IMP logo
IMP Reference Guide  2.11.1
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 2007-2019 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_NUMPY = _IMP_multifit.IMP_KERNEL_HAS_NUMPY
239 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_multifit.IMP_KERNEL_HAS_GPERFTOOLS
240 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_multifit.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
241 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_multifit.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
242 IMPKERNEL_SHOW_WARNINGS = _IMP_multifit.IMPKERNEL_SHOW_WARNINGS
243 
244 import sys
245 class _DirectorObjects(object):
246  """@internal Simple class to keep references to director objects
247  to prevent premature deletion."""
248  def __init__(self):
249  self._objects = []
250  def register(self, obj):
251  """Take a reference to a director object; will only work for
252  refcounted C++ classes"""
253  if hasattr(obj, 'get_ref_count'):
254  self._objects.append(obj)
255  def cleanup(self):
256  """Only drop our reference and allow cleanup by Python if no other
257  Python references exist (we hold 3 references: one in self._objects,
258  one in x, and one in the argument list for getrefcount) *and* no
259  other C++ references exist (the Python object always holds one)"""
260  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
261  or x.get_ref_count() > 1]
262 # Do in two steps so the references are kept until the end of the
263 # function (deleting references may trigger a fresh call to this method)
264  self._objects = objs
265  def get_object_count(self):
266  """Get number of director objects (useful for testing only)"""
267  return len(self._objects)
268 _director_objects = _DirectorObjects()
269 
270 class _ostream(object):
271  """Proxy of C++ std::ostream class."""
272 
273  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
274 
275  def __init__(self, *args, **kwargs):
276  raise AttributeError("No constructor defined")
277  __repr__ = _swig_repr
278 
279  def write(self, osa_buf):
280  """write(_ostream self, char const * osa_buf)"""
281  return _IMP_multifit._ostream_write(self, osa_buf)
282 
283 _ostream_swigregister = _IMP_multifit._ostream_swigregister
284 _ostream_swigregister(_ostream)
285 
286 IMP_COMPILER_HAS_OVERRIDE = _IMP_multifit.IMP_COMPILER_HAS_OVERRIDE
287 IMP_COMPILER_HAS_FINAL = _IMP_multifit.IMP_COMPILER_HAS_FINAL
288 IMP_HAS_NOEXCEPT = _IMP_multifit.IMP_HAS_NOEXCEPT
289 IMP_C_OPEN_BINARY = _IMP_multifit.IMP_C_OPEN_BINARY
290 import IMP
291 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CGAL_HAS_BOOST_FILESYSTEM
292 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
293 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CGAL_HAS_BOOST_RANDOM
294 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CGAL_HAS_BOOST_SYSTEM
295 IMP_CGAL_HAS_NUMPY = _IMP_multifit.IMP_CGAL_HAS_NUMPY
296 IMPCGAL_SHOW_WARNINGS = _IMP_multifit.IMPCGAL_SHOW_WARNINGS
297 import IMP.cgal
298 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_multifit.IMP_ALGEBRA_HAS_IMP_CGAL
299 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
300 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
301 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_RANDOM
302 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_SYSTEM
303 IMP_ALGEBRA_HAS_CGAL = _IMP_multifit.IMP_ALGEBRA_HAS_CGAL
304 IMP_ALGEBRA_HAS_NUMPY = _IMP_multifit.IMP_ALGEBRA_HAS_NUMPY
305 IMP_ALGEBRA_HAS_ANN = _IMP_multifit.IMP_ALGEBRA_HAS_ANN
306 IMPALGEBRA_SHOW_WARNINGS = _IMP_multifit.IMPALGEBRA_SHOW_WARNINGS
307 import IMP.algebra
308 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_multifit.IMP_DISPLAY_HAS_IMP_CGAL
309 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
310 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
311 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_RANDOM
312 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_SYSTEM
313 IMP_DISPLAY_HAS_CGAL = _IMP_multifit.IMP_DISPLAY_HAS_CGAL
314 IMP_DISPLAY_HAS_NUMPY = _IMP_multifit.IMP_DISPLAY_HAS_NUMPY
315 IMPDISPLAY_SHOW_WARNINGS = _IMP_multifit.IMPDISPLAY_SHOW_WARNINGS
316 import IMP.display
317 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
318 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
319 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
320 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
321 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
322 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_CGAL
323 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_HDF5
324 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_NUMPY
325 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_multifit.IMPSCOREFUNCTOR_SHOW_WARNINGS
326 import IMP.score_functor
327 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_multifit.IMP_STATISTICS_HAS_IMP_CGAL
328 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
329 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
330 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_RANDOM
331 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_SYSTEM
332 IMP_STATISTICS_HAS_CGAL = _IMP_multifit.IMP_STATISTICS_HAS_CGAL
333 IMP_STATISTICS_HAS_NUMPY = _IMP_multifit.IMP_STATISTICS_HAS_NUMPY
334 IMPSTATISTICS_SHOW_WARNINGS = _IMP_multifit.IMPSTATISTICS_SHOW_WARNINGS
335 import IMP.statistics
336 IMP_CORE_HAS_IMP_CGAL = _IMP_multifit.IMP_CORE_HAS_IMP_CGAL
337 IMP_CORE_HAS_IMP_KERNEL = _IMP_multifit.IMP_CORE_HAS_IMP_KERNEL
338 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CORE_HAS_BOOST_FILESYSTEM
339 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
340 IMP_CORE_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CORE_HAS_BOOST_RANDOM
341 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CORE_HAS_BOOST_SYSTEM
342 IMP_CORE_HAS_CGAL = _IMP_multifit.IMP_CORE_HAS_CGAL
343 IMP_CORE_HAS_HDF5 = _IMP_multifit.IMP_CORE_HAS_HDF5
344 IMP_CORE_HAS_NUMPY = _IMP_multifit.IMP_CORE_HAS_NUMPY
345 IMPCORE_SHOW_WARNINGS = _IMP_multifit.IMPCORE_SHOW_WARNINGS
346 import IMP.core
347 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_multifit.IMP_CONTAINER_HAS_IMP_ALGEBRA
348 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_multifit.IMP_CONTAINER_HAS_IMP_CGAL
349 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_multifit.IMP_CONTAINER_HAS_IMP_DISPLAY
350 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_multifit.IMP_CONTAINER_HAS_IMP_KERNEL
351 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
352 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
353 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
354 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_RANDOM
355 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_SYSTEM
356 IMP_CONTAINER_HAS_CGAL = _IMP_multifit.IMP_CONTAINER_HAS_CGAL
357 IMP_CONTAINER_HAS_HDF5 = _IMP_multifit.IMP_CONTAINER_HAS_HDF5
358 IMP_CONTAINER_HAS_NUMPY = _IMP_multifit.IMP_CONTAINER_HAS_NUMPY
359 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_multifit.IMP_CONTAINER_HAS_PYTHON_IHM
360 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_multifit.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
361 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_multifit.IMP_CONTAINER_HAS_ROBIN_MAP
362 IMPCONTAINER_SHOW_WARNINGS = _IMP_multifit.IMPCONTAINER_SHOW_WARNINGS
363 import IMP.container
364 IMP_ATOM_HAS_IMP_CGAL = _IMP_multifit.IMP_ATOM_HAS_IMP_CGAL
365 IMP_ATOM_HAS_IMP_KERNEL = _IMP_multifit.IMP_ATOM_HAS_IMP_KERNEL
366 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
367 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
368 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_multifit.IMP_ATOM_HAS_BOOST_RANDOM
369 IMP_ATOM_HAS_BOOST_REGEX = _IMP_multifit.IMP_ATOM_HAS_BOOST_REGEX
370 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_ATOM_HAS_BOOST_SYSTEM
371 IMP_ATOM_HAS_CGAL = _IMP_multifit.IMP_ATOM_HAS_CGAL
372 IMP_ATOM_HAS_HDF5 = _IMP_multifit.IMP_ATOM_HAS_HDF5
373 IMP_ATOM_HAS_NUMPY = _IMP_multifit.IMP_ATOM_HAS_NUMPY
374 IMP_ATOM_HAS_PYTHON_IHM = _IMP_multifit.IMP_ATOM_HAS_PYTHON_IHM
375 IMPATOM_SHOW_WARNINGS = _IMP_multifit.IMPATOM_SHOW_WARNINGS
376 IMP_ATOM_TYPE_INDEX = _IMP_multifit.IMP_ATOM_TYPE_INDEX
377 IMP_RESIDUE_TYPE_INDEX = _IMP_multifit.IMP_RESIDUE_TYPE_INDEX
378 IMP_HIERARCHY_TYPE_INDEX = _IMP_multifit.IMP_HIERARCHY_TYPE_INDEX
379 IMP_CHAIN_TYPE_INDEX = _IMP_multifit.IMP_CHAIN_TYPE_INDEX
380 import IMP.atom
381 IMP_EM_HAS_IMP_CGAL = _IMP_multifit.IMP_EM_HAS_IMP_CGAL
382 IMP_EM_HAS_IMP_CONTAINER = _IMP_multifit.IMP_EM_HAS_IMP_CONTAINER
383 IMP_EM_HAS_IMP_DISPLAY = _IMP_multifit.IMP_EM_HAS_IMP_DISPLAY
384 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_EM_HAS_IMP_SCORE_FUNCTOR
385 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_EM_HAS_BOOST_FILESYSTEM
386 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
387 IMP_EM_HAS_BOOST_RANDOM = _IMP_multifit.IMP_EM_HAS_BOOST_RANDOM
388 IMP_EM_HAS_BOOST_REGEX = _IMP_multifit.IMP_EM_HAS_BOOST_REGEX
389 IMP_EM_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_EM_HAS_BOOST_SYSTEM
390 IMP_EM_HAS_CGAL = _IMP_multifit.IMP_EM_HAS_CGAL
391 IMP_EM_HAS_HDF5 = _IMP_multifit.IMP_EM_HAS_HDF5
392 IMP_EM_HAS_NUMPY = _IMP_multifit.IMP_EM_HAS_NUMPY
393 IMP_EM_HAS_PYTHON_IHM = _IMP_multifit.IMP_EM_HAS_PYTHON_IHM
394 IMPEM_SHOW_WARNINGS = _IMP_multifit.IMPEM_SHOW_WARNINGS
395 import IMP.em
396 IMP_RMF_HAS_IMP_CGAL = _IMP_multifit.IMP_RMF_HAS_IMP_CGAL
397 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
398 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_RMF_HAS_BOOST_FILESYSTEM
399 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
400 IMP_RMF_HAS_BOOST_RANDOM = _IMP_multifit.IMP_RMF_HAS_BOOST_RANDOM
401 IMP_RMF_HAS_BOOST_REGEX = _IMP_multifit.IMP_RMF_HAS_BOOST_REGEX
402 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_RMF_HAS_BOOST_SYSTEM
403 IMP_RMF_HAS_CGAL = _IMP_multifit.IMP_RMF_HAS_CGAL
404 IMP_RMF_HAS_HDF5 = _IMP_multifit.IMP_RMF_HAS_HDF5
405 IMP_RMF_HAS_NUMPY = _IMP_multifit.IMP_RMF_HAS_NUMPY
406 IMP_RMF_HAS_PYTHON_IHM = _IMP_multifit.IMP_RMF_HAS_PYTHON_IHM
407 IMPRMF_SHOW_WARNINGS = _IMP_multifit.IMPRMF_SHOW_WARNINGS
408 import IMP.rmf
409 import RMF
410 IMP_DOMINO_HAS_IMP_ATOM = _IMP_multifit.IMP_DOMINO_HAS_IMP_ATOM
411 IMP_DOMINO_HAS_IMP_CGAL = _IMP_multifit.IMP_DOMINO_HAS_IMP_CGAL
412 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_multifit.IMP_DOMINO_HAS_IMP_KERNEL
413 IMP_DOMINO_HAS_IMP_RMF = _IMP_multifit.IMP_DOMINO_HAS_IMP_RMF
414 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
415 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_FILESYSTEM
416 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
417 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_RANDOM
418 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_multifit.IMP_DOMINO_HAS_BOOST_REGEX
419 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_SYSTEM
420 IMP_DOMINO_HAS_CGAL = _IMP_multifit.IMP_DOMINO_HAS_CGAL
421 IMP_DOMINO_HAS_HDF5 = _IMP_multifit.IMP_DOMINO_HAS_HDF5
422 IMP_DOMINO_HAS_NUMPY = _IMP_multifit.IMP_DOMINO_HAS_NUMPY
423 IMP_DOMINO_HAS_RMF = _IMP_multifit.IMP_DOMINO_HAS_RMF
424 IMP_DOMINO_HAS_PYTHON_IHM = _IMP_multifit.IMP_DOMINO_HAS_PYTHON_IHM
425 IMPDOMINO_SHOW_WARNINGS = _IMP_multifit.IMPDOMINO_SHOW_WARNINGS
426 import RMF_HDF5
427 import IMP.domino
428 IMP_MULTIFIT_HAS_IMP_CGAL = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_CGAL
429 IMP_MULTIFIT_HAS_IMP_CONTAINER = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_CONTAINER
430 IMP_MULTIFIT_HAS_IMP_DISPLAY = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_DISPLAY
431 IMP_MULTIFIT_HAS_IMP_KERNEL = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_KERNEL
432 IMP_MULTIFIT_HAS_IMP_RMF = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_RMF
433 IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR
434 IMP_MULTIFIT_HAS_BOOST_GRAPH = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_GRAPH
435 IMP_MULTIFIT_HAS_BOOST_RANDOM = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_RANDOM
436 IMP_MULTIFIT_HAS_BOOST_REGEX = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_REGEX
437 IMP_MULTIFIT_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_SYSTEM
438 IMP_MULTIFIT_HAS_CGAL = _IMP_multifit.IMP_MULTIFIT_HAS_CGAL
439 IMP_MULTIFIT_HAS_HDF5 = _IMP_multifit.IMP_MULTIFIT_HAS_HDF5
440 IMP_MULTIFIT_HAS_NUMPY = _IMP_multifit.IMP_MULTIFIT_HAS_NUMPY
441 IMP_MULTIFIT_HAS_RMF = _IMP_multifit.IMP_MULTIFIT_HAS_RMF
442 IMP_MULTIFIT_HAS_PYTHON_IHM = _IMP_multifit.IMP_MULTIFIT_HAS_PYTHON_IHM
443 IMPMULTIFIT_SHOW_WARNINGS = _IMP_multifit.IMPMULTIFIT_SHOW_WARNINGS
444 
445 _object_types.append("RadiusOfGyrationRestraint")
446 
447 
448 def _object_cast_to_RadiusOfGyrationRestraint(o):
449  """_object_cast_to_RadiusOfGyrationRestraint(Object o) -> RadiusOfGyrationRestraint"""
450  return _IMP_multifit._object_cast_to_RadiusOfGyrationRestraint(o)
451 
452 _object_types.append("ComponentHeader")
453 
454 
455 def _object_cast_to_ComponentHeader(o):
456  """_object_cast_to_ComponentHeader(Object o) -> ComponentHeader"""
457  return _IMP_multifit._object_cast_to_ComponentHeader(o)
458 
459 _object_types.append("AssemblyHeader")
460 
461 
462 def _object_cast_to_AssemblyHeader(o):
463  """_object_cast_to_AssemblyHeader(Object o) -> AssemblyHeader"""
464  return _IMP_multifit._object_cast_to_AssemblyHeader(o)
465 
466 _object_types.append("SettingsData")
467 
468 
469 def _object_cast_to_SettingsData(o):
470  """_object_cast_to_SettingsData(Object o) -> SettingsData"""
471  return _IMP_multifit._object_cast_to_SettingsData(o)
472 
473 _object_types.append("WeightedExcludedVolumeRestraint")
474 
475 
476 def _object_cast_to_WeightedExcludedVolumeRestraint(o):
477  """_object_cast_to_WeightedExcludedVolumeRestraint(Object o) -> WeightedExcludedVolumeRestraint"""
478  return _IMP_multifit._object_cast_to_WeightedExcludedVolumeRestraint(o)
479 
480 _object_types.append("ComplementarityRestraint")
481 
482 
483 def _object_cast_to_ComplementarityRestraint(o):
484  """_object_cast_to_ComplementarityRestraint(Object o) -> ComplementarityRestraint"""
485  return _IMP_multifit._object_cast_to_ComplementarityRestraint(o)
486 
487 ProteinRecordDataList=list
488 _plural_types.append("ProteinRecordDataList")
489 _value_types.append("ProteinRecordData")
490 
491 
492 FittingSolutionRecords=list
493 _plural_types.append("FittingSolutionRecords")
494 _value_types.append("FittingSolutionRecord")
495 
496 
497 AnchorsDataList=list
498 _plural_types.append("AnchorsDataList")
499 _value_types.append("AnchorsData")
500 
501 
502 DominoParamsList=list
503 _plural_types.append("DominoParamsList")
504 _value_types.append("DominoParams")
505 
506 
507 ComplementarityParamsList=list
508 _plural_types.append("ComplementarityParamsList")
509 _value_types.append("ComplementarityParams")
510 
511 
512 XlinkParamsList=list
513 _plural_types.append("XlinkParamsList")
514 _value_types.append("XlinkParams")
515 
516 
517 ConnectivityParamsList=list
518 _plural_types.append("ConnectivityParamsList")
519 _value_types.append("ConnectivityParams")
520 
521 
522 FragmentsParamsList=list
523 _plural_types.append("FragmentsParamsList")
524 _value_types.append("FragmentsParams")
525 
526 
527 RogParamsList=list
528 _plural_types.append("RogParamsList")
529 _value_types.append("RogParams")
530 
531 
532 EVParamsList=list
533 _plural_types.append("EVParamsList")
534 _value_types.append("EVParams")
535 
536 
537 FiltersParamsList=list
538 _plural_types.append("FiltersParamsList")
539 _value_types.append("FiltersParams")
540 
541 
542 AlignmentParamsList=list
543 _plural_types.append("AlignmentParamsList")
544 _value_types.append("AlignmentParams")
545 
546 
547 FittingParamsList=list
548 _plural_types.append("FittingParamsList")
549 _value_types.append("FittingParams")
550 
551 
552 ProteinsAnchorsSamplingSpaces=list
553 _plural_types.append("ProteinsAnchorsSamplingSpaces")
554 _value_types.append("ProteinsAnchorsSamplingSpace")
555 
556 
557 _object_types.append("ProteomicsData")
558 
559 
560 def _object_cast_to_ProteomicsData(o):
561  """_object_cast_to_ProteomicsData(Object o) -> ProteomicsData"""
562  return _IMP_multifit._object_cast_to_ProteomicsData(o)
563 
564 _object_types.append("FFTFitting")
565 
566 
567 def _object_cast_to_FFTFitting(o):
568  """_object_cast_to_FFTFitting(Object o) -> FFTFitting"""
569  return _IMP_multifit._object_cast_to_FFTFitting(o)
570 
571 _object_types.append("FFTFittingOutput")
572 
573 
574 def _object_cast_to_FFTFittingOutput(o):
575  """_object_cast_to_FFTFittingOutput(Object o) -> FFTFittingOutput"""
576  return _IMP_multifit._object_cast_to_FFTFittingOutput(o)
577 
578 _object_types.append("ProbabilisticAnchorGraph")
579 
580 
581 def _object_cast_to_ProbabilisticAnchorGraph(o):
582  """_object_cast_to_ProbabilisticAnchorGraph(Object o) -> ProbabilisticAnchorGraph"""
583  return _IMP_multifit._object_cast_to_ProbabilisticAnchorGraph(o)
584 
585 _object_types.append("Ensemble")
586 
587 
588 def _object_cast_to_Ensemble(o):
589  """_object_cast_to_Ensemble(Object o) -> Ensemble"""
590  return _IMP_multifit._object_cast_to_Ensemble(o)
591 
592 _object_types.append("ProteomicsEMAlignmentAtomic")
593 
594 
595 def _object_cast_to_ProteomicsEMAlignmentAtomic(o):
596  """_object_cast_to_ProteomicsEMAlignmentAtomic(Object o) -> ProteomicsEMAlignmentAtomic"""
597  return _IMP_multifit._object_cast_to_ProteomicsEMAlignmentAtomic(o)
598 
599 _object_types.append("RigidLeavesRefiner")
600 
601 
602 def _object_cast_to_RigidLeavesRefiner(o):
603  """_object_cast_to_RigidLeavesRefiner(Object o) -> RigidLeavesRefiner"""
604  return _IMP_multifit._object_cast_to_RigidLeavesRefiner(o)
605 
606 def add_surface_index(*args):
607  """
608  add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key, FloatKey radius_key, FloatKey weight_key)
609  add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key, FloatKey radius_key)
610  add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key)
611  add_surface_index(Hierarchy mhd, IMP::Float apix)
612  """
613  return _IMP_multifit.add_surface_index(*args)
614 
616  """
617  create_weighted_excluded_volume_restraint(RigidBody rb1, RigidBody rb2, FloatKey shell_key) -> Restraint
618  create_weighted_excluded_volume_restraint(RigidBody rb1, RigidBody rb2) -> Restraint
619  """
620  return _IMP_multifit.create_weighted_excluded_volume_restraint(*args)
621 class FittingSolutionRecord(object):
622  """Proxy of C++ IMP::multifit::FittingSolutionRecord class."""
623 
624  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
625 
626  def __init__(self):
627  """__init__(IMP::multifit::FittingSolutionRecord self) -> FittingSolutionRecord"""
628  this = _IMP_multifit.new_FittingSolutionRecord()
629  try:
630  self.this.append(this)
631  except __builtin__.Exception:
632  self.this = this
633 
634  def get_index(self):
635  """get_index(FittingSolutionRecord self) -> unsigned int"""
636  return _IMP_multifit.FittingSolutionRecord_get_index(self)
637 
638 
639  def set_index(self, new_ind):
640  """set_index(FittingSolutionRecord self, unsigned int new_ind)"""
641  return _IMP_multifit.FittingSolutionRecord_set_index(self, new_ind)
642 
643 
644  def get_solution_filename(self):
645  """get_solution_filename(FittingSolutionRecord self) -> std::string"""
646  return _IMP_multifit.FittingSolutionRecord_get_solution_filename(self)
647 
648 
649  def set_solution_filename(self, sol_fn):
650  """set_solution_filename(FittingSolutionRecord self, std::string sol_fn)"""
651  return _IMP_multifit.FittingSolutionRecord_set_solution_filename(self, sol_fn)
652 
653 
654  def get_fit_transformation(self):
655  """get_fit_transformation(FittingSolutionRecord self) -> Transformation3D"""
656  return _IMP_multifit.FittingSolutionRecord_get_fit_transformation(self)
657 
658 
659  def set_fit_transformation(self, t):
660  """set_fit_transformation(FittingSolutionRecord self, Transformation3D t)"""
661  return _IMP_multifit.FittingSolutionRecord_set_fit_transformation(self, t)
662 
663 
664  def get_match_size(self):
665  """get_match_size(FittingSolutionRecord self) -> unsigned int"""
666  return _IMP_multifit.FittingSolutionRecord_get_match_size(self)
667 
668 
669  def set_match_size(self, match_size):
670  """set_match_size(FittingSolutionRecord self, unsigned int match_size)"""
671  return _IMP_multifit.FittingSolutionRecord_set_match_size(self, match_size)
672 
673 
674  def get_match_average_distance(self):
675  """get_match_average_distance(FittingSolutionRecord self) -> IMP::Float"""
676  return _IMP_multifit.FittingSolutionRecord_get_match_average_distance(self)
677 
678 
679  def set_match_average_distance(self, match_avg_dist):
680  """set_match_average_distance(FittingSolutionRecord self, IMP::Float match_avg_dist)"""
681  return _IMP_multifit.FittingSolutionRecord_set_match_average_distance(self, match_avg_dist)
682 
683 
684  def get_fitting_score(self):
685  """get_fitting_score(FittingSolutionRecord self) -> IMP::Float"""
686  return _IMP_multifit.FittingSolutionRecord_get_fitting_score(self)
687 
688 
689  def set_fitting_score(self, fit_score):
690  """set_fitting_score(FittingSolutionRecord self, IMP::Float fit_score)"""
691  return _IMP_multifit.FittingSolutionRecord_set_fitting_score(self, fit_score)
692 
693 
694  def get_rmsd_to_reference(self):
695  """get_rmsd_to_reference(FittingSolutionRecord self) -> IMP::Float"""
696  return _IMP_multifit.FittingSolutionRecord_get_rmsd_to_reference(self)
697 
698 
699  def set_rmsd_to_reference(self, rmsd_to_ref):
700  """set_rmsd_to_reference(FittingSolutionRecord self, IMP::Float rmsd_to_ref)"""
701  return _IMP_multifit.FittingSolutionRecord_set_rmsd_to_reference(self, rmsd_to_ref)
702 
703 
704  def get_dock_transformation(self):
705  """get_dock_transformation(FittingSolutionRecord self) -> Transformation3D"""
706  return _IMP_multifit.FittingSolutionRecord_get_dock_transformation(self)
707 
708 
709  def set_dock_transformation(self, t):
710  """set_dock_transformation(FittingSolutionRecord self, Transformation3D t)"""
711  return _IMP_multifit.FittingSolutionRecord_set_dock_transformation(self, t)
712 
713 
714  def get_envelope_penetration_score(self):
715  """get_envelope_penetration_score(FittingSolutionRecord self) -> IMP::Float"""
716  return _IMP_multifit.FittingSolutionRecord_get_envelope_penetration_score(self)
717 
718 
719  def set_envelope_penetration_score(self, s):
720  """set_envelope_penetration_score(FittingSolutionRecord self, IMP::Float s)"""
721  return _IMP_multifit.FittingSolutionRecord_set_envelope_penetration_score(self, s)
722 
723 
724  def show(self, *args):
725  """
726  show(FittingSolutionRecord self, _ostream out)
727  show(FittingSolutionRecord self)
728  """
729  return _IMP_multifit.FittingSolutionRecord_show(self, *args)
730 
731 
732  def get_record_header():
733  """get_record_header() -> std::string"""
734  return _IMP_multifit.FittingSolutionRecord_get_record_header()
735 
736  get_record_header = staticmethod(get_record_header)
737 
738  def __str__(self):
739  """__str__(FittingSolutionRecord self) -> std::string"""
740  return _IMP_multifit.FittingSolutionRecord___str__(self)
741 
742 
743  def __repr__(self):
744  """__repr__(FittingSolutionRecord self) -> std::string"""
745  return _IMP_multifit.FittingSolutionRecord___repr__(self)
746 
747  __swig_destroy__ = _IMP_multifit.delete_FittingSolutionRecord
748  __del__ = lambda self: None
749 FittingSolutionRecord_swigregister = _IMP_multifit.FittingSolutionRecord_swigregister
750 FittingSolutionRecord_swigregister(FittingSolutionRecord)
751 
752 def FittingSolutionRecord_get_record_header():
753  """FittingSolutionRecord_get_record_header() -> std::string"""
754  return _IMP_multifit.FittingSolutionRecord_get_record_header()
755 
756 
757 def pca_based_rigid_fitting(*args):
758  """
759  pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold, FloatKey wei_key, PrincipalComponentAnalysis3D dens_pca_input) -> FittingSolutions
760  pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold, FloatKey wei_key) -> FittingSolutions
761  pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold) -> FittingSolutions
762  pca_based_rigid_fitting(IMP::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold, FloatKey wei_key, PrincipalComponentAnalysis3D dens_pca_input) -> FittingSolutions
763  pca_based_rigid_fitting(IMP::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold, FloatKey wei_key) -> FittingSolutions
764  pca_based_rigid_fitting(IMP::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold) -> FittingSolutions
765  """
766  return _IMP_multifit.pca_based_rigid_fitting(*args)
767 
768 def write_markers(pca, out):
769  """write_markers(PrincipalComponentAnalysis3D pca, _ostream out)"""
770  return _IMP_multifit.write_markers(pca, out)
771 class ComponentHeader(IMP.Object):
772  """Proxy of C++ IMP::multifit::ComponentHeader class."""
773 
774  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
775 
776  def __init__(self):
777  """__init__(IMP::multifit::ComponentHeader self) -> ComponentHeader"""
778  this = _IMP_multifit.new_ComponentHeader()
779  try:
780  self.this.append(this)
781  except __builtin__.Exception:
782  self.this = this
783 
784  def set_name(self, name):
785  """set_name(ComponentHeader self, std::string const & name)"""
786  return _IMP_multifit.ComponentHeader_set_name(self, name)
787 
788 
789  def get_name(self):
790  """get_name(ComponentHeader self) -> std::string"""
791  return _IMP_multifit.ComponentHeader_get_name(self)
792 
793 
794  def get_filename(self):
795  """get_filename(ComponentHeader self) -> std::string"""
796  return _IMP_multifit.ComponentHeader_get_filename(self)
797 
798 
799  def set_filename(self, filename):
800  """set_filename(ComponentHeader self, std::string const & filename)"""
801  return _IMP_multifit.ComponentHeader_set_filename(self, filename)
802 
803 
804  def get_surface_fn(self):
805  """get_surface_fn(ComponentHeader self) -> std::string"""
806  return _IMP_multifit.ComponentHeader_get_surface_fn(self)
807 
808 
809  def set_surface_fn(self, fn):
810  """set_surface_fn(ComponentHeader self, std::string const & fn)"""
811  return _IMP_multifit.ComponentHeader_set_surface_fn(self, fn)
812 
813 
814  def set_txt_ap_fn(self, pdb_ap_fn):
815  """set_txt_ap_fn(ComponentHeader self, std::string const & pdb_ap_fn)"""
816  return _IMP_multifit.ComponentHeader_set_txt_ap_fn(self, pdb_ap_fn)
817 
818 
819  def get_txt_ap_fn(self):
820  """get_txt_ap_fn(ComponentHeader self) -> std::string"""
821  return _IMP_multifit.ComponentHeader_get_txt_ap_fn(self)
822 
823 
824  def set_txt_fine_ap_fn(self, pdb_ap_fn):
825  """set_txt_fine_ap_fn(ComponentHeader self, std::string const & pdb_ap_fn)"""
826  return _IMP_multifit.ComponentHeader_set_txt_fine_ap_fn(self, pdb_ap_fn)
827 
828 
829  def get_txt_fine_ap_fn(self):
830  """get_txt_fine_ap_fn(ComponentHeader self) -> std::string"""
831  return _IMP_multifit.ComponentHeader_get_txt_fine_ap_fn(self)
832 
833 
834  def set_num_ap(self, num_ap):
835  """set_num_ap(ComponentHeader self, int num_ap)"""
836  return _IMP_multifit.ComponentHeader_set_num_ap(self, num_ap)
837 
838 
839  def get_num_ap(self):
840  """get_num_ap(ComponentHeader self) -> int"""
841  return _IMP_multifit.ComponentHeader_get_num_ap(self)
842 
843 
844  def set_num_fine_ap(self, num_ap):
845  """set_num_fine_ap(ComponentHeader self, int num_ap)"""
846  return _IMP_multifit.ComponentHeader_set_num_fine_ap(self, num_ap)
847 
848 
849  def get_num_fine_ap(self):
850  """get_num_fine_ap(ComponentHeader self) -> int"""
851  return _IMP_multifit.ComponentHeader_get_num_fine_ap(self)
852 
853 
854  def set_transformations_fn(self, transformations_fn):
855  """set_transformations_fn(ComponentHeader self, std::string transformations_fn)"""
856  return _IMP_multifit.ComponentHeader_set_transformations_fn(self, transformations_fn)
857 
858 
859  def get_transformations_fn(self):
860  """get_transformations_fn(ComponentHeader self) -> std::string"""
861  return _IMP_multifit.ComponentHeader_get_transformations_fn(self)
862 
863 
864  def set_reference_fn(self, ref_fn):
865  """set_reference_fn(ComponentHeader self, std::string const & ref_fn)"""
866  return _IMP_multifit.ComponentHeader_set_reference_fn(self, ref_fn)
867 
868 
869  def get_reference_fn(self):
870  """get_reference_fn(ComponentHeader self) -> std::string"""
871  return _IMP_multifit.ComponentHeader_get_reference_fn(self)
872 
873 
874  def get_version_info(self):
875  """get_version_info(ComponentHeader self) -> VersionInfo"""
876  return _IMP_multifit.ComponentHeader_get_version_info(self)
877 
878 
879  def __str__(self):
880  """__str__(ComponentHeader self) -> std::string"""
881  return _IMP_multifit.ComponentHeader___str__(self)
882 
883 
884  def __repr__(self):
885  """__repr__(ComponentHeader self) -> std::string"""
886  return _IMP_multifit.ComponentHeader___repr__(self)
887 
888 
889  @staticmethod
890  def get_from(o):
891  return _object_cast_to_ComponentHeader(o)
892 
893 ComponentHeader_swigregister = _IMP_multifit.ComponentHeader_swigregister
894 ComponentHeader_swigregister(ComponentHeader)
895 
896 class AssemblyHeader(IMP.Object):
897  """Proxy of C++ IMP::multifit::AssemblyHeader class."""
898 
899  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
900 
901  def __init__(self):
902  """__init__(IMP::multifit::AssemblyHeader self) -> AssemblyHeader"""
903  this = _IMP_multifit.new_AssemblyHeader()
904  try:
905  self.this.append(this)
906  except __builtin__.Exception:
907  self.this = this
908 
909  def set_dens_fn(self, dens_fn):
910  """set_dens_fn(AssemblyHeader self, std::string const & dens_fn)"""
911  return _IMP_multifit.AssemblyHeader_set_dens_fn(self, dens_fn)
912 
913 
914  def get_dens_fn(self):
915  """get_dens_fn(AssemblyHeader self) -> std::string"""
916  return _IMP_multifit.AssemblyHeader_get_dens_fn(self)
917 
918 
919  def set_resolution(self, res):
920  """set_resolution(AssemblyHeader self, float res)"""
921  return _IMP_multifit.AssemblyHeader_set_resolution(self, res)
922 
923 
924  def get_resolution(self):
925  """get_resolution(AssemblyHeader self) -> float"""
926  return _IMP_multifit.AssemblyHeader_get_resolution(self)
927 
928 
929  def get_spacing(self):
930  """get_spacing(AssemblyHeader self) -> float"""
931  return _IMP_multifit.AssemblyHeader_get_spacing(self)
932 
933 
934  def set_spacing(self, spacing):
935  """set_spacing(AssemblyHeader self, float spacing)"""
936  return _IMP_multifit.AssemblyHeader_set_spacing(self, spacing)
937 
938 
939  def set_threshold(self, t):
940  """set_threshold(AssemblyHeader self, float t)"""
941  return _IMP_multifit.AssemblyHeader_set_threshold(self, t)
942 
943 
944  def get_threshold(self):
945  """get_threshold(AssemblyHeader self) -> float"""
946  return _IMP_multifit.AssemblyHeader_get_threshold(self)
947 
948 
949  def get_origin(self):
950  """get_origin(AssemblyHeader self) -> Vector3D"""
951  return _IMP_multifit.AssemblyHeader_get_origin(self)
952 
953 
954  def set_origin(self, origin):
955  """set_origin(AssemblyHeader self, Vector3D origin)"""
956  return _IMP_multifit.AssemblyHeader_set_origin(self, origin)
957 
958 
959  def get_coarse_ap_fn(self):
960  """get_coarse_ap_fn(AssemblyHeader self) -> std::string"""
961  return _IMP_multifit.AssemblyHeader_get_coarse_ap_fn(self)
962 
963 
964  def set_coarse_ap_fn(self, new_fn):
965  """set_coarse_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
966  return _IMP_multifit.AssemblyHeader_set_coarse_ap_fn(self, new_fn)
967 
968 
969  def get_coarse_over_sampled_ap_fn(self):
970  """get_coarse_over_sampled_ap_fn(AssemblyHeader self) -> std::string"""
971  return _IMP_multifit.AssemblyHeader_get_coarse_over_sampled_ap_fn(self)
972 
973 
974  def set_coarse_over_sampled_ap_fn(self, new_fn):
975  """set_coarse_over_sampled_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
976  return _IMP_multifit.AssemblyHeader_set_coarse_over_sampled_ap_fn(self, new_fn)
977 
978 
979  def get_fine_ap_fn(self):
980  """get_fine_ap_fn(AssemblyHeader self) -> std::string"""
981  return _IMP_multifit.AssemblyHeader_get_fine_ap_fn(self)
982 
983 
984  def set_fine_ap_fn(self, new_fn):
985  """set_fine_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
986  return _IMP_multifit.AssemblyHeader_set_fine_ap_fn(self, new_fn)
987 
988 
989  def get_fine_over_sampled_ap_fn(self):
990  """get_fine_over_sampled_ap_fn(AssemblyHeader self) -> std::string"""
991  return _IMP_multifit.AssemblyHeader_get_fine_over_sampled_ap_fn(self)
992 
993 
994  def set_fine_over_sampled_ap_fn(self, new_fn):
995  """set_fine_over_sampled_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
996  return _IMP_multifit.AssemblyHeader_set_fine_over_sampled_ap_fn(self, new_fn)
997 
998 
999  def get_version_info(self):
1000  """get_version_info(AssemblyHeader self) -> VersionInfo"""
1001  return _IMP_multifit.AssemblyHeader_get_version_info(self)
1002 
1003 
1004  def __str__(self):
1005  """__str__(AssemblyHeader self) -> std::string"""
1006  return _IMP_multifit.AssemblyHeader___str__(self)
1007 
1008 
1009  def __repr__(self):
1010  """__repr__(AssemblyHeader self) -> std::string"""
1011  return _IMP_multifit.AssemblyHeader___repr__(self)
1012 
1013 
1014  @staticmethod
1015  def get_from(o):
1016  return _object_cast_to_AssemblyHeader(o)
1017 
1018 AssemblyHeader_swigregister = _IMP_multifit.AssemblyHeader_swigregister
1019 AssemblyHeader_swigregister(AssemblyHeader)
1020 
1021 class SettingsData(IMP.Object):
1022  """Proxy of C++ IMP::multifit::SettingsData class."""
1023 
1024  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1025 
1026  def __init__(self):
1027  """__init__(IMP::multifit::SettingsData self) -> SettingsData"""
1028  this = _IMP_multifit.new_SettingsData()
1029  try:
1030  self.this.append(this)
1031  except __builtin__.Exception:
1032  self.this = this
1033 
1034  def show_component_header_line(*args):
1035  """
1036  show_component_header_line(_ostream out)
1037  show_component_header_line()
1038  """
1039  return _IMP_multifit.SettingsData_show_component_header_line(*args)
1040 
1041  show_component_header_line = staticmethod(show_component_header_line)
1042 
1043  def get_component_header_line():
1044  """get_component_header_line() -> std::string"""
1045  return _IMP_multifit.SettingsData_get_component_header_line()
1046 
1047  get_component_header_line = staticmethod(get_component_header_line)
1048 
1049  def show_density_header_line(*args):
1050  """
1051  show_density_header_line(_ostream out)
1052  show_density_header_line()
1053  """
1054  return _IMP_multifit.SettingsData_show_density_header_line(*args)
1055 
1056  show_density_header_line = staticmethod(show_density_header_line)
1057 
1058  def get_density_header_line():
1059  """get_density_header_line() -> std::string"""
1060  return _IMP_multifit.SettingsData_get_density_header_line()
1061 
1062  get_density_header_line = staticmethod(get_density_header_line)
1063 
1064  def set_assembly_filename(self, fn):
1065  """set_assembly_filename(SettingsData self, std::string const & fn)"""
1066  return _IMP_multifit.SettingsData_set_assembly_filename(self, fn)
1067 
1068 
1069  def get_assembly_filename(self):
1070  """get_assembly_filename(SettingsData self) -> char const *"""
1071  return _IMP_multifit.SettingsData_get_assembly_filename(self)
1072 
1073 
1074  def set_assembly_header(self, h):
1075  """set_assembly_header(SettingsData self, AssemblyHeader h)"""
1076  return _IMP_multifit.SettingsData_set_assembly_header(self, h)
1077 
1078 
1079  def get_assembly_header(self):
1080  """get_assembly_header(SettingsData self) -> AssemblyHeader"""
1081  return _IMP_multifit.SettingsData_get_assembly_header(self)
1082 
1083 
1084  def set_data_path(self, fn):
1085  """set_data_path(SettingsData self, std::string const & fn)"""
1086  return _IMP_multifit.SettingsData_set_data_path(self, fn)
1087 
1088 
1089  def get_data_path(self):
1090  """get_data_path(SettingsData self) -> std::string"""
1091  return _IMP_multifit.SettingsData_get_data_path(self)
1092 
1093 
1094  def get_version_info(self):
1095  """get_version_info(SettingsData self) -> VersionInfo"""
1096  return _IMP_multifit.SettingsData_get_version_info(self)
1097 
1098 
1099  def remove_component_header(self, d):
1100  """remove_component_header(SettingsData self, ComponentHeader d)"""
1101  return _IMP_multifit.SettingsData_remove_component_header(self, d)
1102 
1103 
1104  def remove_component_headers(self, d):
1105  """remove_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & d)"""
1106  return _IMP_multifit.SettingsData_remove_component_headers(self, d)
1107 
1108 
1109  def set_component_headers(self, ps):
1110  """set_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & ps)"""
1111  return _IMP_multifit.SettingsData_set_component_headers(self, ps)
1112 
1113 
1114  def set_component_headers_order(self, objs):
1115  """set_component_headers_order(SettingsData self, IMP::multifit::ComponentHeaders const & objs)"""
1116  return _IMP_multifit.SettingsData_set_component_headers_order(self, objs)
1117 
1118 
1119  def add_component_header(self, obj):
1120  """add_component_header(SettingsData self, ComponentHeader obj) -> unsigned int"""
1121  return _IMP_multifit.SettingsData_add_component_header(self, obj)
1122 
1123 
1124  def add_component_headers(self, objs):
1125  """add_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & objs)"""
1126  return _IMP_multifit.SettingsData_add_component_headers(self, objs)
1127 
1128 
1129  def clear_component_headers(self):
1130  """clear_component_headers(SettingsData self)"""
1131  return _IMP_multifit.SettingsData_clear_component_headers(self)
1132 
1133 
1134  def get_number_of_component_headers(self):
1135  """get_number_of_component_headers(SettingsData self) -> unsigned int"""
1136  return _IMP_multifit.SettingsData_get_number_of_component_headers(self)
1137 
1138 
1139  def get_has_component_headers(self):
1140  """get_has_component_headers(SettingsData self) -> bool"""
1141  return _IMP_multifit.SettingsData_get_has_component_headers(self)
1142 
1143 
1144  def get_component_header(self, i):
1145  """get_component_header(SettingsData self, unsigned int i) -> ComponentHeader"""
1146  return _IMP_multifit.SettingsData_get_component_header(self, i)
1147 
1148 
1149  def get_component_headers(self):
1150  """get_component_headers(SettingsData self) -> IMP::multifit::ComponentHeaders"""
1151  return _IMP_multifit.SettingsData_get_component_headers(self)
1152 
1153 
1154  def reserve_component_headers(self, sz):
1155  """reserve_component_headers(SettingsData self, unsigned int sz)"""
1156  return _IMP_multifit.SettingsData_reserve_component_headers(self, sz)
1157 
1158 
1159  def __str__(self):
1160  """__str__(SettingsData self) -> std::string"""
1161  return _IMP_multifit.SettingsData___str__(self)
1162 
1163 
1164  def __repr__(self):
1165  """__repr__(SettingsData self) -> std::string"""
1166  return _IMP_multifit.SettingsData___repr__(self)
1167 
1168 
1169  @staticmethod
1170  def get_from(o):
1171  return _object_cast_to_SettingsData(o)
1172 
1173 SettingsData_swigregister = _IMP_multifit.SettingsData_swigregister
1174 SettingsData_swigregister(SettingsData)
1175 
1176 def SettingsData_show_component_header_line(*args):
1177  """
1178  show_component_header_line(_ostream out)
1179  SettingsData_show_component_header_line()
1180  """
1181  return _IMP_multifit.SettingsData_show_component_header_line(*args)
1182 
1183 def SettingsData_get_component_header_line():
1184  """SettingsData_get_component_header_line() -> std::string"""
1185  return _IMP_multifit.SettingsData_get_component_header_line()
1186 
1187 def SettingsData_show_density_header_line(*args):
1188  """
1189  show_density_header_line(_ostream out)
1190  SettingsData_show_density_header_line()
1191  """
1192  return _IMP_multifit.SettingsData_show_density_header_line(*args)
1193 
1194 def SettingsData_get_density_header_line():
1195  """SettingsData_get_density_header_line() -> std::string"""
1196  return _IMP_multifit.SettingsData_get_density_header_line()
1197 
1198 
1199 def read_settings(filename):
1200  """read_settings(char const * filename) -> SettingsData"""
1201  return _IMP_multifit.read_settings(filename)
1202 
1203 def write_settings(filename, sd):
1204  """write_settings(char const * filename, SettingsData sd)"""
1205  return _IMP_multifit.write_settings(filename, sd)
1206 class WeightedExcludedVolumeRestraint(IMP.Restraint):
1207  """Proxy of C++ IMP::multifit::WeightedExcludedVolumeRestraint class."""
1208 
1209  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1210 
1211  def __init__(self, *args):
1212  """
1213  __init__(IMP::multifit::WeightedExcludedVolumeRestraint self, IMP::core::RigidBodies rbs, Refiner refiner, FloatKey weight_key) -> WeightedExcludedVolumeRestraint
1214  __init__(IMP::multifit::WeightedExcludedVolumeRestraint self, IMP::core::RigidBodies rbs, Refiner refiner) -> WeightedExcludedVolumeRestraint
1215  """
1216  this = _IMP_multifit.new_WeightedExcludedVolumeRestraint(*args)
1217  try:
1218  self.this.append(this)
1219  except __builtin__.Exception:
1220  self.this = this
1221 
1222  def do_get_inputs(self):
1223  """do_get_inputs(WeightedExcludedVolumeRestraint self) -> IMP::ModelObjectsTemp"""
1224  return _IMP_multifit.WeightedExcludedVolumeRestraint_do_get_inputs(self)
1225 
1226 
1227  def get_version_info(self):
1228  """get_version_info(WeightedExcludedVolumeRestraint self) -> VersionInfo"""
1229  return _IMP_multifit.WeightedExcludedVolumeRestraint_get_version_info(self)
1230 
1231 
1232  def __str__(self):
1233  """__str__(WeightedExcludedVolumeRestraint self) -> std::string"""
1234  return _IMP_multifit.WeightedExcludedVolumeRestraint___str__(self)
1235 
1236 
1237  def __repr__(self):
1238  """__repr__(WeightedExcludedVolumeRestraint self) -> std::string"""
1239  return _IMP_multifit.WeightedExcludedVolumeRestraint___repr__(self)
1240 
1241 
1242  @staticmethod
1243  def get_from(o):
1244  return _object_cast_to_WeightedExcludedVolumeRestraint(o)
1245 
1246 WeightedExcludedVolumeRestraint_swigregister = _IMP_multifit.WeightedExcludedVolumeRestraint_swigregister
1247 WeightedExcludedVolumeRestraint_swigregister(WeightedExcludedVolumeRestraint)
1248 
1249 class FFTFittingOutput(IMP.Object):
1250  """Proxy of C++ IMP::multifit::FFTFittingOutput class."""
1251 
1252  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1253 
1254  def __init__(self):
1255  """__init__(IMP::multifit::FFTFittingOutput self) -> FFTFittingOutput"""
1256  this = _IMP_multifit.new_FFTFittingOutput()
1257  try:
1258  self.this.append(this)
1259  except __builtin__.Exception:
1260  self.this = this
1261 
1262  def get_version_info(self):
1263  """get_version_info(FFTFittingOutput self) -> VersionInfo"""
1264  return _IMP_multifit.FFTFittingOutput_get_version_info(self)
1265 
1266  best_fits_ = _swig_property(_IMP_multifit.FFTFittingOutput_best_fits__get, _IMP_multifit.FFTFittingOutput_best_fits__set)
1267  best_trans_per_rot_ = _swig_property(_IMP_multifit.FFTFittingOutput_best_trans_per_rot__get, _IMP_multifit.FFTFittingOutput_best_trans_per_rot__set)
1268 
1269  def __str__(self):
1270  """__str__(FFTFittingOutput self) -> std::string"""
1271  return _IMP_multifit.FFTFittingOutput___str__(self)
1272 
1273 
1274  def __repr__(self):
1275  """__repr__(FFTFittingOutput self) -> std::string"""
1276  return _IMP_multifit.FFTFittingOutput___repr__(self)
1277 
1278 
1279  @staticmethod
1280  def get_from(o):
1281  return _object_cast_to_FFTFittingOutput(o)
1282 
1283 FFTFittingOutput_swigregister = _IMP_multifit.FFTFittingOutput_swigregister
1284 FFTFittingOutput_swigregister(FFTFittingOutput)
1285 
1286 class FFTFitting(IMP.Object):
1287  """Proxy of C++ IMP::multifit::FFTFitting class."""
1288 
1289  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1290 
1291  def get_version_info(self):
1292  """get_version_info(FFTFitting self) -> VersionInfo"""
1293  return _IMP_multifit.FFTFitting_get_version_info(self)
1294 
1295 
1296  def __init__(self):
1297  """__init__(IMP::multifit::FFTFitting self) -> FFTFitting"""
1298  this = _IMP_multifit.new_FFTFitting()
1299  try:
1300  self.this.append(this)
1301  except __builtin__.Exception:
1302  self.this = this
1303 
1304  def do_global_fitting(self, *args):
1305  """
1306  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
1307  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
1308  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
1309  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
1310  """
1311  return _IMP_multifit.FFTFitting_do_global_fitting(self, *args)
1312 
1313 
1314  def do_local_fitting(self, *args):
1315  """
1316  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
1317  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
1318  """
1319  return _IMP_multifit.FFTFitting_do_local_fitting(self, *args)
1320 
1321 
1322  def __str__(self):
1323  """__str__(FFTFitting self) -> std::string"""
1324  return _IMP_multifit.FFTFitting___str__(self)
1325 
1326 
1327  def __repr__(self):
1328  """__repr__(FFTFitting self) -> std::string"""
1329  return _IMP_multifit.FFTFitting___repr__(self)
1330 
1331 
1332  @staticmethod
1333  def get_from(o):
1334  return _object_cast_to_FFTFitting(o)
1335 
1336 FFTFitting_swigregister = _IMP_multifit.FFTFitting_swigregister
1337 FFTFitting_swigregister(FFTFitting)
1338 
1339 
1340 def fft_based_rigid_fitting(mol2fit, dmap, density_threshold, angle_sampling_interval_rad):
1341  """fft_based_rigid_fitting(Hierarchy mol2fit, DensityMap dmap, double density_threshold, double angle_sampling_interval_rad) -> IMP::multifit::FittingSolutionRecords"""
1342  return _IMP_multifit.fft_based_rigid_fitting(mol2fit, dmap, density_threshold, angle_sampling_interval_rad)
1343 
1344 def remove_background(dmap, threshold, edge_threshold):
1345  """remove_background(DensityMap dmap, float threshold, float edge_threshold) -> DensityMap"""
1346  return _IMP_multifit.remove_background(dmap, threshold, edge_threshold)
1347 
1348 def get_connected_components(dmap, threshold, edge_threshold):
1349  """get_connected_components(DensityMap dmap, float threshold, float edge_threshold) -> IMP::IntsList"""
1350  return _IMP_multifit.get_connected_components(dmap, threshold, edge_threshold)
1351 
1352 def get_segmentation(dmap, apix, density_threshold, num_means, pdb_filename, cmm_filename, seg_filename, txt_filename):
1353  """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)"""
1354  return _IMP_multifit.get_segmentation(dmap, apix, density_threshold, num_means, pdb_filename, cmm_filename, seg_filename, txt_filename)
1355 class ComplementarityRestraint(IMP.Restraint):
1356  """Proxy of C++ IMP::multifit::ComplementarityRestraint class."""
1357 
1358  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1359 
1360  def __init__(self, *args):
1361  """
1362  __init__(IMP::multifit::ComplementarityRestraint self, IMP::ParticlesTemp const & a, IMP::ParticlesTemp const & b, std::string name) -> ComplementarityRestraint
1363  __init__(IMP::multifit::ComplementarityRestraint self, IMP::ParticlesTemp const & a, IMP::ParticlesTemp const & b) -> ComplementarityRestraint
1364  """
1365  this = _IMP_multifit.new_ComplementarityRestraint(*args)
1366  try:
1367  self.this.append(this)
1368  except __builtin__.Exception:
1369  self.this = this
1370 
1371  def set_maximum_penetration_score(self, s):
1372  """set_maximum_penetration_score(ComplementarityRestraint self, double s)"""
1373  return _IMP_multifit.ComplementarityRestraint_set_maximum_penetration_score(self, s)
1374 
1375 
1376  def set_maximum_penetration(self, d):
1377  """set_maximum_penetration(ComplementarityRestraint self, double d)"""
1378  return _IMP_multifit.ComplementarityRestraint_set_maximum_penetration(self, d)
1379 
1380 
1381  def set_maximum_separation(self, s):
1382  """set_maximum_separation(ComplementarityRestraint self, double s)"""
1383  return _IMP_multifit.ComplementarityRestraint_set_maximum_separation(self, s)
1384 
1385 
1386  def set_complementarity_thickness(self, th):
1387  """set_complementarity_thickness(ComplementarityRestraint self, double th)"""
1388  return _IMP_multifit.ComplementarityRestraint_set_complementarity_thickness(self, th)
1389 
1390 
1391  def set_complementarity_value(self, th):
1392  """set_complementarity_value(ComplementarityRestraint self, double th)"""
1393  return _IMP_multifit.ComplementarityRestraint_set_complementarity_value(self, th)
1394 
1395 
1396  def set_interior_layer_thickness(self, th):
1397  """set_interior_layer_thickness(ComplementarityRestraint self, double th)"""
1398  return _IMP_multifit.ComplementarityRestraint_set_interior_layer_thickness(self, th)
1399 
1400 
1401  def set_penetration_coefficient(self, pc):
1402  """set_penetration_coefficient(ComplementarityRestraint self, double pc)"""
1403  return _IMP_multifit.ComplementarityRestraint_set_penetration_coefficient(self, pc)
1404 
1405 
1406  def set_complementarity_coefficient(self, cc):
1407  """set_complementarity_coefficient(ComplementarityRestraint self, double cc)"""
1408  return _IMP_multifit.ComplementarityRestraint_set_complementarity_coefficient(self, cc)
1409 
1410 
1411  def set_boundary_coefficient(self, bc):
1412  """set_boundary_coefficient(ComplementarityRestraint self, double bc)"""
1413  return _IMP_multifit.ComplementarityRestraint_set_boundary_coefficient(self, bc)
1414 
1415 
1416  def get_voxel_size(self):
1417  """get_voxel_size(ComplementarityRestraint self) -> float"""
1418  return _IMP_multifit.ComplementarityRestraint_get_voxel_size(self)
1419 
1420 
1421  def do_get_inputs(self):
1422  """do_get_inputs(ComplementarityRestraint self) -> IMP::ModelObjectsTemp"""
1423  return _IMP_multifit.ComplementarityRestraint_do_get_inputs(self)
1424 
1425 
1426  def get_version_info(self):
1427  """get_version_info(ComplementarityRestraint self) -> VersionInfo"""
1428  return _IMP_multifit.ComplementarityRestraint_get_version_info(self)
1429 
1430 
1431  def __str__(self):
1432  """__str__(ComplementarityRestraint self) -> std::string"""
1433  return _IMP_multifit.ComplementarityRestraint___str__(self)
1434 
1435 
1436  def __repr__(self):
1437  """__repr__(ComplementarityRestraint self) -> std::string"""
1438  return _IMP_multifit.ComplementarityRestraint___repr__(self)
1439 
1440 
1441  @staticmethod
1442  def get_from(o):
1443  return _object_cast_to_ComplementarityRestraint(o)
1444 
1445 ComplementarityRestraint_swigregister = _IMP_multifit.ComplementarityRestraint_swigregister
1446 ComplementarityRestraint_swigregister(ComplementarityRestraint)
1447 
1448 
1449 def read_fitting_solutions(fitting_fn):
1450  """read_fitting_solutions(char const * fitting_fn) -> IMP::multifit::FittingSolutionRecords"""
1451  return _IMP_multifit.read_fitting_solutions(fitting_fn)
1452 
1453 def write_fitting_solutions(fitting_fn, fit_sols, num_sols=-1):
1454  """
1455  write_fitting_solutions(char const * fitting_fn, IMP::multifit::FittingSolutionRecords const & fit_sols, int num_sols=-1)
1456  write_fitting_solutions(char const * fitting_fn, IMP::multifit::FittingSolutionRecords const & fit_sols)
1457  """
1458  return _IMP_multifit.write_fitting_solutions(fitting_fn, fit_sols, num_sols)
1459 
1460 def convert_em_to_multifit_format(em_fits):
1461  """convert_em_to_multifit_format(FittingSolutions em_fits) -> IMP::multifit::FittingSolutionRecords"""
1462  return _IMP_multifit.convert_em_to_multifit_format(em_fits)
1463 
1464 def convert_multifit_to_em_format(multifit_fits):
1465  """convert_multifit_to_em_format(IMP::multifit::FittingSolutionRecords const & multifit_fits) -> FittingSolutions"""
1466  return _IMP_multifit.convert_multifit_to_em_format(multifit_fits)
1467 
1468 def convert_transformations_to_multifit_format(trans):
1469  """convert_transformations_to_multifit_format(IMP::algebra::Transformation3Ds const & trans) -> IMP::multifit::FittingSolutionRecords"""
1470  return _IMP_multifit.convert_transformations_to_multifit_format(trans)
1471 
1472 def convert_multifit_format_to_transformations(recs):
1473  """convert_multifit_format_to_transformations(IMP::multifit::FittingSolutionRecords const & recs) -> IMP::algebra::Transformation3Ds"""
1474  return _IMP_multifit.convert_multifit_format_to_transformations(recs)
1475 
1476 def get_close_to_point(fit_sols, mh, ap, dist):
1477  """get_close_to_point(IMP::multifit::FittingSolutionRecords const & fit_sols, Hierarchy mh, Particle ap, IMP::Float dist) -> IMP::multifit::FittingSolutionRecords"""
1478  return _IMP_multifit.get_close_to_point(fit_sols, mh, ap, dist)
1479 class ProbabilisticAnchorGraph(IMP.Object):
1480  """Proxy of C++ IMP::multifit::ProbabilisticAnchorGraph class."""
1481 
1482  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1483 
1484  def __init__(self, anchor_positions):
1485  """__init__(IMP::multifit::ProbabilisticAnchorGraph self, IMP::algebra::Vector3Ds anchor_positions) -> ProbabilisticAnchorGraph"""
1486  this = _IMP_multifit.new_ProbabilisticAnchorGraph(anchor_positions)
1487  try:
1488  self.this.append(this)
1489  except __builtin__.Exception:
1490  self.this = this
1491 
1492  def add_edge(self, i, j):
1493  """add_edge(ProbabilisticAnchorGraph self, int i, int j)"""
1494  return _IMP_multifit.ProbabilisticAnchorGraph_add_edge(self, i, j)
1495 
1496 
1497  def set_particle_probabilities_on_anchors(self, p, sols):
1498  """set_particle_probabilities_on_anchors(ProbabilisticAnchorGraph self, Particle p, IMP::multifit::FittingSolutionRecords sols)"""
1499  return _IMP_multifit.ProbabilisticAnchorGraph_set_particle_probabilities_on_anchors(self, p, sols)
1500 
1501 
1502  def show(self, *args):
1503  """
1504  show(ProbabilisticAnchorGraph self, _ostream out)
1505  show(ProbabilisticAnchorGraph self)
1506  """
1507  return _IMP_multifit.ProbabilisticAnchorGraph_show(self, *args)
1508 
1509 
1510  def get_number_of_anchors(self):
1511  """get_number_of_anchors(ProbabilisticAnchorGraph self) -> unsigned int"""
1512  return _IMP_multifit.ProbabilisticAnchorGraph_get_number_of_anchors(self)
1513 
1514 
1515  def get_number_of_edges(self):
1516  """get_number_of_edges(ProbabilisticAnchorGraph self) -> unsigned int"""
1517  return _IMP_multifit.ProbabilisticAnchorGraph_get_number_of_edges(self)
1518 
1519 
1520  def get_edge_list(self):
1521  """get_edge_list(ProbabilisticAnchorGraph self) -> IMP::IntRanges"""
1522  return _IMP_multifit.ProbabilisticAnchorGraph_get_edge_list(self)
1523 
1524 
1525  def get_anchors(self):
1526  """get_anchors(ProbabilisticAnchorGraph self) -> IMP::algebra::Vector3Ds"""
1527  return _IMP_multifit.ProbabilisticAnchorGraph_get_anchors(self)
1528 
1529 
1530  def get_particle_anchors(self, p, min_prob=0):
1531  """
1532  get_particle_anchors(ProbabilisticAnchorGraph self, Particle p, float min_prob=0) -> IMP::algebra::Vector3Ds
1533  get_particle_anchors(ProbabilisticAnchorGraph self, Particle p) -> IMP::algebra::Vector3Ds
1534  """
1535  return _IMP_multifit.ProbabilisticAnchorGraph_get_particle_anchors(self, p, min_prob)
1536 
1537 
1538  def get_are_probabilities_for_particle_set(self, p):
1539  """get_are_probabilities_for_particle_set(ProbabilisticAnchorGraph self, Particle p) -> bool"""
1540  return _IMP_multifit.ProbabilisticAnchorGraph_get_are_probabilities_for_particle_set(self, p)
1541 
1542 
1543  def get_particle_probabilities(self, p):
1544  """get_particle_probabilities(ProbabilisticAnchorGraph self, Particle p) -> IMP::Floats"""
1545  return _IMP_multifit.ProbabilisticAnchorGraph_get_particle_probabilities(self, p)
1546 
1547 
1548  def get_version_info(self):
1549  """get_version_info(ProbabilisticAnchorGraph self) -> VersionInfo"""
1550  return _IMP_multifit.ProbabilisticAnchorGraph_get_version_info(self)
1551 
1552 
1553  def __str__(self):
1554  """__str__(ProbabilisticAnchorGraph self) -> std::string"""
1555  return _IMP_multifit.ProbabilisticAnchorGraph___str__(self)
1556 
1557 
1558  def __repr__(self):
1559  """__repr__(ProbabilisticAnchorGraph self) -> std::string"""
1560  return _IMP_multifit.ProbabilisticAnchorGraph___repr__(self)
1561 
1562 
1563  @staticmethod
1564  def get_from(o):
1565  return _object_cast_to_ProbabilisticAnchorGraph(o)
1566 
1567 ProbabilisticAnchorGraph_swigregister = _IMP_multifit.ProbabilisticAnchorGraph_swigregister
1568 ProbabilisticAnchorGraph_swigregister(ProbabilisticAnchorGraph)
1569 
1570 class ProteinRecordData(object):
1571  """Proxy of C++ IMP::multifit::ProteinRecordData class."""
1572 
1573  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1574 
1575  def reset_all(self):
1576  """reset_all(ProteinRecordData self)"""
1577  return _IMP_multifit.ProteinRecordData_reset_all(self)
1578 
1579 
1580  def __init__(self, *args):
1581  """
1582  __init__(IMP::multifit::ProteinRecordData self) -> ProteinRecordData
1583  __init__(IMP::multifit::ProteinRecordData self, std::string const & name) -> ProteinRecordData
1584  __init__(IMP::multifit::ProteinRecordData self, std::string const & name, std::string const fn) -> ProteinRecordData
1585  __init__(IMP::multifit::ProteinRecordData self, std::string const & name, int start_res, int end_res, std::string const fn) -> ProteinRecordData
1586  __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
1587  """
1588  this = _IMP_multifit.new_ProteinRecordData(*args)
1589  try:
1590  self.this.append(this)
1591  except __builtin__.Exception:
1592  self.this = this
1593 
1594  def show(self, *args):
1595  """
1596  show(ProteinRecordData self, _ostream out)
1597  show(ProteinRecordData self)
1598  """
1599  return _IMP_multifit.ProteinRecordData_show(self, *args)
1600 
1601  name_ = _swig_property(_IMP_multifit.ProteinRecordData_name__get, _IMP_multifit.ProteinRecordData_name__set)
1602  start_res_ = _swig_property(_IMP_multifit.ProteinRecordData_start_res__get, _IMP_multifit.ProteinRecordData_start_res__set)
1603  end_res_ = _swig_property(_IMP_multifit.ProteinRecordData_end_res__get, _IMP_multifit.ProteinRecordData_end_res__set)
1604  filename_ = _swig_property(_IMP_multifit.ProteinRecordData_filename__get, _IMP_multifit.ProteinRecordData_filename__set)
1605  surface_filename_ = _swig_property(_IMP_multifit.ProteinRecordData_surface_filename__get, _IMP_multifit.ProteinRecordData_surface_filename__set)
1606  ref_filename_ = _swig_property(_IMP_multifit.ProteinRecordData_ref_filename__get, _IMP_multifit.ProteinRecordData_ref_filename__set)
1607 
1608  def __str__(self):
1609  """__str__(ProteinRecordData self) -> std::string"""
1610  return _IMP_multifit.ProteinRecordData___str__(self)
1611 
1612 
1613  def __repr__(self):
1614  """__repr__(ProteinRecordData self) -> std::string"""
1615  return _IMP_multifit.ProteinRecordData___repr__(self)
1616 
1617  __swig_destroy__ = _IMP_multifit.delete_ProteinRecordData
1618  __del__ = lambda self: None
1619 ProteinRecordData_swigregister = _IMP_multifit.ProteinRecordData_swigregister
1620 ProteinRecordData_swigregister(ProteinRecordData)
1621 
1622 class ProteomicsData(IMP.Object):
1623  """Proxy of C++ IMP::multifit::ProteomicsData class."""
1624 
1625  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1626 
1627  def __init__(self):
1628  """__init__(IMP::multifit::ProteomicsData self) -> ProteomicsData"""
1629  this = _IMP_multifit.new_ProteomicsData()
1630  try:
1631  self.this.append(this)
1632  except __builtin__.Exception:
1633  self.this = this
1634 
1635  def add_protein(self, *args):
1636  """
1637  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
1638  add_protein(ProteomicsData self, ProteinRecordData rec) -> int
1639  """
1640  return _IMP_multifit.ProteomicsData_add_protein(self, *args)
1641 
1642 
1643  def find(self, name):
1644  """find(ProteomicsData self, std::string const & name) -> int"""
1645  return _IMP_multifit.ProteomicsData_find(self, name)
1646 
1647 
1648  def add_interaction(self, ii, used_for_filter, linker_len):
1649  """add_interaction(ProteomicsData self, IMP::Ints const & ii, bool used_for_filter, float linker_len)"""
1650  return _IMP_multifit.ProteomicsData_add_interaction(self, ii, used_for_filter, linker_len)
1651 
1652 
1653  def add_cross_link_interaction(self, prot1, res1, prot2, res2, used_in_filter, linker_len):
1654  """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)"""
1655  return _IMP_multifit.ProteomicsData_add_cross_link_interaction(self, prot1, res1, prot2, res2, used_in_filter, linker_len)
1656 
1657 
1658  def add_ev_pair(self, prot1, prot2):
1659  """add_ev_pair(ProteomicsData self, IMP::Int prot1, IMP::Int prot2)"""
1660  return _IMP_multifit.ProteomicsData_add_ev_pair(self, prot1, prot2)
1661 
1662 
1663  def get_number_of_proteins(self):
1664  """get_number_of_proteins(ProteomicsData self) -> int"""
1665  return _IMP_multifit.ProteomicsData_get_number_of_proteins(self)
1666 
1667 
1668  def get_number_of_interactions(self):
1669  """get_number_of_interactions(ProteomicsData self) -> int"""
1670  return _IMP_multifit.ProteomicsData_get_number_of_interactions(self)
1671 
1672 
1673  def get_interaction(self, interaction_ind):
1674  """get_interaction(ProteomicsData self, int interaction_ind) -> IMP::Ints"""
1675  return _IMP_multifit.ProteomicsData_get_interaction(self, interaction_ind)
1676 
1677 
1678  def get_interaction_part_of_filter(self, interaction_ind):
1679  """get_interaction_part_of_filter(ProteomicsData self, int interaction_ind) -> bool"""
1680  return _IMP_multifit.ProteomicsData_get_interaction_part_of_filter(self, interaction_ind)
1681 
1682 
1683  def get_interaction_linker_length(self, interaction_ind):
1684  """get_interaction_linker_length(ProteomicsData self, int interaction_ind) -> int"""
1685  return _IMP_multifit.ProteomicsData_get_interaction_linker_length(self, interaction_ind)
1686 
1687 
1688  def get_number_of_cross_links(self):
1689  """get_number_of_cross_links(ProteomicsData self) -> int"""
1690  return _IMP_multifit.ProteomicsData_get_number_of_cross_links(self)
1691 
1692 
1693  def get_cross_link(self, xlink_ind):
1694  """get_cross_link(ProteomicsData self, int xlink_ind) -> std::pair< IMP::IntPair,IMP::IntPair >"""
1695  return _IMP_multifit.ProteomicsData_get_cross_link(self, xlink_ind)
1696 
1697 
1698  def get_cross_link_part_of_filter(self, xlink_ind):
1699  """get_cross_link_part_of_filter(ProteomicsData self, int xlink_ind) -> bool"""
1700  return _IMP_multifit.ProteomicsData_get_cross_link_part_of_filter(self, xlink_ind)
1701 
1702 
1703  def get_cross_link_length(self, xlink_ind):
1704  """get_cross_link_length(ProteomicsData self, int xlink_ind) -> float"""
1705  return _IMP_multifit.ProteomicsData_get_cross_link_length(self, xlink_ind)
1706 
1707 
1708  def get_number_of_ev_pairs(self):
1709  """get_number_of_ev_pairs(ProteomicsData self) -> int"""
1710  return _IMP_multifit.ProteomicsData_get_number_of_ev_pairs(self)
1711 
1712 
1713  def get_ev_pair(self, ev_ind):
1714  """get_ev_pair(ProteomicsData self, int ev_ind) -> IMP::IntPair"""
1715  return _IMP_multifit.ProteomicsData_get_ev_pair(self, ev_ind)
1716 
1717 
1718  def get_protein_name(self, protein_ind):
1719  """get_protein_name(ProteomicsData self, int protein_ind) -> std::string"""
1720  return _IMP_multifit.ProteomicsData_get_protein_name(self, protein_ind)
1721 
1722 
1723  def get_end_res(self, protein_ind):
1724  """get_end_res(ProteomicsData self, int protein_ind) -> int"""
1725  return _IMP_multifit.ProteomicsData_get_end_res(self, protein_ind)
1726 
1727 
1728  def get_start_res(self, protein_ind):
1729  """get_start_res(ProteomicsData self, int protein_ind) -> int"""
1730  return _IMP_multifit.ProteomicsData_get_start_res(self, protein_ind)
1731 
1732 
1733  def get_protein_filename(self, protein_ind):
1734  """get_protein_filename(ProteomicsData self, int protein_ind) -> std::string"""
1735  return _IMP_multifit.ProteomicsData_get_protein_filename(self, protein_ind)
1736 
1737 
1738  def get_reference_filename(self, protein_ind):
1739  """get_reference_filename(ProteomicsData self, int protein_ind) -> std::string"""
1740  return _IMP_multifit.ProteomicsData_get_reference_filename(self, protein_ind)
1741 
1742 
1743  def get_surface_filename(self, protein_ind):
1744  """get_surface_filename(ProteomicsData self, int protein_ind) -> std::string"""
1745  return _IMP_multifit.ProteomicsData_get_surface_filename(self, protein_ind)
1746 
1747 
1748  def get_protein_data(self, protein_ind):
1749  """get_protein_data(ProteomicsData self, int protein_ind) -> ProteinRecordData"""
1750  return _IMP_multifit.ProteomicsData_get_protein_data(self, protein_ind)
1751 
1752 
1753  def get_version_info(self):
1754  """get_version_info(ProteomicsData self) -> VersionInfo"""
1755  return _IMP_multifit.ProteomicsData_get_version_info(self)
1756 
1757 
1758  def get_num_allowed_violated_interactions(self):
1759  """get_num_allowed_violated_interactions(ProteomicsData self) -> int"""
1760  return _IMP_multifit.ProteomicsData_get_num_allowed_violated_interactions(self)
1761 
1762 
1763  def set_num_allowed_violated_interactions(self, n):
1764  """set_num_allowed_violated_interactions(ProteomicsData self, int n)"""
1765  return _IMP_multifit.ProteomicsData_set_num_allowed_violated_interactions(self, n)
1766 
1767 
1768  def get_num_allowed_violated_cross_links(self):
1769  """get_num_allowed_violated_cross_links(ProteomicsData self) -> int"""
1770  return _IMP_multifit.ProteomicsData_get_num_allowed_violated_cross_links(self)
1771 
1772 
1773  def set_num_allowed_violated_cross_links(self, n):
1774  """set_num_allowed_violated_cross_links(ProteomicsData self, int n)"""
1775  return _IMP_multifit.ProteomicsData_set_num_allowed_violated_cross_links(self, n)
1776 
1777 
1778  def get_num_allowed_violated_ev(self):
1779  """get_num_allowed_violated_ev(ProteomicsData self) -> int"""
1780  return _IMP_multifit.ProteomicsData_get_num_allowed_violated_ev(self)
1781 
1782 
1783  def set_num_allowed_violated_ev(self, n):
1784  """set_num_allowed_violated_ev(ProteomicsData self, int n)"""
1785  return _IMP_multifit.ProteomicsData_set_num_allowed_violated_ev(self, n)
1786 
1787 
1788  def __str__(self):
1789  """__str__(ProteomicsData self) -> std::string"""
1790  return _IMP_multifit.ProteomicsData___str__(self)
1791 
1792 
1793  def __repr__(self):
1794  """__repr__(ProteomicsData self) -> std::string"""
1795  return _IMP_multifit.ProteomicsData___repr__(self)
1796 
1797 
1798  @staticmethod
1799  def get_from(o):
1800  return _object_cast_to_ProteomicsData(o)
1801 
1802 ProteomicsData_swigregister = _IMP_multifit.ProteomicsData_swigregister
1803 ProteomicsData_swigregister(ProteomicsData)
1804 
1805 
1806 def read_proteomics_data(proteomics_fn):
1807  """read_proteomics_data(char const * proteomics_fn) -> ProteomicsData"""
1808  return _IMP_multifit.read_proteomics_data(proteomics_fn)
1809 
1810 def get_partial_proteomics_data(pd, prot_names):
1811  """get_partial_proteomics_data(ProteomicsData pd, IMP::Strings const & prot_names) -> ProteomicsData"""
1812  return _IMP_multifit.get_partial_proteomics_data(pd, prot_names)
1813 class AnchorsData(object):
1814  """Proxy of C++ IMP::multifit::AnchorsData class."""
1815 
1816  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1817 
1818  def __init__(self, *args):
1819  """
1820  __init__(IMP::multifit::AnchorsData self) -> AnchorsData
1821  __init__(IMP::multifit::AnchorsData self, IMP::algebra::Vector3Ds points, IMP::IntPairs edges) -> AnchorsData
1822  """
1823  this = _IMP_multifit.new_AnchorsData(*args)
1824  try:
1825  self.this.append(this)
1826  except __builtin__.Exception:
1827  self.this = this
1828 
1829  def remove_edges_for_node(self, node_ind):
1830  """remove_edges_for_node(AnchorsData self, int node_ind)"""
1831  return _IMP_multifit.AnchorsData_remove_edges_for_node(self, node_ind)
1832 
1833 
1834  def get_number_of_points(self):
1835  """get_number_of_points(AnchorsData self) -> int"""
1836  return _IMP_multifit.AnchorsData_get_number_of_points(self)
1837 
1838 
1839  def get_number_of_edges(self):
1840  """get_number_of_edges(AnchorsData self) -> int"""
1841  return _IMP_multifit.AnchorsData_get_number_of_edges(self)
1842 
1843 
1844  def get_is_point_considered(self, node_ind):
1845  """get_is_point_considered(AnchorsData self, int node_ind) -> bool"""
1846  return _IMP_multifit.AnchorsData_get_is_point_considered(self, node_ind)
1847 
1848 
1849  def show(self, *args):
1850  """
1851  show(AnchorsData self, _ostream out)
1852  show(AnchorsData self)
1853  """
1854  return _IMP_multifit.AnchorsData_show(self, *args)
1855 
1856 
1857  def get_secondary_structure_is_set(self):
1858  """get_secondary_structure_is_set(AnchorsData self) -> bool"""
1859  return _IMP_multifit.AnchorsData_get_secondary_structure_is_set(self)
1860 
1861 
1862  def setup_secondary_structure(self, mdl):
1863  """setup_secondary_structure(AnchorsData self, Model mdl)"""
1864  return _IMP_multifit.AnchorsData_setup_secondary_structure(self, mdl)
1865 
1866 
1867  def set_secondary_structure_probabilities(self, *args):
1868  """
1869  set_secondary_structure_probabilities(AnchorsData self, IMP::Particles const & ssres_ps, IMP::Ints const & indices)
1870  set_secondary_structure_probabilities(AnchorsData self, IMP::Particles const & ssres_ps)
1871  """
1872  return _IMP_multifit.AnchorsData_set_secondary_structure_probabilities(self, *args)
1873 
1874 
1875  def get_secondary_structure_particles(self):
1876  """get_secondary_structure_particles(AnchorsData self) -> IMP::Particles"""
1877  return _IMP_multifit.AnchorsData_get_secondary_structure_particles(self)
1878 
1879  points_ = _swig_property(_IMP_multifit.AnchorsData_points__get, _IMP_multifit.AnchorsData_points__set)
1880  consider_point_ = _swig_property(_IMP_multifit.AnchorsData_consider_point__get, _IMP_multifit.AnchorsData_consider_point__set)
1881  edges_ = _swig_property(_IMP_multifit.AnchorsData_edges__get, _IMP_multifit.AnchorsData_edges__set)
1882 
1883  def __str__(self):
1884  """__str__(AnchorsData self) -> std::string"""
1885  return _IMP_multifit.AnchorsData___str__(self)
1886 
1887 
1888  def __repr__(self):
1889  """__repr__(AnchorsData self) -> std::string"""
1890  return _IMP_multifit.AnchorsData___repr__(self)
1891 
1892  __swig_destroy__ = _IMP_multifit.delete_AnchorsData
1893  __del__ = lambda self: None
1894 AnchorsData_swigregister = _IMP_multifit.AnchorsData_swigregister
1895 AnchorsData_swigregister(AnchorsData)
1896 
1897 
1898 def read_anchors_data(txt_filename):
1899  """read_anchors_data(char const * txt_filename) -> AnchorsData"""
1900  return _IMP_multifit.read_anchors_data(txt_filename)
1901 
1902 def write_txt(txt_filename, ad):
1903  """write_txt(std::string const & txt_filename, AnchorsData ad)"""
1904  return _IMP_multifit.write_txt(txt_filename, ad)
1905 
1906 def write_cmm(cmm_filename, marker_set_name, dpa):
1907  """write_cmm(std::string const & cmm_filename, std::string const & marker_set_name, AnchorsData dpa)"""
1908  return _IMP_multifit.write_cmm(cmm_filename, marker_set_name, dpa)
1909 
1910 def create_coarse_molecule_from_density(dmap, dens_threshold, num_beads, mdl, bead_radius):
1911  """create_coarse_molecule_from_density(DensityMap dmap, float dens_threshold, int num_beads, Model mdl, float bead_radius) -> Hierarchy"""
1912  return _IMP_multifit.create_coarse_molecule_from_density(dmap, dens_threshold, num_beads, mdl, bead_radius)
1913 
1914 def create_hit_map(rb, rb_ref, sols, damp):
1915  """create_hit_map(RigidBody rb, Refiner rb_ref, IMP::multifit::FittingSolutionRecords const & sols, DensityMap damp) -> DensityMap"""
1916  return _IMP_multifit.create_hit_map(rb, rb_ref, sols, damp)
1917 
1918 def get_points_close_to_molecule(mh, points, max_dist):
1919  """get_points_close_to_molecule(Hierarchy mh, IMP::algebra::Vector3Ds const points, IMP::Float max_dist) -> IMP::algebra::Vector3Ds"""
1920  return _IMP_multifit.get_points_close_to_molecule(mh, points, max_dist)
1921 
1922 def get_points_far_from_molecule(mh, points, max_dist):
1923  """get_points_far_from_molecule(Hierarchy mh, IMP::algebra::Vector3Ds const points, IMP::Float max_dist) -> IMP::algebra::Vector3Ds"""
1924  return _IMP_multifit.get_points_far_from_molecule(mh, points, max_dist)
1925 class RadiusOfGyrationRestraint(IMP.Restraint):
1926  """Proxy of C++ IMP::multifit::RadiusOfGyrationRestraint class."""
1927 
1928  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1929 
1930  def __init__(self, ps, num_residues, scale=1.):
1931  """
1932  __init__(IMP::multifit::RadiusOfGyrationRestraint self, IMP::Particles ps, int num_residues, IMP::Float scale=1.) -> RadiusOfGyrationRestraint
1933  __init__(IMP::multifit::RadiusOfGyrationRestraint self, IMP::Particles ps, int num_residues) -> RadiusOfGyrationRestraint
1934  """
1935  this = _IMP_multifit.new_RadiusOfGyrationRestraint(ps, num_residues, scale)
1936  try:
1937  self.this.append(this)
1938  except __builtin__.Exception:
1939  self.this = this
1940 
1941  def do_get_inputs(self):
1942  """do_get_inputs(RadiusOfGyrationRestraint self) -> IMP::ModelObjectsTemp"""
1943  return _IMP_multifit.RadiusOfGyrationRestraint_do_get_inputs(self)
1944 
1945 
1946  def get_version_info(self):
1947  """get_version_info(RadiusOfGyrationRestraint self) -> VersionInfo"""
1948  return _IMP_multifit.RadiusOfGyrationRestraint_get_version_info(self)
1949 
1950 
1951  def set_radius_of_gyration(self, r):
1952  """set_radius_of_gyration(RadiusOfGyrationRestraint self, IMP::Float r)"""
1953  return _IMP_multifit.RadiusOfGyrationRestraint_set_radius_of_gyration(self, r)
1954 
1955 
1956  def get_radius_of_gyration(self):
1957  """get_radius_of_gyration(RadiusOfGyrationRestraint self) -> IMP::Float"""
1958  return _IMP_multifit.RadiusOfGyrationRestraint_get_radius_of_gyration(self)
1959 
1960 
1961  def __str__(self):
1962  """__str__(RadiusOfGyrationRestraint self) -> std::string"""
1963  return _IMP_multifit.RadiusOfGyrationRestraint___str__(self)
1964 
1965 
1966  def __repr__(self):
1967  """__repr__(RadiusOfGyrationRestraint self) -> std::string"""
1968  return _IMP_multifit.RadiusOfGyrationRestraint___repr__(self)
1969 
1970 
1971  @staticmethod
1972  def get_from(o):
1973  return _object_cast_to_RadiusOfGyrationRestraint(o)
1974 
1975 RadiusOfGyrationRestraint_swigregister = _IMP_multifit.RadiusOfGyrationRestraint_swigregister
1976 RadiusOfGyrationRestraint_swigregister(RadiusOfGyrationRestraint)
1977 
1978 
1979 def get_approximated_radius_of_gyration(len):
1980  """get_approximated_radius_of_gyration(int len) -> float"""
1981  return _IMP_multifit.get_approximated_radius_of_gyration(len)
1982 
1983 def get_actual_radius_of_gyration(ps):
1984  """get_actual_radius_of_gyration(IMP::ParticlesTemp ps) -> float"""
1985  return _IMP_multifit.get_actual_radius_of_gyration(ps)
1986 
1987 def get_approximated_radius(len):
1988  """get_approximated_radius(int len) -> float"""
1989  return _IMP_multifit.get_approximated_radius(len)
1990 class ProteinsAnchorsSamplingSpace(object):
1991  """Proxy of C++ IMP::multifit::ProteinsAnchorsSamplingSpace class."""
1992 
1993  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1994 
1995  def __init__(self, prots=None):
1996  """
1997  __init__(IMP::multifit::ProteinsAnchorsSamplingSpace self, ProteomicsData prots=None) -> ProteinsAnchorsSamplingSpace
1998  __init__(IMP::multifit::ProteinsAnchorsSamplingSpace self) -> ProteinsAnchorsSamplingSpace
1999  """
2000  this = _IMP_multifit.new_ProteinsAnchorsSamplingSpace(prots)
2001  try:
2002  self.this.append(this)
2003  except __builtin__.Exception:
2004  self.this = this
2005 
2006  def set_anchors(self, data):
2007  """set_anchors(ProteinsAnchorsSamplingSpace self, AnchorsData data)"""
2008  return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_anchors(self, data)
2009 
2010 
2011  def get_anchors(self):
2012  """get_anchors(ProteinsAnchorsSamplingSpace self) -> AnchorsData"""
2013  return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_anchors(self)
2014 
2015 
2016  def get_anchors_filename(self):
2017  """get_anchors_filename(ProteinsAnchorsSamplingSpace self) -> std::string"""
2018  return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_anchors_filename(self)
2019 
2020 
2021  def set_anchors_filename(self, fn):
2022  """set_anchors_filename(ProteinsAnchorsSamplingSpace self, std::string const & fn)"""
2023  return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_anchors_filename(self, fn)
2024 
2025 
2026  def get_proteomics_data(self):
2027  """get_proteomics_data(ProteinsAnchorsSamplingSpace self) -> ProteomicsData"""
2028  return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_proteomics_data(self)
2029 
2030 
2031  def add_protein(self, rec):
2032  """add_protein(ProteinsAnchorsSamplingSpace self, ProteinRecordData rec)"""
2033  return _IMP_multifit.ProteinsAnchorsSamplingSpace_add_protein(self, rec)
2034 
2035 
2036  def get_paths_for_protein(self, prot_name):
2037  """get_paths_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name) -> IMP::IntsList"""
2038  return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_paths_for_protein(self, prot_name)
2039 
2040 
2041  def set_paths_filename_for_protein(self, prot_name, paths_filename):
2042  """set_paths_filename_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name, std::string const & paths_filename)"""
2043  return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_paths_filename_for_protein(self, prot_name, paths_filename)
2044 
2045 
2046  def get_paths_filename_for_protein(self, prot_name):
2047  """get_paths_filename_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name) -> std::string"""
2048  return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_paths_filename_for_protein(self, prot_name)
2049 
2050 
2051  def set_paths_for_protein(self, prot_name, paths):
2052  """set_paths_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name, IMP::IntsList paths)"""
2053  return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_paths_for_protein(self, prot_name, paths)
2054 
2055 
2056  def show(self, *args):
2057  """
2058  show(ProteinsAnchorsSamplingSpace self, _ostream s)
2059  show(ProteinsAnchorsSamplingSpace self)
2060  """
2061  return _IMP_multifit.ProteinsAnchorsSamplingSpace_show(self, *args)
2062 
2063 
2064  def __str__(self):
2065  """__str__(ProteinsAnchorsSamplingSpace self) -> std::string"""
2066  return _IMP_multifit.ProteinsAnchorsSamplingSpace___str__(self)
2067 
2068 
2069  def __repr__(self):
2070  """__repr__(ProteinsAnchorsSamplingSpace self) -> std::string"""
2071  return _IMP_multifit.ProteinsAnchorsSamplingSpace___repr__(self)
2072 
2073  __swig_destroy__ = _IMP_multifit.delete_ProteinsAnchorsSamplingSpace
2074  __del__ = lambda self: None
2075 ProteinsAnchorsSamplingSpace_swigregister = _IMP_multifit.ProteinsAnchorsSamplingSpace_swigregister
2076 ProteinsAnchorsSamplingSpace_swigregister(ProteinsAnchorsSamplingSpace)
2077 
2078 
2079 def read_protein_anchors_mapping(*args):
2080  """
2081  read_protein_anchors_mapping(ProteomicsData prots, std::string const & anchors_prot_map_fn, int max_paths) -> ProteinsAnchorsSamplingSpace
2082  read_protein_anchors_mapping(ProteomicsData prots, std::string const & anchors_prot_map_fn) -> ProteinsAnchorsSamplingSpace
2083  """
2084  return _IMP_multifit.read_protein_anchors_mapping(*args)
2085 
2086 def write_protein_anchors_mapping(*args):
2087  """
2088  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)
2089  write_protein_anchors_mapping(std::string const & anchors_prot_map_fn, ProteinsAnchorsSamplingSpace pa, IMP::Strings const & prot_names)
2090  """
2091  return _IMP_multifit.write_protein_anchors_mapping(*args)
2092 
2093 def get_part_of_sampling_space(prots_ss, prot_names):
2094  """get_part_of_sampling_space(ProteinsAnchorsSamplingSpace prots_ss, IMP::Strings const & prot_names) -> ProteinsAnchorsSamplingSpace"""
2095  return _IMP_multifit.get_part_of_sampling_space(prots_ss, prot_names)
2096 
2097 def get_partial_assembly_setting_data(prots_sd, prot_names):
2098  """get_partial_assembly_setting_data(SettingsData prots_sd, IMP::Strings const & prot_names) -> SettingsData"""
2099  return _IMP_multifit.get_partial_assembly_setting_data(prots_sd, prot_names)
2100 
2101 def read_paths(*args):
2102  """
2103  read_paths(char const * txt_filename, int max_paths) -> IMP::IntsList
2104  read_paths(char const * txt_filename) -> IMP::IntsList
2105  """
2106  return _IMP_multifit.read_paths(*args)
2107 
2108 def write_paths(paths, txt_filename):
2109  """write_paths(IMP::IntsList const & paths, std::string const & txt_filename)"""
2110  return _IMP_multifit.write_paths(paths, txt_filename)
2111 
2112 def molecule2anchors(mh, k):
2113  """molecule2anchors(Hierarchy mh, int k) -> AnchorsData"""
2114  return _IMP_multifit.molecule2anchors(mh, k)
2115 
2116 def get_anchors_for_density(dmap, number_of_means, density_threshold, pdb_filename, cmm_filename, seg_filename, txt_filename):
2117  """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)"""
2118  return _IMP_multifit.get_anchors_for_density(dmap, number_of_means, density_threshold, pdb_filename, cmm_filename, seg_filename, txt_filename)
2119 
2120 def get_anchor_indices_matching_secondary_structure(ad, ssrs, max_rmsd=0.7):
2121  """
2122  get_anchor_indices_matching_secondary_structure(AnchorsData ad, IMP::atom::SecondaryStructureResidues const & ssrs, IMP::Float max_rmsd=0.7) -> IMP::IntsList
2123  get_anchor_indices_matching_secondary_structure(AnchorsData ad, IMP::atom::SecondaryStructureResidues const & ssrs) -> IMP::IntsList
2124  """
2125  return _IMP_multifit.get_anchor_indices_matching_secondary_structure(ad, ssrs, max_rmsd)
2126 class DominoParams(object):
2127  """Proxy of C++ IMP::multifit::DominoParams class."""
2128 
2129  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2130 
2131  def __init__(self):
2132  """__init__(IMP::multifit::DominoParams self) -> DominoParams"""
2133  this = _IMP_multifit.new_DominoParams()
2134  try:
2135  self.this.append(this)
2136  except __builtin__.Exception:
2137  self.this = this
2138 
2139  def add(self, pt):
2140  """add(DominoParams self, boost::property_tree::ptree const & pt)"""
2141  return _IMP_multifit.DominoParams_add(self, pt)
2142 
2143 
2144  def show(self, *args):
2145  """
2146  show(DominoParams self, _ostream s)
2147  show(DominoParams self)
2148  """
2149  return _IMP_multifit.DominoParams_show(self, *args)
2150 
2151  max_value_threshold_ = _swig_property(_IMP_multifit.DominoParams_max_value_threshold__get, _IMP_multifit.DominoParams_max_value_threshold__set)
2152  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)
2153  max_anchor_penetration_ = _swig_property(_IMP_multifit.DominoParams_max_anchor_penetration__get, _IMP_multifit.DominoParams_max_anchor_penetration__set)
2154  heap_size_ = _swig_property(_IMP_multifit.DominoParams_heap_size__get, _IMP_multifit.DominoParams_heap_size__set)
2155  cache_size_ = _swig_property(_IMP_multifit.DominoParams_cache_size__get, _IMP_multifit.DominoParams_cache_size__set)
2156 
2157  def __str__(self):
2158  """__str__(DominoParams self) -> std::string"""
2159  return _IMP_multifit.DominoParams___str__(self)
2160 
2161 
2162  def __repr__(self):
2163  """__repr__(DominoParams self) -> std::string"""
2164  return _IMP_multifit.DominoParams___repr__(self)
2165 
2166  __swig_destroy__ = _IMP_multifit.delete_DominoParams
2167  __del__ = lambda self: None
2168 DominoParams_swigregister = _IMP_multifit.DominoParams_swigregister
2169 DominoParams_swigregister(DominoParams)
2170 
2171 class XlinkParams(object):
2172  """Proxy of C++ IMP::multifit::XlinkParams class."""
2173 
2174  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2175 
2176  def __init__(self):
2177  """__init__(IMP::multifit::XlinkParams self) -> XlinkParams"""
2178  this = _IMP_multifit.new_XlinkParams()
2179  try:
2180  self.this.append(this)
2181  except __builtin__.Exception:
2182  self.this = this
2183 
2184  def add(self, pt):
2185  """add(XlinkParams self, boost::property_tree::ptree const & pt)"""
2186  return _IMP_multifit.XlinkParams_add(self, pt)
2187 
2188 
2189  def show(self, *args):
2190  """
2191  show(XlinkParams self, _ostream s)
2192  show(XlinkParams self)
2193  """
2194  return _IMP_multifit.XlinkParams_show(self, *args)
2195 
2196  upper_bound_ = _swig_property(_IMP_multifit.XlinkParams_upper_bound__get, _IMP_multifit.XlinkParams_upper_bound__set)
2197  k_ = _swig_property(_IMP_multifit.XlinkParams_k__get, _IMP_multifit.XlinkParams_k__set)
2198  max_xlink_val_ = _swig_property(_IMP_multifit.XlinkParams_max_xlink_val__get, _IMP_multifit.XlinkParams_max_xlink_val__set)
2199  treat_between_residues_ = _swig_property(_IMP_multifit.XlinkParams_treat_between_residues__get, _IMP_multifit.XlinkParams_treat_between_residues__set)
2200 
2201  def __str__(self):
2202  """__str__(XlinkParams self) -> std::string"""
2203  return _IMP_multifit.XlinkParams___str__(self)
2204 
2205 
2206  def __repr__(self):
2207  """__repr__(XlinkParams self) -> std::string"""
2208  return _IMP_multifit.XlinkParams___repr__(self)
2209 
2210  __swig_destroy__ = _IMP_multifit.delete_XlinkParams
2211  __del__ = lambda self: None
2212 XlinkParams_swigregister = _IMP_multifit.XlinkParams_swigregister
2213 XlinkParams_swigregister(XlinkParams)
2214 
2215 class ConnectivityParams(object):
2216  """Proxy of C++ IMP::multifit::ConnectivityParams class."""
2217 
2218  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2219 
2220  def __init__(self):
2221  """__init__(IMP::multifit::ConnectivityParams self) -> ConnectivityParams"""
2222  this = _IMP_multifit.new_ConnectivityParams()
2223  try:
2224  self.this.append(this)
2225  except __builtin__.Exception:
2226  self.this = this
2227 
2228  def add(self, pt):
2229  """add(ConnectivityParams self, boost::property_tree::ptree const & pt)"""
2230  return _IMP_multifit.ConnectivityParams_add(self, pt)
2231 
2232 
2233  def show(self, *args):
2234  """
2235  show(ConnectivityParams self, _ostream s)
2236  show(ConnectivityParams self)
2237  """
2238  return _IMP_multifit.ConnectivityParams_show(self, *args)
2239 
2240  upper_bound_ = _swig_property(_IMP_multifit.ConnectivityParams_upper_bound__get, _IMP_multifit.ConnectivityParams_upper_bound__set)
2241  k_ = _swig_property(_IMP_multifit.ConnectivityParams_k__get, _IMP_multifit.ConnectivityParams_k__set)
2242  max_conn_rest_val_ = _swig_property(_IMP_multifit.ConnectivityParams_max_conn_rest_val__get, _IMP_multifit.ConnectivityParams_max_conn_rest_val__set)
2243 
2244  def __str__(self):
2245  """__str__(ConnectivityParams self) -> std::string"""
2246  return _IMP_multifit.ConnectivityParams___str__(self)
2247 
2248 
2249  def __repr__(self):
2250  """__repr__(ConnectivityParams self) -> std::string"""
2251  return _IMP_multifit.ConnectivityParams___repr__(self)
2252 
2253  __swig_destroy__ = _IMP_multifit.delete_ConnectivityParams
2254  __del__ = lambda self: None
2255 ConnectivityParams_swigregister = _IMP_multifit.ConnectivityParams_swigregister
2256 ConnectivityParams_swigregister(ConnectivityParams)
2257 
2258 class FragmentsParams(object):
2259  """Proxy of C++ IMP::multifit::FragmentsParams class."""
2260 
2261  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2262 
2263  def __init__(self):
2264  """__init__(IMP::multifit::FragmentsParams self) -> FragmentsParams"""
2265  this = _IMP_multifit.new_FragmentsParams()
2266  try:
2267  self.this.append(this)
2268  except __builtin__.Exception:
2269  self.this = this
2270 
2271  def add(self, pt):
2272  """add(FragmentsParams self, boost::property_tree::ptree const & pt)"""
2273  return _IMP_multifit.FragmentsParams_add(self, pt)
2274 
2275 
2276  def show(self, *args):
2277  """
2278  show(FragmentsParams self, _ostream s)
2279  show(FragmentsParams self)
2280  """
2281  return _IMP_multifit.FragmentsParams_show(self, *args)
2282 
2283  frag_len_ = _swig_property(_IMP_multifit.FragmentsParams_frag_len__get, _IMP_multifit.FragmentsParams_frag_len__set)
2284  bead_radius_scale_ = _swig_property(_IMP_multifit.FragmentsParams_bead_radius_scale__get, _IMP_multifit.FragmentsParams_bead_radius_scale__set)
2285  load_atomic_ = _swig_property(_IMP_multifit.FragmentsParams_load_atomic__get, _IMP_multifit.FragmentsParams_load_atomic__set)
2286  subunit_rigid_ = _swig_property(_IMP_multifit.FragmentsParams_subunit_rigid__get, _IMP_multifit.FragmentsParams_subunit_rigid__set)
2287 
2288  def __str__(self):
2289  """__str__(FragmentsParams self) -> std::string"""
2290  return _IMP_multifit.FragmentsParams___str__(self)
2291 
2292 
2293  def __repr__(self):
2294  """__repr__(FragmentsParams self) -> std::string"""
2295  return _IMP_multifit.FragmentsParams___repr__(self)
2296 
2297  __swig_destroy__ = _IMP_multifit.delete_FragmentsParams
2298  __del__ = lambda self: None
2299 FragmentsParams_swigregister = _IMP_multifit.FragmentsParams_swigregister
2300 FragmentsParams_swigregister(FragmentsParams)
2301 
2302 class RogParams(object):
2303  """Proxy of C++ IMP::multifit::RogParams class."""
2304 
2305  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2306 
2307  def __init__(self):
2308  """__init__(IMP::multifit::RogParams self) -> RogParams"""
2309  this = _IMP_multifit.new_RogParams()
2310  try:
2311  self.this.append(this)
2312  except __builtin__.Exception:
2313  self.this = this
2314 
2315  def add(self, pt):
2316  """add(RogParams self, boost::property_tree::ptree const & pt)"""
2317  return _IMP_multifit.RogParams_add(self, pt)
2318 
2319 
2320  def get_max_score(self):
2321  """get_max_score(RogParams self) -> float"""
2322  return _IMP_multifit.RogParams_get_max_score(self)
2323 
2324 
2325  def get_scale(self):
2326  """get_scale(RogParams self) -> float"""
2327  return _IMP_multifit.RogParams_get_scale(self)
2328 
2329 
2330  def show(self, *args):
2331  """
2332  show(RogParams self, _ostream s)
2333  show(RogParams self)
2334  """
2335  return _IMP_multifit.RogParams_show(self, *args)
2336 
2337 
2338  def __str__(self):
2339  """__str__(RogParams self) -> std::string"""
2340  return _IMP_multifit.RogParams___str__(self)
2341 
2342 
2343  def __repr__(self):
2344  """__repr__(RogParams self) -> std::string"""
2345  return _IMP_multifit.RogParams___repr__(self)
2346 
2347  __swig_destroy__ = _IMP_multifit.delete_RogParams
2348  __del__ = lambda self: None
2349 RogParams_swigregister = _IMP_multifit.RogParams_swigregister
2350 RogParams_swigregister(RogParams)
2351 
2352 class EVParams(object):
2353  """Proxy of C++ IMP::multifit::EVParams class."""
2354 
2355  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2356 
2357  def __init__(self):
2358  """__init__(IMP::multifit::EVParams self) -> EVParams"""
2359  this = _IMP_multifit.new_EVParams()
2360  try:
2361  self.this.append(this)
2362  except __builtin__.Exception:
2363  self.this = this
2364 
2365  def add(self, pt):
2366  """add(EVParams self, boost::property_tree::ptree const & pt)"""
2367  return _IMP_multifit.EVParams_add(self, pt)
2368 
2369 
2370  def show(self, *args):
2371  """
2372  show(EVParams self, _ostream s)
2373  show(EVParams self)
2374  """
2375  return _IMP_multifit.EVParams_show(self, *args)
2376 
2377  pair_distance_ = _swig_property(_IMP_multifit.EVParams_pair_distance__get, _IMP_multifit.EVParams_pair_distance__set)
2378  pair_slack_ = _swig_property(_IMP_multifit.EVParams_pair_slack__get, _IMP_multifit.EVParams_pair_slack__set)
2379  hlb_mean_ = _swig_property(_IMP_multifit.EVParams_hlb_mean__get, _IMP_multifit.EVParams_hlb_mean__set)
2380  hlb_k_ = _swig_property(_IMP_multifit.EVParams_hlb_k__get, _IMP_multifit.EVParams_hlb_k__set)
2381  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)
2382  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)
2383  scoring_mode_ = _swig_property(_IMP_multifit.EVParams_scoring_mode__get, _IMP_multifit.EVParams_scoring_mode__set)
2384 
2385  def __str__(self):
2386  """__str__(EVParams self) -> std::string"""
2387  return _IMP_multifit.EVParams___str__(self)
2388 
2389 
2390  def __repr__(self):
2391  """__repr__(EVParams self) -> std::string"""
2392  return _IMP_multifit.EVParams___repr__(self)
2393 
2394  __swig_destroy__ = _IMP_multifit.delete_EVParams
2395  __del__ = lambda self: None
2396 EVParams_swigregister = _IMP_multifit.EVParams_swigregister
2397 EVParams_swigregister(EVParams)
2398 
2399 class FiltersParams(object):
2400  """Proxy of C++ IMP::multifit::FiltersParams class."""
2401 
2402  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2403 
2404  def __init__(self):
2405  """__init__(IMP::multifit::FiltersParams self) -> FiltersParams"""
2406  this = _IMP_multifit.new_FiltersParams()
2407  try:
2408  self.this.append(this)
2409  except __builtin__.Exception:
2410  self.this = this
2411 
2412  def add(self, pt):
2413  """add(FiltersParams self, boost::property_tree::ptree const & pt)"""
2414  return _IMP_multifit.FiltersParams_add(self, pt)
2415 
2416 
2417  def show(self, *args):
2418  """
2419  show(FiltersParams self, _ostream s)
2420  show(FiltersParams self)
2421  """
2422  return _IMP_multifit.FiltersParams_show(self, *args)
2423 
2424  max_num_violated_xlink_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_xlink__get, _IMP_multifit.FiltersParams_max_num_violated_xlink__set)
2425  max_num_violated_conn_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_conn__get, _IMP_multifit.FiltersParams_max_num_violated_conn__set)
2426  max_num_violated_ev_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_ev__get, _IMP_multifit.FiltersParams_max_num_violated_ev__set)
2427 
2428  def __str__(self):
2429  """__str__(FiltersParams self) -> std::string"""
2430  return _IMP_multifit.FiltersParams___str__(self)
2431 
2432 
2433  def __repr__(self):
2434  """__repr__(FiltersParams self) -> std::string"""
2435  return _IMP_multifit.FiltersParams___repr__(self)
2436 
2437  __swig_destroy__ = _IMP_multifit.delete_FiltersParams
2438  __del__ = lambda self: None
2439 FiltersParams_swigregister = _IMP_multifit.FiltersParams_swigregister
2440 FiltersParams_swigregister(FiltersParams)
2441 
2442 class FittingParams(object):
2443  """Proxy of C++ IMP::multifit::FittingParams class."""
2444 
2445  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2446 
2447  def __init__(self):
2448  """__init__(IMP::multifit::FittingParams self) -> FittingParams"""
2449  this = _IMP_multifit.new_FittingParams()
2450  try:
2451  self.this.append(this)
2452  except __builtin__.Exception:
2453  self.this = this
2454 
2455  def add(self, pt):
2456  """add(FittingParams self, boost::property_tree::ptree const & pt)"""
2457  return _IMP_multifit.FittingParams_add(self, pt)
2458 
2459 
2460  def show(self, *args):
2461  """
2462  show(FittingParams self, _ostream s)
2463  show(FittingParams self)
2464  """
2465  return _IMP_multifit.FittingParams_show(self, *args)
2466 
2467  pca_max_angle_diff_ = _swig_property(_IMP_multifit.FittingParams_pca_max_angle_diff__get, _IMP_multifit.FittingParams_pca_max_angle_diff__set)
2468  pca_max_size_diff_ = _swig_property(_IMP_multifit.FittingParams_pca_max_size_diff__get, _IMP_multifit.FittingParams_pca_max_size_diff__set)
2469  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)
2470  max_asmb_fit_score_ = _swig_property(_IMP_multifit.FittingParams_max_asmb_fit_score__get, _IMP_multifit.FittingParams_max_asmb_fit_score__set)
2471 
2472  def __str__(self):
2473  """__str__(FittingParams self) -> std::string"""
2474  return _IMP_multifit.FittingParams___str__(self)
2475 
2476 
2477  def __repr__(self):
2478  """__repr__(FittingParams self) -> std::string"""
2479  return _IMP_multifit.FittingParams___repr__(self)
2480 
2481  __swig_destroy__ = _IMP_multifit.delete_FittingParams
2482  __del__ = lambda self: None
2483 FittingParams_swigregister = _IMP_multifit.FittingParams_swigregister
2484 FittingParams_swigregister(FittingParams)
2485 
2486 class ComplementarityParams(object):
2487  """Proxy of C++ IMP::multifit::ComplementarityParams class."""
2488 
2489  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2490 
2491  def __init__(self):
2492  """__init__(IMP::multifit::ComplementarityParams self) -> ComplementarityParams"""
2493  this = _IMP_multifit.new_ComplementarityParams()
2494  try:
2495  self.this.append(this)
2496  except __builtin__.Exception:
2497  self.this = this
2498 
2499  def add(self, pt):
2500  """add(ComplementarityParams self, boost::property_tree::ptree const & pt)"""
2501  return _IMP_multifit.ComplementarityParams_add(self, pt)
2502 
2503 
2504  def show(self, *args):
2505  """
2506  show(ComplementarityParams self, _ostream s)
2507  show(ComplementarityParams self)
2508  """
2509  return _IMP_multifit.ComplementarityParams_show(self, *args)
2510 
2511  max_score_ = _swig_property(_IMP_multifit.ComplementarityParams_max_score__get, _IMP_multifit.ComplementarityParams_max_score__set)
2512  max_penetration_ = _swig_property(_IMP_multifit.ComplementarityParams_max_penetration__get, _IMP_multifit.ComplementarityParams_max_penetration__set)
2513  interior_layer_thickness_ = _swig_property(_IMP_multifit.ComplementarityParams_interior_layer_thickness__get, _IMP_multifit.ComplementarityParams_interior_layer_thickness__set)
2514  boundary_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_boundary_coef__get, _IMP_multifit.ComplementarityParams_boundary_coef__set)
2515  comp_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_comp_coef__get, _IMP_multifit.ComplementarityParams_comp_coef__set)
2516  penetration_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_penetration_coef__get, _IMP_multifit.ComplementarityParams_penetration_coef__set)
2517 
2518  def __str__(self):
2519  """__str__(ComplementarityParams self) -> std::string"""
2520  return _IMP_multifit.ComplementarityParams___str__(self)
2521 
2522 
2523  def __repr__(self):
2524  """__repr__(ComplementarityParams self) -> std::string"""
2525  return _IMP_multifit.ComplementarityParams___repr__(self)
2526 
2527  __swig_destroy__ = _IMP_multifit.delete_ComplementarityParams
2528  __del__ = lambda self: None
2529 ComplementarityParams_swigregister = _IMP_multifit.ComplementarityParams_swigregister
2530 ComplementarityParams_swigregister(ComplementarityParams)
2531 
2532 class AlignmentParams(object):
2533  """Proxy of C++ IMP::multifit::AlignmentParams class."""
2534 
2535  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2536 
2537  def __init__(self, param_filename):
2538  """__init__(IMP::multifit::AlignmentParams self, char const * param_filename) -> AlignmentParams"""
2539  this = _IMP_multifit.new_AlignmentParams(param_filename)
2540  try:
2541  self.this.append(this)
2542  except __builtin__.Exception:
2543  self.this = this
2544 
2545  def get_domino_params(self):
2546  """get_domino_params(AlignmentParams self) -> DominoParams"""
2547  return _IMP_multifit.AlignmentParams_get_domino_params(self)
2548 
2549 
2550  def get_fitting_params(self):
2551  """get_fitting_params(AlignmentParams self) -> FittingParams"""
2552  return _IMP_multifit.AlignmentParams_get_fitting_params(self)
2553 
2554 
2555  def get_complementarity_params(self):
2556  """get_complementarity_params(AlignmentParams self) -> ComplementarityParams"""
2557  return _IMP_multifit.AlignmentParams_get_complementarity_params(self)
2558 
2559 
2560  def get_xlink_params(self):
2561  """get_xlink_params(AlignmentParams self) -> XlinkParams"""
2562  return _IMP_multifit.AlignmentParams_get_xlink_params(self)
2563 
2564 
2565  def get_connectivity_params(self):
2566  """get_connectivity_params(AlignmentParams self) -> ConnectivityParams"""
2567  return _IMP_multifit.AlignmentParams_get_connectivity_params(self)
2568 
2569 
2570  def get_rog_params(self):
2571  """get_rog_params(AlignmentParams self) -> RogParams"""
2572  return _IMP_multifit.AlignmentParams_get_rog_params(self)
2573 
2574 
2575  def get_fragments_params(self):
2576  """get_fragments_params(AlignmentParams self) -> FragmentsParams"""
2577  return _IMP_multifit.AlignmentParams_get_fragments_params(self)
2578 
2579 
2580  def get_filters_params(self):
2581  """get_filters_params(AlignmentParams self) -> FiltersParams"""
2582  return _IMP_multifit.AlignmentParams_get_filters_params(self)
2583 
2584 
2585  def get_ev_params(self):
2586  """get_ev_params(AlignmentParams self) -> EVParams"""
2587  return _IMP_multifit.AlignmentParams_get_ev_params(self)
2588 
2589 
2590  def show(self, *args):
2591  """
2592  show(AlignmentParams self, _ostream s)
2593  show(AlignmentParams self)
2594  """
2595  return _IMP_multifit.AlignmentParams_show(self, *args)
2596 
2597 
2598  def __str__(self):
2599  """__str__(AlignmentParams self) -> std::string"""
2600  return _IMP_multifit.AlignmentParams___str__(self)
2601 
2602 
2603  def __repr__(self):
2604  """__repr__(AlignmentParams self) -> std::string"""
2605  return _IMP_multifit.AlignmentParams___repr__(self)
2606 
2607  __swig_destroy__ = _IMP_multifit.delete_AlignmentParams
2608  __del__ = lambda self: None
2609 AlignmentParams_swigregister = _IMP_multifit.AlignmentParams_swigregister
2610 AlignmentParams_swigregister(AlignmentParams)
2611 
2612 class ProteomicsEMAlignmentAtomic(IMP.Object):
2613  """Proxy of C++ IMP::multifit::ProteomicsEMAlignmentAtomic class."""
2614 
2615  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2616 
2617  def __init__(self, mapping_data, asmb_data, align_param):
2618  """__init__(IMP::multifit::ProteomicsEMAlignmentAtomic self, ProteinsAnchorsSamplingSpace mapping_data, SettingsData asmb_data, AlignmentParams align_param) -> ProteomicsEMAlignmentAtomic"""
2619  this = _IMP_multifit.new_ProteomicsEMAlignmentAtomic(mapping_data, asmb_data, align_param)
2620  try:
2621  self.this.append(this)
2622  except __builtin__.Exception:
2623  self.this = this
2624 
2625  def align(self):
2626  """align(ProteomicsEMAlignmentAtomic self)"""
2627  return _IMP_multifit.ProteomicsEMAlignmentAtomic_align(self)
2628 
2629 
2630  def add_all_restraints(self):
2631  """add_all_restraints(ProteomicsEMAlignmentAtomic self)"""
2632  return _IMP_multifit.ProteomicsEMAlignmentAtomic_add_all_restraints(self)
2633 
2634 
2635  def get_restraint_set(self):
2636  """get_restraint_set(ProteomicsEMAlignmentAtomic self) -> RestraintSet"""
2637  return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_restraint_set(self)
2638 
2639 
2640  def add_states_and_filters(self):
2641  """add_states_and_filters(ProteomicsEMAlignmentAtomic self)"""
2642  return _IMP_multifit.ProteomicsEMAlignmentAtomic_add_states_and_filters(self)
2643 
2644 
2645  def show_domino_merge_tree(self):
2646  """show_domino_merge_tree(ProteomicsEMAlignmentAtomic self)"""
2647  return _IMP_multifit.ProteomicsEMAlignmentAtomic_show_domino_merge_tree(self)
2648 
2649 
2650  def get_combinations(self, uniques=False):
2651  """
2652  get_combinations(ProteomicsEMAlignmentAtomic self, bool uniques=False) -> IMP::domino::Assignments
2653  get_combinations(ProteomicsEMAlignmentAtomic self) -> IMP::domino::Assignments
2654  """
2655  return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_combinations(self, uniques)
2656 
2657 
2658  def set_density_map(self, dmap, threshold):
2659  """set_density_map(ProteomicsEMAlignmentAtomic self, DensityMap dmap, float threshold)"""
2660  return _IMP_multifit.ProteomicsEMAlignmentAtomic_set_density_map(self, dmap, threshold)
2661 
2662 
2663  def get_molecules(self):
2664  """get_molecules(ProteomicsEMAlignmentAtomic self) -> IMP::atom::Hierarchies"""
2665  return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_molecules(self)
2666 
2667 
2668  def get_rigid_bodies(self):
2669  """get_rigid_bodies(ProteomicsEMAlignmentAtomic self) -> IMP::core::RigidBodies"""
2670  return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_rigid_bodies(self)
2671 
2672 
2673  def load_combination_of_states(self, state4particles):
2674  """load_combination_of_states(ProteomicsEMAlignmentAtomic self, IMP::Ints const & state4particles)"""
2675  return _IMP_multifit.ProteomicsEMAlignmentAtomic_load_combination_of_states(self, state4particles)
2676 
2677 
2678  def show_scores_header(self, *args):
2679  """
2680  show_scores_header(ProteomicsEMAlignmentAtomic self, _ostream ous)
2681  show_scores_header(ProteomicsEMAlignmentAtomic self)
2682  """
2683  return _IMP_multifit.ProteomicsEMAlignmentAtomic_show_scores_header(self, *args)
2684 
2685 
2686  def get_model(self):
2687  """get_model(ProteomicsEMAlignmentAtomic self) -> Model"""
2688  return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_model(self)
2689 
2690 
2691  def set_fast_scoring(self, state):
2692  """set_fast_scoring(ProteomicsEMAlignmentAtomic self, bool state)"""
2693  return _IMP_multifit.ProteomicsEMAlignmentAtomic_set_fast_scoring(self, state)
2694 
2695 
2696  def get_version_info(self):
2697  """get_version_info(ProteomicsEMAlignmentAtomic self) -> VersionInfo"""
2698  return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_version_info(self)
2699 
2700 
2701  def __str__(self):
2702  """__str__(ProteomicsEMAlignmentAtomic self) -> std::string"""
2703  return _IMP_multifit.ProteomicsEMAlignmentAtomic___str__(self)
2704 
2705 
2706  def __repr__(self):
2707  """__repr__(ProteomicsEMAlignmentAtomic self) -> std::string"""
2708  return _IMP_multifit.ProteomicsEMAlignmentAtomic___repr__(self)
2709 
2710 
2711  @staticmethod
2712  def get_from(o):
2713  return _object_cast_to_ProteomicsEMAlignmentAtomic(o)
2714 
2715 ProteomicsEMAlignmentAtomic_swigregister = _IMP_multifit.ProteomicsEMAlignmentAtomic_swigregister
2716 ProteomicsEMAlignmentAtomic_swigregister(ProteomicsEMAlignmentAtomic)
2717 
2718 
2719 def write_connolly_surface(atoms, fn, density, probe_radius):
2720  """write_connolly_surface(IMP::atom::Atoms atoms, TextOutput fn, float density, float probe_radius)"""
2721  return _IMP_multifit.write_connolly_surface(atoms, fn, density, probe_radius)
2722 class Ensemble(IMP.Object):
2723  """Proxy of C++ IMP::multifit::Ensemble class."""
2724 
2725  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2726 
2727  def load_combination(self, fit_comb):
2728  """load_combination(Ensemble self, IMP::Ints fit_comb)"""
2729  return _IMP_multifit.Ensemble_load_combination(self, fit_comb)
2730 
2731 
2732  def unload_combination(self, fit_comb):
2733  """unload_combination(Ensemble self, IMP::Ints fit_comb)"""
2734  return _IMP_multifit.Ensemble_unload_combination(self, fit_comb)
2735 
2736 
2737  def add_component_and_fits(self, mh, fits):
2738  """add_component_and_fits(Ensemble self, Hierarchy mh, IMP::multifit::FittingSolutionRecords const & fits)"""
2739  return _IMP_multifit.Ensemble_add_component_and_fits(self, mh, fits)
2740 
2741 
2742  def get_molecules(self):
2743  """get_molecules(Ensemble self) -> IMP::atom::Hierarchies"""
2744  return _IMP_multifit.Ensemble_get_molecules(self)
2745 
2746 
2747  def get_rigid_bodies(self):
2748  """get_rigid_bodies(Ensemble self) -> IMP::core::RigidBodies"""
2749  return _IMP_multifit.Ensemble_get_rigid_bodies(self)
2750 
2751 
2752  def get_rmsd(self, second_xyz):
2753  """get_rmsd(Ensemble self, IMP::core::XYZs const & second_xyz) -> float"""
2754  return _IMP_multifit.Ensemble_get_rmsd(self, second_xyz)
2755 
2756 
2757  def __init__(self, sd, mapping_data):
2758  """__init__(IMP::multifit::Ensemble self, SettingsData sd, ProteinsAnchorsSamplingSpace mapping_data) -> Ensemble"""
2759  this = _IMP_multifit.new_Ensemble(sd, mapping_data)
2760  try:
2761  self.this.append(this)
2762  except __builtin__.Exception:
2763  self.this = this
2764 
2765  def score_by_restraints(self, rs, combinations):
2766  """score_by_restraints(Ensemble self, IMP::Restraints rs, IMP::IntsList const & combinations) -> std::vector< IMP::Floats,std::allocator< IMP::Floats > >"""
2767  return _IMP_multifit.Ensemble_score_by_restraints(self, rs, combinations)
2768 
2769 
2770  def get_version_info(self):
2771  """get_version_info(Ensemble self) -> VersionInfo"""
2772  return _IMP_multifit.Ensemble_get_version_info(self)
2773 
2774 
2775  def __str__(self):
2776  """__str__(Ensemble self) -> std::string"""
2777  return _IMP_multifit.Ensemble___str__(self)
2778 
2779 
2780  def __repr__(self):
2781  """__repr__(Ensemble self) -> std::string"""
2782  return _IMP_multifit.Ensemble___repr__(self)
2783 
2784 
2785  @staticmethod
2786  def get_from(o):
2787  return _object_cast_to_Ensemble(o)
2788 
2789 Ensemble_swigregister = _IMP_multifit.Ensemble_swigregister
2790 Ensemble_swigregister(Ensemble)
2791 
2792 
2793 def load_ensemble(sd, mdl, mapping_data):
2794  """load_ensemble(SettingsData sd, Model mdl, ProteinsAnchorsSamplingSpace mapping_data) -> Ensemble"""
2795  return _IMP_multifit.load_ensemble(sd, mdl, mapping_data)
2796 class RigidLeavesRefiner(IMP.Refiner):
2797  """Proxy of C++ IMP::multifit::RigidLeavesRefiner class."""
2798 
2799  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2800 
2801  def __init__(self, *args):
2802  """
2803  __init__(IMP::multifit::RigidLeavesRefiner self, std::string name) -> RigidLeavesRefiner
2804  __init__(IMP::multifit::RigidLeavesRefiner self) -> RigidLeavesRefiner
2805  """
2806  this = _IMP_multifit.new_RigidLeavesRefiner(*args)
2807  try:
2808  self.this.append(this)
2809  except __builtin__.Exception:
2810  self.this = this
2811 
2812  def do_get_inputs(self, m, pis):
2813  """do_get_inputs(RigidLeavesRefiner self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2814  return _IMP_multifit.RigidLeavesRefiner_do_get_inputs(self, m, pis)
2815 
2816 
2817  def get_version_info(self):
2818  """get_version_info(RigidLeavesRefiner self) -> VersionInfo"""
2819  return _IMP_multifit.RigidLeavesRefiner_get_version_info(self)
2820 
2821 
2822  def __str__(self):
2823  """__str__(RigidLeavesRefiner self) -> std::string"""
2824  return _IMP_multifit.RigidLeavesRefiner___str__(self)
2825 
2826 
2827  def __repr__(self):
2828  """__repr__(RigidLeavesRefiner self) -> std::string"""
2829  return _IMP_multifit.RigidLeavesRefiner___repr__(self)
2830 
2831 
2832  @staticmethod
2833  def get_from(o):
2834  return _object_cast_to_RigidLeavesRefiner(o)
2835 
2836 RigidLeavesRefiner_swigregister = _IMP_multifit.RigidLeavesRefiner_swigregister
2837 RigidLeavesRefiner_swigregister(RigidLeavesRefiner)
2838 
2839 
2840 _all_commands = ["param", "anchors", "fit_fft", "cluster", "add_fit_rmsd",
2841  "indexes", "proteomics", "align", "models", "transforms",
2842  "score", "merge_tree", "reference", "refine_fft", "segment"]
2843 
2844 
2845 def get_module_version():
2846  """get_module_version() -> std::string const"""
2847  return _IMP_multifit.get_module_version()
2848 
2849 def get_example_path(fname):
2850  """get_example_path(std::string fname) -> std::string"""
2851  return _IMP_multifit.get_example_path(fname)
2852 
2853 def get_data_path(fname):
2854  """get_data_path(std::string fname) -> std::string"""
2855  return _IMP_multifit.get_data_path(fname)
2856 
2857 from . import _version_check
2858 _version_check.check_version(get_module_version())
2859 __version__ = get_module_version()
2860 
2861 
2862 
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.