multifit.IMPEM_SHOW_WARNINGS
378 import IMP.em
379 IMP_RMF_HAS_IMP_CGAL = _IMP_multifit.IMP_RMF_HAS_IMP_CGAL
380 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
381 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_RMF_HAS_BOOST_FILESYSTEM
382 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
383 IMP_RMF_HAS_BOOST_RANDOM = _IMP_multifit.IMP_RMF_HAS_BOOST_RANDOM
384 IMP_RMF_HAS_BOOST_REGEX = _IMP_multifit.IMP_RMF_HAS_BOOST_REGEX
385 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_RMF_HAS_BOOST_SYSTEM
386 IMP_RMF_HAS_CGAL = _IMP_multifit.IMP_RMF_HAS_CGAL
387 IMP_RMF_HAS_HDF5 = _IMP_multifit.IMP_RMF_HAS_HDF5
388 IMPRMF_SHOW_WARNINGS = _IMP_multifit.IMPRMF_SHOW_WARNINGS
389 import IMP.rmf
390 import RMF
391 IMP_DOMINO_HAS_IMP_ATOM = _IMP_multifit.IMP_DOMINO_HAS_IMP_ATOM
392 IMP_DOMINO_HAS_IMP_CGAL = _IMP_multifit.IMP_DOMINO_HAS_IMP_CGAL
393 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_multifit.IMP_DOMINO_HAS_IMP_KERNEL
394 IMP_DOMINO_HAS_IMP_RMF = _IMP_multifit.IMP_DOMINO_HAS_IMP_RMF
395 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
396 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_FILESYSTEM
397 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
398 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_RANDOM
399 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_multifit.IMP_DOMINO_HAS_BOOST_REGEX
400 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_SYSTEM
401 IMP_DOMINO_HAS_CGAL = _IMP_multifit.IMP_DOMINO_HAS_CGAL
402 IMP_DOMINO_HAS_HDF5 = _IMP_multifit.IMP_DOMINO_HAS_HDF5
403 IMP_DOMINO_HAS_RMF = _IMP_multifit.IMP_DOMINO_HAS_RMF
404 IMPDOMINO_SHOW_WARNINGS = _IMP_multifit.IMPDOMINO_SHOW_WARNINGS
405 import RMF_HDF5
406 import IMP.domino
407 IMP_MULTIFIT_HAS_IMP_CGAL = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_CGAL
408 IMP_MULTIFIT_HAS_IMP_CONTAINER = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_CONTAINER
409 IMP_MULTIFIT_HAS_IMP_DISPLAY = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_DISPLAY
410 IMP_MULTIFIT_HAS_IMP_KERNEL = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_KERNEL
411 IMP_MULTIFIT_HAS_IMP_RMF = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_RMF
412 IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR
413 IMP_MULTIFIT_HAS_BOOST_GRAPH = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_GRAPH
414 IMP_MULTIFIT_HAS_BOOST_RANDOM = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_RANDOM
415 IMP_MULTIFIT_HAS_BOOST_REGEX = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_REGEX
416 IMP_MULTIFIT_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_SYSTEM
417 IMP_MULTIFIT_HAS_CGAL = _IMP_multifit.IMP_MULTIFIT_HAS_CGAL
418 IMP_MULTIFIT_HAS_HDF5 = _IMP_multifit.IMP_MULTIFIT_HAS_HDF5
419 IMP_MULTIFIT_HAS_RMF = _IMP_multifit.IMP_MULTIFIT_HAS_RMF
420 IMPMULTIFIT_SHOW_WARNINGS = _IMP_multifit.IMPMULTIFIT_SHOW_WARNINGS
421 
422 _object_types.append("RadiusOfGyrationRestraint")
423 
424 
425 def _object_cast_to_RadiusOfGyrationRestraint(o):
426  """_object_cast_to_RadiusOfGyrationRestraint(Object o) -> RadiusOfGyrationRestraint"""
427  return _IMP_multifit._object_cast_to_RadiusOfGyrationRestraint(o)
428 
429 _object_types.append("ComponentHeader")
430 
431 
432 def _object_cast_to_ComponentHeader(o):
433  """_object_cast_to_ComponentHeader(Object o) -> ComponentHeader"""
434  return _IMP_multifit._object_cast_to_ComponentHeader(o)
435 
436 _object_types.append("AssemblyHeader")
437 
438 
439 def _object_cast_to_AssemblyHeader(o):
440  """_object_cast_to_AssemblyHeader(Object o) -> AssemblyHeader"""
441  return _IMP_multifit._object_cast_to_AssemblyHeader(o)
442 
443 _object_types.append("SettingsData")
444 
445 
446 def _object_cast_to_SettingsData(o):
447  """_object_cast_to_SettingsData(Object o) -> SettingsData"""
448  return _IMP_multifit._object_cast_to_SettingsData(o)
449 
450 _object_types.append("WeightedExcludedVolumeRestraint")
451 
452 
453 def _object_cast_to_WeightedExcludedVolumeRestraint(o):
454  """_object_cast_to_WeightedExcludedVolumeRestraint(Object o) -> WeightedExcludedVolumeRestraint"""
455  return _IMP_multifit._object_cast_to_WeightedExcludedVolumeRestraint(o)
456 
457 _object_types.append("ComplementarityRestraint")
458 
459 
460 def _object_cast_to_ComplementarityRestraint(o):
461  """_object_cast_to_ComplementarityRestraint(Object o) -> ComplementarityRestraint"""
462  return _IMP_multifit._object_cast_to_ComplementarityRestraint(o)
463 
464 ProteinRecordDataList=list
465 _plural_types.append("ProteinRecordDataList")
466 _value_types.append("ProteinRecordData")
467 
468 
469 FittingSolutionRecords=list
470 _plural_types.append("FittingSolutionRecords")
471 _value_types.append("FittingSolutionRecord")
472 
473 
474 AnchorsDataList=list
475 _plural_types.append("AnchorsDataList")
476 _value_types.append("AnchorsData")
477 
478 
479 DominoParamsList=list
480 _plural_types.append("DominoParamsList")
481 _value_types.append("DominoParams")
482 
483 
484 ComplementarityParamsList=list
485 _plural_types.append("ComplementarityParamsList")
486 _value_types.append("ComplementarityParams")
487 
488 
489 XlinkParamsList=list
490 _plural_types.append("XlinkParamsList")
491 _value_types.append("XlinkParams")
492 
493 
494 ConnectivityParamsList=list
495 _plural_types.append("ConnectivityParamsList")
496 _value_types.append("ConnectivityParams")
497 
498 
499 FragmentsParamsList=list
500 _plural_types.append("FragmentsParamsList")
501 _value_types.append("FragmentsParams")
502 
503 
504 RogParamsList=list
505 _plural_types.append("RogParamsList")
506 _value_types.append("RogParams")
507 
508 
509 EVParamsList=list
510 _plural_types.append("EVParamsList")
511 _value_types.append("EVParams")
512 
513 
514 FiltersParamsList=list
515 _plural_types.append("FiltersParamsList")
516 _value_types.append("FiltersParams")
517 
518 
519 AlignmentParamsList=list
520 _plural_types.append("AlignmentParamsList")
521 _value_types.append("AlignmentParams")
522 
523 
524 FittingParamsList=list
525 _plural_types.append("FittingParamsList")
526 _value_types.append("FittingParams")
527 
528 
529 ProteinsAnchorsSamplingSpaces=list
530 _plural_types.append("ProteinsAnchorsSamplingSpaces")
531 _value_types.append("ProteinsAnchorsSamplingSpace")
532 
533 
534 _object_types.append("ProteomicsData")
535 
536 
537 def _object_cast_to_ProteomicsData(o):
538  """_object_cast_to_ProteomicsData(Object o) -> ProteomicsData"""
539  return _IMP_multifit._object_cast_to_ProteomicsData(o)
540 
541 _object_types.append("FFTFitting")
542 
543 
544 def _object_cast_to_FFTFitting(o):
545  """_object_cast_to_FFTFitting(Object o) -> FFTFitting"""
546  return _IMP_multifit._object_cast_to_FFTFitting(o)
547 
548 _object_types.append("FFTFittingOutput")
549 
550 
551 def _object_cast_to_FFTFittingOutput(o):
552  """_object_cast_to_FFTFittingOutput(Object o) -> FFTFittingOutput"""
553  return _IMP_multifit._object_cast_to_FFTFittingOutput(o)
554 
555 _object_types.append("ProbabilisticAnchorGraph")
556 
557 
558 def _object_cast_to_ProbabilisticAnchorGraph(o):
559  """_object_cast_to_ProbabilisticAnchorGraph(Object o) -> ProbabilisticAnchorGraph"""
560  return _IMP_multifit._object_cast_to_ProbabilisticAnchorGraph(o)
561 
562 _object_types.append("Ensemble")
563 
564 
565 def _object_cast_to_Ensemble(o):
566  """_object_cast_to_Ensemble(Object o) -> Ensemble"""
567  return _IMP_multifit._object_cast_to_Ensemble(o)
568 
569 _object_types.append("ProteomicsEMAlignmentAtomic")
570 
571 
572 def _object_cast_to_ProteomicsEMAlignmentAtomic(o):
573  """_object_cast_to_ProteomicsEMAlignmentAtomic(Object o) -> ProteomicsEMAlignmentAtomic"""
574  return _IMP_multifit._object_cast_to_ProteomicsEMAlignmentAtomic(o)
575 
576 _object_types.append("RigidLeavesRefiner")
577 
578 
579 def _object_cast_to_RigidLeavesRefiner(o):
580  """_object_cast_to_RigidLeavesRefiner(Object o) -> RigidLeavesRefiner"""
581  return _IMP_multifit._object_cast_to_RigidLeavesRefiner(o)
582 
583 def add_surface_index(*args):
584  """
585  add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key, FloatKey radius_key, FloatKey weight_key)
586  add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key, FloatKey radius_key)
587  add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key)
588  add_surface_index(Hierarchy mhd, IMP::Float apix)
589  """
590  return _IMP_multifit.add_surface_index(*args)
591 
593  """
594  create_weighted_excluded_volume_restraint(RigidBody rb1, RigidBody rb2, FloatKey shell_key) -> Restraint
595  create_weighted_excluded_volume_restraint(RigidBody rb1, RigidBody rb2) -> Restraint
596  """
597  return _IMP_multifit.create_weighted_excluded_volume_restraint(*args)
598 class FittingSolutionRecord(object):
599  """Proxy of C++ IMP::multifit::FittingSolutionRecord class."""
600 
601  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
602 
603  def __init__(self):
604  """__init__(IMP::multifit::FittingSolutionRecord self) -> FittingSolutionRecord"""
605  this = _IMP_multifit.new_FittingSolutionRecord()
606  try:
607  self.this.append(this)
608  except __builtin__.Exception:
609  self.this = this
610 
611  def get_index(self):
612  """get_index(FittingSolutionRecord self) -> unsigned int"""
613  return _IMP_multifit.FittingSolutionRecord_get_index(self)
614 
615 
616  def set_index(self, new_ind):
617  """set_index(FittingSolutionRecord self, unsigned int new_ind)"""
618  return _IMP_multifit.FittingSolutionRecord_set_index(self, new_ind)
619 
620 
621  def get_solution_filename(self):
622  """get_solution_filename(FittingSolutionRecord self) -> std::string"""
623  return _IMP_multifit.FittingSolutionRecord_get_solution_filename(self)
624 
625 
626  def set_solution_filename(self, sol_fn):
627  """set_solution_filename(FittingSolutionRecord self, std::string sol_fn)"""
628  return _IMP_multifit.FittingSolutionRecord_set_solution_filename(self, sol_fn)
629 
630 
631  def get_fit_transformation(self):
632  """get_fit_transformation(FittingSolutionRecord self) -> Transformation3D"""
633  return _IMP_multifit.FittingSolutionRecord_get_fit_transformation(self)
634 
635 
636  def set_fit_transformation(self, t):
637  """set_fit_transformation(FittingSolutionRecord self, Transformation3D t)"""
638  return _IMP_multifit.FittingSolutionRecord_set_fit_transformation(self, t)
639 
640 
641  def get_match_size(self):
642  """get_match_size(FittingSolutionRecord self) -> unsigned int"""
643  return _IMP_multifit.FittingSolutionRecord_get_match_size(self)
644 
645 
646  def set_match_size(self, match_size):
647  """set_match_size(FittingSolutionRecord self, unsigned int match_size)"""
648  return _IMP_multifit.FittingSolutionRecord_set_match_size(self, match_size)
649 
650 
651  def get_match_average_distance(self):
652  """get_match_average_distance(FittingSolutionRecord self) -> IMP::Float"""
653  return _IMP_multifit.FittingSolutionRecord_get_match_average_distance(self)
654 
655 
656  def set_match_average_distance(self, match_avg_dist):
657  """set_match_average_distance(FittingSolutionRecord self, IMP::Float match_avg_dist)"""
658  return _IMP_multifit.FittingSolutionRecord_set_match_average_distance(self, match_avg_dist)
659 
660 
661  def get_fitting_score(self):
662  """get_fitting_score(FittingSolutionRecord self) -> IMP::Float"""
663  return _IMP_multifit.FittingSolutionRecord_get_fitting_score(self)
664 
665 
666  def set_fitting_score(self, fit_score):
667  """set_fitting_score(FittingSolutionRecord self, IMP::Float fit_score)"""
668  return _IMP_multifit.FittingSolutionRecord_set_fitting_score(self, fit_score)
669 
670 
671  def get_rmsd_to_reference(self):
672  """get_rmsd_to_reference(FittingSolutionRecord self) -> IMP::Float"""
673  return _IMP_multifit.FittingSolutionRecord_get_rmsd_to_reference(self)
674 
675 
676  def set_rmsd_to_reference(self, rmsd_to_ref):
677  """set_rmsd_to_reference(FittingSolutionRecord self, IMP::Float rmsd_to_ref)"""
678  return _IMP_multifit.FittingSolutionRecord_set_rmsd_to_reference(self, rmsd_to_ref)
679 
680 
681  def get_dock_transformation(self):
682  """get_dock_transformation(FittingSolutionRecord self) -> Transformation3D"""
683  return _IMP_multifit.FittingSolutionRecord_get_dock_transformation(self)
684 
685 
686  def set_dock_transformation(self, t):
687  """set_dock_transformation(FittingSolutionRecord self, Transformation3D t)"""
688  return _IMP_multifit.FittingSolutionRecord_set_dock_transformation(self, t)
689 
690 
691  def get_envelope_penetration_score(self):
692  """get_envelope_penetration_score(FittingSolutionRecord self) -> IMP::Float"""
693  return _IMP_multifit.FittingSolutionRecord_get_envelope_penetration_score(self)
694 
695 
696  def set_envelope_penetration_score(self, s):
697  """set_envelope_penetration_score(FittingSolutionRecord self, IMP::Float s)"""
698  return _IMP_multifit.FittingSolutionRecord_set_envelope_penetration_score(self, s)
699 
700 
701  def show(self, *args):
702  """
703  show(FittingSolutionRecord self, _ostream out)
704  show(FittingSolutionRecord self)
705  """
706  return _IMP_multifit.FittingSolutionRecord_show(self, *args)
707 
708 
709  def get_record_header():
710  """get_record_header() -> std::string"""
711  return _IMP_multifit.FittingSolutionRecord_get_record_header()
712 
713  get_record_header = staticmethod(get_record_header)
714 
715  def __str__(self):
716  """__str__(FittingSolutionRecord self) -> std::string"""
717  return _IMP_multifit.FittingSolutionRecord___str__(self)
718 
719 
720  def __repr__(self):
721  """__repr__(FittingSolutionRecord self) -> std::string"""
722  return _IMP_multifit.FittingSolutionRecord___repr__(self)
723 
724  __swig_destroy__ = _IMP_multifit.delete_FittingSolutionRecord
725  __del__ = lambda self: None
726 FittingSolutionRecord_swigregister = _IMP_multifit.FittingSolutionRecord_swigregister
727 FittingSolutionRecord_swigregister(FittingSolutionRecord)
728 
729 def FittingSolutionRecord_get_record_header():
730  """FittingSolutionRecord_get_record_header() -> std::string"""
731  return _IMP_multifit.FittingSolutionRecord_get_record_header()
732 
733 
734 def pca_based_rigid_fitting(*args):
735  """
736  pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold, FloatKey wei_key, PrincipalComponentAnalysis3D dens_pca_input) -> FittingSolutions
737  pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold, FloatKey wei_key) -> FittingSolutions
738  pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold) -> FittingSolutions
739  pca_based_rigid_fitting(IMP::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold, FloatKey wei_key, PrincipalComponentAnalysis3D dens_pca_input) -> FittingSolutions
740  pca_based_rigid_fitting(IMP::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold, FloatKey wei_key) -> FittingSolutions
741  pca_based_rigid_fitting(IMP::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold) -> FittingSolutions
742  """
743  return _IMP_multifit.pca_based_rigid_fitting(*args)
744 
745 def write_markers(pca, out):
746  """write_markers(PrincipalComponentAnalysis3D pca, _ostream out)"""
747  return _IMP_multifit.write_markers(pca, out)
748 class ComponentHeader(IMP.Object):
749  """Proxy of C++ IMP::multifit::ComponentHeader class."""
750 
751  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
752 
753  def __init__(self):
754  """__init__(IMP::multifit::ComponentHeader self) -> ComponentHeader"""
755  this = _IMP_multifit.new_ComponentHeader()
756  try:
757  self.this.append(this)
758  except __builtin__.Exception:
759  self.this = this
760 
761  def set_name(self, name):
762  """set_name(ComponentHeader self, std::string const & name)"""
763  return _IMP_multifit.ComponentHeader_set_name(self, name)
764 
765 
766  def get_name(self):
767  """get_name(ComponentHeader self) -> std::string"""
768  return _IMP_multifit.ComponentHeader_get_name(self)
769 
770 
771  def get_filename(self):
772  """get_filename(ComponentHeader self) -> std::string"""
773  return _IMP_multifit.ComponentHeader_get_filename(self)
774 
775 
776  def set_filename(self, filename):
777  """set_filename(ComponentHeader self, std::string const & filename)"""
778  return _IMP_multifit.ComponentHeader_set_filename(self, filename)
779 
780 
781  def get_surface_fn(self):
782  """get_surface_fn(ComponentHeader self) -> std::string"""
783  return _IMP_multifit.ComponentHeader_get_surface_fn(self)
784 
785 
786  def set_surface_fn(self, fn):
787  """set_surface_fn(ComponentHeader self, std::string const & fn)"""
788  return _IMP_multifit.ComponentHeader_set_surface_fn(self, fn)
789 
790 
791  def set_txt_ap_fn(self, pdb_ap_fn):
792  """set_txt_ap_fn(ComponentHeader self, std::string const & pdb_ap_fn)"""
793  return _IMP_multifit.ComponentHeader_set_txt_ap_fn(self, pdb_ap_fn)
794 
795 
796  def get_txt_ap_fn(self):
797  """get_txt_ap_fn(ComponentHeader self) -> std::string"""
798  return _IMP_multifit.ComponentHeader_get_txt_ap_fn(self)
799 
800 
801  def set_txt_fine_ap_fn(self, pdb_ap_fn):
802  """set_txt_fine_ap_fn(ComponentHeader self, std::string const & pdb_ap_fn)"""
803  return _IMP_multifit.ComponentHeader_set_txt_fine_ap_fn(self, pdb_ap_fn)
804 
805 
806  def get_txt_fine_ap_fn(self):
807  """get_txt_fine_ap_fn(ComponentHeader self) -> std::string"""
808  return _IMP_multifit.ComponentHeader_get_txt_fine_ap_fn(self)
809 
810 
811  def set_num_ap(self, num_ap):
812  """set_num_ap(ComponentHeader self, int num_ap)"""
813  return _IMP_multifit.ComponentHeader_set_num_ap(self, num_ap)
814 
815 
816  def get_num_ap(self):
817  """get_num_ap(ComponentHeader self) -> int"""
818  return _IMP_multifit.ComponentHeader_get_num_ap(self)
819 
820 
821  def set_num_fine_ap(self, num_ap):
822  """set_num_fine_ap(ComponentHeader self, int num_ap)"""
823  return _IMP_multifit.ComponentHeader_set_num_fine_ap(self, num_ap)
824 
825 
826  def get_num_fine_ap(self):
827  """get_num_fine_ap(ComponentHeader self) -> int"""
828  return _IMP_multifit.ComponentHeader_get_num_fine_ap(self)
829 
830 
831  def set_transformations_fn(self, transformations_fn):
832  """set_transformations_fn(ComponentHeader self, std::string transformations_fn)"""
833  return _IMP_multifit.ComponentHeader_set_transformations_fn(self, transformations_fn)
834 
835 
836  def get_transformations_fn(self):
837  """get_transformations_fn(ComponentHeader self) -> std::string"""
838  return _IMP_multifit.ComponentHeader_get_transformations_fn(self)
839 
840 
841  def set_reference_fn(self, ref_fn):
842  """set_reference_fn(ComponentHeader self, std::string const & ref_fn)"""
843  return _IMP_multifit.ComponentHeader_set_reference_fn(self, ref_fn)
844 
845 
846  def get_reference_fn(self):
847  """get_reference_fn(ComponentHeader self) -> std::string"""
848  return _IMP_multifit.ComponentHeader_get_reference_fn(self)
849 
850 
851  def get_version_info(self):
852  """get_version_info(ComponentHeader self) -> VersionInfo"""
853  return _IMP_multifit.ComponentHeader_get_version_info(self)
854 
855 
856  def __str__(self):
857  """__str__(ComponentHeader self) -> std::string"""
858  return _IMP_multifit.ComponentHeader___str__(self)
859 
860 
861  def __repr__(self):
862  """__repr__(ComponentHeader self) -> std::string"""
863  return _IMP_multifit.ComponentHeader___repr__(self)
864 
865 
866  @staticmethod
867  def get_from(o):
868  return _object_cast_to_ComponentHeader(o)
869 
870 ComponentHeader_swigregister = _IMP_multifit.ComponentHeader_swigregister
871 ComponentHeader_swigregister(ComponentHeader)
872 
873 class AssemblyHeader(IMP.Object):
874  """Proxy of C++ IMP::multifit::AssemblyHeader class."""
875 
876  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
877 
878  def __init__(self):
879  """__init__(IMP::multifit::AssemblyHeader self) -> AssemblyHeader"""
880  this = _IMP_multifit.new_AssemblyHeader()
881  try:
882  self.this.append(this)
883  except __builtin__.Exception:
884  self.this = this
885 
886  def set_dens_fn(self, dens_fn):
887  """set_dens_fn(AssemblyHeader self, std::string const & dens_fn)"""
888  return _IMP_multifit.AssemblyHeader_set_dens_fn(self, dens_fn)
889 
890 
891  def get_dens_fn(self):
892  """get_dens_fn(AssemblyHeader self) -> std::string"""
893  return _IMP_multifit.AssemblyHeader_get_dens_fn(self)
894 
895 
896  def set_resolution(self, res):
897  """set_resolution(AssemblyHeader self, float res)"""
898  return _IMP_multifit.AssemblyHeader_set_resolution(self, res)
899 
900 
901  def get_resolution(self):
902  """get_resolution(AssemblyHeader self) -> float"""
903  return _IMP_multifit.AssemblyHeader_get_resolution(self)
904 
905 
906  def get_spacing(self):
907  """get_spacing(AssemblyHeader self) -> float"""
908  return _IMP_multifit.AssemblyHeader_get_spacing(self)
909 
910 
911  def set_spacing(self, spacing):
912  """set_spacing(AssemblyHeader self, float spacing)"""
913  return _IMP_multifit.AssemblyHeader_set_spacing(self, spacing)
914 
915 
916  def set_threshold(self, t):
917  """set_threshold(AssemblyHeader self, float t)"""
918  return _IMP_multifit.AssemblyHeader_set_threshold(self, t)
919 
920 
921  def get_threshold(self):
922  """get_threshold(AssemblyHeader self) -> float"""
923  return _IMP_multifit.AssemblyHeader_get_threshold(self)
924 
925 
926  def get_origin(self):
927  """get_origin(AssemblyHeader self) -> Vector3D"""
928  return _IMP_multifit.AssemblyHeader_get_origin(self)
929 
930 
931  def set_origin(self, origin):
932  """set_origin(AssemblyHeader self, Vector3D origin)"""
933  return _IMP_multifit.AssemblyHeader_set_origin(self, origin)
934 
935 
936  def get_coarse_ap_fn(self):
937  """get_coarse_ap_fn(AssemblyHeader self) -> std::string"""
938  return _IMP_multifit.AssemblyHeader_get_coarse_ap_fn(self)
939 
940 
941  def set_coarse_ap_fn(self, new_fn):
942  """set_coarse_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
943  return _IMP_multifit.AssemblyHeader_set_coarse_ap_fn(self, new_fn)
944 
945 
946  def get_coarse_over_sampled_ap_fn(self):
947  """get_coarse_over_sampled_ap_fn(AssemblyHeader self) -> std::string"""
948  return _IMP_multifit.AssemblyHeader_get_coarse_over_sampled_ap_fn(self)
949 
950 
951  def set_coarse_over_sampled_ap_fn(self, new_fn):
952  """set_coarse_over_sampled_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
953  return _IMP_multifit.AssemblyHeader_set_coarse_over_sampled_ap_fn(self, new_fn)
954 
955 
956  def get_fine_ap_fn(self):
957  """get_fine_ap_fn(AssemblyHeader self) -> std::string"""
958  return _IMP_multifit.AssemblyHeader_get_fine_ap_fn(self)
959 
960 
961  def set_fine_ap_fn(self, new_fn):
962  """set_fine_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
963  return _IMP_multifit.AssemblyHeader_set_fine_ap_fn(self, new_fn)
964 
965 
966  def get_fine_over_sampled_ap_fn(self):
967  """get_fine_over_sampled_ap_fn(AssemblyHeader self) -> std::string"""
968  return _IMP_multifit.AssemblyHeader_get_fine_over_sampled_ap_fn(self)
969 
970 
971  def set_fine_over_sampled_ap_fn(self, new_fn):
972  """set_fine_over_sampled_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
973  return _IMP_multifit.AssemblyHeader_set_fine_over_sampled_ap_fn(self, new_fn)
974 
975 
976  def get_version_info(self):
977  """get_version_info(AssemblyHeader self) -> VersionInfo"""
978  return _IMP_multifit.AssemblyHeader_get_version_info(self)
979 
980 
981  def __str__(self):
982  """__str__(AssemblyHeader self) -> std::string"""
983  return _IMP_multifit.AssemblyHeader___str__(self)
984 
985 
986  def __repr__(self):
987  """__repr__(AssemblyHeader self) -> std::string"""
988  return _IMP_multifit.AssemblyHeader___repr__(self)
989 
990 
991  @staticmethod
992  def get_from(o):
993  return _object_cast_to_AssemblyHeader(o)
994 
995 AssemblyHeader_swigregister = _IMP_multifit.AssemblyHeader_swigregister
996 AssemblyHeader_swigregister(AssemblyHeader)
997 
998 class SettingsData(IMP.Object):
999  """Proxy of C++ IMP::multifit::SettingsData class."""
1000 
1001  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1002 
1003  def __init__(self):
1004  """__init__(IMP::multifit::SettingsData self) -> SettingsData"""
1005  this = _IMP_multifit.new_SettingsData()
1006  try:
1007  self.this.append(this)
1008  except __builtin__.Exception:
1009  self.this = this
1010 
1011  def show_component_header_line(*args):
1012  """
1013  show_component_header_line(_ostream out)
1014  show_component_header_line()
1015  """
1016  return _IMP_multifit.SettingsData_show_component_header_line(*args)
1017 
1018  show_component_header_line = staticmethod(show_component_header_line)
1019 
1020  def get_component_header_line():
1021  """get_component_header_line() -> std::string"""
1022  return _IMP_multifit.SettingsData_get_component_header_line()
1023 
1024  get_component_header_line = staticmethod(get_component_header_line)
1025 
1026  def show_density_header_line(*args):
1027  """
1028  show_density_header_line(_ostream out)
1029  show_density_header_line()
1030  """
1031  return _IMP_multifit.SettingsData_show_density_header_line(*args)
1032 
1033  show_density_header_line = staticmethod(show_density_header_line)
1034 
1035  def get_density_header_line():
1036  """get_density_header_line() -> std::string"""
1037  return _IMP_multifit.SettingsData_get_density_header_line()
1038 
1039  get_density_header_line = staticmethod(get_density_header_line)
1040 
1041  def set_assembly_filename(self, fn):
1042  """set_assembly_filename(SettingsData self, std::string const & fn)"""
1043  return _IMP_multifit.SettingsData_set_assembly_filename(self, fn)
1044 
1045 
1046  def get_assembly_filename(self):
1047  """get_assembly_filename(SettingsData self) -> char const *"""
1048  return _IMP_multifit.SettingsData_get_assembly_filename(self)
1049 
1050 
1051  def set_assembly_header(self, h):
1052  """set_assembly_header(SettingsData self, AssemblyHeader h)"""
1053  return _IMP_multifit.SettingsData_set_assembly_header(self, h)
1054 
1055 
1056  def get_assembly_header(self):
1057  """get_assembly_header(SettingsData self) -> AssemblyHeader"""
1058  return _IMP_multifit.SettingsData_get_assembly_header(self)
1059 
1060 
1061  def set_data_path(self, fn):
1062  """set_data_path(SettingsData self, std::string const & fn)"""
1063  return _IMP_multifit.SettingsData_set_data_path(self, fn)
1064 
1065 
1066  def get_data_path(self):
1067  """get_data_path(SettingsData self) -> std::string"""
1068  return _IMP_multifit.SettingsData_get_data_path(self)
1069 
1070 
1071  def get_version_info(self):
1072  """get_version_info(SettingsData self) -> VersionInfo"""
1073  return _IMP_multifit.SettingsData_get_version_info(self)
1074 
1075 
1076  def remove_component_header(self, d):
1077  """remove_component_header(SettingsData self, ComponentHeader d)"""
1078  return _IMP_multifit.SettingsData_remove_component_header(self, d)
1079 
1080 
1081  def remove_component_headers(self, d):
1082  """remove_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & d)"""
1083  return _IMP_multifit.SettingsData_remove_component_headers(self, d)
1084 
1085 
1086  def set_component_headers(self, ps):
1087  """set_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & ps)"""
1088  return _IMP_multifit.SettingsData_set_component_headers(self, ps)
1089 
1090 
1091  def set_component_headers_order(self, objs):
1092  """set_component_headers_order(SettingsData self, IMP::multifit::ComponentHeaders const & objs)"""
1093  return _IMP_multifit.SettingsData_set_component_headers_order(self, objs)
1094 
1095 
1096  def add_component_header(self, obj):
1097  """add_component_header(SettingsData self, ComponentHeader obj) -> unsigned int"""
1098  return _IMP_multifit.SettingsData_add_component_header(self, obj)
1099 
1100 
1101  def add_component_headers(self, objs):
1102  """add_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & objs)"""
1103  return _IMP_multifit.SettingsData_add_component_headers(self, objs)
1104 
1105 
1106  def clear_component_headers(self):
1107  """clear_component_headers(SettingsData self)"""
1108  return _IMP_multifit.SettingsData_clear_component_headers(self)
1109 
1110 
1111  def get_number_of_component_headers(self):
1112  """get_number_of_component_headers(SettingsData self) -> unsigned int"""
1113  return _IMP_multifit.SettingsData_get_number_of_component_headers(self)
1114 
1115 
1116  def get_has_component_headers(self):
1117  """get_has_component_headers(SettingsData self) -> bool"""
1118  return _IMP_multifit.SettingsData_get_has_component_headers(self)
1119 
1120 
1121  def get_component_header(self, i):
1122  """get_component_header(SettingsData self, unsigned int i) -> ComponentHeader"""
1123  return _IMP_multifit.SettingsData_get_component_header(self, i)
1124 
1125 
1126  def get_component_headers(self):
1127  """get_component_headers(SettingsData self) -> IMP::multifit::ComponentHeaders"""
1128  return _IMP_multifit.SettingsData_get_component_headers(self)
1129 
1130 
1131  def reserve_component_headers(self, sz):
1132  """reserve_component_headers(SettingsData self, unsigned int sz)"""
1133  return _IMP_multifit.SettingsData_reserve_component_headers(self, sz)
1134 
1135 
1136  def __str__(self):
1137  """__str__(SettingsData self) -> std::string"""
1138  return _IMP_multifit.SettingsData___str__(self)
1139 
1140 
1141  def __repr__(self):
1142  """__repr__(SettingsData self) -> std::string"""
1143  return _IMP_multifit.SettingsData___repr__(self)
1144 
1145 
1146  @staticmethod
1147  def get_from(o):
1148  return _object_cast_to_SettingsData(o)
1149 
1150 SettingsData_swigregister = _IMP_multifit.SettingsData_swigregister
1151 SettingsData_swigregister(SettingsData)
1152 
1153 def SettingsData_show_component_header_line(*args):
1154  """
1155  show_component_header_line(_ostream out)
1156  SettingsData_show_component_header_line()
1157  """
1158  return _IMP_multifit.SettingsData_show_component_header_line(*args)
1159 
1160 def SettingsData_get_component_header_line():
1161  """SettingsData_get_component_header_line() -> std::string"""
1162  return _IMP_multifit.SettingsData_get_component_header_line()
1163 
1164 def SettingsData_show_density_header_line(*args):
1165  """
1166  show_density_header_line(_ostream out)
1167  SettingsData_show_density_header_line()
1168  """
1169  return _IMP_multifit.SettingsData_show_density_header_line(*args)
1170 
1171 def SettingsData_get_density_header_line():
1172  """SettingsData_get_density_header_line() -> std::string"""
1173  return _IMP_multifit.SettingsData_get_density_header_line()
1174 
1175 
1176 def read_settings(filename):
1177  """read_settings(char const * filename) -> SettingsData"""
1178  return _IMP_multifit.read_settings(filename)
1179 
1180 def write_settings(filename, sd):
1181  """write_settings(char const * filename, SettingsData sd)"""
1182  return _IMP_multifit.write_settings(filename, sd)
1183 class WeightedExcludedVolumeRestraint(IMP.Restraint):
1184  """Proxy of C++ IMP::multifit::WeightedExcludedVolumeRestraint class."""
1185 
1186  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1187 
1188  def __init__(self, *args):
1189  """
1190  __init__(IMP::multifit::WeightedExcludedVolumeRestraint self, IMP::core::RigidBodies rbs, Refiner refiner, FloatKey weight_key) -> WeightedExcludedVolumeRestraint
1191  __init__(IMP::multifit::WeightedExcludedVolumeRestraint self, IMP::core::RigidBodies rbs, Refiner refiner) -> WeightedExcludedVolumeRestraint
1192  """
1193  this = _IMP_multifit.new_WeightedExcludedVolumeRestraint(*args)
1194  try:
1195  self.this.append(this)
1196  except __builtin__.Exception:
1197  self.this = this
1198 
1199  def do_get_inputs(self):
1200  """do_get_inputs(WeightedExcludedVolumeRestraint self) -> IMP::ModelObjectsTemp"""
1201  return _IMP_multifit.WeightedExcludedVolumeRestraint_do_get_inputs(self)
1202 
1203 
1204  def get_version_info(self):
1205  """get_version_info(WeightedExcludedVolumeRestraint self) -> VersionInfo"""
1206  return _IMP_multifit.WeightedExcludedVolumeRestraint_get_version_info(self)
1207 
1208 
1209  def __str__(self):
1210  """__str__(WeightedExcludedVolumeRestraint self) -> std::string"""
1211  return _IMP_multifit.WeightedExcludedVolumeRestraint___str__(self)
1212 
1213 
1214  def __repr__(self):
1215  """__repr__(WeightedExcludedVolumeRestraint self) -> std::string"""
1216  return _IMP_multifit.WeightedExcludedVolumeRestraint___repr__(self)
1217 
1218 
1219  @staticmethod
1220  def get_from(o):
1221  return _object_cast_to_WeightedExcludedVolumeRestraint(o)
1222 
1223 WeightedExcludedVolumeRestraint_swigregister = _IMP_multifit.WeightedExcludedVolumeRestraint_swigregister
1224 WeightedExcludedVolumeRestraint_swigregister(WeightedExcludedVolumeRestraint)
1225 
1226 class FFTFittingOutput(IMP.Object):
1227  """Proxy of C++ IMP::multifit::FFTFittingOutput class."""
1228 
1229  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1230 
1231  def __init__(self):
1232  """__init__(IMP::multifit::FFTFittingOutput self) -> FFTFittingOutput"""
1233  this = _IMP_multifit.new_FFTFittingOutput()
1234  try:
1235  self.this.append(this)
1236  except __builtin__.Exception:
1237  self.this = this
1238 
1239  def get_version_info(self):
1240  """get_version_info(FFTFittingOutput self) -> VersionInfo"""
1241  return _IMP_multifit.FFTFittingOutput_get_version_info(self)
1242 
1243  best_fits_ = _swig_property(_IMP_multifit.FFTFittingOutput_best_fits__get, _IMP_multifit.FFTFittingOutput_best_fits__set)
1244  best_trans_per_rot_ = _swig_property(_IMP_multifit.FFTFittingOutput_best_trans_per_rot__get, _IMP_multifit.FFTFittingOutput_best_trans_per_rot__set)
1245 
1246  def __str__(self):
1247  """__str__(FFTFittingOutput self) -> std::string"""
1248  return _IMP_multifit.FFTFittingOutput___str__(self)
1249 
1250 
1251  def __repr__(self):
1252  """__repr__(FFTFittingOutput self) -> std::string"""
1253  return _IMP_multifit.FFTFittingOutput___repr__(self)
1254 
1255 
1256  @staticmethod
1257  def get_from(o):
1258  return _object_cast_to_FFTFittingOutput(o)
1259 
1260 FFTFittingOutput_swigregister = _IMP_multifit.FFTFittingOutput_swigregister
1261 FFTFittingOutput_swigregister(FFTFittingOutput)
1262 
1263 class FFTFitting(IMP.Object):
1264  """Proxy of C++ IMP::multifit::FFTFitting class."""
1265 
1266  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1267 
1268  def get_version_info(self):
1269  """get_version_info(FFTFitting self) -> VersionInfo"""
1270  return _IMP_multifit.FFTFitting_get_version_info(self)
1271 
1272 
1273  def __init__(self):
1274  """__init__(IMP::multifit::FFTFitting self) -> FFTFitting"""
1275  this = _IMP_multifit.new_FFTFitting()
1276  try:
1277  self.this.append(this)
1278  except __builtin__.Exception:
1279  self.this = this
1280 
1281  def do_global_fitting(self, *args):
1282  """
1283  do_global_fitting(FFTFitting self, DensityMap dmap, double density_threshold, Hierarchy mol2fit, double angle_sampling_interval_rad, int num_fits_to_report, double max_clustering_translation, double max_clustering_angle, bool cluster_fits=True, int num_angle_per_voxel=1, std::string const & angles_filename) -> FFTFittingOutput
1284  do_global_fitting(FFTFitting self, DensityMap dmap, double density_threshold, Hierarchy mol2fit, double angle_sampling_interval_rad, int num_fits_to_report, double max_clustering_translation, double max_clustering_angle, bool cluster_fits=True, int num_angle_per_voxel=1) -> FFTFittingOutput
1285  do_global_fitting(FFTFitting self, DensityMap dmap, double density_threshold, Hierarchy mol2fit, double angle_sampling_interval_rad, int num_fits_to_report, double max_clustering_translation, double max_clustering_angle, bool cluster_fits=True) -> FFTFittingOutput
1286  do_global_fitting(FFTFitting self, DensityMap dmap, double density_threshold, Hierarchy mol2fit, double angle_sampling_interval_rad, int num_fits_to_report, double max_clustering_translation, double max_clustering_angle) -> FFTFittingOutput
1287  """
1288  return _IMP_multifit.FFTFitting_do_global_fitting(self, *args)
1289 
1290 
1291  def do_local_fitting(self, *args):
1292  """
1293  do_local_fitting(FFTFitting self, DensityMap dmap, double density_threshold, Hierarchy mol2fit, double angle_sampling_interval_rad, double max_angle_sampling_rad, double max_translation, int num_fits_to_report, bool cluster_fits, int num_angle_per_voxel, double max_clustering_translation, double max_clustering_rotation, std::string const & angles_filename) -> FFTFittingOutput
1294  do_local_fitting(FFTFitting self, DensityMap dmap, double density_threshold, Hierarchy mol2fit, double angle_sampling_interval_rad, double max_angle_sampling_rad, double max_translation, int num_fits_to_report, bool cluster_fits, int num_angle_per_voxel, double max_clustering_translation, double max_clustering_rotation) -> FFTFittingOutput
1295  """
1296  return _IMP_multifit.FFTFitting_do_local_fitting(self, *args)
1297 
1298 
1299  def __str__(self):
1300  """__str__(FFTFitting self) -> std::string"""
1301  return _IMP_multifit.FFTFitting___str__(self)
1302 
1303 
1304  def __repr__(self):
1305  """__repr__(FFTFitting self) -> std::string"""
1306  return _IMP_multifit.FFTFitting___repr__(self)
1307 
1308 
1309  @staticmethod
1310  def get_from(o):
1311  return _object_cast_to_FFTFitting(o)
1312 
1313 FFTFitting_swigregister = _IMP_multifit.FFTFitting_swigregister
1314 FFTFitting_swigregister(FFTFitting)
1315 
1316 
1317 def fft_based_rigid_fitting(mol2fit, dmap, density_threshold, angle_sampling_interval_rad):
1318  """fft_based_rigid_fitting(Hierarchy mol2fit, DensityMap dmap, double density_threshold, double angle_sampling_interval_rad) -> IMP::multifit::FittingSolutionRecords"""
1319  return _IMP_multifit.fft_based_rigid_fitting(mol2fit, dmap, density_threshold, angle_sampling_interval_rad)
1320 
1321 def remove_background(dmap, threshold, edge_threshold):
1322  """remove_background(DensityMap dmap, float threshold, float edge_threshold) -> DensityMap"""
1323  return _IMP_multifit.remove_background(dmap, threshold, edge_threshold)
1324 
1325 def get_connected_components(dmap, threshold, edge_threshold):
1326  """get_connected_components(DensityMap dmap, float threshold, float edge_threshold) -> IMP::IntsList"""
1327  return _IMP_multifit.get_connected_components(dmap, threshold, edge_threshold)
1328 
1329 def get_segmentation(dmap, apix, density_threshold, num_means, pdb_filename, cmm_filename, seg_filename, txt_filename):
1330  """get_segmentation(DensityMap dmap, double apix, double density_threshold, int num_means, std::string const pdb_filename, std::string const cmm_filename, std::string const seg_filename, std::string const txt_filename)"""
1331  return _IMP_multifit.get_segmentation(dmap, apix, density_threshold, num_means, pdb_filename, cmm_filename, seg_filename, txt_filename)
1332 class ComplementarityRestraint(IMP.Restraint):
1333  """Proxy of C++ IMP::multifit::ComplementarityRestraint class."""
1334 
1335  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1336 
1337  def __init__(self, *args):
1338  """
1339  __init__(IMP::multifit::ComplementarityRestraint self, IMP::ParticlesTemp const & a, IMP::ParticlesTemp const & b, std::string name) -> ComplementarityRestraint
1340  __init__(IMP::multifit::ComplementarityRestraint self, IMP::ParticlesTemp const & a, IMP::ParticlesTemp const & b) -> ComplementarityRestraint
1341  """
1342  this = _IMP_multifit.new_ComplementarityRestraint(*args)
1343  try:
1344  self.this.append(this)
1345  except __builtin__.Exception:
1346  self.this = this
1347 
1348  def set_maximum_penetration_score(self, s):
1349  """set_maximum_penetration_score(ComplementarityRestraint self, double s)"""
1350  return _IMP_multifit.ComplementarityRestraint_set_maximum_penetration_score(self, s)
1351 
1352 
1353  def set_maximum_penetration(self, d):
1354  """set_maximum_penetration(ComplementarityRestraint self, double d)"""
1355  return _IMP_multifit.ComplementarityRestraint_set_maximum_penetration(self, d)
1356 
1357 
1358  def set_maximum_separation(self, s):
1359  """set_maximum_separation(ComplementarityRestraint self, double s)"""
1360  return _IMP_multifit.ComplementarityRestraint_set_maximum_separation(self, s)
1361 
1362 
1363  def set_complementarity_thickness(self, th):
1364  """set_complementarity_thickness(ComplementarityRestraint self, double th)"""
1365  return _IMP_multifit.ComplementarityRestraint_set_complementarity_thickness(self, th)
1366 
1367 
1368  def set_complementarity_value(self, th):
1369  """set_complementarity_value(ComplementarityRestraint self, double th)"""
1370  return _IMP_multifit.ComplementarityRestraint_set_complementarity_value(self, th)
1371 
1372 
1373  def set_interior_layer_thickness(self, th):
1374  """set_interior_layer_thickness(ComplementarityRestraint self, double th)"""
1375  return _IMP_multifit.ComplementarityRestraint_set_interior_layer_thickness(self, th)
1376 
1377 
1378  def set_penetration_coefficient(self, pc):
1379  """set_penetration_coefficient(ComplementarityRestraint self, double pc)"""
1380  return _IMP_multifit.ComplementarityRestraint_set_penetration_coefficient(self, pc)
1381 
1382 
1383  def set_complementarity_coefficient(self, cc):
1384  """set_complementarity_coefficient(ComplementarityRestraint self, double cc)"""
1385  return _IMP_multifit.ComplementarityRestraint_set_complementarity_coefficient(self, cc)
1386 
1387 
1388  def set_boundary_coefficient(self, bc):
1389  """set_boundary_coefficient(ComplementarityRestraint self, double bc)"""
1390  return _IMP_multifit.ComplementarityRestraint_set_boundary_coefficient(self, bc)
1391 
1392 
1393  def get_voxel_size(self):
1394  """get_voxel_size(ComplementarityRestraint self) -> float"""
1395  return _IMP_multifit.ComplementarityRestraint_get_voxel_size(self)
1396 
1397 
1398  def do_get_inputs(self):
1399  """do_get_inputs(ComplementarityRestraint self) -> IMP::ModelObjectsTemp"""
1400  return _IMP_multifit.ComplementarityRestraint_do_get_inputs(self)
1401 
1402 
1403  def get_version_info(self):
1404  """get_version_info(ComplementarityRestraint self) -> VersionInfo"""
1405  return _IMP_multifit.ComplementarityRestraint_get_version_info(self)
1406 
1407 
1408  def __str__(self):
1409  """__str__(ComplementarityRestraint self) -> std::string"""
1410  return _IMP_multifit.ComplementarityRestraint___str__(self)
1411 
1412 
1413  def __repr__(self):
1414  """__repr__(ComplementarityRestraint self) -> std::string"""
1415  return _IMP_multifit.ComplementarityRestraint___repr__(self)
1416 
1417 
1418  @staticmethod
1419  def get_from(o):
1420  return _object_cast_to_ComplementarityRestraint(o)
1421 
1422 ComplementarityRestraint_swigregister = _IMP_multifit.ComplementarityRestraint_swigregister
1423 ComplementarityRestraint_swigregister(ComplementarityRestraint)
1424 
1425 
1426 def read_fitting_solutions(fitting_fn):
1427  """read_fitting_solutions(char const * fitting_fn) -> IMP::multifit::FittingSolutionRecords"""
1428  return _IMP_multifit.read_fitting_solutions(fitting_fn)
1429 
1430 def write_fitting_solutions(fitting_fn, fit_sols, num_sols=-1):
1431  """
1432  write_fitting_solutions(char const * fitting_fn, IMP::multifit::FittingSolutionRecords const & fit_sols, int num_sols=-1)
1433  write_fitting_solutions(char const * fitting_fn, IMP::multifit::FittingSolutionRecords const & fit_sols)
1434  """
1435  return _IMP_multifit.write_fitting_solutions(fitting_fn, fit_sols, num_sols)
1436 
1437 def convert_em_to_multifit_format(em_fits):
1438  """convert_em_to_multifit_format(FittingSolutions em_fits) -> IMP::multifit::FittingSolutionRecords"""
1439  return _IMP_multifit.convert_em_to_multifit_format(em_fits)
1440 
1441 def convert_multifit_to_em_format(multifit_fits):
1442  """convert_multifit_to_em_format(IMP::multifit::FittingSolutionRecords const & multifit_fits) -> FittingSolutions"""
1443  return _IMP_multifit.convert_multifit_to_em_format(multifit_fits)
1444 
1445 def convert_transformations_to_multifit_format(trans):
1446  """convert_transformations_to_multifit_format(IMP::algebra::Transformation3Ds const & trans) -> IMP::multifit::FittingSolutionRecords"""
1447  return _IMP_multifit.convert_transformations_to_multifit_format(trans)
1448 
1449 def convert_multifit_format_to_transformations(recs):
1450  """convert_multifit_format_to_transformations(IMP::multifit::FittingSolutionRecords const & recs) -> IMP::algebra::Transformation3Ds"""
1451  return _IMP_multifit.convert_multifit_format_to_transformations(recs)
1452 
1453 def get_close_to_point(fit_sols, mh, ap, dist):
1454  """get_close_to_point(IMP::multifit::FittingSolutionRecords const & fit_sols, Hierarchy mh, Particle ap, IMP::Float dist) -> IMP::multifit::FittingSolutionRecords"""
1455  return _IMP_multifit.get_close_to_point(fit_sols, mh, ap, dist)
1456 class ProbabilisticAnchorGraph(IMP.Object):
1457  """Proxy of C++ IMP::multifit::ProbabilisticAnchorGraph class."""
1458 
1459  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1460 
1461  def __init__(self, anchor_positions):
1462  """__init__(IMP::multifit::ProbabilisticAnchorGraph self, IMP::algebra::Vector3Ds anchor_positions) -> ProbabilisticAnchorGraph"""
1463  this = _IMP_multifit.new_ProbabilisticAnchorGraph(anchor_positions)
1464  try:
1465  self.this.append(this)
1466  except __builtin__.Exception:
1467  self.this = this
1468 
1469  def add_edge(self, i, j):
1470  """add_edge(ProbabilisticAnchorGraph self, int i, int j)"""
1471  return _IMP_multifit.ProbabilisticAnchorGraph_add_edge(self, i, j)
1472 
1473 
1474  def set_particle_probabilities_on_anchors(self, p, sols):
1475  """set_particle_probabilities_on_anchors(ProbabilisticAnchorGraph self, Particle p, IMP::multifit::FittingSolutionRecords sols)"""
1476  return _IMP_multifit.ProbabilisticAnchorGraph_set_particle_probabilities_on_anchors(self, p, sols)
1477 
1478 
1479  def show(self, *args):
1480  """
1481  show(ProbabilisticAnchorGraph self, _ostream out)
1482  show(ProbabilisticAnchorGraph self)
1483  """
1484  return _IMP_multifit.ProbabilisticAnchorGraph_show(self, *args)
1485 
1486 
1487  def get_number_of_anchors(self):
1488  """get_number_of_anchors(ProbabilisticAnchorGraph self) -> unsigned int"""
1489  return _IMP_multifit.ProbabilisticAnchorGraph_get_number_of_anchors(self)
1490 
1491 
1492  def get_number_of_edges(self):
1493  """get_number_of_edges(ProbabilisticAnchorGraph self) -> unsigned int"""
1494  return _IMP_multifit.ProbabilisticAnchorGraph_get_number_of_edges(self)
1495 
1496 
1497  def get_edge_list(self):
1498  """get_edge_list(ProbabilisticAnchorGraph self) -> IMP::IntRanges"""
1499  return _IMP_multifit.ProbabilisticAnchorGraph_get_edge_list(self)
1500 
1501 
1502  def get_anchors(self):
1503  """get_anchors(ProbabilisticAnchorGraph self) -> IMP::algebra::Vector3Ds"""
1504  return _IMP_multifit.ProbabilisticAnchorGraph_get_anchors(self)
1505 
1506 
1507  def get_particle_anchors(self, p, min_prob=0):
1508  """
1509  get_particle_anchors(ProbabilisticAnchorGraph self, Particle p, float min_prob=0) -> IMP::algebra::Vector3Ds
1510  get_particle_anchors(ProbabilisticAnchorGraph self, Particle p) -> IMP::algebra::Vector3Ds
1511  """
1512  return _IMP_multifit.ProbabilisticAnchorGraph_get_particle_anchors(self, p, min_prob)
1513 
1514 
1515  def get_are_probabilities_for_particle_set(self, p):
1516  """get_are_probabilities_for_particle_set(ProbabilisticAnchorGraph self, Particle p) -> bool"""
1517  return _IMP_multifit.ProbabilisticAnchorGraph_get_are_probabilities_for_particle_set(self, p)
1518 
1519 
1520  def get_particle_probabilities(self, p):
1521  """get_particle_probabilities(ProbabilisticAnchorGraph self, Particle p) -> IMP::Floats"""
1522  return _IMP_multifit.ProbabilisticAnchorGraph_get_particle_probabilities(self, p)
1523 
1524 
1525  def get_version_info(self):
1526  """get_version_info(ProbabilisticAnchorGraph self) -> VersionInfo"""
1527  return _IMP_multifit.ProbabilisticAnchorGraph_get_version_info(self)
1528 
1529 
1530  def __str__(self):
1531  """__str__(ProbabilisticAnchorGraph self) -> std::string"""
1532  return _IMP_multifit.ProbabilisticAnchorGraph___str__(self)
1533 
1534 
1535  def __repr__(self):
1536  """__repr__(ProbabilisticAnchorGraph self) -> std::string"""
1537  return _IMP_multifit.ProbabilisticAnchorGraph___repr__(self)
1538 
1539 
1540  @staticmethod
1541  def get_from(o):
1542  return _object_cast_to_ProbabilisticAnchorGraph(o)
1543 
1544 ProbabilisticAnchorGraph_swigregister = _IMP_multifit.ProbabilisticAnchorGraph_swigregister
1545 ProbabilisticAnchorGraph_swigregister(ProbabilisticAnchorGraph)
1546 
1547 class ProteinRecordData(object):
1548  """Proxy of C++ IMP::multifit::ProteinRecordData class."""
1549 
1550  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1551 
1552  def reset_all(self):
1553  """reset_all(ProteinRecordData self)"""
1554  return _IMP_multifit.ProteinRecordData_reset_all(self)
1555 
1556 
1557  def __init__(self, *args):
1558  """
1559  __init__(IMP::multifit::ProteinRecordData self) -> ProteinRecordData
1560  __init__(IMP::multifit::ProteinRecordData self, std::string const & name) -> ProteinRecordData
1561  __init__(IMP::multifit::ProteinRecordData self, std::string const & name, std::string const fn) -> ProteinRecordData
1562  __init__(IMP::multifit::ProteinRecordData self, std::string const & name, int start_res, int end_res, std::string const fn) -> ProteinRecordData
1563  __init__(IMP::multifit::ProteinRecordData self, std::string const & name, int start_res, int end_res, std::string const & fn, std::string const & surface_fn, std::string const & ref_fn) -> ProteinRecordData
1564  """
1565  this = _IMP_multifit.new_ProteinRecordData(*args)
1566  try:
1567  self.this.append(this)
1568  except __builtin__.Exception:
1569  self.this = this
1570 
1571  def show(self, *args):
1572  """
1573  show(ProteinRecordData self, _ostream out)
1574  show(ProteinRecordData self)
1575  """
1576  return _IMP_multifit.ProteinRecordData_show(self, *args)
1577 
1578  name_ = _swig_property(_IMP_multifit.ProteinRecordData_name__get, _IMP_multifit.ProteinRecordData_name__set)
1579  start_res_ = _swig_property(_IMP_multifit.ProteinRecordData_start_res__get, _IMP_multifit.ProteinRecordData_start_res__set)
1580  end_res_ = _swig_property(_IMP_multifit.ProteinRecordData_end_res__get, _IMP_multifit.ProteinRecordData_end_res__set)
1581  filename_ = _swig_property(_IMP_multifit.ProteinRecordData_filename__get, _IMP_multifit.ProteinRecordData_filename__set)
1582  surface_filename_ = _swig_property(_IMP_multifit.ProteinRecordData_surface_filename__get, _IMP_multifit.ProteinRecordData_surface_filename__set)
1583  ref_filename_ = _swig_property(_IMP_multifit.ProteinRecordData_ref_filename__get, _IMP_multifit.ProteinRecordData_ref_filename__set)
1584 
1585  def __str__(self):
1586  """__str__(ProteinRecordData self) -> std::string"""
1587  return _IMP_multifit.ProteinRecordData___str__(self)
1588 
1589 
1590  def __repr__(self):
1591  """__repr__(ProteinRecordData self) -> std::string"""
1592  return _IMP_multifit.ProteinRecordData___repr__(self)
1593 
1594  __swig_destroy__ = _IMP_multifit.delete_ProteinRecordData
1595  __del__ = lambda self: None
1596 ProteinRecordData_swigregister = _IMP_multifit.ProteinRecordData_swigregister
1597 ProteinRecordData_swigregister(ProteinRecordData)
1598 
1599 class ProteomicsData(IMP.Object):
1600  """Proxy of C++ IMP::multifit::ProteomicsData class."""
1601 
1602  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1603 
1604  def __init__(self):
1605  """__init__(IMP::multifit::ProteomicsData self) -> ProteomicsData"""
1606  this = _IMP_multifit.new_ProteomicsData()
1607  try:
1608  self.this.append(this)
1609  except __builtin__.Exception:
1610  self.this = this
1611 
1612  def add_protein(self, *args):
1613  """
1614  add_protein(ProteomicsData self, std::string name, int start_res, int end_res, std::string const & mol_fn, std::string const & surface_fn, std::string const & ref_fn) -> int
1615  add_protein(ProteomicsData self, ProteinRecordData rec) -> int
1616  """
1617  return _IMP_multifit.ProteomicsData_add_protein(self, *args)
1618 
1619 
1620  def find(self, name):
1621  """find(ProteomicsData self, std::string const & name) -> int"""
1622  return _IMP_multifit.ProteomicsData_find(self, name)
1623 
1624 
1625  def add_interaction(self, ii, used_for_filter, linker_len):
1626  """add_interaction(ProteomicsData self, IMP::Ints const & ii, bool used_for_filter, float linker_len)"""
1627  return _IMP_multifit.ProteomicsData_add_interaction(self, ii, used_for_filter, linker_len)
1628 
1629 
1630  def add_cross_link_interaction(self, prot1, res1, prot2, res2, used_in_filter, linker_len):
1631  """add_cross_link_interaction(ProteomicsData self, IMP::Int prot1, IMP::Int res1, IMP::Int prot2, IMP::Int res2, bool used_in_filter, IMP::Float linker_len)"""
1632  return _IMP_multifit.ProteomicsData_add_cross_link_interaction(self, prot1, res1, prot2, res2, used_in_filter, linker_len)
1633 
1634 
1635  def add_ev_pair(self, prot1, prot2):
1636  """add_ev_pair(ProteomicsData self, IMP::Int prot1, IMP::Int prot2)"""
1637  return _IMP_multifit.ProteomicsData_add_ev_pair(self, prot1, prot2)
1638 
1639 
1640  def get_number_of_proteins(self):
1641  """get_number_of_proteins(ProteomicsData self) -> int"""
1642  return _IMP_multifit.ProteomicsData_get_number_of_proteins(self)
1643 
1644 
1645  def get_number_of_interactions(self):
1646  """get_number_of_interactions(ProteomicsData self) -> int"""
1647  return _IMP_multifit.ProteomicsData_get_number_of_interactions(self)
1648 
1649 
1650  def get_interaction(self, interaction_ind):
1651  """get_interaction(ProteomicsData self, int interaction_ind) -> IMP::Ints"""
1652  return _IMP_multifit.ProteomicsData_get_interaction(self, interaction_ind)
1653 
1654 
1655  def get_interaction_part_of_filter(self, interaction_ind):
1656  """get_interaction_part_of_filter(ProteomicsData self, int interaction_ind) -> bool"""
1657  return _IMP_multifit.ProteomicsData_get_interaction_part_of_filter(self, interaction_ind)
1658 
1659 
1660  def get_interaction_linker_length(self, interaction_ind):
1661  """get_interaction_linker_length(ProteomicsData self, int interaction_ind) -> int"""
1662  return _IMP_multifit.ProteomicsData_get_interaction_linker_length(self, interaction_ind)
1663 
1664 
1665  def get_number_of_cross_links(self):
1666  """get_number_of_cross_links(ProteomicsData self) -> int"""
1667  return _IMP_multifit.ProteomicsData_get_number_of_cross_links(self)
1668 
1669 
1670  def get_cross_link(self, xlink_ind):
1671  """get_cross_link(ProteomicsData self, int xlink_ind) -> std::pair< IMP::IntPair,IMP::IntPair >"""
1672  return _IMP_multifit.ProteomicsData_get_cross_link(self, xlink_ind)
1673 
1674 
1675  def get_cross_link_part_of_filter(self, xlink_ind):
1676  """get_cross_link_part_of_filter(ProteomicsData self, int xlink_ind) -> bool"""
1677  return _IMP_multifit.ProteomicsData_get_cross_link_part_of_filter(self, xlink_ind)
1678 
1679 
1680  def get_cross_link_length(self, xlink_ind):
1681  """get_cross_link_length(ProteomicsData self, int xlink_ind) -> float"""
1682  return _IMP_multifit.ProteomicsData_get_cross_link_length(self, xlink_ind)
1683 
1684 
1685  def get_number_of_ev_pairs(self):
1686  """get_number_of_ev_pairs(ProteomicsData self) -> int"""
1687  return _IMP_multifit.ProteomicsData_get_number_of_ev_pairs(self)
1688 
1689 
1690  def get_ev_pair(self, ev_ind):
1691  """get_ev_pair(ProteomicsData self, int ev_ind) -> IMP::IntPair"""
1692  return _IMP_multifit.ProteomicsData_get_ev_pair(self, ev_ind)
1693 
1694 
1695  def get_protein_name(self, protein_ind):
1696  """get_protein_name(ProteomicsData self, int protein_ind) -> std::string"""
1697  return _IMP_multifit.ProteomicsData_get_protein_name(self, protein_ind)
1698 
1699 
1700  def get_end_res(self, protein_ind):
1701  """get_end_res(ProteomicsData self, int protein_ind) -> int"""
1702  return _IMP_multifit.ProteomicsData_get_end_res(self, protein_ind)
1703 
1704 
1705  def get_start_res(self, protein_ind):
1706  """get_start_res(ProteomicsData self, int protein_ind) -> int"""
1707  return _IMP_multifit.ProteomicsData_get_start_res(self, protein_ind)
1708 
1709 
1710  def get_protein_filename(self, protein_ind):
1711  """get_protein_filename(ProteomicsData self, int protein_ind) -> std::string"""
1712  return _IMP_multifit.ProteomicsData_get_protein_filename(self, protein_ind)
1713 
1714 
1715  def get_reference_filename(self, protein_ind):
1716  """get_reference_filename(ProteomicsData self, int protein_ind) -> std::string"""
1717  return _IMP_multifit.ProteomicsData_get_reference_filename(self, protein_ind)
1718 
1719 
1720  def get_surface_filename(self, protein_ind):
1721  """get_surface_filename(ProteomicsData self, int protein_ind) -> std::string"""
1722  return _IMP_multifit.ProteomicsData_get_surface_filename(self, protein_ind)
1723 
1724 
1725  def get_protein_data(self, protein_ind):
1726  """get_protein_data(ProteomicsData self, int protein_ind) -> ProteinRecordData"""
1727  return _IMP_multifit.ProteomicsData_get_protein_data(self, protein_ind)
1728 
1729 
1730  def get_version_info(self):
1731  """get_version_info(ProteomicsData self) -> VersionInfo"""
1732  return _IMP_multifit.ProteomicsData_get_version_info(self)
1733 
1734 
1735  def get_num_allowed_violated_interactions(self):
1736  """get_num_allowed_violated_interactions(ProteomicsData self) -> int"""
1737  return _IMP_multifit.ProteomicsData_get_num_allowed_violated_interactions(self)
1738 
1739 
1740  def set_num_allowed_violated_interactions(self, n):
1741  """set_num_allowed_violated_interactions(ProteomicsData self, int n)"""
1742  return _IMP_multifit.ProteomicsData_set_num_allowed_violated_interactions(self, n)
1743 
1744 
1745  def get_num_allowed_violated_cross_links(self):
1746  """get_num_allowed_violated_cross_links(ProteomicsData self) -> int"""
1747  return _IMP_multifit.ProteomicsData_get_num_allowed_violated_cross_links(self)
1748 
1749 
1750  def set_num_allowed_violated_cross_links(self, n):
1751  """set_num_allowed_violated_cross_links(ProteomicsData self, int n)"""
1752  return _IMP_multifit.ProteomicsData_set_num_allowed_violated_cross_links(self, n)
1753 
1754 
1755  def get_num_allowed_violated_ev(self):
1756  """get_num_allowed_violated_ev(ProteomicsData self) -> int"""
1757  return _IMP_multifit.ProteomicsData_get_num_allowed_violated_ev(self)
1758 
1759 
1760  def set_num_allowed_violated_ev(self, n):
1761  """set_num_allowed_violated_ev(ProteomicsData self, int n)"""
1762  return _IMP_multifit.ProteomicsData_set_num_allowed_violated_ev(self, n)
1763 
1764 
1765  def __str__(self):
1766  """__str__(ProteomicsData self) -> std::string"""
1767  return _IMP_multifit.ProteomicsData___str__(self)
1768 
1769 
1770  def __repr__(self):
1771  """__repr__(ProteomicsData self) -> std::string"""
1772  return _IMP_multifit.ProteomicsData___repr__(self)
1773 
1774 
1775  @staticmethod
1776  def get_from(o):
1777  return _object_cast_to_ProteomicsData(o)
1778 
1779 ProteomicsData_swigregister = _IMP_multifit.ProteomicsData_swigregister
1780 ProteomicsData_swigregister(ProteomicsData)
1781 
1782 
1783 def read_proteomics_data(proteomics_fn):
1784  """read_proteomics_data(char const * proteomics_fn) -> ProteomicsData"""
1785  return _IMP_multifit.read_proteomics_data(proteomics_fn)
1786 
1787 def get_partial_proteomics_data(pd, prot_names):
1788  """get_partial_proteomics_data(ProteomicsData pd, IMP::Strings const & prot_names) -> ProteomicsData"""
1789  return _IMP_multifit.get_partial_proteomics_data(pd, prot_names)
1790 class AnchorsData(object):
1791  """Proxy of C++ IMP::multifit::AnchorsData class."""
1792 
1793  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1794 
1795  def __init__(self, *args):
1796  """
1797  __init__(IMP::multifit::AnchorsData self) -> AnchorsData
1798  __init__(IMP::multifit::AnchorsData self, IMP::algebra::Vector3Ds points, IMP::IntPairs edges) -> AnchorsData
1799  """
1800  this = _IMP_multifit.new_AnchorsData(*args)
1801  try:
1802  self.this.append(this)
1803  except __builtin__.Exception:
1804  self.this = this
1805 
1806  def remove_edges_for_node(self, node_ind):
1807  """remove_edges_for_node(AnchorsData self, int node_ind)"""
1808  return _IMP_multifit.AnchorsData_remove_edges_for_node(self, node_ind)
1809 
1810 
1811  def get_number_of_points(self):
1812  """get_number_of_points(AnchorsData self) -> int"""
1813  return _IMP_multifit.AnchorsData_get_number_of_points(self)
1814 
1815 
1816  def get_number_of_edges(self):
1817  """get_number_of_edges(AnchorsData self) -> int"""
1818  return _IMP_multifit.AnchorsData_get_number_of_edges(self)
1819 
1820 
1821  def get_is_point_considered(self, node_ind):
1822  """get_is_point_considered(AnchorsData self, int node_ind) -> bool"""
1823  return _IMP_multifit.AnchorsData_get_is_point_considered(self, node_ind)
1824 
1825 
1826  def show(self, *args):
1827  """
1828  show(AnchorsData self, _ostream out)
1829  show(AnchorsData self)
1830  """
1831  return _IMP_multifit.AnchorsData_show(self, *args)
1832 
1833 
1834  def get_secondary_structure_is_set(self):
1835  """get_secondary_structure_is_set(AnchorsData self) -> bool"""
1836  return _IMP_multifit.AnchorsData_get_secondary_structure_is_set(self)
1837 
1838 
1839  def setup_secondary_structure(self, mdl):
1840  """setup_secondary_structure(AnchorsData self, Model mdl)"""
1841  return _IMP_multifit.AnchorsData_setup_secondary_structure(self, mdl)
1842 
1843 
1844  def set_secondary_structure_probabilities(self, *args):
1845  """
1846  set_secondary_structure_probabilities(AnchorsData self, IMP::Particles const & ssres_ps, IMP::Ints const & indices)
1847  set_secondary_structure_probabilities(AnchorsData self, IMP::Particles const & ssres_ps)
1848  """
1849  return _IMP_multifit.AnchorsData_set_secondary_structure_probabilities(self, *args)
1850 
1851 
1852  def get_secondary_structure_particles(self):
1853  """get_secondary_structure_particles(AnchorsData self) -> IMP::Particles"""
1854  return _IMP_multifit.AnchorsData_get_secondary_structure_particles(self)
1855 
1856  points_ = _swig_property(_IMP_multifit.AnchorsData_points__get, _IMP_multifit.AnchorsData_points__set)
1857  consider_point_ = _swig_property(_IMP_multifit.AnchorsData_consider_point__get, _IMP_multifit.AnchorsData_consider_point__set)
1858  edges_ = _swig_property(_IMP_multifit.AnchorsData_edges__get, _IMP_multifit.AnchorsData_edges__set)
1859 
1860  def __str__(self):
1861  """__str__(AnchorsData self) -> std::string"""
1862  return _IMP_multifit.AnchorsData___str__(self)
1863 
1864 
1865  def __repr__(self):
1866  """__repr__(AnchorsData self) -> std::string"""
1867  return _IMP_multifit.AnchorsData___repr__(self)
1868 
1869  __swig_destroy__ = _IMP_multifit.delete_AnchorsData
1870  __del__ = lambda self: None
1871 AnchorsData_swigregister = _IMP_multifit.AnchorsData_swigregister
1872 AnchorsData_swigregister(AnchorsData)
1873 
1874 
1875 def read_anchors_data(txt_filename):
1876  """read_anchors_data(char const * txt_filename) -> AnchorsData"""
1877  return _IMP_multifit.read_anchors_data(txt_filename)
1878 
1879 def write_txt(txt_filename, ad):
1880  """write_txt(std::string const & txt_filename, AnchorsData ad)"""
1881  return _IMP_multifit.write_txt(txt_filename, ad)
1882 
1883 def write_cmm(cmm_filename, marker_set_name, dpa):
1884  """write_cmm(std::string const & cmm_filename, std::string const & marker_set_name, AnchorsData dpa)"""
1885  return _IMP_multifit.write_cmm(cmm_filename, marker_set_name, dpa)
1886 
1887 def create_coarse_molecule_from_density(dmap, dens_threshold, num_beads, mdl, bead_radius):
1888  """create_coarse_molecule_from_density(DensityMap dmap, float dens_threshold, int num_beads, Model mdl, float bead_radius) -> Hierarchy"""
1889  return _IMP_multifit.create_coarse_molecule_from_density(dmap, dens_threshold, num_beads, mdl, bead_radius)
1890 
1891 def create_hit_map(rb, rb_ref, sols, damp):
1892  """create_hit_map(RigidBody rb, Refiner rb_ref, IMP::multifit::FittingSolutionRecords const & sols, DensityMap damp) -> DensityMap"""
1893  return _IMP_multifit.create_hit_map(rb, rb_ref, sols, damp)
1894 
1895 def get_points_close_to_molecule(mh, points, max_dist):
1896  """get_points_close_to_molecule(Hierarchy mh, IMP::algebra::Vector3Ds const points, IMP::Float max_dist) -> IMP::algebra::Vector3Ds"""
1897  return _IMP_multifit.get_points_close_to_molecule(mh, points, max_dist)
1898 
1899 def get_points_far_from_molecule(mh, points, max_dist):
1900  """get_points_far_from_molecule(Hierarchy mh, IMP::algebra::Vector3Ds const points, IMP::Float max_dist) -> IMP::algebra::Vector3Ds"""
1901  return _IMP_multifit.get_points_far_from_molecule(mh, points, max_dist)
1902 class RadiusOfGyrationRestraint(IMP.Restraint):
1903  """Proxy of C++ IMP::multifit::RadiusOfGyrationRestraint class."""
1904 
1905  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1906 
1907  def __init__(self, ps, num_residues, scale=1.):
1908  """
1909  __init__(IMP::multifit::RadiusOfGyrationRestraint self, IMP::Particles ps, int num_residues, IMP::Float scale=1.) -> RadiusOfGyrationRestraint
1910  __init__(IMP::multifit::RadiusOfGyrationRestraint self, IMP::Particles ps, int num_residues) -> RadiusOfGyrationRestraint
1911  """
1912  this = _IMP_multifit.new_RadiusOfGyrationRestraint(ps, num_residues, scale)
1913  try:
1914  self.this.append(this)
1915  except __builtin__.Exception:
1916  self.this = this
1917 
1918  def do_get_inputs(self):
1919  """do_get_inputs(RadiusOfGyrationRestraint self) -> IMP::ModelObjectsTemp"""
1920  return _IMP_multifit.RadiusOfGyrationRestraint_do_get_inputs(self)
1921 
1922 
1923  def get_version_info(self):
1924  """get_version_info(RadiusOfGyrationRestraint self) -> VersionInfo"""
1925  return _IMP_multifit.RadiusOfGyrationRestraint_get_version_info(self)
1926 
1927 
1928  def set_radius_of_gyration(self, r):
1929  """set_radius_of_gyration(RadiusOfGyrationRestraint self, IMP::Float r)"""
1930  return _IMP_multifit.RadiusOfGyrationRestraint_set_radius_of_gyration(self, r)
1931 
1932 
1933  def get_radius_of_gyration(self):
1934  """get_radius_of_gyration(RadiusOfGyrationRestraint self) -> IMP::Float"""
1935  return _IMP_multifit.RadiusOfGyrationRestraint_get_radius_of_gyration(self)
1936 
1937 
1938  def __str__(self):
1939  """__str__(RadiusOfGyrationRestraint self) -> std::string"""
1940  return _IMP_multifit.RadiusOfGyrationRestraint___str__(self)
1941 
1942 
1943  def __repr__(self):
1944  """__repr__(RadiusOfGyrationRestraint self) -> std::string"""
1945  return _IMP_multifit.RadiusOfGyrationRestraint___repr__(self)
1946 
1947 
1948  @staticmethod
1949  def get_from(o):
1950  return _object_cast_to_RadiusOfGyrationRestraint(o)
1951 
1952 RadiusOfGyrationRestraint_swigregister = _IMP_multifit.RadiusOfGyrationRestraint_swigregister
1953 RadiusOfGyrationRestraint_swigregister(RadiusOfGyrationRestraint)
1954 
1955 
1956 def get_approximated_radius_of_gyration(len):
1957  """get_approximated_radius_of_gyration(int len) -> float"""
1958  return _IMP_multifit.get_approximated_radius_of_gyration(len)
1959 
1960 def get_actual_radius_of_gyration(ps):
1961  """get_actual_radius_of_gyration(IMP::ParticlesTemp ps) -> float"""
1962  return _IMP_multifit.get_actual_radius_of_gyration(ps)
1963 
1964 def get_approximated_radius(len):
1965  """get_approximated_radius(int len) -> float"""
1966  return _IMP_multifit.get_approximated_radius(len)
1967 class ProteinsAnchorsSamplingSpace(object):
1968  """Proxy of C++ IMP::multifit::ProteinsAnchorsSamplingSpace class."""
1969 
1970  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1971 
1972  def __init__(self, prots=None):
1973  """
1974  __init__(IMP::multifit::ProteinsAnchorsSamplingSpace self, ProteomicsData prots=None) -> ProteinsAnchorsSamplingSpace
1975  __init__(IMP::multifit::ProteinsAnchorsSamplingSpace self) -> ProteinsAnchorsSamplingSpace
1976  """
1977  this = _IMP_multifit.new_ProteinsAnchorsSamplingSpace(prots)
1978  try:
1979  self.this.append(this)
1980  except __builtin__.Exception:
1981  self.this = this
1982 
1983  def set_anchors(self, data):
1984  """set_anchors(ProteinsAnchorsSamplingSpace self, AnchorsData data)"""
1985  return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_anchors(self, data)
1986 
1987 
1988  def get_anchors(self):
1989  """get_anchors(ProteinsAnchorsSamplingSpace self) -> AnchorsData"""
1990  return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_anchors(self)
1991 
1992 
1993  def get_anchors_filename(self):
1994  """get_anchors_filename(ProteinsAnchorsSamplingSpace self) -> std::string"""
1995  return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_anchors_filename(self)
1996 
1997 
1998  def set_anchors_filename(self, fn):
1999  """set_anchors_filename(ProteinsAnchorsSamplingSpace self, std::string const & fn)"""
2000  return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_anchors_filename(self, fn)
2001 
2002 
2003  def get_proteomics_data(self):
2004  """get_proteomics_data(ProteinsAnchorsSamplingSpace self) -> ProteomicsData"""
2005  return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_proteomics_data(self)
2006 
2007 
2008  def add_protein(self, rec):
2009  """add_protein(ProteinsAnchorsSamplingSpace self, ProteinRecordData rec)"""
2010  return _IMP_multifit.ProteinsAnchorsSamplingSpace_add_protein(self, rec)
2011 
2012 
2013  def get_paths_for_protein(self, prot_name):
2014  """get_paths_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name) -> IMP::IntsList"""
2015  return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_paths_for_protein(self, prot_name)
2016 
2017 
2018  def set_paths_filename_for_protein(self, prot_name, paths_filename):
2019  """set_paths_filename_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name, std::string const & paths_filename)"""
2020  return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_paths_filename_for_protein(self, prot_name, paths_filename)
2021 
2022 
2023  def get_paths_filename_for_protein(self, prot_name):
2024  """get_paths_filename_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name) -> std::string"""
2025  return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_paths_filename_for_protein(self, prot_name)
2026 
2027 
2028  def set_paths_for_protein(self, prot_name, paths):
2029  """set_paths_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name, IMP::IntsList paths)"""
2030  return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_paths_for_protein(self, prot_name, paths)
2031 
2032 
2033  def show(self, *args):
2034  """
2035  show(ProteinsAnchorsSamplingSpace self, _ostream s)
2036  show(ProteinsAnchorsSamplingSpace self)
2037  """
2038  return _IMP_multifit.ProteinsAnchorsSamplingSpace_show(self, *args)
2039 
2040 
2041  def __str__(self):
2042  """__str__(ProteinsAnchorsSamplingSpace self) -> std::string"""
2043  return _IMP_multifit.ProteinsAnchorsSamplingSpace___str__(self)
2044 
2045 
2046  def __repr__(self):
2047  """__repr__(ProteinsAnchorsSamplingSpace self) -> std::string"""
2048  return _IMP_multifit.ProteinsAnchorsSamplingSpace___repr__(self)
2049 
2050  __swig_destroy__ = _IMP_multifit.delete_ProteinsAnchorsSamplingSpace
2051  __del__ = lambda self: None
2052 ProteinsAnchorsSamplingSpace_swigregister = _IMP_multifit.ProteinsAnchorsSamplingSpace_swigregister
2053 ProteinsAnchorsSamplingSpace_swigregister(ProteinsAnchorsSamplingSpace)
2054 
2055 
2056 def read_protein_anchors_mapping(*args):
2057  """
2058  read_protein_anchors_mapping(ProteomicsData prots, std::string const & anchors_prot_map_fn, int max_paths) -> ProteinsAnchorsSamplingSpace
2059  read_protein_anchors_mapping(ProteomicsData prots, std::string const & anchors_prot_map_fn) -> ProteinsAnchorsSamplingSpace
2060  """
2061  return _IMP_multifit.read_protein_anchors_mapping(*args)
2062 
2063 def write_protein_anchors_mapping(*args):
2064  """
2065  write_protein_anchors_mapping(std::string const & anchors_prot_map_fn, std::string const & anchors_fn, std::vector< std::pair< IMP::String,IMP::String >,std::allocator< std::pair< IMP::String,IMP::String > > > const & prot_paths)
2066  write_protein_anchors_mapping(std::string const & anchors_prot_map_fn, ProteinsAnchorsSamplingSpace pa, IMP::Strings const & prot_names)
2067  """
2068  return _IMP_multifit.write_protein_anchors_mapping(*args)
2069 
2070 def get_part_of_sampling_space(prots_ss, prot_names):
2071  """get_part_of_sampling_space(ProteinsAnchorsSamplingSpace prots_ss, IMP::Strings const & prot_names) -> ProteinsAnchorsSamplingSpace"""
2072  return _IMP_multifit.get_part_of_sampling_space(prots_ss, prot_names)
2073 
2074 def get_partial_assembly_setting_data(prots_sd, prot_names):
2075  """get_partial_assembly_setting_data(SettingsData prots_sd, IMP::Strings const & prot_names) -> SettingsData"""
2076  return _IMP_multifit.get_partial_assembly_setting_data(prots_sd, prot_names)
2077 
2078 def read_paths(*args):
2079  """
2080  read_paths(char const * txt_filename, int max_paths) -> IMP::IntsList
2081  read_paths(char const * txt_filename) -> IMP::IntsList
2082  """
2083  return _IMP_multifit.read_paths(*args)
2084 
2085 def write_paths(paths, txt_filename):
2086  """write_paths(IMP::IntsList const & paths, std::string const & txt_filename)"""
2087  return _IMP_multifit.write_paths(paths, txt_filename)
2088 
2089 def molecule2anchors(mh, k):
2090  """molecule2anchors(Hierarchy mh, int k) -> AnchorsData"""
2091  return _IMP_multifit.molecule2anchors(mh, k)
2092 
2093 def get_anchors_for_density(dmap, number_of_means, density_threshold, pdb_filename, cmm_filename, seg_filename, txt_filename):
2094  """get_anchors_for_density(DensityMap dmap, int number_of_means, float density_threshold, std::string pdb_filename, std::string cmm_filename, std::string seg_filename, std::string txt_filename)"""
2095  return _IMP_multifit.get_anchors_for_density(dmap, number_of_means, density_threshold, pdb_filename, cmm_filename, seg_filename, txt_filename)
2096 
2097 def get_anchor_indices_matching_secondary_structure(ad, ssrs, max_rmsd=0.7):
2098  """
2099  get_anchor_indices_matching_secondary_structure(AnchorsData ad, IMP::atom::SecondaryStructureResidues const & ssrs, IMP::Float max_rmsd=0.7) -> IMP::IntsList
2100  get_anchor_indices_matching_secondary_structure(AnchorsData ad, IMP::atom::SecondaryStructureResidues const & ssrs) -> IMP::IntsList
2101  """
2102  return _IMP_multifit.get_anchor_indices_matching_secondary_structure(ad, ssrs, max_rmsd)
2103 class DominoParams(object):
2104  """Proxy of C++ IMP::multifit::DominoParams class."""
2105 
2106  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2107 
2108  def __init__(self):
2109  """__init__(IMP::multifit::DominoParams self) -> DominoParams"""
2110  this = _IMP_multifit.new_DominoParams()
2111  try:
2112  self.this.append(this)
2113  except __builtin__.Exception:
2114  self.this = this
2115 
2116  def add(self, pt):
2117  """add(DominoParams self, boost::property_tree::ptree const & pt)"""
2118  return _IMP_multifit.DominoParams_add(self, pt)
2119 
2120 
2121  def show(self, *args):
2122  """
2123  show(DominoParams self, _ostream s)
2124  show(DominoParams self)
2125  """
2126  return _IMP_multifit.DominoParams_show(self, *args)
2127 
2128  max_value_threshold_ = _swig_property(_IMP_multifit.DominoParams_max_value_threshold__get, _IMP_multifit.DominoParams_max_value_threshold__set)
2129  max_num_states_for_subset_ = _swig_property(_IMP_multifit.DominoParams_max_num_states_for_subset__get, _IMP_multifit.DominoParams_max_num_states_for_subset__set)
2130  max_anchor_penetration_ = _swig_property(_IMP_multifit.DominoParams_max_anchor_penetration__get, _IMP_multifit.DominoParams_max_anchor_penetration__set)
2131  heap_size_ = _swig_property(_IMP_multifit.DominoParams_heap_size__get, _IMP_multifit.DominoParams_heap_size__set)
2132  cache_size_ = _swig_property(_IMP_multifit.DominoParams_cache_size__get, _IMP_multifit.DominoParams_cache_size__set)
2133 
2134  def __str__(self):
2135  """__str__(DominoParams self) -> std::string"""
2136  return _IMP_multifit.DominoParams___str__(self)
2137 
2138 
2139  def __repr__(self):
2140  """__repr__(DominoParams self) -> std::string"""
2141  return _IMP_multifit.DominoParams___repr__(self)
2142 
2143  __swig_destroy__ = _IMP_multifit.delete_DominoParams
2144  __del__ = lambda self: None
2145 DominoParams_swigregister = _IMP_multifit.DominoParams_swigregister
2146 DominoParams_swigregister(DominoParams)
2147 
2148 class XlinkParams(object):
2149  """Proxy of C++ IMP::multifit::XlinkParams class."""
2150 
2151  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2152 
2153  def __init__(self):
2154  """__init__(IMP::multifit::XlinkParams self) -> XlinkParams"""
2155  this = _IMP_multifit.new_XlinkParams()
2156  try:
2157  self.this.append(this)
2158  except __builtin__.Exception:
2159  self.this = this
2160 
2161  def add(self, pt):
2162  """add(XlinkParams self, boost::property_tree::ptree const & pt)"""
2163  return _IMP_multifit.XlinkParams_add(self, pt)
2164 
2165 
2166  def show(self, *args):
2167  """
2168  show(XlinkParams self, _ostream s)
2169  show(XlinkParams self)
2170  """
2171  return _IMP_multifit.XlinkParams_show(self, *args)
2172 
2173  upper_bound_ = _swig_property(_IMP_multifit.XlinkParams_upper_bound__get, _IMP_multifit.XlinkParams_upper_bound__set)
2174  k_ = _swig_property(_IMP_multifit.XlinkParams_k__get, _IMP_multifit.XlinkParams_k__set)
2175  max_xlink_val_ = _swig_property(_IMP_multifit.XlinkParams_max_xlink_val__get, _IMP_multifit.XlinkParams_max_xlink_val__set)
2176  treat_between_residues_ = _swig_property(_IMP_multifit.XlinkParams_treat_between_residues__get, _IMP_multifit.XlinkParams_treat_between_residues__set)
2177 
2178  def __str__(self):
2179  """__str__(XlinkParams self) -> std::string"""
2180  return _IMP_multifit.XlinkParams___str__(self)
2181 
2182 
2183  def __repr__(self):
2184  """__repr__(XlinkParams self) -> std::string"""
2185  return _IMP_multifit.XlinkParams___repr__(self)
2186 
2187  __swig_destroy__ = _IMP_multifit.delete_XlinkParams
2188  __del__ = lambda self: None
2189 XlinkParams_swigregister = _IMP_multifit.XlinkParams_swigregister
2190 XlinkParams_swigregister(XlinkParams)
2191 
2192 class ConnectivityParams(object):
2193  """Proxy of C++ IMP::multifit::ConnectivityParams class."""
2194 
2195  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2196 
2197  def __init__(self):
2198  """__init__(IMP::multifit::ConnectivityParams self) -> ConnectivityParams"""
2199  this = _IMP_multifit.new_ConnectivityParams()
2200  try:
2201  self.this.append(this)
2202  except __builtin__.Exception:
2203  self.this = this
2204 
2205  def add(self, pt):
2206  """add(ConnectivityParams self, boost::property_tree::ptree const & pt)"""
2207  return _IMP_multifit.ConnectivityParams_add(self, pt)
2208 
2209 
2210  def show(self, *args):
2211  """
2212  show(ConnectivityParams self, _ostream s)
2213  show(ConnectivityParams self)
2214  """
2215  return _IMP_multifit.ConnectivityParams_show(self, *args)
2216 
2217  upper_bound_ = _swig_property(_IMP_multifit.ConnectivityParams_upper_bound__get, _IMP_multifit.ConnectivityParams_upper_bound__set)
2218  k_ = _swig_property(_IMP_multifit.ConnectivityParams_k__get, _IMP_multifit.ConnectivityParams_k__set)
2219  max_conn_rest_val_ = _swig_property(_IMP_multifit.ConnectivityParams_max_conn_rest_val__get, _IMP_multifit.ConnectivityParams_max_conn_rest_val__set)
2220 
2221  def __str__(self):
2222  """__str__(ConnectivityParams self) -> std::string"""
2223  return _IMP_multifit.ConnectivityParams___str__(self)
2224 
2225 
2226  def __repr__(self):
2227  """__repr__(ConnectivityParams self) -> std::string"""
2228  return _IMP_multifit.ConnectivityParams___repr__(self)
2229 
2230  __swig_destroy__ = _IMP_multifit.delete_ConnectivityParams
2231  __del__ = lambda self: None
2232 ConnectivityParams_swigregister = _IMP_multifit.ConnectivityParams_swigregister
2233 ConnectivityParams_swigregister(ConnectivityParams)
2234 
2235 class FragmentsParams(object):
2236  """Proxy of C++ IMP::multifit::FragmentsParams class."""
2237 
2238  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2239 
2240  def __init__(self):
2241  """__init__(IMP::multifit::FragmentsParams self) -> FragmentsParams"""
2242  this = _IMP_multifit.new_FragmentsParams()
2243  try:
2244  self.this.append(this)
2245  except __builtin__.Exception:
2246  self.this = this
2247 
2248  def add(self, pt):
2249  """add(FragmentsParams self, boost::property_tree::ptree const & pt)"""
2250  return _IMP_multifit.FragmentsParams_add(self, pt)
2251 
2252 
2253  def show(self, *args):
2254  """
2255  show(FragmentsParams self, _ostream s)
2256  show(FragmentsParams self)
2257  """
2258  return _IMP_multifit.FragmentsParams_show(self, *args)
2259 
2260  frag_len_ = _swig_property(_IMP_multifit.FragmentsParams_frag_len__get, _IMP_multifit.FragmentsParams_frag_len__set)
2261  bead_radius_scale_ = _swig_property(_IMP_multifit.FragmentsParams_bead_radius_scale__get, _IMP_multifit.FragmentsParams_bead_radius_scale__set)
2262  load_atomic_ = _swig_property(_IMP_multifit.FragmentsParams_load_atomic__get, _IMP_multifit.FragmentsParams_load_atomic__set)
2263  subunit_rigid_ = _swig_property(_IMP_multifit.FragmentsParams_subunit_rigid__get, _IMP_multifit.FragmentsParams_subunit_rigid__set)
2264 
2265  def __str__(self):
2266  """__str__(FragmentsParams self) -> std::string"""
2267  return _IMP_multifit.FragmentsParams___str__(self)
2268 
2269 
2270  def __repr__(self):
2271  """__repr__(FragmentsParams self) -> std::string"""
2272  return _IMP_multifit.FragmentsParams___repr__(self)
2273 
2274  __swig_destroy__ = _IMP_multifit.delete_FragmentsParams
2275  __del__ = lambda self: None
2276 FragmentsParams_swigregister = _IMP_multifit.FragmentsParams_swigregister
2277 FragmentsParams_swigregister(FragmentsParams)
2278 
2279 class RogParams(object):
2280  """Proxy of C++ IMP::multifit::RogParams class."""
2281 
2282  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2283 
2284  def __init__(self):
2285  """__init__(IMP::multifit::RogParams self) -> RogParams"""
2286  this = _IMP_multifit.new_RogParams()
2287  try:
2288  self.this.append(this)
2289  except __builtin__.Exception:
2290  self.this = this
2291 
2292  def add(self, pt):
2293  """add(RogParams self, boost::property_tree::ptree const & pt)"""
2294  return _IMP_multifit.RogParams_add(self, pt)
2295 
2296 
2297  def get_max_score(self):
2298  """get_max_score(RogParams self) -> float"""
2299  return _IMP_multifit.RogParams_get_max_score(self)
2300 
2301 
2302  def get_scale(self):
2303  """get_scale(RogParams self) -> float"""
2304  return _IMP_multifit.RogParams_get_scale(self)
2305 
2306 
2307  def show(self, *args):
2308  """
2309  show(RogParams self, _ostream s)
2310  show(RogParams self)
2311  """
2312  return _IMP_multifit.RogParams_show(self, *args)
2313 
2314 
2315  def __str__(self):
2316  """__str__(RogParams self) -> std::string"""
2317  return _IMP_multifit.RogParams___str__(self)
2318 
2319 
2320  def __repr__(self):
2321  """__repr__(RogParams self) -> std::string"""
2322  return _IMP_multifit.RogParams___repr__(self)
2323 
2324  __swig_destroy__ = _IMP_multifit.delete_RogParams
2325  __del__ = lambda self: None
2326 RogParams_swigregister = _IMP_multifit.RogParams_swigregister
2327 RogParams_swigregister(RogParams)
2328 
2329 class EVParams(object):
2330  """Proxy of C++ IMP::multifit::EVParams class."""
2331 
2332  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2333 
2334  def __init__(self):
2335  """__init__(IMP::multifit::EVParams self) -> EVParams"""
2336  this = _IMP_multifit.new_EVParams()
2337  try:
2338  self.this.append(this)
2339  except __builtin__.Exception:
2340  self.this = this
2341 
2342  def add(self, pt):
2343  """add(EVParams self, boost::property_tree::ptree const & pt)"""
2344  return _IMP_multifit.EVParams_add(self, pt)
2345 
2346 
2347  def show(self, *args):
2348  """
2349  show(EVParams self, _ostream s)
2350  show(EVParams self)
2351  """
2352  return _IMP_multifit.EVParams_show(self, *args)
2353 
2354  pair_distance_ = _swig_property(_IMP_multifit.EVParams_pair_distance__get, _IMP_multifit.EVParams_pair_distance__set)
2355  pair_slack_ = _swig_property(_IMP_multifit.EVParams_pair_slack__get, _IMP_multifit.EVParams_pair_slack__set)
2356  hlb_mean_ = _swig_property(_IMP_multifit.EVParams_hlb_mean__get, _IMP_multifit.EVParams_hlb_mean__set)
2357  hlb_k_ = _swig_property(_IMP_multifit.EVParams_hlb_k__get, _IMP_multifit.EVParams_hlb_k__set)
2358  maximum_ev_score_for_pair_ = _swig_property(_IMP_multifit.EVParams_maximum_ev_score_for_pair__get, _IMP_multifit.EVParams_maximum_ev_score_for_pair__set)
2359  allowed_percentage_of_bad_pairs_ = _swig_property(_IMP_multifit.EVParams_allowed_percentage_of_bad_pairs__get, _IMP_multifit.EVParams_allowed_percentage_of_bad_pairs__set)
2360  scoring_mode_ = _swig_property(_IMP_multifit.EVParams_scoring_mode__get, _IMP_multifit.EVParams_scoring_mode__set)
2361 
2362  def __str__(self):
2363  """__str__(EVParams self) -> std::string"""
2364  return _IMP_multifit.EVParams___str__(self)
2365 
2366 
2367  def __repr__(self):
2368  """__repr__(EVParams self) -> std::string"""
2369  return _IMP_multifit.EVParams___repr__(self)
2370 
2371  __swig_destroy__ = _IMP_multifit.delete_EVParams
2372  __del__ = lambda self: None
2373 EVParams_swigregister = _IMP_multifit.EVParams_swigregister
2374 EVParams_swigregister(EVParams)
2375 
2376 class FiltersParams(object):
2377  """Proxy of C++ IMP::multifit::FiltersParams class."""
2378 
2379  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2380 
2381  def __init__(self):
2382  """__init__(IMP::multifit::FiltersParams self) -> FiltersParams"""
2383  this = _IMP_multifit.new_FiltersParams()
2384  try:
2385  self.this.append(this)
2386  except __builtin__.Exception:
2387  self.this = this
2388 
2389  def add(self, pt):
2390  """add(FiltersParams self, boost::property_tree::ptree const & pt)"""
2391  return _IMP_multifit.FiltersParams_add(self, pt)
2392 
2393 
2394  def show(self, *args):
2395  """
2396  show(FiltersParams self, _ostream s)
2397  show(FiltersParams self)
2398  """
2399  return _IMP_multifit.FiltersParams_show(self, *args)
2400 
2401  max_num_violated_xlink_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_xlink__get, _IMP_multifit.FiltersParams_max_num_violated_xlink__set)
2402  max_num_violated_conn_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_conn__get, _IMP_multifit.FiltersParams_max_num_violated_conn__set)
2403  max_num_violated_ev_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_ev__get, _IMP_multifit.FiltersParams_max_num_violated_ev__set)
2404 
2405  def __str__(self):
2406  """__str__(FiltersParams self) -> std::string"""
2407  return _IMP_multifit.FiltersParams___str__(self)
2408 
2409 
2410  def __repr__(self):
2411  """__repr__(FiltersParams self) -> std::string"""
2412  return _IMP_multifit.FiltersParams___repr__(self)
2413 
2414  __swig_destroy__ = _IMP_multifit.delete_FiltersParams
2415  __del__ = lambda self: None
2416 FiltersParams_swigregister = _IMP_multifit.FiltersParams_swigregister
2417 FiltersParams_swigregister(FiltersParams)
2418 
2419 class FittingParams(object):
2420  """Proxy of C++ IMP::multifit::FittingParams class."""
2421 
2422  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2423 
2424  def __init__(self):
2425  """__init__(IMP::multifit::FittingParams self) -> FittingParams"""
2426  this = _IMP_multifit.new_FittingParams()
2427  try:
2428  self.this.append(this)
2429  except __builtin__.Exception:
2430  self.this = this
2431 
2432  def add(self, pt):
2433  """add(FittingParams self, boost::property_tree::ptree const & pt)"""
2434  return _IMP_multifit.FittingParams_add(self, pt)
2435 
2436 
2437  def show(self, *args):
2438  """
2439  show(FittingParams self, _ostream s)
2440  show(FittingParams self)
2441  """
2442  return _IMP_multifit.FittingParams_show(self, *args)
2443 
2444  pca_max_angle_diff_ = _swig_property(_IMP_multifit.FittingParams_pca_max_angle_diff__get, _IMP_multifit.FittingParams_pca_max_angle_diff__set)
2445  pca_max_size_diff_ = _swig_property(_IMP_multifit.FittingParams_pca_max_size_diff__get, _IMP_multifit.FittingParams_pca_max_size_diff__set)
2446  pca_max_cent_dist_diff_ = _swig_property(_IMP_multifit.FittingParams_pca_max_cent_dist_diff__get, _IMP_multifit.FittingParams_pca_max_cent_dist_diff__set)
2447  max_asmb_fit_score_ = _swig_property(_IMP_multifit.FittingParams_max_asmb_fit_score__get, _IMP_multifit.FittingParams_max_asmb_fit_score__set)
2448 
2449  def __str__(self):
2450  """__str__(FittingParams self) -> std::string"""
2451  return _IMP_multifit.FittingParams___str__(self)
2452 
2453 
2454  def __repr__(self):
2455  """__repr__(FittingParams self) -> std::string"""
2456  return _IMP_multifit.FittingParams___repr__(self)
2457 
2458  __swig_destroy__ = _IMP_multifit.delete_FittingParams
2459  __del__ = lambda self: None
2460 FittingParams_swigregister = _IMP_multifit.FittingParams_swigregister
2461 FittingParams_swigregister(FittingParams)
2462 
2463 class ComplementarityParams(object):
2464  """Proxy of C++ IMP::multifit::ComplementarityParams class."""
2465 
2466  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2467 
2468  def __init__(self):
2469  """__init__(IMP::multifit::ComplementarityParams self) -> ComplementarityParams"""
2470  this = _IMP_multifit.new_ComplementarityParams()
2471  try:
2472  self.this.append(this)
2473  except __builtin__.Exception:
2474  self.this = this
2475 
2476  def add(self, pt):
2477  """add(ComplementarityParams self, boost::property_tree::ptree const & pt)"""
2478  return _IMP_multifit.ComplementarityParams_add(self, pt)
2479 
2480 
2481  def show(self, *args):
2482  """
2483  show(ComplementarityParams self, _ostream s)
2484  show(ComplementarityParams self)
2485  """
2486  return _IMP_multifit.ComplementarityParams_show(self, *args)
2487 
2488  max_score_ = _swig_property(_IMP_multifit.ComplementarityParams_max_score__get, _IMP_multifit.ComplementarityParams_max_score__set)
2489  max_penetration_ = _swig_property(_IMP_multifit.ComplementarityParams_max_penetration__get, _IMP_multifit.ComplementarityParams_max_penetration__set)
2490  interior_layer_thickness_ = _swig_property(_IMP_multifit.ComplementarityParams_interior_layer_thickness__get, _IMP_multifit.ComplementarityParams_interior_layer_thickness__set)
2491  boundary_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_boundary_coef__get, _IMP_multifit.ComplementarityParams_boundary_coef__set)
2492  comp_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_comp_coef__get, _IMP_multifit.ComplementarityParams_comp_coef__set)
2493  penetration_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_penetration_coef__get, _IMP_multifit.ComplementarityParams_penetration_coef__set)
2494 
2495  def __str__(self):
2496  """__str__(ComplementarityParams self) -> std::string"""
2497  return _IMP_multifit.ComplementarityParams___str__(self)
2498 
2499 
2500  def __repr__(self):
2501  """__repr__(ComplementarityParams self) -> std::string"""
2502  return _IMP_multifit.ComplementarityParams___repr__(self)
2503 
2504  __swig_destroy__ = _IMP_multifit.delete_ComplementarityParams
2505  __del__ = lambda self: None
2506 ComplementarityParams_swigregister = _IMP_multifit.ComplementarityParams_swigregister
2507 ComplementarityParams_swigregister(ComplementarityParams)
2508 
2509 class AlignmentParams(object):
2510  """Proxy of C++ IMP::multifit::AlignmentParams class."""
2511 
2512  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2513 
2514  def __init__(self, param_filename):
2515  """__init__(IMP::multifit::AlignmentParams self, char const * param_filename) -> AlignmentParams"""
2516  this = _IMP_multifit.new_AlignmentParams(param_filename)
2517  try:
2518  self.this.append(this)
2519  except __builtin__.Exception:
2520  self.this = this
2521 
2522  def get_domino_params(self):
2523  """get_domino_params(AlignmentParams self) -> DominoParams"""
2524  return _IMP_multifit.AlignmentParams_get_domino_params(self)
2525 
2526 
2527  def get_fitting_params(self):
2528  """get_fitting_params(AlignmentParams self) -> FittingParams"""
2529  return _IMP_multifit.AlignmentParams_get_fitting_params(self)
2530 
2531 
2532  def get_complementarity_params(self):
2533  """get_complementarity_params(AlignmentParams self) -> ComplementarityParams"""
2534  return _IMP_multifit.AlignmentParams_get_complementarity_params(self)
2535 
2536 
2537  def get_xlink_params(self):
2538  """get_xlink_params(AlignmentParams self) -> XlinkParams"""
2539  return _IMP_multifit.AlignmentParams_get_xlink_params(self)
2540 
2541 
2542  def get_connectivity_params(self):
2543  """get_connectivity_params(AlignmentParams self) -> ConnectivityParams"""
2544  return _IMP_multifit.AlignmentParams_get_connectivity_params(self)
2545 
2546 
2547  def get_rog_params(self):
2548  """get_rog_params(AlignmentParams self) -> RogParams"""
2549  return _IMP_multifit.AlignmentParams_get_rog_params(self)
2550 
2551 
2552  def get_fragments_params(self):
2553  """get_fragments_params(AlignmentParams self) -> FragmentsParams"""
2554  return _IMP_multifit.AlignmentParams_get_fragments_params(self)
2555 
2556 
2557  def get_filters_params(self):
2558  """get_filters_params(AlignmentParams self) -> FiltersParams"""
2559  return _IMP_multifit.AlignmentParams_get_filters_params(self)
2560 
2561 
2562  def get_ev_params(self):
2563  """get_ev_params(AlignmentParams self) -> EVParams"""
2564  return _IMP_multifit.AlignmentParams_get_ev_params(self)
2565 
2566 
2567  def show(self, *args):
2568  """
2569  show(AlignmentParams self, _ostream s)
2570  show(AlignmentParams self)
2571  """
2572  return _IMP_multifit.AlignmentParams_show(self, *args)
2573 
2574 
2575  def __str__(self):
2576  """__str__(AlignmentParams self) -> std::string"""
2577  return _IMP_multifit.AlignmentParams___str__(self)
2578 
2579 
2580  def __repr__(self):
2581  """__repr__(AlignmentParams self) -> std::string"""
2582  return _IMP_multifit.AlignmentParams___repr__(self)
2583 
2584  __swig_destroy__ = _IMP_multifit.delete_AlignmentParams
2585  __del__ = lambda self: None
2586 AlignmentParams_swigregister = _IMP_multifit.AlignmentParams_swigregister
2587 AlignmentParams_swigregister(AlignmentParams)
2588 
2589 class ProteomicsEMAlignmentAtomic(IMP.Object):
2590  """Proxy of C++ IMP::multifit::ProteomicsEMAlignmentAtomic class."""
2591 
2592  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2593 
2594  def __init__(self, mapping_data, asmb_data, align_param):
2595  """__init__(IMP::multifit::ProteomicsEMAlignmentAtomic self, ProteinsAnchorsSamplingSpace mapping_data, SettingsData asmb_data, AlignmentParams align_param) -> ProteomicsEMAlignmentAtomic"""
2596  this = _IMP_multifit.new_ProteomicsEMAlignmentAtomic(mapping_data, asmb_data, align_param)
2597  try:
2598  self.this.append(this)
2599  except __builtin__.Exception:
2600  self.this = this
2601 
2602  def align(self):
2603  """align(ProteomicsEMAlignmentAtomic self)"""
2604  return _IMP_multifit.ProteomicsEMAlignmentAtomic_align(self)
2605 
2606 
2607  def add_all_restraints(self):
2608  """add_all_restraints(ProteomicsEMAlignmentAtomic self)"""
2609  return _IMP_multifit.ProteomicsEMAlignmentAtomic_add_all_restraints(self)
2610 
2611 
2612  def get_restraint_set(self):
2613  """get_restraint_set(ProteomicsEMAlignmentAtomic self) -> RestraintSet"""
2614  return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_restraint_set(self)
2615 
2616 
2617  def add_states_and_filters(self):
2618  """add_states_and_filters(ProteomicsEMAlignmentAtomic self)"""
2619  return _IMP_multifit.ProteomicsEMAlignmentAtomic_add_states_and_filters(self)
2620 
2621 
2622  def show_domino_merge_tree(self):
2623  """show_domino_merge_tree(ProteomicsEMAlignmentAtomic self)"""
2624  return _IMP_multifit.ProteomicsEMAlignmentAtomic_show_domino_merge_tree(self)
2625 
2626 
2627  def get_combinations(self, uniques=False):
2628  """
2629  get_combinations(ProteomicsEMAlignmentAtomic self, bool uniques=False) -> IMP::domino::Assignments
2630  get_combinations(ProteomicsEMAlignmentAtomic self) -> IMP::domino::Assignments
2631  """
2632  return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_combinations(self, uniques)
2633 
2634 
2635  def set_density_map(self, dmap, threshold):
2636  """set_density_map(ProteomicsEMAlignmentAtomic self, DensityMap dmap, float threshold)"""
2637  return _IMP_multifit.ProteomicsEMAlignmentAtomic_set_density_map(self, dmap, threshold)
2638 
2639 
2640  def get_molecules(self):
2641  """get_molecules(ProteomicsEMAlignmentAtomic self) -> IMP::atom::Hierarchies"""
2642  return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_molecules(self)
2643 
2644 
2645  def get_rigid_bodies(self):
2646  """get_rigid_bodies(ProteomicsEMAlignmentAtomic self) -> IMP::core::RigidBodies"""
2647  return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_rigid_bodies(self)
2648 
2649 
2650  def load_combination_of_states(self, state4particles):
2651  """load_combination_of_states(ProteomicsEMAlignmentAtomic self, IMP::Ints const & state4particles)"""
2652  return _IMP_multifit.ProteomicsEMAlignmentAtomic_load_combination_of_states(self, state4particles)
2653 
2654 
2655  def show_scores_header(self, *args):
2656  """
2657  show_scores_header(ProteomicsEMAlignmentAtomic self, _ostream ous)
2658  show_scores_header(ProteomicsEMAlignmentAtomic self)
2659  """
2660  return _IMP_multifit.ProteomicsEMAlignmentAtomic_show_scores_header(self, *args)
2661 
2662 
2663  def get_model(self):
2664  """get_model(ProteomicsEMAlignmentAtomic self) -> Model"""
2665  return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_model(self)
2666 
2667 
2668  def set_fast_scoring(self, state):
2669  """set_fast_scoring(ProteomicsEMAlignmentAtomic self, bool state)"""
2670  return _IMP_multifit.ProteomicsEMAlignmentAtomic_set_fast_scoring(self, state)
2671 
2672 
2673  def get_version_info(self):
2674  """get_version_info(ProteomicsEMAlignmentAtomic self) -> VersionInfo"""
2675  return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_version_info(self)
2676 
2677 
2678  def __str__(self):
2679  """__str__(ProteomicsEMAlignmentAtomic self) -> std::string"""
2680  return _IMP_multifit.ProteomicsEMAlignmentAtomic___str__(self)
2681 
2682 
2683  def __repr__(self):
2684  """__repr__(ProteomicsEMAlignmentAtomic self) -> std::string"""
2685  return _IMP_multifit.ProteomicsEMAlignmentAtomic___repr__(self)
2686 
2687 
2688  @staticmethod
2689  def get_from(o):
2690  return _object_cast_to_ProteomicsEMAlignmentAtomic(o)
2691 
2692 ProteomicsEMAlignmentAtomic_swigregister = _IMP_multifit.ProteomicsEMAlignmentAtomic_swigregister
2693 ProteomicsEMAlignmentAtomic_swigregister(ProteomicsEMAlignmentAtomic)
2694 
2695 
2696 def write_connolly_surface(atoms, fn, density, probe_radius):
2697  """write_connolly_surface(IMP::atom::Atoms atoms, TextOutput fn, float density, float probe_radius)"""
2698  return _IMP_multifit.write_connolly_surface(atoms, fn, density, probe_radius)
2699 class Ensemble(IMP.Object):
2700  """Proxy of C++ IMP::multifit::Ensemble class."""
2701 
2702  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2703 
2704  def load_combination(self, fit_comb):
2705  """load_combination(Ensemble self, IMP::Ints fit_comb)"""
2706  return _IMP_multifit.Ensemble_load_combination(self, fit_comb)
2707 
2708 
2709  def unload_combination(self, fit_comb):
2710  """unload_combination(Ensemble self, IMP::Ints fit_comb)"""
2711  return _IMP_multifit.Ensemble_unload_combination(self, fit_comb)
2712 
2713 
2714  def add_component_and_fits(self, mh, fits):
2715  """add_component_and_fits(Ensemble self, Hierarchy mh, IMP::multifit::FittingSolutionRecords const & fits)"""
2716  return _IMP_multifit.Ensemble_add_component_and_fits(self, mh, fits)
2717 
2718 
2719  def get_molecules(self):
2720  """get_molecules(Ensemble self) -> IMP::atom::Hierarchies"""
2721  return _IMP_multifit.Ensemble_get_molecules(self)
2722 
2723 
2724  def get_rigid_bodies(self):
2725  """get_rigid_bodies(Ensemble self) -> IMP::core::RigidBodies"""
2726  return _IMP_multifit.Ensemble_get_rigid_bodies(self)
2727 
2728 
2729  def get_rmsd(self, second_xyz):
2730  """get_rmsd(Ensemble self, IMP::core::XYZs const & second_xyz) -> float"""
2731  return _IMP_multifit.Ensemble_get_rmsd(self, second_xyz)
2732 
2733 
2734  def __init__(self, sd, mapping_data):
2735  """__init__(IMP::multifit::Ensemble self, SettingsData sd, ProteinsAnchorsSamplingSpace mapping_data) -> Ensemble"""
2736  this = _IMP_multifit.new_Ensemble(sd, mapping_data)
2737  try:
2738  self.this.append(this)
2739  except __builtin__.Exception:
2740  self.this = this
2741 
2742  def score_by_restraints(self, rs, combinations):
2743  """score_by_restraints(Ensemble self, IMP::Restraints rs, IMP::IntsList const & combinations) -> std::vector< IMP::Floats,std::allocator< IMP::Floats > >"""
2744  return _IMP_multifit.Ensemble_score_by_restraints(self, rs, combinations)
2745 
2746 
2747  def get_version_info(self):
2748  """get_version_info(Ensemble self) -> VersionInfo"""
2749  return _IMP_multifit.Ensemble_get_version_info(self)
2750 
2751 
2752  def __str__(self):
2753  """__str__(Ensemble self) -> std::string"""
2754  return _IMP_multifit.Ensemble___str__(self)
2755 
2756 
2757  def __repr__(self):
2758  """__repr__(Ensemble self) -> std::string"""
2759  return _IMP_multifit.Ensemble___repr__(self)
2760 
2761 
2762  @staticmethod
2763  def get_from(o):
2764  return _object_cast_to_Ensemble(o)
2765 
2766 Ensemble_swigregister = _IMP_multifit.Ensemble_swigregister
2767 Ensemble_swigregister(Ensemble)
2768 
2769 
2770 def load_ensemble(sd, mdl, mapping_data):
2771  """load_ensemble(SettingsData sd, Model mdl, ProteinsAnchorsSamplingSpace mapping_data) -> Ensemble"""
2772  return _IMP_multifit.load_ensemble(sd, mdl, mapping_data)
2773 class RigidLeavesRefiner(IMP.Refiner):
2774  """Proxy of C++ IMP::multifit::RigidLeavesRefiner class."""
2775 
2776  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2777 
2778  def __init__(self, *args):
2779  """
2780  __init__(IMP::multifit::RigidLeavesRefiner self, std::string name) -> RigidLeavesRefiner
2781  __init__(IMP::multifit::RigidLeavesRefiner self) -> RigidLeavesRefiner
2782  """
2783  this = _IMP_multifit.new_RigidLeavesRefiner(*args)
2784  try:
2785  self.this.append(this)
2786  except __builtin__.Exception:
2787  self.this = this
2788 
2789  def do_get_inputs(self, m, pis):
2790  """do_get_inputs(RigidLeavesRefiner self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2791  return _IMP_multifit.RigidLeavesRefiner_do_get_inputs(self, m, pis)
2792 
2793 
2794  def get_version_info(self):
2795  """get_version_info(RigidLeavesRefiner self) -> VersionInfo"""
2796  return _IMP_multifit.RigidLeavesRefiner_get_version_info(self)
2797 
2798 
2799  def __str__(self):
2800  """__str__(RigidLeavesRefiner self) -> std::string"""
2801  return _IMP_multifit.RigidLeavesRefiner___str__(self)
2802 
2803 
2804  def __repr__(self):
2805  """__repr__(RigidLeavesRefiner self) -> std::string"""
2806  return _IMP_multifit.RigidLeavesRefiner___repr__(self)
2807 
2808 
2809  @staticmethod
2810  def get_from(o):
2811  return _object_cast_to_RigidLeavesRefiner(o)
2812 
2813 RigidLeavesRefiner_swigregister = _IMP_multifit.RigidLeavesRefiner_swigregister
2814 RigidLeavesRefiner_swigregister(RigidLeavesRefiner)
2815 
2816 
2817 _all_commands = ["param", "anchors", "fit_fft", "cluster", "add_fit_rmsd",
2818  "indexes", "proteomics", "align", "models", "transforms",
2819  "score", "merge_tree", "reference", "refine_fft", "segment"]
2820 
2821 
2822 def get_module_version():
2823  """get_module_version() -> std::string const"""
2824  return _IMP_multifit.get_module_version()
2825 
2826 def get_example_path(fname):
2827  """get_example_path(std::string fname) -> std::string"""
2828  return _IMP_multifit.get_example_path(fname)
2829 
2830 def get_data_path(fname):
2831  """get_data_path(std::string fname) -> std::string"""
2832  return _IMP_multifit.get_data_path(fname)
2833 
2834 from . import _version_check
2835 _version_check.check_version(get_module_version())
2836 __version__ = get_module_version()
2837 
2838 
2839 
IntsList get_anchor_indices_matching_secondary_structure(const AnchorsData &ad, const atom::SecondaryStructureResidues &ssrs, Float max_rmsd=0.7)
Get lists of anchors that match a sequence of secondary structures.
FittingSolutionRecords get_close_to_point(const FittingSolutionRecords &fit_sols, atom::Hierarchy mh, IMP::Particle *ap, Float dist)
prune solutions by distance to an anchor point
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
IntsList get_connected_components(em::DensityMap *dmap, float threshold, float edge_threshold)
Return connected components based on density values.
Various classes to hold sets of particles.
Make CGAL functionality available to IMP.
em::DensityMap * remove_background(em::DensityMap *dmap, float threshold, float edge_threshold)
Returns a map containing all density without the background.
ProteinsAnchorsSamplingSpace get_part_of_sampling_space(const ProteinsAnchorsSamplingSpace &prots_ss, const Strings &prot_names)
Get the sampling space of few of the proteins.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
multifit::SettingsData * get_partial_assembly_setting_data(multifit::SettingsData *prots_sd, const Strings &prot_names)
Get the assembly data for a few of the proteins.
Composable functors to implement scores via compile-time composition.
em::FittingSolutions pca_based_rigid_fitting(core::RigidBody rb, Refiner *rb_refiner, em::DensityMap *em_map, Float threshold, FloatKey wei_key=atom::Mass::get_mass_key(), algebra::PrincipalComponentAnalysis dens_pca_input=algebra::PrincipalComponentAnalysis())
Compute fitting scores for a given set of rigid transformations.
Code to compute statistical measures.
void add_surface_index(core::Hierarchy mhd, Float apix, FloatKey shell_key=FloatKey("surf_ind"), FloatKey radius_key=core::XYZR::get_radius_key(), FloatKey weight_key=atom::Mass::get_mass_key())
Add shell index to leaves.
Ints get_index(const ParticlesTemp &particles, const Subset &subset, const Subsets &excluded)
Common base class for heavy weight IMP objects.
Definition: Object.h:106
void get_anchors_for_density(em::DensityMap *dmap, int number_of_means, float density_threshold, std::string pdb_filename, std::string cmm_filename, std::string seg_filename, std::string txt_filename)
Generate anchors in several formats for a given density map.
double get_rmsd(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
double get_radius_of_gyration(const Vector3Ds &ps)
Return the radius of gyration of a set of points.
Definition: Vector3D.h:77
Basic utilities for handling cryo-electron microscopy 3D density maps.
void write_fitting_solutions(const char *fitting_fn, const FittingSolutionRecords &fit_sols, int num_sols=-1)
Write fitting solutions to a file.
ProteomicsData * read_proteomics_data(const char *proteomics_fn)
Proteomics reader.
IMP::Restraint * create_weighted_excluded_volume_restraint(core::RigidBody rb1, core::RigidBody rb2, FloatKey shell_key=FloatKey("surf_ind"))
Create a weighted excluded volume restraint between two rigid bodies.
algebra::Vector3Ds get_points_close_to_molecule(const atom::Hierarchy &mh, const algebra::Vector3Ds points, Float max_dist)
void get_segmentation(em::DensityMap *dmap, double apix, double density_threshold, int num_means, const std::string pdb_filename, const std::string cmm_filename, const std::string seg_filename, const std::string txt_filename)
Segment a density map using the anchor graph.
void write_connolly_surface(atom::Atoms atoms, TextOutput fn, float density, float probe_radius)
Write the Connolly surface for a set of atoms to a file.
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
multifit::FittingSolutionRecords fft_based_rigid_fitting(atom::Hierarchy mol2fit, em::DensityMap *dmap, double density_threshold, double angle_sampling_interval_rad)
FFT fit of a molecule in the density.
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...
IntsList read_paths(const char *txt_filename, int max_paths=INT_MAX)
Read paths.
FittingSolutionRecords read_fitting_solutions(const char *fitting_fn)
Fitting solutions reader.
Abstract class to implement hierarchical methods.
Definition: Refiner.h:34
double get_resolution(Model *m, ParticleIndex pi)
Estimate the resolution of the hierarchy as used by Representation.
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.
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:52
atom::Hierarchy create_coarse_molecule_from_density(em::DensityMap *dmap, float dens_threshold, int num_beads, Model *mdl, float bead_radius)
Coarsen a density map based on voxels clustering.