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IMP Reference Guide  2.8.0
The Integrative Modeling Platform
saxs/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.10
3 #
4 # Do not make changes to this file unless you know what you are doing--modify
5 # the SWIG interface file instead.
6 
7 # This wrapper is part of IMP,
8 # Copyright 2007-2017 IMP Inventors. All rights reserved.
9 
10 from __future__ import print_function, division, absolute_import
11 
12 
13 
14 
15 from sys import version_info as _swig_python_version_info
16 if _swig_python_version_info >= (2, 7, 0):
17  def swig_import_helper():
18  import importlib
19  pkg = __name__.rpartition('.')[0]
20  mname = '.'.join((pkg, '_IMP_saxs')).lstrip('.')
21  try:
22  return importlib.import_module(mname)
23  except ImportError:
24  return importlib.import_module('_IMP_saxs')
25  _IMP_saxs = swig_import_helper()
26  del swig_import_helper
27 elif _swig_python_version_info >= (2, 6, 0):
28  def swig_import_helper():
29  from os.path import dirname
30  import imp
31  fp = None
32  try:
33  fp, pathname, description = imp.find_module('_IMP_saxs', [dirname(__file__)])
34  except ImportError:
35  import _IMP_saxs
36  return _IMP_saxs
37  if fp is not None:
38  try:
39  _mod = imp.load_module('_IMP_saxs', fp, pathname, description)
40  finally:
41  fp.close()
42  return _mod
43  _IMP_saxs = swig_import_helper()
44  del swig_import_helper
45 else:
46  import _IMP_saxs
47 del _swig_python_version_info
48 try:
49  _swig_property = property
50 except NameError:
51  pass # Python < 2.2 doesn't have 'property'.
52 
53 try:
54  import builtins as __builtin__
55 except ImportError:
56  import __builtin__
57 
58 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
59  if (name == "thisown"):
60  return self.this.own(value)
61  if (name == "this"):
62  if type(value).__name__ == 'SwigPyObject':
63  self.__dict__[name] = value
64  return
65  method = class_type.__swig_setmethods__.get(name, None)
66  if method:
67  return method(self, value)
68  if (not static):
69  object.__setattr__(self, name, value)
70  else:
71  raise AttributeError("You cannot add attributes to %s" % self)
72 
73 
74 def _swig_setattr(self, class_type, name, value):
75  return _swig_setattr_nondynamic(self, class_type, name, value, 0)
76 
77 
78 def _swig_getattr(self, class_type, name):
79  if (name == "thisown"):
80  return self.this.own()
81  method = class_type.__swig_getmethods__.get(name, None)
82  if method:
83  return method(self)
84  raise AttributeError("'%s' object has no attribute '%s'" % (class_type.__name__, name))
85 
86 
87 def _swig_repr(self):
88  try:
89  strthis = "proxy of " + self.this.__repr__()
90  except __builtin__.Exception:
91  strthis = ""
92  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
93 
94 
95 def _swig_setattr_nondynamic_method(set):
96  def set_attr(self, name, value):
97  if (name == "thisown"):
98  return self.this.own(value)
99  if hasattr(self, name) or (name == "this"):
100  set(self, name, value)
101  else:
102  raise AttributeError("You cannot add attributes to %s" % self)
103  return set_attr
104 
105 
106 try:
107  import weakref
108  weakref_proxy = weakref.proxy
109 except __builtin__.Exception:
110  weakref_proxy = lambda x: x
111 
112 
113 class IMP_SAXS_SwigPyIterator(object):
114  """Proxy of C++ swig::IMP_SAXS_SwigPyIterator class."""
115 
116  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
117 
118  def __init__(self, *args, **kwargs):
119  raise AttributeError("No constructor defined - class is abstract")
120  __repr__ = _swig_repr
121  __swig_destroy__ = _IMP_saxs.delete_IMP_SAXS_SwigPyIterator
122  __del__ = lambda self: None
123 
124  def value(self):
125  """value(IMP_SAXS_SwigPyIterator self) -> PyObject *"""
126  return _IMP_saxs.IMP_SAXS_SwigPyIterator_value(self)
127 
128 
129  def incr(self, n=1):
130  """
131  incr(IMP_SAXS_SwigPyIterator self, size_t n=1) -> IMP_SAXS_SwigPyIterator
132  incr(IMP_SAXS_SwigPyIterator self) -> IMP_SAXS_SwigPyIterator
133  """
134  return _IMP_saxs.IMP_SAXS_SwigPyIterator_incr(self, n)
135 
136 
137  def decr(self, n=1):
138  """
139  decr(IMP_SAXS_SwigPyIterator self, size_t n=1) -> IMP_SAXS_SwigPyIterator
140  decr(IMP_SAXS_SwigPyIterator self) -> IMP_SAXS_SwigPyIterator
141  """
142  return _IMP_saxs.IMP_SAXS_SwigPyIterator_decr(self, n)
143 
144 
145  def distance(self, x):
146  """distance(IMP_SAXS_SwigPyIterator self, IMP_SAXS_SwigPyIterator x) -> ptrdiff_t"""
147  return _IMP_saxs.IMP_SAXS_SwigPyIterator_distance(self, x)
148 
149 
150  def equal(self, x):
151  """equal(IMP_SAXS_SwigPyIterator self, IMP_SAXS_SwigPyIterator x) -> bool"""
152  return _IMP_saxs.IMP_SAXS_SwigPyIterator_equal(self, x)
153 
154 
155  def copy(self):
156  """copy(IMP_SAXS_SwigPyIterator self) -> IMP_SAXS_SwigPyIterator"""
157  return _IMP_saxs.IMP_SAXS_SwigPyIterator_copy(self)
158 
159 
160  def next(self):
161  """next(IMP_SAXS_SwigPyIterator self) -> PyObject *"""
162  return _IMP_saxs.IMP_SAXS_SwigPyIterator_next(self)
163 
164 
165  def __next__(self):
166  """__next__(IMP_SAXS_SwigPyIterator self) -> PyObject *"""
167  return _IMP_saxs.IMP_SAXS_SwigPyIterator___next__(self)
168 
169 
170  def previous(self):
171  """previous(IMP_SAXS_SwigPyIterator self) -> PyObject *"""
172  return _IMP_saxs.IMP_SAXS_SwigPyIterator_previous(self)
173 
174 
175  def advance(self, n):
176  """advance(IMP_SAXS_SwigPyIterator self, ptrdiff_t n) -> IMP_SAXS_SwigPyIterator"""
177  return _IMP_saxs.IMP_SAXS_SwigPyIterator_advance(self, n)
178 
179 
180  def __eq__(self, x):
181  """__eq__(IMP_SAXS_SwigPyIterator self, IMP_SAXS_SwigPyIterator x) -> bool"""
182  return _IMP_saxs.IMP_SAXS_SwigPyIterator___eq__(self, x)
183 
184 
185  def __ne__(self, x):
186  """__ne__(IMP_SAXS_SwigPyIterator self, IMP_SAXS_SwigPyIterator x) -> bool"""
187  return _IMP_saxs.IMP_SAXS_SwigPyIterator___ne__(self, x)
188 
189 
190  def __iadd__(self, n):
191  """__iadd__(IMP_SAXS_SwigPyIterator self, ptrdiff_t n) -> IMP_SAXS_SwigPyIterator"""
192  return _IMP_saxs.IMP_SAXS_SwigPyIterator___iadd__(self, n)
193 
194 
195  def __isub__(self, n):
196  """__isub__(IMP_SAXS_SwigPyIterator self, ptrdiff_t n) -> IMP_SAXS_SwigPyIterator"""
197  return _IMP_saxs.IMP_SAXS_SwigPyIterator___isub__(self, n)
198 
199 
200  def __add__(self, n):
201  """__add__(IMP_SAXS_SwigPyIterator self, ptrdiff_t n) -> IMP_SAXS_SwigPyIterator"""
202  return _IMP_saxs.IMP_SAXS_SwigPyIterator___add__(self, n)
203 
204 
205  def __sub__(self, *args):
206  """
207  __sub__(IMP_SAXS_SwigPyIterator self, ptrdiff_t n) -> IMP_SAXS_SwigPyIterator
208  __sub__(IMP_SAXS_SwigPyIterator self, IMP_SAXS_SwigPyIterator x) -> ptrdiff_t
209  """
210  return _IMP_saxs.IMP_SAXS_SwigPyIterator___sub__(self, *args)
211 
212  def __iter__(self):
213  return self
214 IMP_SAXS_SwigPyIterator_swigregister = _IMP_saxs.IMP_SAXS_SwigPyIterator_swigregister
215 IMP_SAXS_SwigPyIterator_swigregister(IMP_SAXS_SwigPyIterator)
216 
217 
218 _value_types=[]
219 _object_types=[]
220 _raii_types=[]
221 _plural_types=[]
222 
223 IMP_DEBUG = _IMP_saxs.IMP_DEBUG
224 IMP_RELEASE = _IMP_saxs.IMP_RELEASE
225 IMP_SILENT = _IMP_saxs.IMP_SILENT
226 IMP_PROGRESS = _IMP_saxs.IMP_PROGRESS
227 IMP_TERSE = _IMP_saxs.IMP_TERSE
228 IMP_VERBOSE = _IMP_saxs.IMP_VERBOSE
229 IMP_MEMORY = _IMP_saxs.IMP_MEMORY
230 IMP_NONE = _IMP_saxs.IMP_NONE
231 IMP_USAGE = _IMP_saxs.IMP_USAGE
232 IMP_INTERNAL = _IMP_saxs.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_saxs.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_saxs.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_saxs.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_saxs.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_saxs.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_saxs.IMP_KERNEL_HAS_GPERFTOOLS
239 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_saxs.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
240 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_saxs.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
241 IMPKERNEL_SHOW_WARNINGS = _IMP_saxs.IMPKERNEL_SHOW_WARNINGS
242 
243 import sys
244 class _DirectorObjects(object):
245  """@internal Simple class to keep references to director objects
246  to prevent premature deletion."""
247  def __init__(self):
248  self._objects = []
249  def register(self, obj):
250  """Take a reference to a director object; will only work for
251  refcounted C++ classes"""
252  if hasattr(obj, 'get_ref_count'):
253  self._objects.append(obj)
254  def cleanup(self):
255  """Only drop our reference and allow cleanup by Python if no other
256  Python references exist (we hold 3 references: one in self._objects,
257  one in x, and one in the argument list for getrefcount) *and* no
258  other C++ references exist (the Python object always holds one)"""
259  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
260  or x.get_ref_count() > 1]
261 # Do in two steps so the references are kept until the end of the
262 # function (deleting references may trigger a fresh call to this method)
263  self._objects = objs
264  def get_object_count(self):
265  """Get number of director objects (useful for testing only)"""
266  return len(self._objects)
267 _director_objects = _DirectorObjects()
268 
269 class _ostream(object):
270  """Proxy of C++ std::ostream class."""
271 
272  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
273 
274  def __init__(self, *args, **kwargs):
275  raise AttributeError("No constructor defined")
276  __repr__ = _swig_repr
277 
278  def write(self, osa_buf):
279  """write(_ostream self, char const * osa_buf)"""
280  return _IMP_saxs._ostream_write(self, osa_buf)
281 
282 _ostream_swigregister = _IMP_saxs._ostream_swigregister
283 _ostream_swigregister(_ostream)
284 
285 IMP_COMPILER_HAS_OVERRIDE = _IMP_saxs.IMP_COMPILER_HAS_OVERRIDE
286 IMP_COMPILER_HAS_FINAL = _IMP_saxs.IMP_COMPILER_HAS_FINAL
287 IMP_HAS_NOEXCEPT = _IMP_saxs.IMP_HAS_NOEXCEPT
288 import IMP
289 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_saxs.IMP_CGAL_HAS_BOOST_FILESYSTEM
290 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
291 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_saxs.IMP_CGAL_HAS_BOOST_RANDOM
292 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_CGAL_HAS_BOOST_SYSTEM
293 IMPCGAL_SHOW_WARNINGS = _IMP_saxs.IMPCGAL_SHOW_WARNINGS
294 import IMP.cgal
295 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_saxs.IMP_ALGEBRA_HAS_IMP_CGAL
296 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_saxs.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
297 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
298 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_saxs.IMP_ALGEBRA_HAS_BOOST_RANDOM
299 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_ALGEBRA_HAS_BOOST_SYSTEM
300 IMP_ALGEBRA_HAS_CGAL = _IMP_saxs.IMP_ALGEBRA_HAS_CGAL
301 IMP_ALGEBRA_HAS_ANN = _IMP_saxs.IMP_ALGEBRA_HAS_ANN
302 IMPALGEBRA_SHOW_WARNINGS = _IMP_saxs.IMPALGEBRA_SHOW_WARNINGS
303 import IMP.algebra
304 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_saxs.IMP_DISPLAY_HAS_IMP_CGAL
305 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_saxs.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
306 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
307 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_saxs.IMP_DISPLAY_HAS_BOOST_RANDOM
308 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_DISPLAY_HAS_BOOST_SYSTEM
309 IMP_DISPLAY_HAS_CGAL = _IMP_saxs.IMP_DISPLAY_HAS_CGAL
310 IMPDISPLAY_SHOW_WARNINGS = _IMP_saxs.IMPDISPLAY_SHOW_WARNINGS
311 import IMP.display
312 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_saxs.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
313 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_saxs.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
314 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
315 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_saxs.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
316 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
317 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_saxs.IMP_SCORE_FUNCTOR_HAS_CGAL
318 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_saxs.IMP_SCORE_FUNCTOR_HAS_HDF5
319 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_saxs.IMPSCOREFUNCTOR_SHOW_WARNINGS
320 import IMP.score_functor
321 IMP_CORE_HAS_IMP_CGAL = _IMP_saxs.IMP_CORE_HAS_IMP_CGAL
322 IMP_CORE_HAS_IMP_KERNEL = _IMP_saxs.IMP_CORE_HAS_IMP_KERNEL
323 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_saxs.IMP_CORE_HAS_BOOST_FILESYSTEM
324 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
325 IMP_CORE_HAS_BOOST_RANDOM = _IMP_saxs.IMP_CORE_HAS_BOOST_RANDOM
326 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_CORE_HAS_BOOST_SYSTEM
327 IMP_CORE_HAS_CGAL = _IMP_saxs.IMP_CORE_HAS_CGAL
328 IMP_CORE_HAS_HDF5 = _IMP_saxs.IMP_CORE_HAS_HDF5
329 IMPCORE_SHOW_WARNINGS = _IMP_saxs.IMPCORE_SHOW_WARNINGS
330 import IMP.core
331 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_saxs.IMP_CONTAINER_HAS_IMP_ALGEBRA
332 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_saxs.IMP_CONTAINER_HAS_IMP_CGAL
333 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_saxs.IMP_CONTAINER_HAS_IMP_DISPLAY
334 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_saxs.IMP_CONTAINER_HAS_IMP_KERNEL
335 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_saxs.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
336 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_saxs.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
337 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
338 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_saxs.IMP_CONTAINER_HAS_BOOST_RANDOM
339 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_CONTAINER_HAS_BOOST_SYSTEM
340 IMP_CONTAINER_HAS_CGAL = _IMP_saxs.IMP_CONTAINER_HAS_CGAL
341 IMP_CONTAINER_HAS_HDF5 = _IMP_saxs.IMP_CONTAINER_HAS_HDF5
342 IMPCONTAINER_SHOW_WARNINGS = _IMP_saxs.IMPCONTAINER_SHOW_WARNINGS
343 import IMP.container
344 IMP_ATOM_HAS_IMP_CGAL = _IMP_saxs.IMP_ATOM_HAS_IMP_CGAL
345 IMP_ATOM_HAS_IMP_KERNEL = _IMP_saxs.IMP_ATOM_HAS_IMP_KERNEL
346 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_saxs.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
347 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
348 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_saxs.IMP_ATOM_HAS_BOOST_RANDOM
349 IMP_ATOM_HAS_BOOST_REGEX = _IMP_saxs.IMP_ATOM_HAS_BOOST_REGEX
350 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_ATOM_HAS_BOOST_SYSTEM
351 IMP_ATOM_HAS_CGAL = _IMP_saxs.IMP_ATOM_HAS_CGAL
352 IMP_ATOM_HAS_HDF5 = _IMP_saxs.IMP_ATOM_HAS_HDF5
353 IMPATOM_SHOW_WARNINGS = _IMP_saxs.IMPATOM_SHOW_WARNINGS
354 IMP_ATOM_TYPE_INDEX = _IMP_saxs.IMP_ATOM_TYPE_INDEX
355 IMP_RESIDUE_TYPE_INDEX = _IMP_saxs.IMP_RESIDUE_TYPE_INDEX
356 IMP_HIERARCHY_TYPE_INDEX = _IMP_saxs.IMP_HIERARCHY_TYPE_INDEX
357 import IMP.atom
358 IMP_SAXS_HAS_IMP_CGAL = _IMP_saxs.IMP_SAXS_HAS_IMP_CGAL
359 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_saxs.IMP_SAXS_HAS_IMP_CONTAINER
360 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_saxs.IMP_SAXS_HAS_IMP_DISPLAY
361 IMP_SAXS_HAS_IMP_KERNEL = _IMP_saxs.IMP_SAXS_HAS_IMP_KERNEL
362 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_saxs.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
363 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_saxs.IMP_SAXS_HAS_BOOST_FILESYSTEM
364 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
365 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_saxs.IMP_SAXS_HAS_BOOST_RANDOM
366 IMP_SAXS_HAS_BOOST_REGEX = _IMP_saxs.IMP_SAXS_HAS_BOOST_REGEX
367 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_SAXS_HAS_BOOST_SYSTEM
368 IMP_SAXS_HAS_CGAL = _IMP_saxs.IMP_SAXS_HAS_CGAL
369 IMP_SAXS_HAS_HDF5 = _IMP_saxs.IMP_SAXS_HAS_HDF5
370 IMPSAXS_SHOW_WARNINGS = _IMP_saxs.IMPSAXS_SHOW_WARNINGS
371 class DistBase(object):
372  """Proxy of C++ std::vector<(double)> class."""
373 
374  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
375  __repr__ = _swig_repr
376 
377  def iterator(self):
378  """iterator(DistBase self) -> IMP_SAXS_SwigPyIterator"""
379  return _IMP_saxs.DistBase_iterator(self)
380 
381  def __iter__(self):
382  return self.iterator()
383 
384  def __nonzero__(self):
385  """__nonzero__(DistBase self) -> bool"""
386  return _IMP_saxs.DistBase___nonzero__(self)
387 
388 
389  def __bool__(self):
390  """__bool__(DistBase self) -> bool"""
391  return _IMP_saxs.DistBase___bool__(self)
392 
393 
394  def __len__(self):
395  """__len__(DistBase self) -> std::vector< double >::size_type"""
396  return _IMP_saxs.DistBase___len__(self)
397 
398 
399  def __getslice__(self, i, j):
400  """__getslice__(DistBase self, std::vector< double >::difference_type i, std::vector< double >::difference_type j) -> DistBase"""
401  return _IMP_saxs.DistBase___getslice__(self, i, j)
402 
403 
404  def __setslice__(self, *args):
405  """
406  __setslice__(DistBase self, std::vector< double >::difference_type i, std::vector< double >::difference_type j)
407  __setslice__(DistBase self, std::vector< double >::difference_type i, std::vector< double >::difference_type j, DistBase v)
408  """
409  return _IMP_saxs.DistBase___setslice__(self, *args)
410 
411 
412  def __delslice__(self, i, j):
413  """__delslice__(DistBase self, std::vector< double >::difference_type i, std::vector< double >::difference_type j)"""
414  return _IMP_saxs.DistBase___delslice__(self, i, j)
415 
416 
417  def __delitem__(self, *args):
418  """
419  __delitem__(DistBase self, std::vector< double >::difference_type i)
420  __delitem__(DistBase self, PySliceObject * slice)
421  """
422  return _IMP_saxs.DistBase___delitem__(self, *args)
423 
424 
425  def __getitem__(self, *args):
426  """
427  __getitem__(DistBase self, PySliceObject * slice) -> DistBase
428  __getitem__(DistBase self, std::vector< double >::difference_type i) -> std::vector< double >::value_type const &
429  """
430  return _IMP_saxs.DistBase___getitem__(self, *args)
431 
432 
433  def __setitem__(self, *args):
434  """
435  __setitem__(DistBase self, PySliceObject * slice, DistBase v)
436  __setitem__(DistBase self, PySliceObject * slice)
437  __setitem__(DistBase self, std::vector< double >::difference_type i, std::vector< double >::value_type const & x)
438  """
439  return _IMP_saxs.DistBase___setitem__(self, *args)
440 
441 
442  def pop(self):
443  """pop(DistBase self) -> std::vector< double >::value_type"""
444  return _IMP_saxs.DistBase_pop(self)
445 
446 
447  def append(self, x):
448  """append(DistBase self, std::vector< double >::value_type const & x)"""
449  return _IMP_saxs.DistBase_append(self, x)
450 
451 
452  def empty(self):
453  """empty(DistBase self) -> bool"""
454  return _IMP_saxs.DistBase_empty(self)
455 
456 
457  def size(self):
458  """size(DistBase self) -> std::vector< double >::size_type"""
459  return _IMP_saxs.DistBase_size(self)
460 
461 
462  def swap(self, v):
463  """swap(DistBase self, DistBase v)"""
464  return _IMP_saxs.DistBase_swap(self, v)
465 
466 
467  def begin(self):
468  """begin(DistBase self) -> std::vector< double >::iterator"""
469  return _IMP_saxs.DistBase_begin(self)
470 
471 
472  def end(self):
473  """end(DistBase self) -> std::vector< double >::iterator"""
474  return _IMP_saxs.DistBase_end(self)
475 
476 
477  def rbegin(self):
478  """rbegin(DistBase self) -> std::vector< double >::reverse_iterator"""
479  return _IMP_saxs.DistBase_rbegin(self)
480 
481 
482  def rend(self):
483  """rend(DistBase self) -> std::vector< double >::reverse_iterator"""
484  return _IMP_saxs.DistBase_rend(self)
485 
486 
487  def clear(self):
488  """clear(DistBase self)"""
489  return _IMP_saxs.DistBase_clear(self)
490 
491 
492  def get_allocator(self):
493  """get_allocator(DistBase self) -> std::vector< double >::allocator_type"""
494  return _IMP_saxs.DistBase_get_allocator(self)
495 
496 
497  def pop_back(self):
498  """pop_back(DistBase self)"""
499  return _IMP_saxs.DistBase_pop_back(self)
500 
501 
502  def erase(self, *args):
503  """
504  erase(DistBase self, std::vector< double >::iterator pos) -> std::vector< double >::iterator
505  erase(DistBase self, std::vector< double >::iterator first, std::vector< double >::iterator last) -> std::vector< double >::iterator
506  """
507  return _IMP_saxs.DistBase_erase(self, *args)
508 
509 
510  def __init__(self, *args):
511  """
512  __init__(std::vector<(double)> self) -> DistBase
513  __init__(std::vector<(double)> self, DistBase arg2) -> DistBase
514  __init__(std::vector<(double)> self, std::vector< double >::size_type size) -> DistBase
515  __init__(std::vector<(double)> self, std::vector< double >::size_type size, std::vector< double >::value_type const & value) -> DistBase
516  """
517  this = _IMP_saxs.new_DistBase(*args)
518  try:
519  self.this.append(this)
520  except __builtin__.Exception:
521  self.this = this
522 
523  def push_back(self, x):
524  """push_back(DistBase self, std::vector< double >::value_type const & x)"""
525  return _IMP_saxs.DistBase_push_back(self, x)
526 
527 
528  def front(self):
529  """front(DistBase self) -> std::vector< double >::value_type const &"""
530  return _IMP_saxs.DistBase_front(self)
531 
532 
533  def back(self):
534  """back(DistBase self) -> std::vector< double >::value_type const &"""
535  return _IMP_saxs.DistBase_back(self)
536 
537 
538  def assign(self, n, x):
539  """assign(DistBase self, std::vector< double >::size_type n, std::vector< double >::value_type const & x)"""
540  return _IMP_saxs.DistBase_assign(self, n, x)
541 
542 
543  def resize(self, *args):
544  """
545  resize(DistBase self, std::vector< double >::size_type new_size)
546  resize(DistBase self, std::vector< double >::size_type new_size, std::vector< double >::value_type const & x)
547  """
548  return _IMP_saxs.DistBase_resize(self, *args)
549 
550 
551  def insert(self, *args):
552  """
553  insert(DistBase self, std::vector< double >::iterator pos, std::vector< double >::value_type const & x) -> std::vector< double >::iterator
554  insert(DistBase self, std::vector< double >::iterator pos, std::vector< double >::size_type n, std::vector< double >::value_type const & x)
555  """
556  return _IMP_saxs.DistBase_insert(self, *args)
557 
558 
559  def reserve(self, n):
560  """reserve(DistBase self, std::vector< double >::size_type n)"""
561  return _IMP_saxs.DistBase_reserve(self, n)
562 
563 
564  def capacity(self):
565  """capacity(DistBase self) -> std::vector< double >::size_type"""
566  return _IMP_saxs.DistBase_capacity(self)
567 
568  __swig_destroy__ = _IMP_saxs.delete_DistBase
569  __del__ = lambda self: None
570 DistBase_swigregister = _IMP_saxs.DistBase_swigregister
571 DistBase_swigregister(DistBase)
572 
573 
574 _object_types.append("Profile")
575 
576 
577 def _object_cast_to_Profile(o):
578  """_object_cast_to_Profile(Object o) -> Profile"""
579  return _IMP_saxs._object_cast_to_Profile(o)
580 
581 _object_types.append("ChiScore")
582 
583 
584 def _object_cast_to_ChiScore(o):
585  """_object_cast_to_ChiScore(Object o) -> ChiScore"""
586  return _IMP_saxs._object_cast_to_ChiScore(o)
587 
588 _object_types.append("ChiScoreLog")
589 
590 
591 def _object_cast_to_ChiScoreLog(o):
592  """_object_cast_to_ChiScoreLog(Object o) -> ChiScoreLog"""
593  return _IMP_saxs._object_cast_to_ChiScoreLog(o)
594 ALL_ATOMS = _IMP_saxs.ALL_ATOMS
595 HEAVY_ATOMS = _IMP_saxs.HEAVY_ATOMS
596 CA_ATOMS = _IMP_saxs.CA_ATOMS
597 RESIDUES = _IMP_saxs.RESIDUES
598 class FormFactorTable(object):
599  """Proxy of C++ IMP::saxs::FormFactorTable class."""
600 
601  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
602  __repr__ = _swig_repr
603 
604  def __init__(self, *args):
605  """
606  __init__(IMP::saxs::FormFactorTable self) -> FormFactorTable
607  __init__(IMP::saxs::FormFactorTable self, std::string const & table_name, double min_q, double max_q, double delta_q) -> FormFactorTable
608  """
609  this = _IMP_saxs.new_FormFactorTable(*args)
610  try:
611  self.this.append(this)
612  except __builtin__.Exception:
613  self.this = this
614 
615  def get_form_factor(self, *args):
616  """
617  get_form_factor(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type) -> double
618  get_form_factor(FormFactorTable self, Particle p) -> double
619  """
620  return _IMP_saxs.FormFactorTable_get_form_factor(self, *args)
621 
622 
623  def get_vacuum_form_factor(self, *args):
624  """
625  get_vacuum_form_factor(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type) -> double
626  get_vacuum_form_factor(FormFactorTable self, Particle p) -> double
627  """
628  return _IMP_saxs.FormFactorTable_get_vacuum_form_factor(self, *args)
629 
630 
631  def get_dummy_form_factor(self, *args):
632  """
633  get_dummy_form_factor(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type) -> double
634  get_dummy_form_factor(FormFactorTable self, Particle p) -> double
635  """
636  return _IMP_saxs.FormFactorTable_get_dummy_form_factor(self, *args)
637 
638 
639  def get_water_form_factor(self):
640  """get_water_form_factor(FormFactorTable self) -> double"""
641  return _IMP_saxs.FormFactorTable_get_water_form_factor(self)
642 
643 
644  def get_vacuum_water_form_factor(self):
645  """get_vacuum_water_form_factor(FormFactorTable self) -> double"""
646  return _IMP_saxs.FormFactorTable_get_vacuum_water_form_factor(self)
647 
648 
649  def get_dummy_water_form_factor(self):
650  """get_dummy_water_form_factor(FormFactorTable self) -> double"""
651  return _IMP_saxs.FormFactorTable_get_dummy_water_form_factor(self)
652 
653 
654  def get_form_factors(self, *args):
655  """
656  get_form_factors(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type) -> IMP::Vector< double > const
657  get_form_factors(FormFactorTable self, Particle p) -> IMP::Vector< double > const &
658  """
659  return _IMP_saxs.FormFactorTable_get_form_factors(self, *args)
660 
661 
662  def get_vacuum_form_factors(self, *args):
663  """
664  get_vacuum_form_factors(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type) -> IMP::Vector< double > const
665  get_vacuum_form_factors(FormFactorTable self, Particle p) -> IMP::Vector< double > const &
666  """
667  return _IMP_saxs.FormFactorTable_get_vacuum_form_factors(self, *args)
668 
669 
670  def get_dummy_form_factors(self, *args):
671  """
672  get_dummy_form_factors(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type) -> IMP::Vector< double > const
673  get_dummy_form_factors(FormFactorTable self, Particle p) -> IMP::Vector< double > const &
674  """
675  return _IMP_saxs.FormFactorTable_get_dummy_form_factors(self, *args)
676 
677 
678  def get_water_form_factors(self):
679  """get_water_form_factors(FormFactorTable self) -> IMP::Vector< double > const &"""
680  return _IMP_saxs.FormFactorTable_get_water_form_factors(self)
681 
682 
683  def get_water_vacuum_form_factors(self):
684  """get_water_vacuum_form_factors(FormFactorTable self) -> IMP::Vector< double > const &"""
685  return _IMP_saxs.FormFactorTable_get_water_vacuum_form_factors(self)
686 
687 
688  def get_water_dummy_form_factors(self):
689  """get_water_dummy_form_factors(FormFactorTable self) -> IMP::Vector< double > const &"""
690  return _IMP_saxs.FormFactorTable_get_water_dummy_form_factors(self)
691 
692 
693  def get_radius(self, *args):
694  """
695  get_radius(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type) -> double
696  get_radius(FormFactorTable self, Particle p) -> double
697  """
698  return _IMP_saxs.FormFactorTable_get_radius(self, *args)
699 
700 
701  def get_volume(self, *args):
702  """
703  get_volume(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type) -> double
704  get_volume(FormFactorTable self, Particle p) -> double
705  """
706  return _IMP_saxs.FormFactorTable_get_volume(self, *args)
707 
708 
709  def show(self, *args):
710  """
711  show(FormFactorTable self, _ostream out, std::string prefix)
712  show(FormFactorTable self, _ostream out)
713  show(FormFactorTable self)
714  """
715  return _IMP_saxs.FormFactorTable_show(self, *args)
716 
717  rho_ = _swig_property(_IMP_saxs.FormFactorTable_rho__get, _IMP_saxs.FormFactorTable_rho__set)
718  __swig_destroy__ = _IMP_saxs.delete_FormFactorTable
719  __del__ = lambda self: None
720 FormFactorTable_swigregister = _IMP_saxs.FormFactorTable_swigregister
721 FormFactorTable_swigregister(FormFactorTable)
722 cvar = _IMP_saxs.cvar
723 
724 
726  """get_default_form_factor_table() -> FormFactorTable"""
727  return _IMP_saxs.get_default_form_factor_table()
728 class Profile(IMP.Object):
729  """Proxy of C++ IMP::saxs::Profile class."""
730 
731  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
732 
733  def __init__(self, *args):
734  """
735  __init__(IMP::saxs::Profile self, std::string const & file_name, bool fit_file=False, double max_q=0.0) -> Profile
736  __init__(IMP::saxs::Profile self, std::string const & file_name, bool fit_file=False) -> Profile
737  __init__(IMP::saxs::Profile self, std::string const & file_name) -> Profile
738  __init__(IMP::saxs::Profile self, double qmin=0.0, double qmax=0.5, double delta=0.005) -> Profile
739  __init__(IMP::saxs::Profile self, double qmin=0.0, double qmax=0.5) -> Profile
740  __init__(IMP::saxs::Profile self, double qmin=0.0) -> Profile
741  __init__(IMP::saxs::Profile self) -> Profile
742  """
743  this = _IMP_saxs.new_Profile(*args)
744  try:
745  self.this.append(this)
746  except __builtin__.Exception:
747  self.this = this
748 
749  def calculate_profile_partial(self, *args):
750  """
751  calculate_profile_partial(Profile self, IMP::Particles const & particles, IMP::Vector< double > const & surface, IMP::saxs::FormFactorType ff_type)
752  calculate_profile_partial(Profile self, IMP::Particles const & particles, IMP::Vector< double > const & surface)
753  calculate_profile_partial(Profile self, IMP::Particles const & particles)
754  calculate_profile_partial(Profile self, IMP::Particles const & particles1, IMP::Particles const & particles2, IMP::Vector< double > const & surface1, IMP::Vector< double > const & surface2, IMP::saxs::FormFactorType ff_type)
755  calculate_profile_partial(Profile self, IMP::Particles const & particles1, IMP::Particles const & particles2, IMP::Vector< double > const & surface1, IMP::Vector< double > const & surface2)
756  calculate_profile_partial(Profile self, IMP::Particles const & particles1, IMP::Particles const & particles2, IMP::Vector< double > const & surface1)
757  calculate_profile_partial(Profile self, IMP::Particles const & particles1, IMP::Particles const & particles2)
758  """
759  return _IMP_saxs.Profile_calculate_profile_partial(self, *args)
760 
761 
762  def calculate_profile_reciprocal_partial(self, *args):
763  """
764  calculate_profile_reciprocal_partial(Profile self, IMP::Particles const & particles, IMP::Vector< double > const & surface, IMP::saxs::FormFactorType ff_type)
765  calculate_profile_reciprocal_partial(Profile self, IMP::Particles const & particles, IMP::Vector< double > const & surface)
766  calculate_profile_reciprocal_partial(Profile self, IMP::Particles const & particles)
767  """
768  return _IMP_saxs.Profile_calculate_profile_reciprocal_partial(self, *args)
769 
770 
771  def calculate_profile(self, *args):
772  """
773  calculate_profile(Profile self, IMP::Particles const & particles, IMP::saxs::FormFactorType ff_type, bool reciprocal=False)
774  calculate_profile(Profile self, IMP::Particles const & particles, IMP::saxs::FormFactorType ff_type)
775  calculate_profile(Profile self, IMP::Particles const & particles)
776  calculate_profile(Profile self, IMP::Particles const & particles1, IMP::Particles const & particles2, IMP::saxs::FormFactorType ff_type)
777  calculate_profile(Profile self, IMP::Particles const & particles1, IMP::Particles const & particles2)
778  """
779  return _IMP_saxs.Profile_calculate_profile(self, *args)
780 
781 
782  def calculate_I0(self, *args):
783  """
784  calculate_I0(Profile self, IMP::Particles const & particles, IMP::saxs::FormFactorType ff_type) -> double
785  calculate_I0(Profile self, IMP::Particles const & particles) -> double
786  """
787  return _IMP_saxs.Profile_calculate_I0(self, *args)
788 
789 
790  def calculate_profile_constant_form_factor(self, particles, form_factor=1.0):
791  """
792  calculate_profile_constant_form_factor(Profile self, IMP::Particles const & particles, double form_factor=1.0)
793  calculate_profile_constant_form_factor(Profile self, IMP::Particles const & particles)
794  """
795  return _IMP_saxs.Profile_calculate_profile_constant_form_factor(self, particles, form_factor)
796 
797 
798  def calculate_profile_symmetric(self, *args):
799  """
800  calculate_profile_symmetric(Profile self, IMP::Particles const & particles, unsigned int n, IMP::saxs::FormFactorType ff_type)
801  calculate_profile_symmetric(Profile self, IMP::Particles const & particles, unsigned int n)
802  """
803  return _IMP_saxs.Profile_calculate_profile_symmetric(self, *args)
804 
805 
806  def profile_2_distribution(self, rd, max_distance):
807  """profile_2_distribution(Profile self, RadialDistributionFunction rd, double max_distance)"""
808  return _IMP_saxs.Profile_profile_2_distribution(self, rd, max_distance)
809 
810 
811  def distribution_2_profile(self, r_dist):
812  """distribution_2_profile(Profile self, RadialDistributionFunction r_dist)"""
813  return _IMP_saxs.Profile_distribution_2_profile(self, r_dist)
814 
815 
816  def resample(self, exp_profile, resampled_profile):
817  """resample(Profile self, Profile exp_profile, Profile resampled_profile)"""
818  return _IMP_saxs.Profile_resample(self, exp_profile, resampled_profile)
819 
820 
821  def downsample(self, downsampled_profile, point_number):
822  """downsample(Profile self, Profile downsampled_profile, unsigned int point_number)"""
823  return _IMP_saxs.Profile_downsample(self, downsampled_profile, point_number)
824 
825 
826  def radius_of_gyration(self, end_q_rg=1.3):
827  """
828  radius_of_gyration(Profile self, double end_q_rg=1.3) -> double
829  radius_of_gyration(Profile self) -> double
830  """
831  return _IMP_saxs.Profile_radius_of_gyration(self, end_q_rg)
832 
833 
834  def mean_intensity(self):
835  """mean_intensity(Profile self) -> double"""
836  return _IMP_saxs.Profile_mean_intensity(self)
837 
838 
839  def read_SAXS_file(self, file_name, fit_file=False, max_q=0.0):
840  """
841  read_SAXS_file(Profile self, std::string const & file_name, bool fit_file=False, double max_q=0.0)
842  read_SAXS_file(Profile self, std::string const & file_name, bool fit_file=False)
843  read_SAXS_file(Profile self, std::string const & file_name)
844  """
845  return _IMP_saxs.Profile_read_SAXS_file(self, file_name, fit_file, max_q)
846 
847 
848  def write_SAXS_file(self, file_name, max_q=0.0):
849  """
850  write_SAXS_file(Profile self, std::string const & file_name, double max_q=0.0)
851  write_SAXS_file(Profile self, std::string const & file_name)
852  """
853  return _IMP_saxs.Profile_write_SAXS_file(self, file_name, max_q)
854 
855 
856  def read_partial_profiles(self, file_name):
857  """read_partial_profiles(Profile self, std::string const & file_name)"""
858  return _IMP_saxs.Profile_read_partial_profiles(self, file_name)
859 
860 
861  def write_partial_profiles(self, file_name):
862  """write_partial_profiles(Profile self, std::string const & file_name)"""
863  return _IMP_saxs.Profile_write_partial_profiles(self, file_name)
864 
865 
866  def get_delta_q(self):
867  """get_delta_q(Profile self) -> double"""
868  return _IMP_saxs.Profile_get_delta_q(self)
869 
870 
871  def get_min_q(self):
872  """get_min_q(Profile self) -> double"""
873  return _IMP_saxs.Profile_get_min_q(self)
874 
875 
876  def get_max_q(self):
877  """get_max_q(Profile self) -> double"""
878  return _IMP_saxs.Profile_get_max_q(self)
879 
880 
881  def get_intensity(self, i):
882  """get_intensity(Profile self, unsigned int i) -> double"""
883  return _IMP_saxs.Profile_get_intensity(self, i)
884 
885 
886  def get_q(self, i):
887  """get_q(Profile self, unsigned int i) -> double"""
888  return _IMP_saxs.Profile_get_q(self, i)
889 
890 
891  def get_error(self, i):
892  """get_error(Profile self, unsigned int i) -> double"""
893  return _IMP_saxs.Profile_get_error(self, i)
894 
895 
896  def get_weight(self, i):
897  """get_weight(Profile self, unsigned int i) -> double"""
898  return _IMP_saxs.Profile_get_weight(self, i)
899 
900 
901  def get_qs(self):
902  """get_qs(Profile self) -> IMP_Eigen::VectorXf const &"""
903  return _IMP_saxs.Profile_get_qs(self)
904 
905 
906  def get_intensities(self):
907  """get_intensities(Profile self) -> IMP_Eigen::VectorXf const &"""
908  return _IMP_saxs.Profile_get_intensities(self)
909 
910 
911  def get_errors(self):
912  """get_errors(Profile self) -> IMP_Eigen::VectorXf const &"""
913  return _IMP_saxs.Profile_get_errors(self)
914 
915 
916  def get_average_radius(self):
917  """get_average_radius(Profile self) -> double"""
918  return _IMP_saxs.Profile_get_average_radius(self)
919 
920 
921  def size(self):
922  """size(Profile self) -> unsigned int"""
923  return _IMP_saxs.Profile_size(self)
924 
925 
926  def is_uniform_sampling(self):
927  """is_uniform_sampling(Profile self) -> bool"""
928  return _IMP_saxs.Profile_is_uniform_sampling(self)
929 
930 
931  def is_partial_profile(self):
932  """is_partial_profile(Profile self) -> bool"""
933  return _IMP_saxs.Profile_is_partial_profile(self)
934 
935 
936  def get_name(self):
937  """get_name(Profile self) -> std::string"""
938  return _IMP_saxs.Profile_get_name(self)
939 
940 
941  def get_id(self):
942  """get_id(Profile self) -> unsigned int"""
943  return _IMP_saxs.Profile_get_id(self)
944 
945 
946  def set_qs(self, q):
947  """set_qs(Profile self, IMP_Eigen::VectorXf const & q)"""
948  return _IMP_saxs.Profile_set_qs(self, q)
949 
950 
951  def set_intensities(self, i):
952  """set_intensities(Profile self, IMP_Eigen::VectorXf const & i)"""
953  return _IMP_saxs.Profile_set_intensities(self, i)
954 
955 
956  def set_errors(self, e):
957  """set_errors(Profile self, IMP_Eigen::VectorXf const & e)"""
958  return _IMP_saxs.Profile_set_errors(self, e)
959 
960 
961  def set_intensity(self, i, iq):
962  """set_intensity(Profile self, unsigned int i, double iq)"""
963  return _IMP_saxs.Profile_set_intensity(self, i, iq)
964 
965 
966  def set_ff_table(self, ff_table):
967  """set_ff_table(Profile self, FormFactorTable ff_table)"""
968  return _IMP_saxs.Profile_set_ff_table(self, ff_table)
969 
970 
971  def set_average_radius(self, r):
972  """set_average_radius(Profile self, double r)"""
973  return _IMP_saxs.Profile_set_average_radius(self, r)
974 
975 
976  def set_average_volume(self, v):
977  """set_average_volume(Profile self, double v)"""
978  return _IMP_saxs.Profile_set_average_volume(self, v)
979 
980 
981  def set_name(self, name):
982  """set_name(Profile self, std::string name)"""
983  return _IMP_saxs.Profile_set_name(self, name)
984 
985 
986  def set_id(self, id):
987  """set_id(Profile self, unsigned int id)"""
988  return _IMP_saxs.Profile_set_id(self, id)
989 
990 
991  def set_beam_profile(self, beam_profile_file):
992  """set_beam_profile(Profile self, std::string beam_profile_file)"""
993  return _IMP_saxs.Profile_set_beam_profile(self, beam_profile_file)
994 
995 
996  def add_errors(self):
997  """add_errors(Profile self)"""
998  return _IMP_saxs.Profile_add_errors(self)
999 
1000 
1001  def add_noise(self, percentage=0.03):
1002  """
1003  add_noise(Profile self, double percentage=0.03)
1004  add_noise(Profile self)
1005  """
1006  return _IMP_saxs.Profile_add_noise(self, percentage)
1007 
1008 
1009  def sum_partial_profiles(self, c1, c2, check_cashed=True):
1010  """
1011  sum_partial_profiles(Profile self, double c1, double c2, bool check_cashed=True)
1012  sum_partial_profiles(Profile self, double c1, double c2)
1013  """
1014  return _IMP_saxs.Profile_sum_partial_profiles(self, c1, c2, check_cashed)
1015 
1016 
1017  def add(self, *args):
1018  """
1019  add(Profile self, Profile other_profile, double weight=1.0)
1020  add(Profile self, Profile other_profile)
1021  add(Profile self, IMP::Vector< IMP::saxs::Profile * > const & profiles, IMP::Vector< double > const & weights)
1022  add(Profile self, IMP::Vector< IMP::saxs::Profile * > const & profiles)
1023  """
1024  return _IMP_saxs.Profile_add(self, *args)
1025 
1026 
1027  def add_partial_profiles(self, *args):
1028  """
1029  add_partial_profiles(Profile self, Profile other_profile, double weight=1.0)
1030  add_partial_profiles(Profile self, Profile other_profile)
1031  add_partial_profiles(Profile self, IMP::Vector< IMP::saxs::Profile * > const & profiles, IMP::Vector< double > const & weights)
1032  add_partial_profiles(Profile self, IMP::Vector< IMP::saxs::Profile * > const & profiles)
1033  """
1034  return _IMP_saxs.Profile_add_partial_profiles(self, *args)
1035 
1036 
1037  def background_adjust(self, start_q):
1038  """background_adjust(Profile self, double start_q)"""
1039  return _IMP_saxs.Profile_background_adjust(self, start_q)
1040 
1041 
1042  def scale(self, c):
1043  """scale(Profile self, double c)"""
1044  return _IMP_saxs.Profile_scale(self, c)
1045 
1046 
1047  def offset(self, c):
1048  """offset(Profile self, double c)"""
1049  return _IMP_saxs.Profile_offset(self, c)
1050 
1051 
1052  def copy_errors(self, exp_profile):
1053  """copy_errors(Profile self, Profile exp_profile)"""
1054  return _IMP_saxs.Profile_copy_errors(self, exp_profile)
1055 
1056 
1057  def get_version_info(self):
1058  """get_version_info(Profile self) -> VersionInfo"""
1059  return _IMP_saxs.Profile_get_version_info(self)
1060 
1061 
1062  def __str__(self):
1063  """__str__(Profile self) -> std::string"""
1064  return _IMP_saxs.Profile___str__(self)
1065 
1066 
1067  def __repr__(self):
1068  """__repr__(Profile self) -> std::string"""
1069  return _IMP_saxs.Profile___repr__(self)
1070 
1071 
1072  @staticmethod
1073  def get_from(o):
1074  return _object_cast_to_Profile(o)
1075 
1076 Profile_swigregister = _IMP_saxs.Profile_swigregister
1077 Profile_swigregister(Profile)
1078 Profile.modulation_function_parameter_ = _IMP_saxs.cvar.Profile_modulation_function_parameter_
1079 
1080 class FitParameters(object):
1081  """Proxy of C++ IMP::saxs::FitParameters class."""
1082 
1083  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1084  __repr__ = _swig_repr
1085 
1086  def __init__(self, *args):
1087  """
1088  __init__(IMP::saxs::FitParameters self) -> FitParameters
1089  __init__(IMP::saxs::FitParameters self, double chi, double c1, double c2, double c, double o) -> FitParameters
1090  __init__(IMP::saxs::FitParameters self, double chi, double c1, double c2) -> FitParameters
1091  """
1092  this = _IMP_saxs.new_FitParameters(*args)
1093  try:
1094  self.this.append(this)
1095  except __builtin__.Exception:
1096  self.this = this
1097 
1098  def get_score(self):
1099  """get_score(FitParameters self) -> double"""
1100  return _IMP_saxs.FitParameters_get_score(self)
1101 
1102 
1103  def get_chi(self):
1104  """get_chi(FitParameters self) -> double"""
1105  return _IMP_saxs.FitParameters_get_chi(self)
1106 
1107 
1108  def get_c1(self):
1109  """get_c1(FitParameters self) -> double"""
1110  return _IMP_saxs.FitParameters_get_c1(self)
1111 
1112 
1113  def get_c2(self):
1114  """get_c2(FitParameters self) -> double"""
1115  return _IMP_saxs.FitParameters_get_c2(self)
1116 
1117 
1118  def get_scale(self):
1119  """get_scale(FitParameters self) -> double"""
1120  return _IMP_saxs.FitParameters_get_scale(self)
1121 
1122 
1123  def get_offset(self):
1124  """get_offset(FitParameters self) -> double"""
1125  return _IMP_saxs.FitParameters_get_offset(self)
1126 
1127 
1128  def get_default_chi(self):
1129  """get_default_chi(FitParameters self) -> double"""
1130  return _IMP_saxs.FitParameters_get_default_chi(self)
1131 
1132 
1133  def get_pdb_file_name(self):
1134  """get_pdb_file_name(FitParameters self) -> std::string"""
1135  return _IMP_saxs.FitParameters_get_pdb_file_name(self)
1136 
1137 
1138  def get_profile_file_name(self):
1139  """get_profile_file_name(FitParameters self) -> std::string"""
1140  return _IMP_saxs.FitParameters_get_profile_file_name(self)
1141 
1142 
1143  def get_mol_index(self):
1144  """get_mol_index(FitParameters self) -> int"""
1145  return _IMP_saxs.FitParameters_get_mol_index(self)
1146 
1147 
1148  def set_chi(self, chi):
1149  """set_chi(FitParameters self, double chi)"""
1150  return _IMP_saxs.FitParameters_set_chi(self, chi)
1151 
1152 
1153  def set_default_chi(self, chi):
1154  """set_default_chi(FitParameters self, double chi)"""
1155  return _IMP_saxs.FitParameters_set_default_chi(self, chi)
1156 
1157 
1158  def set_profile_file_name(self, file_name):
1159  """set_profile_file_name(FitParameters self, std::string file_name)"""
1160  return _IMP_saxs.FitParameters_set_profile_file_name(self, file_name)
1161 
1162 
1163  def set_pdb_file_name(self, file_name):
1164  """set_pdb_file_name(FitParameters self, std::string file_name)"""
1165  return _IMP_saxs.FitParameters_set_pdb_file_name(self, file_name)
1166 
1167 
1168  def set_mol_index(self, index):
1169  """set_mol_index(FitParameters self, int index)"""
1170  return _IMP_saxs.FitParameters_set_mol_index(self, index)
1171 
1172 
1173  def show(self, s):
1174  """show(FitParameters self, _ostream s)"""
1175  return _IMP_saxs.FitParameters_show(self, s)
1176 
1177  __swig_destroy__ = _IMP_saxs.delete_FitParameters
1178  __del__ = lambda self: None
1179 FitParameters_swigregister = _IMP_saxs.FitParameters_swigregister
1180 FitParameters_swigregister(FitParameters)
1181 
1182 class WeightedFitParameters(FitParameters):
1183  """Proxy of C++ IMP::saxs::WeightedFitParameters class."""
1184 
1185  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1186  __repr__ = _swig_repr
1187 
1188  def __init__(self, *args):
1189  """
1190  __init__(IMP::saxs::WeightedFitParameters self) -> WeightedFitParameters
1191  __init__(IMP::saxs::WeightedFitParameters self, double chi, double c1, double c2, IMP::Vector< double > const & weights) -> WeightedFitParameters
1192  """
1193  this = _IMP_saxs.new_WeightedFitParameters(*args)
1194  try:
1195  self.this.append(this)
1196  except __builtin__.Exception:
1197  self.this = this
1198 
1199  def get_weights(self):
1200  """get_weights(WeightedFitParameters self) -> IMP::Vector< double > const &"""
1201  return _IMP_saxs.WeightedFitParameters_get_weights(self)
1202 
1203 
1204  def set_weights(self, weights):
1205  """set_weights(WeightedFitParameters self, IMP::Vector< double > const & weights)"""
1206  return _IMP_saxs.WeightedFitParameters_set_weights(self, weights)
1207 
1208 
1209  def show(self, s):
1210  """show(WeightedFitParameters self, _ostream s)"""
1211  return _IMP_saxs.WeightedFitParameters_show(self, s)
1212 
1213  __swig_destroy__ = _IMP_saxs.delete_WeightedFitParameters
1214  __del__ = lambda self: None
1215 WeightedFitParameters_swigregister = _IMP_saxs.WeightedFitParameters_swigregister
1216 WeightedFitParameters_swigregister(WeightedFitParameters)
1217 
1218 class ChiScore(IMP.Object):
1219  """Proxy of C++ IMP::saxs::ChiScore class."""
1220 
1221  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1222 
1223  def __init__(self):
1224  """__init__(IMP::saxs::ChiScore self) -> ChiScore"""
1225  this = _IMP_saxs.new_ChiScore()
1226  try:
1227  self.this.append(this)
1228  except __builtin__.Exception:
1229  self.this = this
1230 
1231  def compute_score(self, exp_profile, model_profile, use_offset=False):
1232  """
1233  compute_score(ChiScore self, Profile exp_profile, Profile model_profile, bool use_offset=False) -> double
1234  compute_score(ChiScore self, Profile exp_profile, Profile model_profile) -> double
1235  """
1236  return _IMP_saxs.ChiScore_compute_score(self, exp_profile, model_profile, use_offset)
1237 
1238 
1239  def compute_scale_factor(self, exp_profile, model_profile, offset=0.0):
1240  """
1241  compute_scale_factor(ChiScore self, Profile exp_profile, Profile model_profile, double offset=0.0) -> double
1242  compute_scale_factor(ChiScore self, Profile exp_profile, Profile model_profile) -> double
1243  """
1244  return _IMP_saxs.ChiScore_compute_scale_factor(self, exp_profile, model_profile, offset)
1245 
1246 
1247  def compute_offset(self, exp_profile, model_profile):
1248  """compute_offset(ChiScore self, Profile exp_profile, Profile model_profile) -> double"""
1249  return _IMP_saxs.ChiScore_compute_offset(self, exp_profile, model_profile)
1250 
1251 
1252  def get_version_info(self):
1253  """get_version_info(ChiScore self) -> VersionInfo"""
1254  return _IMP_saxs.ChiScore_get_version_info(self)
1255 
1256 
1257  def __str__(self):
1258  """__str__(ChiScore self) -> std::string"""
1259  return _IMP_saxs.ChiScore___str__(self)
1260 
1261 
1262  def __repr__(self):
1263  """__repr__(ChiScore self) -> std::string"""
1264  return _IMP_saxs.ChiScore___repr__(self)
1265 
1266 
1267  @staticmethod
1268  def get_from(o):
1269  return _object_cast_to_ChiScore(o)
1270 
1271 ChiScore_swigregister = _IMP_saxs.ChiScore_swigregister
1272 ChiScore_swigregister(ChiScore)
1273 
1274 class ChiScoreLog(IMP.Object):
1275  """Proxy of C++ IMP::saxs::ChiScoreLog class."""
1276 
1277  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1278 
1279  def __init__(self):
1280  """__init__(IMP::saxs::ChiScoreLog self) -> ChiScoreLog"""
1281  this = _IMP_saxs.new_ChiScoreLog()
1282  try:
1283  self.this.append(this)
1284  except __builtin__.Exception:
1285  self.this = this
1286 
1287  def compute_score(self, *args):
1288  """
1289  compute_score(ChiScoreLog self, Profile exp_profile, Profile model_profile, bool use_offset=False) -> double
1290  compute_score(ChiScoreLog self, Profile exp_profile, Profile model_profile) -> double
1291  compute_score(ChiScoreLog self, Profile exp_profile, Profile model_profile, double min_q, double max_q) -> double
1292  """
1293  return _IMP_saxs.ChiScoreLog_compute_score(self, *args)
1294 
1295 
1296  def compute_scale_factor(self, exp_profile, model_profile, offset=0.0):
1297  """
1298  compute_scale_factor(ChiScoreLog self, Profile exp_profile, Profile model_profile, double offset=0.0) -> double
1299  compute_scale_factor(ChiScoreLog self, Profile exp_profile, Profile model_profile) -> double
1300  """
1301  return _IMP_saxs.ChiScoreLog_compute_scale_factor(self, exp_profile, model_profile, offset)
1302 
1303 
1304  def compute_offset(self, exp_profile, model_profile):
1305  """compute_offset(ChiScoreLog self, Profile exp_profile, Profile model_profile) -> double"""
1306  return _IMP_saxs.ChiScoreLog_compute_offset(self, exp_profile, model_profile)
1307 
1308 
1309  def get_version_info(self):
1310  """get_version_info(ChiScoreLog self) -> VersionInfo"""
1311  return _IMP_saxs.ChiScoreLog_get_version_info(self)
1312 
1313 
1314  def __str__(self):
1315  """__str__(ChiScoreLog self) -> std::string"""
1316  return _IMP_saxs.ChiScoreLog___str__(self)
1317 
1318 
1319  def __repr__(self):
1320  """__repr__(ChiScoreLog self) -> std::string"""
1321  return _IMP_saxs.ChiScoreLog___repr__(self)
1322 
1323 
1324  @staticmethod
1325  def get_from(o):
1326  return _object_cast_to_ChiScoreLog(o)
1327 
1328 ChiScoreLog_swigregister = _IMP_saxs.ChiScoreLog_swigregister
1329 ChiScoreLog_swigregister(ChiScoreLog)
1330 
1331 class ProfileFitterChi(IMP.Object):
1332  """Proxy of C++ IMP::saxs::ProfileFitter<(IMP::saxs::ChiScore)> class."""
1333 
1334  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1335  __repr__ = _swig_repr
1336 
1337  def __init__(self, *args):
1338  """
1339  __init__(IMP::saxs::ProfileFitter<(IMP::saxs::ChiScore)> self, Profile exp_profile) -> ProfileFitterChi
1340  __init__(IMP::saxs::ProfileFitter<(IMP::saxs::ChiScore)> self, Profile exp_profile, ChiScore sf) -> ProfileFitterChi
1341  """
1342  this = _IMP_saxs.new_ProfileFitterChi(*args)
1343  try:
1344  self.this.append(this)
1345  except __builtin__.Exception:
1346  self.this = this
1347 
1348  def compute_score(self, *args):
1349  """
1350  compute_score(ProfileFitterChi self, Profile model_profile, bool use_offset=False, std::string const fit_file_name) -> double
1351  compute_score(ProfileFitterChi self, Profile model_profile, bool use_offset=False) -> double
1352  compute_score(ProfileFitterChi self, Profile model_profile) -> double
1353  """
1354  return _IMP_saxs.ProfileFitterChi_compute_score(self, *args)
1355 
1356 
1357  def fit_profile(self, *args):
1358  """
1359  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
1360  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) -> FitParameters
1361  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) -> FitParameters
1362  fit_profile(ProfileFitterChi self, Profile partial_profile, double min_c1=0.95, double max_c1=1.05, double min_c2=-2.0) -> FitParameters
1363  fit_profile(ProfileFitterChi self, Profile partial_profile, double min_c1=0.95, double max_c1=1.05) -> FitParameters
1364  fit_profile(ProfileFitterChi self, Profile partial_profile, double min_c1=0.95) -> FitParameters
1365  fit_profile(ProfileFitterChi self, Profile partial_profile) -> FitParameters
1366  """
1367  return _IMP_saxs.ProfileFitterChi_fit_profile(self, *args)
1368 
1369 
1370  def compute_scale_factor(self, model_profile, offset=0.0):
1371  """
1372  compute_scale_factor(ProfileFitterChi self, Profile model_profile, double offset=0.0) -> double
1373  compute_scale_factor(ProfileFitterChi self, Profile model_profile) -> double
1374  """
1375  return _IMP_saxs.ProfileFitterChi_compute_scale_factor(self, model_profile, offset)
1376 
1377 
1378  def compute_offset(self, model_profile):
1379  """compute_offset(ProfileFitterChi self, Profile model_profile) -> double"""
1380  return _IMP_saxs.ProfileFitterChi_compute_offset(self, model_profile)
1381 
1382 
1383  def resample(self, model_profile, resampled_profile):
1384  """resample(ProfileFitterChi self, Profile model_profile, Profile resampled_profile)"""
1385  return _IMP_saxs.ProfileFitterChi_resample(self, model_profile, resampled_profile)
1386 
1387 
1388  def write_SAXS_fit_file(self, file_name, model_profile, chi_square, c=1, offset=0):
1389  """
1390  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)
1391  write_SAXS_fit_file(ProfileFitterChi self, std::string const & file_name, Profile model_profile, double const chi_square, double const c=1)
1392  write_SAXS_fit_file(ProfileFitterChi self, std::string const & file_name, Profile model_profile, double const chi_square)
1393  """
1394  return _IMP_saxs.ProfileFitterChi_write_SAXS_fit_file(self, file_name, model_profile, chi_square, c, offset)
1395 
1396  __swig_destroy__ = _IMP_saxs.delete_ProfileFitterChi
1397  __del__ = lambda self: None
1398 ProfileFitterChi_swigregister = _IMP_saxs.ProfileFitterChi_swigregister
1399 ProfileFitterChi_swigregister(ProfileFitterChi)
1400 
1401 class WeightedProfileFitterChi(ProfileFitterChi):
1402  """Proxy of C++ IMP::saxs::WeightedProfileFitter<(IMP::saxs::ChiScore)> class."""
1403 
1404  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1405  __repr__ = _swig_repr
1406 
1407  def __init__(self, exp_profile):
1408  """__init__(IMP::saxs::WeightedProfileFitter<(IMP::saxs::ChiScore)> self, Profile exp_profile) -> WeightedProfileFitterChi"""
1409  this = _IMP_saxs.new_WeightedProfileFitterChi(exp_profile)
1410  try:
1411  self.this.append(this)
1412  except __builtin__.Exception:
1413  self.this = this
1414 
1415  def compute_score(self, profiles, weights, use_offset=False, NNLS=True):
1416  """
1417  compute_score(WeightedProfileFitterChi self, IMP::saxs::ProfilesTemp const & profiles, IMP::Vector< double > & weights, bool use_offset=False, bool NNLS=True) -> double
1418  compute_score(WeightedProfileFitterChi self, IMP::saxs::ProfilesTemp const & profiles, IMP::Vector< double > & weights, bool use_offset=False) -> double
1419  compute_score(WeightedProfileFitterChi self, IMP::saxs::ProfilesTemp const & profiles, IMP::Vector< double > & weights) -> double
1420  """
1421  return _IMP_saxs.WeightedProfileFitterChi_compute_score(self, profiles, weights, use_offset, NNLS)
1422 
1423 
1424  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):
1425  """
1426  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
1427  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) -> WeightedFitParameters
1428  fit_profile(WeightedProfileFitterChi self, IMP::saxs::ProfilesTemp partial_profiles, double min_c1=0.95, double max_c1=1.05, double min_c2=-2.0) -> WeightedFitParameters
1429  fit_profile(WeightedProfileFitterChi self, IMP::saxs::ProfilesTemp partial_profiles, double min_c1=0.95, double max_c1=1.05) -> WeightedFitParameters
1430  fit_profile(WeightedProfileFitterChi self, IMP::saxs::ProfilesTemp partial_profiles, double min_c1=0.95) -> WeightedFitParameters
1431  fit_profile(WeightedProfileFitterChi self, IMP::saxs::ProfilesTemp partial_profiles) -> WeightedFitParameters
1432  """
1433  return _IMP_saxs.WeightedProfileFitterChi_fit_profile(self, partial_profiles, min_c1, max_c1, min_c2, max_c2, use_offset)
1434 
1435 
1436  def write_fit_file(self, partial_profiles, fp, fit_file_name, use_offset=False):
1437  """
1438  write_fit_file(WeightedProfileFitterChi self, IMP::saxs::ProfilesTemp partial_profiles, WeightedFitParameters fp, std::string const fit_file_name, bool use_offset=False)
1439  write_fit_file(WeightedProfileFitterChi self, IMP::saxs::ProfilesTemp partial_profiles, WeightedFitParameters fp, std::string const fit_file_name)
1440  """
1441  return _IMP_saxs.WeightedProfileFitterChi_write_fit_file(self, partial_profiles, fp, fit_file_name, use_offset)
1442 
1443  __swig_destroy__ = _IMP_saxs.delete_WeightedProfileFitterChi
1444  __del__ = lambda self: None
1445 WeightedProfileFitterChi_swigregister = _IMP_saxs.WeightedProfileFitterChi_swigregister
1446 WeightedProfileFitterChi_swigregister(WeightedProfileFitterChi)
1447 
1448 class Restraint(IMP.Restraint):
1449  """Proxy of C++ IMP::saxs::Restraint class."""
1450 
1451  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1452  __repr__ = _swig_repr
1453 
1454  def __init__(self, *args):
1455  """
1456  __init__(IMP::saxs::Restraint self, IMP::Particles const & particles, Profile exp_profile, IMP::saxs::FormFactorType ff_type) -> Restraint
1457  __init__(IMP::saxs::Restraint self, IMP::Particles const & particles, Profile exp_profile) -> Restraint
1458  """
1459  this = _IMP_saxs.new_Restraint(*args)
1460  try:
1461  self.this.append(this)
1462  except __builtin__.Exception:
1463  self.this = this
1464 
1465  if self.__class__ != Restraint:
1466  _director_objects.register(self)
1467 
1468 
1469 
1470 
1471  def do_get_inputs(self):
1472  """do_get_inputs(Restraint self) -> IMP::ModelObjectsTemp"""
1473  return _IMP_saxs.Restraint_do_get_inputs(self)
1474 
1475 
1476  def get_version_info(self):
1477  """get_version_info(Restraint self) -> VersionInfo"""
1478  return _IMP_saxs.Restraint_get_version_info(self)
1479 
1480 Restraint_swigregister = _IMP_saxs.Restraint_swigregister
1481 Restraint_swigregister(Restraint)
1482 
1483 class RadiusOfGyrationRestraint(Restraint):
1484  """Proxy of C++ IMP::saxs::RadiusOfGyrationRestraint class."""
1485 
1486  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1487  __repr__ = _swig_repr
1488 
1489  def __init__(self, particles, exp_profile, end_q_rg=1.3):
1490  """
1491  __init__(IMP::saxs::RadiusOfGyrationRestraint self, IMP::Particles const & particles, Profile exp_profile, double const end_q_rg=1.3) -> RadiusOfGyrationRestraint
1492  __init__(IMP::saxs::RadiusOfGyrationRestraint self, IMP::Particles const & particles, Profile exp_profile) -> RadiusOfGyrationRestraint
1493  """
1494  this = _IMP_saxs.new_RadiusOfGyrationRestraint(particles, exp_profile, end_q_rg)
1495  try:
1496  self.this.append(this)
1497  except __builtin__.Exception:
1498  self.this = this
1499 RadiusOfGyrationRestraint_swigregister = _IMP_saxs.RadiusOfGyrationRestraint_swigregister
1500 RadiusOfGyrationRestraint_swigregister(RadiusOfGyrationRestraint)
1501 
1502 class FloatDistribution(DistBase):
1503  """Proxy of C++ IMP::saxs::Distribution<(double)> class."""
1504 
1505  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1506  __repr__ = _swig_repr
1507 
1508  def __init__(self, *args):
1509  """
1510  __init__(IMP::saxs::Distribution<(double)> self, double bin_size) -> FloatDistribution
1511  __init__(IMP::saxs::Distribution<(double)> self) -> FloatDistribution
1512  """
1513  this = _IMP_saxs.new_FloatDistribution(*args)
1514  try:
1515  self.this.append(this)
1516  except __builtin__.Exception:
1517  self.this = this
1518 
1519  def get_max_distance(self):
1520  """get_max_distance(FloatDistribution self) -> double"""
1521  return _IMP_saxs.FloatDistribution_get_max_distance(self)
1522 
1523 
1524  def get_bin_size(self):
1525  """get_bin_size(FloatDistribution self) -> double"""
1526  return _IMP_saxs.FloatDistribution_get_bin_size(self)
1527 
1528 
1529  def get_index_from_distance(self, dist):
1530  """get_index_from_distance(FloatDistribution self, double dist) -> unsigned int"""
1531  return _IMP_saxs.FloatDistribution_get_index_from_distance(self, dist)
1532 
1533 
1534  def get_distance_from_index(self, index):
1535  """get_distance_from_index(FloatDistribution self, unsigned int index) -> double"""
1536  return _IMP_saxs.FloatDistribution_get_distance_from_index(self, index)
1537 
1538  __swig_destroy__ = _IMP_saxs.delete_FloatDistribution
1539  __del__ = lambda self: None
1540 FloatDistribution_swigregister = _IMP_saxs.FloatDistribution_swigregister
1541 FloatDistribution_swigregister(FloatDistribution)
1542 
1543 class VectorDistribution(object):
1544  """Proxy of C++ IMP::saxs::Distribution<(IMP::algebra::Vector3D)> class."""
1545 
1546  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1547  __repr__ = _swig_repr
1548 
1549  def __init__(self, *args):
1550  """
1551  __init__(IMP::saxs::Distribution<(IMP::algebra::Vector3D)> self, double bin_size) -> VectorDistribution
1552  __init__(IMP::saxs::Distribution<(IMP::algebra::Vector3D)> self) -> VectorDistribution
1553  """
1554  this = _IMP_saxs.new_VectorDistribution(*args)
1555  try:
1556  self.this.append(this)
1557  except __builtin__.Exception:
1558  self.this = this
1559 
1560  def get_max_distance(self):
1561  """get_max_distance(VectorDistribution self) -> double"""
1562  return _IMP_saxs.VectorDistribution_get_max_distance(self)
1563 
1564 
1565  def get_bin_size(self):
1566  """get_bin_size(VectorDistribution self) -> double"""
1567  return _IMP_saxs.VectorDistribution_get_bin_size(self)
1568 
1569 
1570  def get_index_from_distance(self, dist):
1571  """get_index_from_distance(VectorDistribution self, double dist) -> unsigned int"""
1572  return _IMP_saxs.VectorDistribution_get_index_from_distance(self, dist)
1573 
1574 
1575  def get_distance_from_index(self, index):
1576  """get_distance_from_index(VectorDistribution self, unsigned int index) -> double"""
1577  return _IMP_saxs.VectorDistribution_get_distance_from_index(self, index)
1578 
1579  __swig_destroy__ = _IMP_saxs.delete_VectorDistribution
1580  __del__ = lambda self: None
1581 VectorDistribution_swigregister = _IMP_saxs.VectorDistribution_swigregister
1582 VectorDistribution_swigregister(VectorDistribution)
1583 
1584 class RadialDistributionFunction(FloatDistribution):
1585  """Proxy of C++ IMP::saxs::RadialDistributionFunction class."""
1586 
1587  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1588  __repr__ = _swig_repr
1589 
1590  def __init__(self, *args):
1591  """
1592  __init__(IMP::saxs::RadialDistributionFunction self, double bin_size) -> RadialDistributionFunction
1593  __init__(IMP::saxs::RadialDistributionFunction self) -> RadialDistributionFunction
1594  __init__(IMP::saxs::RadialDistributionFunction self, std::string const & file_name) -> RadialDistributionFunction
1595  """
1596  this = _IMP_saxs.new_RadialDistributionFunction(*args)
1597  try:
1598  self.this.append(this)
1599  except __builtin__.Exception:
1600  self.this = this
1601 
1602  def scale(self, c):
1603  """scale(RadialDistributionFunction self, double c)"""
1604  return _IMP_saxs.RadialDistributionFunction_scale(self, c)
1605 
1606 
1607  def add(self, model_pr):
1608  """add(RadialDistributionFunction self, RadialDistributionFunction model_pr)"""
1609  return _IMP_saxs.RadialDistributionFunction_add(self, model_pr)
1610 
1611 
1612  def show(self, *args):
1613  """
1614  show(RadialDistributionFunction self, _ostream out)
1615  show(RadialDistributionFunction self)
1616  """
1617  return _IMP_saxs.RadialDistributionFunction_show(self, *args)
1618 
1619 
1620  def R_factor_score(self, *args):
1621  """
1622  R_factor_score(RadialDistributionFunction self, RadialDistributionFunction model_pr, std::string const & file_name) -> double
1623  R_factor_score(RadialDistributionFunction self, RadialDistributionFunction model_pr) -> double
1624  """
1625  return _IMP_saxs.RadialDistributionFunction_R_factor_score(self, *args)
1626 
1627 
1628  def fit(self, *args):
1629  """
1630  fit(RadialDistributionFunction self, RadialDistributionFunction model_pr, std::string const & file_name) -> double
1631  fit(RadialDistributionFunction self, RadialDistributionFunction model_pr) -> double
1632  """
1633  return _IMP_saxs.RadialDistributionFunction_fit(self, *args)
1634 
1635 
1636  def normalize(self):
1637  """normalize(RadialDistributionFunction self)"""
1638  return _IMP_saxs.RadialDistributionFunction_normalize(self)
1639 
1640 
1641  def add_to_distribution(self, dist, value):
1642  """add_to_distribution(RadialDistributionFunction self, double dist, double value)"""
1643  return _IMP_saxs.RadialDistributionFunction_add_to_distribution(self, dist, value)
1644 
1645  __swig_destroy__ = _IMP_saxs.delete_RadialDistributionFunction
1646  __del__ = lambda self: None
1647 RadialDistributionFunction_swigregister = _IMP_saxs.RadialDistributionFunction_swigregister
1648 RadialDistributionFunction_swigregister(RadialDistributionFunction)
1649 
1650 class DeltaDistributionFunction(VectorDistribution):
1651  """Proxy of C++ IMP::saxs::DeltaDistributionFunction class."""
1652 
1653  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1654  __repr__ = _swig_repr
1655 
1656  def __init__(self, *args):
1657  """
1658  __init__(IMP::saxs::DeltaDistributionFunction self, IMP::Particles const & particles, double max_distance=0.0, double bin_size) -> DeltaDistributionFunction
1659  __init__(IMP::saxs::DeltaDistributionFunction self, IMP::Particles const & particles, double max_distance=0.0) -> DeltaDistributionFunction
1660  __init__(IMP::saxs::DeltaDistributionFunction self, IMP::Particles const & particles) -> DeltaDistributionFunction
1661  """
1662  this = _IMP_saxs.new_DeltaDistributionFunction(*args)
1663  try:
1664  self.this.append(this)
1665  except __builtin__.Exception:
1666  self.this = this
1667 
1668  def calculate_derivative_distribution(self, particle):
1669  """calculate_derivative_distribution(DeltaDistributionFunction self, Particle particle)"""
1670  return _IMP_saxs.DeltaDistributionFunction_calculate_derivative_distribution(self, particle)
1671 
1672 
1673  def show(self, *args):
1674  """
1675  show(DeltaDistributionFunction self, _ostream out, std::string prefix)
1676  show(DeltaDistributionFunction self, _ostream out)
1677  show(DeltaDistributionFunction self)
1678  """
1679  return _IMP_saxs.DeltaDistributionFunction_show(self, *args)
1680 
1681  __swig_destroy__ = _IMP_saxs.delete_DeltaDistributionFunction
1682  __del__ = lambda self: None
1683 DeltaDistributionFunction_swigregister = _IMP_saxs.DeltaDistributionFunction_swigregister
1684 DeltaDistributionFunction_swigregister(DeltaDistributionFunction)
1685 
1686 class SolventAccessibleSurface(object):
1687  """Proxy of C++ IMP::saxs::SolventAccessibleSurface class."""
1688 
1689  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1690  __repr__ = _swig_repr
1691 
1692  def get_solvent_accessibility(self, points, probe_radius=1.8, density=5.0):
1693  """
1694  get_solvent_accessibility(SolventAccessibleSurface self, IMP::core::XYZRs const & points, double probe_radius=1.8, double density=5.0) -> IMP::Vector< double >
1695  get_solvent_accessibility(SolventAccessibleSurface self, IMP::core::XYZRs const & points, double probe_radius=1.8) -> IMP::Vector< double >
1696  get_solvent_accessibility(SolventAccessibleSurface self, IMP::core::XYZRs const & points) -> IMP::Vector< double >
1697  """
1698  return _IMP_saxs.SolventAccessibleSurface_get_solvent_accessibility(self, points, probe_radius, density)
1699 
1700 
1701  def __init__(self):
1702  """__init__(IMP::saxs::SolventAccessibleSurface self) -> SolventAccessibleSurface"""
1703  this = _IMP_saxs.new_SolventAccessibleSurface()
1704  try:
1705  self.this.append(this)
1706  except __builtin__.Exception:
1707  self.this = this
1708  __swig_destroy__ = _IMP_saxs.delete_SolventAccessibleSurface
1709  __del__ = lambda self: None
1710 SolventAccessibleSurface_swigregister = _IMP_saxs.SolventAccessibleSurface_swigregister
1711 SolventAccessibleSurface_swigregister(SolventAccessibleSurface)
1712 
1713 class ProfileFitterChiLog(IMP.Object):
1714  """Proxy of C++ IMP::saxs::ProfileFitter<(IMP::saxs::ChiScoreLog)> class."""
1715 
1716  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1717  __repr__ = _swig_repr
1718 
1719  def __init__(self, *args):
1720  """
1721  __init__(IMP::saxs::ProfileFitter<(IMP::saxs::ChiScoreLog)> self, Profile exp_profile) -> ProfileFitterChiLog
1722  __init__(IMP::saxs::ProfileFitter<(IMP::saxs::ChiScoreLog)> self, Profile exp_profile, ChiScoreLog sf) -> ProfileFitterChiLog
1723  """
1724  this = _IMP_saxs.new_ProfileFitterChiLog(*args)
1725  try:
1726  self.this.append(this)
1727  except __builtin__.Exception:
1728  self.this = this
1729 
1730  def compute_score(self, *args):
1731  """
1732  compute_score(ProfileFitterChiLog self, Profile model_profile, bool use_offset=False, std::string const fit_file_name) -> double
1733  compute_score(ProfileFitterChiLog self, Profile model_profile, bool use_offset=False) -> double
1734  compute_score(ProfileFitterChiLog self, Profile model_profile) -> double
1735  """
1736  return _IMP_saxs.ProfileFitterChiLog_compute_score(self, *args)
1737 
1738 
1739  def fit_profile(self, *args):
1740  """
1741  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
1742  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) -> FitParameters
1743  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) -> FitParameters
1744  fit_profile(ProfileFitterChiLog self, Profile partial_profile, double min_c1=0.95, double max_c1=1.05, double min_c2=-2.0) -> FitParameters
1745  fit_profile(ProfileFitterChiLog self, Profile partial_profile, double min_c1=0.95, double max_c1=1.05) -> FitParameters
1746  fit_profile(ProfileFitterChiLog self, Profile partial_profile, double min_c1=0.95) -> FitParameters
1747  fit_profile(ProfileFitterChiLog self, Profile partial_profile) -> FitParameters
1748  """
1749  return _IMP_saxs.ProfileFitterChiLog_fit_profile(self, *args)
1750 
1751 
1752  def compute_scale_factor(self, model_profile, offset=0.0):
1753  """
1754  compute_scale_factor(ProfileFitterChiLog self, Profile model_profile, double offset=0.0) -> double
1755  compute_scale_factor(ProfileFitterChiLog self, Profile model_profile) -> double
1756  """
1757  return _IMP_saxs.ProfileFitterChiLog_compute_scale_factor(self, model_profile, offset)
1758 
1759 
1760  def compute_offset(self, model_profile):
1761  """compute_offset(ProfileFitterChiLog self, Profile model_profile) -> double"""
1762  return _IMP_saxs.ProfileFitterChiLog_compute_offset(self, model_profile)
1763 
1764 
1765  def resample(self, model_profile, resampled_profile):
1766  """resample(ProfileFitterChiLog self, Profile model_profile, Profile resampled_profile)"""
1767  return _IMP_saxs.ProfileFitterChiLog_resample(self, model_profile, resampled_profile)
1768 
1769 
1770  def write_SAXS_fit_file(self, file_name, model_profile, chi_square, c=1, offset=0):
1771  """
1772  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)
1773  write_SAXS_fit_file(ProfileFitterChiLog self, std::string const & file_name, Profile model_profile, double const chi_square, double const c=1)
1774  write_SAXS_fit_file(ProfileFitterChiLog self, std::string const & file_name, Profile model_profile, double const chi_square)
1775  """
1776  return _IMP_saxs.ProfileFitterChiLog_write_SAXS_fit_file(self, file_name, model_profile, chi_square, c, offset)
1777 
1778  __swig_destroy__ = _IMP_saxs.delete_ProfileFitterChiLog
1779  __del__ = lambda self: None
1780 ProfileFitterChiLog_swigregister = _IMP_saxs.ProfileFitterChiLog_swigregister
1781 ProfileFitterChiLog_swigregister(ProfileFitterChiLog)
1782 
1783 class ProfileFitterRatioVolatility(IMP.Object):
1784  """Proxy of C++ IMP::saxs::ProfileFitter<(IMP::saxs::RatioVolatilityScore)> class."""
1785 
1786  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1787  __repr__ = _swig_repr
1788 
1789  def __init__(self, *args):
1790  """
1791  __init__(IMP::saxs::ProfileFitter<(IMP::saxs::RatioVolatilityScore)> self, Profile exp_profile) -> ProfileFitterRatioVolatility
1792  __init__(IMP::saxs::ProfileFitter<(IMP::saxs::RatioVolatilityScore)> self, Profile exp_profile, IMP::saxs::RatioVolatilityScore * sf) -> ProfileFitterRatioVolatility
1793  """
1794  this = _IMP_saxs.new_ProfileFitterRatioVolatility(*args)
1795  try:
1796  self.this.append(this)
1797  except __builtin__.Exception:
1798  self.this = this
1799 
1800  def compute_score(self, *args):
1801  """
1802  compute_score(ProfileFitterRatioVolatility self, Profile model_profile, bool use_offset=False, std::string const fit_file_name) -> double
1803  compute_score(ProfileFitterRatioVolatility self, Profile model_profile, bool use_offset=False) -> double
1804  compute_score(ProfileFitterRatioVolatility self, Profile model_profile) -> double
1805  """
1806  return _IMP_saxs.ProfileFitterRatioVolatility_compute_score(self, *args)
1807 
1808 
1809  def fit_profile(self, *args):
1810  """
1811  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
1812  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) -> FitParameters
1813  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) -> FitParameters
1814  fit_profile(ProfileFitterRatioVolatility self, Profile partial_profile, double min_c1=0.95, double max_c1=1.05, double min_c2=-2.0) -> FitParameters
1815  fit_profile(ProfileFitterRatioVolatility self, Profile partial_profile, double min_c1=0.95, double max_c1=1.05) -> FitParameters
1816  fit_profile(ProfileFitterRatioVolatility self, Profile partial_profile, double min_c1=0.95) -> FitParameters
1817  fit_profile(ProfileFitterRatioVolatility self, Profile partial_profile) -> FitParameters
1818  """
1819  return _IMP_saxs.ProfileFitterRatioVolatility_fit_profile(self, *args)
1820 
1821 
1822  def compute_scale_factor(self, model_profile, offset=0.0):
1823  """
1824  compute_scale_factor(ProfileFitterRatioVolatility self, Profile model_profile, double offset=0.0) -> double
1825  compute_scale_factor(ProfileFitterRatioVolatility self, Profile model_profile) -> double
1826  """
1827  return _IMP_saxs.ProfileFitterRatioVolatility_compute_scale_factor(self, model_profile, offset)
1828 
1829 
1830  def compute_offset(self, model_profile):
1831  """compute_offset(ProfileFitterRatioVolatility self, Profile model_profile) -> double"""
1832  return _IMP_saxs.ProfileFitterRatioVolatility_compute_offset(self, model_profile)
1833 
1834 
1835  def resample(self, model_profile, resampled_profile):
1836  """resample(ProfileFitterRatioVolatility self, Profile model_profile, Profile resampled_profile)"""
1837  return _IMP_saxs.ProfileFitterRatioVolatility_resample(self, model_profile, resampled_profile)
1838 
1839 
1840  def write_SAXS_fit_file(self, file_name, model_profile, chi_square, c=1, offset=0):
1841  """
1842  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)
1843  write_SAXS_fit_file(ProfileFitterRatioVolatility self, std::string const & file_name, Profile model_profile, double const chi_square, double const c=1)
1844  write_SAXS_fit_file(ProfileFitterRatioVolatility self, std::string const & file_name, Profile model_profile, double const chi_square)
1845  """
1846  return _IMP_saxs.ProfileFitterRatioVolatility_write_SAXS_fit_file(self, file_name, model_profile, chi_square, c, offset)
1847 
1848  __swig_destroy__ = _IMP_saxs.delete_ProfileFitterRatioVolatility
1849  __del__ = lambda self: None
1850 ProfileFitterRatioVolatility_swigregister = _IMP_saxs.ProfileFitterRatioVolatility_swigregister
1851 ProfileFitterRatioVolatility_swigregister(ProfileFitterRatioVolatility)
1852 
1853 
1854 def get_module_version():
1855  """get_module_version() -> std::string const"""
1856  return _IMP_saxs.get_module_version()
1857 
1858 def get_example_path(fname):
1859  """get_example_path(std::string fname) -> std::string"""
1860  return _IMP_saxs.get_example_path(fname)
1861 
1862 def get_data_path(fname):
1863  """get_data_path(std::string fname) -> std::string"""
1864  return _IMP_saxs.get_data_path(fname)
1865 
1866 from . import _version_check
1867 _version_check.check_version(get_module_version())
1868 __version__ = get_module_version()
1869 
1870 
1871 
Various classes to hold sets of particles.
Make CGAL functionality available to IMP.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
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:163
Common base class for heavy weight IMP objects.
Definition: Object.h:106
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:52