IMP  2.3.0
The Integrative Modeling Platform
multifit/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.2
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 
8 
9 
10 
11 from sys import version_info
12 if version_info >= (2,6,0):
13  def swig_import_helper():
14  from os.path import dirname
15  import imp
16  fp = None
17  try:
18  fp, pathname, description = imp.find_module('_IMP_multifit', [dirname(__file__)])
19  except ImportError:
20  import _IMP_multifit
21  return _IMP_multifit
22  if fp is not None:
23  try:
24  _mod = imp.load_module('_IMP_multifit', fp, pathname, description)
25  finally:
26  fp.close()
27  return _mod
28  _IMP_multifit = swig_import_helper()
29  del swig_import_helper
30 else:
31  import _IMP_multifit
32 del version_info
33 try:
34  _swig_property = property
35 except NameError:
36  pass # Python < 2.2 doesn't have 'property'.
37 def _swig_setattr_nondynamic(self,class_type,name,value,static=1):
38  if (name == "thisown"): return self.this.own(value)
39  if (name == "this"):
40  if type(value).__name__ == 'SwigPyObject':
41  self.__dict__[name] = value
42  return
43  method = class_type.__swig_setmethods__.get(name,None)
44  if method: return method(self,value)
45  if (not static):
46  self.__dict__[name] = value
47  else:
48  raise AttributeError("You cannot add attributes to %s" % self)
49 
50 def _swig_setattr(self,class_type,name,value):
51  return _swig_setattr_nondynamic(self,class_type,name,value,0)
52 
53 def _swig_getattr(self,class_type,name):
54  if (name == "thisown"): return self.this.own()
55  method = class_type.__swig_getmethods__.get(name,None)
56  if method: return method(self)
57  raise AttributeError(name)
58 
59 def _swig_repr(self):
60  try: strthis = "proxy of " + self.this.__repr__()
61  except: strthis = ""
62  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
63 
64 try:
65  _object = object
66  _newclass = 1
67 except AttributeError:
68  class _object : pass
69  _newclass = 0
70 
71 
72 try:
73  import weakref
74  weakref_proxy = weakref.proxy
75 except:
76  weakref_proxy = lambda x: x
77 
78 
79 class IMP_MULTIFIT_SwigPyIterator(_object):
80  """Proxy of C++ swig::IMP_MULTIFIT_SwigPyIterator class"""
81  __swig_setmethods__ = {}
82  __setattr__ = lambda self, name, value: _swig_setattr(self, IMP_MULTIFIT_SwigPyIterator, name, value)
83  __swig_getmethods__ = {}
84  __getattr__ = lambda self, name: _swig_getattr(self, IMP_MULTIFIT_SwigPyIterator, name)
85  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
86  __repr__ = _swig_repr
87  __swig_destroy__ = _IMP_multifit.delete_IMP_MULTIFIT_SwigPyIterator
88  __del__ = lambda self : None;
89  def value(self):
90  """value(IMP_MULTIFIT_SwigPyIterator self) -> PyObject *"""
91  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_value(self)
92 
93  def incr(self, n=1):
94  """
95  incr(IMP_MULTIFIT_SwigPyIterator self, size_t n=1) -> IMP_MULTIFIT_SwigPyIterator
96  incr(IMP_MULTIFIT_SwigPyIterator self) -> IMP_MULTIFIT_SwigPyIterator
97  """
98  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_incr(self, n)
99 
100  def decr(self, n=1):
101  """
102  decr(IMP_MULTIFIT_SwigPyIterator self, size_t n=1) -> IMP_MULTIFIT_SwigPyIterator
103  decr(IMP_MULTIFIT_SwigPyIterator self) -> IMP_MULTIFIT_SwigPyIterator
104  """
105  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_decr(self, n)
106 
107  def distance(self, *args):
108  """distance(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> ptrdiff_t"""
109  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_distance(self, *args)
110 
111  def equal(self, *args):
112  """equal(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> bool"""
113  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_equal(self, *args)
114 
115  def copy(self):
116  """copy(IMP_MULTIFIT_SwigPyIterator self) -> IMP_MULTIFIT_SwigPyIterator"""
117  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_copy(self)
118 
119  def next(self):
120  """next(IMP_MULTIFIT_SwigPyIterator self) -> PyObject *"""
121  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_next(self)
122 
123  def __next__(self):
124  """__next__(IMP_MULTIFIT_SwigPyIterator self) -> PyObject *"""
125  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___next__(self)
126 
127  def previous(self):
128  """previous(IMP_MULTIFIT_SwigPyIterator self) -> PyObject *"""
129  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_previous(self)
130 
131  def advance(self, *args):
132  """advance(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator"""
133  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_advance(self, *args)
134 
135  def __eq__(self, *args):
136  """__eq__(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> bool"""
137  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___eq__(self, *args)
138 
139  def __ne__(self, *args):
140  """__ne__(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> bool"""
141  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___ne__(self, *args)
142 
143  def __iadd__(self, *args):
144  """__iadd__(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator"""
145  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___iadd__(self, *args)
146 
147  def __isub__(self, *args):
148  """__isub__(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator"""
149  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___isub__(self, *args)
150 
151  def __add__(self, *args):
152  """__add__(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator"""
153  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___add__(self, *args)
154 
155  def __sub__(self, *args):
156  """
157  __sub__(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator
158  __sub__(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> ptrdiff_t
159  """
160  return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___sub__(self, *args)
161 
162  def __iter__(self): return self
163 IMP_MULTIFIT_SwigPyIterator_swigregister = _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_swigregister
164 IMP_MULTIFIT_SwigPyIterator_swigregister(IMP_MULTIFIT_SwigPyIterator)
165 
166 _value_types=[]
167 _object_types=[]
168 _raii_types=[]
169 _plural_types=[]
170 
171 IMP_DEBUG = _IMP_multifit.IMP_DEBUG
172 IMP_RELEASE = _IMP_multifit.IMP_RELEASE
173 IMP_SILENT = _IMP_multifit.IMP_SILENT
174 IMP_PROGRESS = _IMP_multifit.IMP_PROGRESS
175 IMP_TERSE = _IMP_multifit.IMP_TERSE
176 IMP_VERBOSE = _IMP_multifit.IMP_VERBOSE
177 IMP_MEMORY = _IMP_multifit.IMP_MEMORY
178 IMP_NONE = _IMP_multifit.IMP_NONE
179 IMP_USAGE = _IMP_multifit.IMP_USAGE
180 IMP_INTERNAL = _IMP_multifit.IMP_INTERNAL
181 IMP_BASE_HAS_LOG4CXX = _IMP_multifit.IMP_BASE_HAS_LOG4CXX
182 IMP_COMPILER_HAS_AUTO = _IMP_multifit.IMP_COMPILER_HAS_AUTO
183 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_multifit.IMP_COMPILER_HAS_DEBUG_VECTOR
184 IMP_BASE_HAS_BOOST_RANDOM = _IMP_multifit.IMP_BASE_HAS_BOOST_RANDOM
185 IMP_BASE_HAS_GPERFTOOLS = _IMP_multifit.IMP_BASE_HAS_GPERFTOOLS
186 IMP_BASE_HAS_TCMALLOC_HEAPCHECKER = _IMP_multifit.IMP_BASE_HAS_TCMALLOC_HEAPCHECKER
187 IMP_BASE_HAS_TCMALLOC_HEAPPROFILER = _IMP_multifit.IMP_BASE_HAS_TCMALLOC_HEAPPROFILER
188 IMPBASE_SHOW_WARNINGS = _IMP_multifit.IMPBASE_SHOW_WARNINGS
189 import sys
190 class _DirectorObjects(object):
191  """@internal Simple class to keep references to director objects
192  to prevent premature deletion."""
193  def __init__(self):
194  self._objects = []
195  def register(self, obj):
196  """Take a reference to a director object; will only work for
197  refcounted C++ classes"""
198  if hasattr(obj, 'get_ref_count'):
199  self._objects.append(obj)
200  def cleanup(self):
201  """Only drop our reference and allow cleanup by Python if no other
202  Python references exist (we hold 3 references: one in self._objects,
203  one in x, and one in the argument list for getrefcount) *and* no
204  other C++ references exist (the Python object always holds one)"""
205  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
206  or x.get_ref_count() > 1]
207 
208 
209  self._objects = objs
210  def get_object_count(self):
211  """Get number of director objects (useful for testing only)"""
212  return len(self._objects)
213 _director_objects = _DirectorObjects()
214 
215 DEFAULT_CHECK = _IMP_multifit.DEFAULT_CHECK
216 NONE = _IMP_multifit.NONE
217 USAGE = _IMP_multifit.USAGE
218 USAGE_AND_INTERNAL = _IMP_multifit.USAGE_AND_INTERNAL
219 
220 def set_check_level(*args):
221  """set_check_level(IMP::base::CheckLevel tf)"""
222  return _IMP_multifit.set_check_level(*args)
223 
224 def get_check_level():
225  """get_check_level() -> IMP::base::CheckLevel"""
226  return _IMP_multifit.get_check_level()
227 class _ostream(_object):
228  """Proxy of C++ std::ostream class"""
229  __swig_setmethods__ = {}
230  __setattr__ = lambda self, name, value: _swig_setattr(self, _ostream, name, value)
231  __swig_getmethods__ = {}
232  __getattr__ = lambda self, name: _swig_getattr(self, _ostream, name)
233  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined")
234  __repr__ = _swig_repr
235  def write(self, *args):
236  """write(_ostream self, char const * osa_buf)"""
237  return _IMP_multifit._ostream_write(self, *args)
238 
239 _ostream_swigregister = _IMP_multifit._ostream_swigregister
240 _ostream_swigregister(_ostream)
241 
242 IMP_COMPILER_HAS_OVERRIDE = _IMP_multifit.IMP_COMPILER_HAS_OVERRIDE
243 IMP_COMPILER_HAS_FINAL = _IMP_multifit.IMP_COMPILER_HAS_FINAL
244 IMP_HAS_NOEXCEPT = _IMP_multifit.IMP_HAS_NOEXCEPT
245 import IMP.base
246 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CGAL_HAS_BOOST_FILESYSTEM
247 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
248 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CGAL_HAS_BOOST_RANDOM
249 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CGAL_HAS_BOOST_SYSTEM
250 IMPCGAL_SHOW_WARNINGS = _IMP_multifit.IMPCGAL_SHOW_WARNINGS
251 import IMP.cgal
252 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_multifit.IMP_ALGEBRA_HAS_IMP_CGAL
253 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
254 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
255 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_RANDOM
256 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_SYSTEM
257 IMP_ALGEBRA_HAS_CGAL = _IMP_multifit.IMP_ALGEBRA_HAS_CGAL
258 IMP_ALGEBRA_HAS_ANN = _IMP_multifit.IMP_ALGEBRA_HAS_ANN
259 IMPALGEBRA_SHOW_WARNINGS = _IMP_multifit.IMPALGEBRA_SHOW_WARNINGS
260 import IMP.algebra
261 IMP_KERNEL_HAS_IMP_CGAL = _IMP_multifit.IMP_KERNEL_HAS_IMP_CGAL
262 IMP_KERNEL_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_KERNEL_HAS_BOOST_PROGRAMOPTIONS
263 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_multifit.IMP_KERNEL_HAS_BOOST_RANDOM
264 IMP_KERNEL_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_KERNEL_HAS_BOOST_SYSTEM
265 IMP_KERNEL_HAS_CGAL = _IMP_multifit.IMP_KERNEL_HAS_CGAL
266 IMPKERNEL_SHOW_WARNINGS = _IMP_multifit.IMPKERNEL_SHOW_WARNINGS
267 import IMP.kernel
268 IMP_DISPLAY_HAS_IMP_BASE = _IMP_multifit.IMP_DISPLAY_HAS_IMP_BASE
269 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_multifit.IMP_DISPLAY_HAS_IMP_CGAL
270 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
271 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
272 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_RANDOM
273 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_SYSTEM
274 IMP_DISPLAY_HAS_CGAL = _IMP_multifit.IMP_DISPLAY_HAS_CGAL
275 IMPDISPLAY_SHOW_WARNINGS = _IMP_multifit.IMPDISPLAY_SHOW_WARNINGS
276 import IMP.display
277 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
278 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
279 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
280 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
281 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
282 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_CGAL
283 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_HDF5
284 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_multifit.IMPSCOREFUNCTOR_SHOW_WARNINGS
285 import IMP.score_functor
286 IMP_STATISTICS_HAS_IMP_BASE = _IMP_multifit.IMP_STATISTICS_HAS_IMP_BASE
287 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_multifit.IMP_STATISTICS_HAS_IMP_CGAL
288 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
289 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
290 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_RANDOM
291 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_SYSTEM
292 IMP_STATISTICS_HAS_CGAL = _IMP_multifit.IMP_STATISTICS_HAS_CGAL
293 IMPSTATISTICS_SHOW_WARNINGS = _IMP_multifit.IMPSTATISTICS_SHOW_WARNINGS
294 import IMP.statistics
295 IMP_CORE_HAS_IMP_BASE = _IMP_multifit.IMP_CORE_HAS_IMP_BASE
296 IMP_CORE_HAS_IMP_CGAL = _IMP_multifit.IMP_CORE_HAS_IMP_CGAL
297 IMP_CORE_HAS_IMP_KERNEL = _IMP_multifit.IMP_CORE_HAS_IMP_KERNEL
298 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CORE_HAS_BOOST_FILESYSTEM
299 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
300 IMP_CORE_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CORE_HAS_BOOST_RANDOM
301 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CORE_HAS_BOOST_SYSTEM
302 IMP_CORE_HAS_CGAL = _IMP_multifit.IMP_CORE_HAS_CGAL
303 IMP_CORE_HAS_HDF5 = _IMP_multifit.IMP_CORE_HAS_HDF5
304 IMPCORE_SHOW_WARNINGS = _IMP_multifit.IMPCORE_SHOW_WARNINGS
305 import IMP.core
306 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_multifit.IMP_CONTAINER_HAS_IMP_ALGEBRA
307 IMP_CONTAINER_HAS_IMP_BASE = _IMP_multifit.IMP_CONTAINER_HAS_IMP_BASE
308 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_multifit.IMP_CONTAINER_HAS_IMP_CGAL
309 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_multifit.IMP_CONTAINER_HAS_IMP_DISPLAY
310 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_multifit.IMP_CONTAINER_HAS_IMP_KERNEL
311 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
312 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
313 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
314 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_RANDOM
315 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_SYSTEM
316 IMP_CONTAINER_HAS_CGAL = _IMP_multifit.IMP_CONTAINER_HAS_CGAL
317 IMP_CONTAINER_HAS_HDF5 = _IMP_multifit.IMP_CONTAINER_HAS_HDF5
318 IMPCONTAINER_SHOW_WARNINGS = _IMP_multifit.IMPCONTAINER_SHOW_WARNINGS
319 import IMP.container
320 IMP_ATOM_HAS_IMP_BASE = _IMP_multifit.IMP_ATOM_HAS_IMP_BASE
321 IMP_ATOM_HAS_IMP_CGAL = _IMP_multifit.IMP_ATOM_HAS_IMP_CGAL
322 IMP_ATOM_HAS_IMP_KERNEL = _IMP_multifit.IMP_ATOM_HAS_IMP_KERNEL
323 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
324 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
325 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_multifit.IMP_ATOM_HAS_BOOST_RANDOM
326 IMP_ATOM_HAS_BOOST_REGEX = _IMP_multifit.IMP_ATOM_HAS_BOOST_REGEX
327 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_ATOM_HAS_BOOST_SYSTEM
328 IMP_ATOM_HAS_CGAL = _IMP_multifit.IMP_ATOM_HAS_CGAL
329 IMP_ATOM_HAS_HDF5 = _IMP_multifit.IMP_ATOM_HAS_HDF5
330 IMPATOM_SHOW_WARNINGS = _IMP_multifit.IMPATOM_SHOW_WARNINGS
331 IMP_ATOM_TYPE_INDEX = _IMP_multifit.IMP_ATOM_TYPE_INDEX
332 IMP_RESIDUE_TYPE_INDEX = _IMP_multifit.IMP_RESIDUE_TYPE_INDEX
333 IMP_HIERARCHY_TYPE_INDEX = _IMP_multifit.IMP_HIERARCHY_TYPE_INDEX
334 import IMP.atom
335 IMP_EM_HAS_IMP_CGAL = _IMP_multifit.IMP_EM_HAS_IMP_CGAL
336 IMP_EM_HAS_IMP_CONTAINER = _IMP_multifit.IMP_EM_HAS_IMP_CONTAINER
337 IMP_EM_HAS_IMP_DISPLAY = _IMP_multifit.IMP_EM_HAS_IMP_DISPLAY
338 IMP_EM_HAS_IMP_KERNEL = _IMP_multifit.IMP_EM_HAS_IMP_KERNEL
339 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_EM_HAS_IMP_SCORE_FUNCTOR
340 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_EM_HAS_BOOST_FILESYSTEM
341 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
342 IMP_EM_HAS_BOOST_RANDOM = _IMP_multifit.IMP_EM_HAS_BOOST_RANDOM
343 IMP_EM_HAS_BOOST_REGEX = _IMP_multifit.IMP_EM_HAS_BOOST_REGEX
344 IMP_EM_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_EM_HAS_BOOST_SYSTEM
345 IMP_EM_HAS_CGAL = _IMP_multifit.IMP_EM_HAS_CGAL
346 IMP_EM_HAS_HDF5 = _IMP_multifit.IMP_EM_HAS_HDF5
347 IMPEM_SHOW_WARNINGS = _IMP_multifit.IMPEM_SHOW_WARNINGS
348 import IMP.em
349 IMP_RMF_HAS_IMP_BASE = _IMP_multifit.IMP_RMF_HAS_IMP_BASE
350 IMP_RMF_HAS_IMP_CGAL = _IMP_multifit.IMP_RMF_HAS_IMP_CGAL
351 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
352 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_RMF_HAS_BOOST_FILESYSTEM
353 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
354 IMP_RMF_HAS_BOOST_RANDOM = _IMP_multifit.IMP_RMF_HAS_BOOST_RANDOM
355 IMP_RMF_HAS_BOOST_REGEX = _IMP_multifit.IMP_RMF_HAS_BOOST_REGEX
356 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_RMF_HAS_BOOST_SYSTEM
357 IMP_RMF_HAS_CGAL = _IMP_multifit.IMP_RMF_HAS_CGAL
358 IMP_RMF_HAS_HDF5 = _IMP_multifit.IMP_RMF_HAS_HDF5
359 IMPRMF_SHOW_WARNINGS = _IMP_multifit.IMPRMF_SHOW_WARNINGS
360 import IMP.rmf
361 import RMF
362 IMP_DOMINO_HAS_IMP_ATOM = _IMP_multifit.IMP_DOMINO_HAS_IMP_ATOM
363 IMP_DOMINO_HAS_IMP_BASE = _IMP_multifit.IMP_DOMINO_HAS_IMP_BASE
364 IMP_DOMINO_HAS_IMP_CGAL = _IMP_multifit.IMP_DOMINO_HAS_IMP_CGAL
365 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_multifit.IMP_DOMINO_HAS_IMP_KERNEL
366 IMP_DOMINO_HAS_IMP_RMF = _IMP_multifit.IMP_DOMINO_HAS_IMP_RMF
367 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
368 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_FILESYSTEM
369 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
370 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_RANDOM
371 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_multifit.IMP_DOMINO_HAS_BOOST_REGEX
372 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_SYSTEM
373 IMP_DOMINO_HAS_CGAL = _IMP_multifit.IMP_DOMINO_HAS_CGAL
374 IMP_DOMINO_HAS_HDF5 = _IMP_multifit.IMP_DOMINO_HAS_HDF5
375 IMP_DOMINO_HAS_RMF = _IMP_multifit.IMP_DOMINO_HAS_RMF
376 IMPDOMINO_SHOW_WARNINGS = _IMP_multifit.IMPDOMINO_SHOW_WARNINGS
377 import RMF_HDF5
378 import IMP.domino
379 IMP_MULTIFIT_HAS_IMP_BASE = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_BASE
380 IMP_MULTIFIT_HAS_IMP_CGAL = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_CGAL
381 IMP_MULTIFIT_HAS_IMP_CONTAINER = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_CONTAINER
382 IMP_MULTIFIT_HAS_IMP_DISPLAY = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_DISPLAY
383 IMP_MULTIFIT_HAS_IMP_KERNEL = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_KERNEL
384 IMP_MULTIFIT_HAS_IMP_RMF = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_RMF
385 IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR
386 IMP_MULTIFIT_HAS_BOOST_GRAPH = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_GRAPH
387 IMP_MULTIFIT_HAS_BOOST_RANDOM = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_RANDOM
388 IMP_MULTIFIT_HAS_BOOST_REGEX = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_REGEX
389 IMP_MULTIFIT_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_SYSTEM
390 IMP_MULTIFIT_HAS_CGAL = _IMP_multifit.IMP_MULTIFIT_HAS_CGAL
391 IMP_MULTIFIT_HAS_HDF5 = _IMP_multifit.IMP_MULTIFIT_HAS_HDF5
392 IMP_MULTIFIT_HAS_RMF = _IMP_multifit.IMP_MULTIFIT_HAS_RMF
393 IMPMULTIFIT_SHOW_WARNINGS = _IMP_multifit.IMPMULTIFIT_SHOW_WARNINGS
394 _object_types.append("RadiusOfGyrationRestraint")
395 
396 
397 def _object_cast_to_RadiusOfGyrationRestraint(*args):
398  """_object_cast_to_RadiusOfGyrationRestraint(Object o) -> RadiusOfGyrationRestraint"""
399  return _IMP_multifit._object_cast_to_RadiusOfGyrationRestraint(*args)
400 _object_types.append("ComponentHeader")
401 
402 
403 def _object_cast_to_ComponentHeader(*args):
404  """_object_cast_to_ComponentHeader(Object o) -> ComponentHeader"""
405  return _IMP_multifit._object_cast_to_ComponentHeader(*args)
406 _object_types.append("AssemblyHeader")
407 
408 
409 def _object_cast_to_AssemblyHeader(*args):
410  """_object_cast_to_AssemblyHeader(Object o) -> AssemblyHeader"""
411  return _IMP_multifit._object_cast_to_AssemblyHeader(*args)
412 _object_types.append("SettingsData")
413 
414 
415 def _object_cast_to_SettingsData(*args):
416  """_object_cast_to_SettingsData(Object o) -> SettingsData"""
417  return _IMP_multifit._object_cast_to_SettingsData(*args)
418 _object_types.append("WeightedExcludedVolumeRestraint")
419 
420 
421 def _object_cast_to_WeightedExcludedVolumeRestraint(*args):
422  """_object_cast_to_WeightedExcludedVolumeRestraint(Object o) -> WeightedExcludedVolumeRestraint"""
423  return _IMP_multifit._object_cast_to_WeightedExcludedVolumeRestraint(*args)
424 _object_types.append("ComplementarityRestraint")
425 
426 
427 def _object_cast_to_ComplementarityRestraint(*args):
428  """_object_cast_to_ComplementarityRestraint(Object o) -> ComplementarityRestraint"""
429  return _IMP_multifit._object_cast_to_ComplementarityRestraint(*args)
430 ProteinRecordDataList=list
431 _plural_types.append("ProteinRecordDataList")
432 _value_types.append("ProteinRecordData")
433 
434 FittingSolutionRecords=list
435 _plural_types.append("FittingSolutionRecords")
436 _value_types.append("FittingSolutionRecord")
437 
438 AnchorsDataList=list
439 _plural_types.append("AnchorsDataList")
440 _value_types.append("AnchorsData")
441 
442 DominoParamsList=list
443 _plural_types.append("DominoParamsList")
444 _value_types.append("DominoParams")
445 
446 ComplementarityParamsList=list
447 _plural_types.append("ComplementarityParamsList")
448 _value_types.append("ComplementarityParams")
449 
450 XlinkParamsList=list
451 _plural_types.append("XlinkParamsList")
452 _value_types.append("XlinkParams")
453 
454 ConnectivityParamsList=list
455 _plural_types.append("ConnectivityParamsList")
456 _value_types.append("ConnectivityParams")
457 
458 FragmentsParamsList=list
459 _plural_types.append("FragmentsParamsList")
460 _value_types.append("FragmentsParams")
461 
462 RogParamsList=list
463 _plural_types.append("RogParamsList")
464 _value_types.append("RogParams")
465 
466 EVParamsList=list
467 _plural_types.append("EVParamsList")
468 _value_types.append("EVParams")
469 
470 FiltersParamsList=list
471 _plural_types.append("FiltersParamsList")
472 _value_types.append("FiltersParams")
473 
474 AlignmentParamsList=list
475 _plural_types.append("AlignmentParamsList")
476 _value_types.append("AlignmentParams")
477 
478 FittingParamsList=list
479 _plural_types.append("FittingParamsList")
480 _value_types.append("FittingParams")
481 
482 ProteinsAnchorsSamplingSpaces=list
483 _plural_types.append("ProteinsAnchorsSamplingSpaces")
484 _value_types.append("ProteinsAnchorsSamplingSpace")
485 
486 _object_types.append("ProteomicsData")
487 
488 
489 def _object_cast_to_ProteomicsData(*args):
490  """_object_cast_to_ProteomicsData(Object o) -> ProteomicsData"""
491  return _IMP_multifit._object_cast_to_ProteomicsData(*args)
492 _object_types.append("FFTFitting")
493 
494 
495 def _object_cast_to_FFTFitting(*args):
496  """_object_cast_to_FFTFitting(Object o) -> FFTFitting"""
497  return _IMP_multifit._object_cast_to_FFTFitting(*args)
498 _object_types.append("FFTFittingOutput")
499 
500 
501 def _object_cast_to_FFTFittingOutput(*args):
502  """_object_cast_to_FFTFittingOutput(Object o) -> FFTFittingOutput"""
503  return _IMP_multifit._object_cast_to_FFTFittingOutput(*args)
504 _object_types.append("ProbabilisticAnchorGraph")
505 
506 
507 def _object_cast_to_ProbabilisticAnchorGraph(*args):
508  """_object_cast_to_ProbabilisticAnchorGraph(Object o) -> ProbabilisticAnchorGraph"""
509  return _IMP_multifit._object_cast_to_ProbabilisticAnchorGraph(*args)
510 _object_types.append("Ensemble")
511 
512 
513 def _object_cast_to_Ensemble(*args):
514  """_object_cast_to_Ensemble(Object o) -> Ensemble"""
515  return _IMP_multifit._object_cast_to_Ensemble(*args)
516 _object_types.append("ProteomicsEMAlignmentAtomic")
517 
518 
519 def _object_cast_to_ProteomicsEMAlignmentAtomic(*args):
520  """_object_cast_to_ProteomicsEMAlignmentAtomic(Object o) -> ProteomicsEMAlignmentAtomic"""
521  return _IMP_multifit._object_cast_to_ProteomicsEMAlignmentAtomic(*args)
522 
523 def add_surface_index(*args):
524  """
525  add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key=FloatKey("surf_ind"), FloatKey radius_key=IMP::core::XYZR::get_radius_key(),
526  FloatKey weight_key=IMP::atom::Mass::get_mass_key())
527  add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key=FloatKey("surf_ind"), FloatKey radius_key=IMP::core::XYZR::get_radius_key())
528  add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key=FloatKey("surf_ind"))
529  add_surface_index(Hierarchy mhd, IMP::Float apix)
530  """
531  return _IMP_multifit.add_surface_index(*args)
532 
534  """
535  create_weighted_excluded_volume_restraint(RigidBody rb1, RigidBody rb2, FloatKey shell_key=FloatKey("surf_ind")) -> Restraint
536  create_weighted_excluded_volume_restraint(RigidBody rb1, RigidBody rb2) -> Restraint
537  """
538  return _IMP_multifit.create_weighted_excluded_volume_restraint(*args)
539 class FittingSolutionRecord(_object):
540  """Proxy of C++ IMP::multifit::FittingSolutionRecord class"""
541  __swig_setmethods__ = {}
542  __setattr__ = lambda self, name, value: _swig_setattr(self, FittingSolutionRecord, name, value)
543  __swig_getmethods__ = {}
544  __getattr__ = lambda self, name: _swig_getattr(self, FittingSolutionRecord, name)
545  def __init__(self):
546  """__init__(IMP::multifit::FittingSolutionRecord self) -> FittingSolutionRecord"""
547  this = _IMP_multifit.new_FittingSolutionRecord()
548  try: self.this.append(this)
549  except: self.this = this
550  def get_index(self):
551  """get_index(FittingSolutionRecord self) -> unsigned int"""
552  return _IMP_multifit.FittingSolutionRecord_get_index(self)
553 
554  def set_index(self, *args):
555  """set_index(FittingSolutionRecord self, unsigned int new_ind)"""
556  return _IMP_multifit.FittingSolutionRecord_set_index(self, *args)
557 
558  def get_solution_filename(self):
559  """get_solution_filename(FittingSolutionRecord self) -> std::string"""
560  return _IMP_multifit.FittingSolutionRecord_get_solution_filename(self)
561 
562  def set_solution_filename(self, *args):
563  """set_solution_filename(FittingSolutionRecord self, std::string sol_fn)"""
564  return _IMP_multifit.FittingSolutionRecord_set_solution_filename(self, *args)
565 
566  def get_fit_transformation(self):
567  """get_fit_transformation(FittingSolutionRecord self) -> Transformation3D"""
568  return _IMP_multifit.FittingSolutionRecord_get_fit_transformation(self)
569 
570  def set_fit_transformation(self, *args):
571  """set_fit_transformation(FittingSolutionRecord self, Transformation3D t)"""
572  return _IMP_multifit.FittingSolutionRecord_set_fit_transformation(self, *args)
573 
574  def get_match_size(self):
575  """get_match_size(FittingSolutionRecord self) -> unsigned int"""
576  return _IMP_multifit.FittingSolutionRecord_get_match_size(self)
577 
578  def set_match_size(self, *args):
579  """set_match_size(FittingSolutionRecord self, unsigned int match_size)"""
580  return _IMP_multifit.FittingSolutionRecord_set_match_size(self, *args)
581 
582  def get_match_average_distance(self):
583  """get_match_average_distance(FittingSolutionRecord self) -> IMP::Float"""
584  return _IMP_multifit.FittingSolutionRecord_get_match_average_distance(self)
585 
586  def set_match_average_distance(self, *args):
587  """set_match_average_distance(FittingSolutionRecord self, IMP::Float match_avg_dist)"""
588  return _IMP_multifit.FittingSolutionRecord_set_match_average_distance(self, *args)
589 
590  def get_fitting_score(self):
591  """get_fitting_score(FittingSolutionRecord self) -> IMP::Float"""
592  return _IMP_multifit.FittingSolutionRecord_get_fitting_score(self)
593 
594  def set_fitting_score(self, *args):
595  """set_fitting_score(FittingSolutionRecord self, IMP::Float fit_score)"""
596  return _IMP_multifit.FittingSolutionRecord_set_fitting_score(self, *args)
597 
598  def get_rmsd_to_reference(self):
599  """get_rmsd_to_reference(FittingSolutionRecord self) -> IMP::Float"""
600  return _IMP_multifit.FittingSolutionRecord_get_rmsd_to_reference(self)
601 
602  def set_rmsd_to_reference(self, *args):
603  """set_rmsd_to_reference(FittingSolutionRecord self, IMP::Float rmsd_to_ref)"""
604  return _IMP_multifit.FittingSolutionRecord_set_rmsd_to_reference(self, *args)
605 
606  def get_dock_transformation(self):
607  """get_dock_transformation(FittingSolutionRecord self) -> Transformation3D"""
608  return _IMP_multifit.FittingSolutionRecord_get_dock_transformation(self)
609 
610  def set_dock_transformation(self, *args):
611  """set_dock_transformation(FittingSolutionRecord self, Transformation3D t)"""
612  return _IMP_multifit.FittingSolutionRecord_set_dock_transformation(self, *args)
613 
614  def get_envelope_penetration_score(self):
615  """get_envelope_penetration_score(FittingSolutionRecord self) -> IMP::Float"""
616  return _IMP_multifit.FittingSolutionRecord_get_envelope_penetration_score(self)
617 
618  def set_envelope_penetration_score(self, *args):
619  """set_envelope_penetration_score(FittingSolutionRecord self, IMP::Float s)"""
620  return _IMP_multifit.FittingSolutionRecord_set_envelope_penetration_score(self, *args)
621 
622  def show(self, *args):
623  """
624  show(FittingSolutionRecord self, _ostream out=std::cout)
625  show(FittingSolutionRecord self)
626  """
627  return _IMP_multifit.FittingSolutionRecord_show(self, *args)
628 
629  def get_record_header():
630  """get_record_header() -> std::string"""
631  return _IMP_multifit.FittingSolutionRecord_get_record_header()
632 
633  if _newclass:get_record_header = staticmethod(get_record_header)
634  __swig_getmethods__["get_record_header"] = lambda x: get_record_header
635  def __str__(self):
636  """__str__(FittingSolutionRecord self) -> std::string"""
637  return _IMP_multifit.FittingSolutionRecord___str__(self)
638 
639  def __repr__(self):
640  """__repr__(FittingSolutionRecord self) -> std::string"""
641  return _IMP_multifit.FittingSolutionRecord___repr__(self)
642 
643  __swig_destroy__ = _IMP_multifit.delete_FittingSolutionRecord
644  __del__ = lambda self : None;
645 FittingSolutionRecord_swigregister = _IMP_multifit.FittingSolutionRecord_swigregister
646 FittingSolutionRecord_swigregister(FittingSolutionRecord)
647 
648 def FittingSolutionRecord_get_record_header():
649  """FittingSolutionRecord_get_record_header() -> std::string"""
650  return _IMP_multifit.FittingSolutionRecord_get_record_header()
651 
652 
653 def pca_based_rigid_fitting(*args):
654  """
655  pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold, FloatKey wei_key=IMP::atom::Mass::get_mass_key(),
656  PrincipalComponentAnalysis3D dens_pca_input=IMP::algebra::PrincipalComponentAnalysis()) -> FittingSolutions
657  pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold, FloatKey wei_key=IMP::atom::Mass::get_mass_key()) -> FittingSolutions
658  pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold) -> FittingSolutions
659  pca_based_rigid_fitting(IMP::kernel::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold, FloatKey wei_key=IMP::atom::Mass::get_mass_key(),
660  PrincipalComponentAnalysis3D dens_pca_input=IMP::algebra::PrincipalComponentAnalysis()) -> FittingSolutions
661  pca_based_rigid_fitting(IMP::kernel::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold, FloatKey wei_key=IMP::atom::Mass::get_mass_key()) -> FittingSolutions
662  pca_based_rigid_fitting(IMP::kernel::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold) -> FittingSolutions
663  """
664  return _IMP_multifit.pca_based_rigid_fitting(*args)
665 
666 def write_markers(*args):
667  """write_markers(PrincipalComponentAnalysis3D pca, _ostream out)"""
668  return _IMP_multifit.write_markers(*args)
669 class ComponentHeader(IMP.base.Object):
670  """Proxy of C++ IMP::multifit::ComponentHeader class"""
671  __swig_setmethods__ = {}
672  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
673  __setattr__ = lambda self, name, value: _swig_setattr(self, ComponentHeader, name, value)
674  __swig_getmethods__ = {}
675  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
676  __getattr__ = lambda self, name: _swig_getattr(self, ComponentHeader, name)
677  def __init__(self):
678  """__init__(IMP::multifit::ComponentHeader self) -> ComponentHeader"""
679  this = _IMP_multifit.new_ComponentHeader()
680  try: self.this.append(this)
681  except: self.this = this
682  def set_name(self, *args):
683  """set_name(ComponentHeader self, std::string const & name)"""
684  return _IMP_multifit.ComponentHeader_set_name(self, *args)
685 
686  def get_name(self):
687  """get_name(ComponentHeader self) -> std::string"""
688  return _IMP_multifit.ComponentHeader_get_name(self)
689 
690  def get_filename(self):
691  """get_filename(ComponentHeader self) -> std::string"""
692  return _IMP_multifit.ComponentHeader_get_filename(self)
693 
694  def set_filename(self, *args):
695  """set_filename(ComponentHeader self, std::string const & filename)"""
696  return _IMP_multifit.ComponentHeader_set_filename(self, *args)
697 
698  def get_surface_fn(self):
699  """get_surface_fn(ComponentHeader self) -> std::string"""
700  return _IMP_multifit.ComponentHeader_get_surface_fn(self)
701 
702  def set_surface_fn(self, *args):
703  """set_surface_fn(ComponentHeader self, std::string const & fn)"""
704  return _IMP_multifit.ComponentHeader_set_surface_fn(self, *args)
705 
706  def set_txt_ap_fn(self, *args):
707  """set_txt_ap_fn(ComponentHeader self, std::string const & pdb_ap_fn)"""
708  return _IMP_multifit.ComponentHeader_set_txt_ap_fn(self, *args)
709 
710  def get_txt_ap_fn(self):
711  """get_txt_ap_fn(ComponentHeader self) -> std::string"""
712  return _IMP_multifit.ComponentHeader_get_txt_ap_fn(self)
713 
714  def set_txt_fine_ap_fn(self, *args):
715  """set_txt_fine_ap_fn(ComponentHeader self, std::string const & pdb_ap_fn)"""
716  return _IMP_multifit.ComponentHeader_set_txt_fine_ap_fn(self, *args)
717 
718  def get_txt_fine_ap_fn(self):
719  """get_txt_fine_ap_fn(ComponentHeader self) -> std::string"""
720  return _IMP_multifit.ComponentHeader_get_txt_fine_ap_fn(self)
721 
722  def set_num_ap(self, *args):
723  """set_num_ap(ComponentHeader self, int num_ap)"""
724  return _IMP_multifit.ComponentHeader_set_num_ap(self, *args)
725 
726  def get_num_ap(self):
727  """get_num_ap(ComponentHeader self) -> int"""
728  return _IMP_multifit.ComponentHeader_get_num_ap(self)
729 
730  def set_num_fine_ap(self, *args):
731  """set_num_fine_ap(ComponentHeader self, int num_ap)"""
732  return _IMP_multifit.ComponentHeader_set_num_fine_ap(self, *args)
733 
734  def get_num_fine_ap(self):
735  """get_num_fine_ap(ComponentHeader self) -> int"""
736  return _IMP_multifit.ComponentHeader_get_num_fine_ap(self)
737 
738  def set_transformations_fn(self, *args):
739  """set_transformations_fn(ComponentHeader self, std::string transformations_fn)"""
740  return _IMP_multifit.ComponentHeader_set_transformations_fn(self, *args)
741 
742  def get_transformations_fn(self):
743  """get_transformations_fn(ComponentHeader self) -> std::string"""
744  return _IMP_multifit.ComponentHeader_get_transformations_fn(self)
745 
746  def set_reference_fn(self, *args):
747  """set_reference_fn(ComponentHeader self, std::string const & ref_fn)"""
748  return _IMP_multifit.ComponentHeader_set_reference_fn(self, *args)
749 
750  def get_reference_fn(self):
751  """get_reference_fn(ComponentHeader self) -> std::string"""
752  return _IMP_multifit.ComponentHeader_get_reference_fn(self)
753 
754  def get_version_info(self):
755  """get_version_info(ComponentHeader self) -> VersionInfo"""
756  return _IMP_multifit.ComponentHeader_get_version_info(self)
757 
758  def __str__(self):
759  """__str__(ComponentHeader self) -> std::string"""
760  return _IMP_multifit.ComponentHeader___str__(self)
761 
762  def __repr__(self):
763  """__repr__(ComponentHeader self) -> std::string"""
764  return _IMP_multifit.ComponentHeader___repr__(self)
765 
766  def get_from(o):
767  return _object_cast_to_ComponentHeader(o)
768  get_from = staticmethod(get_from)
769 
770 ComponentHeader_swigregister = _IMP_multifit.ComponentHeader_swigregister
771 ComponentHeader_swigregister(ComponentHeader)
772 
773 class AssemblyHeader(IMP.base.Object):
774  """Proxy of C++ IMP::multifit::AssemblyHeader class"""
775  __swig_setmethods__ = {}
776  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
777  __setattr__ = lambda self, name, value: _swig_setattr(self, AssemblyHeader, name, value)
778  __swig_getmethods__ = {}
779  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
780  __getattr__ = lambda self, name: _swig_getattr(self, AssemblyHeader, name)
781  def __init__(self):
782  """__init__(IMP::multifit::AssemblyHeader self) -> AssemblyHeader"""
783  this = _IMP_multifit.new_AssemblyHeader()
784  try: self.this.append(this)
785  except: self.this = this
786  def set_dens_fn(self, *args):
787  """set_dens_fn(AssemblyHeader self, std::string const & dens_fn)"""
788  return _IMP_multifit.AssemblyHeader_set_dens_fn(self, *args)
789 
790  def get_dens_fn(self):
791  """get_dens_fn(AssemblyHeader self) -> std::string"""
792  return _IMP_multifit.AssemblyHeader_get_dens_fn(self)
793 
794  def set_resolution(self, *args):
795  """set_resolution(AssemblyHeader self, float res)"""
796  return _IMP_multifit.AssemblyHeader_set_resolution(self, *args)
797 
798  def get_resolution(self):
799  """get_resolution(AssemblyHeader self) -> float"""
800  return _IMP_multifit.AssemblyHeader_get_resolution(self)
801 
802  def get_spacing(self):
803  """get_spacing(AssemblyHeader self) -> float"""
804  return _IMP_multifit.AssemblyHeader_get_spacing(self)
805 
806  def set_spacing(self, *args):
807  """set_spacing(AssemblyHeader self, float spacing)"""
808  return _IMP_multifit.AssemblyHeader_set_spacing(self, *args)
809 
810  def set_threshold(self, *args):
811  """set_threshold(AssemblyHeader self, float t)"""
812  return _IMP_multifit.AssemblyHeader_set_threshold(self, *args)
813 
814  def get_threshold(self):
815  """get_threshold(AssemblyHeader self) -> float"""
816  return _IMP_multifit.AssemblyHeader_get_threshold(self)
817 
818  def get_origin(self):
819  """get_origin(AssemblyHeader self) -> Vector3D"""
820  return _IMP_multifit.AssemblyHeader_get_origin(self)
821 
822  def set_origin(self, *args):
823  """set_origin(AssemblyHeader self, Vector3D origin)"""
824  return _IMP_multifit.AssemblyHeader_set_origin(self, *args)
825 
826  def get_coarse_ap_fn(self):
827  """get_coarse_ap_fn(AssemblyHeader self) -> std::string"""
828  return _IMP_multifit.AssemblyHeader_get_coarse_ap_fn(self)
829 
830  def set_coarse_ap_fn(self, *args):
831  """set_coarse_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
832  return _IMP_multifit.AssemblyHeader_set_coarse_ap_fn(self, *args)
833 
834  def get_coarse_over_sampled_ap_fn(self):
835  """get_coarse_over_sampled_ap_fn(AssemblyHeader self) -> std::string"""
836  return _IMP_multifit.AssemblyHeader_get_coarse_over_sampled_ap_fn(self)
837 
838  def set_coarse_over_sampled_ap_fn(self, *args):
839  """set_coarse_over_sampled_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
840  return _IMP_multifit.AssemblyHeader_set_coarse_over_sampled_ap_fn(self, *args)
841 
842  def get_fine_ap_fn(self):
843  """get_fine_ap_fn(AssemblyHeader self) -> std::string"""
844  return _IMP_multifit.AssemblyHeader_get_fine_ap_fn(self)
845 
846  def set_fine_ap_fn(self, *args):
847  """set_fine_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
848  return _IMP_multifit.AssemblyHeader_set_fine_ap_fn(self, *args)
849 
850  def get_fine_over_sampled_ap_fn(self):
851  """get_fine_over_sampled_ap_fn(AssemblyHeader self) -> std::string"""
852  return _IMP_multifit.AssemblyHeader_get_fine_over_sampled_ap_fn(self)
853 
854  def set_fine_over_sampled_ap_fn(self, *args):
855  """set_fine_over_sampled_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
856  return _IMP_multifit.AssemblyHeader_set_fine_over_sampled_ap_fn(self, *args)
857 
858  def get_version_info(self):
859  """get_version_info(AssemblyHeader self) -> VersionInfo"""
860  return _IMP_multifit.AssemblyHeader_get_version_info(self)
861 
862  def __str__(self):
863  """__str__(AssemblyHeader self) -> std::string"""
864  return _IMP_multifit.AssemblyHeader___str__(self)
865 
866  def __repr__(self):
867  """__repr__(AssemblyHeader self) -> std::string"""
868  return _IMP_multifit.AssemblyHeader___repr__(self)
869 
870  def get_from(o):
871  return _object_cast_to_AssemblyHeader(o)
872  get_from = staticmethod(get_from)
873 
874 AssemblyHeader_swigregister = _IMP_multifit.AssemblyHeader_swigregister
875 AssemblyHeader_swigregister(AssemblyHeader)
876 
877 class SettingsData(IMP.base.Object):
878  """Proxy of C++ IMP::multifit::SettingsData class"""
879  __swig_setmethods__ = {}
880  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
881  __setattr__ = lambda self, name, value: _swig_setattr(self, SettingsData, name, value)
882  __swig_getmethods__ = {}
883  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
884  __getattr__ = lambda self, name: _swig_getattr(self, SettingsData, name)
885  def __init__(self):
886  """__init__(IMP::multifit::SettingsData self) -> SettingsData"""
887  this = _IMP_multifit.new_SettingsData()
888  try: self.this.append(this)
889  except: self.this = this
890  def show_component_header_line(*args):
891  """
892  show_component_header_line(_ostream out=std::cout)
893  show_component_header_line()
894  """
895  return _IMP_multifit.SettingsData_show_component_header_line(*args)
896 
897  if _newclass:show_component_header_line = staticmethod(show_component_header_line)
898  __swig_getmethods__["show_component_header_line"] = lambda x: show_component_header_line
899  def get_component_header_line():
900  """get_component_header_line() -> std::string"""
901  return _IMP_multifit.SettingsData_get_component_header_line()
902 
903  if _newclass:get_component_header_line = staticmethod(get_component_header_line)
904  __swig_getmethods__["get_component_header_line"] = lambda x: get_component_header_line
905  def show_density_header_line(*args):
906  """
907  show_density_header_line(_ostream out=std::cout)
908  show_density_header_line()
909  """
910  return _IMP_multifit.SettingsData_show_density_header_line(*args)
911 
912  if _newclass:show_density_header_line = staticmethod(show_density_header_line)
913  __swig_getmethods__["show_density_header_line"] = lambda x: show_density_header_line
914  def get_density_header_line():
915  """get_density_header_line() -> std::string"""
916  return _IMP_multifit.SettingsData_get_density_header_line()
917 
918  if _newclass:get_density_header_line = staticmethod(get_density_header_line)
919  __swig_getmethods__["get_density_header_line"] = lambda x: get_density_header_line
920  def set_assembly_filename(self, *args):
921  """set_assembly_filename(SettingsData self, std::string const & fn)"""
922  return _IMP_multifit.SettingsData_set_assembly_filename(self, *args)
923 
924  def get_assembly_filename(self):
925  """get_assembly_filename(SettingsData self) -> char const *"""
926  return _IMP_multifit.SettingsData_get_assembly_filename(self)
927 
928  def set_assembly_header(self, *args):
929  """set_assembly_header(SettingsData self, AssemblyHeader h)"""
930  return _IMP_multifit.SettingsData_set_assembly_header(self, *args)
931 
932  def get_assembly_header(self):
933  """get_assembly_header(SettingsData self) -> AssemblyHeader"""
934  return _IMP_multifit.SettingsData_get_assembly_header(self)
935 
936  def set_data_path(self, *args):
937  """set_data_path(SettingsData self, std::string const & fn)"""
938  return _IMP_multifit.SettingsData_set_data_path(self, *args)
939 
940  def get_data_path(self):
941  """get_data_path(SettingsData self) -> std::string"""
942  return _IMP_multifit.SettingsData_get_data_path(self)
943 
944  def get_version_info(self):
945  """get_version_info(SettingsData self) -> VersionInfo"""
946  return _IMP_multifit.SettingsData_get_version_info(self)
947 
948  def remove_component_header(self, *args):
949  """remove_component_header(SettingsData self, ComponentHeader d)"""
950  return _IMP_multifit.SettingsData_remove_component_header(self, *args)
951 
952  def remove_component_headers(self, *args):
953  """remove_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & d)"""
954  return _IMP_multifit.SettingsData_remove_component_headers(self, *args)
955 
956  def set_component_headers(self, *args):
957  """set_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & ps)"""
958  return _IMP_multifit.SettingsData_set_component_headers(self, *args)
959 
960  def set_component_headers_order(self, *args):
961  """set_component_headers_order(SettingsData self, IMP::multifit::ComponentHeaders const & objs)"""
962  return _IMP_multifit.SettingsData_set_component_headers_order(self, *args)
963 
964  def add_component_header(self, *args):
965  """add_component_header(SettingsData self, ComponentHeader obj) -> unsigned int"""
966  return _IMP_multifit.SettingsData_add_component_header(self, *args)
967 
968  def add_component_headers(self, *args):
969  """add_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & objs)"""
970  return _IMP_multifit.SettingsData_add_component_headers(self, *args)
971 
972  def clear_component_headers(self):
973  """clear_component_headers(SettingsData self)"""
974  return _IMP_multifit.SettingsData_clear_component_headers(self)
975 
976  def get_number_of_component_headers(self):
977  """get_number_of_component_headers(SettingsData self) -> unsigned int"""
978  return _IMP_multifit.SettingsData_get_number_of_component_headers(self)
979 
980  def get_has_component_headers(self):
981  """get_has_component_headers(SettingsData self) -> bool"""
982  return _IMP_multifit.SettingsData_get_has_component_headers(self)
983 
984  def get_component_header(self, *args):
985  """get_component_header(SettingsData self, unsigned int i) -> ComponentHeader"""
986  return _IMP_multifit.SettingsData_get_component_header(self, *args)
987 
988  def get_component_headers(self):
989  """get_component_headers(SettingsData self) -> IMP::multifit::ComponentHeaders"""
990  return _IMP_multifit.SettingsData_get_component_headers(self)
991 
992  def reserve_component_headers(self, *args):
993  """reserve_component_headers(SettingsData self, unsigned int sz)"""
994  return _IMP_multifit.SettingsData_reserve_component_headers(self, *args)
995 
996  def __str__(self):
997  """__str__(SettingsData self) -> std::string"""
998  return _IMP_multifit.SettingsData___str__(self)
999 
1000  def __repr__(self):
1001  """__repr__(SettingsData self) -> std::string"""
1002  return _IMP_multifit.SettingsData___repr__(self)
1003 
1004  def get_from(o):
1005  return _object_cast_to_SettingsData(o)
1006  get_from = staticmethod(get_from)
1007 
1008 SettingsData_swigregister = _IMP_multifit.SettingsData_swigregister
1009 SettingsData_swigregister(SettingsData)
1010 
1011 def SettingsData_show_component_header_line(*args):
1012  """
1013  show_component_header_line(_ostream out=std::cout)
1014  SettingsData_show_component_header_line()
1015  """
1016  return _IMP_multifit.SettingsData_show_component_header_line(*args)
1017 
1018 def SettingsData_get_component_header_line():
1019  """SettingsData_get_component_header_line() -> std::string"""
1020  return _IMP_multifit.SettingsData_get_component_header_line()
1021 
1022 def SettingsData_show_density_header_line(*args):
1023  """
1024  show_density_header_line(_ostream out=std::cout)
1025  SettingsData_show_density_header_line()
1026  """
1027  return _IMP_multifit.SettingsData_show_density_header_line(*args)
1028 
1029 def SettingsData_get_density_header_line():
1030  """SettingsData_get_density_header_line() -> std::string"""
1031  return _IMP_multifit.SettingsData_get_density_header_line()
1032 
1033 
1034 def read_settings(*args):
1035  """read_settings(char const * filename) -> SettingsData"""
1036  return _IMP_multifit.read_settings(*args)
1037 
1038 def write_settings(*args):
1039  """write_settings(char const * filename, SettingsData sd)"""
1040  return _IMP_multifit.write_settings(*args)
1041 class WeightedExcludedVolumeRestraint(IMP.kernel.Restraint):
1042  """Proxy of C++ IMP::multifit::WeightedExcludedVolumeRestraint class"""
1043  __swig_setmethods__ = {}
1044  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1045  __setattr__ = lambda self, name, value: _swig_setattr(self, WeightedExcludedVolumeRestraint, name, value)
1046  __swig_getmethods__ = {}
1047  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1048  __getattr__ = lambda self, name: _swig_getattr(self, WeightedExcludedVolumeRestraint, name)
1049  def __init__(self, *args):
1050  """
1051  __init__(IMP::multifit::WeightedExcludedVolumeRestraint self, IMP::core::RigidBodies rbs, Refiner refiner, FloatKey weight_key=IMP::atom::Mass::get_mass_key()) -> WeightedExcludedVolumeRestraint
1052  __init__(IMP::multifit::WeightedExcludedVolumeRestraint self, IMP::core::RigidBodies rbs, Refiner refiner) -> WeightedExcludedVolumeRestraint
1053  """
1054  this = _IMP_multifit.new_WeightedExcludedVolumeRestraint(*args)
1055  try: self.this.append(this)
1056  except: self.this = this
1057  def do_get_inputs(self):
1058  """do_get_inputs(WeightedExcludedVolumeRestraint self) -> IMP::kernel::ModelObjectsTemp"""
1059  return _IMP_multifit.WeightedExcludedVolumeRestraint_do_get_inputs(self)
1060 
1061  def get_version_info(self):
1062  """get_version_info(WeightedExcludedVolumeRestraint self) -> VersionInfo"""
1063  return _IMP_multifit.WeightedExcludedVolumeRestraint_get_version_info(self)
1064 
1065  def __str__(self):
1066  """__str__(WeightedExcludedVolumeRestraint self) -> std::string"""
1067  return _IMP_multifit.WeightedExcludedVolumeRestraint___str__(self)
1068 
1069  def __repr__(self):
1070  """__repr__(WeightedExcludedVolumeRestraint self) -> std::string"""
1071  return _IMP_multifit.WeightedExcludedVolumeRestraint___repr__(self)
1072 
1073  def get_from(o):
1074  return _object_cast_to_WeightedExcludedVolumeRestraint(o)
1075  get_from = staticmethod(get_from)
1076 
1077 WeightedExcludedVolumeRestraint_swigregister = _IMP_multifit.WeightedExcludedVolumeRestraint_swigregister
1078 WeightedExcludedVolumeRestraint_swigregister(WeightedExcludedVolumeRestraint)
1079 
1080 class FFTFittingOutput(IMP.base.Object):
1081  """Proxy of C++ IMP::multifit::FFTFittingOutput class"""
1082  __swig_setmethods__ = {}
1083  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1084  __setattr__ = lambda self, name, value: _swig_setattr(self, FFTFittingOutput, name, value)
1085  __swig_getmethods__ = {}
1086  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1087  __getattr__ = lambda self, name: _swig_getattr(self, FFTFittingOutput, name)
1088  def __init__(self):
1089  """__init__(IMP::multifit::FFTFittingOutput self) -> FFTFittingOutput"""
1090  this = _IMP_multifit.new_FFTFittingOutput()
1091  try: self.this.append(this)
1092  except: self.this = this
1093  def get_version_info(self):
1094  """get_version_info(FFTFittingOutput self) -> VersionInfo"""
1095  return _IMP_multifit.FFTFittingOutput_get_version_info(self)
1096 
1097  __swig_setmethods__["best_fits_"] = _IMP_multifit.FFTFittingOutput_best_fits__set
1098  __swig_getmethods__["best_fits_"] = _IMP_multifit.FFTFittingOutput_best_fits__get
1099  if _newclass:best_fits_ = _swig_property(_IMP_multifit.FFTFittingOutput_best_fits__get, _IMP_multifit.FFTFittingOutput_best_fits__set)
1100  __swig_setmethods__["best_trans_per_rot_"] = _IMP_multifit.FFTFittingOutput_best_trans_per_rot__set
1101  __swig_getmethods__["best_trans_per_rot_"] = _IMP_multifit.FFTFittingOutput_best_trans_per_rot__get
1102  if _newclass:best_trans_per_rot_ = _swig_property(_IMP_multifit.FFTFittingOutput_best_trans_per_rot__get, _IMP_multifit.FFTFittingOutput_best_trans_per_rot__set)
1103  def __str__(self):
1104  """__str__(FFTFittingOutput self) -> std::string"""
1105  return _IMP_multifit.FFTFittingOutput___str__(self)
1106 
1107  def __repr__(self):
1108  """__repr__(FFTFittingOutput self) -> std::string"""
1109  return _IMP_multifit.FFTFittingOutput___repr__(self)
1110 
1111  def get_from(o):
1112  return _object_cast_to_FFTFittingOutput(o)
1113  get_from = staticmethod(get_from)
1114 
1115 FFTFittingOutput_swigregister = _IMP_multifit.FFTFittingOutput_swigregister
1116 FFTFittingOutput_swigregister(FFTFittingOutput)
1117 
1118 class FFTFitting(IMP.base.Object):
1119  """Proxy of C++ IMP::multifit::FFTFitting class"""
1120  __swig_setmethods__ = {}
1121  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1122  __setattr__ = lambda self, name, value: _swig_setattr(self, FFTFitting, name, value)
1123  __swig_getmethods__ = {}
1124  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1125  __getattr__ = lambda self, name: _swig_getattr(self, FFTFitting, name)
1126  def get_version_info(self):
1127  """get_version_info(FFTFitting self) -> VersionInfo"""
1128  return _IMP_multifit.FFTFitting_get_version_info(self)
1129 
1130  def __init__(self):
1131  """__init__(IMP::multifit::FFTFitting self) -> FFTFitting"""
1132  this = _IMP_multifit.new_FFTFitting()
1133  try: self.this.append(this)
1134  except: self.this = this
1135  def do_global_fitting(self, *args):
1136  """
1137  do_global_fitting(FFTFitting self, DensityMap dmap, double density_threshold, Hierarchy mol2fit, double angle_sampling_interval_rad,
1138  int num_fits_to_report, double max_clustering_translation,
1139  double max_clustering_angle, bool cluster_fits=True, int num_angle_per_voxel=1,
1140  std::string const & angles_filename="") -> FFTFittingOutput
1141  do_global_fitting(FFTFitting self, DensityMap dmap, double density_threshold, Hierarchy mol2fit, double angle_sampling_interval_rad,
1142  int num_fits_to_report, double max_clustering_translation,
1143  double max_clustering_angle, bool cluster_fits=True, int num_angle_per_voxel=1) -> FFTFittingOutput
1144  do_global_fitting(FFTFitting self, DensityMap dmap, double density_threshold, Hierarchy mol2fit, double angle_sampling_interval_rad,
1145  int num_fits_to_report, double max_clustering_translation,
1146  double max_clustering_angle, bool cluster_fits=True) -> FFTFittingOutput
1147  do_global_fitting(FFTFitting self, DensityMap dmap, double density_threshold, Hierarchy mol2fit, double angle_sampling_interval_rad,
1148  int num_fits_to_report, double max_clustering_translation,
1149  double max_clustering_angle) -> FFTFittingOutput
1150  """
1151  return _IMP_multifit.FFTFitting_do_global_fitting(self, *args)
1152 
1153  def do_local_fitting(self, *args):
1154  """
1155  do_local_fitting(FFTFitting self, DensityMap dmap, double density_threshold, Hierarchy mol2fit, double angle_sampling_interval_rad,
1156  double max_angle_sampling_rad, double max_translation, int num_fits_to_report,
1157  bool cluster_fits, int num_angle_per_voxel, double max_clustering_translation,
1158  double max_clustering_rotation, std::string const & angles_filename="") -> FFTFittingOutput
1159  do_local_fitting(FFTFitting self, DensityMap dmap, double density_threshold, Hierarchy mol2fit, double angle_sampling_interval_rad,
1160  double max_angle_sampling_rad, double max_translation, int num_fits_to_report,
1161  bool cluster_fits, int num_angle_per_voxel, double max_clustering_translation,
1162  double max_clustering_rotation) -> FFTFittingOutput
1163  """
1164  return _IMP_multifit.FFTFitting_do_local_fitting(self, *args)
1165 
1166  def __str__(self):
1167  """__str__(FFTFitting self) -> std::string"""
1168  return _IMP_multifit.FFTFitting___str__(self)
1169 
1170  def __repr__(self):
1171  """__repr__(FFTFitting self) -> std::string"""
1172  return _IMP_multifit.FFTFitting___repr__(self)
1173 
1174  def get_from(o):
1175  return _object_cast_to_FFTFitting(o)
1176  get_from = staticmethod(get_from)
1177 
1178 FFTFitting_swigregister = _IMP_multifit.FFTFitting_swigregister
1179 FFTFitting_swigregister(FFTFitting)
1180 
1181 
1182 def fft_based_rigid_fitting(*args):
1183  """fft_based_rigid_fitting(Hierarchy mol2fit, DensityMap dmap, double density_threshold, double angle_sampling_interval_rad) -> IMP::multifit::FittingSolutionRecords"""
1184  return _IMP_multifit.fft_based_rigid_fitting(*args)
1185 
1186 def remove_background(*args):
1187  """remove_background(DensityMap dmap, float threshold, float edge_threshold) -> DensityMap"""
1188  return _IMP_multifit.remove_background(*args)
1189 
1190 def get_connected_components(*args):
1191  """get_connected_components(DensityMap dmap, float threshold, float edge_threshold) -> IMP::IntsList"""
1192  return _IMP_multifit.get_connected_components(*args)
1193 
1194 def get_segmentation(*args):
1195  """
1196  get_segmentation(DensityMap dmap, double apix, double density_threshold, int num_means, std::string const pdb_filename,
1197  std::string const cmm_filename, std::string const seg_filename,
1198  std::string const txt_filename)
1199  """
1200  return _IMP_multifit.get_segmentation(*args)
1201 class ComplementarityRestraint(IMP.kernel.Restraint):
1202  """Proxy of C++ IMP::multifit::ComplementarityRestraint class"""
1203  __swig_setmethods__ = {}
1204  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1205  __setattr__ = lambda self, name, value: _swig_setattr(self, ComplementarityRestraint, name, value)
1206  __swig_getmethods__ = {}
1207  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1208  __getattr__ = lambda self, name: _swig_getattr(self, ComplementarityRestraint, name)
1209  def __init__(self, *args):
1210  """
1211  __init__(IMP::multifit::ComplementarityRestraint self, IMP::kernel::ParticlesTemp const & a, IMP::kernel::ParticlesTemp const & b, std::string name="ComplementarityRestraint %1%") -> ComplementarityRestraint
1212  __init__(IMP::multifit::ComplementarityRestraint self, IMP::kernel::ParticlesTemp const & a, IMP::kernel::ParticlesTemp const & b) -> ComplementarityRestraint
1213  """
1214  this = _IMP_multifit.new_ComplementarityRestraint(*args)
1215  try: self.this.append(this)
1216  except: self.this = this
1217  def set_maximum_penetration_score(self, *args):
1218  """set_maximum_penetration_score(ComplementarityRestraint self, double s)"""
1219  return _IMP_multifit.ComplementarityRestraint_set_maximum_penetration_score(self, *args)
1220 
1221  def set_maximum_penetration(self, *args):
1222  """set_maximum_penetration(ComplementarityRestraint self, double d)"""
1223  return _IMP_multifit.ComplementarityRestraint_set_maximum_penetration(self, *args)
1224 
1225  def set_maximum_separation(self, *args):
1226  """set_maximum_separation(ComplementarityRestraint self, double s)"""
1227  return _IMP_multifit.ComplementarityRestraint_set_maximum_separation(self, *args)
1228 
1229  def set_complementarity_thickness(self, *args):
1230  """set_complementarity_thickness(ComplementarityRestraint self, double th)"""
1231  return _IMP_multifit.ComplementarityRestraint_set_complementarity_thickness(self, *args)
1232 
1233  def set_complementarity_value(self, *args):
1234  """set_complementarity_value(ComplementarityRestraint self, double th)"""
1235  return _IMP_multifit.ComplementarityRestraint_set_complementarity_value(self, *args)
1236 
1237  def set_interior_layer_thickness(self, *args):
1238  """set_interior_layer_thickness(ComplementarityRestraint self, double th)"""
1239  return _IMP_multifit.ComplementarityRestraint_set_interior_layer_thickness(self, *args)
1240 
1241  def set_penetration_coefficient(self, *args):
1242  """set_penetration_coefficient(ComplementarityRestraint self, double pc)"""
1243  return _IMP_multifit.ComplementarityRestraint_set_penetration_coefficient(self, *args)
1244 
1245  def set_complementarity_coefficient(self, *args):
1246  """set_complementarity_coefficient(ComplementarityRestraint self, double cc)"""
1247  return _IMP_multifit.ComplementarityRestraint_set_complementarity_coefficient(self, *args)
1248 
1249  def set_boundary_coefficient(self, *args):
1250  """set_boundary_coefficient(ComplementarityRestraint self, double bc)"""
1251  return _IMP_multifit.ComplementarityRestraint_set_boundary_coefficient(self, *args)
1252 
1253  def get_voxel_size(self):
1254  """get_voxel_size(ComplementarityRestraint self) -> float"""
1255  return _IMP_multifit.ComplementarityRestraint_get_voxel_size(self)
1256 
1257  def do_get_inputs(self):
1258  """do_get_inputs(ComplementarityRestraint self) -> IMP::kernel::ModelObjectsTemp"""
1259  return _IMP_multifit.ComplementarityRestraint_do_get_inputs(self)
1260 
1261  def get_version_info(self):
1262  """get_version_info(ComplementarityRestraint self) -> VersionInfo"""
1263  return _IMP_multifit.ComplementarityRestraint_get_version_info(self)
1264 
1265  def __str__(self):
1266  """__str__(ComplementarityRestraint self) -> std::string"""
1267  return _IMP_multifit.ComplementarityRestraint___str__(self)
1268 
1269  def __repr__(self):
1270  """__repr__(ComplementarityRestraint self) -> std::string"""
1271  return _IMP_multifit.ComplementarityRestraint___repr__(self)
1272 
1273  def get_from(o):
1274  return _object_cast_to_ComplementarityRestraint(o)
1275  get_from = staticmethod(get_from)
1276 
1277 ComplementarityRestraint_swigregister = _IMP_multifit.ComplementarityRestraint_swigregister
1278 ComplementarityRestraint_swigregister(ComplementarityRestraint)
1279 
1280 
1281 def read_fitting_solutions(*args):
1282  """read_fitting_solutions(char const * fitting_fn) -> IMP::multifit::FittingSolutionRecords"""
1283  return _IMP_multifit.read_fitting_solutions(*args)
1284 
1285 def write_fitting_solutions(*args):
1286  """
1287  write_fitting_solutions(char const * fitting_fn, IMP::multifit::FittingSolutionRecords const & fit_sols,
1288  int num_sols=-1)
1289  write_fitting_solutions(char const * fitting_fn, IMP::multifit::FittingSolutionRecords const & fit_sols)
1290  """
1291  return _IMP_multifit.write_fitting_solutions(*args)
1292 
1293 def convert_em_to_multifit_format(*args):
1294  """convert_em_to_multifit_format(FittingSolutions em_fits) -> IMP::multifit::FittingSolutionRecords"""
1295  return _IMP_multifit.convert_em_to_multifit_format(*args)
1296 
1297 def convert_multifit_to_em_format(*args):
1298  """convert_multifit_to_em_format(IMP::multifit::FittingSolutionRecords const & multifit_fits) -> FittingSolutions"""
1299  return _IMP_multifit.convert_multifit_to_em_format(*args)
1300 
1301 def convert_transformations_to_multifit_format(*args):
1302  """convert_transformations_to_multifit_format(IMP::algebra::Transformation3Ds const & trans) -> IMP::multifit::FittingSolutionRecords"""
1303  return _IMP_multifit.convert_transformations_to_multifit_format(*args)
1304 
1305 def convert_multifit_format_to_transformations(*args):
1306  """convert_multifit_format_to_transformations(IMP::multifit::FittingSolutionRecords const & recs) -> IMP::algebra::Transformation3Ds"""
1307  return _IMP_multifit.convert_multifit_format_to_transformations(*args)
1308 
1309 def get_close_to_point(*args):
1310  """
1311  get_close_to_point(IMP::multifit::FittingSolutionRecords const & fit_sols, Hierarchy mh, Particle ap,
1312  IMP::Float dist) -> IMP::multifit::FittingSolutionRecords
1313  """
1314  return _IMP_multifit.get_close_to_point(*args)
1315 class ProbabilisticAnchorGraph(IMP.base.Object):
1316  """Proxy of C++ IMP::multifit::ProbabilisticAnchorGraph class"""
1317  __swig_setmethods__ = {}
1318  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1319  __setattr__ = lambda self, name, value: _swig_setattr(self, ProbabilisticAnchorGraph, name, value)
1320  __swig_getmethods__ = {}
1321  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1322  __getattr__ = lambda self, name: _swig_getattr(self, ProbabilisticAnchorGraph, name)
1323  def __init__(self, *args):
1324  """__init__(IMP::multifit::ProbabilisticAnchorGraph self, IMP::algebra::Vector3Ds anchor_positions) -> ProbabilisticAnchorGraph"""
1325  this = _IMP_multifit.new_ProbabilisticAnchorGraph(*args)
1326  try: self.this.append(this)
1327  except: self.this = this
1328  def add_edge(self, *args):
1329  """add_edge(ProbabilisticAnchorGraph self, int i, int j)"""
1330  return _IMP_multifit.ProbabilisticAnchorGraph_add_edge(self, *args)
1331 
1332  def set_particle_probabilities_on_anchors(self, *args):
1333  """set_particle_probabilities_on_anchors(ProbabilisticAnchorGraph self, Particle p, IMP::multifit::FittingSolutionRecords sols)"""
1334  return _IMP_multifit.ProbabilisticAnchorGraph_set_particle_probabilities_on_anchors(self, *args)
1335 
1336  def show(self, *args):
1337  """
1338  show(ProbabilisticAnchorGraph self, _ostream out=std::cout)
1339  show(ProbabilisticAnchorGraph self)
1340  """
1341  return _IMP_multifit.ProbabilisticAnchorGraph_show(self, *args)
1342 
1343  def get_number_of_anchors(self):
1344  """get_number_of_anchors(ProbabilisticAnchorGraph self) -> unsigned int"""
1345  return _IMP_multifit.ProbabilisticAnchorGraph_get_number_of_anchors(self)
1346 
1347  def get_number_of_edges(self):
1348  """get_number_of_edges(ProbabilisticAnchorGraph self) -> unsigned int"""
1349  return _IMP_multifit.ProbabilisticAnchorGraph_get_number_of_edges(self)
1350 
1351  def get_edge_list(self):
1352  """get_edge_list(ProbabilisticAnchorGraph self) -> IMP::IntRanges"""
1353  return _IMP_multifit.ProbabilisticAnchorGraph_get_edge_list(self)
1354 
1355  def get_anchors(self):
1356  """get_anchors(ProbabilisticAnchorGraph self) -> IMP::algebra::Vector3Ds"""
1357  return _IMP_multifit.ProbabilisticAnchorGraph_get_anchors(self)
1358 
1359  def get_particle_anchors(self, *args):
1360  """
1361  get_particle_anchors(ProbabilisticAnchorGraph self, Particle p, float min_prob=0) -> IMP::algebra::Vector3Ds
1362  get_particle_anchors(ProbabilisticAnchorGraph self, Particle p) -> IMP::algebra::Vector3Ds
1363  """
1364  return _IMP_multifit.ProbabilisticAnchorGraph_get_particle_anchors(self, *args)
1365 
1366  def get_are_probabilities_for_particle_set(self, *args):
1367  """get_are_probabilities_for_particle_set(ProbabilisticAnchorGraph self, Particle p) -> bool"""
1368  return _IMP_multifit.ProbabilisticAnchorGraph_get_are_probabilities_for_particle_set(self, *args)
1369 
1370  def get_particle_probabilities(self, *args):
1371  """get_particle_probabilities(ProbabilisticAnchorGraph self, Particle p) -> IMP::Floats"""
1372  return _IMP_multifit.ProbabilisticAnchorGraph_get_particle_probabilities(self, *args)
1373 
1374  def get_version_info(self):
1375  """get_version_info(ProbabilisticAnchorGraph self) -> VersionInfo"""
1376  return _IMP_multifit.ProbabilisticAnchorGraph_get_version_info(self)
1377 
1378  def __str__(self):
1379  """__str__(ProbabilisticAnchorGraph self) -> std::string"""
1380  return _IMP_multifit.ProbabilisticAnchorGraph___str__(self)
1381 
1382  def __repr__(self):
1383  """__repr__(ProbabilisticAnchorGraph self) -> std::string"""
1384  return _IMP_multifit.ProbabilisticAnchorGraph___repr__(self)
1385 
1386  def get_from(o):
1387  return _object_cast_to_ProbabilisticAnchorGraph(o)
1388  get_from = staticmethod(get_from)
1389 
1390 ProbabilisticAnchorGraph_swigregister = _IMP_multifit.ProbabilisticAnchorGraph_swigregister
1391 ProbabilisticAnchorGraph_swigregister(ProbabilisticAnchorGraph)
1392 
1393 class ProteinRecordData(_object):
1394  """Proxy of C++ IMP::multifit::ProteinRecordData class"""
1395  __swig_setmethods__ = {}
1396  __setattr__ = lambda self, name, value: _swig_setattr(self, ProteinRecordData, name, value)
1397  __swig_getmethods__ = {}
1398  __getattr__ = lambda self, name: _swig_getattr(self, ProteinRecordData, name)
1399  def reset_all(self):
1400  """reset_all(ProteinRecordData self)"""
1401  return _IMP_multifit.ProteinRecordData_reset_all(self)
1402 
1403  def __init__(self, *args):
1404  """
1405  __init__(IMP::multifit::ProteinRecordData self) -> ProteinRecordData
1406  __init__(IMP::multifit::ProteinRecordData self, std::string const & name) -> ProteinRecordData
1407  __init__(IMP::multifit::ProteinRecordData self, std::string const & name, std::string const fn) -> ProteinRecordData
1408  __init__(IMP::multifit::ProteinRecordData self, std::string const & name, int start_res, int end_res, std::string const fn) -> ProteinRecordData
1409  __init__(IMP::multifit::ProteinRecordData self, std::string const & name, int start_res, int end_res, std::string const & fn, std::string const & surface_fn,
1410  std::string const & ref_fn) -> ProteinRecordData
1411  """
1412  this = _IMP_multifit.new_ProteinRecordData(*args)
1413  try: self.this.append(this)
1414  except: self.this = this
1415  def show(self, *args):
1416  """
1417  show(ProteinRecordData self, _ostream out=std::cout)
1418  show(ProteinRecordData self)
1419  """
1420  return _IMP_multifit.ProteinRecordData_show(self, *args)
1421 
1422  __swig_setmethods__["name_"] = _IMP_multifit.ProteinRecordData_name__set
1423  __swig_getmethods__["name_"] = _IMP_multifit.ProteinRecordData_name__get
1424  if _newclass:name_ = _swig_property(_IMP_multifit.ProteinRecordData_name__get, _IMP_multifit.ProteinRecordData_name__set)
1425  __swig_setmethods__["start_res_"] = _IMP_multifit.ProteinRecordData_start_res__set
1426  __swig_getmethods__["start_res_"] = _IMP_multifit.ProteinRecordData_start_res__get
1427  if _newclass:start_res_ = _swig_property(_IMP_multifit.ProteinRecordData_start_res__get, _IMP_multifit.ProteinRecordData_start_res__set)
1428  __swig_setmethods__["end_res_"] = _IMP_multifit.ProteinRecordData_end_res__set
1429  __swig_getmethods__["end_res_"] = _IMP_multifit.ProteinRecordData_end_res__get
1430  if _newclass:end_res_ = _swig_property(_IMP_multifit.ProteinRecordData_end_res__get, _IMP_multifit.ProteinRecordData_end_res__set)
1431  __swig_setmethods__["filename_"] = _IMP_multifit.ProteinRecordData_filename__set
1432  __swig_getmethods__["filename_"] = _IMP_multifit.ProteinRecordData_filename__get
1433  if _newclass:filename_ = _swig_property(_IMP_multifit.ProteinRecordData_filename__get, _IMP_multifit.ProteinRecordData_filename__set)
1434  __swig_setmethods__["surface_filename_"] = _IMP_multifit.ProteinRecordData_surface_filename__set
1435  __swig_getmethods__["surface_filename_"] = _IMP_multifit.ProteinRecordData_surface_filename__get
1436  if _newclass:surface_filename_ = _swig_property(_IMP_multifit.ProteinRecordData_surface_filename__get, _IMP_multifit.ProteinRecordData_surface_filename__set)
1437  __swig_setmethods__["ref_filename_"] = _IMP_multifit.ProteinRecordData_ref_filename__set
1438  __swig_getmethods__["ref_filename_"] = _IMP_multifit.ProteinRecordData_ref_filename__get
1439  if _newclass:ref_filename_ = _swig_property(_IMP_multifit.ProteinRecordData_ref_filename__get, _IMP_multifit.ProteinRecordData_ref_filename__set)
1440  def __str__(self):
1441  """__str__(ProteinRecordData self) -> std::string"""
1442  return _IMP_multifit.ProteinRecordData___str__(self)
1443 
1444  def __repr__(self):
1445  """__repr__(ProteinRecordData self) -> std::string"""
1446  return _IMP_multifit.ProteinRecordData___repr__(self)
1447 
1448  __swig_destroy__ = _IMP_multifit.delete_ProteinRecordData
1449  __del__ = lambda self : None;
1450 ProteinRecordData_swigregister = _IMP_multifit.ProteinRecordData_swigregister
1451 ProteinRecordData_swigregister(ProteinRecordData)
1452 
1453 class ProteomicsData(IMP.base.Object):
1454  """Proxy of C++ IMP::multifit::ProteomicsData class"""
1455  __swig_setmethods__ = {}
1456  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1457  __setattr__ = lambda self, name, value: _swig_setattr(self, ProteomicsData, name, value)
1458  __swig_getmethods__ = {}
1459  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1460  __getattr__ = lambda self, name: _swig_getattr(self, ProteomicsData, name)
1461  def __init__(self):
1462  """__init__(IMP::multifit::ProteomicsData self) -> ProteomicsData"""
1463  this = _IMP_multifit.new_ProteomicsData()
1464  try: self.this.append(this)
1465  except: self.this = this
1466  def add_protein(self, *args):
1467  """
1468  add_protein(ProteomicsData self, std::string name, int start_res, int end_res, std::string const & mol_fn, std::string const & surface_fn,
1469  std::string const & ref_fn) -> int
1470  add_protein(ProteomicsData self, ProteinRecordData rec) -> int
1471  """
1472  return _IMP_multifit.ProteomicsData_add_protein(self, *args)
1473 
1474  def find(self, *args):
1475  """find(ProteomicsData self, std::string const & name) -> int"""
1476  return _IMP_multifit.ProteomicsData_find(self, *args)
1477 
1478  def add_interaction(self, *args):
1479  """add_interaction(ProteomicsData self, IMP::Ints const & ii, bool used_for_filter, float linker_len)"""
1480  return _IMP_multifit.ProteomicsData_add_interaction(self, *args)
1481 
1482  def add_cross_link_interaction(self, *args):
1483  """
1484  add_cross_link_interaction(ProteomicsData self, IMP::Int prot1, IMP::Int res1, IMP::Int prot2, IMP::Int res2, bool used_in_filter,
1485  IMP::Float linker_len)
1486  """
1487  return _IMP_multifit.ProteomicsData_add_cross_link_interaction(self, *args)
1488 
1489  def add_ev_pair(self, *args):
1490  """add_ev_pair(ProteomicsData self, IMP::Int prot1, IMP::Int prot2)"""
1491  return _IMP_multifit.ProteomicsData_add_ev_pair(self, *args)
1492 
1493  def get_number_of_proteins(self):
1494  """get_number_of_proteins(ProteomicsData self) -> int"""
1495  return _IMP_multifit.ProteomicsData_get_number_of_proteins(self)
1496 
1497  def get_number_of_interactions(self):
1498  """get_number_of_interactions(ProteomicsData self) -> int"""
1499  return _IMP_multifit.ProteomicsData_get_number_of_interactions(self)
1500 
1501  def get_interaction(self, *args):
1502  """get_interaction(ProteomicsData self, int interaction_ind) -> IMP::Ints"""
1503  return _IMP_multifit.ProteomicsData_get_interaction(self, *args)
1504 
1505  def get_interaction_part_of_filter(self, *args):
1506  """get_interaction_part_of_filter(ProteomicsData self, int interaction_ind) -> bool"""
1507  return _IMP_multifit.ProteomicsData_get_interaction_part_of_filter(self, *args)
1508 
1509  def get_interaction_linker_length(self, *args):
1510  """get_interaction_linker_length(ProteomicsData self, int interaction_ind) -> int"""
1511  return _IMP_multifit.ProteomicsData_get_interaction_linker_length(self, *args)
1512 
1513  def get_number_of_cross_links(self):
1514  """get_number_of_cross_links(ProteomicsData self) -> int"""
1515  return _IMP_multifit.ProteomicsData_get_number_of_cross_links(self)
1516 
1517  def get_cross_link(self, *args):
1518  """get_cross_link(ProteomicsData self, int xlink_ind) -> std::pair< IMP::IntPair,IMP::IntPair >"""
1519  return _IMP_multifit.ProteomicsData_get_cross_link(self, *args)
1520 
1521  def get_cross_link_part_of_filter(self, *args):
1522  """get_cross_link_part_of_filter(ProteomicsData self, int xlink_ind) -> bool"""
1523  return _IMP_multifit.ProteomicsData_get_cross_link_part_of_filter(self, *args)
1524 
1525  def get_cross_link_length(self, *args):
1526  """get_cross_link_length(ProteomicsData self, int xlink_ind) -> float"""
1527  return _IMP_multifit.ProteomicsData_get_cross_link_length(self, *args)
1528 
1529  def get_number_of_ev_pairs(self):
1530  """get_number_of_ev_pairs(ProteomicsData self) -> int"""
1531  return _IMP_multifit.ProteomicsData_get_number_of_ev_pairs(self)
1532 
1533  def get_ev_pair(self, *args):
1534  """get_ev_pair(ProteomicsData self, int ev_ind) -> IMP::IntPair"""
1535  return _IMP_multifit.ProteomicsData_get_ev_pair(self, *args)
1536 
1537  def get_protein_name(self, *args):
1538  """get_protein_name(ProteomicsData self, int protein_ind) -> std::string"""
1539  return _IMP_multifit.ProteomicsData_get_protein_name(self, *args)
1540 
1541  def get_end_res(self, *args):
1542  """get_end_res(ProteomicsData self, int protein_ind) -> int"""
1543  return _IMP_multifit.ProteomicsData_get_end_res(self, *args)
1544 
1545  def get_start_res(self, *args):
1546  """get_start_res(ProteomicsData self, int protein_ind) -> int"""
1547  return _IMP_multifit.ProteomicsData_get_start_res(self, *args)
1548 
1549  def get_protein_filename(self, *args):
1550  """get_protein_filename(ProteomicsData self, int protein_ind) -> std::string"""
1551  return _IMP_multifit.ProteomicsData_get_protein_filename(self, *args)
1552 
1553  def get_reference_filename(self, *args):
1554  """get_reference_filename(ProteomicsData self, int protein_ind) -> std::string"""
1555  return _IMP_multifit.ProteomicsData_get_reference_filename(self, *args)
1556 
1557  def get_surface_filename(self, *args):
1558  """get_surface_filename(ProteomicsData self, int protein_ind) -> std::string"""
1559  return _IMP_multifit.ProteomicsData_get_surface_filename(self, *args)
1560 
1561  def get_protein_data(self, *args):
1562  """get_protein_data(ProteomicsData self, int protein_ind) -> ProteinRecordData"""
1563  return _IMP_multifit.ProteomicsData_get_protein_data(self, *args)
1564 
1565  def get_version_info(self):
1566  """get_version_info(ProteomicsData self) -> VersionInfo"""
1567  return _IMP_multifit.ProteomicsData_get_version_info(self)
1568 
1569  def get_num_allowed_violated_interactions(self):
1570  """get_num_allowed_violated_interactions(ProteomicsData self) -> int"""
1571  return _IMP_multifit.ProteomicsData_get_num_allowed_violated_interactions(self)
1572 
1573  def set_num_allowed_violated_interactions(self, *args):
1574  """set_num_allowed_violated_interactions(ProteomicsData self, int n)"""
1575  return _IMP_multifit.ProteomicsData_set_num_allowed_violated_interactions(self, *args)
1576 
1577  def get_num_allowed_violated_cross_links(self):
1578  """get_num_allowed_violated_cross_links(ProteomicsData self) -> int"""
1579  return _IMP_multifit.ProteomicsData_get_num_allowed_violated_cross_links(self)
1580 
1581  def set_num_allowed_violated_cross_links(self, *args):
1582  """set_num_allowed_violated_cross_links(ProteomicsData self, int n)"""
1583  return _IMP_multifit.ProteomicsData_set_num_allowed_violated_cross_links(self, *args)
1584 
1585  def get_num_allowed_violated_ev(self):
1586  """get_num_allowed_violated_ev(ProteomicsData self) -> int"""
1587  return _IMP_multifit.ProteomicsData_get_num_allowed_violated_ev(self)
1588 
1589  def set_num_allowed_violated_ev(self, *args):
1590  """set_num_allowed_violated_ev(ProteomicsData self, int n)"""
1591  return _IMP_multifit.ProteomicsData_set_num_allowed_violated_ev(self, *args)
1592 
1593  def __str__(self):
1594  """__str__(ProteomicsData self) -> std::string"""
1595  return _IMP_multifit.ProteomicsData___str__(self)
1596 
1597  def __repr__(self):
1598  """__repr__(ProteomicsData self) -> std::string"""
1599  return _IMP_multifit.ProteomicsData___repr__(self)
1600 
1601  def get_from(o):
1602  return _object_cast_to_ProteomicsData(o)
1603  get_from = staticmethod(get_from)
1604 
1605 ProteomicsData_swigregister = _IMP_multifit.ProteomicsData_swigregister
1606 ProteomicsData_swigregister(ProteomicsData)
1607 
1608 
1609 def read_proteomics_data(*args):
1610  """read_proteomics_data(char const * proteomics_fn) -> ProteomicsData"""
1611  return _IMP_multifit.read_proteomics_data(*args)
1612 
1613 def get_partial_proteomics_data(*args):
1614  """get_partial_proteomics_data(ProteomicsData pd, IMP::Strings const & prot_names) -> ProteomicsData"""
1615  return _IMP_multifit.get_partial_proteomics_data(*args)
1616 class AnchorsData(_object):
1617  """Proxy of C++ IMP::multifit::AnchorsData class"""
1618  __swig_setmethods__ = {}
1619  __setattr__ = lambda self, name, value: _swig_setattr(self, AnchorsData, name, value)
1620  __swig_getmethods__ = {}
1621  __getattr__ = lambda self, name: _swig_getattr(self, AnchorsData, name)
1622  def __init__(self, *args):
1623  """
1624  __init__(IMP::multifit::AnchorsData self) -> AnchorsData
1625  __init__(IMP::multifit::AnchorsData self, IMP::algebra::Vector3Ds points, IMP::IntPairs edges) -> AnchorsData
1626  """
1627  this = _IMP_multifit.new_AnchorsData(*args)
1628  try: self.this.append(this)
1629  except: self.this = this
1630  def remove_edges_for_node(self, *args):
1631  """remove_edges_for_node(AnchorsData self, int node_ind)"""
1632  return _IMP_multifit.AnchorsData_remove_edges_for_node(self, *args)
1633 
1634  def get_number_of_points(self):
1635  """get_number_of_points(AnchorsData self) -> int"""
1636  return _IMP_multifit.AnchorsData_get_number_of_points(self)
1637 
1638  def get_number_of_edges(self):
1639  """get_number_of_edges(AnchorsData self) -> int"""
1640  return _IMP_multifit.AnchorsData_get_number_of_edges(self)
1641 
1642  def get_is_point_considered(self, *args):
1643  """get_is_point_considered(AnchorsData self, int node_ind) -> bool"""
1644  return _IMP_multifit.AnchorsData_get_is_point_considered(self, *args)
1645 
1646  def show(self, *args):
1647  """
1648  show(AnchorsData self, _ostream out=std::cout)
1649  show(AnchorsData self)
1650  """
1651  return _IMP_multifit.AnchorsData_show(self, *args)
1652 
1653  def get_secondary_structure_is_set(self):
1654  """get_secondary_structure_is_set(AnchorsData self) -> bool"""
1655  return _IMP_multifit.AnchorsData_get_secondary_structure_is_set(self)
1656 
1657  def setup_secondary_structure(self, *args):
1658  """setup_secondary_structure(AnchorsData self, Model mdl)"""
1659  return _IMP_multifit.AnchorsData_setup_secondary_structure(self, *args)
1660 
1661  def set_secondary_structure_probabilities(self, *args):
1662  """
1663  set_secondary_structure_probabilities(AnchorsData self, IMP::kernel::Particles const & ssres_ps, IMP::Ints const & indices=IMP::Ints())
1664  set_secondary_structure_probabilities(AnchorsData self, IMP::kernel::Particles const & ssres_ps)
1665  """
1666  return _IMP_multifit.AnchorsData_set_secondary_structure_probabilities(self, *args)
1667 
1668  def get_secondary_structure_particles(self):
1669  """get_secondary_structure_particles(AnchorsData self) -> IMP::kernel::Particles"""
1670  return _IMP_multifit.AnchorsData_get_secondary_structure_particles(self)
1671 
1672  __swig_setmethods__["points_"] = _IMP_multifit.AnchorsData_points__set
1673  __swig_getmethods__["points_"] = _IMP_multifit.AnchorsData_points__get
1674  if _newclass:points_ = _swig_property(_IMP_multifit.AnchorsData_points__get, _IMP_multifit.AnchorsData_points__set)
1675  __swig_setmethods__["consider_point_"] = _IMP_multifit.AnchorsData_consider_point__set
1676  __swig_getmethods__["consider_point_"] = _IMP_multifit.AnchorsData_consider_point__get
1677  if _newclass:consider_point_ = _swig_property(_IMP_multifit.AnchorsData_consider_point__get, _IMP_multifit.AnchorsData_consider_point__set)
1678  __swig_setmethods__["edges_"] = _IMP_multifit.AnchorsData_edges__set
1679  __swig_getmethods__["edges_"] = _IMP_multifit.AnchorsData_edges__get
1680  if _newclass:edges_ = _swig_property(_IMP_multifit.AnchorsData_edges__get, _IMP_multifit.AnchorsData_edges__set)
1681  def __str__(self):
1682  """__str__(AnchorsData self) -> std::string"""
1683  return _IMP_multifit.AnchorsData___str__(self)
1684 
1685  def __repr__(self):
1686  """__repr__(AnchorsData self) -> std::string"""
1687  return _IMP_multifit.AnchorsData___repr__(self)
1688 
1689  __swig_destroy__ = _IMP_multifit.delete_AnchorsData
1690  __del__ = lambda self : None;
1691 AnchorsData_swigregister = _IMP_multifit.AnchorsData_swigregister
1692 AnchorsData_swigregister(AnchorsData)
1693 
1694 
1695 def read_anchors_data(*args):
1696  """read_anchors_data(char const * txt_filename) -> AnchorsData"""
1697  return _IMP_multifit.read_anchors_data(*args)
1698 
1699 def write_txt(*args):
1700  """write_txt(std::string const & txt_filename, AnchorsData ad)"""
1701  return _IMP_multifit.write_txt(*args)
1702 
1703 def write_cmm(*args):
1704  """write_cmm(std::string const & cmm_filename, std::string const & marker_set_name, AnchorsData dpa)"""
1705  return _IMP_multifit.write_cmm(*args)
1706 
1708  """
1709  create_coarse_molecule_from_molecule(Hierarchy mh, int num_beads, Model mdl, float bead_radius, bool add_conn_restraint=False) -> Hierarchy
1710  create_coarse_molecule_from_molecule(Hierarchy mh, int num_beads, Model mdl, float bead_radius) -> Hierarchy
1711  """
1712  return _IMP_multifit.create_coarse_molecule_from_molecule(*args)
1713 
1715  """
1716  create_coarse_molecules_from_molecules(IMP::atom::Hierarchies const & mhs, int frag_len, Model mdl, float bead_radius, bool add_conn_restraint=False) -> IMP::atom::Hierarchies
1717  create_coarse_molecules_from_molecules(IMP::atom::Hierarchies const & mhs, int frag_len, Model mdl, float bead_radius) -> IMP::atom::Hierarchies
1718  """
1719  return _IMP_multifit.create_coarse_molecules_from_molecules(*args)
1720 
1722  """create_coarse_molecule_from_density(DensityMap dmap, float dens_threshold, int num_beads, Model mdl, float bead_radius) -> Hierarchy"""
1723  return _IMP_multifit.create_coarse_molecule_from_density(*args)
1724 
1725 def create_hit_map(*args):
1726  """
1727  create_hit_map(RigidBody rb, Refiner rb_ref, IMP::multifit::FittingSolutionRecords const & sols,
1728  DensityMap damp) -> DensityMap
1729  """
1730  return _IMP_multifit.create_hit_map(*args)
1731 
1732 def get_points_close_to_molecule(*args):
1733  """get_points_close_to_molecule(Hierarchy mh, IMP::algebra::Vector3Ds const points, IMP::Float max_dist) -> IMP::algebra::Vector3Ds"""
1734  return _IMP_multifit.get_points_close_to_molecule(*args)
1735 
1736 def get_points_far_from_molecule(*args):
1737  """get_points_far_from_molecule(Hierarchy mh, IMP::algebra::Vector3Ds const points, IMP::Float max_dist) -> IMP::algebra::Vector3Ds"""
1738  return _IMP_multifit.get_points_far_from_molecule(*args)
1739 class RadiusOfGyrationRestraint(IMP.kernel.Restraint):
1740  """Proxy of C++ IMP::multifit::RadiusOfGyrationRestraint class"""
1741  __swig_setmethods__ = {}
1742  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1743  __setattr__ = lambda self, name, value: _swig_setattr(self, RadiusOfGyrationRestraint, name, value)
1744  __swig_getmethods__ = {}
1745  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1746  __getattr__ = lambda self, name: _swig_getattr(self, RadiusOfGyrationRestraint, name)
1747  def __init__(self, *args):
1748  """
1749  __init__(IMP::multifit::RadiusOfGyrationRestraint self, IMP::kernel::Particles ps, int num_residues, IMP::Float scale=1.) -> RadiusOfGyrationRestraint
1750  __init__(IMP::multifit::RadiusOfGyrationRestraint self, IMP::kernel::Particles ps, int num_residues) -> RadiusOfGyrationRestraint
1751  """
1752  this = _IMP_multifit.new_RadiusOfGyrationRestraint(*args)
1753  try: self.this.append(this)
1754  except: self.this = this
1755  def do_get_inputs(self):
1756  """do_get_inputs(RadiusOfGyrationRestraint self) -> IMP::kernel::ModelObjectsTemp"""
1757  return _IMP_multifit.RadiusOfGyrationRestraint_do_get_inputs(self)
1758 
1759  def get_version_info(self):
1760  """get_version_info(RadiusOfGyrationRestraint self) -> VersionInfo"""
1761  return _IMP_multifit.RadiusOfGyrationRestraint_get_version_info(self)
1762 
1763  def set_radius_of_gyration(self, *args):
1764  """set_radius_of_gyration(RadiusOfGyrationRestraint self, IMP::Float r)"""
1765  return _IMP_multifit.RadiusOfGyrationRestraint_set_radius_of_gyration(self, *args)
1766 
1767  def get_radius_of_gyration(self):
1768  """get_radius_of_gyration(RadiusOfGyrationRestraint self) -> IMP::Float"""
1769  return _IMP_multifit.RadiusOfGyrationRestraint_get_radius_of_gyration(self)
1770 
1771  def __str__(self):
1772  """__str__(RadiusOfGyrationRestraint self) -> std::string"""
1773  return _IMP_multifit.RadiusOfGyrationRestraint___str__(self)
1774 
1775  def __repr__(self):
1776  """__repr__(RadiusOfGyrationRestraint self) -> std::string"""
1777  return _IMP_multifit.RadiusOfGyrationRestraint___repr__(self)
1778 
1779  def get_from(o):
1780  return _object_cast_to_RadiusOfGyrationRestraint(o)
1781  get_from = staticmethod(get_from)
1782 
1783 RadiusOfGyrationRestraint_swigregister = _IMP_multifit.RadiusOfGyrationRestraint_swigregister
1784 RadiusOfGyrationRestraint_swigregister(RadiusOfGyrationRestraint)
1785 
1786 
1787 def get_approximated_radius_of_gyration(*args):
1788  """get_approximated_radius_of_gyration(int len) -> float"""
1789  return _IMP_multifit.get_approximated_radius_of_gyration(*args)
1790 
1791 def get_actual_radius_of_gyration(*args):
1792  """get_actual_radius_of_gyration(IMP::kernel::ParticlesTemp ps) -> float"""
1793  return _IMP_multifit.get_actual_radius_of_gyration(*args)
1794 
1795 def get_approximated_radius(*args):
1796  """get_approximated_radius(int len) -> float"""
1797  return _IMP_multifit.get_approximated_radius(*args)
1798 class ProteinsAnchorsSamplingSpace(_object):
1799  """Proxy of C++ IMP::multifit::ProteinsAnchorsSamplingSpace class"""
1800  __swig_setmethods__ = {}
1801  __setattr__ = lambda self, name, value: _swig_setattr(self, ProteinsAnchorsSamplingSpace, name, value)
1802  __swig_getmethods__ = {}
1803  __getattr__ = lambda self, name: _swig_getattr(self, ProteinsAnchorsSamplingSpace, name)
1804  def __init__(self, prots=None):
1805  """
1806  __init__(IMP::multifit::ProteinsAnchorsSamplingSpace self, ProteomicsData prots=None) -> ProteinsAnchorsSamplingSpace
1807  __init__(IMP::multifit::ProteinsAnchorsSamplingSpace self) -> ProteinsAnchorsSamplingSpace
1808  """
1809  this = _IMP_multifit.new_ProteinsAnchorsSamplingSpace(prots)
1810  try: self.this.append(this)
1811  except: self.this = this
1812  def set_anchors(self, *args):
1813  """set_anchors(ProteinsAnchorsSamplingSpace self, AnchorsData data)"""
1814  return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_anchors(self, *args)
1815 
1816  def get_anchors(self):
1817  """get_anchors(ProteinsAnchorsSamplingSpace self) -> AnchorsData"""
1818  return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_anchors(self)
1819 
1820  def get_anchors_filename(self):
1821  """get_anchors_filename(ProteinsAnchorsSamplingSpace self) -> std::string"""
1822  return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_anchors_filename(self)
1823 
1824  def set_anchors_filename(self, *args):
1825  """set_anchors_filename(ProteinsAnchorsSamplingSpace self, std::string const & fn)"""
1826  return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_anchors_filename(self, *args)
1827 
1828  def get_proteomics_data(self):
1829  """get_proteomics_data(ProteinsAnchorsSamplingSpace self) -> ProteomicsData"""
1830  return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_proteomics_data(self)
1831 
1832  def add_protein(self, *args):
1833  """add_protein(ProteinsAnchorsSamplingSpace self, ProteinRecordData rec)"""
1834  return _IMP_multifit.ProteinsAnchorsSamplingSpace_add_protein(self, *args)
1835 
1836  def get_paths_for_protein(self, *args):
1837  """get_paths_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name) -> IMP::IntsList"""
1838  return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_paths_for_protein(self, *args)
1839 
1840  def set_paths_filename_for_protein(self, *args):
1841  """set_paths_filename_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name, std::string const & paths_filename)"""
1842  return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_paths_filename_for_protein(self, *args)
1843 
1844  def get_paths_filename_for_protein(self, *args):
1845  """get_paths_filename_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name) -> std::string"""
1846  return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_paths_filename_for_protein(self, *args)
1847 
1848  def set_paths_for_protein(self, *args):
1849  """set_paths_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name, IMP::IntsList paths)"""
1850  return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_paths_for_protein(self, *args)
1851 
1852  def show(self, *args):
1853  """
1854  show(ProteinsAnchorsSamplingSpace self, _ostream s=std::cout)
1855  show(ProteinsAnchorsSamplingSpace self)
1856  """
1857  return _IMP_multifit.ProteinsAnchorsSamplingSpace_show(self, *args)
1858 
1859  def __str__(self):
1860  """__str__(ProteinsAnchorsSamplingSpace self) -> std::string"""
1861  return _IMP_multifit.ProteinsAnchorsSamplingSpace___str__(self)
1862 
1863  def __repr__(self):
1864  """__repr__(ProteinsAnchorsSamplingSpace self) -> std::string"""
1865  return _IMP_multifit.ProteinsAnchorsSamplingSpace___repr__(self)
1866 
1867  __swig_destroy__ = _IMP_multifit.delete_ProteinsAnchorsSamplingSpace
1868  __del__ = lambda self : None;
1869 ProteinsAnchorsSamplingSpace_swigregister = _IMP_multifit.ProteinsAnchorsSamplingSpace_swigregister
1870 ProteinsAnchorsSamplingSpace_swigregister(ProteinsAnchorsSamplingSpace)
1871 
1872 
1873 def read_protein_anchors_mapping(*args):
1874  """
1875  read_protein_anchors_mapping(ProteomicsData prots, std::string const & anchors_prot_map_fn, int max_paths=INT_MAX) -> ProteinsAnchorsSamplingSpace
1876  read_protein_anchors_mapping(ProteomicsData prots, std::string const & anchors_prot_map_fn) -> ProteinsAnchorsSamplingSpace
1877  """
1878  return _IMP_multifit.read_protein_anchors_mapping(*args)
1879 
1880 def write_protein_anchors_mapping(*args):
1881  """
1882  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)
1883  write_protein_anchors_mapping(std::string const & anchors_prot_map_fn, ProteinsAnchorsSamplingSpace pa, IMP::Strings const & prot_names)
1884  """
1885  return _IMP_multifit.write_protein_anchors_mapping(*args)
1886 
1887 def get_part_of_sampling_space(*args):
1888  """get_part_of_sampling_space(ProteinsAnchorsSamplingSpace prots_ss, IMP::Strings const & prot_names) -> ProteinsAnchorsSamplingSpace"""
1889  return _IMP_multifit.get_part_of_sampling_space(*args)
1890 
1892  """get_partial_assembly_setting_data(SettingsData prots_sd, IMP::Strings const & prot_names) -> SettingsData"""
1893  return _IMP_multifit.get_partial_assembly_setting_data(*args)
1894 
1895 def read_paths(*args):
1896  """
1897  read_paths(char const * txt_filename, int max_paths=INT_MAX) -> IMP::IntsList
1898  read_paths(char const * txt_filename) -> IMP::IntsList
1899  """
1900  return _IMP_multifit.read_paths(*args)
1901 
1902 def write_paths(*args):
1903  """write_paths(IMP::IntsList const & paths, std::string const & txt_filename)"""
1904  return _IMP_multifit.write_paths(*args)
1905 
1906 def molecule2anchors(*args):
1907  """molecule2anchors(Hierarchy mh, int k) -> AnchorsData"""
1908  return _IMP_multifit.molecule2anchors(*args)
1909 
1910 def get_anchors_for_density(*args):
1911  """
1912  get_anchors_for_density(DensityMap dmap, int number_of_means, float density_threshold, std::string pdb_filename,
1913  std::string cmm_filename, std::string seg_filename, std::string txt_filename)
1914  """
1915  return _IMP_multifit.get_anchors_for_density(*args)
1916 
1918  """
1919  get_anchor_indices_matching_secondary_structure(AnchorsData ad, IMP::atom::SecondaryStructureResidues const & ssrs, IMP::Float max_rmsd=0.7) -> IMP::IntsList
1920  get_anchor_indices_matching_secondary_structure(AnchorsData ad, IMP::atom::SecondaryStructureResidues const & ssrs) -> IMP::IntsList
1921  """
1922  return _IMP_multifit.get_anchor_indices_matching_secondary_structure(*args)
1923 class DominoParams(_object):
1924  """Proxy of C++ IMP::multifit::DominoParams class"""
1925  __swig_setmethods__ = {}
1926  __setattr__ = lambda self, name, value: _swig_setattr(self, DominoParams, name, value)
1927  __swig_getmethods__ = {}
1928  __getattr__ = lambda self, name: _swig_getattr(self, DominoParams, name)
1929  def __init__(self):
1930  """__init__(IMP::multifit::DominoParams self) -> DominoParams"""
1931  this = _IMP_multifit.new_DominoParams()
1932  try: self.this.append(this)
1933  except: self.this = this
1934  def add(self, *args):
1935  """add(DominoParams self, boost::property_tree::ptree const & pt)"""
1936  return _IMP_multifit.DominoParams_add(self, *args)
1937 
1938  def show(self, *args):
1939  """
1940  show(DominoParams self, _ostream s=std::cout)
1941  show(DominoParams self)
1942  """
1943  return _IMP_multifit.DominoParams_show(self, *args)
1944 
1945  __swig_setmethods__["max_value_threshold_"] = _IMP_multifit.DominoParams_max_value_threshold__set
1946  __swig_getmethods__["max_value_threshold_"] = _IMP_multifit.DominoParams_max_value_threshold__get
1947  if _newclass:max_value_threshold_ = _swig_property(_IMP_multifit.DominoParams_max_value_threshold__get, _IMP_multifit.DominoParams_max_value_threshold__set)
1948  __swig_setmethods__["max_num_states_for_subset_"] = _IMP_multifit.DominoParams_max_num_states_for_subset__set
1949  __swig_getmethods__["max_num_states_for_subset_"] = _IMP_multifit.DominoParams_max_num_states_for_subset__get
1950  if _newclass: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)
1951  __swig_setmethods__["max_anchor_penetration_"] = _IMP_multifit.DominoParams_max_anchor_penetration__set
1952  __swig_getmethods__["max_anchor_penetration_"] = _IMP_multifit.DominoParams_max_anchor_penetration__get
1953  if _newclass:max_anchor_penetration_ = _swig_property(_IMP_multifit.DominoParams_max_anchor_penetration__get, _IMP_multifit.DominoParams_max_anchor_penetration__set)
1954  __swig_setmethods__["heap_size_"] = _IMP_multifit.DominoParams_heap_size__set
1955  __swig_getmethods__["heap_size_"] = _IMP_multifit.DominoParams_heap_size__get
1956  if _newclass:heap_size_ = _swig_property(_IMP_multifit.DominoParams_heap_size__get, _IMP_multifit.DominoParams_heap_size__set)
1957  __swig_setmethods__["cache_size_"] = _IMP_multifit.DominoParams_cache_size__set
1958  __swig_getmethods__["cache_size_"] = _IMP_multifit.DominoParams_cache_size__get
1959  if _newclass:cache_size_ = _swig_property(_IMP_multifit.DominoParams_cache_size__get, _IMP_multifit.DominoParams_cache_size__set)
1960  def __str__(self):
1961  """__str__(DominoParams self) -> std::string"""
1962  return _IMP_multifit.DominoParams___str__(self)
1963 
1964  def __repr__(self):
1965  """__repr__(DominoParams self) -> std::string"""
1966  return _IMP_multifit.DominoParams___repr__(self)
1967 
1968  __swig_destroy__ = _IMP_multifit.delete_DominoParams
1969  __del__ = lambda self : None;
1970 DominoParams_swigregister = _IMP_multifit.DominoParams_swigregister
1971 DominoParams_swigregister(DominoParams)
1972 
1973 class XlinkParams(_object):
1974  """Proxy of C++ IMP::multifit::XlinkParams class"""
1975  __swig_setmethods__ = {}
1976  __setattr__ = lambda self, name, value: _swig_setattr(self, XlinkParams, name, value)
1977  __swig_getmethods__ = {}
1978  __getattr__ = lambda self, name: _swig_getattr(self, XlinkParams, name)
1979  def __init__(self):
1980  """__init__(IMP::multifit::XlinkParams self) -> XlinkParams"""
1981  this = _IMP_multifit.new_XlinkParams()
1982  try: self.this.append(this)
1983  except: self.this = this
1984  def add(self, *args):
1985  """add(XlinkParams self, boost::property_tree::ptree const & pt)"""
1986  return _IMP_multifit.XlinkParams_add(self, *args)
1987 
1988  def show(self, *args):
1989  """
1990  show(XlinkParams self, _ostream s=std::cout)
1991  show(XlinkParams self)
1992  """
1993  return _IMP_multifit.XlinkParams_show(self, *args)
1994 
1995  __swig_setmethods__["upper_bound_"] = _IMP_multifit.XlinkParams_upper_bound__set
1996  __swig_getmethods__["upper_bound_"] = _IMP_multifit.XlinkParams_upper_bound__get
1997  if _newclass:upper_bound_ = _swig_property(_IMP_multifit.XlinkParams_upper_bound__get, _IMP_multifit.XlinkParams_upper_bound__set)
1998  __swig_setmethods__["k_"] = _IMP_multifit.XlinkParams_k__set
1999  __swig_getmethods__["k_"] = _IMP_multifit.XlinkParams_k__get
2000  if _newclass:k_ = _swig_property(_IMP_multifit.XlinkParams_k__get, _IMP_multifit.XlinkParams_k__set)
2001  __swig_setmethods__["max_xlink_val_"] = _IMP_multifit.XlinkParams_max_xlink_val__set
2002  __swig_getmethods__["max_xlink_val_"] = _IMP_multifit.XlinkParams_max_xlink_val__get
2003  if _newclass:max_xlink_val_ = _swig_property(_IMP_multifit.XlinkParams_max_xlink_val__get, _IMP_multifit.XlinkParams_max_xlink_val__set)
2004  __swig_setmethods__["treat_between_residues_"] = _IMP_multifit.XlinkParams_treat_between_residues__set
2005  __swig_getmethods__["treat_between_residues_"] = _IMP_multifit.XlinkParams_treat_between_residues__get
2006  if _newclass:treat_between_residues_ = _swig_property(_IMP_multifit.XlinkParams_treat_between_residues__get, _IMP_multifit.XlinkParams_treat_between_residues__set)
2007  def __str__(self):
2008  """__str__(XlinkParams self) -> std::string"""
2009  return _IMP_multifit.XlinkParams___str__(self)
2010 
2011  def __repr__(self):
2012  """__repr__(XlinkParams self) -> std::string"""
2013  return _IMP_multifit.XlinkParams___repr__(self)
2014 
2015  __swig_destroy__ = _IMP_multifit.delete_XlinkParams
2016  __del__ = lambda self : None;
2017 XlinkParams_swigregister = _IMP_multifit.XlinkParams_swigregister
2018 XlinkParams_swigregister(XlinkParams)
2019 
2020 class ConnectivityParams(_object):
2021  """Proxy of C++ IMP::multifit::ConnectivityParams class"""
2022  __swig_setmethods__ = {}
2023  __setattr__ = lambda self, name, value: _swig_setattr(self, ConnectivityParams, name, value)
2024  __swig_getmethods__ = {}
2025  __getattr__ = lambda self, name: _swig_getattr(self, ConnectivityParams, name)
2026  def __init__(self):
2027  """__init__(IMP::multifit::ConnectivityParams self) -> ConnectivityParams"""
2028  this = _IMP_multifit.new_ConnectivityParams()
2029  try: self.this.append(this)
2030  except: self.this = this
2031  def add(self, *args):
2032  """add(ConnectivityParams self, boost::property_tree::ptree const & pt)"""
2033  return _IMP_multifit.ConnectivityParams_add(self, *args)
2034 
2035  def show(self, *args):
2036  """
2037  show(ConnectivityParams self, _ostream s=std::cout)
2038  show(ConnectivityParams self)
2039  """
2040  return _IMP_multifit.ConnectivityParams_show(self, *args)
2041 
2042  __swig_setmethods__["upper_bound_"] = _IMP_multifit.ConnectivityParams_upper_bound__set
2043  __swig_getmethods__["upper_bound_"] = _IMP_multifit.ConnectivityParams_upper_bound__get
2044  if _newclass:upper_bound_ = _swig_property(_IMP_multifit.ConnectivityParams_upper_bound__get, _IMP_multifit.ConnectivityParams_upper_bound__set)
2045  __swig_setmethods__["k_"] = _IMP_multifit.ConnectivityParams_k__set
2046  __swig_getmethods__["k_"] = _IMP_multifit.ConnectivityParams_k__get
2047  if _newclass:k_ = _swig_property(_IMP_multifit.ConnectivityParams_k__get, _IMP_multifit.ConnectivityParams_k__set)
2048  __swig_setmethods__["max_conn_rest_val_"] = _IMP_multifit.ConnectivityParams_max_conn_rest_val__set
2049  __swig_getmethods__["max_conn_rest_val_"] = _IMP_multifit.ConnectivityParams_max_conn_rest_val__get
2050  if _newclass:max_conn_rest_val_ = _swig_property(_IMP_multifit.ConnectivityParams_max_conn_rest_val__get, _IMP_multifit.ConnectivityParams_max_conn_rest_val__set)
2051  def __str__(self):
2052  """__str__(ConnectivityParams self) -> std::string"""
2053  return _IMP_multifit.ConnectivityParams___str__(self)
2054 
2055  def __repr__(self):
2056  """__repr__(ConnectivityParams self) -> std::string"""
2057  return _IMP_multifit.ConnectivityParams___repr__(self)
2058 
2059  __swig_destroy__ = _IMP_multifit.delete_ConnectivityParams
2060  __del__ = lambda self : None;
2061 ConnectivityParams_swigregister = _IMP_multifit.ConnectivityParams_swigregister
2062 ConnectivityParams_swigregister(ConnectivityParams)
2063 
2064 class FragmentsParams(_object):
2065  """Proxy of C++ IMP::multifit::FragmentsParams class"""
2066  __swig_setmethods__ = {}
2067  __setattr__ = lambda self, name, value: _swig_setattr(self, FragmentsParams, name, value)
2068  __swig_getmethods__ = {}
2069  __getattr__ = lambda self, name: _swig_getattr(self, FragmentsParams, name)
2070  def __init__(self):
2071  """__init__(IMP::multifit::FragmentsParams self) -> FragmentsParams"""
2072  this = _IMP_multifit.new_FragmentsParams()
2073  try: self.this.append(this)
2074  except: self.this = this
2075  def add(self, *args):
2076  """add(FragmentsParams self, boost::property_tree::ptree const & pt)"""
2077  return _IMP_multifit.FragmentsParams_add(self, *args)
2078 
2079  def show(self, *args):
2080  """
2081  show(FragmentsParams self, _ostream s=std::cout)
2082  show(FragmentsParams self)
2083  """
2084  return _IMP_multifit.FragmentsParams_show(self, *args)
2085 
2086  __swig_setmethods__["frag_len_"] = _IMP_multifit.FragmentsParams_frag_len__set
2087  __swig_getmethods__["frag_len_"] = _IMP_multifit.FragmentsParams_frag_len__get
2088  if _newclass:frag_len_ = _swig_property(_IMP_multifit.FragmentsParams_frag_len__get, _IMP_multifit.FragmentsParams_frag_len__set)
2089  __swig_setmethods__["bead_radius_scale_"] = _IMP_multifit.FragmentsParams_bead_radius_scale__set
2090  __swig_getmethods__["bead_radius_scale_"] = _IMP_multifit.FragmentsParams_bead_radius_scale__get
2091  if _newclass:bead_radius_scale_ = _swig_property(_IMP_multifit.FragmentsParams_bead_radius_scale__get, _IMP_multifit.FragmentsParams_bead_radius_scale__set)
2092  __swig_setmethods__["load_atomic_"] = _IMP_multifit.FragmentsParams_load_atomic__set
2093  __swig_getmethods__["load_atomic_"] = _IMP_multifit.FragmentsParams_load_atomic__get
2094  if _newclass:load_atomic_ = _swig_property(_IMP_multifit.FragmentsParams_load_atomic__get, _IMP_multifit.FragmentsParams_load_atomic__set)
2095  __swig_setmethods__["subunit_rigid_"] = _IMP_multifit.FragmentsParams_subunit_rigid__set
2096  __swig_getmethods__["subunit_rigid_"] = _IMP_multifit.FragmentsParams_subunit_rigid__get
2097  if _newclass:subunit_rigid_ = _swig_property(_IMP_multifit.FragmentsParams_subunit_rigid__get, _IMP_multifit.FragmentsParams_subunit_rigid__set)
2098  def __str__(self):
2099  """__str__(FragmentsParams self) -> std::string"""
2100  return _IMP_multifit.FragmentsParams___str__(self)
2101 
2102  def __repr__(self):
2103  """__repr__(FragmentsParams self) -> std::string"""
2104  return _IMP_multifit.FragmentsParams___repr__(self)
2105 
2106  __swig_destroy__ = _IMP_multifit.delete_FragmentsParams
2107  __del__ = lambda self : None;
2108 FragmentsParams_swigregister = _IMP_multifit.FragmentsParams_swigregister
2109 FragmentsParams_swigregister(FragmentsParams)
2110 
2111 class RogParams(_object):
2112  """Proxy of C++ IMP::multifit::RogParams class"""
2113  __swig_setmethods__ = {}
2114  __setattr__ = lambda self, name, value: _swig_setattr(self, RogParams, name, value)
2115  __swig_getmethods__ = {}
2116  __getattr__ = lambda self, name: _swig_getattr(self, RogParams, name)
2117  def __init__(self):
2118  """__init__(IMP::multifit::RogParams self) -> RogParams"""
2119  this = _IMP_multifit.new_RogParams()
2120  try: self.this.append(this)
2121  except: self.this = this
2122  def add(self, *args):
2123  """add(RogParams self, boost::property_tree::ptree const & pt)"""
2124  return _IMP_multifit.RogParams_add(self, *args)
2125 
2126  def get_max_score(self):
2127  """get_max_score(RogParams self) -> float"""
2128  return _IMP_multifit.RogParams_get_max_score(self)
2129 
2130  def get_scale(self):
2131  """get_scale(RogParams self) -> float"""
2132  return _IMP_multifit.RogParams_get_scale(self)
2133 
2134  def show(self, *args):
2135  """
2136  show(RogParams self, _ostream s=std::cout)
2137  show(RogParams self)
2138  """
2139  return _IMP_multifit.RogParams_show(self, *args)
2140 
2141  def __str__(self):
2142  """__str__(RogParams self) -> std::string"""
2143  return _IMP_multifit.RogParams___str__(self)
2144 
2145  def __repr__(self):
2146  """__repr__(RogParams self) -> std::string"""
2147  return _IMP_multifit.RogParams___repr__(self)
2148 
2149  __swig_destroy__ = _IMP_multifit.delete_RogParams
2150  __del__ = lambda self : None;
2151 RogParams_swigregister = _IMP_multifit.RogParams_swigregister
2152 RogParams_swigregister(RogParams)
2153 
2154 class EVParams(_object):
2155  """Proxy of C++ IMP::multifit::EVParams class"""
2156  __swig_setmethods__ = {}
2157  __setattr__ = lambda self, name, value: _swig_setattr(self, EVParams, name, value)
2158  __swig_getmethods__ = {}
2159  __getattr__ = lambda self, name: _swig_getattr(self, EVParams, name)
2160  def __init__(self):
2161  """__init__(IMP::multifit::EVParams self) -> EVParams"""
2162  this = _IMP_multifit.new_EVParams()
2163  try: self.this.append(this)
2164  except: self.this = this
2165  def add(self, *args):
2166  """add(EVParams self, boost::property_tree::ptree const & pt)"""
2167  return _IMP_multifit.EVParams_add(self, *args)
2168 
2169  def show(self, *args):
2170  """
2171  show(EVParams self, _ostream s=std::cout)
2172  show(EVParams self)
2173  """
2174  return _IMP_multifit.EVParams_show(self, *args)
2175 
2176  __swig_setmethods__["pair_distance_"] = _IMP_multifit.EVParams_pair_distance__set
2177  __swig_getmethods__["pair_distance_"] = _IMP_multifit.EVParams_pair_distance__get
2178  if _newclass:pair_distance_ = _swig_property(_IMP_multifit.EVParams_pair_distance__get, _IMP_multifit.EVParams_pair_distance__set)
2179  __swig_setmethods__["pair_slack_"] = _IMP_multifit.EVParams_pair_slack__set
2180  __swig_getmethods__["pair_slack_"] = _IMP_multifit.EVParams_pair_slack__get
2181  if _newclass:pair_slack_ = _swig_property(_IMP_multifit.EVParams_pair_slack__get, _IMP_multifit.EVParams_pair_slack__set)
2182  __swig_setmethods__["hlb_mean_"] = _IMP_multifit.EVParams_hlb_mean__set
2183  __swig_getmethods__["hlb_mean_"] = _IMP_multifit.EVParams_hlb_mean__get
2184  if _newclass:hlb_mean_ = _swig_property(_IMP_multifit.EVParams_hlb_mean__get, _IMP_multifit.EVParams_hlb_mean__set)
2185  __swig_setmethods__["hlb_k_"] = _IMP_multifit.EVParams_hlb_k__set
2186  __swig_getmethods__["hlb_k_"] = _IMP_multifit.EVParams_hlb_k__get
2187  if _newclass:hlb_k_ = _swig_property(_IMP_multifit.EVParams_hlb_k__get, _IMP_multifit.EVParams_hlb_k__set)
2188  __swig_setmethods__["maximum_ev_score_for_pair_"] = _IMP_multifit.EVParams_maximum_ev_score_for_pair__set
2189  __swig_getmethods__["maximum_ev_score_for_pair_"] = _IMP_multifit.EVParams_maximum_ev_score_for_pair__get
2190  if _newclass: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)
2191  __swig_setmethods__["allowed_percentage_of_bad_pairs_"] = _IMP_multifit.EVParams_allowed_percentage_of_bad_pairs__set
2192  __swig_getmethods__["allowed_percentage_of_bad_pairs_"] = _IMP_multifit.EVParams_allowed_percentage_of_bad_pairs__get
2193  if _newclass: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)
2194  __swig_setmethods__["scoring_mode_"] = _IMP_multifit.EVParams_scoring_mode__set
2195  __swig_getmethods__["scoring_mode_"] = _IMP_multifit.EVParams_scoring_mode__get
2196  if _newclass:scoring_mode_ = _swig_property(_IMP_multifit.EVParams_scoring_mode__get, _IMP_multifit.EVParams_scoring_mode__set)
2197  def __str__(self):
2198  """__str__(EVParams self) -> std::string"""
2199  return _IMP_multifit.EVParams___str__(self)
2200 
2201  def __repr__(self):
2202  """__repr__(EVParams self) -> std::string"""
2203  return _IMP_multifit.EVParams___repr__(self)
2204 
2205  __swig_destroy__ = _IMP_multifit.delete_EVParams
2206  __del__ = lambda self : None;
2207 EVParams_swigregister = _IMP_multifit.EVParams_swigregister
2208 EVParams_swigregister(EVParams)
2209 
2210 class FiltersParams(_object):
2211  """Proxy of C++ IMP::multifit::FiltersParams class"""
2212  __swig_setmethods__ = {}
2213  __setattr__ = lambda self, name, value: _swig_setattr(self, FiltersParams, name, value)
2214  __swig_getmethods__ = {}
2215  __getattr__ = lambda self, name: _swig_getattr(self, FiltersParams, name)
2216  def __init__(self):
2217  """__init__(IMP::multifit::FiltersParams self) -> FiltersParams"""
2218  this = _IMP_multifit.new_FiltersParams()
2219  try: self.this.append(this)
2220  except: self.this = this
2221  def add(self, *args):
2222  """add(FiltersParams self, boost::property_tree::ptree const & pt)"""
2223  return _IMP_multifit.FiltersParams_add(self, *args)
2224 
2225  def show(self, *args):
2226  """
2227  show(FiltersParams self, _ostream s=std::cout)
2228  show(FiltersParams self)
2229  """
2230  return _IMP_multifit.FiltersParams_show(self, *args)
2231 
2232  __swig_setmethods__["max_num_violated_xlink_"] = _IMP_multifit.FiltersParams_max_num_violated_xlink__set
2233  __swig_getmethods__["max_num_violated_xlink_"] = _IMP_multifit.FiltersParams_max_num_violated_xlink__get
2234  if _newclass:max_num_violated_xlink_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_xlink__get, _IMP_multifit.FiltersParams_max_num_violated_xlink__set)
2235  __swig_setmethods__["max_num_violated_conn_"] = _IMP_multifit.FiltersParams_max_num_violated_conn__set
2236  __swig_getmethods__["max_num_violated_conn_"] = _IMP_multifit.FiltersParams_max_num_violated_conn__get
2237  if _newclass:max_num_violated_conn_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_conn__get, _IMP_multifit.FiltersParams_max_num_violated_conn__set)
2238  __swig_setmethods__["max_num_violated_ev_"] = _IMP_multifit.FiltersParams_max_num_violated_ev__set
2239  __swig_getmethods__["max_num_violated_ev_"] = _IMP_multifit.FiltersParams_max_num_violated_ev__get
2240  if _newclass:max_num_violated_ev_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_ev__get, _IMP_multifit.FiltersParams_max_num_violated_ev__set)
2241  def __str__(self):
2242  """__str__(FiltersParams self) -> std::string"""
2243  return _IMP_multifit.FiltersParams___str__(self)
2244 
2245  def __repr__(self):
2246  """__repr__(FiltersParams self) -> std::string"""
2247  return _IMP_multifit.FiltersParams___repr__(self)
2248 
2249  __swig_destroy__ = _IMP_multifit.delete_FiltersParams
2250  __del__ = lambda self : None;
2251 FiltersParams_swigregister = _IMP_multifit.FiltersParams_swigregister
2252 FiltersParams_swigregister(FiltersParams)
2253 
2254 class FittingParams(_object):
2255  """Proxy of C++ IMP::multifit::FittingParams class"""
2256  __swig_setmethods__ = {}
2257  __setattr__ = lambda self, name, value: _swig_setattr(self, FittingParams, name, value)
2258  __swig_getmethods__ = {}
2259  __getattr__ = lambda self, name: _swig_getattr(self, FittingParams, name)
2260  def __init__(self):
2261  """__init__(IMP::multifit::FittingParams self) -> FittingParams"""
2262  this = _IMP_multifit.new_FittingParams()
2263  try: self.this.append(this)
2264  except: self.this = this
2265  def add(self, *args):
2266  """add(FittingParams self, boost::property_tree::ptree const & pt)"""
2267  return _IMP_multifit.FittingParams_add(self, *args)
2268 
2269  def show(self, *args):
2270  """
2271  show(FittingParams self, _ostream s=std::cout)
2272  show(FittingParams self)
2273  """
2274  return _IMP_multifit.FittingParams_show(self, *args)
2275 
2276  __swig_setmethods__["pca_max_angle_diff_"] = _IMP_multifit.FittingParams_pca_max_angle_diff__set
2277  __swig_getmethods__["pca_max_angle_diff_"] = _IMP_multifit.FittingParams_pca_max_angle_diff__get
2278  if _newclass:pca_max_angle_diff_ = _swig_property(_IMP_multifit.FittingParams_pca_max_angle_diff__get, _IMP_multifit.FittingParams_pca_max_angle_diff__set)
2279  __swig_setmethods__["pca_max_size_diff_"] = _IMP_multifit.FittingParams_pca_max_size_diff__set
2280  __swig_getmethods__["pca_max_size_diff_"] = _IMP_multifit.FittingParams_pca_max_size_diff__get
2281  if _newclass:pca_max_size_diff_ = _swig_property(_IMP_multifit.FittingParams_pca_max_size_diff__get, _IMP_multifit.FittingParams_pca_max_size_diff__set)
2282  __swig_setmethods__["pca_max_cent_dist_diff_"] = _IMP_multifit.FittingParams_pca_max_cent_dist_diff__set
2283  __swig_getmethods__["pca_max_cent_dist_diff_"] = _IMP_multifit.FittingParams_pca_max_cent_dist_diff__get
2284  if _newclass: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)
2285  __swig_setmethods__["max_asmb_fit_score_"] = _IMP_multifit.FittingParams_max_asmb_fit_score__set
2286  __swig_getmethods__["max_asmb_fit_score_"] = _IMP_multifit.FittingParams_max_asmb_fit_score__get
2287  if _newclass:max_asmb_fit_score_ = _swig_property(_IMP_multifit.FittingParams_max_asmb_fit_score__get, _IMP_multifit.FittingParams_max_asmb_fit_score__set)
2288  def __str__(self):
2289  """__str__(FittingParams self) -> std::string"""
2290  return _IMP_multifit.FittingParams___str__(self)
2291 
2292  def __repr__(self):
2293  """__repr__(FittingParams self) -> std::string"""
2294  return _IMP_multifit.FittingParams___repr__(self)
2295 
2296  __swig_destroy__ = _IMP_multifit.delete_FittingParams
2297  __del__ = lambda self : None;
2298 FittingParams_swigregister = _IMP_multifit.FittingParams_swigregister
2299 FittingParams_swigregister(FittingParams)
2300 
2301 class ComplementarityParams(_object):
2302  """Proxy of C++ IMP::multifit::ComplementarityParams class"""
2303  __swig_setmethods__ = {}
2304  __setattr__ = lambda self, name, value: _swig_setattr(self, ComplementarityParams, name, value)
2305  __swig_getmethods__ = {}
2306  __getattr__ = lambda self, name: _swig_getattr(self, ComplementarityParams, name)
2307  def __init__(self):
2308  """__init__(IMP::multifit::ComplementarityParams self) -> ComplementarityParams"""
2309  this = _IMP_multifit.new_ComplementarityParams()
2310  try: self.this.append(this)
2311  except: self.this = this
2312  def add(self, *args):
2313  """add(ComplementarityParams self, boost::property_tree::ptree const & pt)"""
2314  return _IMP_multifit.ComplementarityParams_add(self, *args)
2315 
2316  def show(self, *args):
2317  """
2318  show(ComplementarityParams self, _ostream s=std::cout)
2319  show(ComplementarityParams self)
2320  """
2321  return _IMP_multifit.ComplementarityParams_show(self, *args)
2322 
2323  __swig_setmethods__["max_score_"] = _IMP_multifit.ComplementarityParams_max_score__set
2324  __swig_getmethods__["max_score_"] = _IMP_multifit.ComplementarityParams_max_score__get
2325  if _newclass:max_score_ = _swig_property(_IMP_multifit.ComplementarityParams_max_score__get, _IMP_multifit.ComplementarityParams_max_score__set)
2326  __swig_setmethods__["max_penetration_"] = _IMP_multifit.ComplementarityParams_max_penetration__set
2327  __swig_getmethods__["max_penetration_"] = _IMP_multifit.ComplementarityParams_max_penetration__get
2328  if _newclass:max_penetration_ = _swig_property(_IMP_multifit.ComplementarityParams_max_penetration__get, _IMP_multifit.ComplementarityParams_max_penetration__set)
2329  __swig_setmethods__["interior_layer_thickness_"] = _IMP_multifit.ComplementarityParams_interior_layer_thickness__set
2330  __swig_getmethods__["interior_layer_thickness_"] = _IMP_multifit.ComplementarityParams_interior_layer_thickness__get
2331  if _newclass:interior_layer_thickness_ = _swig_property(_IMP_multifit.ComplementarityParams_interior_layer_thickness__get, _IMP_multifit.ComplementarityParams_interior_layer_thickness__set)
2332  __swig_setmethods__["boundary_coef_"] = _IMP_multifit.ComplementarityParams_boundary_coef__set
2333  __swig_getmethods__["boundary_coef_"] = _IMP_multifit.ComplementarityParams_boundary_coef__get
2334  if _newclass:boundary_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_boundary_coef__get, _IMP_multifit.ComplementarityParams_boundary_coef__set)
2335  __swig_setmethods__["comp_coef_"] = _IMP_multifit.ComplementarityParams_comp_coef__set
2336  __swig_getmethods__["comp_coef_"] = _IMP_multifit.ComplementarityParams_comp_coef__get
2337  if _newclass:comp_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_comp_coef__get, _IMP_multifit.ComplementarityParams_comp_coef__set)
2338  __swig_setmethods__["penetration_coef_"] = _IMP_multifit.ComplementarityParams_penetration_coef__set
2339  __swig_getmethods__["penetration_coef_"] = _IMP_multifit.ComplementarityParams_penetration_coef__get
2340  if _newclass:penetration_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_penetration_coef__get, _IMP_multifit.ComplementarityParams_penetration_coef__set)
2341  def __str__(self):
2342  """__str__(ComplementarityParams self) -> std::string"""
2343  return _IMP_multifit.ComplementarityParams___str__(self)
2344 
2345  def __repr__(self):
2346  """__repr__(ComplementarityParams self) -> std::string"""
2347  return _IMP_multifit.ComplementarityParams___repr__(self)
2348 
2349  __swig_destroy__ = _IMP_multifit.delete_ComplementarityParams
2350  __del__ = lambda self : None;
2351 ComplementarityParams_swigregister = _IMP_multifit.ComplementarityParams_swigregister
2352 ComplementarityParams_swigregister(ComplementarityParams)
2353 
2354 class AlignmentParams(_object):
2355  """Proxy of C++ IMP::multifit::AlignmentParams class"""
2356  __swig_setmethods__ = {}
2357  __setattr__ = lambda self, name, value: _swig_setattr(self, AlignmentParams, name, value)
2358  __swig_getmethods__ = {}
2359  __getattr__ = lambda self, name: _swig_getattr(self, AlignmentParams, name)
2360  def __init__(self, *args):
2361  """__init__(IMP::multifit::AlignmentParams self, char const * param_filename) -> AlignmentParams"""
2362  this = _IMP_multifit.new_AlignmentParams(*args)
2363  try: self.this.append(this)
2364  except: self.this = this
2365  def get_domino_params(self):
2366  """get_domino_params(AlignmentParams self) -> DominoParams"""
2367  return _IMP_multifit.AlignmentParams_get_domino_params(self)
2368 
2369  def get_fitting_params(self):
2370  """get_fitting_params(AlignmentParams self) -> FittingParams"""
2371  return _IMP_multifit.AlignmentParams_get_fitting_params(self)
2372 
2373  def get_complementarity_params(self):
2374  """get_complementarity_params(AlignmentParams self) -> ComplementarityParams"""
2375  return _IMP_multifit.AlignmentParams_get_complementarity_params(self)
2376 
2377  def get_xlink_params(self):
2378  """get_xlink_params(AlignmentParams self) -> XlinkParams"""
2379  return _IMP_multifit.AlignmentParams_get_xlink_params(self)
2380 
2381  def get_connectivity_params(self):
2382  """get_connectivity_params(AlignmentParams self) -> ConnectivityParams"""
2383  return _IMP_multifit.AlignmentParams_get_connectivity_params(self)
2384 
2385  def get_rog_params(self):
2386  """get_rog_params(AlignmentParams self) -> RogParams"""
2387  return _IMP_multifit.AlignmentParams_get_rog_params(self)
2388 
2389  def get_fragments_params(self):
2390  """get_fragments_params(AlignmentParams self) -> FragmentsParams"""
2391  return _IMP_multifit.AlignmentParams_get_fragments_params(self)
2392 
2393  def get_filters_params(self):
2394  """get_filters_params(AlignmentParams self) -> FiltersParams"""
2395  return _IMP_multifit.AlignmentParams_get_filters_params(self)
2396 
2397  def get_ev_params(self):
2398  """get_ev_params(AlignmentParams self) -> EVParams"""
2399  return _IMP_multifit.AlignmentParams_get_ev_params(self)
2400 
2401  def show(self, *args):
2402  """
2403  show(AlignmentParams self, _ostream s=std::cout)
2404  show(AlignmentParams self)
2405  """
2406  return _IMP_multifit.AlignmentParams_show(self, *args)
2407 
2408  def __str__(self):
2409  """__str__(AlignmentParams self) -> std::string"""
2410  return _IMP_multifit.AlignmentParams___str__(self)
2411 
2412  def __repr__(self):
2413  """__repr__(AlignmentParams self) -> std::string"""
2414  return _IMP_multifit.AlignmentParams___repr__(self)
2415 
2416  __swig_destroy__ = _IMP_multifit.delete_AlignmentParams
2417  __del__ = lambda self : None;
2418 AlignmentParams_swigregister = _IMP_multifit.AlignmentParams_swigregister
2419 AlignmentParams_swigregister(AlignmentParams)
2420 
2421 class ProteomicsEMAlignmentAtomic(IMP.base.Object):
2422  """Proxy of C++ IMP::multifit::ProteomicsEMAlignmentAtomic class"""
2423  __swig_setmethods__ = {}
2424  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2425  __setattr__ = lambda self, name, value: _swig_setattr(self, ProteomicsEMAlignmentAtomic, name, value)
2426  __swig_getmethods__ = {}
2427  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2428  __getattr__ = lambda self, name: _swig_getattr(self, ProteomicsEMAlignmentAtomic, name)
2429  def __init__(self, *args):
2430  """__init__(IMP::multifit::ProteomicsEMAlignmentAtomic self, ProteinsAnchorsSamplingSpace mapping_data, SettingsData asmb_data, AlignmentParams align_param) -> ProteomicsEMAlignmentAtomic"""
2431  this = _IMP_multifit.new_ProteomicsEMAlignmentAtomic(*args)
2432  try: self.this.append(this)
2433  except: self.this = this
2434  def align(self):
2435  """align(ProteomicsEMAlignmentAtomic self)"""
2436  return _IMP_multifit.ProteomicsEMAlignmentAtomic_align(self)
2437 
2438  def add_all_restraints(self):
2439  """add_all_restraints(ProteomicsEMAlignmentAtomic self)"""
2440  return _IMP_multifit.ProteomicsEMAlignmentAtomic_add_all_restraints(self)
2441 
2442  def add_states_and_filters(self):
2443  """add_states_and_filters(ProteomicsEMAlignmentAtomic self)"""
2444  return _IMP_multifit.ProteomicsEMAlignmentAtomic_add_states_and_filters(self)
2445 
2446  def show_domino_merge_tree(self):
2447  """show_domino_merge_tree(ProteomicsEMAlignmentAtomic self)"""
2448  return _IMP_multifit.ProteomicsEMAlignmentAtomic_show_domino_merge_tree(self)
2449 
2450  def get_combinations(self, uniques=False):
2451  """
2452  get_combinations(ProteomicsEMAlignmentAtomic self, bool uniques=False) -> IMP::domino::Assignments
2453  get_combinations(ProteomicsEMAlignmentAtomic self) -> IMP::domino::Assignments
2454  """
2455  return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_combinations(self, uniques)
2456 
2457  def set_density_map(self, *args):
2458  """set_density_map(ProteomicsEMAlignmentAtomic self, DensityMap dmap, float threshold)"""
2459  return _IMP_multifit.ProteomicsEMAlignmentAtomic_set_density_map(self, *args)
2460 
2461  def get_molecules(self):
2462  """get_molecules(ProteomicsEMAlignmentAtomic self) -> IMP::atom::Hierarchies"""
2463  return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_molecules(self)
2464 
2465  def get_rigid_bodies(self):
2466  """get_rigid_bodies(ProteomicsEMAlignmentAtomic self) -> IMP::core::RigidBodies"""
2467  return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_rigid_bodies(self)
2468 
2469  def load_combination_of_states(self, *args):
2470  """load_combination_of_states(ProteomicsEMAlignmentAtomic self, IMP::Ints const & state4particles)"""
2471  return _IMP_multifit.ProteomicsEMAlignmentAtomic_load_combination_of_states(self, *args)
2472 
2473  def show_scores_header(self, *args):
2474  """
2475  show_scores_header(ProteomicsEMAlignmentAtomic self, _ostream ous=std::cout)
2476  show_scores_header(ProteomicsEMAlignmentAtomic self)
2477  """
2478  return _IMP_multifit.ProteomicsEMAlignmentAtomic_show_scores_header(self, *args)
2479 
2480  def get_model(self):
2481  """get_model(ProteomicsEMAlignmentAtomic self) -> Model"""
2482  return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_model(self)
2483 
2484  def set_fast_scoring(self, *args):
2485  """set_fast_scoring(ProteomicsEMAlignmentAtomic self, bool state)"""
2486  return _IMP_multifit.ProteomicsEMAlignmentAtomic_set_fast_scoring(self, *args)
2487 
2488  def get_version_info(self):
2489  """get_version_info(ProteomicsEMAlignmentAtomic self) -> VersionInfo"""
2490  return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_version_info(self)
2491 
2492  def __str__(self):
2493  """__str__(ProteomicsEMAlignmentAtomic self) -> std::string"""
2494  return _IMP_multifit.ProteomicsEMAlignmentAtomic___str__(self)
2495 
2496  def __repr__(self):
2497  """__repr__(ProteomicsEMAlignmentAtomic self) -> std::string"""
2498  return _IMP_multifit.ProteomicsEMAlignmentAtomic___repr__(self)
2499 
2500  def get_from(o):
2501  return _object_cast_to_ProteomicsEMAlignmentAtomic(o)
2502  get_from = staticmethod(get_from)
2503 
2504 ProteomicsEMAlignmentAtomic_swigregister = _IMP_multifit.ProteomicsEMAlignmentAtomic_swigregister
2505 ProteomicsEMAlignmentAtomic_swigregister(ProteomicsEMAlignmentAtomic)
2506 
2507 
2508 def write_connolly_surface(*args):
2509  """write_connolly_surface(IMP::atom::Atoms as, TextOutput fn, float density, float probe_radius)"""
2510  return _IMP_multifit.write_connolly_surface(*args)
2511 class Ensemble(IMP.base.Object):
2512  """Proxy of C++ IMP::multifit::Ensemble class"""
2513  __swig_setmethods__ = {}
2514  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2515  __setattr__ = lambda self, name, value: _swig_setattr(self, Ensemble, name, value)
2516  __swig_getmethods__ = {}
2517  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2518  __getattr__ = lambda self, name: _swig_getattr(self, Ensemble, name)
2519  def load_combination(self, *args):
2520  """load_combination(Ensemble self, IMP::Ints fit_comb)"""
2521  return _IMP_multifit.Ensemble_load_combination(self, *args)
2522 
2523  def unload_combination(self, *args):
2524  """unload_combination(Ensemble self, IMP::Ints fit_comb)"""
2525  return _IMP_multifit.Ensemble_unload_combination(self, *args)
2526 
2527  def add_component_and_fits(self, *args):
2528  """add_component_and_fits(Ensemble self, Hierarchy mh, IMP::multifit::FittingSolutionRecords const & fits)"""
2529  return _IMP_multifit.Ensemble_add_component_and_fits(self, *args)
2530 
2531  def get_molecules(self):
2532  """get_molecules(Ensemble self) -> IMP::atom::Hierarchies"""
2533  return _IMP_multifit.Ensemble_get_molecules(self)
2534 
2535  def get_rigid_bodies(self):
2536  """get_rigid_bodies(Ensemble self) -> IMP::core::RigidBodies"""
2537  return _IMP_multifit.Ensemble_get_rigid_bodies(self)
2538 
2539  def get_rmsd(self, *args):
2540  """get_rmsd(Ensemble self, IMP::core::XYZs const & second_xyz) -> float"""
2541  return _IMP_multifit.Ensemble_get_rmsd(self, *args)
2542 
2543  def __init__(self, *args):
2544  """__init__(IMP::multifit::Ensemble self, SettingsData sd, ProteinsAnchorsSamplingSpace mapping_data) -> Ensemble"""
2545  this = _IMP_multifit.new_Ensemble(*args)
2546  try: self.this.append(this)
2547  except: self.this = this
2548  def score_by_restraints(self, *args):
2549  """score_by_restraints(Ensemble self, IMP::kernel::Restraints rs, IMP::IntsList const & combinations) -> std::vector< IMP::Floats,std::allocator< IMP::Floats > >"""
2550  return _IMP_multifit.Ensemble_score_by_restraints(self, *args)
2551 
2552  def get_version_info(self):
2553  """get_version_info(Ensemble self) -> VersionInfo"""
2554  return _IMP_multifit.Ensemble_get_version_info(self)
2555 
2556  def __str__(self):
2557  """__str__(Ensemble self) -> std::string"""
2558  return _IMP_multifit.Ensemble___str__(self)
2559 
2560  def __repr__(self):
2561  """__repr__(Ensemble self) -> std::string"""
2562  return _IMP_multifit.Ensemble___repr__(self)
2563 
2564  def get_from(o):
2565  return _object_cast_to_Ensemble(o)
2566  get_from = staticmethod(get_from)
2567 
2568 Ensemble_swigregister = _IMP_multifit.Ensemble_swigregister
2569 Ensemble_swigregister(Ensemble)
2570 
2571 
2572 def load_ensemble(*args):
2573  """load_ensemble(SettingsData sd, Model mdl, ProteinsAnchorsSamplingSpace mapping_data) -> Ensemble"""
2574  return _IMP_multifit.load_ensemble(*args)
2575 _all_commands = ["param", "anchors", "fit_fft", "cluster", "add_fit_rmsd",
2576  "indexes", "proteomics", "align", "models", "transforms",
2577  "score", "merge_tree", "reference", "refine_fft", "segment"]
2578 
2579 
2580 def get_module_version():
2581  """get_module_version() -> std::string const"""
2582  return _IMP_multifit.get_module_version()
2583 
2584 def get_example_path(*args):
2585  """get_example_path(std::string fname) -> std::string"""
2586  return _IMP_multifit.get_example_path(*args)
2587 
2588 def get_data_path(*args):
2589  """get_data_path(std::string fname) -> std::string"""
2590  return _IMP_multifit.get_data_path(*args)
2591 import _version_check
2592 _version_check.check_version(get_module_version())
2593 
2594 # This file is compatible with both classic and new-style classes.
2595 
2596 
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.
Ints get_index(const kernel::ParticlesTemp &particles, const Subset &subset, const Subsets &excluded)
std::string get_example_path(std::string file_name)
Return the path to installed example data for this module.
atom::Hierarchy create_coarse_molecule_from_density(em::DensityMap *dmap, float dens_threshold, int num_beads, kernel::Model *mdl, float bead_radius)
Coarsen a density map based on voxels clustering.
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.
double get_resolution(kernel::Model *m, kernel::ParticleIndex pi)
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
Definition: exception.h:73
ProteinsAnchorsSamplingSpace get_part_of_sampling_space(const ProteinsAnchorsSamplingSpace &prots_ss, const Strings &prot_names)
Get the sampling space of few of the proteins.
Low level functionality (logging, error handling, profiling, command line flags etc) that is used by ...
std::string get_data_path(std::string file_name)
Return the full path to installed data.
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.
void write_connolly_surface(atom::Atoms as, base::TextOutput fn, float density, float probe_radius)
Write the Connolly surface for a set of atoms to a file.
Base functionality and abstract base classes for representation, scoring and sampling.
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)
A restraint is a term in an IMP ScoringFunction.
double get_radius_of_gyration(const Vector3Ds &ps)
Return the radius of gyration of a set of points.
Definition: Vector3D.h:65
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.
Common base class for heavy weight IMP objects.
Definition: Object.h:106
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.
atom::Hierarchy create_coarse_molecule_from_molecule(const atom::Hierarchy &mh, int num_beads, kernel::Model *mdl, float bead_radius, bool add_conn_restraint=false)
Coarsen a molecule based on atom clustering.
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...
FittingSolutionRecords get_close_to_point(const FittingSolutionRecords &fit_sols, atom::Hierarchy mh, IMP::kernel::Particle *ap, Float dist)
prune solutions by distance to an anchor point
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.
void show(Hierarchy h, std::ostream &out=std::cout)
Print out a molecular hierarchy.
atom::Hierarchies create_coarse_molecules_from_molecules(const atom::Hierarchies &mhs, int frag_len, kernel::Model *mdl, float bead_radius, bool add_conn_restraint=false)
Coarsen molecules based on atom clustering.
Output IMP model data in various file formats.
CheckLevel get_check_level()
Get the current audit mode.
Definition: exception.h:81
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.