IMP  2.0.1
The Integrative Modeling Platform
cnmultifit/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 2.0.8
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 from sys import version_info
10 if version_info >= (2,6,0):
11  def swig_import_helper():
12  from os.path import dirname
13  import imp
14  fp = None
15  try:
16  fp, pathname, description = imp.find_module('_IMP_cnmultifit', [dirname(__file__)])
17  except ImportError:
18  import _IMP_cnmultifit
19  return _IMP_cnmultifit
20  if fp is not None:
21  try:
22  _mod = imp.load_module('_IMP_cnmultifit', fp, pathname, description)
23  finally:
24  fp.close()
25  return _mod
26  _IMP_cnmultifit = swig_import_helper()
27  del swig_import_helper
28 else:
29  import _IMP_cnmultifit
30 del version_info
31 try:
32  _swig_property = property
33 except NameError:
34  pass # Python < 2.2 doesn't have 'property'.
35 def _swig_setattr_nondynamic(self,class_type,name,value,static=1):
36  if (name == "thisown"): return self.this.own(value)
37  if (name == "this"):
38  if type(value).__name__ == 'SwigPyObject':
39  self.__dict__[name] = value
40  return
41  method = class_type.__swig_setmethods__.get(name,None)
42  if method: return method(self,value)
43  if (not static):
44  self.__dict__[name] = value
45  else:
46  raise AttributeError("You cannot add attributes to %s" % self)
47 
48 def _swig_setattr(self,class_type,name,value):
49  return _swig_setattr_nondynamic(self,class_type,name,value,0)
50 
51 def _swig_getattr(self,class_type,name):
52  if (name == "thisown"): return self.this.own()
53  method = class_type.__swig_getmethods__.get(name,None)
54  if method: return method(self)
55  raise AttributeError(name)
56 
57 def _swig_repr(self):
58  try: strthis = "proxy of " + self.this.__repr__()
59  except: strthis = ""
60  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
61 
62 try:
63  _object = object
64  _newclass = 1
65 except AttributeError:
66  class _object : pass
67  _newclass = 0
68 
69 
70 try:
71  import weakref
72  weakref_proxy = weakref.proxy
73 except:
74  weakref_proxy = lambda x: x
75 
76 
77 class IMP_CNMULTIFIT_SwigPyIterator(_object):
78  """Proxy of C++ swig::IMP_CNMULTIFIT_SwigPyIterator class"""
79  __swig_setmethods__ = {}
80  __setattr__ = lambda self, name, value: _swig_setattr(self, IMP_CNMULTIFIT_SwigPyIterator, name, value)
81  __swig_getmethods__ = {}
82  __getattr__ = lambda self, name: _swig_getattr(self, IMP_CNMULTIFIT_SwigPyIterator, name)
83  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
84  __repr__ = _swig_repr
85  __swig_destroy__ = _IMP_cnmultifit.delete_IMP_CNMULTIFIT_SwigPyIterator
86  __del__ = lambda self : None;
87  def value(self):
88  """value(IMP_CNMULTIFIT_SwigPyIterator self) -> PyObject *"""
89  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_value(self)
90 
91  def incr(self, n=1):
92  """
93  incr(IMP_CNMULTIFIT_SwigPyIterator self, size_t n=1) -> IMP_CNMULTIFIT_SwigPyIterator
94  incr(IMP_CNMULTIFIT_SwigPyIterator self) -> IMP_CNMULTIFIT_SwigPyIterator
95  """
96  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_incr(self, n)
97 
98  def decr(self, n=1):
99  """
100  decr(IMP_CNMULTIFIT_SwigPyIterator self, size_t n=1) -> IMP_CNMULTIFIT_SwigPyIterator
101  decr(IMP_CNMULTIFIT_SwigPyIterator self) -> IMP_CNMULTIFIT_SwigPyIterator
102  """
103  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_decr(self, n)
104 
105  def distance(self, *args):
106  """distance(IMP_CNMULTIFIT_SwigPyIterator self, IMP_CNMULTIFIT_SwigPyIterator x) -> ptrdiff_t"""
107  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_distance(self, *args)
108 
109  def equal(self, *args):
110  """equal(IMP_CNMULTIFIT_SwigPyIterator self, IMP_CNMULTIFIT_SwigPyIterator x) -> bool"""
111  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_equal(self, *args)
112 
113  def copy(self):
114  """copy(IMP_CNMULTIFIT_SwigPyIterator self) -> IMP_CNMULTIFIT_SwigPyIterator"""
115  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_copy(self)
116 
117  def next(self):
118  """next(IMP_CNMULTIFIT_SwigPyIterator self) -> PyObject *"""
119  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_next(self)
120 
121  def __next__(self):
122  """__next__(IMP_CNMULTIFIT_SwigPyIterator self) -> PyObject *"""
123  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___next__(self)
124 
125  def previous(self):
126  """previous(IMP_CNMULTIFIT_SwigPyIterator self) -> PyObject *"""
127  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_previous(self)
128 
129  def advance(self, *args):
130  """advance(IMP_CNMULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_CNMULTIFIT_SwigPyIterator"""
131  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_advance(self, *args)
132 
133  def __eq__(self, *args):
134  """__eq__(IMP_CNMULTIFIT_SwigPyIterator self, IMP_CNMULTIFIT_SwigPyIterator x) -> bool"""
135  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___eq__(self, *args)
136 
137  def __ne__(self, *args):
138  """__ne__(IMP_CNMULTIFIT_SwigPyIterator self, IMP_CNMULTIFIT_SwigPyIterator x) -> bool"""
139  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___ne__(self, *args)
140 
141  def __iadd__(self, *args):
142  """__iadd__(IMP_CNMULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_CNMULTIFIT_SwigPyIterator"""
143  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___iadd__(self, *args)
144 
145  def __isub__(self, *args):
146  """__isub__(IMP_CNMULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_CNMULTIFIT_SwigPyIterator"""
147  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___isub__(self, *args)
148 
149  def __add__(self, *args):
150  """__add__(IMP_CNMULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_CNMULTIFIT_SwigPyIterator"""
151  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___add__(self, *args)
152 
153  def __sub__(self, *args):
154  """
155  __sub__(IMP_CNMULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_CNMULTIFIT_SwigPyIterator
156  __sub__(IMP_CNMULTIFIT_SwigPyIterator self, IMP_CNMULTIFIT_SwigPyIterator x) -> ptrdiff_t
157  """
158  return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___sub__(self, *args)
159 
160  def __iter__(self): return self
161 IMP_CNMULTIFIT_SwigPyIterator_swigregister = _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_swigregister
162 IMP_CNMULTIFIT_SwigPyIterator_swigregister(IMP_CNMULTIFIT_SwigPyIterator)
163 
164 _value_types=[]
165 _object_types=[]
166 _raii_types=[]
167 _plural_types=[]
168 
169 IMP_HAS_DEPRECATED = _IMP_cnmultifit.IMP_HAS_DEPRECATED
170 IMP_DEBUG = _IMP_cnmultifit.IMP_DEBUG
171 IMP_RELEASE = _IMP_cnmultifit.IMP_RELEASE
172 IMP_SILENT = _IMP_cnmultifit.IMP_SILENT
173 IMP_PROGRESS = _IMP_cnmultifit.IMP_PROGRESS
174 IMP_TERSE = _IMP_cnmultifit.IMP_TERSE
175 IMP_VERBOSE = _IMP_cnmultifit.IMP_VERBOSE
176 IMP_NONE = _IMP_cnmultifit.IMP_NONE
177 IMP_USAGE = _IMP_cnmultifit.IMP_USAGE
178 IMP_INTERNAL = _IMP_cnmultifit.IMP_INTERNAL
179 IMP_COMPILER_HAS_AUTO = _IMP_cnmultifit.IMP_COMPILER_HAS_AUTO
180 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_cnmultifit.IMP_COMPILER_HAS_DEBUG_VECTOR
181 IMP_COMPILER_HAS_NULLPTR = _IMP_cnmultifit.IMP_COMPILER_HAS_NULLPTR
182 IMP_BASE_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_BASE_HAS_BOOST_RANDOM
183 IMP_BASE_HAS_GPERFTOOLS = _IMP_cnmultifit.IMP_BASE_HAS_GPERFTOOLS
184 IMP_BASE_HAS_LOG4CXX = _IMP_cnmultifit.IMP_BASE_HAS_LOG4CXX
185 IMP_BASE_HAS_TCMALLOC_HEAPCHECKER = _IMP_cnmultifit.IMP_BASE_HAS_TCMALLOC_HEAPCHECKER
186 IMP_BASE_HAS_TCMALLOC_HEAPPROFILER = _IMP_cnmultifit.IMP_BASE_HAS_TCMALLOC_HEAPPROFILER
187 import sys
188 class _DirectorObjects(object):
189  """@internal Simple class to keep references to director objects
190  to prevent premature deletion."""
191  def __init__(self):
192  self._objects = []
193  def register(self, obj):
194  """Take a reference to a director object; will only work for
195  refcounted C++ classes"""
196  if hasattr(obj, 'get_ref_count'):
197  self._objects.append(obj)
198  def cleanup(self):
199  """Only drop our reference and allow cleanup by Python if no other
200  Python references exist (we hold 3 references: one in self._objects,
201  one in x, and one in the argument list for getrefcount) *and* no
202  other C++ references exist (the Python object always holds one)"""
203  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
204  or x.get_ref_count() > 1]
205 
206 
207  self._objects = objs
208  def get_object_count(self):
209  """Get number of director objects (useful for testing only)"""
210  return len(self._objects)
211 _director_objects = _DirectorObjects()
212 
213 DEFAULT_CHECK = _IMP_cnmultifit.DEFAULT_CHECK
214 NONE = _IMP_cnmultifit.NONE
215 USAGE = _IMP_cnmultifit.USAGE
216 USAGE_AND_INTERNAL = _IMP_cnmultifit.USAGE_AND_INTERNAL
217 
218 def set_check_level(*args):
219  """set_check_level(IMP::base::CheckLevel tf)"""
220  return _IMP_cnmultifit.set_check_level(*args)
221 
222 def get_check_level():
223  """get_check_level() -> IMP::base::CheckLevel"""
224  return _IMP_cnmultifit.get_check_level()
225 class _ostream(_object):
226  """Proxy of C++ std::ostream class"""
227  __swig_setmethods__ = {}
228  __setattr__ = lambda self, name, value: _swig_setattr(self, _ostream, name, value)
229  __swig_getmethods__ = {}
230  __getattr__ = lambda self, name: _swig_getattr(self, _ostream, name)
231  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined")
232  __repr__ = _swig_repr
233  def write(self, *args):
234  """write(_ostream self, char const * osa_buf)"""
235  return _IMP_cnmultifit._ostream_write(self, *args)
236 
237 _ostream_swigregister = _IMP_cnmultifit._ostream_swigregister
238 _ostream_swigregister(_ostream)
239 
240 IMP_COMPILER_HAS_OVERRIDE = _IMP_cnmultifit.IMP_COMPILER_HAS_OVERRIDE
241 IMP_COMPILER_HAS_FINAL = _IMP_cnmultifit.IMP_COMPILER_HAS_FINAL
242 import IMP.base
243 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_CGAL_HAS_BOOST_FILESYSTEM
244 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
245 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_CGAL_HAS_BOOST_RANDOM
246 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_CGAL_HAS_BOOST_SYSTEM
247 import IMP.cgal
248 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_ALGEBRA_HAS_IMP_CGAL
249 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
250 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
251 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_ALGEBRA_HAS_BOOST_RANDOM
252 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_ALGEBRA_HAS_BOOST_SYSTEM
253 IMP_ALGEBRA_HAS_CGAL = _IMP_cnmultifit.IMP_ALGEBRA_HAS_CGAL
254 IMP_ALGEBRA_HAS_ANN = _IMP_cnmultifit.IMP_ALGEBRA_HAS_ANN
255 import IMP.algebra
256 IMP_KERNEL_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_KERNEL_HAS_IMP_CGAL
257 IMP_KERNEL_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_KERNEL_HAS_BOOST_PROGRAMOPTIONS
258 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_KERNEL_HAS_BOOST_RANDOM
259 IMP_KERNEL_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_KERNEL_HAS_BOOST_SYSTEM
260 IMP_KERNEL_HAS_CGAL = _IMP_cnmultifit.IMP_KERNEL_HAS_CGAL
261 import IMP.kernel
262 IMP_DISPLAY_HAS_IMP_BASE = _IMP_cnmultifit.IMP_DISPLAY_HAS_IMP_BASE
263 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_DISPLAY_HAS_IMP_CGAL
264 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
265 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
266 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_DISPLAY_HAS_BOOST_RANDOM
267 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_DISPLAY_HAS_BOOST_SYSTEM
268 IMP_DISPLAY_HAS_CGAL = _IMP_cnmultifit.IMP_DISPLAY_HAS_CGAL
269 import IMP.display
270 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
271 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
272 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
273 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
274 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
275 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_CGAL
276 import IMP.score_functor
277 IMP_STATISTICS_HAS_IMP_BASE = _IMP_cnmultifit.IMP_STATISTICS_HAS_IMP_BASE
278 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_STATISTICS_HAS_IMP_CGAL
279 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
280 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
281 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_STATISTICS_HAS_BOOST_RANDOM
282 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_STATISTICS_HAS_BOOST_SYSTEM
283 IMP_STATISTICS_HAS_CGAL = _IMP_cnmultifit.IMP_STATISTICS_HAS_CGAL
284 import IMP.statistics
285 IMP_CORE_HAS_IMP_BASE = _IMP_cnmultifit.IMP_CORE_HAS_IMP_BASE
286 IMP_CORE_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_CORE_HAS_IMP_CGAL
287 IMP_CORE_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_CORE_HAS_IMP_KERNEL
288 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_CORE_HAS_BOOST_FILESYSTEM
289 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
290 IMP_CORE_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_CORE_HAS_BOOST_RANDOM
291 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_CORE_HAS_BOOST_SYSTEM
292 IMP_CORE_HAS_CGAL = _IMP_cnmultifit.IMP_CORE_HAS_CGAL
293 import IMP.core
294 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_ALGEBRA
295 IMP_CONTAINER_HAS_IMP_BASE = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_BASE
296 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_CGAL
297 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_DISPLAY
298 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_KERNEL
299 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
300 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
301 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
302 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_CONTAINER_HAS_BOOST_RANDOM
303 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_CONTAINER_HAS_BOOST_SYSTEM
304 IMP_CONTAINER_HAS_CGAL = _IMP_cnmultifit.IMP_CONTAINER_HAS_CGAL
305 import IMP.container
306 IMP_ATOM_HAS_IMP_BASE = _IMP_cnmultifit.IMP_ATOM_HAS_IMP_BASE
307 IMP_ATOM_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_ATOM_HAS_IMP_CGAL
308 IMP_ATOM_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_ATOM_HAS_IMP_KERNEL
309 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
310 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
311 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_ATOM_HAS_BOOST_RANDOM
312 IMP_ATOM_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_ATOM_HAS_BOOST_REGEX
313 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_ATOM_HAS_BOOST_SYSTEM
314 IMP_ATOM_HAS_CGAL = _IMP_cnmultifit.IMP_ATOM_HAS_CGAL
315 IMP_ATOM_TYPE_INDEX = _IMP_cnmultifit.IMP_ATOM_TYPE_INDEX
316 IMP_RESIDUE_TYPE_INDEX = _IMP_cnmultifit.IMP_RESIDUE_TYPE_INDEX
317 IMP_HIERARCHY_TYPE_INDEX = _IMP_cnmultifit.IMP_HIERARCHY_TYPE_INDEX
318 import IMP.atom
319 IMP_EM_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_EM_HAS_IMP_CGAL
320 IMP_EM_HAS_IMP_CONTAINER = _IMP_cnmultifit.IMP_EM_HAS_IMP_CONTAINER
321 IMP_EM_HAS_IMP_DISPLAY = _IMP_cnmultifit.IMP_EM_HAS_IMP_DISPLAY
322 IMP_EM_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_EM_HAS_IMP_KERNEL
323 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_EM_HAS_IMP_SCORE_FUNCTOR
324 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_EM_HAS_BOOST_FILESYSTEM
325 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
326 IMP_EM_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_EM_HAS_BOOST_RANDOM
327 IMP_EM_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_EM_HAS_BOOST_REGEX
328 IMP_EM_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_EM_HAS_BOOST_SYSTEM
329 IMP_EM_HAS_CGAL = _IMP_cnmultifit.IMP_EM_HAS_CGAL
330 import IMP.em
331 IMP_RMF_HAS_IMP_BASE = _IMP_cnmultifit.IMP_RMF_HAS_IMP_BASE
332 IMP_RMF_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_RMF_HAS_IMP_CGAL
333 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
334 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_FILESYSTEM
335 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
336 IMP_RMF_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_RANDOM
337 IMP_RMF_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_REGEX
338 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_SYSTEM
339 IMP_RMF_HAS_CGAL = _IMP_cnmultifit.IMP_RMF_HAS_CGAL
340 import IMP.rmf
341 import RMF
342 IMP_DOMINO_HAS_IMP_ATOM = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_ATOM
343 IMP_DOMINO_HAS_IMP_BASE = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_BASE
344 IMP_DOMINO_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_CGAL
345 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_KERNEL
346 IMP_DOMINO_HAS_IMP_RMF = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_RMF
347 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
348 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_FILESYSTEM
349 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
350 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_RANDOM
351 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_REGEX
352 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_SYSTEM
353 IMP_DOMINO_HAS_CGAL = _IMP_cnmultifit.IMP_DOMINO_HAS_CGAL
354 IMP_DOMINO_HAS_HDF5 = _IMP_cnmultifit.IMP_DOMINO_HAS_HDF5
355 IMP_DOMINO_HAS_RMF = _IMP_cnmultifit.IMP_DOMINO_HAS_RMF
356 import RMF_HDF5
357 import IMP.domino
358 IMP_MULTIFIT_HAS_IMP_BASE = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_BASE
359 IMP_MULTIFIT_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_CGAL
360 IMP_MULTIFIT_HAS_IMP_CONTAINER = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_CONTAINER
361 IMP_MULTIFIT_HAS_IMP_DISPLAY = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_DISPLAY
362 IMP_MULTIFIT_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_KERNEL
363 IMP_MULTIFIT_HAS_IMP_RMF = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_RMF
364 IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR
365 IMP_MULTIFIT_HAS_BOOST_GRAPH = _IMP_cnmultifit.IMP_MULTIFIT_HAS_BOOST_GRAPH
366 IMP_MULTIFIT_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_MULTIFIT_HAS_BOOST_RANDOM
367 IMP_MULTIFIT_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_MULTIFIT_HAS_BOOST_REGEX
368 IMP_MULTIFIT_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_MULTIFIT_HAS_BOOST_SYSTEM
369 IMP_MULTIFIT_HAS_CGAL = _IMP_cnmultifit.IMP_MULTIFIT_HAS_CGAL
370 IMP_MULTIFIT_HAS_HDF5 = _IMP_cnmultifit.IMP_MULTIFIT_HAS_HDF5
371 IMP_MULTIFIT_HAS_RMF = _IMP_cnmultifit.IMP_MULTIFIT_HAS_RMF
372 import IMP.multifit
373 IMP_CNMULTIFIT_HAS_IMP_BASE = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_BASE
374 IMP_CNMULTIFIT_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_CGAL
375 IMP_CNMULTIFIT_HAS_IMP_CONTAINER = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_CONTAINER
376 IMP_CNMULTIFIT_HAS_IMP_DISPLAY = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_DISPLAY
377 IMP_CNMULTIFIT_HAS_IMP_DOMINO = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_DOMINO
378 IMP_CNMULTIFIT_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_KERNEL
379 IMP_CNMULTIFIT_HAS_IMP_RMF = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_RMF
380 IMP_CNMULTIFIT_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_SCORE_FUNCTOR
381 IMP_CNMULTIFIT_HAS_BOOST_GRAPH = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_BOOST_GRAPH
382 IMP_CNMULTIFIT_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_BOOST_RANDOM
383 IMP_CNMULTIFIT_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_BOOST_REGEX
384 IMP_CNMULTIFIT_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_BOOST_SYSTEM
385 IMP_CNMULTIFIT_HAS_CGAL = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_CGAL
386 IMP_CNMULTIFIT_HAS_FFTW3 = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_FFTW3
387 IMP_CNMULTIFIT_HAS_HDF5 = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_HDF5
388 IMP_CNMULTIFIT_HAS_RMF = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_RMF
389 AlignSymmetrics=list
390 _plural_types.append("AlignSymmetrics")
391 _value_types.append("AlignSymmetric")
392 
393 CnSymmAxisDetectors=list
394 _plural_types.append("CnSymmAxisDetectors")
395 _value_types.append("CnSymmAxisDetector")
396 
397 MolCnSymmAxisDetectors=list
398 _plural_types.append("MolCnSymmAxisDetectors")
399 _value_types.append("MolCnSymmAxisDetector")
400 
401 class CnSymmAxisDetector(_object):
402  """Proxy of C++ IMP::cnmultifit::CnSymmAxisDetector class"""
403  __swig_setmethods__ = {}
404  __setattr__ = lambda self, name, value: _swig_setattr(self, CnSymmAxisDetector, name, value)
405  __swig_getmethods__ = {}
406  __getattr__ = lambda self, name: _swig_getattr(self, CnSymmAxisDetector, name)
407  def __init__(self, *args):
408  """
409  __init__(IMP::cnmultifit::CnSymmAxisDetector self, int symm_deg, DensityMap dmap, float density_threshold, float top_p=0.8) -> CnSymmAxisDetector
410  __init__(IMP::cnmultifit::CnSymmAxisDetector self, int symm_deg, DensityMap dmap, float density_threshold) -> CnSymmAxisDetector
411  __init__(IMP::cnmultifit::CnSymmAxisDetector self, int symm_deg, IMP::atom::Hierarchies const & mhs) -> CnSymmAxisDetector
412  """
413  this = _IMP_cnmultifit.new_CnSymmAxisDetector(*args)
414  try: self.this.append(this)
415  except: self.this = this
416  def get_pca(self):
417  """get_pca(CnSymmAxisDetector self) -> PrincipalComponentAnalysis3D"""
418  return _IMP_cnmultifit.CnSymmAxisDetector_get_pca(self)
419 
420  def calc_symm_score(self, *args):
421  """calc_symm_score(CnSymmAxisDetector self, int symm_axis_ind) -> float"""
422  return _IMP_cnmultifit.CnSymmAxisDetector_calc_symm_score(self, *args)
423 
424  def get_symmetry_axis(self):
425  """get_symmetry_axis(CnSymmAxisDetector self) -> Vector3D"""
426  return _IMP_cnmultifit.CnSymmAxisDetector_get_symmetry_axis(self)
427 
428  def get_symmetry_axis_index(self):
429  """get_symmetry_axis_index(CnSymmAxisDetector self) -> int"""
430  return _IMP_cnmultifit.CnSymmAxisDetector_get_symmetry_axis_index(self)
431 
432  def get_non_symmetry_axis_length(self):
433  """get_non_symmetry_axis_length(CnSymmAxisDetector self) -> int"""
434  return _IMP_cnmultifit.CnSymmAxisDetector_get_non_symmetry_axis_length(self)
435 
436  def show(self, *args):
437  """
438  show(CnSymmAxisDetector self, _ostream out=std::cout)
439  show(CnSymmAxisDetector self)
440  """
441  return _IMP_cnmultifit.CnSymmAxisDetector_show(self, *args)
442 
443  def __str__(self):
444  """__str__(CnSymmAxisDetector self) -> std::string"""
445  return _IMP_cnmultifit.CnSymmAxisDetector___str__(self)
446 
447  def __repr__(self):
448  """__repr__(CnSymmAxisDetector self) -> std::string"""
449  return _IMP_cnmultifit.CnSymmAxisDetector___repr__(self)
450 
451  __swig_destroy__ = _IMP_cnmultifit.delete_CnSymmAxisDetector
452  __del__ = lambda self : None;
453 CnSymmAxisDetector_swigregister = _IMP_cnmultifit.CnSymmAxisDetector_swigregister
454 CnSymmAxisDetector_swigregister(CnSymmAxisDetector)
455 
456 class MolCnSymmAxisDetector(_object):
457  """Proxy of C++ IMP::cnmultifit::MolCnSymmAxisDetector class"""
458  __swig_setmethods__ = {}
459  __setattr__ = lambda self, name, value: _swig_setattr(self, MolCnSymmAxisDetector, name, value)
460  __swig_getmethods__ = {}
461  __getattr__ = lambda self, name: _swig_getattr(self, MolCnSymmAxisDetector, name)
462  def __init__(self, *args):
463  """__init__(IMP::cnmultifit::MolCnSymmAxisDetector self, int symm_deg, IMP::atom::Hierarchies const & mhs) -> MolCnSymmAxisDetector"""
464  this = _IMP_cnmultifit.new_MolCnSymmAxisDetector(*args)
465  try: self.this.append(this)
466  except: self.this = this
467  def get_pca(self):
468  """get_pca(MolCnSymmAxisDetector self) -> PrincipalComponentAnalysis3D"""
469  return _IMP_cnmultifit.MolCnSymmAxisDetector_get_pca(self)
470 
471  def get_symmetry_axis(self):
472  """get_symmetry_axis(MolCnSymmAxisDetector self) -> Vector3D"""
473  return _IMP_cnmultifit.MolCnSymmAxisDetector_get_symmetry_axis(self)
474 
475  def get_symmetry_axis_index(self):
476  """get_symmetry_axis_index(MolCnSymmAxisDetector self) -> int"""
477  return _IMP_cnmultifit.MolCnSymmAxisDetector_get_symmetry_axis_index(self)
478 
479  def show(self, *args):
480  """
481  show(MolCnSymmAxisDetector self, _ostream out=std::cout)
482  show(MolCnSymmAxisDetector self)
483  """
484  return _IMP_cnmultifit.MolCnSymmAxisDetector_show(self, *args)
485 
486  def calc_symm_score(self, *args):
487  """calc_symm_score(MolCnSymmAxisDetector self, int symm_axis_ind) -> float"""
488  return _IMP_cnmultifit.MolCnSymmAxisDetector_calc_symm_score(self, *args)
489 
490  def __str__(self):
491  """__str__(MolCnSymmAxisDetector self) -> std::string"""
492  return _IMP_cnmultifit.MolCnSymmAxisDetector___str__(self)
493 
494  def __repr__(self):
495  """__repr__(MolCnSymmAxisDetector self) -> std::string"""
496  return _IMP_cnmultifit.MolCnSymmAxisDetector___repr__(self)
497 
498  __swig_destroy__ = _IMP_cnmultifit.delete_MolCnSymmAxisDetector
499  __del__ = lambda self : None;
500 MolCnSymmAxisDetector_swigregister = _IMP_cnmultifit.MolCnSymmAxisDetector_swigregister
501 MolCnSymmAxisDetector_swigregister(MolCnSymmAxisDetector)
502 
503 class AlignSymmetric(_object):
504  """Proxy of C++ IMP::cnmultifit::AlignSymmetric class"""
505  __swig_setmethods__ = {}
506  __setattr__ = lambda self, name, value: _swig_setattr(self, AlignSymmetric, name, value)
507  __swig_getmethods__ = {}
508  __getattr__ = lambda self, name: _swig_getattr(self, AlignSymmetric, name)
509  def __init__(self, *args):
510  """__init__(IMP::cnmultifit::AlignSymmetric self, DensityMap dmap, float threshold, int cn_symm_deg) -> AlignSymmetric"""
511  this = _IMP_cnmultifit.new_AlignSymmetric(*args)
512  try: self.this.append(this)
513  except: self.this = this
514  def get_sorted_principal_values(self):
515  """get_sorted_principal_values(AlignSymmetric self) -> IMP::Floats"""
516  return _IMP_cnmultifit.AlignSymmetric_get_sorted_principal_values(self)
517 
518  def score_alignment(self, *args):
519  """score_alignment(AlignSymmetric self, IMP::atom::Hierarchies mhs, float max_allowed_diff) -> int"""
520  return _IMP_cnmultifit.AlignSymmetric_score_alignment(self, *args)
521 
522  def get_symm_axis_alignments_from_model_to_density(self, *args):
523  """
524  get_symm_axis_alignments_from_model_to_density(AlignSymmetric self, IMP::atom::Hierarchies mhs, bool sample_translation, bool fine_rotation_sampling=True) -> IMP::algebra::Transformation3Ds
525  get_symm_axis_alignments_from_model_to_density(AlignSymmetric self, IMP::atom::Hierarchies mhs, bool sample_translation) -> IMP::algebra::Transformation3Ds
526  """
527  return _IMP_cnmultifit.AlignSymmetric_get_symm_axis_alignments_from_model_to_density(self, *args)
528 
529  def show(self, *args):
530  """
531  show(AlignSymmetric self, _ostream out=std::cout)
532  show(AlignSymmetric self)
533  """
534  return _IMP_cnmultifit.AlignSymmetric_show(self, *args)
535 
536  def __str__(self):
537  """__str__(AlignSymmetric self) -> std::string"""
538  return _IMP_cnmultifit.AlignSymmetric___str__(self)
539 
540  def __repr__(self):
541  """__repr__(AlignSymmetric self) -> std::string"""
542  return _IMP_cnmultifit.AlignSymmetric___repr__(self)
543 
544  __swig_destroy__ = _IMP_cnmultifit.delete_AlignSymmetric
545  __del__ = lambda self : None;
546 AlignSymmetric_swigregister = _IMP_cnmultifit.AlignSymmetric_swigregister
547 AlignSymmetric_swigregister(AlignSymmetric)
548 
549 
550 def generate_cn_transformations(*args):
551  """generate_cn_transformations(IMP::atom::Hierarchies mhs, int symm_deg) -> IMP::algebra::Transformation3Ds"""
552  return _IMP_cnmultifit.generate_cn_transformations(*args)
553 
554 def generate_translations_along_symm_axis(*args):
555  """generate_translations_along_symm_axis(IMP::atom::Hierarchies mhs, int symm_deg) -> IMP::algebra::Transformation3Ds"""
556  return _IMP_cnmultifit.generate_translations_along_symm_axis(*args)
557 
558 def symmetry_local_fitting(*args):
559  """symmetry_local_fitting(IMP::atom::Hierarchies mhs, int cn_symm_deg, int dn_symm_deg, DensityMap dmap, int num_of_trans_to_consider) -> FittingSolutions"""
560  return _IMP_cnmultifit.symmetry_local_fitting(*args)
561 
562 def build_cn_dens_assembly(*args):
563  """
564  build_cn_dens_assembly(DensityMap subunit_dens, DensityHeader asmb_dens_header, Transformation3D monomer_t,
565  int symm_deg) -> DensityMap
566  """
567  return _IMP_cnmultifit.build_cn_dens_assembly(*args)
568 
569 def transform_cn_assembly(*args):
570  """transform_cn_assembly(IMP::atom::Hierarchies mhs, Transformation3D monomer_t)"""
571  return _IMP_cnmultifit.transform_cn_assembly(*args)
572 
573 def fit_cn_assembly(*args):
574  """
575  fit_cn_assembly(IMP::atom::Hierarchies mhs, int dn_symm_deg, DensityMap dmap, float threshold, AlignSymmetric aligner,
576  bool sample_translation=False, bool fine_rotational_sampling=True) -> FittingSolutions
577  fit_cn_assembly(IMP::atom::Hierarchies mhs, int dn_symm_deg, DensityMap dmap, float threshold, AlignSymmetric aligner,
578  bool sample_translation=False) -> FittingSolutions
579  fit_cn_assembly(IMP::atom::Hierarchies mhs, int dn_symm_deg, DensityMap dmap, float threshold, AlignSymmetric aligner) -> FittingSolutions
580  fit_cn_assembly(DensityMap asmb_map, MolCnSymmAxisDetector symm_mol, DensityMap dmap, CnSymmAxisDetector symm_map,
581  int symm_deg, float threshold) -> FittingSolutions
582  """
583  return _IMP_cnmultifit.fit_cn_assembly(*args)
584 
585 def pca_matching(*args):
586  """pca_matching(PrincipalComponentAnalysis3D pca1, PrincipalComponentAnalysis3D pca2, float resolution) -> bool"""
587  return _IMP_cnmultifit.pca_matching(*args)
588 
589 def cn_symm_score(*args):
590  """cn_symm_score(IMP::atom::Hierarchies mhs, Vector3D center, Vector3D direction, int symm_deg) -> float"""
591  return _IMP_cnmultifit.cn_symm_score(*args)
592 
593 def prune_by_pca(*args):
594  """
595  prune_by_pca(std::string const & param_fn, IMP::multifit::FittingSolutionRecords const & sols,
596  int dn=1) -> IMP::multifit::FittingSolutionRecords
597  prune_by_pca(std::string const & param_fn, IMP::multifit::FittingSolutionRecords const & sols) -> IMP::multifit::FittingSolutionRecords
598  """
599  return _IMP_cnmultifit.prune_by_pca(*args)
600 
601 def calc_transformation_around_axis(*args):
602  """calc_transformation_around_axis(Vector3D a, Vector3D b, float angle_rad) -> Transformation3D"""
603  return _IMP_cnmultifit.calc_transformation_around_axis(*args)
604 
605 def get_cn_rmsd(*args):
606  """get_cn_rmsd(IMP::atom::Hierarchies mh1, IMP::atom::Hierarchies mh2) -> float"""
607  return _IMP_cnmultifit.get_cn_rmsd(*args)
608 
609 def do_all_fitting(*args):
610  """
611  do_all_fitting(std::string const param_filename, std::string const chimera_filename="")
612  do_all_fitting(std::string const param_filename)
613  """
614  return _IMP_cnmultifit.do_all_fitting(*args)
615 
616 def get_rmsd_for_models(*args):
617  """
618  get_rmsd_for_models(std::string const param_filename, std::string const trans_filename, std::string const ref_filename,
619  int start_model=0, int end_model=-1) -> IMP::Floats
620  get_rmsd_for_models(std::string const param_filename, std::string const trans_filename, std::string const ref_filename,
621  int start_model=0) -> IMP::Floats
622  get_rmsd_for_models(std::string const param_filename, std::string const trans_filename, std::string const ref_filename) -> IMP::Floats
623  """
624  return _IMP_cnmultifit.get_rmsd_for_models(*args)
625 _all_commands = ["build", "rmsd", "surface",
626  "param", "chimera_models"]
627 
628 
629 def get_module_version():
630  """get_module_version() -> std::string const"""
631  return _IMP_cnmultifit.get_module_version()
632 
633 def get_example_path(*args):
634  """get_example_path(std::string fname) -> std::string"""
635  return _IMP_cnmultifit.get_example_path(*args)
636 
637 def get_data_path(*args):
638  """get_data_path(std::string fname) -> std::string"""
639  return _IMP_cnmultifit.get_data_path(*args)
640 import _version_check
641 _version_check.check_version(get_module_version())
642 
643 # This file is compatible with both classic and new-style classes.
644 
645