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IMP Reference Guide  2.9.0
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 2007-2018 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 IMP_C_OPEN_BINARY = _IMP_multifit.IMP_C_OPEN_BINARY
289 import IMP
290 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CGAL_HAS_BOOST_FILESYSTEM
291 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
292 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CGAL_HAS_BOOST_RANDOM
293 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CGAL_HAS_BOOST_SYSTEM
294 IMPCGAL_SHOW_WARNINGS = _IMP_multifit.IMPCGAL_SHOW_WARNINGS
295 import IMP.cgal
296 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_multifit.IMP_ALGEBRA_HAS_IMP_CGAL
297 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
298 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
299 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_RANDOM
300 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_SYSTEM
301 IMP_ALGEBRA_HAS_CGAL = _IMP_multifit.IMP_ALGEBRA_HAS_CGAL
302 IMP_ALGEBRA_HAS_ANN = _IMP_multifit.IMP_ALGEBRA_HAS_ANN
303 IMPALGEBRA_SHOW_WARNINGS = _IMP_multifit.IMPALGEBRA_SHOW_WARNINGS
304 import IMP.algebra
305 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_multifit.IMP_DISPLAY_HAS_IMP_CGAL
306 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
307 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
308 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_RANDOM
309 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_SYSTEM
310 IMP_DISPLAY_HAS_CGAL = _IMP_multifit.IMP_DISPLAY_HAS_CGAL
311 IMPDISPLAY_SHOW_WARNINGS = _IMP_multifit.IMPDISPLAY_SHOW_WARNINGS
312 import IMP.display
313 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
314 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
315 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
316 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
317 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
318 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_CGAL
319 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_HDF5
320 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_multifit.IMPSCOREFUNCTOR_SHOW_WARNINGS
321 import IMP.score_functor
322 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_multifit.IMP_STATISTICS_HAS_IMP_CGAL
323 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
324 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
325 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_RANDOM
326 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_SYSTEM
327 IMP_STATISTICS_HAS_CGAL = _IMP_multifit.IMP_STATISTICS_HAS_CGAL
328 IMPSTATISTICS_SHOW_WARNINGS = _IMP_multifit.IMPSTATISTICS_SHOW_WARNINGS
329 import IMP.statistics
330 IMP_CORE_HAS_IMP_CGAL = _IMP_multifit.IMP_CORE_HAS_IMP_CGAL
331 IMP_CORE_HAS_IMP_KERNEL = _IMP_multifit.IMP_CORE_HAS_IMP_KERNEL
332 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CORE_HAS_BOOST_FILESYSTEM
333 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
334 IMP_CORE_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CORE_HAS_BOOST_RANDOM
335 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CORE_HAS_BOOST_SYSTEM
336 IMP_CORE_HAS_CGAL = _IMP_multifit.IMP_CORE_HAS_CGAL
337 IMP_CORE_HAS_HDF5 = _IMP_multifit.IMP_CORE_HAS_HDF5
338 IMPCORE_SHOW_WARNINGS = _IMP_multifit.IMPCORE_SHOW_WARNINGS
339 import IMP.core
340 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_multifit.IMP_CONTAINER_HAS_IMP_ALGEBRA
341 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_multifit.IMP_CONTAINER_HAS_IMP_CGAL
342 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_multifit.IMP_CONTAINER_HAS_IMP_DISPLAY
343 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_multifit.IMP_CONTAINER_HAS_IMP_KERNEL
344 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
345 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
346 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
347 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_RANDOM
348 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_SYSTEM
349 IMP_CONTAINER_HAS_CGAL = _IMP_multifit.IMP_CONTAINER_HAS_CGAL
350 IMP_CONTAINER_HAS_HDF5 = _IMP_multifit.IMP_CONTAINER_HAS_HDF5
351 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_multifit.IMP_CONTAINER_HAS_PYTHON_IHM
352 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_multifit.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
353 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_multifit.IMP_CONTAINER_HAS_ROBIN_MAP
354 IMPCONTAINER_SHOW_WARNINGS = _IMP_multifit.IMPCONTAINER_SHOW_WARNINGS
355 import IMP.container
356 IMP_ATOM_HAS_IMP_CGAL = _IMP_multifit.IMP_ATOM_HAS_IMP_CGAL
357 IMP_ATOM_HAS_IMP_KERNEL = _IMP_multifit.IMP_ATOM_HAS_IMP_KERNEL
358 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
359 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
360 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_multifit.IMP_ATOM_HAS_BOOST_RANDOM
361 IMP_ATOM_HAS_BOOST_REGEX = _IMP_multifit.IMP_ATOM_HAS_BOOST_REGEX
362 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_ATOM_HAS_BOOST_SYSTEM
363 IMP_ATOM_HAS_CGAL = _IMP_multifit.IMP_ATOM_HAS_CGAL
364 IMP_ATOM_HAS_HDF5 = _IMP_multifit.IMP_ATOM_HAS_HDF5
365 IMP_ATOM_HAS_PYTHON_IHM = _IMP_multifit.IMP_ATOM_HAS_PYTHON_IHM
366 IMPATOM_SHOW_WARNINGS = _IMP_multifit.IMPATOM_SHOW_WARNINGS
367 IMP_ATOM_TYPE_INDEX = _IMP_multifit.IMP_ATOM_TYPE_INDEX
368 IMP_RESIDUE_TYPE_INDEX = _IMP_multifit.IMP_RESIDUE_TYPE_INDEX
369 IMP_HIERARCHY_TYPE_INDEX = _IMP_multifit.IMP_HIERARCHY_TYPE_INDEX
370 IMP_CHAIN_TYPE_INDEX = _IMP_multifit.IMP_CHAIN_TYPE_INDEX
371 import IMP.atom
372 IMP_EM_HAS_IMP_CGAL = _IMP_multifit.IMP_EM_HAS_IMP_CGAL
373 IMP_EM_HAS_IMP_CONTAINER = _IMP_multifit.IMP_EM_HAS_IMP_CONTAINER
374 IMP_EM_HAS_IMP_DISPLAY = _IMP_multifit.IMP_EM_HAS_IMP_DISPLAY
375 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_EM_HAS_IMP_SCORE_FUNCTOR
376 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_EM_HAS_BOOST_FILESYSTEM
377 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
378 IMP_EM_HAS_BOOST_RANDOM = _IMP_multifit.IMP_EM_HAS_BOOST_RANDOM
379 IMP_EM_HAS_BOOST_REGEX = _IMP_multifit.IMP_EM_HAS_BOOST_REGEX
380 IMP_EM_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_EM_HAS_BOOST_SYSTEM
381 IMP_EM_HAS_CGAL = _IMP_multifit.IMP_EM_HAS_CGAL
382 IMP_EM_HAS_HDF5 = _IMP_multifit.IMP_EM_HAS_HDF5
383 IMP_EM_HAS_PYTHON_IHM = _IMP_multifit.IMP_EM_HAS_PYTHON_IHM
384 IMPEM_SHOW_WARNINGS = _IMP_multifit.IMPEM_SHOW_WARNINGS
385 import IMP.em
386 IMP_RMF_HAS_IMP_CGAL = _IMP_multifit.IMP_RMF_HAS_IMP_CGAL
387 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
388 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_RMF_HAS_BOOST_FILESYSTEM
389 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
390 IMP_RMF_HAS_BOOST_RANDOM = _IMP_multifit.IMP_RMF_HAS_BOOST_RANDOM
391 IMP_RMF_HAS_BOOST_REGEX = _IMP_multifit.IMP_RMF_HAS_BOOST_REGEX
392 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_RMF_HAS_BOOST_SYSTEM
393 IMP_RMF_HAS_CGAL = _IMP_multifit.IMP_RMF_HAS_CGAL
394 IMP_RMF_HAS_HDF5 = _IMP_multifit.IMP_RMF_HAS_HDF5
395 IMP_RMF_HAS_PYTHON_IHM = _IMP_multifit.IMP_RMF_HAS_PYTHON_IHM
396 IMPRMF_SHOW_WARNINGS = _IMP_multifit.IMPRMF_SHOW_WARNINGS
397 import IMP.rmf
398 import RMF
399 IMP_DOMINO_HAS_IMP_ATOM = _IMP_multifit.IMP_DOMINO_HAS_IMP_ATOM
400 IMP_DOMINO_HAS_IMP_CGAL = _IMP_multifit.IMP_DOMINO_HAS_IMP_CGAL
401 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_multifit.IMP_DOMINO_HAS_IMP_KERNEL
402 IMP_DOMINO_HAS_IMP_RMF = _IMP_multifit.IMP_DOMINO_HAS_IMP_RMF
403 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
404 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_FILESYSTEM
405 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
406 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_RANDOM
407 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_multifit.IMP_DOMINO_HAS_BOOST_REGEX
408 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_SYSTEM
409 IMP_DOMINO_HAS_CGAL = _IMP_multifit.IMP_DOMINO_HAS_CGAL
410 IMP_DOMINO_HAS_HDF5 = _IMP_multifit.IMP_DOMINO_HAS_HDF5
411 IMP_DOMINO_HAS_RMF = _IMP_multifit.IMP_DOMINO_HAS_RMF
412 IMP_DOMINO_HAS_PYTHON_IHM = _IMP_multifit.IMP_DOMINO_HAS_PYTHON_IHM
413 IMPDOMINO_SHOW_WARNINGS = _IMP_multifit.IMPDOMINO_SHOW_WARNINGS
414 import RMF_HDF5
415 import IMP.domino
416 IMP_MULTIFIT_HAS_IMP_CGAL = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_CGAL
417 IMP_MULTIFIT_HAS_IMP_CONTAINER = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_CONTAINER
418 IMP_MULTIFIT_HAS_IMP_DISPLAY = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_DISPLAY
419 IMP_MULTIFIT_HAS_IMP_KERNEL = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_KERNEL
420 IMP_MULTIFIT_HAS_IMP_RMF = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_RMF
421 IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR
422 IMP_MULTIFIT_HAS_BOOST_GRAPH = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_GRAPH
423 IMP_MULTIFIT_HAS_BOOST_RANDOM = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_RANDOM
424 IMP_MULTIFIT_HAS_BOOST_REGEX = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_REGEX
425 IMP_MULTIFIT_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_SYSTEM
426 IMP_MULTIFIT_HAS_CGAL = _IMP_multifit.IMP_MULTIFIT_HAS_CGAL
427 IMP_MULTIFIT_HAS_HDF5 = _IMP_multifit.IMP_MULTIFIT_HAS_HDF5
428 IMP_MULTIFIT_HAS_RMF = _IMP_multifit.IMP_MULTIFIT_HAS_RMF
429 IMP_MULTIFIT_HAS_PYTHON_IHM = _IMP_multifit.IMP_MULTIFIT_HAS_PYTHON_IHM
430 IMPMULTIFIT_SHOW_WARNINGS = _IMP_multifit.IMPMULTIFIT_SHOW_WARNINGS
431 
432 _object_types.append("RadiusOfGyrationRestraint")
433 
434 
435 def _object_cast_to_RadiusOfGyrationRestraint(o):
436  """_object_cast_to_RadiusOfGyrationRestraint(Object o) -> RadiusOfGyrationRestraint"""
437  return _IMP_multifit._object_cast_to_RadiusOfGyrationRestraint(o)
438 
439 _object_types.append("ComponentHeader")
440 
441 
442 def _object_cast_to_ComponentHeader(o):
443  """_object_cast_to_ComponentHeader(Object o) -> ComponentHeader"""
444  return _IMP_multifit._object_cast_to_ComponentHeader(o)
445 
446 _object_types.append("AssemblyHeader")
447 
448 
449 def _object_cast_to_AssemblyHeader(o):
450  """_object_cast_to_AssemblyHeader(Object o) -> AssemblyHeader"""
451  return _IMP_multifit._object_cast_to_AssemblyHeader(o)
452 
453 _object_types.append("SettingsData")
454 
455 
456 def _object_cast_to_SettingsData(o):
457  """_object_cast_to_SettingsData(Object o) -> SettingsData"""
458  return _IMP_multifit._object_cast_to_SettingsData(o)
459 
460 _object_types.append("WeightedExcludedVolumeRestraint")
461 
462 
463 def _object_cast_to_WeightedExcludedVolumeRestraint(o):
464  """_object_cast_to_WeightedExcludedVolumeRestraint(Object o) -> WeightedExcludedVolumeRestraint"""
465  return _IMP_multifit._object_cast_to_WeightedExcludedVolumeRestraint(o)
466 
467 _object_types.append("ComplementarityRestraint")
468 
469 
470 def _object_cast_to_ComplementarityRestraint(o):
471  """_object_cast_to_ComplementarityRestraint(Object o) -> ComplementarityRestraint"""
472  return _IMP_multifit._object_cast_to_ComplementarityRestraint(o)
473 
474 ProteinRecordDataList=list
475 _plural_types.append("ProteinRecordDataList")
476 _value_types.append("ProteinRecordData")
477 
478 
479 FittingSolutionRecords=list
480 _plural_types.append("FittingSolutionRecords")
481 _value_types.append("FittingSolutionRecord")
482 
483 
484 AnchorsDataList=list
485 _plural_types.append("AnchorsDataList")
486 _value_types.append("AnchorsData")
487 
488 
489 DominoParamsList=list
490 _plural_types.append("DominoParamsList")
491 _value_types.append("DominoParams")
492 
493 
494 ComplementarityParamsList=list
495 _plural_types.append("ComplementarityParamsList")
496 _value_types.append("ComplementarityParams")
497 
498 
499 XlinkParamsList=list
500 _plural_types.append("XlinkParamsList")
501 _value_types.append("XlinkParams")
502 
503 
504 ConnectivityParamsList=list
505 _plural_types.append("ConnectivityParamsList")
506 _value_types.append("ConnectivityParams")
507 
508 
509 FragmentsParamsList=list
510 _plural_types.append("FragmentsParamsList")
511 _value_types.append("FragmentsParams")
512 
513 
514 RogParamsList=list
515 _plural_types.append("RogParamsList")
516 _value_types.append("RogParams")
517 
518 
519 EVParamsList=list
520 _plural_types.append("EVParamsList")
521 _value_types.append("EVParams")
522 
523 
524 FiltersParamsList=list
525 _plural_types.append("FiltersParamsList")
526 _value_types.append("FiltersParams")
527 
528 
529 AlignmentParamsList=list
530 _plural_types.append("AlignmentParamsList")
531 _value_types.append("AlignmentParams")
532 
533 
534 FittingParamsList=list
535 _plural_types.append("FittingParamsList")
536 _value_types.append("FittingParams")
537 
538 
539 ProteinsAnchorsSamplingSpaces=list
540 _plural_types.append("ProteinsAnchorsSamplingSpaces")
541 _value_types.append("ProteinsAnchorsSamplingSpace")
542 
543 
544 _object_types.append("ProteomicsData")
545 
546 
547 def _object_cast_to_ProteomicsData(o):
548  """_object_cast_to_ProteomicsData(Object o) -> ProteomicsData"""
549  return _IMP_multifit._object_cast_to_ProteomicsData(o)
550 
551 _object_types.append("FFTFitting")
552 
553 
554 def _object_cast_to_FFTFitting(o):
555  """_object_cast_to_FFTFitting(Object o) -> FFTFitting"""
556  return _IMP_multifit._object_cast_to_FFTFitting(o)
557 
558 _object_types.append("FFTFittingOutput")
559 
560 
561 def _object_cast_to_FFTFittingOutput(o):
562  """_object_cast_to_FFTFittingOutput(Object o) -> FFTFittingOutput"""
563  return _IMP_multifit._object_cast_to_FFTFittingOutput(o)
564 
565 _object_types.append("ProbabilisticAnchorGraph")
566 
567 
568 def _object_cast_to_ProbabilisticAnchorGraph(o):
569  """_object_cast_to_ProbabilisticAnchorGraph(Object o) -> ProbabilisticAnchorGraph"""
570  return _IMP_multifit._object_cast_to_ProbabilisticAnchorGraph(o)
571 
572 _object_types.append("Ensemble")
573 
574 
575 def _object_cast_to_Ensemble(o):
576  """_object_cast_to_Ensemble(Object o) -> Ensemble"""
577  return _IMP_multifit._object_cast_to_Ensemble(o)
578 
579 _object_types.append("ProteomicsEMAlignmentAtomic")
580 
581 
582 def _object_cast_to_ProteomicsEMAlignmentAtomic(o):
583  """_object_cast_to_ProteomicsEMAlignmentAtomic(Object o) -> ProteomicsEMAlignmentAtomic"""
584  return _IMP_multifit._object_cast_to_ProteomicsEMAlignmentAtomic(o)
585 
586 _object_types.append("RigidLeavesRefiner")
587 
588 
589 def _object_cast_to_RigidLeavesRefiner(o):
590  """_object_cast_to_RigidLeavesRefiner(Object o) -> RigidLeavesRefiner"""
591  return _IMP_multifit._object_cast_to_RigidLeavesRefiner(o)
592 
593 def add_surface_index(*args):
594  """
595  add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key, FloatKey radius_key, FloatKey weight_key)
596  add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key, FloatKey radius_key)
597  add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key)
598  add_surface_index(Hierarchy mhd, IMP::Float apix)
599  """
600  return _IMP_multifit.add_surface_index(*args)
601 
603  """
604  create_weighted_excluded_volume_restraint(RigidBody rb1, RigidBody rb2, FloatKey shell_key) -> Restraint
605  create_weighted_excluded_volume_restraint(RigidBody rb1, RigidBody rb2) -> Restraint
606  """
607  return _IMP_multifit.create_weighted_excluded_volume_restraint(*args)
608 class FittingSolutionRecord(object):
609  """Proxy of C++ IMP::multifit::FittingSolutionRecord class."""
610 
611  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
612 
613  def __init__(self):
614  """__init__(IMP::multifit::FittingSolutionRecord self) -> FittingSolutionRecord"""
615  this = _IMP_multifit.new_FittingSolutionRecord()
616  try:
617  self.this.append(this)
618  except __builtin__.Exception:
619  self.this = this
620 
621  def get_index(self):
622  """get_index(FittingSolutionRecord self) -> unsigned int"""
623  return _IMP_multifit.FittingSolutionRecord_get_index(self)
624 
625 
626  def set_index(self, new_ind):
627  """set_index(FittingSolutionRecord self, unsigned int new_ind)"""
628  return _IMP_multifit.FittingSolutionRecord_set_index(self, new_ind)
629 
630 
631  def get_solution_filename(self):
632  """get_solution_filename(FittingSolutionRecord self) -> std::string"""
633  return _IMP_multifit.FittingSolutionRecord_get_solution_filename(self)
634 
635 
636  def set_solution_filename(self, sol_fn):
637  """set_solution_filename(FittingSolutionRecord self, std::string sol_fn)"""
638  return _IMP_multifit.FittingSolutionRecord_set_solution_filename(self, sol_fn)
639 
640 
641  def get_fit_transformation(self):
642  """get_fit_transformation(FittingSolutionRecord self) -> Transformation3D"""
643  return _IMP_multifit.FittingSolutionRecord_get_fit_transformation(self)
644 
645 
646  def set_fit_transformation(self, t):
647  """set_fit_transformation(FittingSolutionRecord self, Transformation3D t)"""
648  return _IMP_multifit.FittingSolutionRecord_set_fit_transformation(self, t)
649 
650 
651  def get_match_size(self):
652  """get_match_size(FittingSolutionRecord self) -> unsigned int"""
653  return _IMP_multifit.FittingSolutionRecord_get_match_size(self)
654 
655 
656  def set_match_size(self, match_size):
657  """set_match_size(FittingSolutionRecord self, unsigned int match_size)"""
658  return _IMP_multifit.FittingSolutionRecord_set_match_size(self, match_size)
659 
660 
661  def get_match_average_distance(self):
662  """get_match_average_distance(FittingSolutionRecord self) -> IMP::Float"""
663  return _IMP_multifit.FittingSolutionRecord_get_match_average_distance(self)
664 
665 
666  def set_match_average_distance(self, match_avg_dist):
667  """set_match_average_distance(FittingSolutionRecord self, IMP::Float match_avg_dist)"""
668  return _IMP_multifit.FittingSolutionRecord_set_match_average_distance(self, match_avg_dist)
669 
670 
671  def get_fitting_score(self):
672  """get_fitting_score(FittingSolutionRecord self) -> IMP::Float"""
673  return _IMP_multifit.FittingSolutionRecord_get_fitting_score(self)
674 
675 
676  def set_fitting_score(self, fit_score):
677  """set_fitting_score(FittingSolutionRecord self, IMP::Float fit_score)"""
678  return _IMP_multifit.FittingSolutionRecord_set_fitting_score(self, fit_score)
679 
680 
681  def get_rmsd_to_reference(self):
682  """get_rmsd_to_reference(FittingSolutionRecord self) -> IMP::Float"""
683  return _IMP_multifit.FittingSolutionRecord_get_rmsd_to_reference(self)
684 
685 
686  def set_rmsd_to_reference(self, rmsd_to_ref):
687  """set_rmsd_to_reference(FittingSolutionRecord self, IMP::Float rmsd_to_ref)"""
688  return _IMP_multifit.FittingSolutionRecord_set_rmsd_to_reference(self, rmsd_to_ref)
689 
690 
691  def get_dock_transformation(self):
692  """get_dock_transformation(FittingSolutionRecord self) -> Transformation3D"""
693  return _IMP_multifit.FittingSolutionRecord_get_dock_transformation(self)
694 
695 
696  def set_dock_transformation(self, t):
697  """set_dock_transformation(FittingSolutionRecord self, Transformation3D t)"""
698  return _IMP_multifit.FittingSolutionRecord_set_dock_transformation(self, t)
699 
700 
701  def get_envelope_penetration_score(self):
702  """get_envelope_penetration_score(FittingSolutionRecord self) -> IMP::Float"""
703  return _IMP_multifit.FittingSolutionRecord_get_envelope_penetration_score(self)
704 
705 
706  def set_envelope_penetration_score(self, s):
707  """set_envelope_penetration_score(FittingSolutionRecord self, IMP::Float s)"""
708  return _IMP_multifit.FittingSolutionRecord_set_envelope_penetration_score(self, s)
709 
710 
711  def show(self, *args):
712  """
713  show(FittingSolutionRecord self, _ostream out)
714  show(FittingSolutionRecord self)
715  """
716  return _IMP_multifit.FittingSolutionRecord_show(self, *args)
717 
718 
719  def get_record_header():
720  """get_record_header() -> std::string"""
721  return _IMP_multifit.FittingSolutionRecord_get_record_header()
722 
723  get_record_header = staticmethod(get_record_header)
724 
725  def __str__(self):
726  """__str__(FittingSolutionRecord self) -> std::string"""
727  return _IMP_multifit.FittingSolutionRecord___str__(self)
728 
729 
730  def __repr__(self):
731  """__repr__(FittingSolutionRecord self) -> std::string"""
732  return _IMP_multifit.FittingSolutionRecord___repr__(self)
733 
734  __swig_destroy__ = _IMP_multifit.delete_FittingSolutionRecord
735  __del__ = lambda self: None
736 FittingSolutionRecord_swigregister = _IMP_multifit.FittingSolutionRecord_swigregister
737 FittingSolutionRecord_swigregister(FittingSolutionRecord)
738 
739 def FittingSolutionRecord_get_record_header():
740  """FittingSolutionRecord_get_record_header() -> std::string"""
741  return _IMP_multifit.FittingSolutionRecord_get_record_header()
742 
743 
744 def pca_based_rigid_fitting(*args):
745  """
746  pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold, FloatKey wei_key, PrincipalComponentAnalysis3D dens_pca_input) -> FittingSolutions
747  pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold, FloatKey wei_key) -> FittingSolutions
748  pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold) -> FittingSolutions
749  pca_based_rigid_fitting(IMP::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold, FloatKey wei_key, PrincipalComponentAnalysis3D dens_pca_input) -> FittingSolutions
750  pca_based_rigid_fitting(IMP::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold, FloatKey wei_key) -> FittingSolutions
751  pca_based_rigid_fitting(IMP::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold) -> FittingSolutions
752  """
753  return _IMP_multifit.pca_based_rigid_fitting(*args)
754 
755 def write_markers(pca, out):
756  """write_markers(PrincipalComponentAnalysis3D pca, _ostream out)"""
757  return _IMP_multifit.write_markers(pca, out)
758 class ComponentHeader(IMP.Object):
759  """Proxy of C++ IMP::multifit::ComponentHeader class."""
760 
761  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
762 
763  def __init__(self):
764  """__init__(IMP::multifit::ComponentHeader self) -> ComponentHeader"""
765  this = _IMP_multifit.new_ComponentHeader()
766  try:
767  self.this.append(this)
768  except __builtin__.Exception:
769  self.this = this
770 
771  def set_name(self, name):
772  """set_name(ComponentHeader self, std::string const & name)"""
773  return _IMP_multifit.ComponentHeader_set_name(self, name)
774 
775 
776  def get_name(self):
777  """get_name(ComponentHeader self) -> std::string"""
778  return _IMP_multifit.ComponentHeader_get_name(self)
779 
780 
781  def get_filename(self):
782  """get_filename(ComponentHeader self) -> std::string"""
783  return _IMP_multifit.ComponentHeader_get_filename(self)
784 
785 
786  def set_filename(self, filename):
787  """set_filename(ComponentHeader self, std::string const & filename)"""
788  return _IMP_multifit.ComponentHeader_set_filename(self, filename)
789 
790 
791  def get_surface_fn(self):
792  """get_surface_fn(ComponentHeader self) -> std::string"""
793  return _IMP_multifit.ComponentHeader_get_surface_fn(self)
794 
795 
796  def set_surface_fn(self, fn):
797  """set_surface_fn(ComponentHeader self, std::string const & fn)"""
798  return _IMP_multifit.ComponentHeader_set_surface_fn(self, fn)
799 
800 
801  def set_txt_ap_fn(self, pdb_ap_fn):
802  """set_txt_ap_fn(ComponentHeader self, std::string const & pdb_ap_fn)"""
803  return _IMP_multifit.ComponentHeader_set_txt_ap_fn(self, pdb_ap_fn)
804 
805 
806  def get_txt_ap_fn(self):
807  """get_txt_ap_fn(ComponentHeader self) -> std::string"""
808  return _IMP_multifit.ComponentHeader_get_txt_ap_fn(self)
809 
810 
811  def set_txt_fine_ap_fn(self, pdb_ap_fn):
812  """set_txt_fine_ap_fn(ComponentHeader self, std::string const & pdb_ap_fn)"""
813  return _IMP_multifit.ComponentHeader_set_txt_fine_ap_fn(self, pdb_ap_fn)
814 
815 
816  def get_txt_fine_ap_fn(self):
817  """get_txt_fine_ap_fn(ComponentHeader self) -> std::string"""
818  return _IMP_multifit.ComponentHeader_get_txt_fine_ap_fn(self)
819 
820 
821  def set_num_ap(self, num_ap):
822  """set_num_ap(ComponentHeader self, int num_ap)"""
823  return _IMP_multifit.ComponentHeader_set_num_ap(self, num_ap)
824 
825 
826  def get_num_ap(self):
827  """get_num_ap(ComponentHeader self) -> int"""
828  return _IMP_multifit.ComponentHeader_get_num_ap(self)
829 
830 
831  def set_num_fine_ap(self, num_ap):
832  """set_num_fine_ap(ComponentHeader self, int num_ap)"""
833  return _IMP_multifit.ComponentHeader_set_num_fine_ap(self, num_ap)
834 
835 
836  def get_num_fine_ap(self):
837  """get_num_fine_ap(ComponentHeader self) -> int"""
838  return _IMP_multifit.ComponentHeader_get_num_fine_ap(self)
839 
840 
841  def set_transformations_fn(self, transformations_fn):
842  """set_transformations_fn(ComponentHeader self, std::string transformations_fn)"""
843  return _IMP_multifit.ComponentHeader_set_transformations_fn(self, transformations_fn)
844 
845 
846  def get_transformations_fn(self):
847  """get_transformations_fn(ComponentHeader self) -> std::string"""
848  return _IMP_multifit.ComponentHeader_get_transformations_fn(self)
849 
850 
851  def set_reference_fn(self, ref_fn):
852  """set_reference_fn(ComponentHeader self, std::string const & ref_fn)"""
853  return _IMP_multifit.ComponentHeader_set_reference_fn(self, ref_fn)
854 
855 
856  def get_reference_fn(self):
857  """get_reference_fn(ComponentHeader self) -> std::string"""
858  return _IMP_multifit.ComponentHeader_get_reference_fn(self)
859 
860 
861  def get_version_info(self):
862  """get_version_info(ComponentHeader self) -> VersionInfo"""
863  return _IMP_multifit.ComponentHeader_get_version_info(self)
864 
865 
866  def __str__(self):
867  """__str__(ComponentHeader self) -> std::string"""
868  return _IMP_multifit.ComponentHeader___str__(self)
869 
870 
871  def __repr__(self):
872  """__repr__(ComponentHeader self) -> std::string"""
873  return _IMP_multifit.ComponentHeader___repr__(self)
874 
875 
876  @staticmethod
877  def get_from(o):
878  return _object_cast_to_ComponentHeader(o)
879 
880 ComponentHeader_swigregister = _IMP_multifit.ComponentHeader_swigregister
881 ComponentHeader_swigregister(ComponentHeader)
882 
883 class AssemblyHeader(IMP.Object):
884  """Proxy of C++ IMP::multifit::AssemblyHeader class."""
885 
886  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
887 
888  def __init__(self):
889  """__init__(IMP::multifit::AssemblyHeader self) -> AssemblyHeader"""
890  this = _IMP_multifit.new_AssemblyHeader()
891  try:
892  self.this.append(this)
893  except __builtin__.Exception:
894  self.this = this
895 
896  def set_dens_fn(self, dens_fn):
897  """set_dens_fn(AssemblyHeader self, std::string const & dens_fn)"""
898  return _IMP_multifit.AssemblyHeader_set_dens_fn(self, dens_fn)
899 
900 
901  def get_dens_fn(self):
902  """get_dens_fn(AssemblyHeader self) -> std::string"""
903  return _IMP_multifit.AssemblyHeader_get_dens_fn(self)
904 
905 
906  def set_resolution(self, res):
907  """set_resolution(AssemblyHeader self, float res)"""
908  return _IMP_multifit.AssemblyHeader_set_resolution(self, res)
909 
910 
911  def get_resolution(self):
912  """get_resolution(AssemblyHeader self) -> float"""
913  return _IMP_multifit.AssemblyHeader_get_resolution(self)
914 
915 
916  def get_spacing(self):
917  """get_spacing(AssemblyHeader self) -> float"""
918  return _IMP_multifit.AssemblyHeader_get_spacing(self)
919 
920 
921  def set_spacing(self, spacing):
922  """set_spacing(AssemblyHeader self, float spacing)"""
923  return _IMP_multifit.AssemblyHeader_set_spacing(self, spacing)
924 
925 
926  def set_threshold(self, t):
927  """set_threshold(AssemblyHeader self, float t)"""
928  return _IMP_multifit.AssemblyHeader_set_threshold(self, t)
929 
930 
931  def get_threshold(self):
932  """get_threshold(AssemblyHeader self) -> float"""
933  return _IMP_multifit.AssemblyHeader_get_threshold(self)
934 
935 
936  def get_origin(self):
937  """get_origin(AssemblyHeader self) -> Vector3D"""
938  return _IMP_multifit.AssemblyHeader_get_origin(self)
939 
940 
941  def set_origin(self, origin):
942  """set_origin(AssemblyHeader self, Vector3D origin)"""
943  return _IMP_multifit.AssemblyHeader_set_origin(self, origin)
944 
945 
946  def get_coarse_ap_fn(self):
947  """get_coarse_ap_fn(AssemblyHeader self) -> std::string"""
948  return _IMP_multifit.AssemblyHeader_get_coarse_ap_fn(self)
949 
950 
951  def set_coarse_ap_fn(self, new_fn):
952  """set_coarse_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
953  return _IMP_multifit.AssemblyHeader_set_coarse_ap_fn(self, new_fn)
954 
955 
956  def get_coarse_over_sampled_ap_fn(self):
957  """get_coarse_over_sampled_ap_fn(AssemblyHeader self) -> std::string"""
958  return _IMP_multifit.AssemblyHeader_get_coarse_over_sampled_ap_fn(self)
959 
960 
961  def set_coarse_over_sampled_ap_fn(self, new_fn):
962  """set_coarse_over_sampled_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
963  return _IMP_multifit.AssemblyHeader_set_coarse_over_sampled_ap_fn(self, new_fn)
964 
965 
966  def get_fine_ap_fn(self):
967  """get_fine_ap_fn(AssemblyHeader self) -> std::string"""
968  return _IMP_multifit.AssemblyHeader_get_fine_ap_fn(self)
969 
970 
971  def set_fine_ap_fn(self, new_fn):
972  """set_fine_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
973  return _IMP_multifit.AssemblyHeader_set_fine_ap_fn(self, new_fn)
974 
975 
976  def get_fine_over_sampled_ap_fn(self):
977  """get_fine_over_sampled_ap_fn(AssemblyHeader self) -> std::string"""
978  return _IMP_multifit.AssemblyHeader_get_fine_over_sampled_ap_fn(self)
979 
980 
981  def set_fine_over_sampled_ap_fn(self, new_fn):
982  """set_fine_over_sampled_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
983  return _IMP_multifit.AssemblyHeader_set_fine_over_sampled_ap_fn(self, new_fn)
984 
985 
986  def get_version_info(self):
987  """get_version_info(AssemblyHeader self) -> VersionInfo"""
988  return _IMP_multifit.AssemblyHeader_get_version_info(self)
989 
990 
991  def __str__(self):
992  """__str__(AssemblyHeader self) -> std::string"""
993  return _IMP_multifit.AssemblyHeader___str__(self)
994 
995 
996  def __repr__(self):
997  """__repr__(AssemblyHeader self) -> std::string"""
998  return _IMP_multifit.AssemblyHeader___repr__(self)
999 
1000 
1001  @staticmethod
1002  def get_from(o):
1003  return _object_cast_to_AssemblyHeader(o)
1004 
1005 AssemblyHeader_swigregister = _IMP_multifit.AssemblyHeader_swigregister
1006 AssemblyHeader_swigregister(AssemblyHeader)
1007 
1008 class SettingsData(IMP.Object):
1009  """Proxy of C++ IMP::multifit::SettingsData class."""
1010 
1011  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1012 
1013  def __init__(self):
1014  """__init__(IMP::multifit::SettingsData self) -> SettingsData"""
1015  this = _IMP_multifit.new_SettingsData()
1016  try:
1017  self.this.append(this)
1018  except __builtin__.Exception:
1019  self.this = this
1020 
1021  def show_component_header_line(*args):
1022  """
1023  show_component_header_line(_ostream out)
1024  show_component_header_line()
1025  """
1026  return _IMP_multifit.SettingsData_show_component_header_line(*args)
1027 
1028  show_component_header_line = staticmethod(show_component_header_line)
1029 
1030  def get_component_header_line():
1031  """get_component_header_line() -> std::string"""
1032  return _IMP_multifit.SettingsData_get_component_header_line()
1033 
1034  get_component_header_line = staticmethod(get_component_header_line)
1035 
1036  def show_density_header_line(*args):
1037  """
1038  show_density_header_line(_ostream out)
1039  show_density_header_line()
1040  """
1041  return _IMP_multifit.SettingsData_show_density_header_line(*args)
1042 
1043  show_density_header_line = staticmethod(show_density_header_line)
1044 
1045  def get_density_header_line():
1046  """get_density_header_line() -> std::string"""
1047  return _IMP_multifit.SettingsData_get_density_header_line()
1048 
1049  get_density_header_line = staticmethod(get_density_header_line)
1050 
1051  def set_assembly_filename(self, fn):
1052  """set_assembly_filename(SettingsData self, std::string const & fn)"""
1053  return _IMP_multifit.SettingsData_set_assembly_filename(self, fn)
1054 
1055 
1056  def get_assembly_filename(self):
1057  """get_assembly_filename(SettingsData self) -> char const *"""
1058  return _IMP_multifit.SettingsData_get_assembly_filename(self)
1059 
1060 
1061  def set_assembly_header(self, h):
1062  """set_assembly_header(SettingsData self, AssemblyHeader h)"""
1063  return _IMP_multifit.SettingsData_set_assembly_header(self, h)
1064 
1065 
1066  def get_assembly_header(self):
1067  """get_assembly_header(SettingsData self) -> AssemblyHeader"""
1068  return _IMP_multifit.SettingsData_get_assembly_header(self)
1069 
1070 
1071  def set_data_path(self, fn):
1072  """set_data_path(SettingsData self, std::string const & fn)"""
1073  return _IMP_multifit.SettingsData_set_data_path(self, fn)
1074 
1075 
1076  def get_data_path(self):
1077  """get_data_path(SettingsData self) -> std::string"""
1078  return _IMP_multifit.SettingsData_get_data_path(self)
1079 
1080 
1081  def get_version_info(self):
1082  """get_version_info(SettingsData self) -> VersionInfo"""
1083  return _IMP_multifit.SettingsData_get_version_info(self)
1084 
1085 
1086  def remove_component_header(self, d):
1087  """remove_component_header(SettingsData self, ComponentHeader d)"""
1088  return _IMP_multifit.SettingsData_remove_component_header(self, d)
1089 
1090 
1091  def remove_component_headers(self, d):
1092  """remove_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & d)"""
1093  return _IMP_multifit.SettingsData_remove_component_headers(self, d)
1094 
1095 
1096  def set_component_headers(self, ps):
1097  """set_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & ps)"""
1098  return _IMP_multifit.SettingsData_set_component_headers(self, ps)
1099 
1100 
1101  def set_component_headers_order(self, objs):
1102  """set_component_headers_order(SettingsData self, IMP::multifit::ComponentHeaders const & objs)"""
1103  return _IMP_multifit.SettingsData_set_component_headers_order(self, objs)
1104 
1105 
1106  def add_component_header(self, obj):
1107  """add_component_header(SettingsData self, ComponentHeader obj) -> unsigned int"""
1108  return _IMP_multifit.SettingsData_add_component_header(self, obj)
1109 
1110 
1111  def add_component_headers(self, objs):
1112  """add_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & objs)"""
1113  return _IMP_multifit.SettingsData_add_component_headers(self, objs)
1114 
1115 
1116  def clear_component_headers(self):
1117  """clear_component_headers(SettingsData self)"""
1118  return _IMP_multifit.SettingsData_clear_component_headers(self)
1119 
1120 
1121  def get_number_of_component_headers(self):
1122  """get_number_of_component_headers(SettingsData self) -> unsigned int"""
1123  return _IMP_multifit.SettingsData_get_number_of_component_headers(self)
1124 
1125 
1126  def get_has_component_headers(self):
1127  """get_has_component_headers(SettingsData self) -> bool"""
1128  return _IMP_multifit.SettingsData_get_has_component_headers(self)
1129 
1130 
1131  def get_component_header(self, i):
1132  """get_component_header(SettingsData self, unsigned int i) -> ComponentHeader"""
1133  return _IMP_multifit.SettingsData_get_component_header(self, i)
1134 
1135 
1136  def get_component_headers(self):
1137  """get_component_headers(SettingsData self) -> IMP::multifit::ComponentHeaders"""
1138  return _IMP_multifit.SettingsData_get_component_headers(self)
1139 
1140 
1141  def reserve_component_headers(self, sz):
1142  """reserve_component_headers(SettingsData self, unsigned int sz)"""
1143  return _IMP_multifit.SettingsData_reserve_component_headers(self, sz)
1144 
1145 
1146  def __str__(self):
1147  """__str__(SettingsData self) -> std::string"""
1148  return _IMP_multifit.SettingsData___str__(self)
1149 
1150 
1151  def __repr__(self):
1152  """__repr__(SettingsData self) -> std::string"""
1153  return _IMP_multifit.SettingsData___repr__(self)
1154 
1155 
1156  @staticmethod
1157  def get_from(o):
1158  return _object_cast_to_SettingsData(o)
1159 
1160 SettingsData_swigregister = _IMP_multifit.SettingsData_swigregister
1161 SettingsData_swigregister(SettingsData)
1162 
1163 def SettingsData_show_component_header_line(*args):
1164  """
1165  show_component_header_line(_ostream out)
1166  SettingsData_show_component_header_line()
1167  """
1168  return _IMP_multifit.SettingsData_show_component_header_line(*args)
1169 
1170 def SettingsData_get_component_header_line():
1171  """SettingsData_get_component_header_line() -> std::string"""
1172  return _IMP_multifit.SettingsData_get_component_header_line()
1173 
1174 def SettingsData_show_density_header_line(*args):
1175  """
1176  show_density_header_line(_ostream out)
1177  SettingsData_show_density_header_line()
1178  """
1179  return _IMP_multifit.SettingsData_show_density_header_line(*args)
1180 
1181 def SettingsData_get_density_header_line():
1182  """SettingsData_get_density_header_line() -> std::string"""
1183  return _IMP_multifit.SettingsData_get_density_header_line()
1184 
1185 
1186 def read_settings(filename):
1187  """read_settings(char const * filename) -> SettingsData"""
1188  return _IMP_multifit.read_settings(filename)
1189 
1190 def write_settings(filename, sd):
1191  """write_settings(char const * filename, SettingsData sd)"""
1192  return _IMP_multifit.write_settings(filename, sd)
1193 class WeightedExcludedVolumeRestraint(IMP.Restraint):
1194  """Proxy of C++ IMP::multifit::WeightedExcludedVolumeRestraint class."""
1195 
1196  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1197 
1198  def __init__(self, *args):
1199  """
1200  __init__(IMP::multifit::WeightedExcludedVolumeRestraint self, IMP::core::RigidBodies rbs, Refiner refiner, FloatKey weight_key) -> WeightedExcludedVolumeRestraint
1201  __init__(IMP::multifit::WeightedExcludedVolumeRestraint self, IMP::core::RigidBodies rbs, Refiner refiner) -> WeightedExcludedVolumeRestraint
1202  """
1203  this = _IMP_multifit.new_WeightedExcludedVolumeRestraint(*args)
1204  try:
1205  self.this.append(this)
1206  except __builtin__.Exception:
1207  self.this = this
1208 
1209  def do_get_inputs(self):
1210  """do_get_inputs(WeightedExcludedVolumeRestraint self) -> IMP::ModelObjectsTemp"""
1211  return _IMP_multifit.WeightedExcludedVolumeRestraint_do_get_inputs(self)
1212 
1213 
1214  def get_version_info(self):
1215  """get_version_info(WeightedExcludedVolumeRestraint self) -> VersionInfo"""
1216  return _IMP_multifit.WeightedExcludedVolumeRestraint_get_version_info(self)
1217 
1218 
1219  def __str__(self):
1220  """__str__(WeightedExcludedVolumeRestraint self) -> std::string"""
1221  return _IMP_multifit.WeightedExcludedVolumeRestraint___str__(self)
1222 
1223 
1224  def __repr__(self):
1225  """__repr__(WeightedExcludedVolumeRestraint self) -> std::string"""
1226  return _IMP_multifit.WeightedExcludedVolumeRestraint___repr__(self)
1227 
1228 
1229  @staticmethod
1230  def get_from(o):
1231  return _object_cast_to_WeightedExcludedVolumeRestraint(o)
1232 
1233 WeightedExcludedVolumeRestraint_swigregister = _IMP_multifit.WeightedExcludedVolumeRestraint_swigregister
1234 WeightedExcludedVolumeRestraint_swigregister(WeightedExcludedVolumeRestraint)
1235 
1236 class FFTFittingOutput(IMP.Object):
1237  """Proxy of C++ IMP::multifit::FFTFittingOutput class."""
1238 
1239  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1240 
1241  def __init__(self):
1242  """__init__(IMP::multifit::FFTFittingOutput self) -> FFTFittingOutput"""
1243  this = _IMP_multifit.new_FFTFittingOutput()
1244  try:
1245  self.this.append(this)
1246  except __builtin__.Exception:
1247  self.this = this
1248 
1249  def get_version_info(self):
1250  """get_version_info(FFTFittingOutput self) -> VersionInfo"""
1251  return _IMP_multifit.FFTFittingOutput_get_version_info(self)
1252 
1253  best_fits_ = _swig_property(_IMP_multifit.FFTFittingOutput_best_fits__get, _IMP_multifit.FFTFittingOutput_best_fits__set)
1254  best_trans_per_rot_ = _swig_property(_IMP_multifit.FFTFittingOutput_best_trans_per_rot__get, _IMP_multifit.FFTFittingOutput_best_trans_per_rot__set)
1255 
1256  def __str__(self):
1257  """__str__(FFTFittingOutput self) -> std::string"""
1258  return _IMP_multifit.FFTFittingOutput___str__(self)
1259 
1260 
1261  def __repr__(self):
1262  """__repr__(FFTFittingOutput self) -> std::string"""
1263  return _IMP_multifit.FFTFittingOutput___repr__(self)
1264 
1265 
1266  @staticmethod
1267  def get_from(o):
1268  return _object_cast_to_FFTFittingOutput(o)
1269 
1270 FFTFittingOutput_swigregister = _IMP_multifit.FFTFittingOutput_swigregister
1271 FFTFittingOutput_swigregister(FFTFittingOutput)
1272 
1273 class FFTFitting(IMP.Object):
1274  """Proxy of C++ IMP::multifit::FFTFitting class."""
1275 
1276  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1277 
1278  def get_version_info(self):
1279  """get_version_info(FFTFitting self) -> VersionInfo"""
1280  return _IMP_multifit.FFTFitting_get_version_info(self)
1281 
1282 
1283  def __init__(self):
1284  """__init__(IMP::multifit::FFTFitting self) -> FFTFitting"""
1285  this = _IMP_multifit.new_FFTFitting()
1286  try:
1287  self.this.append(this)
1288  except __builtin__.Exception:
1289  self.this = this
1290 
1291  def do_global_fitting(self, *args):
1292  """
1293  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
1294  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
1295  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
1296  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
1297  """
1298  return _IMP_multifit.FFTFitting_do_global_fitting(self, *args)
1299 
1300 
1301  def do_local_fitting(self, *args):
1302  """
1303  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
1304  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
1305  """
1306  return _IMP_multifit.FFTFitting_do_local_fitting(self, *args)
1307 
1308 
1309  def __str__(self):
1310  """__str__(FFTFitting self) -> std::string"""
1311  return _IMP_multifit.FFTFitting___str__(self)
1312 
1313 
1314  def __repr__(self):
1315  """__repr__(FFTFitting self) -> std::string"""
1316  return _IMP_multifit.FFTFitting___repr__(self)
1317 
1318 
1319  @staticmethod
1320  def get_from(o):
1321  return _object_cast_to_FFTFitting(o)
1322 
1323 FFTFitting_swigregister = _IMP_multifit.FFTFitting_swigregister
1324 FFTFitting_swigregister(FFTFitting)
1325 
1326 
1327 def fft_based_rigid_fitting(mol2fit, dmap, density_threshold, angle_sampling_interval_rad):
1328  """fft_based_rigid_fitting(Hierarchy mol2fit, DensityMap dmap, double density_threshold, double angle_sampling_interval_rad) -> IMP::multifit::FittingSolutionRecords"""
1329  return _IMP_multifit.fft_based_rigid_fitting(mol2fit, dmap, density_threshold, angle_sampling_interval_rad)
1330 
1331 def remove_background(dmap, threshold, edge_threshold):
1332  """remove_background(DensityMap dmap, float threshold, float edge_threshold) -> DensityMap"""
1333  return _IMP_multifit.remove_background(dmap, threshold, edge_threshold)
1334 
1335 def get_connected_components(dmap, threshold, edge_threshold):
1336  """get_connected_components(DensityMap dmap, float threshold, float edge_threshold) -> IMP::IntsList"""
1337  return _IMP_multifit.get_connected_components(dmap, threshold, edge_threshold)
1338 
1339 def get_segmentation(dmap, apix, density_threshold, num_means, pdb_filename, cmm_filename, seg_filename, txt_filename):
1340  """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)"""
1341  return _IMP_multifit.get_segmentation(dmap, apix, density_threshold, num_means, pdb_filename, cmm_filename, seg_filename, txt_filename)
1342 class ComplementarityRestraint(IMP.Restraint):
1343  """Proxy of C++ IMP::multifit::ComplementarityRestraint class."""
1344 
1345  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1346 
1347  def __init__(self, *args):
1348  """
1349  __init__(IMP::multifit::ComplementarityRestraint self, IMP::ParticlesTemp const & a, IMP::ParticlesTemp const & b, std::string name) -> ComplementarityRestraint
1350  __init__(IMP::multifit::ComplementarityRestraint self, IMP::ParticlesTemp const & a, IMP::ParticlesTemp const & b) -> ComplementarityRestraint
1351  """
1352  this = _IMP_multifit.new_ComplementarityRestraint(*args)
1353  try:
1354  self.this.append(this)
1355  except __builtin__.Exception:
1356  self.this = this
1357 
1358  def set_maximum_penetration_score(self, s):
1359  """set_maximum_penetration_score(ComplementarityRestraint self, double s)"""
1360  return _IMP_multifit.ComplementarityRestraint_set_maximum_penetration_score(self, s)
1361 
1362 
1363  def set_maximum_penetration(self, d):
1364  """set_maximum_penetration(ComplementarityRestraint self, double d)"""
1365  return _IMP_multifit.ComplementarityRestraint_set_maximum_penetration(self, d)
1366 
1367 
1368  def set_maximum_separation(self, s):
1369  """set_maximum_separation(ComplementarityRestraint self, double s)"""
1370  return _IMP_multifit.ComplementarityRestraint_set_maximum_separation(self, s)
1371 
1372 
1373  def set_complementarity_thickness(self, th):
1374  """set_complementarity_thickness(ComplementarityRestraint self, double th)"""
1375  return _IMP_multifit.ComplementarityRestraint_set_complementarity_thickness(self, th)
1376 
1377 
1378  def set_complementarity_value(self, th):
1379  """set_complementarity_value(ComplementarityRestraint self, double th)"""
1380  return _IMP_multifit.ComplementarityRestraint_set_complementarity_value(self, th)
1381 
1382 
1383  def set_interior_layer_thickness(self, th):
1384  """set_interior_layer_thickness(ComplementarityRestraint self, double th)"""
1385  return _IMP_multifit.ComplementarityRestraint_set_interior_layer_thickness(self, th)
1386 
1387 
1388  def set_penetration_coefficient(self, pc):
1389  """set_penetration_coefficient(ComplementarityRestraint self, double pc)"""
1390  return _IMP_multifit.ComplementarityRestraint_set_penetration_coefficient(self, pc)
1391 
1392 
1393  def set_complementarity_coefficient(self, cc):
1394  """set_complementarity_coefficient(ComplementarityRestraint self, double cc)"""
1395  return _IMP_multifit.ComplementarityRestraint_set_complementarity_coefficient(self, cc)
1396 
1397 
1398  def set_boundary_coefficient(self, bc):
1399  """set_boundary_coefficient(ComplementarityRestraint self, double bc)"""
1400  return _IMP_multifit.ComplementarityRestraint_set_boundary_coefficient(self, bc)
1401 
1402 
1403  def get_voxel_size(self):
1404  """get_voxel_size(ComplementarityRestraint self) -> float"""
1405  return _IMP_multifit.ComplementarityRestraint_get_voxel_size(self)
1406 
1407 
1408  def do_get_inputs(self):
1409  """do_get_inputs(ComplementarityRestraint self) -> IMP::ModelObjectsTemp"""
1410  return _IMP_multifit.ComplementarityRestraint_do_get_inputs(self)
1411 
1412 
1413  def get_version_info(self):
1414  """get_version_info(ComplementarityRestraint self) -> VersionInfo"""
1415  return _IMP_multifit.ComplementarityRestraint_get_version_info(self)
1416 
1417 
1418  def __str__(self):
1419  """__str__(ComplementarityRestraint self) -> std::string"""
1420  return _IMP_multifit.ComplementarityRestraint___str__(self)
1421 
1422 
1423  def __repr__(self):
1424  """__repr__(ComplementarityRestraint self) -> std::string"""
1425  return _IMP_multifit.ComplementarityRestraint___repr__(self)
1426 
1427 
1428  @staticmethod
1429  def get_from(o):
1430  return _object_cast_to_ComplementarityRestraint(o)
1431 
1432 ComplementarityRestraint_swigregister = _IMP_multifit.ComplementarityRestraint_swigregister
1433 ComplementarityRestraint_swigregister(ComplementarityRestraint)
1434 
1435 
1436 def read_fitting_solutions(fitting_fn):
1437  """read_fitting_solutions(char const * fitting_fn) -> IMP::multifit::FittingSolutionRecords"""
1438  return _IMP_multifit.read_fitting_solutions(fitting_fn)
1439 
1440 def write_fitting_solutions(fitting_fn, fit_sols, num_sols=-1):
1441  """
1442  write_fitting_solutions(char const * fitting_fn, IMP::multifit::FittingSolutionRecords const & fit_sols, int num_sols=-1)
1443  write_fitting_solutions(char const * fitting_fn, IMP::multifit::FittingSolutionRecords const & fit_sols)
1444  """
1445  return _IMP_multifit.write_fitting_solutions(fitting_fn, fit_sols, num_sols)
1446 
1447 def convert_em_to_multifit_format(em_fits):
1448  """convert_em_to_multifit_format(FittingSolutions em_fits) -> IMP::multifit::FittingSolutionRecords"""
1449  return _IMP_multifit.convert_em_to_multifit_format(em_fits)
1450 
1451 def convert_multifit_to_em_format(multifit_fits):
1452  """convert_multifit_to_em_format(IMP::multifit::FittingSolutionRecords const & multifit_fits) -> FittingSolutions"""
1453  return _IMP_multifit.convert_multifit_to_em_format(multifit_fits)
1454 
1455 def convert_transformations_to_multifit_format(trans):
1456  """convert_transformations_to_multifit_format(IMP::algebra::Transformation3Ds const & trans) -> IMP::multifit::FittingSolutionRecords"""
1457  return _IMP_multifit.convert_transformations_to_multifit_format(trans)
1458 
1459 def convert_multifit_format_to_transformations(recs):
1460  """convert_multifit_format_to_transformations(IMP::multifit::FittingSolutionRecords const & recs) -> IMP::algebra::Transformation3Ds"""
1461  return _IMP_multifit.convert_multifit_format_to_transformations(recs)
1462 
1463 def get_close_to_point(fit_sols, mh, ap, dist):
1464  """get_close_to_point(IMP::multifit::FittingSolutionRecords const & fit_sols, Hierarchy mh, Particle ap, IMP::Float dist) -> IMP::multifit::FittingSolutionRecords"""
1465  return _IMP_multifit.get_close_to_point(fit_sols, mh, ap, dist)
1466 class ProbabilisticAnchorGraph(IMP.Object):
1467  """Proxy of C++ IMP::multifit::ProbabilisticAnchorGraph class."""
1468 
1469  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1470 
1471  def __init__(self, anchor_positions):
1472  """__init__(IMP::multifit::ProbabilisticAnchorGraph self, IMP::algebra::Vector3Ds anchor_positions) -> ProbabilisticAnchorGraph"""
1473  this = _IMP_multifit.new_ProbabilisticAnchorGraph(anchor_positions)
1474  try:
1475  self.this.append(this)
1476  except __builtin__.Exception:
1477  self.this = this
1478 
1479  def add_edge(self, i, j):
1480  """add_edge(ProbabilisticAnchorGraph self, int i, int j)"""
1481  return _IMP_multifit.ProbabilisticAnchorGraph_add_edge(self, i, j)
1482 
1483 
1484  def set_particle_probabilities_on_anchors(self, p, sols):
1485  """set_particle_probabilities_on_anchors(ProbabilisticAnchorGraph self, Particle p, IMP::multifit::FittingSolutionRecords sols)"""
1486  return _IMP_multifit.ProbabilisticAnchorGraph_set_particle_probabilities_on_anchors(self, p, sols)
1487 
1488 
1489  def show(self, *args):
1490  """
1491  show(ProbabilisticAnchorGraph self, _ostream out)
1492  show(ProbabilisticAnchorGraph self)
1493  """
1494  return _IMP_multifit.ProbabilisticAnchorGraph_show(self, *args)
1495 
1496 
1497  def get_number_of_anchors(self):
1498  """get_number_of_anchors(ProbabilisticAnchorGraph self) -> unsigned int"""
1499  return _IMP_multifit.ProbabilisticAnchorGraph_get_number_of_anchors(self)
1500 
1501 
1502  def get_number_of_edges(self):
1503  """get_number_of_edges(ProbabilisticAnchorGraph self) -> unsigned int"""
1504  return _IMP_multifit.ProbabilisticAnchorGraph_get_number_of_edges(self)
1505 
1506 
1507  def get_edge_list(self):
1508  """get_edge_list(ProbabilisticAnchorGraph self) -> IMP::IntRanges"""
1509  return _IMP_multifit.ProbabilisticAnchorGraph_get_edge_list(self)
1510 
1511 
1512  def get_anchors(self):
1513  """get_anchors(ProbabilisticAnchorGraph self) -> IMP::algebra::Vector3Ds"""
1514  return _IMP_multifit.ProbabilisticAnchorGraph_get_anchors(self)
1515 
1516 
1517  def get_particle_anchors(self, p, min_prob=0):
1518  """
1519  get_particle_anchors(ProbabilisticAnchorGraph self, Particle p, float min_prob=0) -> IMP::algebra::Vector3Ds
1520  get_particle_anchors(ProbabilisticAnchorGraph self, Particle p) -> IMP::algebra::Vector3Ds
1521  """
1522  return _IMP_multifit.ProbabilisticAnchorGraph_get_particle_anchors(self, p, min_prob)
1523 
1524 
1525  def get_are_probabilities_for_particle_set(self, p):
1526  """get_are_probabilities_for_particle_set(ProbabilisticAnchorGraph self, Particle p) -> bool"""
1527  return _IMP_multifit.ProbabilisticAnchorGraph_get_are_probabilities_for_particle_set(self, p)
1528 
1529 
1530  def get_particle_probabilities(self, p):
1531  """get_particle_probabilities(ProbabilisticAnchorGraph self, Particle p) -> IMP::Floats"""
1532  return _IMP_multifit.ProbabilisticAnchorGraph_get_particle_probabilities(self, p)
1533 
1534 
1535  def get_version_info(self):
1536  """get_version_info(ProbabilisticAnchorGraph self) -> VersionInfo"""
1537  return _IMP_multifit.ProbabilisticAnchorGraph_get_version_info(self)
1538 
1539 
1540  def __str__(self):
1541  """__str__(ProbabilisticAnchorGraph self) -> std::string"""
1542  return _IMP_multifit.ProbabilisticAnchorGraph___str__(self)
1543 
1544 
1545  def __repr__(self):
1546  """__repr__(ProbabilisticAnchorGraph self) -> std::string"""
1547  return _IMP_multifit.ProbabilisticAnchorGraph___repr__(self)
1548 
1549 
1550  @staticmethod
1551  def get_from(o):
1552  return _object_cast_to_ProbabilisticAnchorGraph(o)
1553 
1554 ProbabilisticAnchorGraph_swigregister = _IMP_multifit.ProbabilisticAnchorGraph_swigregister
1555 ProbabilisticAnchorGraph_swigregister(ProbabilisticAnchorGraph)
1556 
1557 class ProteinRecordData(object):
1558  """Proxy of C++ IMP::multifit::ProteinRecordData class."""
1559 
1560  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1561 
1562  def reset_all(self):
1563  """reset_all(ProteinRecordData self)"""
1564  return _IMP_multifit.ProteinRecordData_reset_all(self)
1565 
1566 
1567  def __init__(self, *args):
1568  """
1569  __init__(IMP::multifit::ProteinRecordData self) -> ProteinRecordData
1570  __init__(IMP::multifit::ProteinRecordData self, std::string const & name) -> ProteinRecordData
1571  __init__(IMP::multifit::ProteinRecordData self, std::string const & name, std::string const fn) -> ProteinRecordData
1572  __init__(IMP::multifit::ProteinRecordData self, std::string const & name, int start_res, int end_res, std::string const fn) -> ProteinRecordData
1573  __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
1574  """
1575  this = _IMP_multifit.new_ProteinRecordData(*args)
1576  try:
1577  self.this.append(this)
1578  except __builtin__.Exception:
1579  self.this = this
1580 
1581  def show(self, *args):
1582  """
1583  show(ProteinRecordData self, _ostream out)
1584  show(ProteinRecordData self)
1585  """
1586  return _IMP_multifit.ProteinRecordData_show(self, *args)
1587 
1588  name_ = _swig_property(_IMP_multifit.ProteinRecordData_name__get, _IMP_multifit.ProteinRecordData_name__set)
1589  start_res_ = _swig_property(_IMP_multifit.ProteinRecordData_start_res__get, _IMP_multifit.ProteinRecordData_start_res__set)
1590  end_res_ = _swig_property(_IMP_multifit.ProteinRecordData_end_res__get, _IMP_multifit.ProteinRecordData_end_res__set)
1591  filename_ = _swig_property(_IMP_multifit.ProteinRecordData_filename__get, _IMP_multifit.ProteinRecordData_filename__set)
1592  surface_filename_ = _swig_property(_IMP_multifit.ProteinRecordData_surface_filename__get, _IMP_multifit.ProteinRecordData_surface_filename__set)
1593  ref_filename_ = _swig_property(_IMP_multifit.ProteinRecordData_ref_filename__get, _IMP_multifit.ProteinRecordData_ref_filename__set)
1594 
1595  def __str__(self):
1596  """__str__(ProteinRecordData self) -> std::string"""
1597  return _IMP_multifit.ProteinRecordData___str__(self)
1598 
1599 
1600  def __repr__(self):
1601  """__repr__(ProteinRecordData self) -> std::string"""
1602  return _IMP_multifit.ProteinRecordData___repr__(self)
1603 
1604  __swig_destroy__ = _IMP_multifit.delete_ProteinRecordData
1605  __del__ = lambda self: None
1606 ProteinRecordData_swigregister = _IMP_multifit.ProteinRecordData_swigregister
1607 ProteinRecordData_swigregister(ProteinRecordData)
1608 
1609 class ProteomicsData(IMP.Object):
1610  """Proxy of C++ IMP::multifit::ProteomicsData class."""
1611 
1612  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1613 
1614  def __init__(self):
1615  """__init__(IMP::multifit::ProteomicsData self) -> ProteomicsData"""
1616  this = _IMP_multifit.new_ProteomicsData()
1617  try:
1618  self.this.append(this)
1619  except __builtin__.Exception:
1620  self.this = this
1621 
1622  def add_protein(self, *args):
1623  """
1624  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
1625  add_protein(ProteomicsData self, ProteinRecordData rec) -> int
1626  """
1627  return _IMP_multifit.ProteomicsData_add_protein(self, *args)
1628 
1629 
1630  def find(self, name):
1631  """find(ProteomicsData self, std::string const & name) -> int"""
1632  return _IMP_multifit.ProteomicsData_find(self, name)
1633 
1634 
1635  def add_interaction(self, ii, used_for_filter, linker_len):
1636  """add_interaction(ProteomicsData self, IMP::Ints const & ii, bool used_for_filter, float linker_len)"""
1637  return _IMP_multifit.ProteomicsData_add_interaction(self, ii, used_for_filter, linker_len)
1638 
1639 
1640  def add_cross_link_interaction(self, prot1, res1, prot2, res2, used_in_filter, linker_len):
1641  """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)"""
1642  return _IMP_multifit.ProteomicsData_add_cross_link_interaction(self, prot1, res1, prot2, res2, used_in_filter, linker_len)
1643 
1644 
1645  def add_ev_pair(self, prot1, prot2):
1646  """add_ev_pair(ProteomicsData self, IMP::Int prot1, IMP::Int prot2)"""
1647  return _IMP_multifit.ProteomicsData_add_ev_pair(self, prot1, prot2)
1648 
1649 
1650  def get_number_of_proteins(self):
1651  """get_number_of_proteins(ProteomicsData self) -> int"""
1652  return _IMP_multifit.ProteomicsData_get_number_of_proteins(self)
1653 
1654 
1655  def get_number_of_interactions(self):
1656  """get_number_of_interactions(ProteomicsData self) -> int"""
1657  return _IMP_multifit.ProteomicsData_get_number_of_interactions(self)
1658 
1659 
1660  def get_interaction(self, interaction_ind):
1661  """get_interaction(ProteomicsData self, int interaction_ind) -> IMP::Ints"""
1662  return _IMP_multifit.ProteomicsData_get_interaction(self, interaction_ind)
1663 
1664 
1665  def get_interaction_part_of_filter(self, interaction_ind):
1666  """get_interaction_part_of_filter(ProteomicsData self, int interaction_ind) -> bool"""
1667  return _IMP_multifit.ProteomicsData_get_interaction_part_of_filter(self, interaction_ind)
1668 
1669 
1670  def get_interaction_linker_length(self, interaction_ind):
1671  """get_interaction_linker_length(ProteomicsData self, int interaction_ind) -> int"""
1672  return _IMP_multifit.ProteomicsData_get_interaction_linker_length(self, interaction_ind)
1673 
1674 
1675  def get_number_of_cross_links(self):
1676  """get_number_of_cross_links(ProteomicsData self) -> int"""
1677  return _IMP_multifit.ProteomicsData_get_number_of_cross_links(self)
1678 
1679 
1680  def get_cross_link(self, xlink_ind):
1681  """get_cross_link(ProteomicsData self, int xlink_ind) -> std::pair< IMP::IntPair,IMP::IntPair >"""
1682  return _IMP_multifit.ProteomicsData_get_cross_link(self, xlink_ind)
1683 
1684 
1685  def get_cross_link_part_of_filter(self, xlink_ind):
1686  """get_cross_link_part_of_filter(ProteomicsData self, int xlink_ind) -> bool"""
1687  return _IMP_multifit.ProteomicsData_get_cross_link_part_of_filter(self, xlink_ind)
1688 
1689 
1690  def get_cross_link_length(self, xlink_ind):
1691  """get_cross_link_length(ProteomicsData self, int xlink_ind) -> float"""
1692  return _IMP_multifit.ProteomicsData_get_cross_link_length(self, xlink_ind)
1693 
1694 
1695  def get_number_of_ev_pairs(self):
1696  """get_number_of_ev_pairs(ProteomicsData self) -> int"""
1697  return _IMP_multifit.ProteomicsData_get_number_of_ev_pairs(self)
1698 
1699 
1700  def get_ev_pair(self, ev_ind):
1701  """get_ev_pair(ProteomicsData self, int ev_ind) -> IMP::IntPair"""
1702  return _IMP_multifit.ProteomicsData_get_ev_pair(self, ev_ind)
1703 
1704 
1705  def get_protein_name(self, protein_ind):
1706  """get_protein_name(ProteomicsData self, int protein_ind) -> std::string"""
1707  return _IMP_multifit.ProteomicsData_get_protein_name(self, protein_ind)
1708 
1709 
1710  def get_end_res(self, protein_ind):
1711  """get_end_res(ProteomicsData self, int protein_ind) -> int"""
1712  return _IMP_multifit.ProteomicsData_get_end_res(self, protein_ind)
1713 
1714 
1715  def get_start_res(self, protein_ind):
1716  """get_start_res(ProteomicsData self, int protein_ind) -> int"""
1717  return _IMP_multifit.ProteomicsData_get_start_res(self, protein_ind)
1718 
1719 
1720  def get_protein_filename(self, protein_ind):
1721  """get_protein_filename(ProteomicsData self, int protein_ind) -> std::string"""
1722  return _IMP_multifit.ProteomicsData_get_protein_filename(self, protein_ind)
1723 
1724 
1725  def get_reference_filename(self, protein_ind):
1726  """get_reference_filename(ProteomicsData self, int protein_ind) -> std::string"""
1727  return _IMP_multifit.ProteomicsData_get_reference_filename(self, protein_ind)
1728 
1729 
1730  def get_surface_filename(self, protein_ind):
1731  """get_surface_filename(ProteomicsData self, int protein_ind) -> std::string"""
1732  return _IMP_multifit.ProteomicsData_get_surface_filename(self, protein_ind)
1733 
1734 
1735  def get_protein_data(self, protein_ind):
1736  """get_protein_data(ProteomicsData self, int protein_ind) -> ProteinRecordData"""
1737  return _IMP_multifit.ProteomicsData_get_protein_data(self, protein_ind)
1738 
1739 
1740  def get_version_info(self):
1741  """get_version_info(ProteomicsData self) -> VersionInfo"""
1742  return _IMP_multifit.ProteomicsData_get_version_info(self)
1743 
1744 
1745  def get_num_allowed_violated_interactions(self):
1746  """get_num_allowed_violated_interactions(ProteomicsData self) -> int"""
1747  return _IMP_multifit.ProteomicsData_get_num_allowed_violated_interactions(self)
1748 
1749 
1750  def set_num_allowed_violated_interactions(self, n):
1751  """set_num_allowed_violated_interactions(ProteomicsData self, int n)"""
1752  return _IMP_multifit.ProteomicsData_set_num_allowed_violated_interactions(self, n)
1753 
1754 
1755  def get_num_allowed_violated_cross_links(self):
1756  """get_num_allowed_violated_cross_links(ProteomicsData self) -> int"""
1757  return _IMP_multifit.ProteomicsData_get_num_allowed_violated_cross_links(self)
1758 
1759 
1760  def set_num_allowed_violated_cross_links(self, n):
1761  """set_num_allowed_violated_cross_links(ProteomicsData self, int n)"""
1762  return _IMP_multifit.ProteomicsData_set_num_allowed_violated_cross_links(self, n)
1763 
1764 
1765  def get_num_allowed_violated_ev(self):
1766  """get_num_allowed_violated_ev(ProteomicsData self) -> int"""
1767  return _IMP_multifit.ProteomicsData_get_num_allowed_violated_ev(self)
1768 
1769 
1770  def set_num_allowed_violated_ev(self, n):
1771  """set_num_allowed_violated_ev(ProteomicsData self, int n)"""
1772  return _IMP_multifit.ProteomicsData_set_num_allowed_violated_ev(self, n)
1773 
1774 
1775  def __str__(self):
1776  """__str__(ProteomicsData self) -> std::string"""
1777  return _IMP_multifit.ProteomicsData___str__(self)
1778 
1779 
1780  def __repr__(self):
1781  """__repr__(ProteomicsData self) -> std::string"""
1782  return _IMP_multifit.ProteomicsData___repr__(self)
1783 
1784 
1785  @staticmethod
1786  def get_from(o):
1787  return _object_cast_to_ProteomicsData(o)
1788 
1789 ProteomicsData_swigregister = _IMP_multifit.ProteomicsData_swigregister
1790 ProteomicsData_swigregister(ProteomicsData)
1791 
1792 
1793 def read_proteomics_data(proteomics_fn):
1794  """read_proteomics_data(char const * proteomics_fn) -> ProteomicsData"""
1795  return _IMP_multifit.read_proteomics_data(proteomics_fn)
1796 
1797 def get_partial_proteomics_data(pd, prot_names):
1798  """get_partial_proteomics_data(ProteomicsData pd, IMP::Strings const & prot_names) -> ProteomicsData"""
1799  return _IMP_multifit.get_partial_proteomics_data(pd, prot_names)
1800 class AnchorsData(object):
1801  """Proxy of C++ IMP::multifit::AnchorsData class."""
1802 
1803  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1804 
1805  def __init__(self, *args):
1806  """
1807  __init__(IMP::multifit::AnchorsData self) -> AnchorsData
1808  __init__(IMP::multifit::AnchorsData self, IMP::algebra::Vector3Ds points, IMP::IntPairs edges) -> AnchorsData
1809  """
1810  this = _IMP_multifit.new_AnchorsData(*args)
1811  try:
1812  self.this.append(this)
1813  except __builtin__.Exception:
1814  self.this = this
1815 
1816  def remove_edges_for_node(self, node_ind):
1817  """remove_edges_for_node(AnchorsData self, int node_ind)"""
1818  return _IMP_multifit.AnchorsData_remove_edges_for_node(self, node_ind)
1819 
1820 
1821  def get_number_of_points(self):
1822  """get_number_of_points(AnchorsData self) -> int"""
1823  return _IMP_multifit.AnchorsData_get_number_of_points(self)
1824 
1825 
1826  def get_number_of_edges(self):
1827  """get_number_of_edges(AnchorsData self) -> int"""
1828  return _IMP_multifit.AnchorsData_get_number_of_edges(self)
1829 
1830 
1831  def get_is_point_considered(self, node_ind):
1832  """get_is_point_considered(AnchorsData self, int node_ind) -> bool"""
1833  return _IMP_multifit.AnchorsData_get_is_point_considered(self, node_ind)
1834 
1835 
1836  def show(self, *args):
1837  """
1838  show(AnchorsData self, _ostream out)
1839  show(AnchorsData self)
1840  """
1841  return _IMP_multifit.AnchorsData_show(self, *args)
1842 
1843 
1844  def get_secondary_structure_is_set(self):
1845  """get_secondary_structure_is_set(AnchorsData self) -> bool"""
1846  return _IMP_multifit.AnchorsData_get_secondary_structure_is_set(self)
1847 
1848 
1849  def setup_secondary_structure(self, mdl):
1850  """setup_secondary_structure(AnchorsData self, Model mdl)"""
1851  return _IMP_multifit.AnchorsData_setup_secondary_structure(self, mdl)
1852 
1853 
1854  def set_secondary_structure_probabilities(self, *args):
1855  """
1856  set_secondary_structure_probabilities(AnchorsData self, IMP::Particles const & ssres_ps, IMP::Ints const & indices)
1857  set_secondary_structure_probabilities(AnchorsData self, IMP::Particles const & ssres_ps)
1858  """
1859  return _IMP_multifit.AnchorsData_set_secondary_structure_probabilities(self, *args)
1860 
1861 
1862  def get_secondary_structure_particles(self):
1863  """get_secondary_structure_particles(AnchorsData self) -> IMP::Particles"""
1864  return _IMP_multifit.AnchorsData_get_secondary_structure_particles(self)
1865 
1866  points_ = _swig_property(_IMP_multifit.AnchorsData_points__get, _IMP_multifit.AnchorsData_points__set)
1867  consider_point_ = _swig_property(_IMP_multifit.AnchorsData_consider_point__get, _IMP_multifit.AnchorsData_consider_point__set)
1868  edges_ = _swig_property(_IMP_multifit.AnchorsData_edges__get, _IMP_multifit.AnchorsData_edges__set)
1869 
1870  def __str__(self):
1871  """__str__(AnchorsData self) -> std::string"""
1872  return _IMP_multifit.AnchorsData___str__(self)
1873 
1874 
1875  def __repr__(self):
1876  """__repr__(AnchorsData self) -> std::string"""
1877  return _IMP_multifit.AnchorsData___repr__(self)
1878 
1879  __swig_destroy__ = _IMP_multifit.delete_AnchorsData
1880  __del__ = lambda self: None
1881 AnchorsData_swigregister = _IMP_multifit.AnchorsData_swigregister
1882 AnchorsData_swigregister(AnchorsData)
1883 
1884 
1885 def read_anchors_data(txt_filename):
1886  """read_anchors_data(char const * txt_filename) -> AnchorsData"""
1887  return _IMP_multifit.read_anchors_data(txt_filename)
1888 
1889 def write_txt(txt_filename, ad):
1890  """write_txt(std::string const & txt_filename, AnchorsData ad)"""
1891  return _IMP_multifit.write_txt(txt_filename, ad)
1892 
1893 def write_cmm(cmm_filename, marker_set_name, dpa):
1894  """write_cmm(std::string const & cmm_filename, std::string const & marker_set_name, AnchorsData dpa)"""
1895  return _IMP_multifit.write_cmm(cmm_filename, marker_set_name, dpa)
1896 
1897 def create_coarse_molecule_from_density(dmap, dens_threshold, num_beads, mdl, bead_radius):
1898  """create_coarse_molecule_from_density(DensityMap dmap, float dens_threshold, int num_beads, Model mdl, float bead_radius) -> Hierarchy"""
1899  return _IMP_multifit.create_coarse_molecule_from_density(dmap, dens_threshold, num_beads, mdl, bead_radius)
1900 
1901 def create_hit_map(rb, rb_ref, sols, damp):
1902  """create_hit_map(RigidBody rb, Refiner rb_ref, IMP::multifit::FittingSolutionRecords const & sols, DensityMap damp) -> DensityMap"""
1903  return _IMP_multifit.create_hit_map(rb, rb_ref, sols, damp)
1904 
1905 def get_points_close_to_molecule(mh, points, max_dist):
1906  """get_points_close_to_molecule(Hierarchy mh, IMP::algebra::Vector3Ds const points, IMP::Float max_dist) -> IMP::algebra::Vector3Ds"""
1907  return _IMP_multifit.get_points_close_to_molecule(mh, points, max_dist)
1908 
1909 def get_points_far_from_molecule(mh, points, max_dist):
1910  """get_points_far_from_molecule(Hierarchy mh, IMP::algebra::Vector3Ds const points, IMP::Float max_dist) -> IMP::algebra::Vector3Ds"""
1911  return _IMP_multifit.get_points_far_from_molecule(mh, points, max_dist)
1912 class RadiusOfGyrationRestraint(IMP.Restraint):
1913  """Proxy of C++ IMP::multifit::RadiusOfGyrationRestraint class."""
1914 
1915  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1916 
1917  def __init__(self, ps, num_residues, scale=1.):
1918  """
1919  __init__(IMP::multifit::RadiusOfGyrationRestraint self, IMP::Particles ps, int num_residues, IMP::Float scale=1.) -> RadiusOfGyrationRestraint
1920  __init__(IMP::multifit::RadiusOfGyrationRestraint self, IMP::Particles ps, int num_residues) -> RadiusOfGyrationRestraint
1921  """
1922  this = _IMP_multifit.new_RadiusOfGyrationRestraint(ps, num_residues, scale)
1923  try:
1924  self.this.append(this)
1925  except __builtin__.Exception:
1926  self.this = this
1927 
1928  def do_get_inputs(self):
1929  """do_get_inputs(RadiusOfGyrationRestraint self) -> IMP::ModelObjectsTemp"""
1930  return _IMP_multifit.RadiusOfGyrationRestraint_do_get_inputs(self)
1931 
1932 
1933  def get_version_info(self):
1934  """get_version_info(RadiusOfGyrationRestraint self) -> VersionInfo"""
1935  return _IMP_multifit.RadiusOfGyrationRestraint_get_version_info(self)
1936 
1937 
1938  def set_radius_of_gyration(self, r):
1939  """set_radius_of_gyration(RadiusOfGyrationRestraint self, IMP::Float r)"""
1940  return _IMP_multifit.RadiusOfGyrationRestraint_set_radius_of_gyration(self, r)
1941 
1942 
1943  def get_radius_of_gyration(self):
1944  """get_radius_of_gyration(RadiusOfGyrationRestraint self) -> IMP::Float"""
1945  return _IMP_multifit.RadiusOfGyrationRestraint_get_radius_of_gyration(self)
1946 
1947 
1948  def __str__(self):
1949  """__str__(RadiusOfGyrationRestraint self) -> std::string"""
1950  return _IMP_multifit.RadiusOfGyrationRestraint___str__(self)
1951 
1952 
1953  def __repr__(self):
1954  """__repr__(RadiusOfGyrationRestraint self) -> std::string"""
1955  return _IMP_multifit.RadiusOfGyrationRestraint___repr__(self)
1956 
1957 
1958  @staticmethod
1959  def get_from(o):
1960  return _object_cast_to_RadiusOfGyrationRestraint(o)
1961 
1962 RadiusOfGyrationRestraint_swigregister = _IMP_multifit.RadiusOfGyrationRestraint_swigregister
1963 RadiusOfGyrationRestraint_swigregister(RadiusOfGyrationRestraint)
1964 
1965 
1966 def get_approximated_radius_of_gyration(len):
1967  """get_approximated_radius_of_gyration(int len) -> float"""
1968  return _IMP_multifit.get_approximated_radius_of_gyration(len)
1969 
1970 def get_actual_radius_of_gyration(ps):
1971  """get_actual_radius_of_gyration(IMP::ParticlesTemp ps) -> float"""
1972  return _IMP_multifit.get_actual_radius_of_gyration(ps)
1973 
1974 def get_approximated_radius(len):
1975  """get_approximated_radius(int len) -> float"""
1976  return _IMP_multifit.get_approximated_radius(len)
1977 class ProteinsAnchorsSamplingSpace(object):
1978  """Proxy of C++ IMP::multifit::ProteinsAnchorsSamplingSpace class."""
1979 
1980  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1981 
1982  def __init__(self, prots=None):
1983  """
1984  __init__(IMP::multifit::ProteinsAnchorsSamplingSpace self, ProteomicsData prots=None) -> ProteinsAnchorsSamplingSpace
1985  __init__(IMP::multifit::ProteinsAnchorsSamplingSpace self) -> ProteinsAnchorsSamplingSpace
1986  """
1987  this = _IMP_multifit.new_ProteinsAnchorsSamplingSpace(prots)
1988  try:
1989  self.this.append(this)
1990  except __builtin__.Exception:
1991  self.this = this
1992 
1993  def set_anchors(self, data):
1994  """set_anchors(ProteinsAnchorsSamplingSpace self, AnchorsData data)"""
1995  return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_anchors(self, data)
1996 
1997 
1998  def get_anchors(self):
1999  """get_anchors(ProteinsAnchorsSamplingSpace self) -> AnchorsData"""
2000  return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_anchors(self)
2001 
2002 
2003  def get_anchors_filename(self):
2004  """get_anchors_filename(ProteinsAnchorsSamplingSpace self) -> std::string"""
2005  return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_anchors_filename(self)
2006 
2007 
2008  def set_anchors_filename(self, fn):
2009  """set_anchors_filename(ProteinsAnchorsSamplingSpace self, std::string const & fn)"""
2010  return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_anchors_filename(self, fn)
2011 
2012 
2013  def get_proteomics_data(self):
2014  """get_proteomics_data(ProteinsAnchorsSamplingSpace self) -> ProteomicsData"""
2015  return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_proteomics_data(self)
2016 
2017 
2018  def add_protein(self, rec):
2019  """add_protein(ProteinsAnchorsSamplingSpace self, ProteinRecordData rec)"""
2020  return _IMP_multifit.ProteinsAnchorsSamplingSpace_add_protein(self, rec)
2021 
2022 
2023  def get_paths_for_protein(self, prot_name):
2024  """get_paths_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name) -> IMP::IntsList"""
2025  return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_paths_for_protein(self, prot_name)
2026 
2027 
2028  def set_paths_filename_for_protein(self, prot_name, paths_filename):
2029  """set_paths_filename_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name, std::string const & paths_filename)"""
2030  return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_paths_filename_for_protein(self, prot_name, paths_filename)
2031 
2032 
2033  def get_paths_filename_for_protein(self, prot_name):
2034  """get_paths_filename_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name) -> std::string"""
2035  return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_paths_filename_for_protein(self, prot_name)
2036 
2037 
2038  def set_paths_for_protein(self, prot_name, paths):
2039  """set_paths_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name, IMP::IntsList paths)"""
2040  return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_paths_for_protein(self, prot_name, paths)
2041 
2042 
2043  def show(self, *args):
2044  """
2045  show(ProteinsAnchorsSamplingSpace self, _ostream s)
2046  show(ProteinsAnchorsSamplingSpace self)
2047  """
2048  return _IMP_multifit.ProteinsAnchorsSamplingSpace_show(self, *args)
2049 
2050 
2051  def __str__(self):
2052  """__str__(ProteinsAnchorsSamplingSpace self) -> std::string"""
2053  return _IMP_multifit.ProteinsAnchorsSamplingSpace___str__(self)
2054 
2055 
2056  def __repr__(self):
2057  """__repr__(ProteinsAnchorsSamplingSpace self) -> std::string"""
2058  return _IMP_multifit.ProteinsAnchorsSamplingSpace___repr__(self)
2059 
2060  __swig_destroy__ = _IMP_multifit.delete_ProteinsAnchorsSamplingSpace
2061  __del__ = lambda self: None
2062 ProteinsAnchorsSamplingSpace_swigregister = _IMP_multifit.ProteinsAnchorsSamplingSpace_swigregister
2063 ProteinsAnchorsSamplingSpace_swigregister(ProteinsAnchorsSamplingSpace)
2064 
2065 
2066 def read_protein_anchors_mapping(*args):
2067  """
2068  read_protein_anchors_mapping(ProteomicsData prots, std::string const & anchors_prot_map_fn, int max_paths) -> ProteinsAnchorsSamplingSpace
2069  read_protein_anchors_mapping(ProteomicsData prots, std::string const & anchors_prot_map_fn) -> ProteinsAnchorsSamplingSpace
2070  """
2071  return _IMP_multifit.read_protein_anchors_mapping(*args)
2072 
2073 def write_protein_anchors_mapping(*args):
2074  """
2075  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)
2076  write_protein_anchors_mapping(std::string const & anchors_prot_map_fn, ProteinsAnchorsSamplingSpace pa, IMP::Strings const & prot_names)
2077  """
2078  return _IMP_multifit.write_protein_anchors_mapping(*args)
2079 
2080 def get_part_of_sampling_space(prots_ss, prot_names):
2081  """get_part_of_sampling_space(ProteinsAnchorsSamplingSpace prots_ss, IMP::Strings const & prot_names) -> ProteinsAnchorsSamplingSpace"""
2082  return _IMP_multifit.get_part_of_sampling_space(prots_ss, prot_names)
2083 
2084 def get_partial_assembly_setting_data(prots_sd, prot_names):
2085  """get_partial_assembly_setting_data(SettingsData prots_sd, IMP::Strings const & prot_names) -> SettingsData"""
2086  return _IMP_multifit.get_partial_assembly_setting_data(prots_sd, prot_names)
2087 
2088 def read_paths(*args):
2089  """
2090  read_paths(char const * txt_filename, int max_paths) -> IMP::IntsList
2091  read_paths(char const * txt_filename) -> IMP::IntsList
2092  """
2093  return _IMP_multifit.read_paths(*args)
2094 
2095 def write_paths(paths, txt_filename):
2096  """write_paths(IMP::IntsList const & paths, std::string const & txt_filename)"""
2097  return _IMP_multifit.write_paths(paths, txt_filename)
2098 
2099 def molecule2anchors(mh, k):
2100  """molecule2anchors(Hierarchy mh, int k) -> AnchorsData"""
2101  return _IMP_multifit.molecule2anchors(mh, k)
2102 
2103 def get_anchors_for_density(dmap, number_of_means, density_threshold, pdb_filename, cmm_filename, seg_filename, txt_filename):
2104  """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)"""
2105  return _IMP_multifit.get_anchors_for_density(dmap, number_of_means, density_threshold, pdb_filename, cmm_filename, seg_filename, txt_filename)
2106 
2107 def get_anchor_indices_matching_secondary_structure(ad, ssrs, max_rmsd=0.7):
2108  """
2109  get_anchor_indices_matching_secondary_structure(AnchorsData ad, IMP::atom::SecondaryStructureResidues const & ssrs, IMP::Float max_rmsd=0.7) -> IMP::IntsList
2110  get_anchor_indices_matching_secondary_structure(AnchorsData ad, IMP::atom::SecondaryStructureResidues const & ssrs) -> IMP::IntsList
2111  """
2112  return _IMP_multifit.get_anchor_indices_matching_secondary_structure(ad, ssrs, max_rmsd)
2113 class DominoParams(object):
2114  """Proxy of C++ IMP::multifit::DominoParams class."""
2115 
2116  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2117 
2118  def __init__(self):
2119  """__init__(IMP::multifit::DominoParams self) -> DominoParams"""
2120  this = _IMP_multifit.new_DominoParams()
2121  try:
2122  self.this.append(this)
2123  except __builtin__.Exception:
2124  self.this = this
2125 
2126  def add(self, pt):
2127  """add(DominoParams self, boost::property_tree::ptree const & pt)"""
2128  return _IMP_multifit.DominoParams_add(self, pt)
2129 
2130 
2131  def show(self, *args):
2132  """
2133  show(DominoParams self, _ostream s)
2134  show(DominoParams self)
2135  """
2136  return _IMP_multifit.DominoParams_show(self, *args)
2137 
2138  max_value_threshold_ = _swig_property(_IMP_multifit.DominoParams_max_value_threshold__get, _IMP_multifit.DominoParams_max_value_threshold__set)
2139  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)
2140  max_anchor_penetration_ = _swig_property(_IMP_multifit.DominoParams_max_anchor_penetration__get, _IMP_multifit.DominoParams_max_anchor_penetration__set)
2141  heap_size_ = _swig_property(_IMP_multifit.DominoParams_heap_size__get, _IMP_multifit.DominoParams_heap_size__set)
2142  cache_size_ = _swig_property(_IMP_multifit.DominoParams_cache_size__get, _IMP_multifit.DominoParams_cache_size__set)
2143 
2144  def __str__(self):
2145  """__str__(DominoParams self) -> std::string"""
2146  return _IMP_multifit.DominoParams___str__(self)
2147 
2148 
2149  def __repr__(self):
2150  """__repr__(DominoParams self) -> std::string"""
2151  return _IMP_multifit.DominoParams___repr__(self)
2152 
2153  __swig_destroy__ = _IMP_multifit.delete_DominoParams
2154  __del__ = lambda self: None
2155 DominoParams_swigregister = _IMP_multifit.DominoParams_swigregister
2156 DominoParams_swigregister(DominoParams)
2157 
2158 class XlinkParams(object):
2159  """Proxy of C++ IMP::multifit::XlinkParams class."""
2160 
2161  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2162 
2163  def __init__(self):
2164  """__init__(IMP::multifit::XlinkParams self) -> XlinkParams"""
2165  this = _IMP_multifit.new_XlinkParams()
2166  try:
2167  self.this.append(this)
2168  except __builtin__.Exception:
2169  self.this = this
2170 
2171  def add(self, pt):
2172  """add(XlinkParams self, boost::property_tree::ptree const & pt)"""
2173  return _IMP_multifit.XlinkParams_add(self, pt)
2174 
2175 
2176  def show(self, *args):
2177  """
2178  show(XlinkParams self, _ostream s)
2179  show(XlinkParams self)
2180  """
2181  return _IMP_multifit.XlinkParams_show(self, *args)
2182 
2183  upper_bound_ = _swig_property(_IMP_multifit.XlinkParams_upper_bound__get, _IMP_multifit.XlinkParams_upper_bound__set)
2184  k_ = _swig_property(_IMP_multifit.XlinkParams_k__get, _IMP_multifit.XlinkParams_k__set)
2185  max_xlink_val_ = _swig_property(_IMP_multifit.XlinkParams_max_xlink_val__get, _IMP_multifit.XlinkParams_max_xlink_val__set)
2186  treat_between_residues_ = _swig_property(_IMP_multifit.XlinkParams_treat_between_residues__get, _IMP_multifit.XlinkParams_treat_between_residues__set)
2187 
2188  def __str__(self):
2189  """__str__(XlinkParams self) -> std::string"""
2190  return _IMP_multifit.XlinkParams___str__(self)
2191 
2192 
2193  def __repr__(self):
2194  """__repr__(XlinkParams self) -> std::string"""
2195  return _IMP_multifit.XlinkParams___repr__(self)
2196 
2197  __swig_destroy__ = _IMP_multifit.delete_XlinkParams
2198  __del__ = lambda self: None
2199 XlinkParams_swigregister = _IMP_multifit.XlinkParams_swigregister
2200 XlinkParams_swigregister(XlinkParams)
2201 
2202 class ConnectivityParams(object):
2203  """Proxy of C++ IMP::multifit::ConnectivityParams class."""
2204 
2205  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2206 
2207  def __init__(self):
2208  """__init__(IMP::multifit::ConnectivityParams self) -> ConnectivityParams"""
2209  this = _IMP_multifit.new_ConnectivityParams()
2210  try:
2211  self.this.append(this)
2212  except __builtin__.Exception:
2213  self.this = this
2214 
2215  def add(self, pt):
2216  """add(ConnectivityParams self, boost::property_tree::ptree const & pt)"""
2217  return _IMP_multifit.ConnectivityParams_add(self, pt)
2218 
2219 
2220  def show(self, *args):
2221  """
2222  show(ConnectivityParams self, _ostream s)
2223  show(ConnectivityParams self)
2224  """
2225  return _IMP_multifit.ConnectivityParams_show(self, *args)
2226 
2227  upper_bound_ = _swig_property(_IMP_multifit.ConnectivityParams_upper_bound__get, _IMP_multifit.ConnectivityParams_upper_bound__set)
2228  k_ = _swig_property(_IMP_multifit.ConnectivityParams_k__get, _IMP_multifit.ConnectivityParams_k__set)
2229  max_conn_rest_val_ = _swig_property(_IMP_multifit.ConnectivityParams_max_conn_rest_val__get, _IMP_multifit.ConnectivityParams_max_conn_rest_val__set)
2230 
2231  def __str__(self):
2232  """__str__(ConnectivityParams self) -> std::string"""
2233  return _IMP_multifit.ConnectivityParams___str__(self)
2234 
2235 
2236  def __repr__(self):
2237  """__repr__(ConnectivityParams self) -> std::string"""
2238  return _IMP_multifit.ConnectivityParams___repr__(self)
2239 
2240  __swig_destroy__ = _IMP_multifit.delete_ConnectivityParams
2241  __del__ = lambda self: None
2242 ConnectivityParams_swigregister = _IMP_multifit.ConnectivityParams_swigregister
2243 ConnectivityParams_swigregister(ConnectivityParams)
2244 
2245 class FragmentsParams(object):
2246  """Proxy of C++ IMP::multifit::FragmentsParams class."""
2247 
2248  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2249 
2250  def __init__(self):
2251  """__init__(IMP::multifit::FragmentsParams self) -> FragmentsParams"""
2252  this = _IMP_multifit.new_FragmentsParams()
2253  try:
2254  self.this.append(this)
2255  except __builtin__.Exception:
2256  self.this = this
2257 
2258  def add(self, pt):
2259  """add(FragmentsParams self, boost::property_tree::ptree const & pt)"""
2260  return _IMP_multifit.FragmentsParams_add(self, pt)
2261 
2262 
2263  def show(self, *args):
2264  """
2265  show(FragmentsParams self, _ostream s)
2266  show(FragmentsParams self)
2267  """
2268  return _IMP_multifit.FragmentsParams_show(self, *args)
2269 
2270  frag_len_ = _swig_property(_IMP_multifit.FragmentsParams_frag_len__get, _IMP_multifit.FragmentsParams_frag_len__set)
2271  bead_radius_scale_ = _swig_property(_IMP_multifit.FragmentsParams_bead_radius_scale__get, _IMP_multifit.FragmentsParams_bead_radius_scale__set)
2272  load_atomic_ = _swig_property(_IMP_multifit.FragmentsParams_load_atomic__get, _IMP_multifit.FragmentsParams_load_atomic__set)
2273  subunit_rigid_ = _swig_property(_IMP_multifit.FragmentsParams_subunit_rigid__get, _IMP_multifit.FragmentsParams_subunit_rigid__set)
2274 
2275  def __str__(self):
2276  """__str__(FragmentsParams self) -> std::string"""
2277  return _IMP_multifit.FragmentsParams___str__(self)
2278 
2279 
2280  def __repr__(self):
2281  """__repr__(FragmentsParams self) -> std::string"""
2282  return _IMP_multifit.FragmentsParams___repr__(self)
2283 
2284  __swig_destroy__ = _IMP_multifit.delete_FragmentsParams
2285  __del__ = lambda self: None
2286 FragmentsParams_swigregister = _IMP_multifit.FragmentsParams_swigregister
2287 FragmentsParams_swigregister(FragmentsParams)
2288 
2289 class RogParams(object):
2290  """Proxy of C++ IMP::multifit::RogParams class."""
2291 
2292  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2293 
2294  def __init__(self):
2295  """__init__(IMP::multifit::RogParams self) -> RogParams"""
2296  this = _IMP_multifit.new_RogParams()
2297  try:
2298  self.this.append(this)
2299  except __builtin__.Exception:
2300  self.this = this
2301 
2302  def add(self, pt):
2303  """add(RogParams self, boost::property_tree::ptree const & pt)"""
2304  return _IMP_multifit.RogParams_add(self, pt)
2305 
2306 
2307  def get_max_score(self):
2308  """get_max_score(RogParams self) -> float"""
2309  return _IMP_multifit.RogParams_get_max_score(self)
2310 
2311 
2312  def get_scale(self):
2313  """get_scale(RogParams self) -> float"""
2314  return _IMP_multifit.RogParams_get_scale(self)
2315 
2316 
2317  def show(self, *args):
2318  """
2319  show(RogParams self, _ostream s)
2320  show(RogParams self)
2321  """
2322  return _IMP_multifit.RogParams_show(self, *args)
2323 
2324 
2325  def __str__(self):
2326  """__str__(RogParams self) -> std::string"""
2327  return _IMP_multifit.RogParams___str__(self)
2328 
2329 
2330  def __repr__(self):
2331  """__repr__(RogParams self) -> std::string"""
2332  return _IMP_multifit.RogParams___repr__(self)
2333 
2334  __swig_destroy__ = _IMP_multifit.delete_RogParams
2335  __del__ = lambda self: None
2336 RogParams_swigregister = _IMP_multifit.RogParams_swigregister
2337 RogParams_swigregister(RogParams)
2338 
2339 class EVParams(object):
2340  """Proxy of C++ IMP::multifit::EVParams class."""
2341 
2342  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2343 
2344  def __init__(self):
2345  """__init__(IMP::multifit::EVParams self) -> EVParams"""
2346  this = _IMP_multifit.new_EVParams()
2347  try:
2348  self.this.append(this)
2349  except __builtin__.Exception:
2350  self.this = this
2351 
2352  def add(self, pt):
2353  """add(EVParams self, boost::property_tree::ptree const & pt)"""
2354  return _IMP_multifit.EVParams_add(self, pt)
2355 
2356 
2357  def show(self, *args):
2358  """
2359  show(EVParams self, _ostream s)
2360  show(EVParams self)
2361  """
2362  return _IMP_multifit.EVParams_show(self, *args)
2363 
2364  pair_distance_ = _swig_property(_IMP_multifit.EVParams_pair_distance__get, _IMP_multifit.EVParams_pair_distance__set)
2365  pair_slack_ = _swig_property(_IMP_multifit.EVParams_pair_slack__get, _IMP_multifit.EVParams_pair_slack__set)
2366  hlb_mean_ = _swig_property(_IMP_multifit.EVParams_hlb_mean__get, _IMP_multifit.EVParams_hlb_mean__set)
2367  hlb_k_ = _swig_property(_IMP_multifit.EVParams_hlb_k__get, _IMP_multifit.EVParams_hlb_k__set)
2368  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)
2369  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)
2370  scoring_mode_ = _swig_property(_IMP_multifit.EVParams_scoring_mode__get, _IMP_multifit.EVParams_scoring_mode__set)
2371 
2372  def __str__(self):
2373  """__str__(EVParams self) -> std::string"""
2374  return _IMP_multifit.EVParams___str__(self)
2375 
2376 
2377  def __repr__(self):
2378  """__repr__(EVParams self) -> std::string"""
2379  return _IMP_multifit.EVParams___repr__(self)
2380 
2381  __swig_destroy__ = _IMP_multifit.delete_EVParams
2382  __del__ = lambda self: None
2383 EVParams_swigregister = _IMP_multifit.EVParams_swigregister
2384 EVParams_swigregister(EVParams)
2385 
2386 class FiltersParams(object):
2387  """Proxy of C++ IMP::multifit::FiltersParams class."""
2388 
2389  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2390 
2391  def __init__(self):
2392  """__init__(IMP::multifit::FiltersParams self) -> FiltersParams"""
2393  this = _IMP_multifit.new_FiltersParams()
2394  try:
2395  self.this.append(this)
2396  except __builtin__.Exception:
2397  self.this = this
2398 
2399  def add(self, pt):
2400  """add(FiltersParams self, boost::property_tree::ptree const & pt)"""
2401  return _IMP_multifit.FiltersParams_add(self, pt)
2402 
2403 
2404  def show(self, *args):
2405  """
2406  show(FiltersParams self, _ostream s)
2407  show(FiltersParams self)
2408  """
2409  return _IMP_multifit.FiltersParams_show(self, *args)
2410 
2411  max_num_violated_xlink_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_xlink__get, _IMP_multifit.FiltersParams_max_num_violated_xlink__set)
2412  max_num_violated_conn_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_conn__get, _IMP_multifit.FiltersParams_max_num_violated_conn__set)
2413  max_num_violated_ev_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_ev__get, _IMP_multifit.FiltersParams_max_num_violated_ev__set)
2414 
2415  def __str__(self):
2416  """__str__(FiltersParams self) -> std::string"""
2417  return _IMP_multifit.FiltersParams___str__(self)
2418 
2419 
2420  def __repr__(self):
2421  """__repr__(FiltersParams self) -> std::string"""
2422  return _IMP_multifit.FiltersParams___repr__(self)
2423 
2424  __swig_destroy__ = _IMP_multifit.delete_FiltersParams
2425  __del__ = lambda self: None
2426 FiltersParams_swigregister = _IMP_multifit.FiltersParams_swigregister
2427 FiltersParams_swigregister(FiltersParams)
2428 
2429 class FittingParams(object):
2430  """Proxy of C++ IMP::multifit::FittingParams class."""
2431 
2432  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2433 
2434  def __init__(self):
2435  """__init__(IMP::multifit::FittingParams self) -> FittingParams"""
2436  this = _IMP_multifit.new_FittingParams()
2437  try:
2438  self.this.append(this)
2439  except __builtin__.Exception:
2440  self.this = this
2441 
2442  def add(self, pt):
2443  """add(FittingParams self, boost::property_tree::ptree const & pt)"""
2444  return _IMP_multifit.FittingParams_add(self, pt)
2445 
2446 
2447  def show(self, *args):
2448  """
2449  show(FittingParams self, _ostream s)
2450  show(FittingParams self)
2451  """
2452  return _IMP_multifit.FittingParams_show(self, *args)
2453 
2454  pca_max_angle_diff_ = _swig_property(_IMP_multifit.FittingParams_pca_max_angle_diff__get, _IMP_multifit.FittingParams_pca_max_angle_diff__set)
2455  pca_max_size_diff_ = _swig_property(_IMP_multifit.FittingParams_pca_max_size_diff__get, _IMP_multifit.FittingParams_pca_max_size_diff__set)
2456  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)
2457  max_asmb_fit_score_ = _swig_property(_IMP_multifit.FittingParams_max_asmb_fit_score__get, _IMP_multifit.FittingParams_max_asmb_fit_score__set)
2458 
2459  def __str__(self):
2460  """__str__(FittingParams self) -> std::string"""
2461  return _IMP_multifit.FittingParams___str__(self)
2462 
2463 
2464  def __repr__(self):
2465  """__repr__(FittingParams self) -> std::string"""
2466  return _IMP_multifit.FittingParams___repr__(self)
2467 
2468  __swig_destroy__ = _IMP_multifit.delete_FittingParams
2469  __del__ = lambda self: None
2470 FittingParams_swigregister = _IMP_multifit.FittingParams_swigregister
2471 FittingParams_swigregister(FittingParams)
2472 
2473 class ComplementarityParams(object):
2474  """Proxy of C++ IMP::multifit::ComplementarityParams class."""
2475 
2476  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2477 
2478  def __init__(self):
2479  """__init__(IMP::multifit::ComplementarityParams self) -> ComplementarityParams"""
2480  this = _IMP_multifit.new_ComplementarityParams()
2481  try:
2482  self.this.append(this)
2483  except __builtin__.Exception:
2484  self.this = this
2485 
2486  def add(self, pt):
2487  """add(ComplementarityParams self, boost::property_tree::ptree const & pt)"""
2488  return _IMP_multifit.ComplementarityParams_add(self, pt)
2489 
2490 
2491  def show(self, *args):
2492  """
2493  show(ComplementarityParams self, _ostream s)
2494  show(ComplementarityParams self)
2495  """
2496  return _IMP_multifit.ComplementarityParams_show(self, *args)
2497 
2498  max_score_ = _swig_property(_IMP_multifit.ComplementarityParams_max_score__get, _IMP_multifit.ComplementarityParams_max_score__set)
2499  max_penetration_ = _swig_property(_IMP_multifit.ComplementarityParams_max_penetration__get, _IMP_multifit.ComplementarityParams_max_penetration__set)
2500  interior_layer_thickness_ = _swig_property(_IMP_multifit.ComplementarityParams_interior_layer_thickness__get, _IMP_multifit.ComplementarityParams_interior_layer_thickness__set)
2501  boundary_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_boundary_coef__get, _IMP_multifit.ComplementarityParams_boundary_coef__set)
2502  comp_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_comp_coef__get, _IMP_multifit.ComplementarityParams_comp_coef__set)
2503  penetration_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_penetration_coef__get, _IMP_multifit.ComplementarityParams_penetration_coef__set)
2504 
2505  def __str__(self):
2506  """__str__(ComplementarityParams self) -> std::string"""
2507  return _IMP_multifit.ComplementarityParams___str__(self)
2508 
2509 
2510  def __repr__(self):
2511  """__repr__(ComplementarityParams self) -> std::string"""
2512  return _IMP_multifit.ComplementarityParams___repr__(self)
2513 
2514  __swig_destroy__ = _IMP_multifit.delete_ComplementarityParams
2515  __del__ = lambda self: None
2516 ComplementarityParams_swigregister = _IMP_multifit.ComplementarityParams_swigregister
2517 ComplementarityParams_swigregister(ComplementarityParams)
2518 
2519 class AlignmentParams(object):
2520  """Proxy of C++ IMP::multifit::AlignmentParams class."""
2521 
2522  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2523 
2524  def __init__(self, param_filename):
2525  """__init__(IMP::multifit::AlignmentParams self, char const * param_filename) -> AlignmentParams"""
2526  this = _IMP_multifit.new_AlignmentParams(param_filename)
2527  try:
2528  self.this.append(this)
2529  except __builtin__.Exception:
2530  self.this = this
2531 
2532  def get_domino_params(self):
2533  """get_domino_params(AlignmentParams self) -> DominoParams"""
2534  return _IMP_multifit.AlignmentParams_get_domino_params(self)
2535 
2536 
2537  def get_fitting_params(self):
2538  """get_fitting_params(AlignmentParams self) -> FittingParams"""
2539  return _IMP_multifit.AlignmentParams_get_fitting_params(self)
2540 
2541 
2542  def get_complementarity_params(self):
2543  """get_complementarity_params(AlignmentParams self) -> ComplementarityParams"""
2544  return _IMP_multifit.AlignmentParams_get_complementarity_params(self)
2545 
2546 
2547  def get_xlink_params(self):
2548  """get_xlink_params(AlignmentParams self) -> XlinkParams"""
2549  return _IMP_multifit.AlignmentParams_get_xlink_params(self)
2550 
2551 
2552  def get_connectivity_params(self):
2553  """get_connectivity_params(AlignmentParams self) -> ConnectivityParams"""
2554  return _IMP_multifit.AlignmentParams_get_connectivity_params(self)
2555 
2556 
2557  def get_rog_params(self):
2558  """get_rog_params(AlignmentParams self) -> RogParams"""
2559  return _IMP_multifit.AlignmentParams_get_rog_params(self)
2560 
2561 
2562  def get_fragments_params(self):
2563  """get_fragments_params(AlignmentParams self) -> FragmentsParams"""
2564  return _IMP_multifit.AlignmentParams_get_fragments_params(self)
2565 
2566 
2567  def get_filters_params(self):
2568  """get_filters_params(AlignmentParams self) -> FiltersParams"""
2569  return _IMP_multifit.AlignmentParams_get_filters_params(self)
2570 
2571 
2572  def get_ev_params(self):
2573  """get_ev_params(AlignmentParams self) -> EVParams"""
2574  return _IMP_multifit.AlignmentParams_get_ev_params(self)
2575 
2576 
2577  def show(self, *args):
2578  """
2579  show(AlignmentParams self, _ostream s)
2580  show(AlignmentParams self)
2581  """
2582  return _IMP_multifit.AlignmentParams_show(self, *args)
2583 
2584 
2585  def __str__(self):
2586  """__str__(AlignmentParams self) -> std::string"""
2587  return _IMP_multifit.AlignmentParams___str__(self)
2588 
2589 
2590  def __repr__(self):
2591  """__repr__(AlignmentParams self) -> std::string"""
2592  return _IMP_multifit.AlignmentParams___repr__(self)
2593 
2594  __swig_destroy__ = _IMP_multifit.delete_AlignmentParams
2595  __del__ = lambda self: None
2596 AlignmentParams_swigregister = _IMP_multifit.AlignmentParams_swigregister
2597 AlignmentParams_swigregister(AlignmentParams)
2598 
2599 class ProteomicsEMAlignmentAtomic(IMP.Object):
2600  """Proxy of C++ IMP::multifit::ProteomicsEMAlignmentAtomic class."""
2601 
2602  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2603 
2604  def __init__(self, mapping_data, asmb_data, align_param):
2605  """__init__(IMP::multifit::ProteomicsEMAlignmentAtomic self, ProteinsAnchorsSamplingSpace mapping_data, SettingsData asmb_data, AlignmentParams align_param) -> ProteomicsEMAlignmentAtomic"""
2606  this = _IMP_multifit.new_ProteomicsEMAlignmentAtomic(mapping_data, asmb_data, align_param)
2607  try:
2608  self.this.append(this)
2609  except __builtin__.Exception:
2610  self.this = this
2611 
2612  def align(self):
2613  """align(ProteomicsEMAlignmentAtomic self)"""
2614  return _IMP_multifit.ProteomicsEMAlignmentAtomic_align(self)
2615 
2616 
2617  def add_all_restraints(self):
2618  """add_all_restraints(ProteomicsEMAlignmentAtomic self)"""
2619  return _IMP_multifit.ProteomicsEMAlignmentAtomic_add_all_restraints(self)
2620 
2621 
2622  def get_restraint_set(self):
2623  """get_restraint_set(ProteomicsEMAlignmentAtomic self) -> RestraintSet"""
2624  return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_restraint_set(self)
2625 
2626 
2627  def add_states_and_filters(self):
2628  """add_states_and_filters(ProteomicsEMAlignmentAtomic self)"""
2629  return _IMP_multifit.ProteomicsEMAlignmentAtomic_add_states_and_filters(self)
2630 
2631 
2632  def show_domino_merge_tree(self):
2633  """show_domino_merge_tree(ProteomicsEMAlignmentAtomic self)"""
2634  return _IMP_multifit.ProteomicsEMAlignmentAtomic_show_domino_merge_tree(self)
2635 
2636 
2637  def get_combinations(self, uniques=False):
2638  """
2639  get_combinations(ProteomicsEMAlignmentAtomic self, bool uniques=False) -> IMP::domino::Assignments
2640  get_combinations(ProteomicsEMAlignmentAtomic self) -> IMP::domino::Assignments
2641  """
2642  return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_combinations(self, uniques)
2643 
2644 
2645  def set_density_map(self, dmap, threshold):
2646  """set_density_map(ProteomicsEMAlignmentAtomic self, DensityMap dmap, float threshold)"""
2647  return _IMP_multifit.ProteomicsEMAlignmentAtomic_set_density_map(self, dmap, threshold)
2648 
2649 
2650  def get_molecules(self):
2651  """get_molecules(ProteomicsEMAlignmentAtomic self) -> IMP::atom::Hierarchies"""
2652  return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_molecules(self)
2653 
2654 
2655  def get_rigid_bodies(self):
2656  """get_rigid_bodies(ProteomicsEMAlignmentAtomic self) -> IMP::core::RigidBodies"""
2657  return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_rigid_bodies(self)
2658 
2659 
2660  def load_combination_of_states(self, state4particles):
2661  """load_combination_of_states(ProteomicsEMAlignmentAtomic self, IMP::Ints const & state4particles)"""
2662  return _IMP_multifit.ProteomicsEMAlignmentAtomic_load_combination_of_states(self, state4particles)
2663 
2664 
2665  def show_scores_header(self, *args):
2666  """
2667  show_scores_header(ProteomicsEMAlignmentAtomic self, _ostream ous)
2668  show_scores_header(ProteomicsEMAlignmentAtomic self)
2669  """
2670  return _IMP_multifit.ProteomicsEMAlignmentAtomic_show_scores_header(self, *args)
2671 
2672 
2673  def get_model(self):
2674  """get_model(ProteomicsEMAlignmentAtomic self) -> Model"""
2675  return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_model(self)
2676 
2677 
2678  def set_fast_scoring(self, state):
2679  """set_fast_scoring(ProteomicsEMAlignmentAtomic self, bool state)"""
2680  return _IMP_multifit.ProteomicsEMAlignmentAtomic_set_fast_scoring(self, state)
2681 
2682 
2683  def get_version_info(self):
2684  """get_version_info(ProteomicsEMAlignmentAtomic self) -> VersionInfo"""
2685  return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_version_info(self)
2686 
2687 
2688  def __str__(self):
2689  """__str__(ProteomicsEMAlignmentAtomic self) -> std::string"""
2690  return _IMP_multifit.ProteomicsEMAlignmentAtomic___str__(self)
2691 
2692 
2693  def __repr__(self):
2694  """__repr__(ProteomicsEMAlignmentAtomic self) -> std::string"""
2695  return _IMP_multifit.ProteomicsEMAlignmentAtomic___repr__(self)
2696 
2697 
2698  @staticmethod
2699  def get_from(o):
2700  return _object_cast_to_ProteomicsEMAlignmentAtomic(o)
2701 
2702 ProteomicsEMAlignmentAtomic_swigregister = _IMP_multifit.ProteomicsEMAlignmentAtomic_swigregister
2703 ProteomicsEMAlignmentAtomic_swigregister(ProteomicsEMAlignmentAtomic)
2704 
2705 
2706 def write_connolly_surface(atoms, fn, density, probe_radius):
2707  """write_connolly_surface(IMP::atom::Atoms atoms, TextOutput fn, float density, float probe_radius)"""
2708  return _IMP_multifit.write_connolly_surface(atoms, fn, density, probe_radius)
2709 class Ensemble(IMP.Object):
2710  """Proxy of C++ IMP::multifit::Ensemble class."""
2711 
2712  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2713 
2714  def load_combination(self, fit_comb):
2715  """load_combination(Ensemble self, IMP::Ints fit_comb)"""
2716  return _IMP_multifit.Ensemble_load_combination(self, fit_comb)
2717 
2718 
2719  def unload_combination(self, fit_comb):
2720  """unload_combination(Ensemble self, IMP::Ints fit_comb)"""
2721  return _IMP_multifit.Ensemble_unload_combination(self, fit_comb)
2722 
2723 
2724  def add_component_and_fits(self, mh, fits):
2725  """add_component_and_fits(Ensemble self, Hierarchy mh, IMP::multifit::FittingSolutionRecords const & fits)"""
2726  return _IMP_multifit.Ensemble_add_component_and_fits(self, mh, fits)
2727 
2728 
2729  def get_molecules(self):
2730  """get_molecules(Ensemble self) -> IMP::atom::Hierarchies"""
2731  return _IMP_multifit.Ensemble_get_molecules(self)
2732 
2733 
2734  def get_rigid_bodies(self):
2735  """get_rigid_bodies(Ensemble self) -> IMP::core::RigidBodies"""
2736  return _IMP_multifit.Ensemble_get_rigid_bodies(self)
2737 
2738 
2739  def get_rmsd(self, second_xyz):
2740  """get_rmsd(Ensemble self, IMP::core::XYZs const & second_xyz) -> float"""
2741  return _IMP_multifit.Ensemble_get_rmsd(self, second_xyz)
2742 
2743 
2744  def __init__(self, sd, mapping_data):
2745  """__init__(IMP::multifit::Ensemble self, SettingsData sd, ProteinsAnchorsSamplingSpace mapping_data) -> Ensemble"""
2746  this = _IMP_multifit.new_Ensemble(sd, mapping_data)
2747  try:
2748  self.this.append(this)
2749  except __builtin__.Exception:
2750  self.this = this
2751 
2752  def score_by_restraints(self, rs, combinations):
2753  """score_by_restraints(Ensemble self, IMP::Restraints rs, IMP::IntsList const & combinations) -> std::vector< IMP::Floats,std::allocator< IMP::Floats > >"""
2754  return _IMP_multifit.Ensemble_score_by_restraints(self, rs, combinations)
2755 
2756 
2757  def get_version_info(self):
2758  """get_version_info(Ensemble self) -> VersionInfo"""
2759  return _IMP_multifit.Ensemble_get_version_info(self)
2760 
2761 
2762  def __str__(self):
2763  """__str__(Ensemble self) -> std::string"""
2764  return _IMP_multifit.Ensemble___str__(self)
2765 
2766 
2767  def __repr__(self):
2768  """__repr__(Ensemble self) -> std::string"""
2769  return _IMP_multifit.Ensemble___repr__(self)
2770 
2771 
2772  @staticmethod
2773  def get_from(o):
2774  return _object_cast_to_Ensemble(o)
2775 
2776 Ensemble_swigregister = _IMP_multifit.Ensemble_swigregister
2777 Ensemble_swigregister(Ensemble)
2778 
2779 
2780 def load_ensemble(sd, mdl, mapping_data):
2781  """load_ensemble(SettingsData sd, Model mdl, ProteinsAnchorsSamplingSpace mapping_data) -> Ensemble"""
2782  return _IMP_multifit.load_ensemble(sd, mdl, mapping_data)
2783 class RigidLeavesRefiner(IMP.Refiner):
2784  """Proxy of C++ IMP::multifit::RigidLeavesRefiner class."""
2785 
2786  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2787 
2788  def __init__(self, *args):
2789  """
2790  __init__(IMP::multifit::RigidLeavesRefiner self, std::string name) -> RigidLeavesRefiner
2791  __init__(IMP::multifit::RigidLeavesRefiner self) -> RigidLeavesRefiner
2792  """
2793  this = _IMP_multifit.new_RigidLeavesRefiner(*args)
2794  try:
2795  self.this.append(this)
2796  except __builtin__.Exception:
2797  self.this = this
2798 
2799  def do_get_inputs(self, m, pis):
2800  """do_get_inputs(RigidLeavesRefiner self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2801  return _IMP_multifit.RigidLeavesRefiner_do_get_inputs(self, m, pis)
2802 
2803 
2804  def get_version_info(self):
2805  """get_version_info(RigidLeavesRefiner self) -> VersionInfo"""
2806  return _IMP_multifit.RigidLeavesRefiner_get_version_info(self)
2807 
2808 
2809  def __str__(self):
2810  """__str__(RigidLeavesRefiner self) -> std::string"""
2811  return _IMP_multifit.RigidLeavesRefiner___str__(self)
2812 
2813 
2814  def __repr__(self):
2815  """__repr__(RigidLeavesRefiner self) -> std::string"""
2816  return _IMP_multifit.RigidLeavesRefiner___repr__(self)
2817 
2818 
2819  @staticmethod
2820  def get_from(o):
2821  return _object_cast_to_RigidLeavesRefiner(o)
2822 
2823 RigidLeavesRefiner_swigregister = _IMP_multifit.RigidLeavesRefiner_swigregister
2824 RigidLeavesRefiner_swigregister(RigidLeavesRefiner)
2825 
2826 
2827 _all_commands = ["param", "anchors", "fit_fft", "cluster", "add_fit_rmsd",
2828  "indexes", "proteomics", "align", "models", "transforms",
2829  "score", "merge_tree", "reference", "refine_fft", "segment"]
2830 
2831 
2832 def get_module_version():
2833  """get_module_version() -> std::string const"""
2834  return _IMP_multifit.get_module_version()
2835 
2836 def get_example_path(fname):
2837  """get_example_path(std::string fname) -> std::string"""
2838  return _IMP_multifit.get_example_path(fname)
2839 
2840 def get_data_path(fname):
2841  """get_data_path(std::string fname) -> std::string"""
2842  return _IMP_multifit.get_data_path(fname)
2843 
2844 from . import _version_check
2845 _version_check.check_version(get_module_version())
2846 __version__ = get_module_version()
2847 
2848 
2849 
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:54
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.