IMP  2.3.0
The Integrative Modeling Platform
saxs/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.2
3 #
4 # Do not make changes to this file unless you know what you are doing--modify
5 # the SWIG interface file instead.
6 
7 
8 
9 
10 
11 from sys import version_info
12 if version_info >= (2,6,0):
13  def swig_import_helper():
14  from os.path import dirname
15  import imp
16  fp = None
17  try:
18  fp, pathname, description = imp.find_module('_IMP_saxs', [dirname(__file__)])
19  except ImportError:
20  import _IMP_saxs
21  return _IMP_saxs
22  if fp is not None:
23  try:
24  _mod = imp.load_module('_IMP_saxs', fp, pathname, description)
25  finally:
26  fp.close()
27  return _mod
28  _IMP_saxs = swig_import_helper()
29  del swig_import_helper
30 else:
31  import _IMP_saxs
32 del version_info
33 try:
34  _swig_property = property
35 except NameError:
36  pass # Python < 2.2 doesn't have 'property'.
37 def _swig_setattr_nondynamic(self,class_type,name,value,static=1):
38  if (name == "thisown"): return self.this.own(value)
39  if (name == "this"):
40  if type(value).__name__ == 'SwigPyObject':
41  self.__dict__[name] = value
42  return
43  method = class_type.__swig_setmethods__.get(name,None)
44  if method: return method(self,value)
45  if (not static):
46  self.__dict__[name] = value
47  else:
48  raise AttributeError("You cannot add attributes to %s" % self)
49 
50 def _swig_setattr(self,class_type,name,value):
51  return _swig_setattr_nondynamic(self,class_type,name,value,0)
52 
53 def _swig_getattr(self,class_type,name):
54  if (name == "thisown"): return self.this.own()
55  method = class_type.__swig_getmethods__.get(name,None)
56  if method: return method(self)
57  raise AttributeError(name)
58 
59 def _swig_repr(self):
60  try: strthis = "proxy of " + self.this.__repr__()
61  except: strthis = ""
62  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
63 
64 try:
65  _object = object
66  _newclass = 1
67 except AttributeError:
68  class _object : pass
69  _newclass = 0
70 
71 
72 try:
73  import weakref
74  weakref_proxy = weakref.proxy
75 except:
76  weakref_proxy = lambda x: x
77 
78 
79 class IMP_SAXS_SwigPyIterator(_object):
80  """Proxy of C++ swig::IMP_SAXS_SwigPyIterator class"""
81  __swig_setmethods__ = {}
82  __setattr__ = lambda self, name, value: _swig_setattr(self, IMP_SAXS_SwigPyIterator, name, value)
83  __swig_getmethods__ = {}
84  __getattr__ = lambda self, name: _swig_getattr(self, IMP_SAXS_SwigPyIterator, name)
85  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
86  __repr__ = _swig_repr
87  __swig_destroy__ = _IMP_saxs.delete_IMP_SAXS_SwigPyIterator
88  __del__ = lambda self : None;
89  def value(self):
90  """value(IMP_SAXS_SwigPyIterator self) -> PyObject *"""
91  return _IMP_saxs.IMP_SAXS_SwigPyIterator_value(self)
92 
93  def incr(self, n=1):
94  """
95  incr(IMP_SAXS_SwigPyIterator self, size_t n=1) -> IMP_SAXS_SwigPyIterator
96  incr(IMP_SAXS_SwigPyIterator self) -> IMP_SAXS_SwigPyIterator
97  """
98  return _IMP_saxs.IMP_SAXS_SwigPyIterator_incr(self, n)
99 
100  def decr(self, n=1):
101  """
102  decr(IMP_SAXS_SwigPyIterator self, size_t n=1) -> IMP_SAXS_SwigPyIterator
103  decr(IMP_SAXS_SwigPyIterator self) -> IMP_SAXS_SwigPyIterator
104  """
105  return _IMP_saxs.IMP_SAXS_SwigPyIterator_decr(self, n)
106 
107  def distance(self, *args):
108  """distance(IMP_SAXS_SwigPyIterator self, IMP_SAXS_SwigPyIterator x) -> ptrdiff_t"""
109  return _IMP_saxs.IMP_SAXS_SwigPyIterator_distance(self, *args)
110 
111  def equal(self, *args):
112  """equal(IMP_SAXS_SwigPyIterator self, IMP_SAXS_SwigPyIterator x) -> bool"""
113  return _IMP_saxs.IMP_SAXS_SwigPyIterator_equal(self, *args)
114 
115  def copy(self):
116  """copy(IMP_SAXS_SwigPyIterator self) -> IMP_SAXS_SwigPyIterator"""
117  return _IMP_saxs.IMP_SAXS_SwigPyIterator_copy(self)
118 
119  def next(self):
120  """next(IMP_SAXS_SwigPyIterator self) -> PyObject *"""
121  return _IMP_saxs.IMP_SAXS_SwigPyIterator_next(self)
122 
123  def __next__(self):
124  """__next__(IMP_SAXS_SwigPyIterator self) -> PyObject *"""
125  return _IMP_saxs.IMP_SAXS_SwigPyIterator___next__(self)
126 
127  def previous(self):
128  """previous(IMP_SAXS_SwigPyIterator self) -> PyObject *"""
129  return _IMP_saxs.IMP_SAXS_SwigPyIterator_previous(self)
130 
131  def advance(self, *args):
132  """advance(IMP_SAXS_SwigPyIterator self, ptrdiff_t n) -> IMP_SAXS_SwigPyIterator"""
133  return _IMP_saxs.IMP_SAXS_SwigPyIterator_advance(self, *args)
134 
135  def __eq__(self, *args):
136  """__eq__(IMP_SAXS_SwigPyIterator self, IMP_SAXS_SwigPyIterator x) -> bool"""
137  return _IMP_saxs.IMP_SAXS_SwigPyIterator___eq__(self, *args)
138 
139  def __ne__(self, *args):
140  """__ne__(IMP_SAXS_SwigPyIterator self, IMP_SAXS_SwigPyIterator x) -> bool"""
141  return _IMP_saxs.IMP_SAXS_SwigPyIterator___ne__(self, *args)
142 
143  def __iadd__(self, *args):
144  """__iadd__(IMP_SAXS_SwigPyIterator self, ptrdiff_t n) -> IMP_SAXS_SwigPyIterator"""
145  return _IMP_saxs.IMP_SAXS_SwigPyIterator___iadd__(self, *args)
146 
147  def __isub__(self, *args):
148  """__isub__(IMP_SAXS_SwigPyIterator self, ptrdiff_t n) -> IMP_SAXS_SwigPyIterator"""
149  return _IMP_saxs.IMP_SAXS_SwigPyIterator___isub__(self, *args)
150 
151  def __add__(self, *args):
152  """__add__(IMP_SAXS_SwigPyIterator self, ptrdiff_t n) -> IMP_SAXS_SwigPyIterator"""
153  return _IMP_saxs.IMP_SAXS_SwigPyIterator___add__(self, *args)
154 
155  def __sub__(self, *args):
156  """
157  __sub__(IMP_SAXS_SwigPyIterator self, ptrdiff_t n) -> IMP_SAXS_SwigPyIterator
158  __sub__(IMP_SAXS_SwigPyIterator self, IMP_SAXS_SwigPyIterator x) -> ptrdiff_t
159  """
160  return _IMP_saxs.IMP_SAXS_SwigPyIterator___sub__(self, *args)
161 
162  def __iter__(self): return self
163 IMP_SAXS_SwigPyIterator_swigregister = _IMP_saxs.IMP_SAXS_SwigPyIterator_swigregister
164 IMP_SAXS_SwigPyIterator_swigregister(IMP_SAXS_SwigPyIterator)
165 
166 _value_types=[]
167 _object_types=[]
168 _raii_types=[]
169 _plural_types=[]
170 
171 IMP_DEBUG = _IMP_saxs.IMP_DEBUG
172 IMP_RELEASE = _IMP_saxs.IMP_RELEASE
173 IMP_SILENT = _IMP_saxs.IMP_SILENT
174 IMP_PROGRESS = _IMP_saxs.IMP_PROGRESS
175 IMP_TERSE = _IMP_saxs.IMP_TERSE
176 IMP_VERBOSE = _IMP_saxs.IMP_VERBOSE
177 IMP_MEMORY = _IMP_saxs.IMP_MEMORY
178 IMP_NONE = _IMP_saxs.IMP_NONE
179 IMP_USAGE = _IMP_saxs.IMP_USAGE
180 IMP_INTERNAL = _IMP_saxs.IMP_INTERNAL
181 IMP_BASE_HAS_LOG4CXX = _IMP_saxs.IMP_BASE_HAS_LOG4CXX
182 IMP_COMPILER_HAS_AUTO = _IMP_saxs.IMP_COMPILER_HAS_AUTO
183 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_saxs.IMP_COMPILER_HAS_DEBUG_VECTOR
184 IMP_BASE_HAS_BOOST_RANDOM = _IMP_saxs.IMP_BASE_HAS_BOOST_RANDOM
185 IMP_BASE_HAS_GPERFTOOLS = _IMP_saxs.IMP_BASE_HAS_GPERFTOOLS
186 IMP_BASE_HAS_TCMALLOC_HEAPCHECKER = _IMP_saxs.IMP_BASE_HAS_TCMALLOC_HEAPCHECKER
187 IMP_BASE_HAS_TCMALLOC_HEAPPROFILER = _IMP_saxs.IMP_BASE_HAS_TCMALLOC_HEAPPROFILER
188 IMPBASE_SHOW_WARNINGS = _IMP_saxs.IMPBASE_SHOW_WARNINGS
189 import sys
190 class _DirectorObjects(object):
191  """@internal Simple class to keep references to director objects
192  to prevent premature deletion."""
193  def __init__(self):
194  self._objects = []
195  def register(self, obj):
196  """Take a reference to a director object; will only work for
197  refcounted C++ classes"""
198  if hasattr(obj, 'get_ref_count'):
199  self._objects.append(obj)
200  def cleanup(self):
201  """Only drop our reference and allow cleanup by Python if no other
202  Python references exist (we hold 3 references: one in self._objects,
203  one in x, and one in the argument list for getrefcount) *and* no
204  other C++ references exist (the Python object always holds one)"""
205  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
206  or x.get_ref_count() > 1]
207 
208 
209  self._objects = objs
210  def get_object_count(self):
211  """Get number of director objects (useful for testing only)"""
212  return len(self._objects)
213 _director_objects = _DirectorObjects()
214 
215 DEFAULT_CHECK = _IMP_saxs.DEFAULT_CHECK
216 NONE = _IMP_saxs.NONE
217 USAGE = _IMP_saxs.USAGE
218 USAGE_AND_INTERNAL = _IMP_saxs.USAGE_AND_INTERNAL
219 
220 def set_check_level(*args):
221  """set_check_level(IMP::base::CheckLevel tf)"""
222  return _IMP_saxs.set_check_level(*args)
223 
224 def get_check_level():
225  """get_check_level() -> IMP::base::CheckLevel"""
226  return _IMP_saxs.get_check_level()
227 class _ostream(_object):
228  """Proxy of C++ std::ostream class"""
229  __swig_setmethods__ = {}
230  __setattr__ = lambda self, name, value: _swig_setattr(self, _ostream, name, value)
231  __swig_getmethods__ = {}
232  __getattr__ = lambda self, name: _swig_getattr(self, _ostream, name)
233  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined")
234  __repr__ = _swig_repr
235  def write(self, *args):
236  """write(_ostream self, char const * osa_buf)"""
237  return _IMP_saxs._ostream_write(self, *args)
238 
239 _ostream_swigregister = _IMP_saxs._ostream_swigregister
240 _ostream_swigregister(_ostream)
241 
242 IMP_COMPILER_HAS_OVERRIDE = _IMP_saxs.IMP_COMPILER_HAS_OVERRIDE
243 IMP_COMPILER_HAS_FINAL = _IMP_saxs.IMP_COMPILER_HAS_FINAL
244 IMP_HAS_NOEXCEPT = _IMP_saxs.IMP_HAS_NOEXCEPT
245 import IMP.base
246 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_saxs.IMP_CGAL_HAS_BOOST_FILESYSTEM
247 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
248 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_saxs.IMP_CGAL_HAS_BOOST_RANDOM
249 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_CGAL_HAS_BOOST_SYSTEM
250 IMPCGAL_SHOW_WARNINGS = _IMP_saxs.IMPCGAL_SHOW_WARNINGS
251 import IMP.cgal
252 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_saxs.IMP_ALGEBRA_HAS_IMP_CGAL
253 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_saxs.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
254 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
255 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_saxs.IMP_ALGEBRA_HAS_BOOST_RANDOM
256 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_ALGEBRA_HAS_BOOST_SYSTEM
257 IMP_ALGEBRA_HAS_CGAL = _IMP_saxs.IMP_ALGEBRA_HAS_CGAL
258 IMP_ALGEBRA_HAS_ANN = _IMP_saxs.IMP_ALGEBRA_HAS_ANN
259 IMPALGEBRA_SHOW_WARNINGS = _IMP_saxs.IMPALGEBRA_SHOW_WARNINGS
260 import IMP.algebra
261 IMP_KERNEL_HAS_IMP_CGAL = _IMP_saxs.IMP_KERNEL_HAS_IMP_CGAL
262 IMP_KERNEL_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_KERNEL_HAS_BOOST_PROGRAMOPTIONS
263 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_saxs.IMP_KERNEL_HAS_BOOST_RANDOM
264 IMP_KERNEL_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_KERNEL_HAS_BOOST_SYSTEM
265 IMP_KERNEL_HAS_CGAL = _IMP_saxs.IMP_KERNEL_HAS_CGAL
266 IMPKERNEL_SHOW_WARNINGS = _IMP_saxs.IMPKERNEL_SHOW_WARNINGS
267 import IMP.kernel
268 IMP_DISPLAY_HAS_IMP_BASE = _IMP_saxs.IMP_DISPLAY_HAS_IMP_BASE
269 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_saxs.IMP_DISPLAY_HAS_IMP_CGAL
270 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_saxs.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
271 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
272 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_saxs.IMP_DISPLAY_HAS_BOOST_RANDOM
273 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_DISPLAY_HAS_BOOST_SYSTEM
274 IMP_DISPLAY_HAS_CGAL = _IMP_saxs.IMP_DISPLAY_HAS_CGAL
275 IMPDISPLAY_SHOW_WARNINGS = _IMP_saxs.IMPDISPLAY_SHOW_WARNINGS
276 import IMP.display
277 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_saxs.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
278 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_saxs.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
279 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
280 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_saxs.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
281 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
282 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_saxs.IMP_SCORE_FUNCTOR_HAS_CGAL
283 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_saxs.IMP_SCORE_FUNCTOR_HAS_HDF5
284 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_saxs.IMPSCOREFUNCTOR_SHOW_WARNINGS
285 import IMP.score_functor
286 IMP_CORE_HAS_IMP_BASE = _IMP_saxs.IMP_CORE_HAS_IMP_BASE
287 IMP_CORE_HAS_IMP_CGAL = _IMP_saxs.IMP_CORE_HAS_IMP_CGAL
288 IMP_CORE_HAS_IMP_KERNEL = _IMP_saxs.IMP_CORE_HAS_IMP_KERNEL
289 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_saxs.IMP_CORE_HAS_BOOST_FILESYSTEM
290 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
291 IMP_CORE_HAS_BOOST_RANDOM = _IMP_saxs.IMP_CORE_HAS_BOOST_RANDOM
292 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_CORE_HAS_BOOST_SYSTEM
293 IMP_CORE_HAS_CGAL = _IMP_saxs.IMP_CORE_HAS_CGAL
294 IMP_CORE_HAS_HDF5 = _IMP_saxs.IMP_CORE_HAS_HDF5
295 IMPCORE_SHOW_WARNINGS = _IMP_saxs.IMPCORE_SHOW_WARNINGS
296 import IMP.core
297 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_saxs.IMP_CONTAINER_HAS_IMP_ALGEBRA
298 IMP_CONTAINER_HAS_IMP_BASE = _IMP_saxs.IMP_CONTAINER_HAS_IMP_BASE
299 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_saxs.IMP_CONTAINER_HAS_IMP_CGAL
300 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_saxs.IMP_CONTAINER_HAS_IMP_DISPLAY
301 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_saxs.IMP_CONTAINER_HAS_IMP_KERNEL
302 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_saxs.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
303 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_saxs.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
304 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
305 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_saxs.IMP_CONTAINER_HAS_BOOST_RANDOM
306 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_CONTAINER_HAS_BOOST_SYSTEM
307 IMP_CONTAINER_HAS_CGAL = _IMP_saxs.IMP_CONTAINER_HAS_CGAL
308 IMP_CONTAINER_HAS_HDF5 = _IMP_saxs.IMP_CONTAINER_HAS_HDF5
309 IMPCONTAINER_SHOW_WARNINGS = _IMP_saxs.IMPCONTAINER_SHOW_WARNINGS
310 import IMP.container
311 IMP_ATOM_HAS_IMP_BASE = _IMP_saxs.IMP_ATOM_HAS_IMP_BASE
312 IMP_ATOM_HAS_IMP_CGAL = _IMP_saxs.IMP_ATOM_HAS_IMP_CGAL
313 IMP_ATOM_HAS_IMP_KERNEL = _IMP_saxs.IMP_ATOM_HAS_IMP_KERNEL
314 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_saxs.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
315 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
316 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_saxs.IMP_ATOM_HAS_BOOST_RANDOM
317 IMP_ATOM_HAS_BOOST_REGEX = _IMP_saxs.IMP_ATOM_HAS_BOOST_REGEX
318 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_ATOM_HAS_BOOST_SYSTEM
319 IMP_ATOM_HAS_CGAL = _IMP_saxs.IMP_ATOM_HAS_CGAL
320 IMP_ATOM_HAS_HDF5 = _IMP_saxs.IMP_ATOM_HAS_HDF5
321 IMPATOM_SHOW_WARNINGS = _IMP_saxs.IMPATOM_SHOW_WARNINGS
322 IMP_ATOM_TYPE_INDEX = _IMP_saxs.IMP_ATOM_TYPE_INDEX
323 IMP_RESIDUE_TYPE_INDEX = _IMP_saxs.IMP_RESIDUE_TYPE_INDEX
324 IMP_HIERARCHY_TYPE_INDEX = _IMP_saxs.IMP_HIERARCHY_TYPE_INDEX
325 import IMP.atom
326 IMP_SAXS_HAS_IMP_BASE = _IMP_saxs.IMP_SAXS_HAS_IMP_BASE
327 IMP_SAXS_HAS_IMP_CGAL = _IMP_saxs.IMP_SAXS_HAS_IMP_CGAL
328 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_saxs.IMP_SAXS_HAS_IMP_CONTAINER
329 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_saxs.IMP_SAXS_HAS_IMP_DISPLAY
330 IMP_SAXS_HAS_IMP_KERNEL = _IMP_saxs.IMP_SAXS_HAS_IMP_KERNEL
331 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_saxs.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
332 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_saxs.IMP_SAXS_HAS_BOOST_FILESYSTEM
333 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_saxs.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
334 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_saxs.IMP_SAXS_HAS_BOOST_RANDOM
335 IMP_SAXS_HAS_BOOST_REGEX = _IMP_saxs.IMP_SAXS_HAS_BOOST_REGEX
336 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_saxs.IMP_SAXS_HAS_BOOST_SYSTEM
337 IMP_SAXS_HAS_CGAL = _IMP_saxs.IMP_SAXS_HAS_CGAL
338 IMP_SAXS_HAS_HDF5 = _IMP_saxs.IMP_SAXS_HAS_HDF5
339 IMPSAXS_SHOW_WARNINGS = _IMP_saxs.IMPSAXS_SHOW_WARNINGS
340 class DistBase(_object):
341  """Proxy of C++ std::vector<(double)> class"""
342  __swig_setmethods__ = {}
343  __setattr__ = lambda self, name, value: _swig_setattr(self, DistBase, name, value)
344  __swig_getmethods__ = {}
345  __getattr__ = lambda self, name: _swig_getattr(self, DistBase, name)
346  __repr__ = _swig_repr
347  def iterator(self):
348  """iterator(DistBase self) -> IMP_SAXS_SwigPyIterator"""
349  return _IMP_saxs.DistBase_iterator(self)
350 
351  def __iter__(self): return self.iterator()
352  def __nonzero__(self):
353  """__nonzero__(DistBase self) -> bool"""
354  return _IMP_saxs.DistBase___nonzero__(self)
355 
356  def __bool__(self):
357  """__bool__(DistBase self) -> bool"""
358  return _IMP_saxs.DistBase___bool__(self)
359 
360  def __len__(self):
361  """__len__(DistBase self) -> std::vector< double >::size_type"""
362  return _IMP_saxs.DistBase___len__(self)
363 
364  def pop(self):
365  """pop(DistBase self) -> std::vector< double >::value_type"""
366  return _IMP_saxs.DistBase_pop(self)
367 
368  def __getslice__(self, *args):
369  """__getslice__(DistBase self, std::vector< double >::difference_type i, std::vector< double >::difference_type j) -> DistBase"""
370  return _IMP_saxs.DistBase___getslice__(self, *args)
371 
372  def __setslice__(self, *args):
373  """
374  __setslice__(DistBase self, std::vector< double >::difference_type i, std::vector< double >::difference_type j,
375  DistBase v=std::vector< double,std::allocator< double > >())
376  __setslice__(DistBase self, std::vector< double >::difference_type i, std::vector< double >::difference_type j)
377  """
378  return _IMP_saxs.DistBase___setslice__(self, *args)
379 
380  def __delslice__(self, *args):
381  """__delslice__(DistBase self, std::vector< double >::difference_type i, std::vector< double >::difference_type j)"""
382  return _IMP_saxs.DistBase___delslice__(self, *args)
383 
384  def __delitem__(self, *args):
385  """
386  __delitem__(DistBase self, std::vector< double >::difference_type i)
387  __delitem__(DistBase self, PySliceObject * slice)
388  """
389  return _IMP_saxs.DistBase___delitem__(self, *args)
390 
391  def __getitem__(self, *args):
392  """
393  __getitem__(DistBase self, PySliceObject * slice) -> DistBase
394  __getitem__(DistBase self, std::vector< double >::difference_type i) -> std::vector< double >::value_type const &
395  """
396  return _IMP_saxs.DistBase___getitem__(self, *args)
397 
398  def __setitem__(self, *args):
399  """
400  __setitem__(DistBase self, PySliceObject * slice, DistBase v)
401  __setitem__(DistBase self, PySliceObject * slice)
402  __setitem__(DistBase self, std::vector< double >::difference_type i, std::vector< double >::value_type const & x)
403  """
404  return _IMP_saxs.DistBase___setitem__(self, *args)
405 
406  def append(self, *args):
407  """append(DistBase self, std::vector< double >::value_type const & x)"""
408  return _IMP_saxs.DistBase_append(self, *args)
409 
410  def empty(self):
411  """empty(DistBase self) -> bool"""
412  return _IMP_saxs.DistBase_empty(self)
413 
414  def size(self):
415  """size(DistBase self) -> std::vector< double >::size_type"""
416  return _IMP_saxs.DistBase_size(self)
417 
418  def clear(self):
419  """clear(DistBase self)"""
420  return _IMP_saxs.DistBase_clear(self)
421 
422  def swap(self, *args):
423  """swap(DistBase self, DistBase v)"""
424  return _IMP_saxs.DistBase_swap(self, *args)
425 
426  def get_allocator(self):
427  """get_allocator(DistBase self) -> std::vector< double >::allocator_type"""
428  return _IMP_saxs.DistBase_get_allocator(self)
429 
430  def begin(self):
431  """begin(DistBase self) -> std::vector< double >::iterator"""
432  return _IMP_saxs.DistBase_begin(self)
433 
434  def end(self):
435  """end(DistBase self) -> std::vector< double >::iterator"""
436  return _IMP_saxs.DistBase_end(self)
437 
438  def rbegin(self):
439  """rbegin(DistBase self) -> std::vector< double >::reverse_iterator"""
440  return _IMP_saxs.DistBase_rbegin(self)
441 
442  def rend(self):
443  """rend(DistBase self) -> std::vector< double >::reverse_iterator"""
444  return _IMP_saxs.DistBase_rend(self)
445 
446  def pop_back(self):
447  """pop_back(DistBase self)"""
448  return _IMP_saxs.DistBase_pop_back(self)
449 
450  def erase(self, *args):
451  """
452  erase(DistBase self, std::vector< double >::iterator pos) -> std::vector< double >::iterator
453  erase(DistBase self, std::vector< double >::iterator first, std::vector< double >::iterator last) -> std::vector< double >::iterator
454  """
455  return _IMP_saxs.DistBase_erase(self, *args)
456 
457  def __init__(self, *args):
458  """
459  __init__(std::vector<(double)> self) -> DistBase
460  __init__(std::vector<(double)> self, DistBase arg2) -> DistBase
461  __init__(std::vector<(double)> self, std::vector< double >::size_type size) -> DistBase
462  __init__(std::vector<(double)> self, std::vector< double >::size_type size, std::vector< double >::value_type const & value) -> DistBase
463  """
464  this = _IMP_saxs.new_DistBase(*args)
465  try: self.this.append(this)
466  except: self.this = this
467  def push_back(self, *args):
468  """push_back(DistBase self, std::vector< double >::value_type const & x)"""
469  return _IMP_saxs.DistBase_push_back(self, *args)
470 
471  def front(self):
472  """front(DistBase self) -> std::vector< double >::value_type const &"""
473  return _IMP_saxs.DistBase_front(self)
474 
475  def back(self):
476  """back(DistBase self) -> std::vector< double >::value_type const &"""
477  return _IMP_saxs.DistBase_back(self)
478 
479  def assign(self, *args):
480  """assign(DistBase self, std::vector< double >::size_type n, std::vector< double >::value_type const & x)"""
481  return _IMP_saxs.DistBase_assign(self, *args)
482 
483  def resize(self, *args):
484  """
485  resize(DistBase self, std::vector< double >::size_type new_size)
486  resize(DistBase self, std::vector< double >::size_type new_size, std::vector< double >::value_type const & x)
487  """
488  return _IMP_saxs.DistBase_resize(self, *args)
489 
490  def insert(self, *args):
491  """
492  insert(DistBase self, std::vector< double >::iterator pos, std::vector< double >::value_type const & x) -> std::vector< double >::iterator
493  insert(DistBase self, std::vector< double >::iterator pos, std::vector< double >::size_type n, std::vector< double >::value_type const & x)
494  """
495  return _IMP_saxs.DistBase_insert(self, *args)
496 
497  def reserve(self, *args):
498  """reserve(DistBase self, std::vector< double >::size_type n)"""
499  return _IMP_saxs.DistBase_reserve(self, *args)
500 
501  def capacity(self):
502  """capacity(DistBase self) -> std::vector< double >::size_type"""
503  return _IMP_saxs.DistBase_capacity(self)
504 
505  __swig_destroy__ = _IMP_saxs.delete_DistBase
506  __del__ = lambda self : None;
507 DistBase_swigregister = _IMP_saxs.DistBase_swigregister
508 DistBase_swigregister(DistBase)
509 
510 _object_types.append("Profile")
511 
512 
513 def _object_cast_to_Profile(*args):
514  """_object_cast_to_Profile(Object o) -> Profile"""
515  return _IMP_saxs._object_cast_to_Profile(*args)
516 ALL_ATOMS = _IMP_saxs.ALL_ATOMS
517 HEAVY_ATOMS = _IMP_saxs.HEAVY_ATOMS
518 CA_ATOMS = _IMP_saxs.CA_ATOMS
519 class FormFactorTable(_object):
520  """Proxy of C++ IMP::saxs::FormFactorTable class"""
521  __swig_setmethods__ = {}
522  __setattr__ = lambda self, name, value: _swig_setattr(self, FormFactorTable, name, value)
523  __swig_getmethods__ = {}
524  __getattr__ = lambda self, name: _swig_getattr(self, FormFactorTable, name)
525  __repr__ = _swig_repr
526  def __init__(self, *args):
527  """
528  __init__(IMP::saxs::FormFactorTable self) -> FormFactorTable
529  __init__(IMP::saxs::FormFactorTable self, IMP::String const & table_name, IMP::Float min_q, IMP::Float max_q, IMP::Float delta_q) -> FormFactorTable
530  """
531  this = _IMP_saxs.new_FormFactorTable(*args)
532  try: self.this.append(this)
533  except: self.this = this
534  def get_form_factor(self, *args):
535  """
536  get_form_factor(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS) -> IMP::Float
537  get_form_factor(FormFactorTable self, Particle p) -> IMP::Float
538  """
539  return _IMP_saxs.FormFactorTable_get_form_factor(self, *args)
540 
541  def get_vacuum_form_factor(self, *args):
542  """
543  get_vacuum_form_factor(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS) -> IMP::Float
544  get_vacuum_form_factor(FormFactorTable self, Particle p) -> IMP::Float
545  """
546  return _IMP_saxs.FormFactorTable_get_vacuum_form_factor(self, *args)
547 
548  def get_dummy_form_factor(self, *args):
549  """
550  get_dummy_form_factor(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS) -> IMP::Float
551  get_dummy_form_factor(FormFactorTable self, Particle p) -> IMP::Float
552  """
553  return _IMP_saxs.FormFactorTable_get_dummy_form_factor(self, *args)
554 
555  def get_water_form_factor(self):
556  """get_water_form_factor(FormFactorTable self) -> IMP::Float"""
557  return _IMP_saxs.FormFactorTable_get_water_form_factor(self)
558 
559  def get_vacuum_water_form_factor(self):
560  """get_vacuum_water_form_factor(FormFactorTable self) -> IMP::Float"""
561  return _IMP_saxs.FormFactorTable_get_vacuum_water_form_factor(self)
562 
563  def get_dummy_water_form_factor(self):
564  """get_dummy_water_form_factor(FormFactorTable self) -> IMP::Float"""
565  return _IMP_saxs.FormFactorTable_get_dummy_water_form_factor(self)
566 
567  def get_form_factors(self, *args):
568  """
569  get_form_factors(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS) -> IMP::Floats const
570  get_form_factors(FormFactorTable self, Particle p) -> IMP::Floats const &
571  """
572  return _IMP_saxs.FormFactorTable_get_form_factors(self, *args)
573 
574  def get_vacuum_form_factors(self, *args):
575  """
576  get_vacuum_form_factors(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS) -> IMP::Floats const
577  get_vacuum_form_factors(FormFactorTable self, Particle p) -> IMP::Floats const &
578  """
579  return _IMP_saxs.FormFactorTable_get_vacuum_form_factors(self, *args)
580 
581  def get_dummy_form_factors(self, *args):
582  """
583  get_dummy_form_factors(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS) -> IMP::Floats const
584  get_dummy_form_factors(FormFactorTable self, Particle p) -> IMP::Floats const &
585  """
586  return _IMP_saxs.FormFactorTable_get_dummy_form_factors(self, *args)
587 
588  def get_water_form_factors(self):
589  """get_water_form_factors(FormFactorTable self) -> IMP::Floats const &"""
590  return _IMP_saxs.FormFactorTable_get_water_form_factors(self)
591 
592  def get_water_vacuum_form_factors(self):
593  """get_water_vacuum_form_factors(FormFactorTable self) -> IMP::Floats const &"""
594  return _IMP_saxs.FormFactorTable_get_water_vacuum_form_factors(self)
595 
596  def get_water_dummy_form_factors(self):
597  """get_water_dummy_form_factors(FormFactorTable self) -> IMP::Floats const &"""
598  return _IMP_saxs.FormFactorTable_get_water_dummy_form_factors(self)
599 
600  def get_radius(self, *args):
601  """
602  get_radius(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS) -> IMP::Float
603  get_radius(FormFactorTable self, Particle p) -> IMP::Float
604  """
605  return _IMP_saxs.FormFactorTable_get_radius(self, *args)
606 
607  def get_volume(self, *args):
608  """
609  get_volume(FormFactorTable self, Particle p, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS) -> IMP::Float
610  get_volume(FormFactorTable self, Particle p) -> IMP::Float
611  """
612  return _IMP_saxs.FormFactorTable_get_volume(self, *args)
613 
614  def show(self, *args):
615  """
616  show(FormFactorTable self, _ostream out=std::cout, std::string prefix="")
617  show(FormFactorTable self, _ostream out=std::cout)
618  show(FormFactorTable self)
619  """
620  return _IMP_saxs.FormFactorTable_show(self, *args)
621 
622  __swig_setmethods__["rho_"] = _IMP_saxs.FormFactorTable_rho__set
623  __swig_getmethods__["rho_"] = _IMP_saxs.FormFactorTable_rho__get
624  if _newclass:rho_ = _swig_property(_IMP_saxs.FormFactorTable_rho__get, _IMP_saxs.FormFactorTable_rho__set)
625  __swig_destroy__ = _IMP_saxs.delete_FormFactorTable
626  __del__ = lambda self : None;
627 FormFactorTable_swigregister = _IMP_saxs.FormFactorTable_swigregister
628 FormFactorTable_swigregister(FormFactorTable)
629 cvar = _IMP_saxs.cvar
630 
631 
633  """get_default_form_factor_table() -> FormFactorTable"""
634  return _IMP_saxs.get_default_form_factor_table()
635 class Profile(IMP.base.Object):
636  """Proxy of C++ IMP::saxs::Profile class"""
637  __swig_setmethods__ = {}
638  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
639  __setattr__ = lambda self, name, value: _swig_setattr(self, Profile, name, value)
640  __swig_getmethods__ = {}
641  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
642  __getattr__ = lambda self, name: _swig_getattr(self, Profile, name)
643  def __init__(self, *args):
644  """
645  __init__(IMP::saxs::Profile self, IMP::String const & file_name, bool fit_file=False) -> Profile
646  __init__(IMP::saxs::Profile self, IMP::String const & file_name) -> Profile
647  __init__(IMP::saxs::Profile self, IMP::Float qmin=0.0, IMP::Float qmax=0.5, IMP::Float delta=0.005) -> Profile
648  __init__(IMP::saxs::Profile self, IMP::Float qmin=0.0, IMP::Float qmax=0.5) -> Profile
649  __init__(IMP::saxs::Profile self, IMP::Float qmin=0.0) -> Profile
650  __init__(IMP::saxs::Profile self) -> Profile
651  """
652  this = _IMP_saxs.new_Profile(*args)
653  try: self.this.append(this)
654  except: self.this = this
655  def calculate_profile_partial(self, *args):
656  """
657  calculate_profile_partial(Profile self, IMP::kernel::Particles const & particles, IMP::Floats const & surface=IMP::Floats(),
658  IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS)
659  calculate_profile_partial(Profile self, IMP::kernel::Particles const & particles, IMP::Floats const & surface=IMP::Floats())
660  calculate_profile_partial(Profile self, IMP::kernel::Particles const & particles)
661  calculate_profile_partial(Profile self, IMP::kernel::Particles const & particles1, IMP::kernel::Particles const & particles2,
662  IMP::Floats const & surface1=IMP::Floats(), IMP::Floats const & surface2=IMP::Floats(),
663  IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS)
664  calculate_profile_partial(Profile self, IMP::kernel::Particles const & particles1, IMP::kernel::Particles const & particles2,
665  IMP::Floats const & surface1=IMP::Floats(), IMP::Floats const & surface2=IMP::Floats())
666  calculate_profile_partial(Profile self, IMP::kernel::Particles const & particles1, IMP::kernel::Particles const & particles2,
667  IMP::Floats const & surface1=IMP::Floats())
668  calculate_profile_partial(Profile self, IMP::kernel::Particles const & particles1, IMP::kernel::Particles const & particles2)
669  """
670  return _IMP_saxs.Profile_calculate_profile_partial(self, *args)
671 
672  def calculate_profile_reciprocal_partial(self, *args):
673  """
674  calculate_profile_reciprocal_partial(Profile self, IMP::kernel::Particles const & particles, IMP::Floats const & surface=IMP::Floats(),
675  IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS)
676  calculate_profile_reciprocal_partial(Profile self, IMP::kernel::Particles const & particles, IMP::Floats const & surface=IMP::Floats())
677  calculate_profile_reciprocal_partial(Profile self, IMP::kernel::Particles const & particles)
678  """
679  return _IMP_saxs.Profile_calculate_profile_reciprocal_partial(self, *args)
680 
681  def calculate_profile(self, *args):
682  """
683  calculate_profile(Profile self, IMP::kernel::Particles const & particles, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS,
684  bool reciprocal=False)
685  calculate_profile(Profile self, IMP::kernel::Particles const & particles, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS)
686  calculate_profile(Profile self, IMP::kernel::Particles const & particles)
687  calculate_profile(Profile self, IMP::kernel::Particles const & particles1, IMP::kernel::Particles const & particles2,
688  IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS)
689  calculate_profile(Profile self, IMP::kernel::Particles const & particles1, IMP::kernel::Particles const & particles2)
690  """
691  return _IMP_saxs.Profile_calculate_profile(self, *args)
692 
693  def calculate_I0(self, *args):
694  """
695  calculate_I0(Profile self, IMP::kernel::Particles const & particles, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS) -> IMP::Float
696  calculate_I0(Profile self, IMP::kernel::Particles const & particles) -> IMP::Float
697  """
698  return _IMP_saxs.Profile_calculate_I0(self, *args)
699 
700  def calculate_profile_constant_form_factor(self, *args):
701  """
702  calculate_profile_constant_form_factor(Profile self, IMP::kernel::Particles const & particles, IMP::Float form_factor=1.0)
703  calculate_profile_constant_form_factor(Profile self, IMP::kernel::Particles const & particles)
704  """
705  return _IMP_saxs.Profile_calculate_profile_constant_form_factor(self, *args)
706 
707  def calculate_profile_symmetric(self, *args):
708  """
709  calculate_profile_symmetric(Profile self, IMP::kernel::Particles const & particles, unsigned int n, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS)
710  calculate_profile_symmetric(Profile self, IMP::kernel::Particles const & particles, unsigned int n)
711  """
712  return _IMP_saxs.Profile_calculate_profile_symmetric(self, *args)
713 
714  def profile_2_distribution(self, *args):
715  """profile_2_distribution(Profile self, RadialDistributionFunction rd, IMP::Float max_distance)"""
716  return _IMP_saxs.Profile_profile_2_distribution(self, *args)
717 
718  def distribution_2_profile(self, *args):
719  """distribution_2_profile(Profile self, RadialDistributionFunction r_dist)"""
720  return _IMP_saxs.Profile_distribution_2_profile(self, *args)
721 
722  def resample(self, *args):
723  """
724  resample(Profile self, Profile exp_profile, Profile resampled_profile, bool partial_profiles=False)
725  resample(Profile self, Profile exp_profile, Profile resampled_profile)
726  """
727  return _IMP_saxs.Profile_resample(self, *args)
728 
729  def downsample(self, *args):
730  """downsample(Profile self, Profile downsampled_profile, unsigned int point_number)"""
731  return _IMP_saxs.Profile_downsample(self, *args)
732 
733  def radius_of_gyration(self, end_q_rg=1.3):
734  """
735  radius_of_gyration(Profile self, double end_q_rg=1.3) -> double
736  radius_of_gyration(Profile self) -> double
737  """
738  return _IMP_saxs.Profile_radius_of_gyration(self, end_q_rg)
739 
740  def read_SAXS_file(self, *args):
741  """
742  read_SAXS_file(Profile self, IMP::String const & file_name, bool fit_file=False)
743  read_SAXS_file(Profile self, IMP::String const & file_name)
744  """
745  return _IMP_saxs.Profile_read_SAXS_file(self, *args)
746 
747  def write_SAXS_file(self, *args):
748  """
749  write_SAXS_file(Profile self, IMP::String const & file_name, IMP::Float max_q=0.0)
750  write_SAXS_file(Profile self, IMP::String const & file_name)
751  """
752  return _IMP_saxs.Profile_write_SAXS_file(self, *args)
753 
754  def read_partial_profiles(self, *args):
755  """read_partial_profiles(Profile self, IMP::String const & file_name)"""
756  return _IMP_saxs.Profile_read_partial_profiles(self, *args)
757 
758  def write_partial_profiles(self, *args):
759  """write_partial_profiles(Profile self, IMP::String const & file_name)"""
760  return _IMP_saxs.Profile_write_partial_profiles(self, *args)
761 
762  def get_delta_q(self):
763  """get_delta_q(Profile self) -> IMP::Float"""
764  return _IMP_saxs.Profile_get_delta_q(self)
765 
766  def get_min_q(self):
767  """get_min_q(Profile self) -> IMP::Float"""
768  return _IMP_saxs.Profile_get_min_q(self)
769 
770  def get_max_q(self):
771  """get_max_q(Profile self) -> IMP::Float"""
772  return _IMP_saxs.Profile_get_max_q(self)
773 
774  def get_intensity(self, *args):
775  """get_intensity(Profile self, unsigned int i) -> IMP::Float"""
776  return _IMP_saxs.Profile_get_intensity(self, *args)
777 
778  def get_q(self, *args):
779  """get_q(Profile self, unsigned int i) -> IMP::Float"""
780  return _IMP_saxs.Profile_get_q(self, *args)
781 
782  def get_error(self, *args):
783  """get_error(Profile self, unsigned int i) -> IMP::Float"""
784  return _IMP_saxs.Profile_get_error(self, *args)
785 
786  def get_weight(self, *args):
787  """get_weight(Profile self, unsigned int i) -> IMP::Float"""
788  return _IMP_saxs.Profile_get_weight(self, *args)
789 
790  def get_average_radius(self):
791  """get_average_radius(Profile self) -> IMP::Float"""
792  return _IMP_saxs.Profile_get_average_radius(self)
793 
794  def size(self):
795  """size(Profile self) -> unsigned int"""
796  return _IMP_saxs.Profile_size(self)
797 
798  def is_uniform_sampling(self):
799  """is_uniform_sampling(Profile self) -> bool"""
800  return _IMP_saxs.Profile_is_uniform_sampling(self)
801 
802  def get_name(self):
803  """get_name(Profile self) -> std::string"""
804  return _IMP_saxs.Profile_get_name(self)
805 
806  def get_id(self):
807  """get_id(Profile self) -> unsigned int"""
808  return _IMP_saxs.Profile_get_id(self)
809 
810  def set_intensity(self, *args):
811  """set_intensity(Profile self, unsigned int i, IMP::Float iq)"""
812  return _IMP_saxs.Profile_set_intensity(self, *args)
813 
814  def set_ff_table(self, *args):
815  """set_ff_table(Profile self, FormFactorTable ff_table)"""
816  return _IMP_saxs.Profile_set_ff_table(self, *args)
817 
818  def set_average_radius(self, *args):
819  """set_average_radius(Profile self, IMP::Float r)"""
820  return _IMP_saxs.Profile_set_average_radius(self, *args)
821 
822  def set_average_volume(self, *args):
823  """set_average_volume(Profile self, IMP::Float v)"""
824  return _IMP_saxs.Profile_set_average_volume(self, *args)
825 
826  def set_name(self, *args):
827  """set_name(Profile self, std::string name)"""
828  return _IMP_saxs.Profile_set_name(self, *args)
829 
830  def set_id(self, *args):
831  """set_id(Profile self, unsigned int id)"""
832  return _IMP_saxs.Profile_set_id(self, *args)
833 
834  def set_beam_profile(self, *args):
835  """set_beam_profile(Profile self, std::string beam_profile_file)"""
836  return _IMP_saxs.Profile_set_beam_profile(self, *args)
837 
838  def add_entry(self, *args):
839  """
840  add_entry(Profile self, IMP::Float q, IMP::Float intensity, IMP::Float error=1.0)
841  add_entry(Profile self, IMP::Float q, IMP::Float intensity)
842  """
843  return _IMP_saxs.Profile_add_entry(self, *args)
844 
845  def add_errors(self):
846  """add_errors(Profile self)"""
847  return _IMP_saxs.Profile_add_errors(self)
848 
849  def add_noise(self, percentage=0.03):
850  """
851  add_noise(Profile self, IMP::Float percentage=0.03)
852  add_noise(Profile self)
853  """
854  return _IMP_saxs.Profile_add_noise(self, percentage)
855 
856  def sum_partial_profiles(self, *args):
857  """
858  sum_partial_profiles(Profile self, IMP::Float c1, IMP::Float c2, bool check_cashed=True)
859  sum_partial_profiles(Profile self, IMP::Float c1, IMP::Float c2)
860  """
861  return _IMP_saxs.Profile_sum_partial_profiles(self, *args)
862 
863  def add(self, *args):
864  """
865  add(Profile self, Profile other_profile, IMP::Float weight=1.0)
866  add(Profile self, Profile other_profile)
867  add(Profile self, std::vector< IMP::saxs::Profile *,std::allocator< IMP::saxs::Profile * > > const & profiles,
868  DistBase weights=std::vector< IMP::Float >())
869  add(Profile self, std::vector< IMP::saxs::Profile *,std::allocator< IMP::saxs::Profile * > > const & profiles)
870  """
871  return _IMP_saxs.Profile_add(self, *args)
872 
873  def add_partial_profiles(self, *args):
874  """
875  add_partial_profiles(Profile self, Profile other_profile, IMP::Float weight=1.0)
876  add_partial_profiles(Profile self, Profile other_profile)
877  add_partial_profiles(Profile self, std::vector< IMP::saxs::Profile *,std::allocator< IMP::saxs::Profile * > > const & profiles,
878  DistBase weights=std::vector< IMP::Float >())
879  add_partial_profiles(Profile self, std::vector< IMP::saxs::Profile *,std::allocator< IMP::saxs::Profile * > > const & profiles)
880  """
881  return _IMP_saxs.Profile_add_partial_profiles(self, *args)
882 
883  def background_adjust(self, *args):
884  """background_adjust(Profile self, double start_q)"""
885  return _IMP_saxs.Profile_background_adjust(self, *args)
886 
887  def scale(self, *args):
888  """scale(Profile self, IMP::Float c)"""
889  return _IMP_saxs.Profile_scale(self, *args)
890 
891  def offset(self, *args):
892  """offset(Profile self, IMP::Float c)"""
893  return _IMP_saxs.Profile_offset(self, *args)
894 
895  def copy_errors(self, *args):
896  """copy_errors(Profile self, Profile exp_profile)"""
897  return _IMP_saxs.Profile_copy_errors(self, *args)
898 
899  def get_version_info(self):
900  """get_version_info(Profile self) -> VersionInfo"""
901  return _IMP_saxs.Profile_get_version_info(self)
902 
903  def __str__(self):
904  """__str__(Profile self) -> std::string"""
905  return _IMP_saxs.Profile___str__(self)
906 
907  def __repr__(self):
908  """__repr__(Profile self) -> std::string"""
909  return _IMP_saxs.Profile___repr__(self)
910 
911  def get_from(o):
912  return _object_cast_to_Profile(o)
913  get_from = staticmethod(get_from)
914 
915 Profile_swigregister = _IMP_saxs.Profile_swigregister
916 Profile_swigregister(Profile)
917 Profile.modulation_function_parameter_ = _IMP_saxs.cvar.Profile_modulation_function_parameter_
918 
919 class FitParameters(_object):
920  """Proxy of C++ IMP::saxs::FitParameters class"""
921  __swig_setmethods__ = {}
922  __setattr__ = lambda self, name, value: _swig_setattr(self, FitParameters, name, value)
923  __swig_getmethods__ = {}
924  __getattr__ = lambda self, name: _swig_getattr(self, FitParameters, name)
925  __repr__ = _swig_repr
926  def __init__(self, *args):
927  """
928  __init__(IMP::saxs::FitParameters self) -> FitParameters
929  __init__(IMP::saxs::FitParameters self, float chi, float c1, float c2, float c, float o) -> FitParameters
930  __init__(IMP::saxs::FitParameters self, float chi, float c1, float c2) -> FitParameters
931  """
932  this = _IMP_saxs.new_FitParameters(*args)
933  try: self.this.append(this)
934  except: self.this = this
935  def get_score(self):
936  """get_score(FitParameters self) -> float"""
937  return _IMP_saxs.FitParameters_get_score(self)
938 
939  def get_chi(self):
940  """get_chi(FitParameters self) -> float"""
941  return _IMP_saxs.FitParameters_get_chi(self)
942 
943  def get_c1(self):
944  """get_c1(FitParameters self) -> float"""
945  return _IMP_saxs.FitParameters_get_c1(self)
946 
947  def get_c2(self):
948  """get_c2(FitParameters self) -> float"""
949  return _IMP_saxs.FitParameters_get_c2(self)
950 
951  def get_scale(self):
952  """get_scale(FitParameters self) -> float"""
953  return _IMP_saxs.FitParameters_get_scale(self)
954 
955  def get_offset(self):
956  """get_offset(FitParameters self) -> float"""
957  return _IMP_saxs.FitParameters_get_offset(self)
958 
959  def get_default_chi(self):
960  """get_default_chi(FitParameters self) -> float"""
961  return _IMP_saxs.FitParameters_get_default_chi(self)
962 
963  def get_pdb_file_name(self):
964  """get_pdb_file_name(FitParameters self) -> std::string"""
965  return _IMP_saxs.FitParameters_get_pdb_file_name(self)
966 
967  def get_profile_file_name(self):
968  """get_profile_file_name(FitParameters self) -> std::string"""
969  return _IMP_saxs.FitParameters_get_profile_file_name(self)
970 
971  def get_mol_index(self):
972  """get_mol_index(FitParameters self) -> int"""
973  return _IMP_saxs.FitParameters_get_mol_index(self)
974 
975  def set_chi(self, *args):
976  """set_chi(FitParameters self, float chi)"""
977  return _IMP_saxs.FitParameters_set_chi(self, *args)
978 
979  def set_default_chi(self, *args):
980  """set_default_chi(FitParameters self, float chi)"""
981  return _IMP_saxs.FitParameters_set_default_chi(self, *args)
982 
983  def set_profile_file_name(self, *args):
984  """set_profile_file_name(FitParameters self, std::string file_name)"""
985  return _IMP_saxs.FitParameters_set_profile_file_name(self, *args)
986 
987  def set_pdb_file_name(self, *args):
988  """set_pdb_file_name(FitParameters self, std::string file_name)"""
989  return _IMP_saxs.FitParameters_set_pdb_file_name(self, *args)
990 
991  def set_mol_index(self, *args):
992  """set_mol_index(FitParameters self, int index)"""
993  return _IMP_saxs.FitParameters_set_mol_index(self, *args)
994 
995  def show(self, *args):
996  """show(FitParameters self, _ostream s)"""
997  return _IMP_saxs.FitParameters_show(self, *args)
998 
999  __swig_destroy__ = _IMP_saxs.delete_FitParameters
1000  __del__ = lambda self : None;
1001 FitParameters_swigregister = _IMP_saxs.FitParameters_swigregister
1002 FitParameters_swigregister(FitParameters)
1003 
1004 class WeightedFitParameters(FitParameters):
1005  """Proxy of C++ IMP::saxs::WeightedFitParameters class"""
1006  __swig_setmethods__ = {}
1007  for _s in [FitParameters]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1008  __setattr__ = lambda self, name, value: _swig_setattr(self, WeightedFitParameters, name, value)
1009  __swig_getmethods__ = {}
1010  for _s in [FitParameters]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1011  __getattr__ = lambda self, name: _swig_getattr(self, WeightedFitParameters, name)
1012  __repr__ = _swig_repr
1013  def __init__(self, *args):
1014  """__init__(IMP::saxs::WeightedFitParameters self, float chi, float c1, float c2, IMP::Floats weights) -> WeightedFitParameters"""
1015  this = _IMP_saxs.new_WeightedFitParameters(*args)
1016  try: self.this.append(this)
1017  except: self.this = this
1018  def get_weights(self):
1019  """get_weights(WeightedFitParameters self) -> IMP::Floats const &"""
1020  return _IMP_saxs.WeightedFitParameters_get_weights(self)
1021 
1022  def set_weights(self, *args):
1023  """set_weights(WeightedFitParameters self, IMP::Floats const & weights)"""
1024  return _IMP_saxs.WeightedFitParameters_set_weights(self, *args)
1025 
1026  def show(self, *args):
1027  """show(WeightedFitParameters self, _ostream s)"""
1028  return _IMP_saxs.WeightedFitParameters_show(self, *args)
1029 
1030  __swig_destroy__ = _IMP_saxs.delete_WeightedFitParameters
1031  __del__ = lambda self : None;
1032 WeightedFitParameters_swigregister = _IMP_saxs.WeightedFitParameters_swigregister
1033 WeightedFitParameters_swigregister(WeightedFitParameters)
1034 
1035 class ChiScore(_object):
1036  """Proxy of C++ IMP::saxs::ChiScore class"""
1037  __swig_setmethods__ = {}
1038  __setattr__ = lambda self, name, value: _swig_setattr(self, ChiScore, name, value)
1039  __swig_getmethods__ = {}
1040  __getattr__ = lambda self, name: _swig_getattr(self, ChiScore, name)
1041  __repr__ = _swig_repr
1042  def compute_score(self, *args):
1043  """
1044  compute_score(ChiScore self, Profile exp_profile, Profile model_profile, bool use_offset=False) -> IMP::Float
1045  compute_score(ChiScore self, Profile exp_profile, Profile model_profile) -> IMP::Float
1046  compute_score(ChiScore self, Profile exp_profile, Profile model_profile, IMP::Float min_q, IMP::Float max_q) -> IMP::Float
1047  """
1048  return _IMP_saxs.ChiScore_compute_score(self, *args)
1049 
1050  def compute_scale_factor(self, *args):
1051  """
1052  compute_scale_factor(ChiScore self, Profile exp_profile, Profile model_profile, IMP::Float offset=0.0) -> IMP::Float
1053  compute_scale_factor(ChiScore self, Profile exp_profile, Profile model_profile) -> IMP::Float
1054  """
1055  return _IMP_saxs.ChiScore_compute_scale_factor(self, *args)
1056 
1057  def compute_offset(self, *args):
1058  """compute_offset(ChiScore self, Profile exp_profile, Profile model_profile) -> IMP::Float"""
1059  return _IMP_saxs.ChiScore_compute_offset(self, *args)
1060 
1061  def __init__(self):
1062  """__init__(IMP::saxs::ChiScore self) -> ChiScore"""
1063  this = _IMP_saxs.new_ChiScore()
1064  try: self.this.append(this)
1065  except: self.this = this
1066  __swig_destroy__ = _IMP_saxs.delete_ChiScore
1067  __del__ = lambda self : None;
1068 ChiScore_swigregister = _IMP_saxs.ChiScore_swigregister
1069 ChiScore_swigregister(ChiScore)
1070 
1071 class ChiScoreLog(_object):
1072  """Proxy of C++ IMP::saxs::ChiScoreLog class"""
1073  __swig_setmethods__ = {}
1074  __setattr__ = lambda self, name, value: _swig_setattr(self, ChiScoreLog, name, value)
1075  __swig_getmethods__ = {}
1076  __getattr__ = lambda self, name: _swig_getattr(self, ChiScoreLog, name)
1077  __repr__ = _swig_repr
1078  def compute_score(self, *args):
1079  """
1080  compute_score(ChiScoreLog self, Profile exp_profile, Profile model_profile, bool use_offset=False) -> IMP::Float
1081  compute_score(ChiScoreLog self, Profile exp_profile, Profile model_profile) -> IMP::Float
1082  compute_score(ChiScoreLog self, Profile exp_profile, Profile model_profile, IMP::Float min_q, IMP::Float max_q) -> IMP::Float
1083  """
1084  return _IMP_saxs.ChiScoreLog_compute_score(self, *args)
1085 
1086  def compute_scale_factor(self, *args):
1087  """
1088  compute_scale_factor(ChiScoreLog self, Profile exp_profile, Profile model_profile, IMP::Float offset=0.0) -> IMP::Float
1089  compute_scale_factor(ChiScoreLog self, Profile exp_profile, Profile model_profile) -> IMP::Float
1090  """
1091  return _IMP_saxs.ChiScoreLog_compute_scale_factor(self, *args)
1092 
1093  def compute_offset(self, *args):
1094  """compute_offset(ChiScoreLog self, Profile exp_profile, Profile model_profile) -> IMP::Float"""
1095  return _IMP_saxs.ChiScoreLog_compute_offset(self, *args)
1096 
1097  def __init__(self):
1098  """__init__(IMP::saxs::ChiScoreLog self) -> ChiScoreLog"""
1099  this = _IMP_saxs.new_ChiScoreLog()
1100  try: self.this.append(this)
1101  except: self.this = this
1102  __swig_destroy__ = _IMP_saxs.delete_ChiScoreLog
1103  __del__ = lambda self : None;
1104 ChiScoreLog_swigregister = _IMP_saxs.ChiScoreLog_swigregister
1105 ChiScoreLog_swigregister(ChiScoreLog)
1106 
1107 class ProfileFitterChi(IMP.base.Object):
1108  """Proxy of C++ IMP::saxs::ProfileFitter<(IMP::saxs::ChiScore)> class"""
1109  __swig_setmethods__ = {}
1110  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1111  __setattr__ = lambda self, name, value: _swig_setattr(self, ProfileFitterChi, name, value)
1112  __swig_getmethods__ = {}
1113  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1114  __getattr__ = lambda self, name: _swig_getattr(self, ProfileFitterChi, name)
1115  __repr__ = _swig_repr
1116  def __init__(self, *args):
1117  """
1118  __init__(IMP::saxs::ProfileFitter<(IMP::saxs::ChiScore)> self, Profile exp_profile) -> ProfileFitterChi
1119  __init__(IMP::saxs::ProfileFitter<(IMP::saxs::ChiScore)> self, Profile exp_profile, ChiScore sf) -> ProfileFitterChi
1120  """
1121  this = _IMP_saxs.new_ProfileFitterChi(*args)
1122  try: self.this.append(this)
1123  except: self.this = this
1124  def compute_score(self, *args):
1125  """
1126  compute_score(ProfileFitterChi self, Profile model_profile, bool use_offset=False, std::string const fit_file_name="") -> IMP::Float
1127  compute_score(ProfileFitterChi self, Profile model_profile, bool use_offset=False) -> IMP::Float
1128  compute_score(ProfileFitterChi self, Profile model_profile) -> IMP::Float
1129  compute_score(ProfileFitterChi self, Profile model_profile, IMP::Float min_q, IMP::Float max_q) -> IMP::Float
1130  """
1131  return _IMP_saxs.ProfileFitterChi_compute_score(self, *args)
1132 
1133  def fit_profile(self, *args):
1134  """
1135  fit_profile(ProfileFitterChi self, Profile partial_profile, float min_c1=0.95, float max_c1=1.05, float min_c2=-2.0,
1136  float max_c2=4.0, bool use_offset=False, std::string const fit_file_name="") -> FitParameters
1137  fit_profile(ProfileFitterChi self, Profile partial_profile, float min_c1=0.95, float max_c1=1.05, float min_c2=-2.0,
1138  float max_c2=4.0, bool use_offset=False) -> FitParameters
1139  fit_profile(ProfileFitterChi self, Profile partial_profile, float min_c1=0.95, float max_c1=1.05, float min_c2=-2.0,
1140  float max_c2=4.0) -> FitParameters
1141  fit_profile(ProfileFitterChi self, Profile partial_profile, float min_c1=0.95, float max_c1=1.05, float min_c2=-2.0) -> FitParameters
1142  fit_profile(ProfileFitterChi self, Profile partial_profile, float min_c1=0.95, float max_c1=1.05) -> FitParameters
1143  fit_profile(ProfileFitterChi self, Profile partial_profile, float min_c1=0.95) -> FitParameters
1144  fit_profile(ProfileFitterChi self, Profile partial_profile) -> FitParameters
1145  """
1146  return _IMP_saxs.ProfileFitterChi_fit_profile(self, *args)
1147 
1148  def compute_scale_factor(self, *args):
1149  """
1150  compute_scale_factor(ProfileFitterChi self, Profile model_profile, IMP::Float offset=0.0) -> IMP::Float
1151  compute_scale_factor(ProfileFitterChi self, Profile model_profile) -> IMP::Float
1152  """
1153  return _IMP_saxs.ProfileFitterChi_compute_scale_factor(self, *args)
1154 
1155  def compute_offset(self, *args):
1156  """compute_offset(ProfileFitterChi self, Profile model_profile) -> IMP::Float"""
1157  return _IMP_saxs.ProfileFitterChi_compute_offset(self, *args)
1158 
1159  def resample(self, *args):
1160  """resample(ProfileFitterChi self, Profile model_profile, Profile resampled_profile)"""
1161  return _IMP_saxs.ProfileFitterChi_resample(self, *args)
1162 
1163  def write_SAXS_fit_file(self, *args):
1164  """
1165  write_SAXS_fit_file(ProfileFitterChi self, std::string const & file_name, Profile model_profile, IMP::Float const chi_square,
1166  IMP::Float const c=1, IMP::Float const offset=0)
1167  write_SAXS_fit_file(ProfileFitterChi self, std::string const & file_name, Profile model_profile, IMP::Float const chi_square,
1168  IMP::Float const c=1)
1169  write_SAXS_fit_file(ProfileFitterChi self, std::string const & file_name, Profile model_profile, IMP::Float const chi_square)
1170  """
1171  return _IMP_saxs.ProfileFitterChi_write_SAXS_fit_file(self, *args)
1172 
1173  __swig_destroy__ = _IMP_saxs.delete_ProfileFitterChi
1174  __del__ = lambda self : None;
1175 ProfileFitterChi_swigregister = _IMP_saxs.ProfileFitterChi_swigregister
1176 ProfileFitterChi_swigregister(ProfileFitterChi)
1177 
1178 class WeightedProfileFitter(ProfileFitterChi):
1179  """Proxy of C++ IMP::saxs::WeightedProfileFitter class"""
1180  __swig_setmethods__ = {}
1181  for _s in [ProfileFitterChi]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1182  __setattr__ = lambda self, name, value: _swig_setattr(self, WeightedProfileFitter, name, value)
1183  __swig_getmethods__ = {}
1184  for _s in [ProfileFitterChi]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1185  __getattr__ = lambda self, name: _swig_getattr(self, WeightedProfileFitter, name)
1186  __repr__ = _swig_repr
1187  def __init__(self, *args):
1188  """__init__(IMP::saxs::WeightedProfileFitter self, Profile exp_profile) -> WeightedProfileFitter"""
1189  this = _IMP_saxs.new_WeightedProfileFitter(*args)
1190  try: self.this.append(this)
1191  except: self.this = this
1192  def compute_score(self, *args):
1193  """
1194  compute_score(WeightedProfileFitter self, IMP::saxs::ProfilesTemp const & profiles, DistBase weights, bool NNLS=True) -> IMP::Float
1195  compute_score(WeightedProfileFitter self, IMP::saxs::ProfilesTemp const & profiles, DistBase weights) -> IMP::Float
1196  """
1197  return _IMP_saxs.WeightedProfileFitter_compute_score(self, *args)
1198 
1199  def fit_profile(self, *args):
1200  """
1201  fit_profile(WeightedProfileFitter self, IMP::saxs::ProfilesTemp partial_profiles, float min_c1=0.95, float max_c1=1.05, float min_c2=-2.0,
1202  float max_c2=4.0) -> WeightedFitParameters
1203  fit_profile(WeightedProfileFitter self, IMP::saxs::ProfilesTemp partial_profiles, float min_c1=0.95, float max_c1=1.05, float min_c2=-2.0) -> WeightedFitParameters
1204  fit_profile(WeightedProfileFitter self, IMP::saxs::ProfilesTemp partial_profiles, float min_c1=0.95, float max_c1=1.05) -> WeightedFitParameters
1205  fit_profile(WeightedProfileFitter self, IMP::saxs::ProfilesTemp partial_profiles, float min_c1=0.95) -> WeightedFitParameters
1206  fit_profile(WeightedProfileFitter self, IMP::saxs::ProfilesTemp partial_profiles) -> WeightedFitParameters
1207  """
1208  return _IMP_saxs.WeightedProfileFitter_fit_profile(self, *args)
1209 
1210  def write_fit_file(self, *args):
1211  """write_fit_file(WeightedProfileFitter self, IMP::saxs::ProfilesTemp partial_profiles, WeightedFitParameters fp, std::string const fit_file_name)"""
1212  return _IMP_saxs.WeightedProfileFitter_write_fit_file(self, *args)
1213 
1214  __swig_destroy__ = _IMP_saxs.delete_WeightedProfileFitter
1215  __del__ = lambda self : None;
1216 WeightedProfileFitter_swigregister = _IMP_saxs.WeightedProfileFitter_swigregister
1217 WeightedProfileFitter_swigregister(WeightedProfileFitter)
1218 
1219 class DerivativeCalculator(IMP.base.Object):
1220  """Proxy of C++ IMP::saxs::DerivativeCalculator class"""
1221  __swig_setmethods__ = {}
1222  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1223  __setattr__ = lambda self, name, value: _swig_setattr(self, DerivativeCalculator, name, value)
1224  __swig_getmethods__ = {}
1225  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1226  __getattr__ = lambda self, name: _swig_getattr(self, DerivativeCalculator, name)
1227  __repr__ = _swig_repr
1228  def __init__(self, *args):
1229  """__init__(IMP::saxs::DerivativeCalculator self, Profile exp_profile) -> DerivativeCalculator"""
1230  this = _IMP_saxs.new_DerivativeCalculator(*args)
1231  try: self.this.append(this)
1232  except: self.this = this
1233  def compute_chisquare_derivative(self, *args):
1234  """
1235  compute_chisquare_derivative(DerivativeCalculator self, Profile model_profile, IMP::kernel::Particles const & particles1, IMP::kernel::Particles const & particles2,
1236  std::vector< IMP::algebra::Vector3D,std::allocator< IMP::algebra::Vector3D > > & derivatives,
1237  DistBase effect_size)
1238  compute_chisquare_derivative(DerivativeCalculator self, Profile model_profile, IMP::kernel::Particles const & particles, std::vector< IMP::algebra::Vector3D,std::allocator< IMP::algebra::Vector3D > > & derivatives,
1239  DistBase effect_size)
1240  """
1241  return _IMP_saxs.DerivativeCalculator_compute_chisquare_derivative(self, *args)
1242 
1243  def compute_gaussian_effect_size(self, *args):
1244  """compute_gaussian_effect_size(DerivativeCalculator self, Profile model_profile, IMP::Float const c, IMP::Float const offset, DistBase effect_size)"""
1245  return _IMP_saxs.DerivativeCalculator_compute_gaussian_effect_size(self, *args)
1246 
1247  __swig_destroy__ = _IMP_saxs.delete_DerivativeCalculator
1248  __del__ = lambda self : None;
1249 DerivativeCalculator_swigregister = _IMP_saxs.DerivativeCalculator_swigregister
1250 DerivativeCalculator_swigregister(DerivativeCalculator)
1251 
1253  """Proxy of C++ IMP::saxs::Restraint class"""
1254  __swig_setmethods__ = {}
1255  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1256  __setattr__ = lambda self, name, value: _swig_setattr(self, Restraint, name, value)
1257  __swig_getmethods__ = {}
1258  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1259  __getattr__ = lambda self, name: _swig_getattr(self, Restraint, name)
1260  __repr__ = _swig_repr
1261  def __init__(self, *args):
1262  """
1263  __init__(IMP::saxs::Restraint self, IMP::kernel::Particles const & particles, Profile exp_profile, IMP::saxs::FormFactorType ff_type=HEAVY_ATOMS) -> Restraint
1264  __init__(IMP::saxs::Restraint self, IMP::kernel::Particles const & particles, Profile exp_profile) -> Restraint
1265  """
1266  this = _IMP_saxs.new_Restraint(*args)
1267  try: self.this.append(this)
1268  except: self.this = this
1269  if self.__class__ != Restraint:
1270  import IMP.base
1271  IMP.base._director_objects.register(self)
1272 
1273 
1274 
1275  def do_get_inputs(self):
1276  """do_get_inputs(Restraint self) -> IMP::kernel::ModelObjectsTemp"""
1277  return _IMP_saxs.Restraint_do_get_inputs(self)
1278 
1279  def get_version_info(self):
1280  """get_version_info(Restraint self) -> VersionInfo"""
1281  return _IMP_saxs.Restraint_get_version_info(self)
1282 
1283 Restraint_swigregister = _IMP_saxs.Restraint_swigregister
1284 Restraint_swigregister(Restraint)
1285 
1286 class RadiusOfGyrationRestraint(IMP.kernel.Restraint):
1287  """Proxy of C++ IMP::saxs::RadiusOfGyrationRestraint class"""
1288  __swig_setmethods__ = {}
1289  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1290  __setattr__ = lambda self, name, value: _swig_setattr(self, RadiusOfGyrationRestraint, name, value)
1291  __swig_getmethods__ = {}
1292  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1293  __getattr__ = lambda self, name: _swig_getattr(self, RadiusOfGyrationRestraint, name)
1294  __repr__ = _swig_repr
1295  def __init__(self, *args):
1296  """
1297  __init__(IMP::saxs::RadiusOfGyrationRestraint self, IMP::kernel::Particles const & particles, Profile exp_profile, double const end_q_rg=1.3) -> RadiusOfGyrationRestraint
1298  __init__(IMP::saxs::RadiusOfGyrationRestraint self, IMP::kernel::Particles const & particles, Profile exp_profile) -> RadiusOfGyrationRestraint
1299  """
1300  this = _IMP_saxs.new_RadiusOfGyrationRestraint(*args)
1301  try: self.this.append(this)
1302  except: self.this = this
1303  def do_get_inputs(self):
1304  """do_get_inputs(RadiusOfGyrationRestraint self) -> IMP::kernel::ModelObjectsTemp"""
1305  return _IMP_saxs.RadiusOfGyrationRestraint_do_get_inputs(self)
1306 
1307  def get_version_info(self):
1308  """get_version_info(RadiusOfGyrationRestraint self) -> VersionInfo"""
1309  return _IMP_saxs.RadiusOfGyrationRestraint_get_version_info(self)
1310 
1311 RadiusOfGyrationRestraint_swigregister = _IMP_saxs.RadiusOfGyrationRestraint_swigregister
1312 RadiusOfGyrationRestraint_swigregister(RadiusOfGyrationRestraint)
1313 
1314 class FloatDistribution(DistBase):
1315  """Proxy of C++ IMP::saxs::Distribution<(IMP::Float)> class"""
1316  __swig_setmethods__ = {}
1317  for _s in [DistBase]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1318  __setattr__ = lambda self, name, value: _swig_setattr(self, FloatDistribution, name, value)
1319  __swig_getmethods__ = {}
1320  for _s in [DistBase]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1321  __getattr__ = lambda self, name: _swig_getattr(self, FloatDistribution, name)
1322  __repr__ = _swig_repr
1323  def __init__(self, *args):
1324  """
1325  __init__(IMP::saxs::Distribution<(IMP::Float)> self, IMP::Float bin_size=pr_resolution) -> FloatDistribution
1326  __init__(IMP::saxs::Distribution<(IMP::Float)> self) -> FloatDistribution
1327  """
1328  this = _IMP_saxs.new_FloatDistribution(*args)
1329  try: self.this.append(this)
1330  except: self.this = this
1331  def get_max_distance(self):
1332  """get_max_distance(FloatDistribution self) -> IMP::Float"""
1333  return _IMP_saxs.FloatDistribution_get_max_distance(self)
1334 
1335  def get_bin_size(self):
1336  """get_bin_size(FloatDistribution self) -> IMP::Float"""
1337  return _IMP_saxs.FloatDistribution_get_bin_size(self)
1338 
1339  def get_index_from_distance(self, *args):
1340  """get_index_from_distance(FloatDistribution self, IMP::Float dist) -> unsigned int"""
1341  return _IMP_saxs.FloatDistribution_get_index_from_distance(self, *args)
1342 
1343  def get_distance_from_index(self, *args):
1344  """get_distance_from_index(FloatDistribution self, unsigned int index) -> IMP::Float"""
1345  return _IMP_saxs.FloatDistribution_get_distance_from_index(self, *args)
1346 
1347  __swig_destroy__ = _IMP_saxs.delete_FloatDistribution
1348  __del__ = lambda self : None;
1349 FloatDistribution_swigregister = _IMP_saxs.FloatDistribution_swigregister
1350 FloatDistribution_swigregister(FloatDistribution)
1351 
1352 class VectorDistribution(_object):
1353  """Proxy of C++ IMP::saxs::Distribution<(IMP::algebra::Vector3D)> class"""
1354  __swig_setmethods__ = {}
1355  __setattr__ = lambda self, name, value: _swig_setattr(self, VectorDistribution, name, value)
1356  __swig_getmethods__ = {}
1357  __getattr__ = lambda self, name: _swig_getattr(self, VectorDistribution, name)
1358  __repr__ = _swig_repr
1359  def __init__(self, *args):
1360  """
1361  __init__(IMP::saxs::Distribution<(IMP::algebra::Vector3D)> self, IMP::Float bin_size=pr_resolution) -> VectorDistribution
1362  __init__(IMP::saxs::Distribution<(IMP::algebra::Vector3D)> self) -> VectorDistribution
1363  """
1364  this = _IMP_saxs.new_VectorDistribution(*args)
1365  try: self.this.append(this)
1366  except: self.this = this
1367  def get_max_distance(self):
1368  """get_max_distance(VectorDistribution self) -> IMP::Float"""
1369  return _IMP_saxs.VectorDistribution_get_max_distance(self)
1370 
1371  def get_bin_size(self):
1372  """get_bin_size(VectorDistribution self) -> IMP::Float"""
1373  return _IMP_saxs.VectorDistribution_get_bin_size(self)
1374 
1375  def get_index_from_distance(self, *args):
1376  """get_index_from_distance(VectorDistribution self, IMP::Float dist) -> unsigned int"""
1377  return _IMP_saxs.VectorDistribution_get_index_from_distance(self, *args)
1378 
1379  def get_distance_from_index(self, *args):
1380  """get_distance_from_index(VectorDistribution self, unsigned int index) -> IMP::Float"""
1381  return _IMP_saxs.VectorDistribution_get_distance_from_index(self, *args)
1382 
1383  __swig_destroy__ = _IMP_saxs.delete_VectorDistribution
1384  __del__ = lambda self : None;
1385 VectorDistribution_swigregister = _IMP_saxs.VectorDistribution_swigregister
1386 VectorDistribution_swigregister(VectorDistribution)
1387 
1388 class RadialDistributionFunction(FloatDistribution):
1389  """Proxy of C++ IMP::saxs::RadialDistributionFunction class"""
1390  __swig_setmethods__ = {}
1391  for _s in [FloatDistribution]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1392  __setattr__ = lambda self, name, value: _swig_setattr(self, RadialDistributionFunction, name, value)
1393  __swig_getmethods__ = {}
1394  for _s in [FloatDistribution]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1395  __getattr__ = lambda self, name: _swig_getattr(self, RadialDistributionFunction, name)
1396  __repr__ = _swig_repr
1397  def __init__(self, *args):
1398  """
1399  __init__(IMP::saxs::RadialDistributionFunction self, IMP::Float bin_size=pr_resolution) -> RadialDistributionFunction
1400  __init__(IMP::saxs::RadialDistributionFunction self) -> RadialDistributionFunction
1401  __init__(IMP::saxs::RadialDistributionFunction self, std::string const & file_name) -> RadialDistributionFunction
1402  """
1403  this = _IMP_saxs.new_RadialDistributionFunction(*args)
1404  try: self.this.append(this)
1405  except: self.this = this
1406  def scale(self, *args):
1407  """scale(RadialDistributionFunction self, IMP::Float c)"""
1408  return _IMP_saxs.RadialDistributionFunction_scale(self, *args)
1409 
1410  def add(self, *args):
1411  """add(RadialDistributionFunction self, RadialDistributionFunction model_pr)"""
1412  return _IMP_saxs.RadialDistributionFunction_add(self, *args)
1413 
1414  def show(self, *args):
1415  """
1416  show(RadialDistributionFunction self, _ostream out=std::cout)
1417  show(RadialDistributionFunction self)
1418  """
1419  return _IMP_saxs.RadialDistributionFunction_show(self, *args)
1420 
1421  def R_factor_score(self, *args):
1422  """
1423  R_factor_score(RadialDistributionFunction self, RadialDistributionFunction model_pr, std::string const & file_name="") -> IMP::Float
1424  R_factor_score(RadialDistributionFunction self, RadialDistributionFunction model_pr) -> IMP::Float
1425  """
1426  return _IMP_saxs.RadialDistributionFunction_R_factor_score(self, *args)
1427 
1428  def fit(self, *args):
1429  """
1430  fit(RadialDistributionFunction self, RadialDistributionFunction model_pr, std::string const & file_name="") -> IMP::Float
1431  fit(RadialDistributionFunction self, RadialDistributionFunction model_pr) -> IMP::Float
1432  """
1433  return _IMP_saxs.RadialDistributionFunction_fit(self, *args)
1434 
1435  def normalize(self):
1436  """normalize(RadialDistributionFunction self)"""
1437  return _IMP_saxs.RadialDistributionFunction_normalize(self)
1438 
1439  def add_to_distribution(self, *args):
1440  """add_to_distribution(RadialDistributionFunction self, IMP::Float dist, IMP::Float value)"""
1441  return _IMP_saxs.RadialDistributionFunction_add_to_distribution(self, *args)
1442 
1443  __swig_destroy__ = _IMP_saxs.delete_RadialDistributionFunction
1444  __del__ = lambda self : None;
1445 RadialDistributionFunction_swigregister = _IMP_saxs.RadialDistributionFunction_swigregister
1446 RadialDistributionFunction_swigregister(RadialDistributionFunction)
1447 
1448 class DeltaDistributionFunction(VectorDistribution):
1449  """Proxy of C++ IMP::saxs::DeltaDistributionFunction class"""
1450  __swig_setmethods__ = {}
1451  for _s in [VectorDistribution]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1452  __setattr__ = lambda self, name, value: _swig_setattr(self, DeltaDistributionFunction, name, value)
1453  __swig_getmethods__ = {}
1454  for _s in [VectorDistribution]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1455  __getattr__ = lambda self, name: _swig_getattr(self, DeltaDistributionFunction, name)
1456  __repr__ = _swig_repr
1457  def __init__(self, *args):
1458  """
1459  __init__(IMP::saxs::DeltaDistributionFunction self, IMP::kernel::Particles const & particles, IMP::Float max_distance=0.0, IMP::Float bin_size=pr_resolution) -> DeltaDistributionFunction
1460  __init__(IMP::saxs::DeltaDistributionFunction self, IMP::kernel::Particles const & particles, IMP::Float max_distance=0.0) -> DeltaDistributionFunction
1461  __init__(IMP::saxs::DeltaDistributionFunction self, IMP::kernel::Particles const & particles) -> DeltaDistributionFunction
1462  """
1463  this = _IMP_saxs.new_DeltaDistributionFunction(*args)
1464  try: self.this.append(this)
1465  except: self.this = this
1466  def calculate_derivative_distribution(self, *args):
1467  """calculate_derivative_distribution(DeltaDistributionFunction self, Particle particle)"""
1468  return _IMP_saxs.DeltaDistributionFunction_calculate_derivative_distribution(self, *args)
1469 
1470  def show(self, *args):
1471  """
1472  show(DeltaDistributionFunction self, _ostream out=std::cout, std::string prefix="")
1473  show(DeltaDistributionFunction self, _ostream out=std::cout)
1474  show(DeltaDistributionFunction self)
1475  """
1476  return _IMP_saxs.DeltaDistributionFunction_show(self, *args)
1477 
1478  __swig_destroy__ = _IMP_saxs.delete_DeltaDistributionFunction
1479  __del__ = lambda self : None;
1480 DeltaDistributionFunction_swigregister = _IMP_saxs.DeltaDistributionFunction_swigregister
1481 DeltaDistributionFunction_swigregister(DeltaDistributionFunction)
1482 
1483 class SolventAccessibleSurface(_object):
1484  """Proxy of C++ IMP::saxs::SolventAccessibleSurface class"""
1485  __swig_setmethods__ = {}
1486  __setattr__ = lambda self, name, value: _swig_setattr(self, SolventAccessibleSurface, name, value)
1487  __swig_getmethods__ = {}
1488  __getattr__ = lambda self, name: _swig_getattr(self, SolventAccessibleSurface, name)
1489  __repr__ = _swig_repr
1490  def get_solvent_accessibility(self, *args):
1491  """
1492  get_solvent_accessibility(SolventAccessibleSurface self, IMP::core::XYZRs const & points, float probe_radius=1.8, float density=5.0) -> IMP::Floats
1493  get_solvent_accessibility(SolventAccessibleSurface self, IMP::core::XYZRs const & points, float probe_radius=1.8) -> IMP::Floats
1494  get_solvent_accessibility(SolventAccessibleSurface self, IMP::core::XYZRs const & points) -> IMP::Floats
1495  """
1496  return _IMP_saxs.SolventAccessibleSurface_get_solvent_accessibility(self, *args)
1497 
1498  def __init__(self):
1499  """__init__(IMP::saxs::SolventAccessibleSurface self) -> SolventAccessibleSurface"""
1500  this = _IMP_saxs.new_SolventAccessibleSurface()
1501  try: self.this.append(this)
1502  except: self.this = this
1503  __swig_destroy__ = _IMP_saxs.delete_SolventAccessibleSurface
1504  __del__ = lambda self : None;
1505 SolventAccessibleSurface_swigregister = _IMP_saxs.SolventAccessibleSurface_swigregister
1506 SolventAccessibleSurface_swigregister(SolventAccessibleSurface)
1507 
1508 class ProfileFitterChiLog(IMP.base.Object):
1509  """Proxy of C++ IMP::saxs::ProfileFitter<(IMP::saxs::ChiScoreLog)> class"""
1510  __swig_setmethods__ = {}
1511  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1512  __setattr__ = lambda self, name, value: _swig_setattr(self, ProfileFitterChiLog, name, value)
1513  __swig_getmethods__ = {}
1514  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1515  __getattr__ = lambda self, name: _swig_getattr(self, ProfileFitterChiLog, name)
1516  __repr__ = _swig_repr
1517  def __init__(self, *args):
1518  """
1519  __init__(IMP::saxs::ProfileFitter<(IMP::saxs::ChiScoreLog)> self, Profile exp_profile) -> ProfileFitterChiLog
1520  __init__(IMP::saxs::ProfileFitter<(IMP::saxs::ChiScoreLog)> self, Profile exp_profile, ChiScoreLog sf) -> ProfileFitterChiLog
1521  """
1522  this = _IMP_saxs.new_ProfileFitterChiLog(*args)
1523  try: self.this.append(this)
1524  except: self.this = this
1525  def compute_score(self, *args):
1526  """
1527  compute_score(ProfileFitterChiLog self, Profile model_profile, bool use_offset=False, std::string const fit_file_name="") -> IMP::Float
1528  compute_score(ProfileFitterChiLog self, Profile model_profile, bool use_offset=False) -> IMP::Float
1529  compute_score(ProfileFitterChiLog self, Profile model_profile) -> IMP::Float
1530  compute_score(ProfileFitterChiLog self, Profile model_profile, IMP::Float min_q, IMP::Float max_q) -> IMP::Float
1531  """
1532  return _IMP_saxs.ProfileFitterChiLog_compute_score(self, *args)
1533 
1534  def fit_profile(self, *args):
1535  """
1536  fit_profile(ProfileFitterChiLog self, Profile partial_profile, float min_c1=0.95, float max_c1=1.05, float min_c2=-2.0,
1537  float max_c2=4.0, bool use_offset=False, std::string const fit_file_name="") -> FitParameters
1538  fit_profile(ProfileFitterChiLog self, Profile partial_profile, float min_c1=0.95, float max_c1=1.05, float min_c2=-2.0,
1539  float max_c2=4.0, bool use_offset=False) -> FitParameters
1540  fit_profile(ProfileFitterChiLog self, Profile partial_profile, float min_c1=0.95, float max_c1=1.05, float min_c2=-2.0,
1541  float max_c2=4.0) -> FitParameters
1542  fit_profile(ProfileFitterChiLog self, Profile partial_profile, float min_c1=0.95, float max_c1=1.05, float min_c2=-2.0) -> FitParameters
1543  fit_profile(ProfileFitterChiLog self, Profile partial_profile, float min_c1=0.95, float max_c1=1.05) -> FitParameters
1544  fit_profile(ProfileFitterChiLog self, Profile partial_profile, float min_c1=0.95) -> FitParameters
1545  fit_profile(ProfileFitterChiLog self, Profile partial_profile) -> FitParameters
1546  """
1547  return _IMP_saxs.ProfileFitterChiLog_fit_profile(self, *args)
1548 
1549  def compute_scale_factor(self, *args):
1550  """
1551  compute_scale_factor(ProfileFitterChiLog self, Profile model_profile, IMP::Float offset=0.0) -> IMP::Float
1552  compute_scale_factor(ProfileFitterChiLog self, Profile model_profile) -> IMP::Float
1553  """
1554  return _IMP_saxs.ProfileFitterChiLog_compute_scale_factor(self, *args)
1555 
1556  def compute_offset(self, *args):
1557  """compute_offset(ProfileFitterChiLog self, Profile model_profile) -> IMP::Float"""
1558  return _IMP_saxs.ProfileFitterChiLog_compute_offset(self, *args)
1559 
1560  def resample(self, *args):
1561  """resample(ProfileFitterChiLog self, Profile model_profile, Profile resampled_profile)"""
1562  return _IMP_saxs.ProfileFitterChiLog_resample(self, *args)
1563 
1564  def write_SAXS_fit_file(self, *args):
1565  """
1566  write_SAXS_fit_file(ProfileFitterChiLog self, std::string const & file_name, Profile model_profile, IMP::Float const chi_square,
1567  IMP::Float const c=1, IMP::Float const offset=0)
1568  write_SAXS_fit_file(ProfileFitterChiLog self, std::string const & file_name, Profile model_profile, IMP::Float const chi_square,
1569  IMP::Float const c=1)
1570  write_SAXS_fit_file(ProfileFitterChiLog self, std::string const & file_name, Profile model_profile, IMP::Float const chi_square)
1571  """
1572  return _IMP_saxs.ProfileFitterChiLog_write_SAXS_fit_file(self, *args)
1573 
1574  __swig_destroy__ = _IMP_saxs.delete_ProfileFitterChiLog
1575  __del__ = lambda self : None;
1576 ProfileFitterChiLog_swigregister = _IMP_saxs.ProfileFitterChiLog_swigregister
1577 ProfileFitterChiLog_swigregister(ProfileFitterChiLog)
1578 
1579 
1580 def get_module_version():
1581  """get_module_version() -> std::string const"""
1582  return _IMP_saxs.get_module_version()
1583 
1584 def get_example_path(*args):
1585  """get_example_path(std::string fname) -> std::string"""
1586  return _IMP_saxs.get_example_path(*args)
1587 
1588 def get_data_path(*args):
1589  """get_data_path(std::string fname) -> std::string"""
1590  return _IMP_saxs.get_data_path(*args)
1591 import _version_check
1592 _version_check.check_version(get_module_version())
1593 
1594 # This file is compatible with both classic and new-style classes.
1595 
1596 
std::string get_data_path(std::string file_name)
Return the full path to installed data.
Various classes to hold sets of particles.
Make CGAL functionality available to IMP.
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
Definition: exception.h:73
Low level functionality (logging, error handling, profiling, command line flags etc) that is used by ...
FormFactorTable * get_default_form_factor_table()
Composable functors to implement scores via compile-time composition.
double get_volume(const BoundingBoxD< D > &bb)
Definition: BoundingBoxD.h:147
Base functionality and abstract base classes for representation, scoring and sampling.
std::string get_example_path(std::string file_name)
Return the path to installed example data for this module.
A restraint is a term in an IMP ScoringFunction.
Common base class for heavy weight IMP objects.
Definition: Object.h:106
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...
void show(Hierarchy h, std::ostream &out=std::cout)
Print out a molecular hierarchy.
Float radius_of_gyration(const kernel::Particles &particles)
compute radius_of_gyration
Definition: saxs/utility.h:73
Output IMP model data in various file formats.
CheckLevel get_check_level()
Get the current audit mode.
Definition: exception.h:81
Functionality for loading, creating, manipulating and scoring atomic structures.
IMP::kernel::Restraint Restraint