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IMP Reference Guide  2.20.0
The Integrative Modeling Platform
saxs/__init__.py
1 # This file was automatically generated by SWIG (https://www.swig.org).
2 # Version 4.1.1
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 # This wrapper is part of IMP,
9 # Copyright 2007-2023 IMP Inventors. All rights reserved.
10 
11 from __future__ import print_function, division, absolute_import
12 
13 
14 
15 from sys import version_info as _swig_python_version_info
16 import _IMP_saxs
17 
18 try:
19  import builtins as __builtin__
20 except ImportError:
21  import __builtin__
22 
23 def _swig_repr(self):
24  try:
25  strthis = "proxy of " + self.this.__repr__()
26  except __builtin__.Exception:
27  strthis = ""
28  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
29 
30 
31 def _swig_setattr_nondynamic_instance_variable(set):
32  def set_instance_attr(self, name, value):
33  if name == "this":
34  set(self, name, value)
35  elif name == "thisown":
36  self.this.own(value)
37  elif hasattr(self, name) and isinstance(getattr(type(self), name), property):
38  set(self, name, value)
39  else:
40  raise AttributeError("You cannot add instance attributes to %s" % self)
41  return set_instance_attr
42 
43 
44 def _swig_setattr_nondynamic_class_variable(set):
45  def set_class_attr(cls, name, value):
46  if hasattr(cls, name) and not isinstance(getattr(cls, name), property):
47  set(cls, name, value)
48  else:
49  raise AttributeError("You cannot add class attributes to %s" % cls)
50  return set_class_attr
51 
52 
53 def _swig_add_metaclass(metaclass):
54  """Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""
55  def wrapper(cls):
56  return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
57  return wrapper
58 
59 
60 class _SwigNonDynamicMeta(type):
61  """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
62  __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
63 
64 
65 import weakref
66 
67 class IMP_SAXS_SwigPyIterator(object):
68  r"""Proxy of C++ swig::IMP_SAXS_SwigPyIterator class."""
69 
70  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
71 
72  def __init__(self, *args, **kwargs):
73  raise AttributeError("No constructor defined - class is abstract")
74  __repr__ = _swig_repr
75  __swig_destroy__ = _IMP_saxs.delete_IMP_SAXS_SwigPyIterator
76 
77  def value(self):
78  r"""value(IMP_SAXS_SwigPyIterator self) -> PyObject *"""
79  return _IMP_saxs.IMP_SAXS_SwigPyIterator_value(self)
80 
81  def incr(self, n=1):
82  r"""incr(IMP_SAXS_SwigPyIterator self, size_t n=1) -> IMP_SAXS_SwigPyIterator"""
83  return _IMP_saxs.IMP_SAXS_SwigPyIterator_incr(self, n)
84 
85  def decr(self, n=1):
86  r"""decr(IMP_SAXS_SwigPyIterator self, size_t n=1) -> IMP_SAXS_SwigPyIterator"""
87  return _IMP_saxs.IMP_SAXS_SwigPyIterator_decr(self, n)
88 
89  def distance(self, x):
90  r"""distance(IMP_SAXS_SwigPyIterator self, IMP_SAXS_SwigPyIterator x) -> ptrdiff_t"""
91  return _IMP_saxs.IMP_SAXS_SwigPyIterator_distance(self, x)
92 
93  def equal(self, x):
94  r"""equal(IMP_SAXS_SwigPyIterator self, IMP_SAXS_SwigPyIterator x) -> bool"""
95  return _IMP_saxs.IMP_SAXS_SwigPyIterator_equal(self, x)
96 
97  def copy(self):
98  r"""copy(IMP_SAXS_SwigPyIterator self) -> IMP_SAXS_SwigPyIterator"""
99  return _IMP_saxs.IMP_SAXS_SwigPyIterator_copy(self)
100 
101  def next(self):
102  r"""next(IMP_SAXS_SwigPyIterator self) -> PyObject *"""
103  return _IMP_saxs.IMP_SAXS_SwigPyIterator_next(self)
104 
105  def __next__(self):
106  r"""__next__(IMP_SAXS_SwigPyIterator self) -> PyObject *"""
107  return _IMP_saxs.IMP_SAXS_SwigPyIterator___next__(self)
108 
109  def previous(self):
110  r"""previous(IMP_SAXS_SwigPyIterator self) -> PyObject *"""
111  return _IMP_saxs.IMP_SAXS_SwigPyIterator_previous(self)
112 
113  def advance(self, n):
114  r"""advance(IMP_SAXS_SwigPyIterator self, ptrdiff_t n) -> IMP_SAXS_SwigPyIterator"""
115  return _IMP_saxs.IMP_SAXS_SwigPyIterator_advance(self, n)
116 
117  def __eq__(self, x):
118  r"""__eq__(IMP_SAXS_SwigPyIterator self, IMP_SAXS_SwigPyIterator x) -> bool"""
119  return _IMP_saxs.IMP_SAXS_SwigPyIterator___eq__(self, x)
120 
121  def __ne__(self, x):
122  r"""__ne__(IMP_SAXS_SwigPyIterator self, IMP_SAXS_SwigPyIterator x) -> bool"""
123  return _IMP_saxs.IMP_SAXS_SwigPyIterator___ne__(self, x)
124 
125  def __iadd__(self, n):
126  r"""__iadd__(IMP_SAXS_SwigPyIterator self, ptrdiff_t n) -> IMP_SAXS_SwigPyIterator"""
127  return _IMP_saxs.IMP_SAXS_SwigPyIterator___iadd__(self, n)
128 
129  def __isub__(self, n):
130  r"""__isub__(IMP_SAXS_SwigPyIterator self, ptrdiff_t n) -> IMP_SAXS_SwigPyIterator"""
131  return _IMP_saxs.IMP_SAXS_SwigPyIterator___isub__(self, n)
132 
133  def __add__(self, n):
134  r"""__add__(IMP_SAXS_SwigPyIterator self, ptrdiff_t n) -> IMP_SAXS_SwigPyIterator"""
135  return _IMP_saxs.IMP_SAXS_SwigPyIterator___add__(self, n)
136 
137  def __sub__(self, *args):
138  r"""
139  __sub__(IMP_SAXS_SwigPyIterator self, ptrdiff_t n) -> IMP_SAXS_SwigPyIterator
140  __sub__(IMP_SAXS_SwigPyIterator self, IMP_SAXS_SwigPyIterator x) -> ptrdiff_t
141  """
142  return _IMP_saxs.IMP_SAXS_SwigPyIterator___sub__(self, *args)
143  def __iter__(self):
144  return self
145 
146 # Register IMP_SAXS_SwigPyIterator in _IMP_saxs:
147 _IMP_saxs.IMP_SAXS_SwigPyIterator_swigregister(IMP_SAXS_SwigPyIterator)
148 
149 _value_types=[]
150 _object_types=[]
151 _raii_types=[]
152 _plural_types=[]
153 
154 IMP_DEBUG = _IMP_saxs.IMP_DEBUG
155 
156 IMP_RELEASE = _IMP_saxs.IMP_RELEASE
157 
158 IMP_SILENT = _IMP_saxs.IMP_SILENT
159 
160 IMP_PROGRESS = _IMP_saxs.IMP_PROGRESS
161 
162 IMP_TERSE = _IMP_saxs.IMP_TERSE
163 
164 IMP_VERBOSE = _IMP_saxs.IMP_VERBOSE
165 
166 IMP_MEMORY = _IMP_saxs.IMP_MEMORY
167 
168 IMP_NONE = _IMP_saxs.IMP_NONE
169 
170 IMP_USAGE = _IMP_saxs.IMP_USAGE
171 
172 IMP_INTERNAL = _IMP_saxs.IMP_INTERNAL
173 
174 IMP_KERNEL_HAS_LOG4CXX = _IMP_saxs.IMP_KERNEL_HAS_LOG4CXX
175 
176 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_saxs.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
177 
178 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_saxs.IMP_COMPILER_HAS_DEBUG_VECTOR
179 
180 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_saxs.IMP_COMPILER_HAS_RANDOM_SHUFFLE
181 
182 IMP_COMPILER_HAS_THREE_WAY = _IMP_saxs.IMP_COMPILER_HAS_THREE_WAY
183 
184 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_saxs.IMP_KERNEL_HAS_BOOST_RANDOM
185 
186 IMP_KERNEL_HAS_NUMPY = _IMP_saxs.IMP_KERNEL_HAS_NUMPY
187 
188 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_saxs.IMP_KERNEL_HAS_GPERFTOOLS
189 
190 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_saxs.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
191 
192 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_saxs.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
193 
194 IMPKERNEL_SHOW_WARNINGS = _IMP_saxs.IMPKERNEL_SHOW_WARNINGS
195 
196 
197 import sys
198 class _DirectorObjects(object):
199  """@internal Simple class to keep references to director objects
200  to prevent premature deletion."""
201  def __init__(self):
202  self._objects = []
203  def register(self, obj):
204  """Take a reference to a director object; will only work for
205  refcounted C++ classes"""
206  if hasattr(obj, 'get_ref_count'):
207  self._objects.append(obj)
208  def cleanup(self):
209  """Only drop our reference and allow cleanup by Python if no other
210  Python references exist (we hold 3 references: one in self._objects,
211  one in x, and one in the argument list for getrefcount) *and* no
212  other C++ references exist (the Python object always holds one)"""
213  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
214  or x.get_ref_count() > 1]
215 # Do in two steps so the references are kept until the end of the
216 # function (deleting references may trigger a fresh call to this method)
217  self._objects = objs
218  def get_object_count(self):
219  """Get number of director objects (useful for testing only)"""
220  return len(self._objects)
221 _director_objects = _DirectorObjects()
222 
223 class _ostream(object):
224  r"""Proxy of C++ std::ostream class."""
225 
226  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
227 
228  def __init__(self, *args, **kwargs):
229  raise AttributeError("No constructor defined")
230  __repr__ = _swig_repr
231 
232  def write(self, osa_buf):
233  r"""write(_ostream self, char const * osa_buf)"""
234  return _IMP_saxs._ostream_write(self, osa_buf)
235 
236 # Register _ostream in _IMP_saxs:
237 _IMP_saxs._ostream_swigregister(_ostream)
238 IMP_C_OPEN_BINARY = _IMP_saxs.IMP_C_OPEN_BINARY
239 
240 import IMP
241 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_saxs.IMP_CGAL_HAS_BOOST_FILESYSTEM
242 
243 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
244 
245 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_saxs.IMP_CGAL_HAS_BOOST_RANDOM
246 
247 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_CGAL_HAS_BOOST_SYSTEM
248 
249 IMP_CGAL_HAS_NUMPY = _IMP_saxs.IMP_CGAL_HAS_NUMPY
250 
251 IMPCGAL_SHOW_WARNINGS = _IMP_saxs.IMPCGAL_SHOW_WARNINGS
252 
253 import IMP.cgal
254 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_saxs.IMP_ALGEBRA_HAS_IMP_CGAL
255 
256 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_saxs.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
257 
258 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
259 
260 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_saxs.IMP_ALGEBRA_HAS_BOOST_RANDOM
261 
262 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_ALGEBRA_HAS_BOOST_SYSTEM
263 
264 IMP_ALGEBRA_HAS_CGAL = _IMP_saxs.IMP_ALGEBRA_HAS_CGAL
265 
266 IMP_ALGEBRA_HAS_NUMPY = _IMP_saxs.IMP_ALGEBRA_HAS_NUMPY
267 
268 IMP_ALGEBRA_HAS_ANN = _IMP_saxs.IMP_ALGEBRA_HAS_ANN
269 
270 IMPALGEBRA_SHOW_WARNINGS = _IMP_saxs.IMPALGEBRA_SHOW_WARNINGS
271 
272 import IMP.algebra
273 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_saxs.IMP_DISPLAY_HAS_IMP_CGAL
274 
275 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_saxs.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
276 
277 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
278 
279 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_saxs.IMP_DISPLAY_HAS_BOOST_RANDOM
280 
281 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_DISPLAY_HAS_BOOST_SYSTEM
282 
283 IMP_DISPLAY_HAS_CGAL = _IMP_saxs.IMP_DISPLAY_HAS_CGAL
284 
285 IMP_DISPLAY_HAS_NUMPY = _IMP_saxs.IMP_DISPLAY_HAS_NUMPY
286 
287 IMPDISPLAY_SHOW_WARNINGS = _IMP_saxs.IMPDISPLAY_SHOW_WARNINGS
288 
289 import IMP.display
290 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_saxs.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
291 
292 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_saxs.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
293 
294 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
295 
296 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_saxs.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
297 
298 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
299 
300 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_saxs.IMP_SCORE_FUNCTOR_HAS_CGAL
301 
302 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_saxs.IMP_SCORE_FUNCTOR_HAS_HDF5
303 
304 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_saxs.IMP_SCORE_FUNCTOR_HAS_NUMPY
305 
306 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_saxs.IMPSCOREFUNCTOR_SHOW_WARNINGS
307 
308 import IMP.score_functor
309 IMP_CORE_HAS_IMP_CGAL = _IMP_saxs.IMP_CORE_HAS_IMP_CGAL
310 
311 IMP_CORE_HAS_IMP_KERNEL = _IMP_saxs.IMP_CORE_HAS_IMP_KERNEL
312 
313 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_saxs.IMP_CORE_HAS_BOOST_FILESYSTEM
314 
315 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
316 
317 IMP_CORE_HAS_BOOST_RANDOM = _IMP_saxs.IMP_CORE_HAS_BOOST_RANDOM
318 
319 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_CORE_HAS_BOOST_SYSTEM
320 
321 IMP_CORE_HAS_CGAL = _IMP_saxs.IMP_CORE_HAS_CGAL
322 
323 IMP_CORE_HAS_HDF5 = _IMP_saxs.IMP_CORE_HAS_HDF5
324 
325 IMP_CORE_HAS_NUMPY = _IMP_saxs.IMP_CORE_HAS_NUMPY
326 
327 IMPCORE_SHOW_WARNINGS = _IMP_saxs.IMPCORE_SHOW_WARNINGS
328 
329 import IMP.core
330 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_saxs.IMP_CONTAINER_HAS_IMP_ALGEBRA
331 
332 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_saxs.IMP_CONTAINER_HAS_IMP_CGAL
333 
334 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_saxs.IMP_CONTAINER_HAS_IMP_DISPLAY
335 
336 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_saxs.IMP_CONTAINER_HAS_IMP_KERNEL
337 
338 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_saxs.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
339 
340 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_saxs.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
341 
342 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
343 
344 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_saxs.IMP_CONTAINER_HAS_BOOST_RANDOM
345 
346 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_CONTAINER_HAS_BOOST_SYSTEM
347 
348 IMP_CONTAINER_HAS_CGAL = _IMP_saxs.IMP_CONTAINER_HAS_CGAL
349 
350 IMP_CONTAINER_HAS_HDF5 = _IMP_saxs.IMP_CONTAINER_HAS_HDF5
351 
352 IMP_CONTAINER_HAS_NUMPY = _IMP_saxs.IMP_CONTAINER_HAS_NUMPY
353 
354 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_saxs.IMP_CONTAINER_HAS_PYTHON_IHM
355 
356 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_saxs.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
357 
358 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_saxs.IMP_CONTAINER_HAS_ROBIN_MAP
359 
360 IMPCONTAINER_SHOW_WARNINGS = _IMP_saxs.IMPCONTAINER_SHOW_WARNINGS
361 
362 import IMP.container
363 IMP_ATOM_HAS_IMP_CGAL = _IMP_saxs.IMP_ATOM_HAS_IMP_CGAL
364 
365 IMP_ATOM_HAS_IMP_KERNEL = _IMP_saxs.IMP_ATOM_HAS_IMP_KERNEL
366 
367 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_saxs.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
368 
369 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
370 
371 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_saxs.IMP_ATOM_HAS_BOOST_RANDOM
372 
373 IMP_ATOM_HAS_BOOST_REGEX = _IMP_saxs.IMP_ATOM_HAS_BOOST_REGEX
374 
375 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_ATOM_HAS_BOOST_SYSTEM
376 
377 IMP_ATOM_HAS_CGAL = _IMP_saxs.IMP_ATOM_HAS_CGAL
378 
379 IMP_ATOM_HAS_HDF5 = _IMP_saxs.IMP_ATOM_HAS_HDF5
380 
381 IMP_ATOM_HAS_NUMPY = _IMP_saxs.IMP_ATOM_HAS_NUMPY
382 
383 IMP_ATOM_HAS_PYTHON_IHM = _IMP_saxs.IMP_ATOM_HAS_PYTHON_IHM
384 
385 IMPATOM_SHOW_WARNINGS = _IMP_saxs.IMPATOM_SHOW_WARNINGS
386 
387 IMP_ATOM_TYPE_INDEX = _IMP_saxs.IMP_ATOM_TYPE_INDEX
388 
389 IMP_RESIDUE_TYPE_INDEX = _IMP_saxs.IMP_RESIDUE_TYPE_INDEX
390 
391 IMP_HIERARCHY_TYPE_INDEX = _IMP_saxs.IMP_HIERARCHY_TYPE_INDEX
392 
393 IMP_CHAIN_TYPE_INDEX = _IMP_saxs.IMP_CHAIN_TYPE_INDEX
394 
395 import IMP.atom
396 IMP_SAXS_HAS_IMP_CGAL = _IMP_saxs.IMP_SAXS_HAS_IMP_CGAL
397 
398 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_saxs.IMP_SAXS_HAS_IMP_CONTAINER
399 
400 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_saxs.IMP_SAXS_HAS_IMP_DISPLAY
401 
402 IMP_SAXS_HAS_IMP_KERNEL = _IMP_saxs.IMP_SAXS_HAS_IMP_KERNEL
403 
404 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_saxs.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
405 
406 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_saxs.IMP_SAXS_HAS_BOOST_FILESYSTEM
407 
408 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
409 
410 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_saxs.IMP_SAXS_HAS_BOOST_RANDOM
411 
412 IMP_SAXS_HAS_BOOST_REGEX = _IMP_saxs.IMP_SAXS_HAS_BOOST_REGEX
413 
414 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_SAXS_HAS_BOOST_SYSTEM
415 
416 IMP_SAXS_HAS_CGAL = _IMP_saxs.IMP_SAXS_HAS_CGAL
417 
418 IMP_SAXS_HAS_HDF5 = _IMP_saxs.IMP_SAXS_HAS_HDF5
419 
420 IMP_SAXS_HAS_NUMPY = _IMP_saxs.IMP_SAXS_HAS_NUMPY
421 
422 IMP_SAXS_HAS_PYTHON_IHM = _IMP_saxs.IMP_SAXS_HAS_PYTHON_IHM
423 
424 IMPSAXS_SHOW_WARNINGS = _IMP_saxs.IMPSAXS_SHOW_WARNINGS
425 
426 class DistBase(object):
427  r"""Proxy of C++ std::vector< double > class."""
428 
429  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
430  __repr__ = _swig_repr
431 
432  def iterator(self):
433  r"""iterator(DistBase self) -> IMP_SAXS_SwigPyIterator"""
434  return _IMP_saxs.DistBase_iterator(self)
435  def __iter__(self):
436  return self.iterator()
437 
438  def __nonzero__(self):
439  r"""__nonzero__(DistBase self) -> bool"""
440  return _IMP_saxs.DistBase___nonzero__(self)
441 
442  def __bool__(self):
443  r"""__bool__(DistBase self) -> bool"""
444  return _IMP_saxs.DistBase___bool__(self)
445 
446  def __len__(self):
447  r"""__len__(DistBase self) -> std::vector< double >::size_type"""
448  return _IMP_saxs.DistBase___len__(self)
449 
450  def __getslice__(self, i, j):
451  r"""__getslice__(DistBase self, std::vector< double >::difference_type i, std::vector< double >::difference_type j) -> DistBase"""
452  return _IMP_saxs.DistBase___getslice__(self, i, j)
453 
454  def __setslice__(self, *args):
455  r"""
456  __setslice__(DistBase self, std::vector< double >::difference_type i, std::vector< double >::difference_type j)
457  __setslice__(DistBase self, std::vector< double >::difference_type i, std::vector< double >::difference_type j, DistBase v)
458  """
459  return _IMP_saxs.DistBase___setslice__(self, *args)
460 
461  def __delslice__(self, i, j):
462  r"""__delslice__(DistBase self, std::vector< double >::difference_type i, std::vector< double >::difference_type j)"""
463  return _IMP_saxs.DistBase___delslice__(self, i, j)
464 
465  def __delitem__(self, *args):
466  r"""
467  __delitem__(DistBase self, std::vector< double >::difference_type i)
468  __delitem__(DistBase self, SWIGPY_SLICEOBJECT * slice)
469  """
470  return _IMP_saxs.DistBase___delitem__(self, *args)
471 
472  def __getitem__(self, *args):
473  r"""
474  __getitem__(DistBase self, SWIGPY_SLICEOBJECT * slice) -> DistBase
475  __getitem__(DistBase self, std::vector< double >::difference_type i) -> std::vector< double >::value_type const &
476  """
477  return _IMP_saxs.DistBase___getitem__(self, *args)
478 
479  def __setitem__(self, *args):
480  r"""
481  __setitem__(DistBase self, SWIGPY_SLICEOBJECT * slice, DistBase v)
482  __setitem__(DistBase self, SWIGPY_SLICEOBJECT * slice)
483  __setitem__(DistBase self, std::vector< double >::difference_type i, std::vector< double >::value_type const & x)
484  """
485  return _IMP_saxs.DistBase___setitem__(self, *args)
486 
487  def pop(self):
488  r"""pop(DistBase self) -> std::vector< double >::value_type"""
489  return _IMP_saxs.DistBase_pop(self)
490 
491  def append(self, x):
492  r"""append(DistBase self, std::vector< double >::value_type const & x)"""
493  return _IMP_saxs.DistBase_append(self, x)
494 
495  def empty(self):
496  r"""empty(DistBase self) -> bool"""
497  return _IMP_saxs.DistBase_empty(self)
498 
499  def size(self):
500  r"""size(DistBase self) -> std::vector< double >::size_type"""
501  return _IMP_saxs.DistBase_size(self)
502 
503  def swap(self, v):
504  r"""swap(DistBase self, DistBase v)"""
505  return _IMP_saxs.DistBase_swap(self, v)
506 
507  def begin(self):
508  r"""begin(DistBase self) -> std::vector< double >::iterator"""
509  return _IMP_saxs.DistBase_begin(self)
510 
511  def end(self):
512  r"""end(DistBase self) -> std::vector< double >::iterator"""
513  return _IMP_saxs.DistBase_end(self)
514 
515  def rbegin(self):
516  r"""rbegin(DistBase self) -> std::vector< double >::reverse_iterator"""
517  return _IMP_saxs.DistBase_rbegin(self)
518 
519  def rend(self):
520  r"""rend(DistBase self) -> std::vector< double >::reverse_iterator"""
521  return _IMP_saxs.DistBase_rend(self)
522 
523  def clear(self):
524  r"""clear(DistBase self)"""
525  return _IMP_saxs.DistBase_clear(self)
526 
527  def get_allocator(self):
528  r"""get_allocator(DistBase self) -> std::vector< double >::allocator_type"""
529  return _IMP_saxs.DistBase_get_allocator(self)
530 
531  def pop_back(self):
532  r"""pop_back(DistBase self)"""
533  return _IMP_saxs.DistBase_pop_back(self)
534 
535  def erase(self, *args):
536  r"""
537  erase(DistBase self, std::vector< double >::iterator pos) -> std::vector< double >::iterator
538  erase(DistBase self, std::vector< double >::iterator first, std::vector< double >::iterator last) -> std::vector< double >::iterator
539  """
540  return _IMP_saxs.DistBase_erase(self, *args)
541 
542  def __init__(self, *args):
543  r"""
544  __init__(DistBase self) -> DistBase
545  __init__(DistBase self, DistBase other) -> DistBase
546  __init__(DistBase self, std::vector< double >::size_type size) -> DistBase
547  __init__(DistBase self, std::vector< double >::size_type size, std::vector< double >::value_type const & value) -> DistBase
548  """
549  _IMP_saxs.DistBase_swiginit(self, _IMP_saxs.new_DistBase(*args))
550 
551  def push_back(self, x):
552  r"""push_back(DistBase self, std::vector< double >::value_type const & x)"""
553  return _IMP_saxs.DistBase_push_back(self, x)
554 
555  def front(self):
556  r"""front(DistBase self) -> std::vector< double >::value_type const &"""
557  return _IMP_saxs.DistBase_front(self)
558 
559  def back(self):
560  r"""back(DistBase self) -> std::vector< double >::value_type const &"""
561  return _IMP_saxs.DistBase_back(self)
562 
563  def assign(self, n, x):
564  r"""assign(DistBase self, std::vector< double >::size_type n, std::vector< double >::value_type const & x)"""
565  return _IMP_saxs.DistBase_assign(self, n, x)
566 
567  def resize(self, *args):
568  r"""
569  resize(DistBase self, std::vector< double >::size_type new_size)
570  resize(DistBase self, std::vector< double >::size_type new_size, std::vector< double >::value_type const & x)
571  """
572  return _IMP_saxs.DistBase_resize(self, *args)
573 
574  def insert(self, *args):
575  r"""
576  insert(DistBase self, std::vector< double >::iterator pos, std::vector< double >::value_type const & x) -> std::vector< double >::iterator
577  insert(DistBase self, std::vector< double >::iterator pos, std::vector< double >::size_type n, std::vector< double >::value_type const & x)
578  """
579  return _IMP_saxs.DistBase_insert(self, *args)
580 
581  def reserve(self, n):
582  r"""reserve(DistBase self, std::vector< double >::size_type n)"""
583  return _IMP_saxs.DistBase_reserve(self, n)
584 
585  def capacity(self):
586  r"""capacity(DistBase self) -> std::vector< double >::size_type"""
587  return _IMP_saxs.DistBase_capacity(self)
588  __swig_destroy__ = _IMP_saxs.delete_DistBase
589 
590 # Register DistBase in _IMP_saxs:
591 _IMP_saxs.DistBase_swigregister(DistBase)
592 
593 _object_types.append("Profile")
594 
595 
596 def _object_cast_to_Profile(o):
597  r"""_object_cast_to_Profile(Object o) -> Profile"""
598  return _IMP_saxs._object_cast_to_Profile(o)
599 
600 _object_types.append("ChiScore")
601 
602 
603 def _object_cast_to_ChiScore(o):
604  r"""_object_cast_to_ChiScore(Object o) -> ChiScore"""
605  return _IMP_saxs._object_cast_to_ChiScore(o)
606 
607 _object_types.append("ChiScoreLog")
608 
609 
610 def _object_cast_to_ChiScoreLog(o):
611  r"""_object_cast_to_ChiScoreLog(Object o) -> ChiScoreLog"""
612  return _IMP_saxs._object_cast_to_ChiScoreLog(o)
613 
614 _object_types.append("Restraint")
615 
616 ALL_ATOMS = _IMP_saxs.ALL_ATOMS
617 
618 HEAVY_ATOMS = _IMP_saxs.HEAVY_ATOMS
619 
620 CA_ATOMS = _IMP_saxs.CA_ATOMS
621 
622 RESIDUES = _IMP_saxs.RESIDUES
623 
624 class FormFactorTable(object):
625  r"""Proxy of C++ IMP::saxs::FormFactorTable class."""
626 
627  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
628  __repr__ = _swig_repr
629 
630  def __init__(self, *args):
631  r"""
632  __init__(FormFactorTable self) -> FormFactorTable
633  __init__(FormFactorTable self, std::string const & table_name, double min_q, double max_q, double delta_q) -> FormFactorTable
634  """
635  _IMP_saxs.FormFactorTable_swiginit(self, _IMP_saxs.new_FormFactorTable(*args))
636 
637  def get_form_factor(self, *args):
638  r"""get_form_factor(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS) -> double"""
639  return _IMP_saxs.FormFactorTable_get_form_factor(self, *args)
640 
641  def get_vacuum_form_factor(self, *args):
642  r"""get_vacuum_form_factor(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS) -> double"""
643  return _IMP_saxs.FormFactorTable_get_vacuum_form_factor(self, *args)
644 
645  def get_dummy_form_factor(self, *args):
646  r"""get_dummy_form_factor(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS) -> double"""
647  return _IMP_saxs.FormFactorTable_get_dummy_form_factor(self, *args)
648 
649  def get_water_form_factor(self):
650  r"""get_water_form_factor(FormFactorTable self) -> double"""
651  return _IMP_saxs.FormFactorTable_get_water_form_factor(self)
652 
653  def get_vacuum_water_form_factor(self):
654  r"""get_vacuum_water_form_factor(FormFactorTable self) -> double"""
655  return _IMP_saxs.FormFactorTable_get_vacuum_water_form_factor(self)
656 
657  def get_dummy_water_form_factor(self):
658  r"""get_dummy_water_form_factor(FormFactorTable self) -> double"""
659  return _IMP_saxs.FormFactorTable_get_dummy_water_form_factor(self)
660 
661  def get_form_factors(self, *args):
662  r"""get_form_factors(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS) -> IMP::Vector< double > const"""
663  return _IMP_saxs.FormFactorTable_get_form_factors(self, *args)
664 
665  def get_vacuum_form_factors(self, *args):
666  r"""get_vacuum_form_factors(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS) -> IMP::Vector< double > const"""
667  return _IMP_saxs.FormFactorTable_get_vacuum_form_factors(self, *args)
668 
669  def get_dummy_form_factors(self, *args):
670  r"""get_dummy_form_factors(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS) -> IMP::Vector< double > const"""
671  return _IMP_saxs.FormFactorTable_get_dummy_form_factors(self, *args)
672 
673  def get_water_form_factors(self):
674  r"""get_water_form_factors(FormFactorTable self) -> IMP::Vector< double > const &"""
675  return _IMP_saxs.FormFactorTable_get_water_form_factors(self)
676 
677  def get_water_vacuum_form_factors(self):
678  r"""get_water_vacuum_form_factors(FormFactorTable self) -> IMP::Vector< double > const &"""
679  return _IMP_saxs.FormFactorTable_get_water_vacuum_form_factors(self)
680 
681  def get_water_dummy_form_factors(self):
682  r"""get_water_dummy_form_factors(FormFactorTable self) -> IMP::Vector< double > const &"""
683  return _IMP_saxs.FormFactorTable_get_water_dummy_form_factors(self)
684 
685  def get_radius(self, *args):
686  r"""get_radius(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS) -> double"""
687  return _IMP_saxs.FormFactorTable_get_radius(self, *args)
688 
689  def get_volume(self, *args):
690  r"""get_volume(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS) -> double"""
691  return _IMP_saxs.FormFactorTable_get_volume(self, *args)
692 
693  def show(self, *args):
694  r"""show(FormFactorTable self, _ostream out=std::cout, std::string prefix="")"""
695  return _IMP_saxs.FormFactorTable_show(self, *args)
696  rho_ = property(_IMP_saxs.FormFactorTable_rho__get, _IMP_saxs.FormFactorTable_rho__set, doc=r"""rho_ : double""")
697  __swig_destroy__ = _IMP_saxs.delete_FormFactorTable
698 
699 # Register FormFactorTable in _IMP_saxs:
700 _IMP_saxs.FormFactorTable_swigregister(FormFactorTable)
701 cvar = _IMP_saxs.cvar
702 
703 
705  r"""get_default_form_factor_table() -> FormFactorTable"""
706  return _IMP_saxs.get_default_form_factor_table()
707 class Profile(IMP.Object):
708  r"""Proxy of C++ IMP::saxs::Profile class."""
709 
710  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
711 
712  def __init__(self, *args):
713  r"""
714  __init__(Profile self, std::string const & file_name, bool fit_file=False, double max_q=0.0, int units=1) -> Profile
715  __init__(Profile self, double qmin=0.0, double qmax=0.5, double delta=0.005) -> Profile
716  """
717  _IMP_saxs.Profile_swiginit(self, _IMP_saxs.new_Profile(*args))
718 
719  def calculate_profile_partial(self, *args):
720  r"""
721  calculate_profile_partial(Profile self, IMP::Particles const & particles, IMP::Vector< double > const & surface=IMP::Vector< double >(), IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS)
722  calculate_profile_partial(Profile self, IMP::Particles const & particles1, IMP::Particles const & particles2, IMP::Vector< double > const & surface1=IMP::Vector< double >(), IMP::Vector< double > const & surface2=IMP::Vector< double >(), IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS)
723  """
724  return _IMP_saxs.Profile_calculate_profile_partial(self, *args)
725 
726  def calculate_profile_reciprocal_partial(self, *args):
727  r"""calculate_profile_reciprocal_partial(Profile self, IMP::Particles const & particles, IMP::Vector< double > const & surface=IMP::Vector< double >(), IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS)"""
728  return _IMP_saxs.Profile_calculate_profile_reciprocal_partial(self, *args)
729 
730  def calculate_profile(self, *args):
731  r"""
732  calculate_profile(Profile self, IMP::Particles const & particles, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS, bool reciprocal=False)
733  calculate_profile(Profile self, IMP::Particles const & particles1, IMP::Particles const & particles2, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS)
734  """
735  return _IMP_saxs.Profile_calculate_profile(self, *args)
736 
737  def calculate_I0(self, *args):
738  r"""calculate_I0(Profile self, IMP::Particles const & particles, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS) -> double"""
739  return _IMP_saxs.Profile_calculate_I0(self, *args)
740 
741  def calculate_profile_constant_form_factor(self, particles, form_factor=1.0):
742  r"""calculate_profile_constant_form_factor(Profile self, IMP::Particles const & particles, double form_factor=1.0)"""
743  return _IMP_saxs.Profile_calculate_profile_constant_form_factor(self, particles, form_factor)
744 
745  def calculate_profile_symmetric(self, *args):
746  r"""calculate_profile_symmetric(Profile self, IMP::Particles const & particles, unsigned int n, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS)"""
747  return _IMP_saxs.Profile_calculate_profile_symmetric(self, *args)
748 
749  def profile_2_distribution(self, rd, max_distance):
750  r"""profile_2_distribution(Profile self, RadialDistributionFunction rd, double max_distance)"""
751  return _IMP_saxs.Profile_profile_2_distribution(self, rd, max_distance)
752 
753  def distribution_2_profile(self, r_dist):
754  r"""distribution_2_profile(Profile self, RadialDistributionFunction r_dist)"""
755  return _IMP_saxs.Profile_distribution_2_profile(self, r_dist)
756 
757  def resample(self, exp_profile, resampled_profile):
758  r"""resample(Profile self, Profile exp_profile, Profile resampled_profile)"""
759  return _IMP_saxs.Profile_resample(self, exp_profile, resampled_profile)
760 
761  def downsample(self, downsampled_profile, point_number):
762  r"""downsample(Profile self, Profile downsampled_profile, unsigned int point_number)"""
763  return _IMP_saxs.Profile_downsample(self, downsampled_profile, point_number)
764 
765  def radius_of_gyration(self, end_q_rg=1.3):
766  r"""radius_of_gyration(Profile self, double end_q_rg=1.3) -> double"""
767  return _IMP_saxs.Profile_radius_of_gyration(self, end_q_rg)
768 
769  def mean_intensity(self):
770  r"""mean_intensity(Profile self) -> double"""
771  return _IMP_saxs.Profile_mean_intensity(self)
772 
773  def read_SAXS_file(self, file_name, fit_file=False, max_q=0.0, units=1):
774  r"""read_SAXS_file(Profile self, std::string const & file_name, bool fit_file=False, double max_q=0.0, int units=1)"""
775  return _IMP_saxs.Profile_read_SAXS_file(self, file_name, fit_file, max_q, units)
776 
777  def write_SAXS_file(self, file_name, max_q=0.0):
778  r"""write_SAXS_file(Profile self, std::string const & file_name, double max_q=0.0)"""
779  return _IMP_saxs.Profile_write_SAXS_file(self, file_name, max_q)
780 
781  def read_partial_profiles(self, file_name):
782  r"""read_partial_profiles(Profile self, std::string const & file_name)"""
783  return _IMP_saxs.Profile_read_partial_profiles(self, file_name)
784 
785  def write_partial_profiles(self, file_name):
786  r"""write_partial_profiles(Profile self, std::string const & file_name)"""
787  return _IMP_saxs.Profile_write_partial_profiles(self, file_name)
788 
789  def get_delta_q(self):
790  r"""get_delta_q(Profile self) -> double"""
791  return _IMP_saxs.Profile_get_delta_q(self)
792 
793  def get_min_q(self):
794  r"""get_min_q(Profile self) -> double"""
795  return _IMP_saxs.Profile_get_min_q(self)
796 
797  def get_max_q(self):
798  r"""get_max_q(Profile self) -> double"""
799  return _IMP_saxs.Profile_get_max_q(self)
800 
801  def get_intensity(self, i):
802  r"""get_intensity(Profile self, unsigned int i) -> double"""
803  return _IMP_saxs.Profile_get_intensity(self, i)
804 
805  def get_q(self, i):
806  r"""get_q(Profile self, unsigned int i) -> double"""
807  return _IMP_saxs.Profile_get_q(self, i)
808 
809  def get_error(self, i):
810  r"""get_error(Profile self, unsigned int i) -> double"""
811  return _IMP_saxs.Profile_get_error(self, i)
812 
813  def get_weight(self, i):
814  r"""get_weight(Profile self, unsigned int i) -> double"""
815  return _IMP_saxs.Profile_get_weight(self, i)
816 
817  def get_qs(self):
818  r"""get_qs(Profile self) -> Eigen::VectorXf const &"""
819  return _IMP_saxs.Profile_get_qs(self)
820 
821  def get_intensities(self):
822  r"""get_intensities(Profile self) -> Eigen::VectorXf const &"""
823  return _IMP_saxs.Profile_get_intensities(self)
824 
825  def get_errors(self):
826  r"""get_errors(Profile self) -> Eigen::VectorXf const &"""
827  return _IMP_saxs.Profile_get_errors(self)
828 
829  def get_average_radius(self):
830  r"""get_average_radius(Profile self) -> double"""
831  return _IMP_saxs.Profile_get_average_radius(self)
832 
833  def size(self):
834  r"""size(Profile self) -> unsigned int"""
835  return _IMP_saxs.Profile_size(self)
836 
837  def is_uniform_sampling(self):
838  r"""is_uniform_sampling(Profile self) -> bool"""
839  return _IMP_saxs.Profile_is_uniform_sampling(self)
840 
841  def is_partial_profile(self):
842  r"""is_partial_profile(Profile self) -> bool"""
843  return _IMP_saxs.Profile_is_partial_profile(self)
844 
845  def get_name(self):
846  r"""get_name(Profile self) -> std::string"""
847  return _IMP_saxs.Profile_get_name(self)
848 
849  def get_id(self):
850  r"""get_id(Profile self) -> unsigned int"""
851  return _IMP_saxs.Profile_get_id(self)
852 
853  def set_qs(self, q):
854  r"""set_qs(Profile self, Eigen::VectorXf const & q)"""
855  return _IMP_saxs.Profile_set_qs(self, q)
856 
857  def set_intensities(self, i):
858  r"""set_intensities(Profile self, Eigen::VectorXf const & i)"""
859  return _IMP_saxs.Profile_set_intensities(self, i)
860 
861  def set_errors(self, e):
862  r"""set_errors(Profile self, Eigen::VectorXf const & e)"""
863  return _IMP_saxs.Profile_set_errors(self, e)
864 
865  def set_intensity(self, i, iq):
866  r"""set_intensity(Profile self, unsigned int i, double iq)"""
867  return _IMP_saxs.Profile_set_intensity(self, i, iq)
868 
869  def set_ff_table(self, ff_table):
870  r"""set_ff_table(Profile self, FormFactorTable ff_table)"""
871  return _IMP_saxs.Profile_set_ff_table(self, ff_table)
872 
873  def set_average_radius(self, r):
874  r"""set_average_radius(Profile self, double r)"""
875  return _IMP_saxs.Profile_set_average_radius(self, r)
876 
877  def set_average_volume(self, v):
878  r"""set_average_volume(Profile self, double v)"""
879  return _IMP_saxs.Profile_set_average_volume(self, v)
880 
881  def set_name(self, name):
882  r"""set_name(Profile self, std::string name)"""
883  return _IMP_saxs.Profile_set_name(self, name)
884 
885  def set_id(self, id):
886  r"""set_id(Profile self, unsigned int id)"""
887  return _IMP_saxs.Profile_set_id(self, id)
888 
889  def set_beam_profile(self, beam_profile_file):
890  r"""set_beam_profile(Profile self, std::string beam_profile_file)"""
891  return _IMP_saxs.Profile_set_beam_profile(self, beam_profile_file)
892 
893  def add_errors(self):
894  r"""add_errors(Profile self)"""
895  return _IMP_saxs.Profile_add_errors(self)
896 
897  def add_noise(self, percentage=0.03):
898  r"""add_noise(Profile self, double percentage=0.03)"""
899  return _IMP_saxs.Profile_add_noise(self, percentage)
900 
901  def sum_partial_profiles(self, c1, c2, check_cashed=True):
902  r"""sum_partial_profiles(Profile self, double c1, double c2, bool check_cashed=True)"""
903  return _IMP_saxs.Profile_sum_partial_profiles(self, c1, c2, check_cashed)
904 
905  def add(self, *args):
906  r"""
907  add(Profile self, Profile other_profile, double weight=1.0)
908  add(Profile self, IMP::Vector< IMP::saxs::Profile * > const & profiles, IMP::Vector< double > const & weights=IMP::Vector< double >())
909  """
910  return _IMP_saxs.Profile_add(self, *args)
911 
912  def add_partial_profiles(self, *args):
913  r"""
914  add_partial_profiles(Profile self, Profile other_profile, double weight=1.0)
915  add_partial_profiles(Profile self, IMP::Vector< IMP::saxs::Profile * > const & profiles, IMP::Vector< double > const & weights=IMP::Vector< double >())
916  """
917  return _IMP_saxs.Profile_add_partial_profiles(self, *args)
918 
919  def background_adjust(self, start_q):
920  r"""background_adjust(Profile self, double start_q)"""
921  return _IMP_saxs.Profile_background_adjust(self, start_q)
922 
923  def scale(self, c):
924  r"""scale(Profile self, double c)"""
925  return _IMP_saxs.Profile_scale(self, c)
926 
927  def offset(self, c):
928  r"""offset(Profile self, double c)"""
929  return _IMP_saxs.Profile_offset(self, c)
930 
931  def copy_errors(self, exp_profile):
932  r"""copy_errors(Profile self, Profile exp_profile)"""
933  return _IMP_saxs.Profile_copy_errors(self, exp_profile)
934 
935  def get_version_info(self):
936  r"""get_version_info(Profile self) -> VersionInfo"""
937  return _IMP_saxs.Profile_get_version_info(self)
938  __swig_destroy__ = _IMP_saxs.delete_Profile
939 
940  def __str__(self):
941  r"""__str__(Profile self) -> std::string"""
942  return _IMP_saxs.Profile___str__(self)
943 
944  def __repr__(self):
945  r"""__repr__(Profile self) -> std::string"""
946  return _IMP_saxs.Profile___repr__(self)
947 
948  @staticmethod
949  def get_from(o):
950  return _object_cast_to_Profile(o)
951 
952 
953  def _get_as_binary(self):
954  r"""_get_as_binary(Profile self) -> PyObject *"""
955  return _IMP_saxs.Profile__get_as_binary(self)
956 
957  def _set_from_binary(self, p):
958  r"""_set_from_binary(Profile self, PyObject * p)"""
959  return _IMP_saxs.Profile__set_from_binary(self, p)
960 
961  def __getstate__(self):
962  p = self._get_as_binary()
963  if len(self.__dict__) > 1:
964  d = self.__dict__.copy()
965  del d['this']
966  p = (d, p)
967  return p
968 
969  def __setstate__(self, p):
970  if not hasattr(self, 'this'):
971  self.__init__()
972  if isinstance(p, tuple):
973  d, p = p
974  self.__dict__.update(d)
975  return self._set_from_binary(p)
976 
977 
978 # Register Profile in _IMP_saxs:
979 _IMP_saxs.Profile_swigregister(Profile)
980 Profile.modulation_function_parameter_ = _IMP_saxs.cvar.Profile_modulation_function_parameter_
981 
982 class FitParameters(object):
983  r"""Proxy of C++ IMP::saxs::FitParameters class."""
984 
985  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
986  __repr__ = _swig_repr
987 
988  def __init__(self, *args):
989  r"""
990  __init__(FitParameters self) -> FitParameters
991  __init__(FitParameters self, double chi_square, double c1, double c2, double c, double o) -> FitParameters
992  __init__(FitParameters self, double chi_square, double c1, double c2) -> FitParameters
993  """
994  _IMP_saxs.FitParameters_swiginit(self, _IMP_saxs.new_FitParameters(*args))
995 
996  def get_score(self):
997  r"""get_score(FitParameters self) -> double"""
998  return _IMP_saxs.FitParameters_get_score(self)
999 
1000  def get_chi_square(self):
1001  r"""get_chi_square(FitParameters self) -> double"""
1002  return _IMP_saxs.FitParameters_get_chi_square(self)
1003 
1004  def get_c1(self):
1005  r"""get_c1(FitParameters self) -> double"""
1006  return _IMP_saxs.FitParameters_get_c1(self)
1007 
1008  def get_c2(self):
1009  r"""get_c2(FitParameters self) -> double"""
1010  return _IMP_saxs.FitParameters_get_c2(self)
1011 
1012  def get_scale(self):
1013  r"""get_scale(FitParameters self) -> double"""
1014  return _IMP_saxs.FitParameters_get_scale(self)
1015 
1016  def get_offset(self):
1017  r"""get_offset(FitParameters self) -> double"""
1018  return _IMP_saxs.FitParameters_get_offset(self)
1019 
1020  def get_default_chi_square(self):
1021  r"""get_default_chi_square(FitParameters self) -> double"""
1022  return _IMP_saxs.FitParameters_get_default_chi_square(self)
1023 
1024  def get_pdb_file_name(self):
1025  r"""get_pdb_file_name(FitParameters self) -> std::string"""
1026  return _IMP_saxs.FitParameters_get_pdb_file_name(self)
1027 
1028  def get_profile_file_name(self):
1029  r"""get_profile_file_name(FitParameters self) -> std::string"""
1030  return _IMP_saxs.FitParameters_get_profile_file_name(self)
1031 
1032  def get_mol_index(self):
1033  r"""get_mol_index(FitParameters self) -> int"""
1034  return _IMP_saxs.FitParameters_get_mol_index(self)
1035 
1036  def set_score(self, score):
1037  r"""set_score(FitParameters self, double score)"""
1038  return _IMP_saxs.FitParameters_set_score(self, score)
1039 
1040  def set_chi_square(self, chi_square):
1041  r"""set_chi_square(FitParameters self, double chi_square)"""
1042  return _IMP_saxs.FitParameters_set_chi_square(self, chi_square)
1043 
1044  def set_default_chi_square(self, chi_square):
1045  r"""set_default_chi_square(FitParameters self, double chi_square)"""
1046  return _IMP_saxs.FitParameters_set_default_chi_square(self, chi_square)
1047 
1048  def set_profile_file_name(self, file_name):
1049  r"""set_profile_file_name(FitParameters self, std::string file_name)"""
1050  return _IMP_saxs.FitParameters_set_profile_file_name(self, file_name)
1051 
1052  def set_pdb_file_name(self, file_name):
1053  r"""set_pdb_file_name(FitParameters self, std::string file_name)"""
1054  return _IMP_saxs.FitParameters_set_pdb_file_name(self, file_name)
1055 
1056  def set_mol_index(self, index):
1057  r"""set_mol_index(FitParameters self, int index)"""
1058  return _IMP_saxs.FitParameters_set_mol_index(self, index)
1059 
1060  def show(self, s):
1061  r"""show(FitParameters self, _ostream s)"""
1062  return _IMP_saxs.FitParameters_show(self, s)
1063  __swig_destroy__ = _IMP_saxs.delete_FitParameters
1064 
1065 # Register FitParameters in _IMP_saxs:
1066 _IMP_saxs.FitParameters_swigregister(FitParameters)
1067 class WeightedFitParameters(FitParameters):
1068  r"""Proxy of C++ IMP::saxs::WeightedFitParameters class."""
1069 
1070  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1071  __repr__ = _swig_repr
1072 
1073  def __init__(self, *args):
1074  r"""
1075  __init__(WeightedFitParameters self) -> WeightedFitParameters
1076  __init__(WeightedFitParameters self, double chi_square, double c1, double c2, IMP::Vector< double > const & weights=IMP::Vector< double >()) -> WeightedFitParameters
1077  __init__(WeightedFitParameters self, FitParameters fp) -> WeightedFitParameters
1078  """
1079  _IMP_saxs.WeightedFitParameters_swiginit(self, _IMP_saxs.new_WeightedFitParameters(*args))
1080 
1081  def get_weights(self):
1082  r"""get_weights(WeightedFitParameters self) -> IMP::Vector< double > const &"""
1083  return _IMP_saxs.WeightedFitParameters_get_weights(self)
1084 
1085  def set_weights(self, weights):
1086  r"""set_weights(WeightedFitParameters self, IMP::Vector< double > const & weights)"""
1087  return _IMP_saxs.WeightedFitParameters_set_weights(self, weights)
1088 
1089  def show(self, s):
1090  r"""show(WeightedFitParameters self, _ostream s)"""
1091  return _IMP_saxs.WeightedFitParameters_show(self, s)
1092  __swig_destroy__ = _IMP_saxs.delete_WeightedFitParameters
1093 
1094 # Register WeightedFitParameters in _IMP_saxs:
1095 _IMP_saxs.WeightedFitParameters_swigregister(WeightedFitParameters)
1096 class ChiScore(IMP.Object):
1097  r"""Proxy of C++ IMP::saxs::ChiScore class."""
1098 
1099  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1100 
1101  def __init__(self):
1102  r"""__init__(ChiScore self) -> ChiScore"""
1103  _IMP_saxs.ChiScore_swiginit(self, _IMP_saxs.new_ChiScore())
1104 
1105  def compute_score(self, exp_profile, model_profile, use_offset=False):
1106  r"""compute_score(ChiScore self, Profile exp_profile, Profile model_profile, bool use_offset=False) -> double"""
1107  return _IMP_saxs.ChiScore_compute_score(self, exp_profile, model_profile, use_offset)
1108 
1109  def compute_scale_factor(self, exp_profile, model_profile, offset=0.0):
1110  r"""compute_scale_factor(ChiScore self, Profile exp_profile, Profile model_profile, double offset=0.0) -> double"""
1111  return _IMP_saxs.ChiScore_compute_scale_factor(self, exp_profile, model_profile, offset)
1112 
1113  def compute_offset(self, exp_profile, model_profile):
1114  r"""compute_offset(ChiScore self, Profile exp_profile, Profile model_profile) -> double"""
1115  return _IMP_saxs.ChiScore_compute_offset(self, exp_profile, model_profile)
1116 
1117  def get_version_info(self):
1118  r"""get_version_info(ChiScore self) -> VersionInfo"""
1119  return _IMP_saxs.ChiScore_get_version_info(self)
1120  __swig_destroy__ = _IMP_saxs.delete_ChiScore
1121 
1122  def __str__(self):
1123  r"""__str__(ChiScore self) -> std::string"""
1124  return _IMP_saxs.ChiScore___str__(self)
1125 
1126  def __repr__(self):
1127  r"""__repr__(ChiScore self) -> std::string"""
1128  return _IMP_saxs.ChiScore___repr__(self)
1129 
1130  @staticmethod
1131  def get_from(o):
1132  return _object_cast_to_ChiScore(o)
1133 
1134 
1135 # Register ChiScore in _IMP_saxs:
1136 _IMP_saxs.ChiScore_swigregister(ChiScore)
1137 class ChiScoreLog(IMP.Object):
1138  r"""Proxy of C++ IMP::saxs::ChiScoreLog class."""
1139 
1140  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1141 
1142  def __init__(self):
1143  r"""__init__(ChiScoreLog self) -> ChiScoreLog"""
1144  _IMP_saxs.ChiScoreLog_swiginit(self, _IMP_saxs.new_ChiScoreLog())
1145 
1146  def compute_score(self, *args):
1147  r"""
1148  compute_score(ChiScoreLog self, Profile exp_profile, Profile model_profile, bool use_offset=False) -> double
1149  compute_score(ChiScoreLog self, Profile exp_profile, Profile model_profile, double min_q, double max_q) -> double
1150  """
1151  return _IMP_saxs.ChiScoreLog_compute_score(self, *args)
1152 
1153  def compute_scale_factor(self, exp_profile, model_profile, offset=0.0):
1154  r"""compute_scale_factor(ChiScoreLog self, Profile exp_profile, Profile model_profile, double offset=0.0) -> double"""
1155  return _IMP_saxs.ChiScoreLog_compute_scale_factor(self, exp_profile, model_profile, offset)
1156 
1157  def compute_offset(self, exp_profile, model_profile):
1158  r"""compute_offset(ChiScoreLog self, Profile exp_profile, Profile model_profile) -> double"""
1159  return _IMP_saxs.ChiScoreLog_compute_offset(self, exp_profile, model_profile)
1160 
1161  def get_version_info(self):
1162  r"""get_version_info(ChiScoreLog self) -> VersionInfo"""
1163  return _IMP_saxs.ChiScoreLog_get_version_info(self)
1164  __swig_destroy__ = _IMP_saxs.delete_ChiScoreLog
1165 
1166  def __str__(self):
1167  r"""__str__(ChiScoreLog self) -> std::string"""
1168  return _IMP_saxs.ChiScoreLog___str__(self)
1169 
1170  def __repr__(self):
1171  r"""__repr__(ChiScoreLog self) -> std::string"""
1172  return _IMP_saxs.ChiScoreLog___repr__(self)
1173 
1174  @staticmethod
1175  def get_from(o):
1176  return _object_cast_to_ChiScoreLog(o)
1177 
1178 
1179 # Register ChiScoreLog in _IMP_saxs:
1180 _IMP_saxs.ChiScoreLog_swigregister(ChiScoreLog)
1181 class ProfileFitterChi(IMP.Object):
1182  r"""Proxy of C++ IMP::saxs::ProfileFitter< IMP::saxs::ChiScore > class."""
1183 
1184  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1185  __repr__ = _swig_repr
1186 
1187  def __init__(self, *args):
1188  r"""
1189  __init__(ProfileFitterChi self, Profile exp_profile) -> ProfileFitterChi
1190  __init__(ProfileFitterChi self, Profile exp_profile, ChiScore sf) -> ProfileFitterChi
1191  """
1192  _IMP_saxs.ProfileFitterChi_swiginit(self, _IMP_saxs.new_ProfileFitterChi(*args))
1193 
1194  def compute_score(self, *args):
1195  r"""compute_score(ProfileFitterChi self, Profile model_profile, bool use_offset=False, std::string const fit_file_name="") -> double"""
1196  return _IMP_saxs.ProfileFitterChi_compute_score(self, *args)
1197 
1198  def fit_profile(self, *args):
1199  r"""fit_profile(ProfileFitterChi self, Profile partial_profile, double min_c1=0.95, double max_c1=1.05, double min_c2=-2.0, double max_c2=4.0, bool use_offset=False, std::string const fit_file_name="") -> FitParameters"""
1200  return _IMP_saxs.ProfileFitterChi_fit_profile(self, *args)
1201 
1202  def compute_scale_factor(self, model_profile, offset=0.0):
1203  r"""compute_scale_factor(ProfileFitterChi self, Profile model_profile, double offset=0.0) -> double"""
1204  return _IMP_saxs.ProfileFitterChi_compute_scale_factor(self, model_profile, offset)
1205 
1206  def compute_offset(self, model_profile):
1207  r"""compute_offset(ProfileFitterChi self, Profile model_profile) -> double"""
1208  return _IMP_saxs.ProfileFitterChi_compute_offset(self, model_profile)
1209 
1210  def resample(self, model_profile, resampled_profile):
1211  r"""resample(ProfileFitterChi self, Profile model_profile, Profile resampled_profile)"""
1212  return _IMP_saxs.ProfileFitterChi_resample(self, model_profile, resampled_profile)
1213 
1214  def write_SAXS_fit_file(self, file_name, model_profile, chi_square, c=1, offset=0):
1215  r"""write_SAXS_fit_file(ProfileFitterChi self, std::string const & file_name, Profile model_profile, double const chi_square, double const c=1, double const offset=0)"""
1216  return _IMP_saxs.ProfileFitterChi_write_SAXS_fit_file(self, file_name, model_profile, chi_square, c, offset)
1217 
1218  def get_profile(self):
1219  r"""get_profile(ProfileFitterChi self) -> Profile"""
1220  return _IMP_saxs.ProfileFitterChi_get_profile(self)
1221  __swig_destroy__ = _IMP_saxs.delete_ProfileFitterChi
1222 
1223 # Register ProfileFitterChi in _IMP_saxs:
1224 _IMP_saxs.ProfileFitterChi_swigregister(ProfileFitterChi)
1225 class WeightedProfileFitterChi(ProfileFitterChi):
1226  r"""Proxy of C++ IMP::saxs::WeightedProfileFitter< IMP::saxs::ChiScore > class."""
1227 
1228  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1229  __repr__ = _swig_repr
1230 
1231  def __init__(self, exp_profile):
1232  r"""__init__(WeightedProfileFitterChi self, Profile exp_profile) -> WeightedProfileFitterChi"""
1233  _IMP_saxs.WeightedProfileFitterChi_swiginit(self, _IMP_saxs.new_WeightedProfileFitterChi(exp_profile))
1234 
1235  def compute_score(self, profiles, weights, use_offset=False, NNLS=True):
1236  r"""compute_score(WeightedProfileFitterChi self, IMP::saxs::ProfilesTemp const & profiles, IMP::Vector< double > & weights, bool use_offset=False, bool NNLS=True) -> double"""
1237  return _IMP_saxs.WeightedProfileFitterChi_compute_score(self, profiles, weights, use_offset, NNLS)
1238 
1239  def fit_profile(self, partial_profiles, min_c1=0.95, max_c1=1.05, min_c2=-2.0, max_c2=4.0, use_offset=False):
1240  r"""fit_profile(WeightedProfileFitterChi self, IMP::saxs::ProfilesTemp partial_profiles, double min_c1=0.95, double max_c1=1.05, double min_c2=-2.0, double max_c2=4.0, bool use_offset=False) -> WeightedFitParameters"""
1241  return _IMP_saxs.WeightedProfileFitterChi_fit_profile(self, partial_profiles, min_c1, max_c1, min_c2, max_c2, use_offset)
1242 
1243  def write_fit_file(self, partial_profiles, fp, fit_file_name, use_offset=False):
1244  r"""write_fit_file(WeightedProfileFitterChi self, IMP::saxs::ProfilesTemp partial_profiles, WeightedFitParameters fp, std::string const fit_file_name, bool use_offset=False)"""
1245  return _IMP_saxs.WeightedProfileFitterChi_write_fit_file(self, partial_profiles, fp, fit_file_name, use_offset)
1246  __swig_destroy__ = _IMP_saxs.delete_WeightedProfileFitterChi
1247 
1248 # Register WeightedProfileFitterChi in _IMP_saxs:
1249 _IMP_saxs.WeightedProfileFitterChi_swigregister(WeightedProfileFitterChi)
1250 class Restraint(IMP.Restraint):
1251  r"""Proxy of C++ IMP::saxs::Restraint class."""
1252 
1253  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1254 
1255  def __init__(self, *args):
1256  r"""
1257  __init__(Restraint self, IMP::Particles const & particles, Profile exp_profile, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS) -> Restraint
1258  __init__(Restraint self) -> Restraint
1259  """
1260  _IMP_saxs.Restraint_swiginit(self, _IMP_saxs.new_Restraint(*args))
1261 
1262  if self.__class__ != Restraint:
1263  _director_objects.register(self)
1264 
1265 
1266 
1267 
1268  def do_get_inputs(self):
1269  r"""do_get_inputs(Restraint self) -> IMP::ModelObjectsTemp"""
1270  return _IMP_saxs.Restraint_do_get_inputs(self)
1271 
1272  def get_version_info(self):
1273  r"""get_version_info(Restraint self) -> VersionInfo"""
1274  return _IMP_saxs.Restraint_get_version_info(self)
1275  __swig_destroy__ = _IMP_saxs.delete_Restraint
1276 
1277  def __str__(self):
1278  r"""__str__(Restraint self) -> std::string"""
1279  return _IMP_saxs.Restraint___str__(self)
1280 
1281  def __repr__(self):
1282  r"""__repr__(Restraint self) -> std::string"""
1283  return _IMP_saxs.Restraint___repr__(self)
1284 
1285  @staticmethod
1286  def get_from(o):
1287  return _object_cast_to_Restraint(o)
1288 
1289 
1290  def _get_as_binary(self):
1291  r"""_get_as_binary(Restraint self) -> PyObject *"""
1292  return _IMP_saxs.Restraint__get_as_binary(self)
1293 
1294  def _set_from_binary(self, p):
1295  r"""_set_from_binary(Restraint self, PyObject * p)"""
1296  return _IMP_saxs.Restraint__set_from_binary(self, p)
1297 
1298  def __getstate__(self):
1299  p = self._get_as_binary()
1300  if len(self.__dict__) > 1:
1301  d = self.__dict__.copy()
1302  del d['this']
1303  p = (d, p)
1304  return p
1305 
1306  def __setstate__(self, p):
1307  if not hasattr(self, 'this'):
1308  self.__init__()
1309  if isinstance(p, tuple):
1310  d, p = p
1311  self.__dict__.update(d)
1312  return self._set_from_binary(p)
1313 
1314 
1315 # Register Restraint in _IMP_saxs:
1316 _IMP_saxs.Restraint_swigregister(Restraint)
1317 class RadiusOfGyrationRestraint(Restraint):
1318  r"""Proxy of C++ IMP::saxs::RadiusOfGyrationRestraint class."""
1319 
1320  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1321  __repr__ = _swig_repr
1322 
1323  def __init__(self, particles, exp_profile, end_q_rg=1.3):
1324  r"""__init__(RadiusOfGyrationRestraint self, IMP::Particles const & particles, Profile exp_profile, double const end_q_rg=1.3) -> RadiusOfGyrationRestraint"""
1325  _IMP_saxs.RadiusOfGyrationRestraint_swiginit(self, _IMP_saxs.new_RadiusOfGyrationRestraint(particles, exp_profile, end_q_rg))
1326  __swig_destroy__ = _IMP_saxs.delete_RadiusOfGyrationRestraint
1327 
1328 # Register RadiusOfGyrationRestraint in _IMP_saxs:
1329 _IMP_saxs.RadiusOfGyrationRestraint_swigregister(RadiusOfGyrationRestraint)
1330 class FloatDistribution(DistBase):
1331  r"""Proxy of C++ IMP::saxs::Distribution< double > class."""
1332 
1333  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1334  __repr__ = _swig_repr
1335 
1336  def __init__(self, *args):
1337  r"""__init__(FloatDistribution self, double bin_size=pr_resolution) -> FloatDistribution"""
1338  _IMP_saxs.FloatDistribution_swiginit(self, _IMP_saxs.new_FloatDistribution(*args))
1339 
1340  def get_max_distance(self):
1341  r"""get_max_distance(FloatDistribution self) -> double"""
1342  return _IMP_saxs.FloatDistribution_get_max_distance(self)
1343 
1344  def get_bin_size(self):
1345  r"""get_bin_size(FloatDistribution self) -> double"""
1346  return _IMP_saxs.FloatDistribution_get_bin_size(self)
1347 
1348  def get_index_from_distance(self, dist):
1349  r"""get_index_from_distance(FloatDistribution self, double dist) -> unsigned int"""
1350  return _IMP_saxs.FloatDistribution_get_index_from_distance(self, dist)
1351 
1352  def get_distance_from_index(self, index):
1353  r"""get_distance_from_index(FloatDistribution self, unsigned int index) -> double"""
1354  return _IMP_saxs.FloatDistribution_get_distance_from_index(self, index)
1355  __swig_destroy__ = _IMP_saxs.delete_FloatDistribution
1356 
1357 # Register FloatDistribution in _IMP_saxs:
1358 _IMP_saxs.FloatDistribution_swigregister(FloatDistribution)
1359 class VectorDistribution(object):
1360  r"""Proxy of C++ IMP::saxs::Distribution< IMP::algebra::Vector3D > class."""
1361 
1362  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1363  __repr__ = _swig_repr
1364 
1365  def __init__(self, *args):
1366  r"""__init__(VectorDistribution self, double bin_size=pr_resolution) -> VectorDistribution"""
1367  _IMP_saxs.VectorDistribution_swiginit(self, _IMP_saxs.new_VectorDistribution(*args))
1368 
1369  def get_max_distance(self):
1370  r"""get_max_distance(VectorDistribution self) -> double"""
1371  return _IMP_saxs.VectorDistribution_get_max_distance(self)
1372 
1373  def get_bin_size(self):
1374  r"""get_bin_size(VectorDistribution self) -> double"""
1375  return _IMP_saxs.VectorDistribution_get_bin_size(self)
1376 
1377  def get_index_from_distance(self, dist):
1378  r"""get_index_from_distance(VectorDistribution self, double dist) -> unsigned int"""
1379  return _IMP_saxs.VectorDistribution_get_index_from_distance(self, dist)
1380 
1381  def get_distance_from_index(self, index):
1382  r"""get_distance_from_index(VectorDistribution self, unsigned int index) -> double"""
1383  return _IMP_saxs.VectorDistribution_get_distance_from_index(self, index)
1384  __swig_destroy__ = _IMP_saxs.delete_VectorDistribution
1385 
1386 # Register VectorDistribution in _IMP_saxs:
1387 _IMP_saxs.VectorDistribution_swigregister(VectorDistribution)
1388 class RadialDistributionFunction(FloatDistribution):
1389  r"""Proxy of C++ IMP::saxs::RadialDistributionFunction class."""
1390 
1391  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1392  __repr__ = _swig_repr
1393 
1394  def __init__(self, *args):
1395  r"""
1396  __init__(RadialDistributionFunction self, double bin_size=pr_resolution) -> RadialDistributionFunction
1397  __init__(RadialDistributionFunction self, std::string const & file_name) -> RadialDistributionFunction
1398  """
1399  _IMP_saxs.RadialDistributionFunction_swiginit(self, _IMP_saxs.new_RadialDistributionFunction(*args))
1400 
1401  def get_square_root_distances(self):
1402  r"""get_square_root_distances(RadialDistributionFunction self) -> DistBase"""
1403  return _IMP_saxs.RadialDistributionFunction_get_square_root_distances(self)
1404 
1405  def scale(self, c):
1406  r"""scale(RadialDistributionFunction self, double c)"""
1407  return _IMP_saxs.RadialDistributionFunction_scale(self, c)
1408 
1409  def add(self, model_pr):
1410  r"""add(RadialDistributionFunction self, RadialDistributionFunction model_pr)"""
1411  return _IMP_saxs.RadialDistributionFunction_add(self, model_pr)
1412 
1413  def show(self, *args):
1414  r"""show(RadialDistributionFunction self, _ostream out=std::cout)"""
1415  return _IMP_saxs.RadialDistributionFunction_show(self, *args)
1416 
1417  def R_factor_score(self, *args):
1418  r"""R_factor_score(RadialDistributionFunction self, RadialDistributionFunction model_pr, std::string const & file_name="") -> double"""
1419  return _IMP_saxs.RadialDistributionFunction_R_factor_score(self, *args)
1420 
1421  def fit(self, *args):
1422  r"""fit(RadialDistributionFunction self, RadialDistributionFunction model_pr, std::string const & file_name="") -> double"""
1423  return _IMP_saxs.RadialDistributionFunction_fit(self, *args)
1424 
1425  def normalize(self):
1426  r"""normalize(RadialDistributionFunction self)"""
1427  return _IMP_saxs.RadialDistributionFunction_normalize(self)
1428 
1429  def add_to_distribution(self, dist, value):
1430  r"""add_to_distribution(RadialDistributionFunction self, double dist, double value)"""
1431  return _IMP_saxs.RadialDistributionFunction_add_to_distribution(self, dist, value)
1432  __swig_destroy__ = _IMP_saxs.delete_RadialDistributionFunction
1433 
1434 # Register RadialDistributionFunction in _IMP_saxs:
1435 _IMP_saxs.RadialDistributionFunction_swigregister(RadialDistributionFunction)
1436 class DeltaDistributionFunction(VectorDistribution):
1437  r"""Proxy of C++ IMP::saxs::DeltaDistributionFunction class."""
1438 
1439  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1440  __repr__ = _swig_repr
1441 
1442  def __init__(self, *args):
1443  r"""__init__(DeltaDistributionFunction self, IMP::Particles const & particles, double max_distance=0.0, double bin_size=pr_resolution) -> DeltaDistributionFunction"""
1444  _IMP_saxs.DeltaDistributionFunction_swiginit(self, _IMP_saxs.new_DeltaDistributionFunction(*args))
1445 
1446  def calculate_derivative_distribution(self, particle):
1447  r"""calculate_derivative_distribution(DeltaDistributionFunction self, Particle particle)"""
1448  return _IMP_saxs.DeltaDistributionFunction_calculate_derivative_distribution(self, particle)
1449 
1450  def show(self, *args):
1451  r"""show(DeltaDistributionFunction self, _ostream out=std::cout, std::string prefix="")"""
1452  return _IMP_saxs.DeltaDistributionFunction_show(self, *args)
1453  __swig_destroy__ = _IMP_saxs.delete_DeltaDistributionFunction
1454 
1455 # Register DeltaDistributionFunction in _IMP_saxs:
1456 _IMP_saxs.DeltaDistributionFunction_swigregister(DeltaDistributionFunction)
1457 class SolventAccessibleSurface(object):
1458  r"""Proxy of C++ IMP::saxs::SolventAccessibleSurface class."""
1459 
1460  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1461  __repr__ = _swig_repr
1462 
1463  def get_solvent_accessibility(self, points, probe_radius=1.8, density=5.0):
1464  r"""get_solvent_accessibility(SolventAccessibleSurface self, IMP::core::XYZRs const & points, double probe_radius=1.8, double density=5.0) -> IMP::Vector< double >"""
1465  return _IMP_saxs.SolventAccessibleSurface_get_solvent_accessibility(self, points, probe_radius, density)
1466 
1467  def __init__(self):
1468  r"""__init__(SolventAccessibleSurface self) -> SolventAccessibleSurface"""
1469  _IMP_saxs.SolventAccessibleSurface_swiginit(self, _IMP_saxs.new_SolventAccessibleSurface())
1470  __swig_destroy__ = _IMP_saxs.delete_SolventAccessibleSurface
1471 
1472 # Register SolventAccessibleSurface in _IMP_saxs:
1473 _IMP_saxs.SolventAccessibleSurface_swigregister(SolventAccessibleSurface)
1474 class ProfileFitterChiLog(IMP.Object):
1475  r"""Proxy of C++ IMP::saxs::ProfileFitter< IMP::saxs::ChiScoreLog > class."""
1476 
1477  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1478  __repr__ = _swig_repr
1479 
1480  def __init__(self, *args):
1481  r"""
1482  __init__(ProfileFitterChiLog self, Profile exp_profile) -> ProfileFitterChiLog
1483  __init__(ProfileFitterChiLog self, Profile exp_profile, ChiScoreLog sf) -> ProfileFitterChiLog
1484  """
1485  _IMP_saxs.ProfileFitterChiLog_swiginit(self, _IMP_saxs.new_ProfileFitterChiLog(*args))
1486 
1487  def compute_score(self, *args):
1488  r"""compute_score(ProfileFitterChiLog self, Profile model_profile, bool use_offset=False, std::string const fit_file_name="") -> double"""
1489  return _IMP_saxs.ProfileFitterChiLog_compute_score(self, *args)
1490 
1491  def fit_profile(self, *args):
1492  r"""fit_profile(ProfileFitterChiLog self, Profile partial_profile, double min_c1=0.95, double max_c1=1.05, double min_c2=-2.0, double max_c2=4.0, bool use_offset=False, std::string const fit_file_name="") -> FitParameters"""
1493  return _IMP_saxs.ProfileFitterChiLog_fit_profile(self, *args)
1494 
1495  def compute_scale_factor(self, model_profile, offset=0.0):
1496  r"""compute_scale_factor(ProfileFitterChiLog self, Profile model_profile, double offset=0.0) -> double"""
1497  return _IMP_saxs.ProfileFitterChiLog_compute_scale_factor(self, model_profile, offset)
1498 
1499  def compute_offset(self, model_profile):
1500  r"""compute_offset(ProfileFitterChiLog self, Profile model_profile) -> double"""
1501  return _IMP_saxs.ProfileFitterChiLog_compute_offset(self, model_profile)
1502 
1503  def resample(self, model_profile, resampled_profile):
1504  r"""resample(ProfileFitterChiLog self, Profile model_profile, Profile resampled_profile)"""
1505  return _IMP_saxs.ProfileFitterChiLog_resample(self, model_profile, resampled_profile)
1506 
1507  def write_SAXS_fit_file(self, file_name, model_profile, chi_square, c=1, offset=0):
1508  r"""write_SAXS_fit_file(ProfileFitterChiLog self, std::string const & file_name, Profile model_profile, double const chi_square, double const c=1, double const offset=0)"""
1509  return _IMP_saxs.ProfileFitterChiLog_write_SAXS_fit_file(self, file_name, model_profile, chi_square, c, offset)
1510 
1511  def get_profile(self):
1512  r"""get_profile(ProfileFitterChiLog self) -> Profile"""
1513  return _IMP_saxs.ProfileFitterChiLog_get_profile(self)
1514  __swig_destroy__ = _IMP_saxs.delete_ProfileFitterChiLog
1515 
1516 # Register ProfileFitterChiLog in _IMP_saxs:
1517 _IMP_saxs.ProfileFitterChiLog_swigregister(ProfileFitterChiLog)
1518 class ProfileFitterRatioVolatility(IMP.Object):
1519  r"""Proxy of C++ IMP::saxs::ProfileFitter< IMP::saxs::RatioVolatilityScore > class."""
1520 
1521  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1522  __repr__ = _swig_repr
1523 
1524  def __init__(self, *args):
1525  r"""
1526  __init__(ProfileFitterRatioVolatility self, Profile exp_profile) -> ProfileFitterRatioVolatility
1527  __init__(ProfileFitterRatioVolatility self, Profile exp_profile, IMP::saxs::RatioVolatilityScore * sf) -> ProfileFitterRatioVolatility
1528  """
1529  _IMP_saxs.ProfileFitterRatioVolatility_swiginit(self, _IMP_saxs.new_ProfileFitterRatioVolatility(*args))
1530 
1531  def compute_score(self, *args):
1532  r"""compute_score(ProfileFitterRatioVolatility self, Profile model_profile, bool use_offset=False, std::string const fit_file_name="") -> double"""
1533  return _IMP_saxs.ProfileFitterRatioVolatility_compute_score(self, *args)
1534 
1535  def fit_profile(self, *args):
1536  r"""fit_profile(ProfileFitterRatioVolatility self, Profile partial_profile, double min_c1=0.95, double max_c1=1.05, double min_c2=-2.0, double max_c2=4.0, bool use_offset=False, std::string const fit_file_name="") -> FitParameters"""
1537  return _IMP_saxs.ProfileFitterRatioVolatility_fit_profile(self, *args)
1538 
1539  def compute_scale_factor(self, model_profile, offset=0.0):
1540  r"""compute_scale_factor(ProfileFitterRatioVolatility self, Profile model_profile, double offset=0.0) -> double"""
1541  return _IMP_saxs.ProfileFitterRatioVolatility_compute_scale_factor(self, model_profile, offset)
1542 
1543  def compute_offset(self, model_profile):
1544  r"""compute_offset(ProfileFitterRatioVolatility self, Profile model_profile) -> double"""
1545  return _IMP_saxs.ProfileFitterRatioVolatility_compute_offset(self, model_profile)
1546 
1547  def resample(self, model_profile, resampled_profile):
1548  r"""resample(ProfileFitterRatioVolatility self, Profile model_profile, Profile resampled_profile)"""
1549  return _IMP_saxs.ProfileFitterRatioVolatility_resample(self, model_profile, resampled_profile)
1550 
1551  def write_SAXS_fit_file(self, file_name, model_profile, chi_square, c=1, offset=0):
1552  r"""write_SAXS_fit_file(ProfileFitterRatioVolatility self, std::string const & file_name, Profile model_profile, double const chi_square, double const c=1, double const offset=0)"""
1553  return _IMP_saxs.ProfileFitterRatioVolatility_write_SAXS_fit_file(self, file_name, model_profile, chi_square, c, offset)
1554 
1555  def get_profile(self):
1556  r"""get_profile(ProfileFitterRatioVolatility self) -> Profile"""
1557  return _IMP_saxs.ProfileFitterRatioVolatility_get_profile(self)
1558  __swig_destroy__ = _IMP_saxs.delete_ProfileFitterRatioVolatility
1559 
1560 # Register ProfileFitterRatioVolatility in _IMP_saxs:
1561 _IMP_saxs.ProfileFitterRatioVolatility_swigregister(ProfileFitterRatioVolatility)
1562 
1563 def get_module_version():
1564  r"""get_module_version() -> std::string const"""
1565  return _IMP_saxs.get_module_version()
1566 
1567 def get_example_path(fname):
1568  r"""get_example_path(std::string fname) -> std::string"""
1569  return _IMP_saxs.get_example_path(fname)
1570 
1571 def get_data_path(fname):
1572  r"""get_data_path(std::string fname) -> std::string"""
1573  return _IMP_saxs.get_data_path(fname)
1574 
1575 from . import _version_check
1576 _version_check.check_version(get_module_version())
1577 __version__ = get_module_version()
1578 
1579 
def get_example_path
Return the full path to one of this module's example files.
Various classes to hold sets of particles.
def get_data_path
Return the full path to one of this module's data files.
Make CGAL functionality available to IMP.
def get_module_version
Return the version of this module, as a string.
FormFactorTable * get_default_form_factor_table()
Composable functors to implement scores via compile-time composition.
double get_volume(const BoundingBoxD< D > &bb)
See BoundingBoxD.
Definition: BoundingBoxD.h:170
Common base class for heavy weight IMP objects.
Definition: Object.h:111
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
Basic functionality that is expected to be used by a wide variety of IMP users.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
double radius_of_gyration(const Particles &particles)
compute radius_of_gyration
Definition: saxs/utility.h:74
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:56