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
288 IMP_C_OPEN_BINARY = _IMP_example.IMP_C_OPEN_BINARY
290 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CGAL_HAS_BOOST_FILESYSTEM
291 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
292 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_example.IMP_CGAL_HAS_BOOST_RANDOM
293 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_example.IMP_CGAL_HAS_BOOST_SYSTEM
294 IMPCGAL_SHOW_WARNINGS = _IMP_example.IMPCGAL_SHOW_WARNINGS
296 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_example.IMP_ALGEBRA_HAS_IMP_CGAL
297 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
298 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
299 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_example.IMP_ALGEBRA_HAS_BOOST_RANDOM
300 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_example.IMP_ALGEBRA_HAS_BOOST_SYSTEM
301 IMP_ALGEBRA_HAS_CGAL = _IMP_example.IMP_ALGEBRA_HAS_CGAL
302 IMP_ALGEBRA_HAS_ANN = _IMP_example.IMP_ALGEBRA_HAS_ANN
303 IMPALGEBRA_SHOW_WARNINGS = _IMP_example.IMPALGEBRA_SHOW_WARNINGS
305 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_example.IMP_DISPLAY_HAS_IMP_CGAL
306 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
307 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
308 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_example.IMP_DISPLAY_HAS_BOOST_RANDOM
309 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_example.IMP_DISPLAY_HAS_BOOST_SYSTEM
310 IMP_DISPLAY_HAS_CGAL = _IMP_example.IMP_DISPLAY_HAS_CGAL
311 IMPDISPLAY_SHOW_WARNINGS = _IMP_example.IMPDISPLAY_SHOW_WARNINGS
313 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_example.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
314 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
315 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
316 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
317 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
318 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_example.IMP_SCORE_FUNCTOR_HAS_CGAL
319 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_example.IMP_SCORE_FUNCTOR_HAS_HDF5
320 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_example.IMPSCOREFUNCTOR_SHOW_WARNINGS
322 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_example.IMP_STATISTICS_HAS_IMP_CGAL
323 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
324 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
325 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_example.IMP_STATISTICS_HAS_BOOST_RANDOM
326 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_example.IMP_STATISTICS_HAS_BOOST_SYSTEM
327 IMP_STATISTICS_HAS_CGAL = _IMP_example.IMP_STATISTICS_HAS_CGAL
328 IMPSTATISTICS_SHOW_WARNINGS = _IMP_example.IMPSTATISTICS_SHOW_WARNINGS
330 IMP_CORE_HAS_IMP_CGAL = _IMP_example.IMP_CORE_HAS_IMP_CGAL
331 IMP_CORE_HAS_IMP_KERNEL = _IMP_example.IMP_CORE_HAS_IMP_KERNEL
332 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CORE_HAS_BOOST_FILESYSTEM
333 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
334 IMP_CORE_HAS_BOOST_RANDOM = _IMP_example.IMP_CORE_HAS_BOOST_RANDOM
335 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_example.IMP_CORE_HAS_BOOST_SYSTEM
336 IMP_CORE_HAS_CGAL = _IMP_example.IMP_CORE_HAS_CGAL
337 IMP_CORE_HAS_HDF5 = _IMP_example.IMP_CORE_HAS_HDF5
338 IMPCORE_SHOW_WARNINGS = _IMP_example.IMPCORE_SHOW_WARNINGS
340 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_example.IMP_CONTAINER_HAS_IMP_ALGEBRA
341 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_example.IMP_CONTAINER_HAS_IMP_CGAL
342 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_example.IMP_CONTAINER_HAS_IMP_DISPLAY
343 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_example.IMP_CONTAINER_HAS_IMP_KERNEL
344 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
345 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
346 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
347 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_example.IMP_CONTAINER_HAS_BOOST_RANDOM
348 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_example.IMP_CONTAINER_HAS_BOOST_SYSTEM
349 IMP_CONTAINER_HAS_CGAL = _IMP_example.IMP_CONTAINER_HAS_CGAL
350 IMP_CONTAINER_HAS_HDF5 = _IMP_example.IMP_CONTAINER_HAS_HDF5
351 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_example.IMP_CONTAINER_HAS_PYTHON_IHM
352 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_example.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
353 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_example.IMP_CONTAINER_HAS_ROBIN_MAP
354 IMPCONTAINER_SHOW_WARNINGS = _IMP_example.IMPCONTAINER_SHOW_WARNINGS
356 IMP_ATOM_HAS_IMP_CGAL = _IMP_example.IMP_ATOM_HAS_IMP_CGAL
357 IMP_ATOM_HAS_IMP_KERNEL = _IMP_example.IMP_ATOM_HAS_IMP_KERNEL
358 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
359 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
360 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_example.IMP_ATOM_HAS_BOOST_RANDOM
361 IMP_ATOM_HAS_BOOST_REGEX = _IMP_example.IMP_ATOM_HAS_BOOST_REGEX
362 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_example.IMP_ATOM_HAS_BOOST_SYSTEM
363 IMP_ATOM_HAS_CGAL = _IMP_example.IMP_ATOM_HAS_CGAL
364 IMP_ATOM_HAS_HDF5 = _IMP_example.IMP_ATOM_HAS_HDF5
365 IMP_ATOM_HAS_PYTHON_IHM = _IMP_example.IMP_ATOM_HAS_PYTHON_IHM
366 IMPATOM_SHOW_WARNINGS = _IMP_example.IMPATOM_SHOW_WARNINGS
367 IMP_ATOM_TYPE_INDEX = _IMP_example.IMP_ATOM_TYPE_INDEX
368 IMP_RESIDUE_TYPE_INDEX = _IMP_example.IMP_RESIDUE_TYPE_INDEX
369 IMP_HIERARCHY_TYPE_INDEX = _IMP_example.IMP_HIERARCHY_TYPE_INDEX
370 IMP_CHAIN_TYPE_INDEX = _IMP_example.IMP_CHAIN_TYPE_INDEX
372 IMP_RMF_HAS_IMP_CGAL = _IMP_example.IMP_RMF_HAS_IMP_CGAL
373 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
374 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_RMF_HAS_BOOST_FILESYSTEM
375 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
376 IMP_RMF_HAS_BOOST_RANDOM = _IMP_example.IMP_RMF_HAS_BOOST_RANDOM
377 IMP_RMF_HAS_BOOST_REGEX = _IMP_example.IMP_RMF_HAS_BOOST_REGEX
378 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_example.IMP_RMF_HAS_BOOST_SYSTEM
379 IMP_RMF_HAS_CGAL = _IMP_example.IMP_RMF_HAS_CGAL
380 IMP_RMF_HAS_HDF5 = _IMP_example.IMP_RMF_HAS_HDF5
381 IMP_RMF_HAS_PYTHON_IHM = _IMP_example.IMP_RMF_HAS_PYTHON_IHM
382 IMPRMF_SHOW_WARNINGS = _IMP_example.IMPRMF_SHOW_WARNINGS
385 IMP_DOMINO_HAS_IMP_ATOM = _IMP_example.IMP_DOMINO_HAS_IMP_ATOM
386 IMP_DOMINO_HAS_IMP_CGAL = _IMP_example.IMP_DOMINO_HAS_IMP_CGAL
387 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_example.IMP_DOMINO_HAS_IMP_KERNEL
388 IMP_DOMINO_HAS_IMP_RMF = _IMP_example.IMP_DOMINO_HAS_IMP_RMF
389 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
390 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_DOMINO_HAS_BOOST_FILESYSTEM
391 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
392 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_example.IMP_DOMINO_HAS_BOOST_RANDOM
393 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_example.IMP_DOMINO_HAS_BOOST_REGEX
394 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_example.IMP_DOMINO_HAS_BOOST_SYSTEM
395 IMP_DOMINO_HAS_CGAL = _IMP_example.IMP_DOMINO_HAS_CGAL
396 IMP_DOMINO_HAS_HDF5 = _IMP_example.IMP_DOMINO_HAS_HDF5
397 IMP_DOMINO_HAS_RMF = _IMP_example.IMP_DOMINO_HAS_RMF
398 IMP_DOMINO_HAS_PYTHON_IHM = _IMP_example.IMP_DOMINO_HAS_PYTHON_IHM
399 IMPDOMINO_SHOW_WARNINGS = _IMP_example.IMPDOMINO_SHOW_WARNINGS
402 IMP_EXAMPLE_HAS_IMP_ALGEBRA = _IMP_example.IMP_EXAMPLE_HAS_IMP_ALGEBRA
403 IMP_EXAMPLE_HAS_IMP_CGAL = _IMP_example.IMP_EXAMPLE_HAS_IMP_CGAL
404 IMP_EXAMPLE_HAS_IMP_DISPLAY = _IMP_example.IMP_EXAMPLE_HAS_IMP_DISPLAY
405 IMP_EXAMPLE_HAS_IMP_KERNEL = _IMP_example.IMP_EXAMPLE_HAS_IMP_KERNEL
406 IMP_EXAMPLE_HAS_IMP_RMF = _IMP_example.IMP_EXAMPLE_HAS_IMP_RMF
407 IMP_EXAMPLE_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_EXAMPLE_HAS_IMP_SCORE_FUNCTOR
408 IMP_EXAMPLE_HAS_IMP_STATISTICS = _IMP_example.IMP_EXAMPLE_HAS_IMP_STATISTICS
409 IMP_EXAMPLE_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_FILESYSTEM
410 IMP_EXAMPLE_HAS_BOOST_GRAPH = _IMP_example.IMP_EXAMPLE_HAS_BOOST_GRAPH
411 IMP_EXAMPLE_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_EXAMPLE_HAS_BOOST_PROGRAMOPTIONS
412 IMP_EXAMPLE_HAS_BOOST_RANDOM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_RANDOM
413 IMP_EXAMPLE_HAS_BOOST_REGEX = _IMP_example.IMP_EXAMPLE_HAS_BOOST_REGEX
414 IMP_EXAMPLE_HAS_BOOST_SYSTEM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_SYSTEM
415 IMP_EXAMPLE_HAS_CGAL = _IMP_example.IMP_EXAMPLE_HAS_CGAL
416 IMP_EXAMPLE_HAS_HDF5 = _IMP_example.IMP_EXAMPLE_HAS_HDF5
417 IMP_EXAMPLE_HAS_RMF = _IMP_example.IMP_EXAMPLE_HAS_RMF
418 IMP_EXAMPLE_HAS_PYTHON_IHM = _IMP_example.IMP_EXAMPLE_HAS_PYTHON_IHM
419 IMP_EXAMPLE_HAS_EXAMPLEDEPENDENCY = _IMP_example.IMP_EXAMPLE_HAS_EXAMPLEDEPENDENCY
420 IMPEXAMPLE_SHOW_WARNINGS = _IMP_example.IMPEXAMPLE_SHOW_WARNINGS
422 _object_types.append(
"ExampleRestraint")
425 def _object_cast_to_ExampleRestraint(o):
426 """_object_cast_to_ExampleRestraint(Object o) -> ExampleRestraint"""
427 return _IMP_example._object_cast_to_ExampleRestraint(o)
429 def ExampleDecorators(l=[]):
430 return [ExampleDecorator(x)
for x
in l]
431 _plural_types.append(
"ExampleDecorators")
434 _value_types.append(
"ExampleDecorator")
437 _object_types.append(
"ExampleUnaryFunction")
440 def _object_cast_to_ExampleUnaryFunction(o):
441 """_object_cast_to_ExampleUnaryFunction(Object o) -> ExampleUnaryFunction"""
442 return _IMP_example._object_cast_to_ExampleUnaryFunction(o)
444 _object_types.append(
"ExampleSingletonModifier")
447 def _object_cast_to_ExampleSingletonModifier(o):
448 """_object_cast_to_ExampleSingletonModifier(Object o) -> ExampleSingletonModifier"""
449 return _IMP_example._object_cast_to_ExampleSingletonModifier(o)
451 _object_types.append(
"ExamplePairScore")
454 def _object_cast_to_ExamplePairScore(o):
455 """_object_cast_to_ExamplePairScore(Object o) -> ExamplePairScore"""
456 return _IMP_example._object_cast_to_ExamplePairScore(o)
458 _object_types.append(
"ExampleSubsetFilterTable")
461 def _object_cast_to_ExampleSubsetFilterTable(o):
462 """_object_cast_to_ExampleSubsetFilterTable(Object o) -> ExampleSubsetFilterTable"""
463 return _IMP_example._object_cast_to_ExampleSubsetFilterTable(o)
465 _object_types.append(
"ExampleConstraint")
468 def _object_cast_to_ExampleConstraint(o):
469 """_object_cast_to_ExampleConstraint(Object o) -> ExampleConstraint"""
470 return _IMP_example._object_cast_to_ExampleConstraint(o)
472 _object_types.append(
"ExampleObject")
475 def _object_cast_to_ExampleObject(o):
476 """_object_cast_to_ExampleObject(Object o) -> ExampleObject"""
477 return _IMP_example._object_cast_to_ExampleObject(o)
479 ExampleTemplateClass3Ds=list
480 _plural_types.append(
"ExampleTemplateClass3Ds")
481 _value_types.append(
"ExampleTemplateClass3D")
484 def create_model_and_particles():
489 for i
in range(0,100):
490 p = m.add_particle(
"p")
494 d.set_coordinates_are_optimized(
True)
500 """An example restraint written in Python.
501 This should be functionally equivalent to the C++ ExampleRestraint.
503 def __init__(self, m, p, k):
504 IMP.Restraint.__init__(self, m,
"PythonExampleRestraint%1%")
505 self.p, self.k = p, k
509 score = .5 * self.k * d.get_z() * d.get_z()
510 if sa.get_derivative_accumulator():
511 deriv = self.k * d.get_z()
512 d.add_to_derivative(2, deriv, sa.get_derivative_accumulator())
516 return [self.
get_model().get_particle(self.p)]
522 """An example PairScore written in Python.
523 This should be functionally equivalent to the C++ ExamplePairScore.
525 def __init__(self, x0, k):
526 IMP.PairScore.__init__(self)
527 self.x0, self.k = x0, k
532 diff = (d0.get_coordinates()
533 - d1.get_coordinates()).get_magnitude() - self.x0
534 score = .5 * self.k * diff * diff
537 delta = d0.get_coordinates() - d1.get_coordinates()
538 udelta = delta.get_unit_vector()
540 d0.add_to_derivatives(udelta * dv, da)
541 d1.add_to_derivatives(-udelta * dv, da)
551 """An example UnaryFunction written in Python.
552 This should be functionally equivalent to the C++ ExampleUnaryFunction.
554 def __init__(self, center, k):
555 IMP.UnaryFunction.__init__(self)
556 self.center, self.k = center, k
559 return (self.
evaluate(feature), self.k * (feature - self.center))
562 return .5 * self.k * (feature - self.center) * (feature - self.center)
568 """An example Constraint written in Python.
569 This should be functionally equivalent to the C++ ExampleConstraint.
574 def __init__(self, p):
575 IMP.Constraint.__init__(self, p.get_model(),
"ExampleConstraint%1%")
578 PythonExampleConstraint.k =
IMP.IntKey(
"Constraint key")
579 if not p.has_attribute(self.k):
580 p.add_attribute(self.k, 0)
582 def do_update_attributes(self):
583 self.p.set_value(self.k, self.p.get_value(self.k) + 1)
585 def do_update_derivatives(self, da):
598 """An example SingletonModifier written in Python.
599 This should be functionally equivalent to the C++
600 ExampleSingletonModifier.
603 def __init__(self, bb):
604 IMP.SingletonModifier.__init__(self,
"ExampleSingletonModifier%1%")
611 while d.get_coordinate(i) < self.bb.get_corner(0)[i]:
612 d.set_coordinate(i,d.get_coordinate(i) + \
613 (self.bb.get_corner(1)[i] - self.bb.get_corner(0)[i]))
614 while d.get_coordinate(i) > self.bb.get_corner(1)[i]:
615 d.set_coordinate(i,d.get_coordinate(i) - \
616 (self.bb.get_corner(1)[i] - self.bb.get_corner(0)[i]))
626 """Proxy of C++ IMP::example::ExampleRestraint class."""
628 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
630 def __init__(self, m, p, k):
631 """__init__(IMP::example::ExampleRestraint self, Model m, ParticleIndex p, double k) -> ExampleRestraint"""
632 this = _IMP_example.new_ExampleRestraint(m, p, k)
634 self.this.append(this)
635 except __builtin__.Exception:
638 def do_add_score_and_derivatives(self, sa):
639 """do_add_score_and_derivatives(ExampleRestraint self, ScoreAccumulator sa)"""
640 return _IMP_example.ExampleRestraint_do_add_score_and_derivatives(self, sa)
644 """do_get_inputs(ExampleRestraint self) -> IMP::ModelObjectsTemp"""
645 return _IMP_example.ExampleRestraint_do_get_inputs(self)
649 """get_version_info(ExampleRestraint self) -> VersionInfo"""
650 return _IMP_example.ExampleRestraint_get_version_info(self)
654 """__str__(ExampleRestraint self) -> std::string"""
655 return _IMP_example.ExampleRestraint___str__(self)
659 """__repr__(ExampleRestraint self) -> std::string"""
660 return _IMP_example.ExampleRestraint___repr__(self)
665 return _object_cast_to_ExampleRestraint(o)
667 ExampleRestraint_swigregister = _IMP_example.ExampleRestraint_swigregister
668 ExampleRestraint_swigregister(ExampleRestraint)
671 """Proxy of C++ IMP::example::ExampleDecorator class."""
673 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
675 def get_decorator_name(self):
676 """get_decorator_name(ExampleDecorator self) -> std::string"""
677 return _IMP_example.ExampleDecorator_get_decorator_name(self)
680 def set_decorator_name(self, nm):
681 """set_decorator_name(ExampleDecorator self, std::string nm)"""
682 return _IMP_example.ExampleDecorator_set_decorator_name(self, nm)
685 def __init__(self, *args):
687 __init__(IMP::example::ExampleDecorator self) -> ExampleDecorator
688 __init__(IMP::example::ExampleDecorator self, Model m, ParticleIndex id) -> ExampleDecorator
689 __init__(IMP::example::ExampleDecorator self, _ParticleAdaptor d) -> ExampleDecorator
691 this = _IMP_example.new_ExampleDecorator(*args)
693 self.this.append(this)
694 except __builtin__.Exception:
697 def get_is_setup(*args):
699 get_is_setup(Model m, ParticleIndex pi) -> bool
700 get_is_setup(_ParticleAdaptor p) -> bool
702 return _IMP_example.ExampleDecorator_get_is_setup(*args)
704 get_is_setup = staticmethod(get_is_setup)
706 def show(self, *args):
708 show(ExampleDecorator self, _ostream out)
709 show(ExampleDecorator self)
711 return _IMP_example.ExampleDecorator_show(self, *args)
714 def setup_particle(*args):
716 setup_particle(Model m, ParticleIndex pi, std::string name) -> ExampleDecorator
717 setup_particle(_ParticleAdaptor decorator, std::string name) -> ExampleDecorator
719 return _IMP_example.ExampleDecorator_setup_particle(*args)
721 setup_particle = staticmethod(setup_particle)
723 def add_attribute(self, *args):
725 add_attribute(ExampleDecorator self, FloatKey k, IMP::Float v, bool opt)
726 add_attribute(ExampleDecorator self, FloatKey a0, IMP::Float a1)
727 add_attribute(ExampleDecorator self, IntKey a0, IMP::Int a1)
728 add_attribute(ExampleDecorator self, StringKey a0, IMP::String a1)
729 add_attribute(ExampleDecorator self, ParticleIndexKey a0, Particle a1)
730 add_attribute(ExampleDecorator self, ObjectKey a0, Object a1)
732 return _IMP_example.ExampleDecorator_add_attribute(self, *args)
735 def get_value(self, *args):
737 get_value(ExampleDecorator self, FloatKey a0) -> IMP::Float
738 get_value(ExampleDecorator self, IntKey a0) -> IMP::Int
739 get_value(ExampleDecorator self, StringKey a0) -> IMP::String
740 get_value(ExampleDecorator self, ParticleIndexKey a0) -> Particle
741 get_value(ExampleDecorator self, ObjectKey a0) -> Object
743 return _IMP_example.ExampleDecorator_get_value(self, *args)
746 def set_value(self, *args):
748 set_value(ExampleDecorator self, FloatKey a0, IMP::Float a1)
749 set_value(ExampleDecorator self, IntKey a0, IMP::Int a1)
750 set_value(ExampleDecorator self, StringKey a0, IMP::String a1)
751 set_value(ExampleDecorator self, ParticleIndexKey a0, Particle a1)
752 set_value(ExampleDecorator self, ObjectKey a0, Object a1)
754 return _IMP_example.ExampleDecorator_set_value(self, *args)
757 def remove_attribute(self, *args):
759 remove_attribute(ExampleDecorator self, FloatKey a0)
760 remove_attribute(ExampleDecorator self, IntKey a0)
761 remove_attribute(ExampleDecorator self, StringKey a0)
762 remove_attribute(ExampleDecorator self, ParticleIndexKey a0)
763 remove_attribute(ExampleDecorator self, ObjectKey a0)
765 return _IMP_example.ExampleDecorator_remove_attribute(self, *args)
768 def has_attribute(self, *args):
770 has_attribute(ExampleDecorator self, FloatKey a0) -> bool
771 has_attribute(ExampleDecorator self, IntKey a0) -> bool
772 has_attribute(ExampleDecorator self, StringKey a0) -> bool
773 has_attribute(ExampleDecorator self, ParticleIndexKey a0) -> bool
774 has_attribute(ExampleDecorator self, ObjectKey a0) -> bool
776 return _IMP_example.ExampleDecorator_has_attribute(self, *args)
779 def get_derivative(self, a0):
780 """get_derivative(ExampleDecorator self, FloatKey a0) -> double"""
781 return _IMP_example.ExampleDecorator_get_derivative(self, a0)
785 """get_name(ExampleDecorator self) -> std::string"""
786 return _IMP_example.ExampleDecorator_get_name(self)
790 """clear_caches(ExampleDecorator self)"""
791 return _IMP_example.ExampleDecorator_clear_caches(self)
794 def set_name(self, a0):
795 """set_name(ExampleDecorator self, std::string a0)"""
796 return _IMP_example.ExampleDecorator_set_name(self, a0)
800 """set_check_level(ExampleDecorator self, IMP::CheckLevel a0)"""
801 return _IMP_example.ExampleDecorator_set_check_level(self, a0)
804 def add_to_derivative(self, a0, a1, a2):
805 """add_to_derivative(ExampleDecorator self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
806 return _IMP_example.ExampleDecorator_add_to_derivative(self, a0, a1, a2)
809 def set_is_optimized(self, a0, a1):
810 """set_is_optimized(ExampleDecorator self, FloatKey a0, bool a1)"""
811 return _IMP_example.ExampleDecorator_set_is_optimized(self, a0, a1)
814 def get_is_optimized(self, a0):
815 """get_is_optimized(ExampleDecorator self, FloatKey a0) -> bool"""
816 return _IMP_example.ExampleDecorator_get_is_optimized(self, a0)
819 def get_check_level(self):
820 """get_check_level(ExampleDecorator self) -> IMP::CheckLevel"""
821 return _IMP_example.ExampleDecorator_get_check_level(self)
824 def __eq__(self, *args):
826 __eq__(ExampleDecorator self, ExampleDecorator o) -> bool
827 __eq__(ExampleDecorator self, Particle d) -> bool
829 return _IMP_example.ExampleDecorator___eq__(self, *args)
832 def __ne__(self, *args):
834 __ne__(ExampleDecorator self, ExampleDecorator o) -> bool
835 __ne__(ExampleDecorator self, Particle d) -> bool
837 return _IMP_example.ExampleDecorator___ne__(self, *args)
840 def __le__(self, *args):
842 __le__(ExampleDecorator self, ExampleDecorator o) -> bool
843 __le__(ExampleDecorator self, Particle d) -> bool
845 return _IMP_example.ExampleDecorator___le__(self, *args)
848 def __lt__(self, *args):
850 __lt__(ExampleDecorator self, ExampleDecorator o) -> bool
851 __lt__(ExampleDecorator self, Particle d) -> bool
853 return _IMP_example.ExampleDecorator___lt__(self, *args)
856 def __ge__(self, *args):
858 __ge__(ExampleDecorator self, ExampleDecorator o) -> bool
859 __ge__(ExampleDecorator self, Particle d) -> bool
861 return _IMP_example.ExampleDecorator___ge__(self, *args)
864 def __gt__(self, *args):
866 __gt__(ExampleDecorator self, ExampleDecorator o) -> bool
867 __gt__(ExampleDecorator self, Particle d) -> bool
869 return _IMP_example.ExampleDecorator___gt__(self, *args)
873 """__hash__(ExampleDecorator self) -> std::size_t"""
874 return _IMP_example.ExampleDecorator___hash__(self)
878 """__str__(ExampleDecorator self) -> std::string"""
879 return _IMP_example.ExampleDecorator___str__(self)
883 """__repr__(ExampleDecorator self) -> std::string"""
884 return _IMP_example.ExampleDecorator___repr__(self)
886 __swig_destroy__ = _IMP_example.delete_ExampleDecorator
887 __del__ =
lambda self:
None
888 ExampleDecorator_swigregister = _IMP_example.ExampleDecorator_swigregister
889 ExampleDecorator_swigregister(ExampleDecorator)
891 def ExampleDecorator_get_is_setup(*args):
893 get_is_setup(Model m, ParticleIndex pi) -> bool
894 ExampleDecorator_get_is_setup(_ParticleAdaptor p) -> bool
896 return _IMP_example.ExampleDecorator_get_is_setup(*args)
898 def ExampleDecorator_setup_particle(*args):
900 setup_particle(Model m, ParticleIndex pi, std::string name) -> ExampleDecorator
901 ExampleDecorator_setup_particle(_ParticleAdaptor decorator, std::string name) -> ExampleDecorator
903 return _IMP_example.ExampleDecorator_setup_particle(*args)
906 def __lshift__(out, n):
907 """__lshift__(_ostream out, ExampleDecorator n) -> _ostream"""
908 return _IMP_example.__lshift__(out, n)
910 """Proxy of C++ IMP::example::ExampleUnaryFunction class."""
912 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
914 def __init__(self, center, k):
915 """__init__(IMP::example::ExampleUnaryFunction self, IMP::Float center, IMP::Float k) -> ExampleUnaryFunction"""
916 this = _IMP_example.new_ExampleUnaryFunction(center, k)
918 self.this.append(this)
919 except __builtin__.Exception:
923 """get_version_info(ExampleUnaryFunction self) -> VersionInfo"""
924 return _IMP_example.ExampleUnaryFunction_get_version_info(self)
928 """__str__(ExampleUnaryFunction self) -> std::string"""
929 return _IMP_example.ExampleUnaryFunction___str__(self)
933 """__repr__(ExampleUnaryFunction self) -> std::string"""
934 return _IMP_example.ExampleUnaryFunction___repr__(self)
939 return _object_cast_to_ExampleUnaryFunction(o)
941 ExampleUnaryFunction_swigregister = _IMP_example.ExampleUnaryFunction_swigregister
942 ExampleUnaryFunction_swigregister(ExampleUnaryFunction)
945 """Proxy of C++ IMP::example::ExampleObject class."""
947 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
949 def __init__(self, data):
950 """__init__(IMP::example::ExampleObject self, IMP::Floats const & data) -> ExampleObject"""
951 this = _IMP_example.new_ExampleObject(data)
953 self.this.append(this)
954 except __builtin__.Exception:
957 def get_data(self, i):
958 """get_data(ExampleObject self, unsigned int i) -> double"""
959 return _IMP_example.ExampleObject_get_data(self, i)
963 """get_version_info(ExampleObject self) -> VersionInfo"""
964 return _IMP_example.ExampleObject_get_version_info(self)
968 """__str__(ExampleObject self) -> std::string"""
969 return _IMP_example.ExampleObject___str__(self)
973 """__repr__(ExampleObject self) -> std::string"""
974 return _IMP_example.ExampleObject___repr__(self)
979 return _object_cast_to_ExampleObject(o)
981 ExampleObject_swigregister = _IMP_example.ExampleObject_swigregister
982 ExampleObject_swigregister(ExampleObject)
985 """Proxy of C++ IMP::example::ExampleSingletonModifier class."""
987 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
989 def __init__(self, bb):
990 """__init__(IMP::example::ExampleSingletonModifier self, BoundingBox3D bb) -> ExampleSingletonModifier"""
991 this = _IMP_example.new_ExampleSingletonModifier(bb)
993 self.this.append(this)
994 except __builtin__.Exception:
998 """do_get_inputs(ExampleSingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
999 return _IMP_example.ExampleSingletonModifier_do_get_inputs(self, m, pis)
1003 """do_get_outputs(ExampleSingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1004 return _IMP_example.ExampleSingletonModifier_do_get_outputs(self, m, pis)
1008 """get_version_info(ExampleSingletonModifier self) -> VersionInfo"""
1009 return _IMP_example.ExampleSingletonModifier_get_version_info(self)
1013 """__str__(ExampleSingletonModifier self) -> std::string"""
1014 return _IMP_example.ExampleSingletonModifier___str__(self)
1018 """__repr__(ExampleSingletonModifier self) -> std::string"""
1019 return _IMP_example.ExampleSingletonModifier___repr__(self)
1024 return _object_cast_to_ExampleSingletonModifier(o)
1026 ExampleSingletonModifier_swigregister = _IMP_example.ExampleSingletonModifier_swigregister
1027 ExampleSingletonModifier_swigregister(ExampleSingletonModifier)
1030 """Proxy of C++ IMP::example::ExamplePairScore class."""
1032 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1034 def __init__(self, x0, k):
1035 """__init__(IMP::example::ExamplePairScore self, double x0, double k) -> ExamplePairScore"""
1036 this = _IMP_example.new_ExamplePairScore(x0, k)
1038 self.this.append(this)
1039 except __builtin__.Exception:
1043 """do_get_inputs(ExamplePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1044 return _IMP_example.ExamplePairScore_do_get_inputs(self, m, pis)
1048 """get_version_info(ExamplePairScore self) -> VersionInfo"""
1049 return _IMP_example.ExamplePairScore_get_version_info(self)
1053 """__str__(ExamplePairScore self) -> std::string"""
1054 return _IMP_example.ExamplePairScore___str__(self)
1058 """__repr__(ExamplePairScore self) -> std::string"""
1059 return _IMP_example.ExamplePairScore___repr__(self)
1064 return _object_cast_to_ExamplePairScore(o)
1066 ExamplePairScore_swigregister = _IMP_example.ExamplePairScore_swigregister
1067 ExamplePairScore_swigregister(ExamplePairScore)
1070 """Proxy of C++ IMP::example::ExampleSubsetFilterTable class."""
1072 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1074 def __init__(self, max_diff, pt):
1075 """__init__(IMP::example::ExampleSubsetFilterTable self, unsigned int max_diff, IMP::ParticlesTemp const & pt) -> ExampleSubsetFilterTable"""
1076 this = _IMP_example.new_ExampleSubsetFilterTable(max_diff, pt)
1078 self.this.append(this)
1079 except __builtin__.Exception:
1083 """get_version_info(ExampleSubsetFilterTable self) -> VersionInfo"""
1084 return _IMP_example.ExampleSubsetFilterTable_get_version_info(self)
1088 """__str__(ExampleSubsetFilterTable self) -> std::string"""
1089 return _IMP_example.ExampleSubsetFilterTable___str__(self)
1093 """__repr__(ExampleSubsetFilterTable self) -> std::string"""
1094 return _IMP_example.ExampleSubsetFilterTable___repr__(self)
1099 return _object_cast_to_ExampleSubsetFilterTable(o)
1101 ExampleSubsetFilterTable_swigregister = _IMP_example.ExampleSubsetFilterTable_swigregister
1102 ExampleSubsetFilterTable_swigregister(ExampleSubsetFilterTable)
1105 """Proxy of C++ IMP::example::ExampleConstraint class."""
1107 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1109 def __init__(self, p):
1110 """__init__(IMP::example::ExampleConstraint self, Particle p) -> ExampleConstraint"""
1111 this = _IMP_example.new_ExampleConstraint(p)
1113 self.this.append(this)
1114 except __builtin__.Exception:
1118 """do_get_inputs(ExampleConstraint self) -> IMP::ModelObjectsTemp"""
1119 return _IMP_example.ExampleConstraint_do_get_inputs(self)
1123 """do_get_outputs(ExampleConstraint self) -> IMP::ModelObjectsTemp"""
1124 return _IMP_example.ExampleConstraint_do_get_outputs(self)
1128 """get_key() -> IntKey"""
1129 return _IMP_example.ExampleConstraint_get_key()
1131 get_key = staticmethod(get_key)
1134 """get_version_info(ExampleConstraint self) -> VersionInfo"""
1135 return _IMP_example.ExampleConstraint_get_version_info(self)
1139 """__str__(ExampleConstraint self) -> std::string"""
1140 return _IMP_example.ExampleConstraint___str__(self)
1144 """__repr__(ExampleConstraint self) -> std::string"""
1145 return _IMP_example.ExampleConstraint___repr__(self)
1150 return _object_cast_to_ExampleConstraint(o)
1152 ExampleConstraint_swigregister = _IMP_example.ExampleConstraint_swigregister
1153 ExampleConstraint_swigregister(ExampleConstraint)
1155 def ExampleConstraint_get_key():
1156 """ExampleConstraint_get_key() -> IntKey"""
1157 return _IMP_example.ExampleConstraint_get_key()
1161 """create_serial_mover(Model m, IMP::ParticleIndexes const & pis) -> MonteCarloMover"""
1162 return _IMP_example.create_serial_mover(m, pis)
1166 optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs, IMP::PairPredicates const & excluded, IMP::OptimizerStates const & opt_states, IMP::LogLevel ll)
1167 optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs, IMP::PairPredicates const & excluded, IMP::OptimizerStates const & opt_states)
1168 optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs, IMP::PairPredicates const & excluded)
1169 optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs)
1170 optimize_balls(Model m, IMP::ParticleIndexes const & pis)
1172 return _IMP_example.optimize_balls(*args)
1176 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)
1177 optimize_assembly(Model m, IMP::ParticleIndexes const & components, IMP::RestraintsTemp const & interactions, IMP::RestraintsTemp const & other_restraints, BoundingBox3D bb, PairScore ev, double cutoff)
1179 return _IMP_example.optimize_assembly(*args)
1182 """get_number_of_incidences(IMP::ParticlesTemp const & psa, IMP::ParticlesTemp const & psb, double point_distance) -> unsigned int"""
1183 return _IMP_example.get_number_of_incidences(psa, psb, point_distance)
1186 """create_chain_restraint(Model m, IMP::ParticleIndexes const & ps, double length_factor, double k, std::string name) -> Restraint"""
1187 return _IMP_example.create_chain_restraint(m, ps, length_factor, k, name)
1190 """create_excluded_volume(Model m, IMP::ParticleIndexes const & ps, double k, std::string name) -> Restraint"""
1191 return _IMP_example.create_excluded_volume(m, ps, k, name)
1193 """Proxy of C++ IMP::example::ExampleTemplateClassD<(3)> class."""
1195 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1197 def __init__(self, *args):
1199 __init__(IMP::example::ExampleTemplateClassD<(3)> self) -> ExampleTemplateClass3D
1200 __init__(IMP::example::ExampleTemplateClassD<(3)> self, Vector3D a, Vector3D b) -> ExampleTemplateClass3D
1202 this = _IMP_example.new_ExampleTemplateClass3D(*args)
1204 self.this.append(this)
1205 except __builtin__.Exception:
1208 def get_point(self, i):
1209 """get_point(ExampleTemplateClass3D self, unsigned int i) -> Vector3D"""
1210 return _IMP_example.ExampleTemplateClass3D_get_point(self, i)
1213 def show(self, *args):
1215 show(ExampleTemplateClass3D self, _ostream out)
1216 show(ExampleTemplateClass3D self)
1218 return _IMP_example.ExampleTemplateClass3D_show(self, *args)
1222 """__str__(ExampleTemplateClass3D self) -> std::string"""
1223 return _IMP_example.ExampleTemplateClass3D___str__(self)
1227 """__repr__(ExampleTemplateClass3D self) -> std::string"""
1228 return _IMP_example.ExampleTemplateClass3D___repr__(self)
1230 __swig_destroy__ = _IMP_example.delete_ExampleTemplateClass3D
1231 __del__ =
lambda self:
None
1232 ExampleTemplateClass3D_swigregister = _IMP_example.ExampleTemplateClass3D_swigregister
1233 ExampleTemplateClass3D_swigregister(ExampleTemplateClass3D)
1236 def get_module_version():
1237 """get_module_version() -> std::string const"""
1238 return _IMP_example.get_module_version()
1241 """get_example_path(std::string fname) -> std::string"""
1242 return _IMP_example.get_example_path(fname)
1245 """get_data_path(std::string fname) -> std::string"""
1246 return _IMP_example.get_data_path(fname)
1248 from .
import _version_check
1249 _version_check.check_version(get_module_version())
1250 __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.
Restraint * create_excluded_volume(Model *m, const ParticleIndexes &ps, double k, std::string name)
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.
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.