IMP  2.1.0
The Integrative Modeling Platform
restrainer/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 2.0.11
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_restrainer', [dirname(__file__)])
19  except ImportError:
20  import _IMP_restrainer
21  return _IMP_restrainer
22  if fp is not None:
23  try:
24  _mod = imp.load_module('_IMP_restrainer', fp, pathname, description)
25  finally:
26  fp.close()
27  return _mod
28  _IMP_restrainer = swig_import_helper()
29  del swig_import_helper
30 else:
31  import _IMP_restrainer
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_RESTRAINER_SwigPyIterator(_object):
80  """Proxy of C++ swig::IMP_RESTRAINER_SwigPyIterator class"""
81  __swig_setmethods__ = {}
82  __setattr__ = lambda self, name, value: _swig_setattr(self, IMP_RESTRAINER_SwigPyIterator, name, value)
83  __swig_getmethods__ = {}
84  __getattr__ = lambda self, name: _swig_getattr(self, IMP_RESTRAINER_SwigPyIterator, name)
85  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
86  __repr__ = _swig_repr
87  __swig_destroy__ = _IMP_restrainer.delete_IMP_RESTRAINER_SwigPyIterator
88  __del__ = lambda self : None;
89  def value(self):
90  """value(IMP_RESTRAINER_SwigPyIterator self) -> PyObject *"""
91  return _IMP_restrainer.IMP_RESTRAINER_SwigPyIterator_value(self)
92 
93  def incr(self, n=1):
94  """
95  incr(IMP_RESTRAINER_SwigPyIterator self, size_t n=1) -> IMP_RESTRAINER_SwigPyIterator
96  incr(IMP_RESTRAINER_SwigPyIterator self) -> IMP_RESTRAINER_SwigPyIterator
97  """
98  return _IMP_restrainer.IMP_RESTRAINER_SwigPyIterator_incr(self, n)
99 
100  def decr(self, n=1):
101  """
102  decr(IMP_RESTRAINER_SwigPyIterator self, size_t n=1) -> IMP_RESTRAINER_SwigPyIterator
103  decr(IMP_RESTRAINER_SwigPyIterator self) -> IMP_RESTRAINER_SwigPyIterator
104  """
105  return _IMP_restrainer.IMP_RESTRAINER_SwigPyIterator_decr(self, n)
106 
107  def distance(self, *args):
108  """distance(IMP_RESTRAINER_SwigPyIterator self, IMP_RESTRAINER_SwigPyIterator x) -> ptrdiff_t"""
109  return _IMP_restrainer.IMP_RESTRAINER_SwigPyIterator_distance(self, *args)
110 
111  def equal(self, *args):
112  """equal(IMP_RESTRAINER_SwigPyIterator self, IMP_RESTRAINER_SwigPyIterator x) -> bool"""
113  return _IMP_restrainer.IMP_RESTRAINER_SwigPyIterator_equal(self, *args)
114 
115  def copy(self):
116  """copy(IMP_RESTRAINER_SwigPyIterator self) -> IMP_RESTRAINER_SwigPyIterator"""
117  return _IMP_restrainer.IMP_RESTRAINER_SwigPyIterator_copy(self)
118 
119  def next(self):
120  """next(IMP_RESTRAINER_SwigPyIterator self) -> PyObject *"""
121  return _IMP_restrainer.IMP_RESTRAINER_SwigPyIterator_next(self)
122 
123  def __next__(self):
124  """__next__(IMP_RESTRAINER_SwigPyIterator self) -> PyObject *"""
125  return _IMP_restrainer.IMP_RESTRAINER_SwigPyIterator___next__(self)
126 
127  def previous(self):
128  """previous(IMP_RESTRAINER_SwigPyIterator self) -> PyObject *"""
129  return _IMP_restrainer.IMP_RESTRAINER_SwigPyIterator_previous(self)
130 
131  def advance(self, *args):
132  """advance(IMP_RESTRAINER_SwigPyIterator self, ptrdiff_t n) -> IMP_RESTRAINER_SwigPyIterator"""
133  return _IMP_restrainer.IMP_RESTRAINER_SwigPyIterator_advance(self, *args)
134 
135  def __eq__(self, *args):
136  """__eq__(IMP_RESTRAINER_SwigPyIterator self, IMP_RESTRAINER_SwigPyIterator x) -> bool"""
137  return _IMP_restrainer.IMP_RESTRAINER_SwigPyIterator___eq__(self, *args)
138 
139  def __ne__(self, *args):
140  """__ne__(IMP_RESTRAINER_SwigPyIterator self, IMP_RESTRAINER_SwigPyIterator x) -> bool"""
141  return _IMP_restrainer.IMP_RESTRAINER_SwigPyIterator___ne__(self, *args)
142 
143  def __iadd__(self, *args):
144  """__iadd__(IMP_RESTRAINER_SwigPyIterator self, ptrdiff_t n) -> IMP_RESTRAINER_SwigPyIterator"""
145  return _IMP_restrainer.IMP_RESTRAINER_SwigPyIterator___iadd__(self, *args)
146 
147  def __isub__(self, *args):
148  """__isub__(IMP_RESTRAINER_SwigPyIterator self, ptrdiff_t n) -> IMP_RESTRAINER_SwigPyIterator"""
149  return _IMP_restrainer.IMP_RESTRAINER_SwigPyIterator___isub__(self, *args)
150 
151  def __add__(self, *args):
152  """__add__(IMP_RESTRAINER_SwigPyIterator self, ptrdiff_t n) -> IMP_RESTRAINER_SwigPyIterator"""
153  return _IMP_restrainer.IMP_RESTRAINER_SwigPyIterator___add__(self, *args)
154 
155  def __sub__(self, *args):
156  """
157  __sub__(IMP_RESTRAINER_SwigPyIterator self, ptrdiff_t n) -> IMP_RESTRAINER_SwigPyIterator
158  __sub__(IMP_RESTRAINER_SwigPyIterator self, IMP_RESTRAINER_SwigPyIterator x) -> ptrdiff_t
159  """
160  return _IMP_restrainer.IMP_RESTRAINER_SwigPyIterator___sub__(self, *args)
161 
162  def __iter__(self): return self
163 IMP_RESTRAINER_SwigPyIterator_swigregister = _IMP_restrainer.IMP_RESTRAINER_SwigPyIterator_swigregister
164 IMP_RESTRAINER_SwigPyIterator_swigregister(IMP_RESTRAINER_SwigPyIterator)
165 
166 _value_types=[]
167 _object_types=[]
168 _raii_types=[]
169 _plural_types=[]
170 
171 IMP_DEBUG = _IMP_restrainer.IMP_DEBUG
172 IMP_RELEASE = _IMP_restrainer.IMP_RELEASE
173 IMP_SILENT = _IMP_restrainer.IMP_SILENT
174 IMP_PROGRESS = _IMP_restrainer.IMP_PROGRESS
175 IMP_TERSE = _IMP_restrainer.IMP_TERSE
176 IMP_VERBOSE = _IMP_restrainer.IMP_VERBOSE
177 IMP_MEMORY = _IMP_restrainer.IMP_MEMORY
178 IMP_NONE = _IMP_restrainer.IMP_NONE
179 IMP_USAGE = _IMP_restrainer.IMP_USAGE
180 IMP_INTERNAL = _IMP_restrainer.IMP_INTERNAL
181 IMP_BASE_HAS_LOG4CXX = _IMP_restrainer.IMP_BASE_HAS_LOG4CXX
182 IMP_COMPILER_HAS_AUTO = _IMP_restrainer.IMP_COMPILER_HAS_AUTO
183 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_restrainer.IMP_COMPILER_HAS_DEBUG_VECTOR
184 IMP_BASE_HAS_BOOST_RANDOM = _IMP_restrainer.IMP_BASE_HAS_BOOST_RANDOM
185 IMP_BASE_HAS_GPERFTOOLS = _IMP_restrainer.IMP_BASE_HAS_GPERFTOOLS
186 IMP_BASE_HAS_TCMALLOC_HEAPCHECKER = _IMP_restrainer.IMP_BASE_HAS_TCMALLOC_HEAPCHECKER
187 IMP_BASE_HAS_TCMALLOC_HEAPPROFILER = _IMP_restrainer.IMP_BASE_HAS_TCMALLOC_HEAPPROFILER
188 IMPBASE_SHOW_WARNINGS = _IMP_restrainer.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_restrainer.DEFAULT_CHECK
216 NONE = _IMP_restrainer.NONE
217 USAGE = _IMP_restrainer.USAGE
218 USAGE_AND_INTERNAL = _IMP_restrainer.USAGE_AND_INTERNAL
219 
220 def set_check_level(*args):
221  """set_check_level(IMP::base::CheckLevel tf)"""
222  return _IMP_restrainer.set_check_level(*args)
223 
224 def get_check_level():
225  """get_check_level() -> IMP::base::CheckLevel"""
226  return _IMP_restrainer.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_restrainer._ostream_write(self, *args)
238 
239 _ostream_swigregister = _IMP_restrainer._ostream_swigregister
240 _ostream_swigregister(_ostream)
241 
242 IMP_COMPILER_HAS_OVERRIDE = _IMP_restrainer.IMP_COMPILER_HAS_OVERRIDE
243 IMP_COMPILER_HAS_FINAL = _IMP_restrainer.IMP_COMPILER_HAS_FINAL
244 IMP_HAS_NOEXCEPT = _IMP_restrainer.IMP_HAS_NOEXCEPT
245 import IMP.base
246 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_restrainer.IMP_CGAL_HAS_BOOST_FILESYSTEM
247 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_restrainer.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
248 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_restrainer.IMP_CGAL_HAS_BOOST_RANDOM
249 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_restrainer.IMP_CGAL_HAS_BOOST_SYSTEM
250 IMPCGAL_SHOW_WARNINGS = _IMP_restrainer.IMPCGAL_SHOW_WARNINGS
251 import IMP.cgal
252 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_restrainer.IMP_ALGEBRA_HAS_IMP_CGAL
253 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_restrainer.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
254 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_restrainer.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
255 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_restrainer.IMP_ALGEBRA_HAS_BOOST_RANDOM
256 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_restrainer.IMP_ALGEBRA_HAS_BOOST_SYSTEM
257 IMP_ALGEBRA_HAS_CGAL = _IMP_restrainer.IMP_ALGEBRA_HAS_CGAL
258 IMP_ALGEBRA_HAS_ANN = _IMP_restrainer.IMP_ALGEBRA_HAS_ANN
259 IMPALGEBRA_SHOW_WARNINGS = _IMP_restrainer.IMPALGEBRA_SHOW_WARNINGS
260 import IMP.algebra
261 IMP_KERNEL_HAS_IMP_CGAL = _IMP_restrainer.IMP_KERNEL_HAS_IMP_CGAL
262 IMP_KERNEL_HAS_BOOST_PROGRAMOPTIONS = _IMP_restrainer.IMP_KERNEL_HAS_BOOST_PROGRAMOPTIONS
263 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_restrainer.IMP_KERNEL_HAS_BOOST_RANDOM
264 IMP_KERNEL_HAS_BOOST_SYSTEM = _IMP_restrainer.IMP_KERNEL_HAS_BOOST_SYSTEM
265 IMP_KERNEL_HAS_CGAL = _IMP_restrainer.IMP_KERNEL_HAS_CGAL
266 IMPKERNEL_SHOW_WARNINGS = _IMP_restrainer.IMPKERNEL_SHOW_WARNINGS
267 import IMP.kernel
268 IMP_DISPLAY_HAS_IMP_BASE = _IMP_restrainer.IMP_DISPLAY_HAS_IMP_BASE
269 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_restrainer.IMP_DISPLAY_HAS_IMP_CGAL
270 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_restrainer.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
271 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_restrainer.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
272 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_restrainer.IMP_DISPLAY_HAS_BOOST_RANDOM
273 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_restrainer.IMP_DISPLAY_HAS_BOOST_SYSTEM
274 IMP_DISPLAY_HAS_CGAL = _IMP_restrainer.IMP_DISPLAY_HAS_CGAL
275 IMPDISPLAY_SHOW_WARNINGS = _IMP_restrainer.IMPDISPLAY_SHOW_WARNINGS
276 import IMP.display
277 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_restrainer.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
278 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_restrainer.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
279 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_restrainer.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
280 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_restrainer.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
281 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_restrainer.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
282 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_restrainer.IMP_SCORE_FUNCTOR_HAS_CGAL
283 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_restrainer.IMPSCOREFUNCTOR_SHOW_WARNINGS
284 import IMP.score_functor
285 IMP_STATISTICS_HAS_IMP_BASE = _IMP_restrainer.IMP_STATISTICS_HAS_IMP_BASE
286 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_restrainer.IMP_STATISTICS_HAS_IMP_CGAL
287 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_restrainer.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
288 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_restrainer.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
289 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_restrainer.IMP_STATISTICS_HAS_BOOST_RANDOM
290 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_restrainer.IMP_STATISTICS_HAS_BOOST_SYSTEM
291 IMP_STATISTICS_HAS_CGAL = _IMP_restrainer.IMP_STATISTICS_HAS_CGAL
292 IMPSTATISTICS_SHOW_WARNINGS = _IMP_restrainer.IMPSTATISTICS_SHOW_WARNINGS
293 import IMP.statistics
294 IMP_CORE_HAS_IMP_BASE = _IMP_restrainer.IMP_CORE_HAS_IMP_BASE
295 IMP_CORE_HAS_IMP_CGAL = _IMP_restrainer.IMP_CORE_HAS_IMP_CGAL
296 IMP_CORE_HAS_IMP_KERNEL = _IMP_restrainer.IMP_CORE_HAS_IMP_KERNEL
297 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_restrainer.IMP_CORE_HAS_BOOST_FILESYSTEM
298 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_restrainer.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
299 IMP_CORE_HAS_BOOST_RANDOM = _IMP_restrainer.IMP_CORE_HAS_BOOST_RANDOM
300 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_restrainer.IMP_CORE_HAS_BOOST_SYSTEM
301 IMP_CORE_HAS_CGAL = _IMP_restrainer.IMP_CORE_HAS_CGAL
302 IMPCORE_SHOW_WARNINGS = _IMP_restrainer.IMPCORE_SHOW_WARNINGS
303 import IMP.core
304 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_restrainer.IMP_CONTAINER_HAS_IMP_ALGEBRA
305 IMP_CONTAINER_HAS_IMP_BASE = _IMP_restrainer.IMP_CONTAINER_HAS_IMP_BASE
306 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_restrainer.IMP_CONTAINER_HAS_IMP_CGAL
307 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_restrainer.IMP_CONTAINER_HAS_IMP_DISPLAY
308 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_restrainer.IMP_CONTAINER_HAS_IMP_KERNEL
309 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_restrainer.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
310 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_restrainer.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
311 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_restrainer.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
312 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_restrainer.IMP_CONTAINER_HAS_BOOST_RANDOM
313 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_restrainer.IMP_CONTAINER_HAS_BOOST_SYSTEM
314 IMP_CONTAINER_HAS_CGAL = _IMP_restrainer.IMP_CONTAINER_HAS_CGAL
315 IMPCONTAINER_SHOW_WARNINGS = _IMP_restrainer.IMPCONTAINER_SHOW_WARNINGS
316 import IMP.container
317 IMP_ATOM_HAS_IMP_BASE = _IMP_restrainer.IMP_ATOM_HAS_IMP_BASE
318 IMP_ATOM_HAS_IMP_CGAL = _IMP_restrainer.IMP_ATOM_HAS_IMP_CGAL
319 IMP_ATOM_HAS_IMP_KERNEL = _IMP_restrainer.IMP_ATOM_HAS_IMP_KERNEL
320 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_restrainer.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
321 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_restrainer.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
322 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_restrainer.IMP_ATOM_HAS_BOOST_RANDOM
323 IMP_ATOM_HAS_BOOST_REGEX = _IMP_restrainer.IMP_ATOM_HAS_BOOST_REGEX
324 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_restrainer.IMP_ATOM_HAS_BOOST_SYSTEM
325 IMP_ATOM_HAS_CGAL = _IMP_restrainer.IMP_ATOM_HAS_CGAL
326 IMPATOM_SHOW_WARNINGS = _IMP_restrainer.IMPATOM_SHOW_WARNINGS
327 IMP_ATOM_TYPE_INDEX = _IMP_restrainer.IMP_ATOM_TYPE_INDEX
328 IMP_RESIDUE_TYPE_INDEX = _IMP_restrainer.IMP_RESIDUE_TYPE_INDEX
329 IMP_HIERARCHY_TYPE_INDEX = _IMP_restrainer.IMP_HIERARCHY_TYPE_INDEX
330 import IMP.atom
331 IMP_EM_HAS_IMP_CGAL = _IMP_restrainer.IMP_EM_HAS_IMP_CGAL
332 IMP_EM_HAS_IMP_CONTAINER = _IMP_restrainer.IMP_EM_HAS_IMP_CONTAINER
333 IMP_EM_HAS_IMP_DISPLAY = _IMP_restrainer.IMP_EM_HAS_IMP_DISPLAY
334 IMP_EM_HAS_IMP_KERNEL = _IMP_restrainer.IMP_EM_HAS_IMP_KERNEL
335 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_restrainer.IMP_EM_HAS_IMP_SCORE_FUNCTOR
336 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_restrainer.IMP_EM_HAS_BOOST_FILESYSTEM
337 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_restrainer.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
338 IMP_EM_HAS_BOOST_RANDOM = _IMP_restrainer.IMP_EM_HAS_BOOST_RANDOM
339 IMP_EM_HAS_BOOST_REGEX = _IMP_restrainer.IMP_EM_HAS_BOOST_REGEX
340 IMP_EM_HAS_BOOST_SYSTEM = _IMP_restrainer.IMP_EM_HAS_BOOST_SYSTEM
341 IMP_EM_HAS_CGAL = _IMP_restrainer.IMP_EM_HAS_CGAL
342 IMPEM_SHOW_WARNINGS = _IMP_restrainer.IMPEM_SHOW_WARNINGS
343 import IMP.em
344 IMP_SAXS_HAS_IMP_BASE = _IMP_restrainer.IMP_SAXS_HAS_IMP_BASE
345 IMP_SAXS_HAS_IMP_CGAL = _IMP_restrainer.IMP_SAXS_HAS_IMP_CGAL
346 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_restrainer.IMP_SAXS_HAS_IMP_CONTAINER
347 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_restrainer.IMP_SAXS_HAS_IMP_DISPLAY
348 IMP_SAXS_HAS_IMP_KERNEL = _IMP_restrainer.IMP_SAXS_HAS_IMP_KERNEL
349 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_restrainer.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
350 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_restrainer.IMP_SAXS_HAS_BOOST_FILESYSTEM
351 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_restrainer.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
352 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_restrainer.IMP_SAXS_HAS_BOOST_RANDOM
353 IMP_SAXS_HAS_BOOST_REGEX = _IMP_restrainer.IMP_SAXS_HAS_BOOST_REGEX
354 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_restrainer.IMP_SAXS_HAS_BOOST_SYSTEM
355 IMP_SAXS_HAS_CGAL = _IMP_restrainer.IMP_SAXS_HAS_CGAL
356 IMPSAXS_SHOW_WARNINGS = _IMP_restrainer.IMPSAXS_SHOW_WARNINGS
357 import IMP.saxs
358 IMP_RESTRAINER_HAS_IMP_ALGEBRA = _IMP_restrainer.IMP_RESTRAINER_HAS_IMP_ALGEBRA
359 IMP_RESTRAINER_HAS_IMP_BASE = _IMP_restrainer.IMP_RESTRAINER_HAS_IMP_BASE
360 IMP_RESTRAINER_HAS_IMP_CGAL = _IMP_restrainer.IMP_RESTRAINER_HAS_IMP_CGAL
361 IMP_RESTRAINER_HAS_IMP_CONTAINER = _IMP_restrainer.IMP_RESTRAINER_HAS_IMP_CONTAINER
362 IMP_RESTRAINER_HAS_IMP_DISPLAY = _IMP_restrainer.IMP_RESTRAINER_HAS_IMP_DISPLAY
363 IMP_RESTRAINER_HAS_IMP_KERNEL = _IMP_restrainer.IMP_RESTRAINER_HAS_IMP_KERNEL
364 IMP_RESTRAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_restrainer.IMP_RESTRAINER_HAS_IMP_SCORE_FUNCTOR
365 IMP_RESTRAINER_HAS_IMP_STATISTICS = _IMP_restrainer.IMP_RESTRAINER_HAS_IMP_STATISTICS
366 IMP_RESTRAINER_HAS_BOOST_FILESYSTEM = _IMP_restrainer.IMP_RESTRAINER_HAS_BOOST_FILESYSTEM
367 IMP_RESTRAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_restrainer.IMP_RESTRAINER_HAS_BOOST_PROGRAMOPTIONS
368 IMP_RESTRAINER_HAS_BOOST_RANDOM = _IMP_restrainer.IMP_RESTRAINER_HAS_BOOST_RANDOM
369 IMP_RESTRAINER_HAS_BOOST_REGEX = _IMP_restrainer.IMP_RESTRAINER_HAS_BOOST_REGEX
370 IMP_RESTRAINER_HAS_BOOST_SYSTEM = _IMP_restrainer.IMP_RESTRAINER_HAS_BOOST_SYSTEM
371 IMP_RESTRAINER_HAS_CGAL = _IMP_restrainer.IMP_RESTRAINER_HAS_CGAL
372 IMPRESTRAINER_SHOW_WARNINGS = _IMP_restrainer.IMPRESTRAINER_SHOW_WARNINGS
373 SimpleConnectivities=list
374 _plural_types.append("SimpleConnectivities")
375 _value_types.append("SimpleConnectivity")
376 
377 SimpleDistances=list
378 _plural_types.append("SimpleDistances")
379 _value_types.append("SimpleDistance")
380 
381 SimpleDiameters=list
382 _plural_types.append("SimpleDiameters")
383 _value_types.append("SimpleDiameter")
384 
385 SimpleExcludedVolumes=list
386 _plural_types.append("SimpleExcludedVolumes")
387 _value_types.append("SimpleExcludedVolume")
388 
389 SimpleEMFits=list
390 _plural_types.append("SimpleEMFits")
391 _value_types.append("SimpleEMFit")
392 
393 import _representation
394 import _restraint
395 import _xml_parser
396 import _display
397 import _optimization
398 import _main
399 
400 class Representation(_representation.Representation):
401  """Store Representation."""
402  def __init__(self):
403  _representation.Representation.__init__(self)
404  def get_imp_hierarchy_by_id(self, id):
405  """Return an IMP::atom::Hierarchy by particle id.
406  @param id Particle id.
407  @return An IMP::atom::Hierarchy hierarchy."""
408  return _representation.Representation.get_imp_hierarchy_by_id(self,id)
409 
411  """Return the root of the IMP::atom::Hierarchy"""
412  return _representation.Representation.get_root_imp_hierarchy(self)
413 
414  def find_all_by_id(self, id): # assuming there are many obj with the same id
415  """Return a list of all nodes that have the id given by the parameter"""
416  return _representation.Representation.gind_all_by_id(self, id)
417 
418  def find_by_id(self, id): # assuming there is just one obj with the same id
419  """Return a node that have the id given by the parameter"""
420  return _representation.Representation.find_by_id(self,id)
421 
422  def get_model(self, model=None):
423  """Return an IMP::Model that contains the representation"""
424  return _representation.Representation.get_model(self, model)
425 
426 class Restraint(_restraint.Restraint):
427  """Store Restraint"""
428  def __init__(self):
429  """"""
430  _restraint.Restraint.__init__(self)
431 
432  def add_to_representation(self, repr):
433  """ Place restraint into IMP Model."""
434  return _restraint.Restraint.add_to_representation(self, repr)
435 
437  """Show restraint name, initial weight, and score for the current state of the model"""
438  return _restraint.Restraint.show_all_restraints(self)
439 
440 
441  def get_all_restraints_by_name(self, name):
442  """Assuming there are many restraint objects with the same name.
443  @param[in] name The name to search for"""
444  return _restraint.Restraint.get_all_restraints_by_name(self,name)
445 
446  def get_restraint_by_name(self, name):
447  """Assuming there is just one restraint object with the same name."""
448  return restraint.Restraint.get_restraint_by_name(self,name)
449 
450  def get_rigid_body_by_id(self, id):
451  """Get rigid body by particle id."""
452  return _restraint.Restraint.get_rigid_body_by_id(self,id)
453 
454 
456  """Get all rigid bodies."""
457  return _restraint.Restraint.get_all_rigid_bodies(self)
458 
459 class XMLRepresentation(_xml_parser.XMLRepresentation):
460  """Construct Representation from XML file"""
461  def __init__(self, filename):
462  _xml_parser.XMLRepresentation.__init__(self, filename)
463  def run(self):
464  """Return IMP.restrainer.Representation
465  object such that each node in the representation
466  corresponds to the node in the XML nodes"""
467  return _xml_parser.XMLRepresentation.run(self)
468 
469 class XMLDisplay(_xml_parser.XMLDisplay):
470  """Construct Display from XML file"""
471  def __init__(self, filename):
472  _xml_parser.XMLDisplay.__init__(self, filename)
473 
474  def run(self):
475  """Return display object such that each node in the display
476  corresponds to the node in the XML nodes"""
477  return _xml_parser.XMLDisplay.run(self)
478 
479 class XMLRestraint(_xml_parser.XMLRestraint):
480  """Construct Restraint from XML file"""
481  def __init__(self, filename):
482  """ @param[in] filename the name of the file to read """
483  _xml_parser.XMLRestraint.__init__(self, filename)
484  def run(self):
485  """Return Restraint
486  object such that each node in the restraint
487  corresponds to the node in the XML nodes"""
488  return _xml_parser.XMLRestraint.run(self)
489 
490 class XMLOptimization(_xml_parser.XMLOptimization):
491  def __init__(self, filename):
492  _xml_parser.XMLOptimization.__init__(self, filename)
493  def run(self):
494  return _xml_parser.XMLOptimization.run(self)
495 
496 class Display(_display.Display):
497  """A class to display the configuration"""
498  def __init__(self):
499  _display.Display.__init__(self)
500 
501  def create_log(self, repr, log_name):
502  """Create Chimera log.
503  @param Representation object.
504  @param log_name Log name
505  @return IMP::dispay::WriteOptimizerState"""
506  return _display.Display.create_log(self, repr, log_name)
507 
508 class Main(_main.Main):
509  def __init__(self):
510  _main.Main.__init__(self)
511  def add_representation(self, fname):
512  return _main.Main.add_representation(self, fname)
513  def add_restraint(self, fname):
514  return _main.Main.add_restraint(self, fname)
515  def add_optimization(self, fname):
516  return _main.Main.add_optimization(self, fname)
517  def add_display(self, fname, logname=None):
518  return _main.Main.add_display(self, fname, logname)
519  def optimize(self):
520  _main.Main.optimize(self)
521  def get_model(self):
522  return _main.Main.get_model(self)
523 
524 
525 
527  """
528  create_simple_connectivity_on_rigid_bodies(IMP::core::RigidBodies const & rbs, Refiner ref=IMP::core::internal::get_rigid_members_refiner()) -> SimpleConnectivity
529  create_simple_connectivity_on_rigid_bodies(IMP::core::RigidBodies const & rbs) -> SimpleConnectivity
530  """
531  return _IMP_restrainer.create_simple_connectivity_on_rigid_bodies(*args)
532 
534  """create_simple_connectivity_on_molecules(IMP::atom::Hierarchies const & mhs) -> SimpleConnectivity"""
535  return _IMP_restrainer.create_simple_connectivity_on_molecules(*args)
536 
537 def create_simple_distance(*args):
538  """create_simple_distance(IMP::kernel::Particles const & ps) -> SimpleDistance"""
539  return _IMP_restrainer.create_simple_distance(*args)
540 
541 def create_simple_diameter(*args):
542  """create_simple_diameter(IMP::kernel::Particles const & ps, IMP::Float diameter) -> SimpleDiameter"""
543  return _IMP_restrainer.create_simple_diameter(*args)
544 
546  """
547  create_simple_excluded_volume_on_rigid_bodies(IMP::core::RigidBodies const & rbs, Refiner ref=IMP::core::internal::get_rigid_members_refiner()) -> SimpleExcludedVolume
548  create_simple_excluded_volume_on_rigid_bodies(IMP::core::RigidBodies const & rbs) -> SimpleExcludedVolume
549  """
550  return _IMP_restrainer.create_simple_excluded_volume_on_rigid_bodies(*args)
551 
553  """create_simple_excluded_volume_on_molecules(IMP::atom::Hierarchies const & mhs) -> SimpleExcludedVolume"""
554  return _IMP_restrainer.create_simple_excluded_volume_on_molecules(*args)
555 
556 def create_simple_em_fit(*args):
557  """
558  create_simple_em_fit(IMP::atom::Hierarchies const & mhs, DensityMap dmap) -> SimpleEMFit
559  create_simple_em_fit(Hierarchy mh, DensityMap dmap) -> SimpleEMFit
560  """
561  return _IMP_restrainer.create_simple_em_fit(*args)
562 
563 def load_em_density_map(*args):
564  """load_em_density_map(char const * map_fn, float spacing, float resolution) -> DensityMap"""
565  return _IMP_restrainer.load_em_density_map(*args)
566 
567 def set_rigid_bodies(*args):
568  """set_rigid_bodies(IMP::atom::Hierarchies const & mhs) -> IMP::core::RigidBodies"""
569  return _IMP_restrainer.set_rigid_bodies(*args)
570 class SimpleConnectivity(_object):
571  """Proxy of C++ IMP::restrainer::SimpleConnectivity class"""
572  __swig_setmethods__ = {}
573  __setattr__ = lambda self, name, value: _swig_setattr(self, SimpleConnectivity, name, value)
574  __swig_getmethods__ = {}
575  __getattr__ = lambda self, name: _swig_getattr(self, SimpleConnectivity, name)
576  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined")
577  def get_restraint(self):
578  """get_restraint(SimpleConnectivity self) -> ConnectivityRestraint"""
579  return _IMP_restrainer.SimpleConnectivity_get_restraint(self)
580 
581  def get_harmonic_upper_bound(self):
582  """get_harmonic_upper_bound(SimpleConnectivity self) -> HarmonicUpperBound"""
583  return _IMP_restrainer.SimpleConnectivity_get_harmonic_upper_bound(self)
584 
585  def get_sphere_distance_pair_score(self):
586  """get_sphere_distance_pair_score(SimpleConnectivity self) -> SphereDistancePairScore"""
587  return _IMP_restrainer.SimpleConnectivity_get_sphere_distance_pair_score(self)
588 
589  def set_mean(self, *args):
590  """set_mean(SimpleConnectivity self, IMP::Float mean)"""
591  return _IMP_restrainer.SimpleConnectivity_set_mean(self, *args)
592 
593  def set_standard_deviation(self, *args):
594  """set_standard_deviation(SimpleConnectivity self, IMP::Float sd)"""
595  return _IMP_restrainer.SimpleConnectivity_set_standard_deviation(self, *args)
596 
597  def set_k(self, *args):
598  """set_k(SimpleConnectivity self, IMP::Float k)"""
599  return _IMP_restrainer.SimpleConnectivity_set_k(self, *args)
600 
601  def get_version_info(self):
602  """get_version_info(SimpleConnectivity self) -> VersionInfo"""
603  return _IMP_restrainer.SimpleConnectivity_get_version_info(self)
604 
605  def show(self, *args):
606  """
607  show(SimpleConnectivity self, _ostream out=std::cout)
608  show(SimpleConnectivity self)
609  """
610  return _IMP_restrainer.SimpleConnectivity_show(self, *args)
611 
612  def __str__(self):
613  """__str__(SimpleConnectivity self) -> std::string"""
614  return _IMP_restrainer.SimpleConnectivity___str__(self)
615 
616  def __repr__(self):
617  """__repr__(SimpleConnectivity self) -> std::string"""
618  return _IMP_restrainer.SimpleConnectivity___repr__(self)
619 
620  __swig_destroy__ = _IMP_restrainer.delete_SimpleConnectivity
621  __del__ = lambda self : None;
622 SimpleConnectivity_swigregister = _IMP_restrainer.SimpleConnectivity_swigregister
623 SimpleConnectivity_swigregister(SimpleConnectivity)
624 
625 class SimpleDistance(_object):
626  """Proxy of C++ IMP::restrainer::SimpleDistance class"""
627  __swig_setmethods__ = {}
628  __setattr__ = lambda self, name, value: _swig_setattr(self, SimpleDistance, name, value)
629  __swig_getmethods__ = {}
630  __getattr__ = lambda self, name: _swig_getattr(self, SimpleDistance, name)
631  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined")
632  def get_restraint(self):
633  """get_restraint(SimpleDistance self) -> DistanceRestraint"""
634  return _IMP_restrainer.SimpleDistance_get_restraint(self)
635 
636  def get_harmonic_upper_bound(self):
637  """get_harmonic_upper_bound(SimpleDistance self) -> HarmonicUpperBound"""
638  return _IMP_restrainer.SimpleDistance_get_harmonic_upper_bound(self)
639 
640  def set_mean(self, *args):
641  """set_mean(SimpleDistance self, IMP::Float mean)"""
642  return _IMP_restrainer.SimpleDistance_set_mean(self, *args)
643 
644  def set_standard_deviation(self, *args):
645  """set_standard_deviation(SimpleDistance self, IMP::Float sd)"""
646  return _IMP_restrainer.SimpleDistance_set_standard_deviation(self, *args)
647 
648  def set_k(self, *args):
649  """set_k(SimpleDistance self, IMP::Float k)"""
650  return _IMP_restrainer.SimpleDistance_set_k(self, *args)
651 
652  def get_version_info(self):
653  """get_version_info(SimpleDistance self) -> VersionInfo"""
654  return _IMP_restrainer.SimpleDistance_get_version_info(self)
655 
656  def show(self, *args):
657  """
658  show(SimpleDistance self, _ostream out=std::cout)
659  show(SimpleDistance self)
660  """
661  return _IMP_restrainer.SimpleDistance_show(self, *args)
662 
663  def __str__(self):
664  """__str__(SimpleDistance self) -> std::string"""
665  return _IMP_restrainer.SimpleDistance___str__(self)
666 
667  def __repr__(self):
668  """__repr__(SimpleDistance self) -> std::string"""
669  return _IMP_restrainer.SimpleDistance___repr__(self)
670 
671  __swig_destroy__ = _IMP_restrainer.delete_SimpleDistance
672  __del__ = lambda self : None;
673 SimpleDistance_swigregister = _IMP_restrainer.SimpleDistance_swigregister
674 SimpleDistance_swigregister(SimpleDistance)
675 
676 class SimpleDiameter(_object):
677  """Proxy of C++ IMP::restrainer::SimpleDiameter class"""
678  __swig_setmethods__ = {}
679  __setattr__ = lambda self, name, value: _swig_setattr(self, SimpleDiameter, name, value)
680  __swig_getmethods__ = {}
681  __getattr__ = lambda self, name: _swig_getattr(self, SimpleDiameter, name)
682  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined")
683  def get_restraint(self):
684  """get_restraint(SimpleDiameter self) -> DiameterRestraint"""
685  return _IMP_restrainer.SimpleDiameter_get_restraint(self)
686 
687  def get_harmonic_upper_bound(self):
688  """get_harmonic_upper_bound(SimpleDiameter self) -> HarmonicUpperBound"""
689  return _IMP_restrainer.SimpleDiameter_get_harmonic_upper_bound(self)
690 
691  def set_mean(self, *args):
692  """set_mean(SimpleDiameter self, IMP::Float mean)"""
693  return _IMP_restrainer.SimpleDiameter_set_mean(self, *args)
694 
695  def set_standard_deviation(self, *args):
696  """set_standard_deviation(SimpleDiameter self, IMP::Float sd)"""
697  return _IMP_restrainer.SimpleDiameter_set_standard_deviation(self, *args)
698 
699  def set_k(self, *args):
700  """set_k(SimpleDiameter self, IMP::Float k)"""
701  return _IMP_restrainer.SimpleDiameter_set_k(self, *args)
702 
703  def get_version_info(self):
704  """get_version_info(SimpleDiameter self) -> VersionInfo"""
705  return _IMP_restrainer.SimpleDiameter_get_version_info(self)
706 
707  def show(self, *args):
708  """
709  show(SimpleDiameter self, _ostream out=std::cout)
710  show(SimpleDiameter self)
711  """
712  return _IMP_restrainer.SimpleDiameter_show(self, *args)
713 
714  def __str__(self):
715  """__str__(SimpleDiameter self) -> std::string"""
716  return _IMP_restrainer.SimpleDiameter___str__(self)
717 
718  def __repr__(self):
719  """__repr__(SimpleDiameter self) -> std::string"""
720  return _IMP_restrainer.SimpleDiameter___repr__(self)
721 
722  __swig_destroy__ = _IMP_restrainer.delete_SimpleDiameter
723  __del__ = lambda self : None;
724 SimpleDiameter_swigregister = _IMP_restrainer.SimpleDiameter_swigregister
725 SimpleDiameter_swigregister(SimpleDiameter)
726 
727 class SimpleExcludedVolume(_object):
728  """Proxy of C++ IMP::restrainer::SimpleExcludedVolume class"""
729  __swig_setmethods__ = {}
730  __setattr__ = lambda self, name, value: _swig_setattr(self, SimpleExcludedVolume, name, value)
731  __swig_getmethods__ = {}
732  __getattr__ = lambda self, name: _swig_getattr(self, SimpleExcludedVolume, name)
733  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined")
734  def get_restraint(self):
735  """get_restraint(SimpleExcludedVolume self) -> ExcludedVolumeRestraint"""
736  return _IMP_restrainer.SimpleExcludedVolume_get_restraint(self)
737 
738  def get_version_info(self):
739  """get_version_info(SimpleExcludedVolume self) -> VersionInfo"""
740  return _IMP_restrainer.SimpleExcludedVolume_get_version_info(self)
741 
742  def show(self, *args):
743  """
744  show(SimpleExcludedVolume self, _ostream out=std::cout)
745  show(SimpleExcludedVolume self)
746  """
747  return _IMP_restrainer.SimpleExcludedVolume_show(self, *args)
748 
749  def __str__(self):
750  """__str__(SimpleExcludedVolume self) -> std::string"""
751  return _IMP_restrainer.SimpleExcludedVolume___str__(self)
752 
753  def __repr__(self):
754  """__repr__(SimpleExcludedVolume self) -> std::string"""
755  return _IMP_restrainer.SimpleExcludedVolume___repr__(self)
756 
757  __swig_destroy__ = _IMP_restrainer.delete_SimpleExcludedVolume
758  __del__ = lambda self : None;
759 SimpleExcludedVolume_swigregister = _IMP_restrainer.SimpleExcludedVolume_swigregister
760 SimpleExcludedVolume_swigregister(SimpleExcludedVolume)
761 
762 class SimpleEMFit(_object):
763  """Proxy of C++ IMP::restrainer::SimpleEMFit class"""
764  __swig_setmethods__ = {}
765  __setattr__ = lambda self, name, value: _swig_setattr(self, SimpleEMFit, name, value)
766  __swig_getmethods__ = {}
767  __getattr__ = lambda self, name: _swig_getattr(self, SimpleEMFit, name)
768  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined")
769  def get_restraint(self):
770  """get_restraint(SimpleEMFit self) -> FitRestraint"""
771  return _IMP_restrainer.SimpleEMFit_get_restraint(self)
772 
773  def get_version_info(self):
774  """get_version_info(SimpleEMFit self) -> VersionInfo"""
775  return _IMP_restrainer.SimpleEMFit_get_version_info(self)
776 
777  def show(self, *args):
778  """
779  show(SimpleEMFit self, _ostream out=std::cout)
780  show(SimpleEMFit self)
781  """
782  return _IMP_restrainer.SimpleEMFit_show(self, *args)
783 
784  def __str__(self):
785  """__str__(SimpleEMFit self) -> std::string"""
786  return _IMP_restrainer.SimpleEMFit___str__(self)
787 
788  def __repr__(self):
789  """__repr__(SimpleEMFit self) -> std::string"""
790  return _IMP_restrainer.SimpleEMFit___repr__(self)
791 
792  __swig_destroy__ = _IMP_restrainer.delete_SimpleEMFit
793  __del__ = lambda self : None;
794 SimpleEMFit_swigregister = _IMP_restrainer.SimpleEMFit_swigregister
795 SimpleEMFit_swigregister(SimpleEMFit)
796 
797 
798 def get_module_version():
799  """get_module_version() -> std::string const"""
800  return _IMP_restrainer.get_module_version()
801 
802 def get_example_path(*args):
803  """get_example_path(std::string fname) -> std::string"""
804  return _IMP_restrainer.get_example_path(*args)
805 
806 def get_data_path(*args):
807  """get_data_path(std::string fname) -> std::string"""
808  return _IMP_restrainer.get_data_path(*args)
809 import _version_check
810 _version_check.check_version(get_module_version())
811 
812 # This file is compatible with both classic and new-style classes.
813 
814 
def run
Return display object such that each node in the display corresponds to the node in the XML nodes...
SimpleDiameter create_simple_diameter(const kernel::Particles &ps, Float diameter)
def find_all_by_id
Return a list of all nodes that have the id given by the parameter.
def get_model
Return an IMP::Model that contains the representation.
See IMP.container for more information.
def get_imp_hierarchy_by_id
Return an IMP::atom::Hierarchy by particle id.
See IMP.cgal for more information.
Definition: cgal_config.h:107
A class to display the configuration.
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
See IMP.base for more information.
Definition: base/Array.h:20
Construct Restraint from XML file.
def create_log
Create Chimera log.
def run
Return Restraint object such that each node in the restraint corresponds to the node in the XML nodes...
def show_all_restraints
Show restraint name, initial weight, and score for the current state of the model.
See IMP.score_functor for more information.
Definition: AddScores.h:14
SimpleEMFit create_simple_em_fit(atom::Hierarchies const &mhs, em::DensityMap *dmap)
See IMP.statistics for more information.
Construct Representation from XML file.
SimpleExcludedVolume create_simple_excluded_volume_on_molecules(const atom::Hierarchies &mhs)
std::string get_data_path(std::string file_name)
Return the full path to installed data.
See IMP.kernel for more information.
def run
Return IMP.restrainer.Representation object such that each node in the representation corresponds to ...
Simple connectivity restraint.
SimpleConnectivity create_simple_connectivity_on_rigid_bodies(const core::RigidBodies &rbs, Refiner *ref=IMP::core::internal::get_rigid_members_refiner())
SimpleConnectivity create_simple_connectivity_on_molecules(const atom::Hierarchies &mhs)
Simple EM fit restraint.
See IMP.em for more information.
Definition: CoarseCC.h:23
def get_all_rigid_bodies
Get all rigid bodies.
Simple distance restraint between two particles.
std::string get_example_path(std::string file_name)
Return the path to installed example data for this module.
def find_by_id
Return a node that have the id given by the parameter.
def get_all_restraints_by_name
Assuming there are many restraint objects with the same name.
See IMP.core for more information.
See IMP.algebra for more information.
def get_restraint_by_name
Assuming there is just one restraint object with the same name.
void show(Hierarchy h, std::ostream &out=std::cout)
Print out a molecular hierarchy.
def get_rigid_body_by_id
Get rigid body by particle id.
core::RigidBodies set_rigid_bodies(atom::Hierarchies const &mhs)
def get_root_imp_hierarchy
Return the root of the IMP::atom::Hierarchy.
SimpleDistance create_simple_distance(const kernel::Particles &ps)
Simple diameter restraint.
em::DensityMap * load_em_density_map(char const *map_fn, float spacing, float resolution)
SimpleExcludedVolume create_simple_excluded_volume_on_rigid_bodies(const core::RigidBodies &rbs, Refiner *ref=IMP::core::internal::get_rigid_members_refiner())
def add_to_representation
Place restraint into IMP Model.
Simple excluded volume restraint.
See IMP.display for more information.
Definition: BildWriter.h:20
CheckLevel get_check_level()
Get the current audit mode.
See IMP.atom for more information.
Construct Display from XML file.
void add_restraint(RMF::FileHandle fh, kernel::Restraint *hs)
See IMP.saxs for more information.
Definition: ChiFreeScore.h:14