10 from __future__
import print_function, division, absolute_import
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():
19 pkg = __name__.rpartition(
'.')[0]
20 mname =
'.'.join((pkg,
'_IMP_example')).lstrip(
'.')
22 return importlib.import_module(mname)
24 return importlib.import_module(
'_IMP_example')
25 _IMP_example = 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
33 fp, pathname, description = imp.find_module(
'_IMP_example', [dirname(__file__)])
39 _mod = imp.load_module(
'_IMP_example', fp, pathname, description)
43 _IMP_example = swig_import_helper()
44 del swig_import_helper
47 del _swig_python_version_info
49 _swig_property = property
54 import builtins
as __builtin__
58 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
59 if (name ==
"thisown"):
60 return self.this.own(value)
62 if type(value).__name__ ==
'SwigPyObject':
63 self.__dict__[name] = value
65 method = class_type.__swig_setmethods__.get(name,
None)
67 return method(self, value)
69 object.__setattr__(self, name, value)
71 raise AttributeError(
"You cannot add attributes to %s" % self)
74 def _swig_setattr(self, class_type, name, value):
75 return _swig_setattr_nondynamic(self, class_type, name, value, 0)
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)
84 raise AttributeError(
"'%s' object has no attribute '%s'" % (class_type.__name__, name))
89 strthis =
"proxy of " + self.this.__repr__()
90 except __builtin__.Exception:
92 return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
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)
102 raise AttributeError(
"You cannot add attributes to %s" % self)
108 weakref_proxy = weakref.proxy
109 except __builtin__.Exception:
110 weakref_proxy =
lambda x: x
113 class IMP_EXAMPLE_SwigPyIterator(object):
114 """Proxy of C++ swig::IMP_EXAMPLE_SwigPyIterator class."""
116 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
118 def __init__(self, *args, **kwargs):
119 raise AttributeError(
"No constructor defined - class is abstract")
120 __repr__ = _swig_repr
121 __swig_destroy__ = _IMP_example.delete_IMP_EXAMPLE_SwigPyIterator
122 __del__ =
lambda self:
None
125 """value(IMP_EXAMPLE_SwigPyIterator self) -> PyObject *"""
126 return _IMP_example.IMP_EXAMPLE_SwigPyIterator_value(self)
131 incr(IMP_EXAMPLE_SwigPyIterator self, size_t n=1) -> IMP_EXAMPLE_SwigPyIterator
132 incr(IMP_EXAMPLE_SwigPyIterator self) -> IMP_EXAMPLE_SwigPyIterator
134 return _IMP_example.IMP_EXAMPLE_SwigPyIterator_incr(self, n)
139 decr(IMP_EXAMPLE_SwigPyIterator self, size_t n=1) -> IMP_EXAMPLE_SwigPyIterator
140 decr(IMP_EXAMPLE_SwigPyIterator self) -> IMP_EXAMPLE_SwigPyIterator
142 return _IMP_example.IMP_EXAMPLE_SwigPyIterator_decr(self, n)
145 def distance(self, x):
146 """distance(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> ptrdiff_t"""
147 return _IMP_example.IMP_EXAMPLE_SwigPyIterator_distance(self, x)
151 """equal(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> bool"""
152 return _IMP_example.IMP_EXAMPLE_SwigPyIterator_equal(self, x)
156 """copy(IMP_EXAMPLE_SwigPyIterator self) -> IMP_EXAMPLE_SwigPyIterator"""
157 return _IMP_example.IMP_EXAMPLE_SwigPyIterator_copy(self)
161 """next(IMP_EXAMPLE_SwigPyIterator self) -> PyObject *"""
162 return _IMP_example.IMP_EXAMPLE_SwigPyIterator_next(self)
166 """__next__(IMP_EXAMPLE_SwigPyIterator self) -> PyObject *"""
167 return _IMP_example.IMP_EXAMPLE_SwigPyIterator___next__(self)
171 """previous(IMP_EXAMPLE_SwigPyIterator self) -> PyObject *"""
172 return _IMP_example.IMP_EXAMPLE_SwigPyIterator_previous(self)
175 def advance(self, n):
176 """advance(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator"""
177 return _IMP_example.IMP_EXAMPLE_SwigPyIterator_advance(self, n)
181 """__eq__(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> bool"""
182 return _IMP_example.IMP_EXAMPLE_SwigPyIterator___eq__(self, x)
186 """__ne__(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> bool"""
187 return _IMP_example.IMP_EXAMPLE_SwigPyIterator___ne__(self, x)
190 def __iadd__(self, n):
191 """__iadd__(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator"""
192 return _IMP_example.IMP_EXAMPLE_SwigPyIterator___iadd__(self, n)
195 def __isub__(self, n):
196 """__isub__(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator"""
197 return _IMP_example.IMP_EXAMPLE_SwigPyIterator___isub__(self, n)
200 def __add__(self, n):
201 """__add__(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator"""
202 return _IMP_example.IMP_EXAMPLE_SwigPyIterator___add__(self, n)
205 def __sub__(self, *args):
207 __sub__(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator
208 __sub__(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> ptrdiff_t
210 return _IMP_example.IMP_EXAMPLE_SwigPyIterator___sub__(self, *args)
214 IMP_EXAMPLE_SwigPyIterator_swigregister = _IMP_example.IMP_EXAMPLE_SwigPyIterator_swigregister
215 IMP_EXAMPLE_SwigPyIterator_swigregister(IMP_EXAMPLE_SwigPyIterator)
223 IMP_DEBUG = _IMP_example.IMP_DEBUG
224 IMP_RELEASE = _IMP_example.IMP_RELEASE
225 IMP_SILENT = _IMP_example.IMP_SILENT
226 IMP_PROGRESS = _IMP_example.IMP_PROGRESS
227 IMP_TERSE = _IMP_example.IMP_TERSE
228 IMP_VERBOSE = _IMP_example.IMP_VERBOSE
229 IMP_MEMORY = _IMP_example.IMP_MEMORY
230 IMP_NONE = _IMP_example.IMP_NONE
231 IMP_USAGE = _IMP_example.IMP_USAGE
232 IMP_INTERNAL = _IMP_example.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_example.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_example.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_example.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_example.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_example.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_example.IMP_KERNEL_HAS_GPERFTOOLS
239 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_example.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
240 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_example.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
241 IMPKERNEL_SHOW_WARNINGS = _IMP_example.IMPKERNEL_SHOW_WARNINGS
244 class _DirectorObjects(object):
245 """@internal Simple class to keep references to director objects
246 to prevent premature deletion."""
249 def register(self, obj):
250 """Take a reference to a director object; will only work for
251 refcounted C++ classes"""
252 if hasattr(obj,
'get_ref_count'):
253 self._objects.append(obj)
255 """Only drop our reference and allow cleanup by Python if no other
256 Python references exist (we hold 3 references: one in self._objects,
257 one in x, and one in the argument list for getrefcount) *and* no
258 other C++ references exist (the Python object always holds one)"""
259 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
260 or x.get_ref_count() > 1]
264 def get_object_count(self):
265 """Get number of director objects (useful for testing only)"""
266 return len(self._objects)
267 _director_objects = _DirectorObjects()
269 class _ostream(object):
270 """Proxy of C++ std::ostream class."""
272 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
274 def __init__(self, *args, **kwargs):
275 raise AttributeError(
"No constructor defined")
276 __repr__ = _swig_repr
278 def write(self, osa_buf):
279 """write(_ostream self, char const * osa_buf)"""
280 return _IMP_example._ostream_write(self, osa_buf)
282 _ostream_swigregister = _IMP_example._ostream_swigregister
283 _ostream_swigregister(_ostream)
285 IMP_COMPILER_HAS_OVERRIDE = _IMP_example.IMP_COMPILER_HAS_OVERRIDE
286 IMP_COMPILER_HAS_FINAL = _IMP_example.IMP_COMPILER_HAS_FINAL
287 IMP_HAS_NOEXCEPT = _IMP_example.IMP_HAS_NOEXCEPT
289 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CGAL_HAS_BOOST_FILESYSTEM
290 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
291 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_example.IMP_CGAL_HAS_BOOST_RANDOM
292 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_example.IMP_CGAL_HAS_BOOST_SYSTEM
293 IMPCGAL_SHOW_WARNINGS = _IMP_example.IMPCGAL_SHOW_WARNINGS
295 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_example.IMP_ALGEBRA_HAS_IMP_CGAL
296 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
297 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
298 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_example.IMP_ALGEBRA_HAS_BOOST_RANDOM
299 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_example.IMP_ALGEBRA_HAS_BOOST_SYSTEM
300 IMP_ALGEBRA_HAS_CGAL = _IMP_example.IMP_ALGEBRA_HAS_CGAL
301 IMP_ALGEBRA_HAS_ANN = _IMP_example.IMP_ALGEBRA_HAS_ANN
302 IMPALGEBRA_SHOW_WARNINGS = _IMP_example.IMPALGEBRA_SHOW_WARNINGS
304 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_example.IMP_DISPLAY_HAS_IMP_CGAL
305 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
306 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
307 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_example.IMP_DISPLAY_HAS_BOOST_RANDOM
308 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_example.IMP_DISPLAY_HAS_BOOST_SYSTEM
309 IMP_DISPLAY_HAS_CGAL = _IMP_example.IMP_DISPLAY_HAS_CGAL
310 IMPDISPLAY_SHOW_WARNINGS = _IMP_example.IMPDISPLAY_SHOW_WARNINGS
312 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_example.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
313 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
314 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
315 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
316 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
317 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_example.IMP_SCORE_FUNCTOR_HAS_CGAL
318 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_example.IMP_SCORE_FUNCTOR_HAS_HDF5
319 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_example.IMPSCOREFUNCTOR_SHOW_WARNINGS
321 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_example.IMP_STATISTICS_HAS_IMP_CGAL
322 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
323 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
324 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_example.IMP_STATISTICS_HAS_BOOST_RANDOM
325 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_example.IMP_STATISTICS_HAS_BOOST_SYSTEM
326 IMP_STATISTICS_HAS_CGAL = _IMP_example.IMP_STATISTICS_HAS_CGAL
327 IMPSTATISTICS_SHOW_WARNINGS = _IMP_example.IMPSTATISTICS_SHOW_WARNINGS
329 IMP_CORE_HAS_IMP_CGAL = _IMP_example.IMP_CORE_HAS_IMP_CGAL
330 IMP_CORE_HAS_IMP_KERNEL = _IMP_example.IMP_CORE_HAS_IMP_KERNEL
331 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CORE_HAS_BOOST_FILESYSTEM
332 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
333 IMP_CORE_HAS_BOOST_RANDOM = _IMP_example.IMP_CORE_HAS_BOOST_RANDOM
334 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_example.IMP_CORE_HAS_BOOST_SYSTEM
335 IMP_CORE_HAS_CGAL = _IMP_example.IMP_CORE_HAS_CGAL
336 IMP_CORE_HAS_HDF5 = _IMP_example.IMP_CORE_HAS_HDF5
337 IMPCORE_SHOW_WARNINGS = _IMP_example.IMPCORE_SHOW_WARNINGS
339 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_example.IMP_CONTAINER_HAS_IMP_ALGEBRA
340 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_example.IMP_CONTAINER_HAS_IMP_CGAL
341 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_example.IMP_CONTAINER_HAS_IMP_DISPLAY
342 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_example.IMP_CONTAINER_HAS_IMP_KERNEL
343 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
344 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
345 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
346 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_example.IMP_CONTAINER_HAS_BOOST_RANDOM
347 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_example.IMP_CONTAINER_HAS_BOOST_SYSTEM
348 IMP_CONTAINER_HAS_CGAL = _IMP_example.IMP_CONTAINER_HAS_CGAL
349 IMP_CONTAINER_HAS_HDF5 = _IMP_example.IMP_CONTAINER_HAS_HDF5
350 IMPCONTAINER_SHOW_WARNINGS = _IMP_example.IMPCONTAINER_SHOW_WARNINGS
352 IMP_ATOM_HAS_IMP_CGAL = _IMP_example.IMP_ATOM_HAS_IMP_CGAL
353 IMP_ATOM_HAS_IMP_KERNEL = _IMP_example.IMP_ATOM_HAS_IMP_KERNEL
354 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
355 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
356 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_example.IMP_ATOM_HAS_BOOST_RANDOM
357 IMP_ATOM_HAS_BOOST_REGEX = _IMP_example.IMP_ATOM_HAS_BOOST_REGEX
358 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_example.IMP_ATOM_HAS_BOOST_SYSTEM
359 IMP_ATOM_HAS_CGAL = _IMP_example.IMP_ATOM_HAS_CGAL
360 IMP_ATOM_HAS_HDF5 = _IMP_example.IMP_ATOM_HAS_HDF5
361 IMPATOM_SHOW_WARNINGS = _IMP_example.IMPATOM_SHOW_WARNINGS
362 IMP_ATOM_TYPE_INDEX = _IMP_example.IMP_ATOM_TYPE_INDEX
363 IMP_RESIDUE_TYPE_INDEX = _IMP_example.IMP_RESIDUE_TYPE_INDEX
364 IMP_HIERARCHY_TYPE_INDEX = _IMP_example.IMP_HIERARCHY_TYPE_INDEX
366 IMP_RMF_HAS_IMP_CGAL = _IMP_example.IMP_RMF_HAS_IMP_CGAL
367 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
368 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_RMF_HAS_BOOST_FILESYSTEM
369 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
370 IMP_RMF_HAS_BOOST_RANDOM = _IMP_example.IMP_RMF_HAS_BOOST_RANDOM
371 IMP_RMF_HAS_BOOST_REGEX = _IMP_example.IMP_RMF_HAS_BOOST_REGEX
372 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_example.IMP_RMF_HAS_BOOST_SYSTEM
373 IMP_RMF_HAS_CGAL = _IMP_example.IMP_RMF_HAS_CGAL
374 IMP_RMF_HAS_HDF5 = _IMP_example.IMP_RMF_HAS_HDF5
375 IMPRMF_SHOW_WARNINGS = _IMP_example.IMPRMF_SHOW_WARNINGS
378 IMP_DOMINO_HAS_IMP_ATOM = _IMP_example.IMP_DOMINO_HAS_IMP_ATOM
379 IMP_DOMINO_HAS_IMP_CGAL = _IMP_example.IMP_DOMINO_HAS_IMP_CGAL
380 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_example.IMP_DOMINO_HAS_IMP_KERNEL
381 IMP_DOMINO_HAS_IMP_RMF = _IMP_example.IMP_DOMINO_HAS_IMP_RMF
382 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
383 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_DOMINO_HAS_BOOST_FILESYSTEM
384 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
385 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_example.IMP_DOMINO_HAS_BOOST_RANDOM
386 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_example.IMP_DOMINO_HAS_BOOST_REGEX
387 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_example.IMP_DOMINO_HAS_BOOST_SYSTEM
388 IMP_DOMINO_HAS_CGAL = _IMP_example.IMP_DOMINO_HAS_CGAL
389 IMP_DOMINO_HAS_HDF5 = _IMP_example.IMP_DOMINO_HAS_HDF5
390 IMP_DOMINO_HAS_RMF = _IMP_example.IMP_DOMINO_HAS_RMF
391 IMPDOMINO_SHOW_WARNINGS = _IMP_example.IMPDOMINO_SHOW_WARNINGS
394 IMP_EXAMPLE_HAS_IMP_ALGEBRA = _IMP_example.IMP_EXAMPLE_HAS_IMP_ALGEBRA
395 IMP_EXAMPLE_HAS_IMP_CGAL = _IMP_example.IMP_EXAMPLE_HAS_IMP_CGAL
396 IMP_EXAMPLE_HAS_IMP_DISPLAY = _IMP_example.IMP_EXAMPLE_HAS_IMP_DISPLAY
397 IMP_EXAMPLE_HAS_IMP_KERNEL = _IMP_example.IMP_EXAMPLE_HAS_IMP_KERNEL
398 IMP_EXAMPLE_HAS_IMP_RMF = _IMP_example.IMP_EXAMPLE_HAS_IMP_RMF
399 IMP_EXAMPLE_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_EXAMPLE_HAS_IMP_SCORE_FUNCTOR
400 IMP_EXAMPLE_HAS_IMP_STATISTICS = _IMP_example.IMP_EXAMPLE_HAS_IMP_STATISTICS
401 IMP_EXAMPLE_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_FILESYSTEM
402 IMP_EXAMPLE_HAS_BOOST_GRAPH = _IMP_example.IMP_EXAMPLE_HAS_BOOST_GRAPH
403 IMP_EXAMPLE_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_EXAMPLE_HAS_BOOST_PROGRAMOPTIONS
404 IMP_EXAMPLE_HAS_BOOST_RANDOM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_RANDOM
405 IMP_EXAMPLE_HAS_BOOST_REGEX = _IMP_example.IMP_EXAMPLE_HAS_BOOST_REGEX
406 IMP_EXAMPLE_HAS_BOOST_SYSTEM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_SYSTEM
407 IMP_EXAMPLE_HAS_CGAL = _IMP_example.IMP_EXAMPLE_HAS_CGAL
408 IMP_EXAMPLE_HAS_HDF5 = _IMP_example.IMP_EXAMPLE_HAS_HDF5
409 IMP_EXAMPLE_HAS_RMF = _IMP_example.IMP_EXAMPLE_HAS_RMF
410 IMP_EXAMPLE_HAS_EXAMPLEDEPENDENCY = _IMP_example.IMP_EXAMPLE_HAS_EXAMPLEDEPENDENCY
411 IMPEXAMPLE_SHOW_WARNINGS = _IMP_example.IMPEXAMPLE_SHOW_WARNINGS
413 _object_types.append(
"ExampleRestraint")
416 def _object_cast_to_ExampleRestraint(o):
417 """_object_cast_to_ExampleRestraint(Object o) -> ExampleRestraint"""
418 return _IMP_example._object_cast_to_ExampleRestraint(o)
420 def ExampleDecorators(l=[]):
421 return [ExampleDecorator(x)
for x
in l]
422 _plural_types.append(
"ExampleDecorators")
425 _value_types.append(
"ExampleDecorator")
428 _object_types.append(
"ExampleUnaryFunction")
431 def _object_cast_to_ExampleUnaryFunction(o):
432 """_object_cast_to_ExampleUnaryFunction(Object o) -> ExampleUnaryFunction"""
433 return _IMP_example._object_cast_to_ExampleUnaryFunction(o)
435 _object_types.append(
"ExampleSingletonModifier")
438 def _object_cast_to_ExampleSingletonModifier(o):
439 """_object_cast_to_ExampleSingletonModifier(Object o) -> ExampleSingletonModifier"""
440 return _IMP_example._object_cast_to_ExampleSingletonModifier(o)
442 _object_types.append(
"ExamplePairScore")
445 def _object_cast_to_ExamplePairScore(o):
446 """_object_cast_to_ExamplePairScore(Object o) -> ExamplePairScore"""
447 return _IMP_example._object_cast_to_ExamplePairScore(o)
449 _object_types.append(
"ExampleSubsetFilterTable")
452 def _object_cast_to_ExampleSubsetFilterTable(o):
453 """_object_cast_to_ExampleSubsetFilterTable(Object o) -> ExampleSubsetFilterTable"""
454 return _IMP_example._object_cast_to_ExampleSubsetFilterTable(o)
456 _object_types.append(
"ExampleConstraint")
459 def _object_cast_to_ExampleConstraint(o):
460 """_object_cast_to_ExampleConstraint(Object o) -> ExampleConstraint"""
461 return _IMP_example._object_cast_to_ExampleConstraint(o)
463 _object_types.append(
"ExampleObject")
466 def _object_cast_to_ExampleObject(o):
467 """_object_cast_to_ExampleObject(Object o) -> ExampleObject"""
468 return _IMP_example._object_cast_to_ExampleObject(o)
470 ExampleTemplateClass3Ds=list
471 _plural_types.append(
"ExampleTemplateClass3Ds")
472 _value_types.append(
"ExampleTemplateClass3D")
475 def create_model_and_particles():
480 for i
in range(0,100):
481 p = m.add_particle(
"p")
485 d.set_coordinates_are_optimized(
True)
491 """An example restraint written in Python.
492 This should be functionally equivalent to the C++ ExampleRestraint.
494 def __init__(self, m, p, k):
495 IMP.Restraint.__init__(self, m,
"PythonExampleRestraint%1%")
496 self.p, self.k = p, k
500 score = .5 * self.k * d.get_z() * d.get_z()
501 if sa.get_derivative_accumulator():
502 deriv = self.k * d.get_z()
503 d.add_to_derivative(2, deriv, sa.get_derivative_accumulator())
507 return [self.
get_model().get_particle(self.p)]
513 """An example PairScore written in Python.
514 This should be functionally equivalent to the C++ ExamplePairScore.
516 def __init__(self, x0, k):
517 IMP.PairScore.__init__(self)
518 self.x0, self.k = x0, k
523 diff = (d0.get_coordinates()
524 - d1.get_coordinates()).get_magnitude() - self.x0
525 score = .5 * self.k * diff * diff
528 delta = d0.get_coordinates() - d1.get_coordinates()
529 udelta = delta.get_unit_vector()
531 d0.add_to_derivatives(udelta * dv, da)
532 d1.add_to_derivatives(-udelta * dv, da)
542 """An example UnaryFunction written in Python.
543 This should be functionally equivalent to the C++ ExampleUnaryFunction.
545 def __init__(self, center, k):
546 IMP.UnaryFunction.__init__(self)
547 self.center, self.k = center, k
550 return (self.
evaluate(feature), self.k * (feature - self.center))
553 return .5 * self.k * (feature - self.center) * (feature - self.center)
559 """An example Constraint written in Python.
560 This should be functionally equivalent to the C++ ExampleConstraint.
565 def __init__(self, p):
566 IMP.Constraint.__init__(self, p.get_model(),
"ExampleConstraint%1%")
569 PythonExampleConstraint.k =
IMP.IntKey(
"Constraint key")
570 if not p.has_attribute(self.k):
571 p.add_attribute(self.k, 0)
573 def do_update_attributes(self):
574 self.p.set_value(self.k, self.p.get_value(self.k) + 1)
576 def do_update_derivatives(self, da):
589 """An example SingletonModifier written in Python.
590 This should be functionally equivalent to the C++
591 ExampleSingletonModifier.
594 def __init__(self, bb):
595 IMP.SingletonModifier.__init__(self,
"ExampleSingletonModifier%1%")
602 while d.get_coordinate(i) < self.bb.get_corner(0)[i]:
603 d.set_coordinate(i,d.get_coordinate(i) + \
604 (self.bb.get_corner(1)[i] - self.bb.get_corner(0)[i]))
605 while d.get_coordinate(i) > self.bb.get_corner(1)[i]:
606 d.set_coordinate(i,d.get_coordinate(i) - \
607 (self.bb.get_corner(1)[i] - self.bb.get_corner(0)[i]))
617 """Proxy of C++ IMP::example::ExampleRestraint class."""
619 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
621 def __init__(self, m, p, k):
622 """__init__(IMP::example::ExampleRestraint self, Model m, ParticleIndex p, double k) -> ExampleRestraint"""
623 this = _IMP_example.new_ExampleRestraint(m, p, k)
625 self.this.append(this)
626 except __builtin__.Exception:
629 def do_add_score_and_derivatives(self, sa):
630 """do_add_score_and_derivatives(ExampleRestraint self, ScoreAccumulator sa)"""
631 return _IMP_example.ExampleRestraint_do_add_score_and_derivatives(self, sa)
635 """do_get_inputs(ExampleRestraint self) -> IMP::ModelObjectsTemp"""
636 return _IMP_example.ExampleRestraint_do_get_inputs(self)
640 """get_version_info(ExampleRestraint self) -> VersionInfo"""
641 return _IMP_example.ExampleRestraint_get_version_info(self)
645 """__str__(ExampleRestraint self) -> std::string"""
646 return _IMP_example.ExampleRestraint___str__(self)
650 """__repr__(ExampleRestraint self) -> std::string"""
651 return _IMP_example.ExampleRestraint___repr__(self)
656 return _object_cast_to_ExampleRestraint(o)
658 ExampleRestraint_swigregister = _IMP_example.ExampleRestraint_swigregister
659 ExampleRestraint_swigregister(ExampleRestraint)
662 """Proxy of C++ IMP::example::ExampleDecorator class."""
664 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
666 def get_decorator_name(self):
667 """get_decorator_name(ExampleDecorator self) -> std::string"""
668 return _IMP_example.ExampleDecorator_get_decorator_name(self)
671 def set_decorator_name(self, nm):
672 """set_decorator_name(ExampleDecorator self, std::string nm)"""
673 return _IMP_example.ExampleDecorator_set_decorator_name(self, nm)
676 def __init__(self, *args):
678 __init__(IMP::example::ExampleDecorator self) -> ExampleDecorator
679 __init__(IMP::example::ExampleDecorator self, Model m, ParticleIndex id) -> ExampleDecorator
680 __init__(IMP::example::ExampleDecorator self, _ParticleAdaptor d) -> ExampleDecorator
682 this = _IMP_example.new_ExampleDecorator(*args)
684 self.this.append(this)
685 except __builtin__.Exception:
688 def get_is_setup(*args):
690 get_is_setup(Model m, ParticleIndex pi) -> bool
691 get_is_setup(_ParticleAdaptor p) -> bool
693 return _IMP_example.ExampleDecorator_get_is_setup(*args)
695 get_is_setup = staticmethod(get_is_setup)
697 def show(self, *args):
699 show(ExampleDecorator self, _ostream out)
700 show(ExampleDecorator self)
702 return _IMP_example.ExampleDecorator_show(self, *args)
705 def setup_particle(*args):
707 setup_particle(Model m, ParticleIndex pi, std::string name) -> ExampleDecorator
708 setup_particle(_ParticleAdaptor decorator, std::string name) -> ExampleDecorator
710 return _IMP_example.ExampleDecorator_setup_particle(*args)
712 setup_particle = staticmethod(setup_particle)
714 def add_attribute(self, *args):
716 add_attribute(ExampleDecorator self, FloatKey k, IMP::Float v, bool opt)
717 add_attribute(ExampleDecorator self, FloatKey a0, IMP::Float a1)
718 add_attribute(ExampleDecorator self, IntKey a0, IMP::Int a1)
719 add_attribute(ExampleDecorator self, StringKey a0, IMP::String a1)
720 add_attribute(ExampleDecorator self, ParticleIndexKey a0, Particle a1)
721 add_attribute(ExampleDecorator self, ObjectKey a0, Object a1)
723 return _IMP_example.ExampleDecorator_add_attribute(self, *args)
726 def get_value(self, *args):
728 get_value(ExampleDecorator self, FloatKey a0) -> IMP::Float
729 get_value(ExampleDecorator self, IntKey a0) -> IMP::Int
730 get_value(ExampleDecorator self, StringKey a0) -> IMP::String
731 get_value(ExampleDecorator self, ParticleIndexKey a0) -> Particle
732 get_value(ExampleDecorator self, ObjectKey a0) -> Object
734 return _IMP_example.ExampleDecorator_get_value(self, *args)
737 def set_value(self, *args):
739 set_value(ExampleDecorator self, FloatKey a0, IMP::Float a1)
740 set_value(ExampleDecorator self, IntKey a0, IMP::Int a1)
741 set_value(ExampleDecorator self, StringKey a0, IMP::String a1)
742 set_value(ExampleDecorator self, ParticleIndexKey a0, Particle a1)
743 set_value(ExampleDecorator self, ObjectKey a0, Object a1)
745 return _IMP_example.ExampleDecorator_set_value(self, *args)
748 def remove_attribute(self, *args):
750 remove_attribute(ExampleDecorator self, FloatKey a0)
751 remove_attribute(ExampleDecorator self, IntKey a0)
752 remove_attribute(ExampleDecorator self, StringKey a0)
753 remove_attribute(ExampleDecorator self, ParticleIndexKey a0)
754 remove_attribute(ExampleDecorator self, ObjectKey a0)
756 return _IMP_example.ExampleDecorator_remove_attribute(self, *args)
759 def has_attribute(self, *args):
761 has_attribute(ExampleDecorator self, FloatKey a0) -> bool
762 has_attribute(ExampleDecorator self, IntKey a0) -> bool
763 has_attribute(ExampleDecorator self, StringKey a0) -> bool
764 has_attribute(ExampleDecorator self, ParticleIndexKey a0) -> bool
765 has_attribute(ExampleDecorator self, ObjectKey a0) -> bool
767 return _IMP_example.ExampleDecorator_has_attribute(self, *args)
770 def get_derivative(self, a0):
771 """get_derivative(ExampleDecorator self, FloatKey a0) -> double"""
772 return _IMP_example.ExampleDecorator_get_derivative(self, a0)
776 """get_name(ExampleDecorator self) -> std::string"""
777 return _IMP_example.ExampleDecorator_get_name(self)
781 """clear_caches(ExampleDecorator self)"""
782 return _IMP_example.ExampleDecorator_clear_caches(self)
785 def set_name(self, a0):
786 """set_name(ExampleDecorator self, std::string a0)"""
787 return _IMP_example.ExampleDecorator_set_name(self, a0)
791 """set_check_level(ExampleDecorator self, IMP::CheckLevel a0)"""
792 return _IMP_example.ExampleDecorator_set_check_level(self, a0)
795 def add_to_derivative(self, a0, a1, a2):
796 """add_to_derivative(ExampleDecorator self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
797 return _IMP_example.ExampleDecorator_add_to_derivative(self, a0, a1, a2)
800 def set_is_optimized(self, a0, a1):
801 """set_is_optimized(ExampleDecorator self, FloatKey a0, bool a1)"""
802 return _IMP_example.ExampleDecorator_set_is_optimized(self, a0, a1)
805 def get_is_optimized(self, a0):
806 """get_is_optimized(ExampleDecorator self, FloatKey a0) -> bool"""
807 return _IMP_example.ExampleDecorator_get_is_optimized(self, a0)
810 def get_check_level(self):
811 """get_check_level(ExampleDecorator self) -> IMP::CheckLevel"""
812 return _IMP_example.ExampleDecorator_get_check_level(self)
815 def __eq__(self, *args):
817 __eq__(ExampleDecorator self, ExampleDecorator o) -> bool
818 __eq__(ExampleDecorator self, Particle d) -> bool
820 return _IMP_example.ExampleDecorator___eq__(self, *args)
823 def __ne__(self, *args):
825 __ne__(ExampleDecorator self, ExampleDecorator o) -> bool
826 __ne__(ExampleDecorator self, Particle d) -> bool
828 return _IMP_example.ExampleDecorator___ne__(self, *args)
831 def __le__(self, *args):
833 __le__(ExampleDecorator self, ExampleDecorator o) -> bool
834 __le__(ExampleDecorator self, Particle d) -> bool
836 return _IMP_example.ExampleDecorator___le__(self, *args)
839 def __lt__(self, *args):
841 __lt__(ExampleDecorator self, ExampleDecorator o) -> bool
842 __lt__(ExampleDecorator self, Particle d) -> bool
844 return _IMP_example.ExampleDecorator___lt__(self, *args)
847 def __ge__(self, *args):
849 __ge__(ExampleDecorator self, ExampleDecorator o) -> bool
850 __ge__(ExampleDecorator self, Particle d) -> bool
852 return _IMP_example.ExampleDecorator___ge__(self, *args)
855 def __gt__(self, *args):
857 __gt__(ExampleDecorator self, ExampleDecorator o) -> bool
858 __gt__(ExampleDecorator self, Particle d) -> bool
860 return _IMP_example.ExampleDecorator___gt__(self, *args)
864 """__hash__(ExampleDecorator self) -> std::size_t"""
865 return _IMP_example.ExampleDecorator___hash__(self)
869 """__str__(ExampleDecorator self) -> std::string"""
870 return _IMP_example.ExampleDecorator___str__(self)
874 """__repr__(ExampleDecorator self) -> std::string"""
875 return _IMP_example.ExampleDecorator___repr__(self)
877 __swig_destroy__ = _IMP_example.delete_ExampleDecorator
878 __del__ =
lambda self:
None
879 ExampleDecorator_swigregister = _IMP_example.ExampleDecorator_swigregister
880 ExampleDecorator_swigregister(ExampleDecorator)
882 def ExampleDecorator_get_is_setup(*args):
884 get_is_setup(Model m, ParticleIndex pi) -> bool
885 ExampleDecorator_get_is_setup(_ParticleAdaptor p) -> bool
887 return _IMP_example.ExampleDecorator_get_is_setup(*args)
889 def ExampleDecorator_setup_particle(*args):
891 setup_particle(Model m, ParticleIndex pi, std::string name) -> ExampleDecorator
892 ExampleDecorator_setup_particle(_ParticleAdaptor decorator, std::string name) -> ExampleDecorator
894 return _IMP_example.ExampleDecorator_setup_particle(*args)
897 def __lshift__(out, n):
898 """__lshift__(_ostream out, ExampleDecorator n) -> _ostream"""
899 return _IMP_example.__lshift__(out, n)
901 """Proxy of C++ IMP::example::ExampleUnaryFunction class."""
903 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
905 def __init__(self, center, k):
906 """__init__(IMP::example::ExampleUnaryFunction self, IMP::Float center, IMP::Float k) -> ExampleUnaryFunction"""
907 this = _IMP_example.new_ExampleUnaryFunction(center, k)
909 self.this.append(this)
910 except __builtin__.Exception:
914 """get_version_info(ExampleUnaryFunction self) -> VersionInfo"""
915 return _IMP_example.ExampleUnaryFunction_get_version_info(self)
919 """__str__(ExampleUnaryFunction self) -> std::string"""
920 return _IMP_example.ExampleUnaryFunction___str__(self)
924 """__repr__(ExampleUnaryFunction self) -> std::string"""
925 return _IMP_example.ExampleUnaryFunction___repr__(self)
930 return _object_cast_to_ExampleUnaryFunction(o)
932 ExampleUnaryFunction_swigregister = _IMP_example.ExampleUnaryFunction_swigregister
933 ExampleUnaryFunction_swigregister(ExampleUnaryFunction)
936 """Proxy of C++ IMP::example::ExampleObject class."""
938 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
940 def __init__(self, data):
941 """__init__(IMP::example::ExampleObject self, IMP::Floats const & data) -> ExampleObject"""
942 this = _IMP_example.new_ExampleObject(data)
944 self.this.append(this)
945 except __builtin__.Exception:
948 def get_data(self, i):
949 """get_data(ExampleObject self, unsigned int i) -> double"""
950 return _IMP_example.ExampleObject_get_data(self, i)
954 """get_version_info(ExampleObject self) -> VersionInfo"""
955 return _IMP_example.ExampleObject_get_version_info(self)
959 """__str__(ExampleObject self) -> std::string"""
960 return _IMP_example.ExampleObject___str__(self)
964 """__repr__(ExampleObject self) -> std::string"""
965 return _IMP_example.ExampleObject___repr__(self)
970 return _object_cast_to_ExampleObject(o)
972 ExampleObject_swigregister = _IMP_example.ExampleObject_swigregister
973 ExampleObject_swigregister(ExampleObject)
976 """Proxy of C++ IMP::example::ExampleSingletonModifier class."""
978 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
980 def __init__(self, bb):
981 """__init__(IMP::example::ExampleSingletonModifier self, BoundingBox3D bb) -> ExampleSingletonModifier"""
982 this = _IMP_example.new_ExampleSingletonModifier(bb)
984 self.this.append(this)
985 except __builtin__.Exception:
989 """do_get_inputs(ExampleSingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
990 return _IMP_example.ExampleSingletonModifier_do_get_inputs(self, m, pis)
994 """do_get_outputs(ExampleSingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
995 return _IMP_example.ExampleSingletonModifier_do_get_outputs(self, m, pis)
999 """get_version_info(ExampleSingletonModifier self) -> VersionInfo"""
1000 return _IMP_example.ExampleSingletonModifier_get_version_info(self)
1004 """__str__(ExampleSingletonModifier self) -> std::string"""
1005 return _IMP_example.ExampleSingletonModifier___str__(self)
1009 """__repr__(ExampleSingletonModifier self) -> std::string"""
1010 return _IMP_example.ExampleSingletonModifier___repr__(self)
1015 return _object_cast_to_ExampleSingletonModifier(o)
1017 ExampleSingletonModifier_swigregister = _IMP_example.ExampleSingletonModifier_swigregister
1018 ExampleSingletonModifier_swigregister(ExampleSingletonModifier)
1021 """Proxy of C++ IMP::example::ExamplePairScore class."""
1023 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1025 def __init__(self, x0, k):
1026 """__init__(IMP::example::ExamplePairScore self, double x0, double k) -> ExamplePairScore"""
1027 this = _IMP_example.new_ExamplePairScore(x0, k)
1029 self.this.append(this)
1030 except __builtin__.Exception:
1034 """do_get_inputs(ExamplePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1035 return _IMP_example.ExamplePairScore_do_get_inputs(self, m, pis)
1039 """get_version_info(ExamplePairScore self) -> VersionInfo"""
1040 return _IMP_example.ExamplePairScore_get_version_info(self)
1044 """__str__(ExamplePairScore self) -> std::string"""
1045 return _IMP_example.ExamplePairScore___str__(self)
1049 """__repr__(ExamplePairScore self) -> std::string"""
1050 return _IMP_example.ExamplePairScore___repr__(self)
1055 return _object_cast_to_ExamplePairScore(o)
1057 ExamplePairScore_swigregister = _IMP_example.ExamplePairScore_swigregister
1058 ExamplePairScore_swigregister(ExamplePairScore)
1061 """Proxy of C++ IMP::example::ExampleSubsetFilterTable class."""
1063 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1065 def __init__(self, max_diff, pt):
1066 """__init__(IMP::example::ExampleSubsetFilterTable self, unsigned int max_diff, IMP::ParticlesTemp const & pt) -> ExampleSubsetFilterTable"""
1067 this = _IMP_example.new_ExampleSubsetFilterTable(max_diff, pt)
1069 self.this.append(this)
1070 except __builtin__.Exception:
1074 """get_version_info(ExampleSubsetFilterTable self) -> VersionInfo"""
1075 return _IMP_example.ExampleSubsetFilterTable_get_version_info(self)
1079 """__str__(ExampleSubsetFilterTable self) -> std::string"""
1080 return _IMP_example.ExampleSubsetFilterTable___str__(self)
1084 """__repr__(ExampleSubsetFilterTable self) -> std::string"""
1085 return _IMP_example.ExampleSubsetFilterTable___repr__(self)
1090 return _object_cast_to_ExampleSubsetFilterTable(o)
1092 ExampleSubsetFilterTable_swigregister = _IMP_example.ExampleSubsetFilterTable_swigregister
1093 ExampleSubsetFilterTable_swigregister(ExampleSubsetFilterTable)
1096 """Proxy of C++ IMP::example::ExampleConstraint class."""
1098 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1100 def __init__(self, p):
1101 """__init__(IMP::example::ExampleConstraint self, Particle p) -> ExampleConstraint"""
1102 this = _IMP_example.new_ExampleConstraint(p)
1104 self.this.append(this)
1105 except __builtin__.Exception:
1109 """do_get_inputs(ExampleConstraint self) -> IMP::ModelObjectsTemp"""
1110 return _IMP_example.ExampleConstraint_do_get_inputs(self)
1114 """do_get_outputs(ExampleConstraint self) -> IMP::ModelObjectsTemp"""
1115 return _IMP_example.ExampleConstraint_do_get_outputs(self)
1119 """get_key() -> IntKey"""
1120 return _IMP_example.ExampleConstraint_get_key()
1122 get_key = staticmethod(get_key)
1125 """get_version_info(ExampleConstraint self) -> VersionInfo"""
1126 return _IMP_example.ExampleConstraint_get_version_info(self)
1130 """__str__(ExampleConstraint self) -> std::string"""
1131 return _IMP_example.ExampleConstraint___str__(self)
1135 """__repr__(ExampleConstraint self) -> std::string"""
1136 return _IMP_example.ExampleConstraint___repr__(self)
1141 return _object_cast_to_ExampleConstraint(o)
1143 ExampleConstraint_swigregister = _IMP_example.ExampleConstraint_swigregister
1144 ExampleConstraint_swigregister(ExampleConstraint)
1146 def ExampleConstraint_get_key():
1147 """ExampleConstraint_get_key() -> IntKey"""
1148 return _IMP_example.ExampleConstraint_get_key()
1152 """create_serial_mover(Model m, IMP::ParticleIndexes const & pis) -> MonteCarloMover"""
1153 return _IMP_example.create_serial_mover(m, pis)
1157 optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs, IMP::PairPredicates const & excluded, IMP::OptimizerStates const & opt_states, IMP::LogLevel ll)
1158 optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs, IMP::PairPredicates const & excluded, IMP::OptimizerStates const & opt_states)
1159 optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs, IMP::PairPredicates const & excluded)
1160 optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs)
1161 optimize_balls(Model m, IMP::ParticleIndexes const & pis)
1163 return _IMP_example.optimize_balls(*args)
1167 optimize_assembly(Model m, IMP::ParticleIndexes const & components, IMP::RestraintsTemp const & interactions, IMP::RestraintsTemp const & other_restraints, BoundingBox3D bb, PairScore ev, double cutoff, IMP::PairPredicates const & excluded)
1168 optimize_assembly(Model m, IMP::ParticleIndexes const & components, IMP::RestraintsTemp const & interactions, IMP::RestraintsTemp const & other_restraints, BoundingBox3D bb, PairScore ev, double cutoff)
1170 return _IMP_example.optimize_assembly(*args)
1173 """get_number_of_incidences(IMP::ParticlesTemp const & psa, IMP::ParticlesTemp const & psb, double point_distance) -> unsigned int"""
1174 return _IMP_example.get_number_of_incidences(psa, psb, point_distance)
1177 """create_chain_restraint(Model m, IMP::ParticleIndexes const & ps, double length_factor, double k, std::string name) -> Restraint"""
1178 return _IMP_example.create_chain_restraint(m, ps, length_factor, k, name)
1181 """create_excluded_volume(IMP::ParticlesTemp const & ps, double k, std::string name) -> Restraint"""
1182 return _IMP_example.create_excluded_volume(ps, k, name)
1184 """Proxy of C++ IMP::example::ExampleTemplateClassD<(3)> class."""
1186 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1188 def __init__(self, *args):
1190 __init__(IMP::example::ExampleTemplateClassD<(3)> self) -> ExampleTemplateClass3D
1191 __init__(IMP::example::ExampleTemplateClassD<(3)> self, Vector3D a, Vector3D b) -> ExampleTemplateClass3D
1193 this = _IMP_example.new_ExampleTemplateClass3D(*args)
1195 self.this.append(this)
1196 except __builtin__.Exception:
1199 def get_point(self, i):
1200 """get_point(ExampleTemplateClass3D self, unsigned int i) -> Vector3D"""
1201 return _IMP_example.ExampleTemplateClass3D_get_point(self, i)
1204 def show(self, *args):
1206 show(ExampleTemplateClass3D self, _ostream out)
1207 show(ExampleTemplateClass3D self)
1209 return _IMP_example.ExampleTemplateClass3D_show(self, *args)
1213 """__str__(ExampleTemplateClass3D self) -> std::string"""
1214 return _IMP_example.ExampleTemplateClass3D___str__(self)
1218 """__repr__(ExampleTemplateClass3D self) -> std::string"""
1219 return _IMP_example.ExampleTemplateClass3D___repr__(self)
1221 __swig_destroy__ = _IMP_example.delete_ExampleTemplateClass3D
1222 __del__ =
lambda self:
None
1223 ExampleTemplateClass3D_swigregister = _IMP_example.ExampleTemplateClass3D_swigregister
1224 ExampleTemplateClass3D_swigregister(ExampleTemplateClass3D)
1227 def get_module_version():
1228 """get_module_version() -> std::string const"""
1229 return _IMP_example.get_module_version()
1232 """get_example_path(std::string fname) -> std::string"""
1233 return _IMP_example.get_example_path(fname)
1236 """get_data_path(std::string fname) -> std::string"""
1237 return _IMP_example.get_data_path(fname)
1239 from .
import _version_check
1240 _version_check.check_version(get_module_version())
1241 __version__ = get_module_version()
unsigned int get_number_of_incidences(const ParticlesTemp &psa, const ParticlesTemp &psb, double point_distance)
A base class for modifiers of ParticlesTemp.
Abstract class for scoring object(s) of type ParticleIndexPair.
virtual double evaluate(double feature) const
Calculate score with respect to the given feature.
An example PairScore written in Python.
An example SingletonModifier written in Python.
Various classes to hold sets of particles.
static XYZR setup_particle(Model *m, ParticleIndex pi)
An example UnaryFunction written in Python.
virtual void do_add_score_and_derivatives(ScoreAccumulator sa) const
A restraint should override this to compute the score and derivatives.
Make CGAL functionality available to IMP.
A line segment templated on the dimension.
ParticlesTemp get_particles(Model *m, const ParticleIndexes &ps)
virtual void clear_caches()
virtual ModelObjectsTemp do_get_outputs(Model *m, const ParticleIndexes &pis) const =0
Overload this method to specify the outputs.
Composable functors to implement scores via compile-time composition.
Vector3D get_random_vector_in(const Cylinder3D &c)
Generate a random vector in a cylinder with uniform density.
core::MonteCarloMover * create_serial_mover(Model *m, const ParticleIndexes &pis)
Code to compute statistical measures.
Implement a constraint on the Model.
Class for storing model, its restraints, constraints, and particles.
An example simple object which is reference counted.
A simple decorator which adds a name to a particle.
An example Constraint written in Python.
An example singleton modifier.
Common base class for heavy weight IMP objects.
Store a list of ParticleIndexes.
An example restraint written in Python.
Restraint * create_excluded_volume(const ParticlesTemp &ps, double k, std::string name)
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const =0
Overload this method to specify the inputs.
void optimize_balls(Model *m, const ParticleIndexes &pis, const RestraintsTemp &rs=RestraintsTemp(), const PairPredicates &excluded=PairPredicates(), const OptimizerStates &opt_states=OptimizerStates(), LogLevel ll=DEFAULT)
Restrain a particle to be in the x,y plane.
void optimize_assembly(Model *m, const ParticleIndexes &components, const RestraintsTemp &interactions, const RestraintsTemp &other_restraints, const algebra::BoundingBox3D &bb, PairScore *ev, double cutoff, const PairPredicates &excluded=PairPredicates())
A decorator for a particle with x,y,z coordinates.
Interface to specialized Particle types (e.g. atoms)
virtual ModelObjectsTemp do_get_outputs() const =0
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...
virtual void apply_index(Model *m, ParticleIndex v) const =0
virtual VersionInfo get_version_info() const
Get information about the module and version of the object.
virtual DerivativePair evaluate_with_derivative(double feature) const
Calculate score and derivative with respect to the given feature.
void set_check_level(CheckLevel l)
Apply a harmonic to the distance between two particles.
Restraint * create_chain_restraint(Model *m, const ParticleIndexes &ps, double length_factor, double k, std::string name)
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Model * get_model() const
A trivial constraint that just increments a counter.
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
Support for the RMF file format for storing hierarchical molecular data and markup.
Abstract single variable functor class for score functions.
virtual ModelObjectsTemp do_get_inputs() const =0
Divide-and-conquer inferential optimization in discrete space.
virtual double evaluate_index(Model *m, const ParticleIndexPair &vt, DerivativeAccumulator *da) const =0
Compute the score and the derivative if needed.
A restraint is a term in an IMP ScoringFunction.