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IMP Reference Guide  2.14.0
The Integrative Modeling Platform
rotamer/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.10
3 #
4 # Do not make changes to this file unless you know what you are doing--modify
5 # the SWIG interface file instead.
6 
7 # This wrapper is part of IMP,
8 # Copyright 2007-2020 IMP Inventors. All rights reserved.
9 
10 from __future__ import print_function, division, absolute_import
11 
12 
13 
14 
15 from sys import version_info as _swig_python_version_info
16 if _swig_python_version_info >= (2, 7, 0):
17  def swig_import_helper():
18  import importlib
19  pkg = __name__.rpartition('.')[0]
20  mname = '.'.join((pkg, '_IMP_rotamer')).lstrip('.')
21  try:
22  return importlib.import_module(mname)
23  except ImportError:
24  return importlib.import_module('_IMP_rotamer')
25  _IMP_rotamer = swig_import_helper()
26  del swig_import_helper
27 elif _swig_python_version_info >= (2, 6, 0):
28  def swig_import_helper():
29  from os.path import dirname
30  import imp
31  fp = None
32  try:
33  fp, pathname, description = imp.find_module('_IMP_rotamer', [dirname(__file__)])
34  except ImportError:
35  import _IMP_rotamer
36  return _IMP_rotamer
37  if fp is not None:
38  try:
39  _mod = imp.load_module('_IMP_rotamer', fp, pathname, description)
40  finally:
41  fp.close()
42  return _mod
43  _IMP_rotamer = swig_import_helper()
44  del swig_import_helper
45 else:
46  import _IMP_rotamer
47 del _swig_python_version_info
48 try:
49  _swig_property = property
50 except NameError:
51  pass # Python < 2.2 doesn't have 'property'.
52 
53 try:
54  import builtins as __builtin__
55 except ImportError:
56  import __builtin__
57 
58 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
59  if (name == "thisown"):
60  return self.this.own(value)
61  if (name == "this"):
62  if type(value).__name__ == 'SwigPyObject':
63  self.__dict__[name] = value
64  return
65  method = class_type.__swig_setmethods__.get(name, None)
66  if method:
67  return method(self, value)
68  if (not static):
69  object.__setattr__(self, name, value)
70  else:
71  raise AttributeError("You cannot add attributes to %s" % self)
72 
73 
74 def _swig_setattr(self, class_type, name, value):
75  return _swig_setattr_nondynamic(self, class_type, name, value, 0)
76 
77 
78 def _swig_getattr(self, class_type, name):
79  if (name == "thisown"):
80  return self.this.own()
81  method = class_type.__swig_getmethods__.get(name, None)
82  if method:
83  return method(self)
84  raise AttributeError("'%s' object has no attribute '%s'" % (class_type.__name__, name))
85 
86 
87 def _swig_repr(self):
88  try:
89  strthis = "proxy of " + self.this.__repr__()
90  except __builtin__.Exception:
91  strthis = ""
92  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
93 
94 
95 def _swig_setattr_nondynamic_method(set):
96  def set_attr(self, name, value):
97  if (name == "thisown"):
98  return self.this.own(value)
99  if hasattr(self, name) or (name == "this"):
100  set(self, name, value)
101  else:
102  raise AttributeError("You cannot add attributes to %s" % self)
103  return set_attr
104 
105 
106 try:
107  import weakref
108  weakref_proxy = weakref.proxy
109 except __builtin__.Exception:
110  weakref_proxy = lambda x: x
111 
112 
113 class IMP_ROTAMER_SwigPyIterator(object):
114  """Proxy of C++ swig::IMP_ROTAMER_SwigPyIterator class."""
115 
116  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
117 
118  def __init__(self, *args, **kwargs):
119  raise AttributeError("No constructor defined - class is abstract")
120  __repr__ = _swig_repr
121  __swig_destroy__ = _IMP_rotamer.delete_IMP_ROTAMER_SwigPyIterator
122  __del__ = lambda self: None
123 
124  def value(self):
125  """value(IMP_ROTAMER_SwigPyIterator self) -> PyObject *"""
126  return _IMP_rotamer.IMP_ROTAMER_SwigPyIterator_value(self)
127 
128 
129  def incr(self, n=1):
130  """
131  incr(IMP_ROTAMER_SwigPyIterator self, size_t n=1) -> IMP_ROTAMER_SwigPyIterator
132  incr(IMP_ROTAMER_SwigPyIterator self) -> IMP_ROTAMER_SwigPyIterator
133  """
134  return _IMP_rotamer.IMP_ROTAMER_SwigPyIterator_incr(self, n)
135 
136 
137  def decr(self, n=1):
138  """
139  decr(IMP_ROTAMER_SwigPyIterator self, size_t n=1) -> IMP_ROTAMER_SwigPyIterator
140  decr(IMP_ROTAMER_SwigPyIterator self) -> IMP_ROTAMER_SwigPyIterator
141  """
142  return _IMP_rotamer.IMP_ROTAMER_SwigPyIterator_decr(self, n)
143 
144 
145  def distance(self, x):
146  """distance(IMP_ROTAMER_SwigPyIterator self, IMP_ROTAMER_SwigPyIterator x) -> ptrdiff_t"""
147  return _IMP_rotamer.IMP_ROTAMER_SwigPyIterator_distance(self, x)
148 
149 
150  def equal(self, x):
151  """equal(IMP_ROTAMER_SwigPyIterator self, IMP_ROTAMER_SwigPyIterator x) -> bool"""
152  return _IMP_rotamer.IMP_ROTAMER_SwigPyIterator_equal(self, x)
153 
154 
155  def copy(self):
156  """copy(IMP_ROTAMER_SwigPyIterator self) -> IMP_ROTAMER_SwigPyIterator"""
157  return _IMP_rotamer.IMP_ROTAMER_SwigPyIterator_copy(self)
158 
159 
160  def next(self):
161  """next(IMP_ROTAMER_SwigPyIterator self) -> PyObject *"""
162  return _IMP_rotamer.IMP_ROTAMER_SwigPyIterator_next(self)
163 
164 
165  def __next__(self):
166  """__next__(IMP_ROTAMER_SwigPyIterator self) -> PyObject *"""
167  return _IMP_rotamer.IMP_ROTAMER_SwigPyIterator___next__(self)
168 
169 
170  def previous(self):
171  """previous(IMP_ROTAMER_SwigPyIterator self) -> PyObject *"""
172  return _IMP_rotamer.IMP_ROTAMER_SwigPyIterator_previous(self)
173 
174 
175  def advance(self, n):
176  """advance(IMP_ROTAMER_SwigPyIterator self, ptrdiff_t n) -> IMP_ROTAMER_SwigPyIterator"""
177  return _IMP_rotamer.IMP_ROTAMER_SwigPyIterator_advance(self, n)
178 
179 
180  def __eq__(self, x):
181  """__eq__(IMP_ROTAMER_SwigPyIterator self, IMP_ROTAMER_SwigPyIterator x) -> bool"""
182  return _IMP_rotamer.IMP_ROTAMER_SwigPyIterator___eq__(self, x)
183 
184 
185  def __ne__(self, x):
186  """__ne__(IMP_ROTAMER_SwigPyIterator self, IMP_ROTAMER_SwigPyIterator x) -> bool"""
187  return _IMP_rotamer.IMP_ROTAMER_SwigPyIterator___ne__(self, x)
188 
189 
190  def __iadd__(self, n):
191  """__iadd__(IMP_ROTAMER_SwigPyIterator self, ptrdiff_t n) -> IMP_ROTAMER_SwigPyIterator"""
192  return _IMP_rotamer.IMP_ROTAMER_SwigPyIterator___iadd__(self, n)
193 
194 
195  def __isub__(self, n):
196  """__isub__(IMP_ROTAMER_SwigPyIterator self, ptrdiff_t n) -> IMP_ROTAMER_SwigPyIterator"""
197  return _IMP_rotamer.IMP_ROTAMER_SwigPyIterator___isub__(self, n)
198 
199 
200  def __add__(self, n):
201  """__add__(IMP_ROTAMER_SwigPyIterator self, ptrdiff_t n) -> IMP_ROTAMER_SwigPyIterator"""
202  return _IMP_rotamer.IMP_ROTAMER_SwigPyIterator___add__(self, n)
203 
204 
205  def __sub__(self, *args):
206  """
207  __sub__(IMP_ROTAMER_SwigPyIterator self, ptrdiff_t n) -> IMP_ROTAMER_SwigPyIterator
208  __sub__(IMP_ROTAMER_SwigPyIterator self, IMP_ROTAMER_SwigPyIterator x) -> ptrdiff_t
209  """
210  return _IMP_rotamer.IMP_ROTAMER_SwigPyIterator___sub__(self, *args)
211 
212  def __iter__(self):
213  return self
214 IMP_ROTAMER_SwigPyIterator_swigregister = _IMP_rotamer.IMP_ROTAMER_SwigPyIterator_swigregister
215 IMP_ROTAMER_SwigPyIterator_swigregister(IMP_ROTAMER_SwigPyIterator)
216 
217 
218 _value_types=[]
219 _object_types=[]
220 _raii_types=[]
221 _plural_types=[]
222 
223 IMP_DEBUG = _IMP_rotamer.IMP_DEBUG
224 IMP_RELEASE = _IMP_rotamer.IMP_RELEASE
225 IMP_SILENT = _IMP_rotamer.IMP_SILENT
226 IMP_PROGRESS = _IMP_rotamer.IMP_PROGRESS
227 IMP_TERSE = _IMP_rotamer.IMP_TERSE
228 IMP_VERBOSE = _IMP_rotamer.IMP_VERBOSE
229 IMP_MEMORY = _IMP_rotamer.IMP_MEMORY
230 IMP_NONE = _IMP_rotamer.IMP_NONE
231 IMP_USAGE = _IMP_rotamer.IMP_USAGE
232 IMP_INTERNAL = _IMP_rotamer.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_rotamer.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_rotamer.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_rotamer.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_rotamer.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_rotamer.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_NUMPY = _IMP_rotamer.IMP_KERNEL_HAS_NUMPY
239 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_rotamer.IMP_KERNEL_HAS_GPERFTOOLS
240 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_rotamer.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
241 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_rotamer.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
242 IMPKERNEL_SHOW_WARNINGS = _IMP_rotamer.IMPKERNEL_SHOW_WARNINGS
243 
244 import sys
245 class _DirectorObjects(object):
246  """@internal Simple class to keep references to director objects
247  to prevent premature deletion."""
248  def __init__(self):
249  self._objects = []
250  def register(self, obj):
251  """Take a reference to a director object; will only work for
252  refcounted C++ classes"""
253  if hasattr(obj, 'get_ref_count'):
254  self._objects.append(obj)
255  def cleanup(self):
256  """Only drop our reference and allow cleanup by Python if no other
257  Python references exist (we hold 3 references: one in self._objects,
258  one in x, and one in the argument list for getrefcount) *and* no
259  other C++ references exist (the Python object always holds one)"""
260  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
261  or x.get_ref_count() > 1]
262 # Do in two steps so the references are kept until the end of the
263 # function (deleting references may trigger a fresh call to this method)
264  self._objects = objs
265  def get_object_count(self):
266  """Get number of director objects (useful for testing only)"""
267  return len(self._objects)
268 _director_objects = _DirectorObjects()
269 
270 class _ostream(object):
271  """Proxy of C++ std::ostream class."""
272 
273  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
274 
275  def __init__(self, *args, **kwargs):
276  raise AttributeError("No constructor defined")
277  __repr__ = _swig_repr
278 
279  def write(self, osa_buf):
280  """write(_ostream self, char const * osa_buf)"""
281  return _IMP_rotamer._ostream_write(self, osa_buf)
282 
283 _ostream_swigregister = _IMP_rotamer._ostream_swigregister
284 _ostream_swigregister(_ostream)
285 
286 IMP_COMPILER_HAS_OVERRIDE = _IMP_rotamer.IMP_COMPILER_HAS_OVERRIDE
287 IMP_COMPILER_HAS_FINAL = _IMP_rotamer.IMP_COMPILER_HAS_FINAL
288 IMP_HAS_NOEXCEPT = _IMP_rotamer.IMP_HAS_NOEXCEPT
289 IMP_C_OPEN_BINARY = _IMP_rotamer.IMP_C_OPEN_BINARY
290 import IMP
291 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_rotamer.IMP_CGAL_HAS_BOOST_FILESYSTEM
292 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_rotamer.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
293 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_rotamer.IMP_CGAL_HAS_BOOST_RANDOM
294 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_rotamer.IMP_CGAL_HAS_BOOST_SYSTEM
295 IMP_CGAL_HAS_NUMPY = _IMP_rotamer.IMP_CGAL_HAS_NUMPY
296 IMPCGAL_SHOW_WARNINGS = _IMP_rotamer.IMPCGAL_SHOW_WARNINGS
297 import IMP.cgal
298 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_rotamer.IMP_ALGEBRA_HAS_IMP_CGAL
299 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_rotamer.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
300 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_rotamer.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
301 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_rotamer.IMP_ALGEBRA_HAS_BOOST_RANDOM
302 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_rotamer.IMP_ALGEBRA_HAS_BOOST_SYSTEM
303 IMP_ALGEBRA_HAS_CGAL = _IMP_rotamer.IMP_ALGEBRA_HAS_CGAL
304 IMP_ALGEBRA_HAS_NUMPY = _IMP_rotamer.IMP_ALGEBRA_HAS_NUMPY
305 IMP_ALGEBRA_HAS_ANN = _IMP_rotamer.IMP_ALGEBRA_HAS_ANN
306 IMPALGEBRA_SHOW_WARNINGS = _IMP_rotamer.IMPALGEBRA_SHOW_WARNINGS
307 import IMP.algebra
308 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_rotamer.IMP_DISPLAY_HAS_IMP_CGAL
309 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_rotamer.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
310 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_rotamer.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
311 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_rotamer.IMP_DISPLAY_HAS_BOOST_RANDOM
312 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_rotamer.IMP_DISPLAY_HAS_BOOST_SYSTEM
313 IMP_DISPLAY_HAS_CGAL = _IMP_rotamer.IMP_DISPLAY_HAS_CGAL
314 IMP_DISPLAY_HAS_NUMPY = _IMP_rotamer.IMP_DISPLAY_HAS_NUMPY
315 IMPDISPLAY_SHOW_WARNINGS = _IMP_rotamer.IMPDISPLAY_SHOW_WARNINGS
316 import IMP.display
317 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_rotamer.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
318 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_rotamer.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
319 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_rotamer.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
320 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_rotamer.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
321 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_rotamer.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
322 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_rotamer.IMP_SCORE_FUNCTOR_HAS_CGAL
323 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_rotamer.IMP_SCORE_FUNCTOR_HAS_HDF5
324 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_rotamer.IMP_SCORE_FUNCTOR_HAS_NUMPY
325 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_rotamer.IMPSCOREFUNCTOR_SHOW_WARNINGS
326 import IMP.score_functor
327 IMP_CORE_HAS_IMP_CGAL = _IMP_rotamer.IMP_CORE_HAS_IMP_CGAL
328 IMP_CORE_HAS_IMP_KERNEL = _IMP_rotamer.IMP_CORE_HAS_IMP_KERNEL
329 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_rotamer.IMP_CORE_HAS_BOOST_FILESYSTEM
330 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_rotamer.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
331 IMP_CORE_HAS_BOOST_RANDOM = _IMP_rotamer.IMP_CORE_HAS_BOOST_RANDOM
332 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_rotamer.IMP_CORE_HAS_BOOST_SYSTEM
333 IMP_CORE_HAS_CGAL = _IMP_rotamer.IMP_CORE_HAS_CGAL
334 IMP_CORE_HAS_HDF5 = _IMP_rotamer.IMP_CORE_HAS_HDF5
335 IMP_CORE_HAS_NUMPY = _IMP_rotamer.IMP_CORE_HAS_NUMPY
336 IMPCORE_SHOW_WARNINGS = _IMP_rotamer.IMPCORE_SHOW_WARNINGS
337 import IMP.core
338 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_rotamer.IMP_CONTAINER_HAS_IMP_ALGEBRA
339 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_rotamer.IMP_CONTAINER_HAS_IMP_CGAL
340 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_rotamer.IMP_CONTAINER_HAS_IMP_DISPLAY
341 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_rotamer.IMP_CONTAINER_HAS_IMP_KERNEL
342 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_rotamer.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
343 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_rotamer.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
344 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_rotamer.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
345 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_rotamer.IMP_CONTAINER_HAS_BOOST_RANDOM
346 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_rotamer.IMP_CONTAINER_HAS_BOOST_SYSTEM
347 IMP_CONTAINER_HAS_CGAL = _IMP_rotamer.IMP_CONTAINER_HAS_CGAL
348 IMP_CONTAINER_HAS_HDF5 = _IMP_rotamer.IMP_CONTAINER_HAS_HDF5
349 IMP_CONTAINER_HAS_NUMPY = _IMP_rotamer.IMP_CONTAINER_HAS_NUMPY
350 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_rotamer.IMP_CONTAINER_HAS_PYTHON_IHM
351 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_rotamer.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
352 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_rotamer.IMP_CONTAINER_HAS_ROBIN_MAP
353 IMPCONTAINER_SHOW_WARNINGS = _IMP_rotamer.IMPCONTAINER_SHOW_WARNINGS
354 import IMP.container
355 IMP_ATOM_HAS_IMP_CGAL = _IMP_rotamer.IMP_ATOM_HAS_IMP_CGAL
356 IMP_ATOM_HAS_IMP_KERNEL = _IMP_rotamer.IMP_ATOM_HAS_IMP_KERNEL
357 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_rotamer.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
358 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_rotamer.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
359 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_rotamer.IMP_ATOM_HAS_BOOST_RANDOM
360 IMP_ATOM_HAS_BOOST_REGEX = _IMP_rotamer.IMP_ATOM_HAS_BOOST_REGEX
361 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_rotamer.IMP_ATOM_HAS_BOOST_SYSTEM
362 IMP_ATOM_HAS_CGAL = _IMP_rotamer.IMP_ATOM_HAS_CGAL
363 IMP_ATOM_HAS_HDF5 = _IMP_rotamer.IMP_ATOM_HAS_HDF5
364 IMP_ATOM_HAS_NUMPY = _IMP_rotamer.IMP_ATOM_HAS_NUMPY
365 IMP_ATOM_HAS_PYTHON_IHM = _IMP_rotamer.IMP_ATOM_HAS_PYTHON_IHM
366 IMPATOM_SHOW_WARNINGS = _IMP_rotamer.IMPATOM_SHOW_WARNINGS
367 IMP_ATOM_TYPE_INDEX = _IMP_rotamer.IMP_ATOM_TYPE_INDEX
368 IMP_RESIDUE_TYPE_INDEX = _IMP_rotamer.IMP_RESIDUE_TYPE_INDEX
369 IMP_HIERARCHY_TYPE_INDEX = _IMP_rotamer.IMP_HIERARCHY_TYPE_INDEX
370 IMP_CHAIN_TYPE_INDEX = _IMP_rotamer.IMP_CHAIN_TYPE_INDEX
371 import IMP.atom
372 IMP_ROTAMER_HAS_IMP_ALGEBRA = _IMP_rotamer.IMP_ROTAMER_HAS_IMP_ALGEBRA
373 IMP_ROTAMER_HAS_IMP_CGAL = _IMP_rotamer.IMP_ROTAMER_HAS_IMP_CGAL
374 IMP_ROTAMER_HAS_IMP_CONTAINER = _IMP_rotamer.IMP_ROTAMER_HAS_IMP_CONTAINER
375 IMP_ROTAMER_HAS_IMP_DISPLAY = _IMP_rotamer.IMP_ROTAMER_HAS_IMP_DISPLAY
376 IMP_ROTAMER_HAS_IMP_KERNEL = _IMP_rotamer.IMP_ROTAMER_HAS_IMP_KERNEL
377 IMP_ROTAMER_HAS_IMP_SCORE_FUNCTOR = _IMP_rotamer.IMP_ROTAMER_HAS_IMP_SCORE_FUNCTOR
378 IMP_ROTAMER_HAS_BOOST_FILESYSTEM = _IMP_rotamer.IMP_ROTAMER_HAS_BOOST_FILESYSTEM
379 IMP_ROTAMER_HAS_BOOST_PROGRAMOPTIONS = _IMP_rotamer.IMP_ROTAMER_HAS_BOOST_PROGRAMOPTIONS
380 IMP_ROTAMER_HAS_BOOST_RANDOM = _IMP_rotamer.IMP_ROTAMER_HAS_BOOST_RANDOM
381 IMP_ROTAMER_HAS_BOOST_REGEX = _IMP_rotamer.IMP_ROTAMER_HAS_BOOST_REGEX
382 IMP_ROTAMER_HAS_BOOST_SYSTEM = _IMP_rotamer.IMP_ROTAMER_HAS_BOOST_SYSTEM
383 IMP_ROTAMER_HAS_CGAL = _IMP_rotamer.IMP_ROTAMER_HAS_CGAL
384 IMP_ROTAMER_HAS_HDF5 = _IMP_rotamer.IMP_ROTAMER_HAS_HDF5
385 IMP_ROTAMER_HAS_NUMPY = _IMP_rotamer.IMP_ROTAMER_HAS_NUMPY
386 IMP_ROTAMER_HAS_PYTHON_IHM = _IMP_rotamer.IMP_ROTAMER_HAS_PYTHON_IHM
387 IMPROTAMER_SHOW_WARNINGS = _IMP_rotamer.IMPROTAMER_SHOW_WARNINGS
388 
389 RotamerAngleTuples=list
390 _plural_types.append("RotamerAngleTuples")
391 _value_types.append("RotamerAngleTuple")
392 
393 
394 ResidueRotamers=list
395 _plural_types.append("ResidueRotamers")
396 _value_types.append("ResidueRotamer")
397 
398 
399 _object_types.append("RotamerLibrary")
400 
401 
402 def _object_cast_to_RotamerLibrary(o):
403  """_object_cast_to_RotamerLibrary(Object o) -> RotamerLibrary"""
404  return _IMP_rotamer._object_cast_to_RotamerLibrary(o)
405 
406 _object_types.append("RotamerCalculator")
407 
408 
409 def _object_cast_to_RotamerCalculator(o):
410  """_object_cast_to_RotamerCalculator(Object o) -> RotamerCalculator"""
411  return _IMP_rotamer._object_cast_to_RotamerCalculator(o)
412 class RotamerAngleTuple(object):
413  """Proxy of C++ IMP::rotamer::RotamerAngleTuple class."""
414 
415  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
416 
417  def __init__(self, *args):
418  """
419  __init__(IMP::rotamer::RotamerAngleTuple self) -> RotamerAngleTuple
420  __init__(IMP::rotamer::RotamerAngleTuple self, float chi1, float chi2, float chi3, float chi4, float probability) -> RotamerAngleTuple
421  """
422  this = _IMP_rotamer.new_RotamerAngleTuple(*args)
423  try:
424  self.this.append(this)
425  except __builtin__.Exception:
426  self.this = this
427 
428  def get_chi1(self):
429  """get_chi1(RotamerAngleTuple self) -> float"""
430  return _IMP_rotamer.RotamerAngleTuple_get_chi1(self)
431 
432 
433  def get_chi2(self):
434  """get_chi2(RotamerAngleTuple self) -> float"""
435  return _IMP_rotamer.RotamerAngleTuple_get_chi2(self)
436 
437 
438  def get_chi3(self):
439  """get_chi3(RotamerAngleTuple self) -> float"""
440  return _IMP_rotamer.RotamerAngleTuple_get_chi3(self)
441 
442 
443  def get_chi4(self):
444  """get_chi4(RotamerAngleTuple self) -> float"""
445  return _IMP_rotamer.RotamerAngleTuple_get_chi4(self)
446 
447 
448  def get_probability(self):
449  """get_probability(RotamerAngleTuple self) -> float"""
450  return _IMP_rotamer.RotamerAngleTuple_get_probability(self)
451 
452 
453  def show(self, *args):
454  """
455  show(RotamerAngleTuple self, _ostream out)
456  show(RotamerAngleTuple self)
457  """
458  return _IMP_rotamer.RotamerAngleTuple_show(self, *args)
459 
460 
461  def __str__(self):
462  """__str__(RotamerAngleTuple self) -> std::string"""
463  return _IMP_rotamer.RotamerAngleTuple___str__(self)
464 
465 
466  def __repr__(self):
467  """__repr__(RotamerAngleTuple self) -> std::string"""
468  return _IMP_rotamer.RotamerAngleTuple___repr__(self)
469 
470  __swig_destroy__ = _IMP_rotamer.delete_RotamerAngleTuple
471  __del__ = lambda self: None
472 RotamerAngleTuple_swigregister = _IMP_rotamer.RotamerAngleTuple_swigregister
473 RotamerAngleTuple_swigregister(RotamerAngleTuple)
474 
475 class RotamerLibrary(IMP.Object):
476  """Proxy of C++ IMP::rotamer::RotamerLibrary class."""
477 
478  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
479 
480  def __init__(self, angle_step=10):
481  """
482  __init__(IMP::rotamer::RotamerLibrary self, unsigned int angle_step=10) -> RotamerLibrary
483  __init__(IMP::rotamer::RotamerLibrary self) -> RotamerLibrary
484  """
485  this = _IMP_rotamer.new_RotamerLibrary(angle_step)
486  try:
487  self.this.append(this)
488  except __builtin__.Exception:
489  self.this = this
490 
491  def get_rotamers(self, residue, phi, psi, probability_thr):
492  """get_rotamers(RotamerLibrary self, ResidueType residue, float phi, float psi, float probability_thr) -> IMP::rotamer::RotamerAngleTuples"""
493  return _IMP_rotamer.RotamerLibrary_get_rotamers(self, residue, phi, psi, probability_thr)
494 
495 
496  def read_library_file(self, lib_file_name):
497  """read_library_file(RotamerLibrary self, std::string const & lib_file_name)"""
498  return _IMP_rotamer.RotamerLibrary_read_library_file(self, lib_file_name)
499 
500 
501  def get_version_info(self):
502  """get_version_info(RotamerLibrary self) -> VersionInfo"""
503  return _IMP_rotamer.RotamerLibrary_get_version_info(self)
504 
505 
506  def __str__(self):
507  """__str__(RotamerLibrary self) -> std::string"""
508  return _IMP_rotamer.RotamerLibrary___str__(self)
509 
510 
511  def __repr__(self):
512  """__repr__(RotamerLibrary self) -> std::string"""
513  return _IMP_rotamer.RotamerLibrary___repr__(self)
514 
515 
516  @staticmethod
517  def get_from(o):
518  return _object_cast_to_RotamerLibrary(o)
519 
520 RotamerLibrary_swigregister = _IMP_rotamer.RotamerLibrary_swigregister
521 RotamerLibrary_swigregister(RotamerLibrary)
522 
523 class ResidueRotamer(object):
524  """Proxy of C++ IMP::rotamer::ResidueRotamer class."""
525 
526  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
527 
528  def __init__(self, *args):
529  """
530  __init__(IMP::rotamer::ResidueRotamer self, ResidueType rt) -> ResidueRotamer
531  __init__(IMP::rotamer::ResidueRotamer self) -> ResidueRotamer
532  """
533  this = _IMP_rotamer.new_ResidueRotamer(*args)
534  try:
535  self.this.append(this)
536  except __builtin__.Exception:
537  self.this = this
538 
539  def get_coordinates(self, index, at):
540  """get_coordinates(ResidueRotamer self, unsigned int index, AtomType at) -> Vector3D"""
541  return _IMP_rotamer.ResidueRotamer_get_coordinates(self, index, at)
542 
543 
544  def get_number_of_cases(self, at):
545  """get_number_of_cases(ResidueRotamer self, AtomType at) -> unsigned int"""
546  return _IMP_rotamer.ResidueRotamer_get_number_of_cases(self, at)
547 
548 
549  def get_atom_exists(self, at):
550  """get_atom_exists(ResidueRotamer self, AtomType at) -> bool"""
551  return _IMP_rotamer.ResidueRotamer_get_atom_exists(self, at)
552 
553 
554  def get_size(self):
555  """get_size(ResidueRotamer self) -> unsigned int"""
556  return _IMP_rotamer.ResidueRotamer_get_size(self)
557 
558 
559  def get_probability(self, index):
560  """get_probability(ResidueRotamer self, unsigned int index) -> double"""
561  return _IMP_rotamer.ResidueRotamer_get_probability(self, index)
562 
563 
564  def show(self, *args):
565  """
566  show(ResidueRotamer self, _ostream out)
567  show(ResidueRotamer self)
568  """
569  return _IMP_rotamer.ResidueRotamer_show(self, *args)
570 
571 
572  def __str__(self):
573  """__str__(ResidueRotamer self) -> std::string"""
574  return _IMP_rotamer.ResidueRotamer___str__(self)
575 
576 
577  def __repr__(self):
578  """__repr__(ResidueRotamer self) -> std::string"""
579  return _IMP_rotamer.ResidueRotamer___repr__(self)
580 
581  __swig_destroy__ = _IMP_rotamer.delete_ResidueRotamer
582  __del__ = lambda self: None
583 ResidueRotamer_swigregister = _IMP_rotamer.ResidueRotamer_swigregister
584 ResidueRotamer_swigregister(ResidueRotamer)
585 
586 class RotamerCalculator(IMP.Object):
587  """Proxy of C++ IMP::rotamer::RotamerCalculator class."""
588 
589  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
590 
591  def __init__(self, rl):
592  """__init__(IMP::rotamer::RotamerCalculator self, RotamerLibrary rl) -> RotamerCalculator"""
593  this = _IMP_rotamer.new_RotamerCalculator(rl)
594  try:
595  self.this.append(this)
596  except __builtin__.Exception:
597  self.this = this
598 
599  def get_rotamer(self, rd, thr):
600  """get_rotamer(RotamerCalculator self, Residue rd, double thr) -> ResidueRotamer"""
601  return _IMP_rotamer.RotamerCalculator_get_rotamer(self, rd, thr)
602 
603 
604  def get_version_info(self):
605  """get_version_info(RotamerCalculator self) -> VersionInfo"""
606  return _IMP_rotamer.RotamerCalculator_get_version_info(self)
607 
608 
609  def transform(self, protein, score, thr, K, num_iter):
610  """transform(RotamerCalculator self, Hierarchy protein, PairScore score, double thr, double K, int num_iter)"""
611  return _IMP_rotamer.RotamerCalculator_transform(self, protein, score, thr, K, num_iter)
612 
613 
614  def __str__(self):
615  """__str__(RotamerCalculator self) -> std::string"""
616  return _IMP_rotamer.RotamerCalculator___str__(self)
617 
618 
619  def __repr__(self):
620  """__repr__(RotamerCalculator self) -> std::string"""
621  return _IMP_rotamer.RotamerCalculator___repr__(self)
622 
623 
624  @staticmethod
625  def get_from(o):
626  return _object_cast_to_RotamerCalculator(o)
627 
628 RotamerCalculator_swigregister = _IMP_rotamer.RotamerCalculator_swigregister
629 RotamerCalculator_swigregister(RotamerCalculator)
630 
631 
632 def get_module_version():
633  """get_module_version() -> std::string const"""
634  return _IMP_rotamer.get_module_version()
635 
636 def get_example_path(fname):
637  """get_example_path(std::string fname) -> std::string"""
638  return _IMP_rotamer.get_example_path(fname)
639 
640 def get_data_path(fname):
641  """get_data_path(std::string fname) -> std::string"""
642  return _IMP_rotamer.get_data_path(fname)
643 
644 from . import _version_check
645 _version_check.check_version(get_module_version())
646 __version__ = get_module_version()
647 
648 
649 
Various classes to hold sets of particles.
Make CGAL functionality available to IMP.
Composable functors to implement scores via compile-time composition.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
std::string get_module_version()
Return the version of this module, as a string.
void transform(Hierarchy h, const algebra::Transformation3D &tr)
Transform a hierarchy. This is aware of rigid bodies.
Common base class for heavy weight IMP objects.
Definition: Object.h:106
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Basic functionality that is expected to be used by a wide variety of IMP users.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.