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_NUMPY = _IMP_example.IMP_KERNEL_HAS_NUMPY
239 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_example.IMP_KERNEL_HAS_GPERFTOOLS
240 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_example.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
241 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_example.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
242 IMPKERNEL_SHOW_WARNINGS = _IMP_example.IMPKERNEL_SHOW_WARNINGS
245 class _DirectorObjects(object):
246 """@internal Simple class to keep references to director objects
247 to prevent premature deletion."""
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)
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]
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()
270 class _ostream(object):
271 """Proxy of C++ std::ostream class."""
273 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
275 def __init__(self, *args, **kwargs):
276 raise AttributeError(
"No constructor defined")
277 __repr__ = _swig_repr
279 def write(self, osa_buf):
280 """write(_ostream self, char const * osa_buf)"""
281 return _IMP_example._ostream_write(self, osa_buf)
283 _ostream_swigregister = _IMP_example._ostream_swigregister
284 _ostream_swigregister(_ostream)
286 IMP_COMPILER_HAS_OVERRIDE = _IMP_example.IMP_COMPILER_HAS_OVERRIDE
287 IMP_COMPILER_HAS_FINAL = _IMP_example.IMP_COMPILER_HAS_FINAL
288 IMP_HAS_NOEXCEPT = _IMP_example.IMP_HAS_NOEXCEPT
289 IMP_C_OPEN_BINARY = _IMP_example.IMP_C_OPEN_BINARY
291 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CGAL_HAS_BOOST_FILESYSTEM
292 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
293 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_example.IMP_CGAL_HAS_BOOST_RANDOM
294 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_example.IMP_CGAL_HAS_BOOST_SYSTEM
295 IMP_CGAL_HAS_NUMPY = _IMP_example.IMP_CGAL_HAS_NUMPY
296 IMPCGAL_SHOW_WARNINGS = _IMP_example.IMPCGAL_SHOW_WARNINGS
298 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_example.IMP_ALGEBRA_HAS_IMP_CGAL
299 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
300 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
301 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_example.IMP_ALGEBRA_HAS_BOOST_RANDOM
302 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_example.IMP_ALGEBRA_HAS_BOOST_SYSTEM
303 IMP_ALGEBRA_HAS_CGAL = _IMP_example.IMP_ALGEBRA_HAS_CGAL
304 IMP_ALGEBRA_HAS_NUMPY = _IMP_example.IMP_ALGEBRA_HAS_NUMPY
305 IMP_ALGEBRA_HAS_ANN = _IMP_example.IMP_ALGEBRA_HAS_ANN
306 IMPALGEBRA_SHOW_WARNINGS = _IMP_example.IMPALGEBRA_SHOW_WARNINGS
308 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_example.IMP_DISPLAY_HAS_IMP_CGAL
309 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
310 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
311 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_example.IMP_DISPLAY_HAS_BOOST_RANDOM
312 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_example.IMP_DISPLAY_HAS_BOOST_SYSTEM
313 IMP_DISPLAY_HAS_CGAL = _IMP_example.IMP_DISPLAY_HAS_CGAL
314 IMP_DISPLAY_HAS_NUMPY = _IMP_example.IMP_DISPLAY_HAS_NUMPY
315 IMPDISPLAY_SHOW_WARNINGS = _IMP_example.IMPDISPLAY_SHOW_WARNINGS
317 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_example.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
318 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
319 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
320 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
321 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
322 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_example.IMP_SCORE_FUNCTOR_HAS_CGAL
323 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_example.IMP_SCORE_FUNCTOR_HAS_HDF5
324 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_example.IMP_SCORE_FUNCTOR_HAS_NUMPY
325 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_example.IMPSCOREFUNCTOR_SHOW_WARNINGS
327 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_example.IMP_STATISTICS_HAS_IMP_CGAL
328 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
329 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
330 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_example.IMP_STATISTICS_HAS_BOOST_RANDOM
331 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_example.IMP_STATISTICS_HAS_BOOST_SYSTEM
332 IMP_STATISTICS_HAS_CGAL = _IMP_example.IMP_STATISTICS_HAS_CGAL
333 IMP_STATISTICS_HAS_NUMPY = _IMP_example.IMP_STATISTICS_HAS_NUMPY
334 IMPSTATISTICS_SHOW_WARNINGS = _IMP_example.IMPSTATISTICS_SHOW_WARNINGS
336 IMP_CORE_HAS_IMP_CGAL = _IMP_example.IMP_CORE_HAS_IMP_CGAL
337 IMP_CORE_HAS_IMP_KERNEL = _IMP_example.IMP_CORE_HAS_IMP_KERNEL
338 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CORE_HAS_BOOST_FILESYSTEM
339 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
340 IMP_CORE_HAS_BOOST_RANDOM = _IMP_example.IMP_CORE_HAS_BOOST_RANDOM
341 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_example.IMP_CORE_HAS_BOOST_SYSTEM
342 IMP_CORE_HAS_CGAL = _IMP_example.IMP_CORE_HAS_CGAL
343 IMP_CORE_HAS_HDF5 = _IMP_example.IMP_CORE_HAS_HDF5
344 IMP_CORE_HAS_NUMPY = _IMP_example.IMP_CORE_HAS_NUMPY
345 IMPCORE_SHOW_WARNINGS = _IMP_example.IMPCORE_SHOW_WARNINGS
347 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_example.IMP_CONTAINER_HAS_IMP_ALGEBRA
348 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_example.IMP_CONTAINER_HAS_IMP_CGAL
349 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_example.IMP_CONTAINER_HAS_IMP_DISPLAY
350 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_example.IMP_CONTAINER_HAS_IMP_KERNEL
351 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
352 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
353 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
354 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_example.IMP_CONTAINER_HAS_BOOST_RANDOM
355 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_example.IMP_CONTAINER_HAS_BOOST_SYSTEM
356 IMP_CONTAINER_HAS_CGAL = _IMP_example.IMP_CONTAINER_HAS_CGAL
357 IMP_CONTAINER_HAS_HDF5 = _IMP_example.IMP_CONTAINER_HAS_HDF5
358 IMP_CONTAINER_HAS_NUMPY = _IMP_example.IMP_CONTAINER_HAS_NUMPY
359 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_example.IMP_CONTAINER_HAS_PYTHON_IHM
360 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_example.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
361 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_example.IMP_CONTAINER_HAS_ROBIN_MAP
362 IMPCONTAINER_SHOW_WARNINGS = _IMP_example.IMPCONTAINER_SHOW_WARNINGS
364 IMP_ATOM_HAS_IMP_CGAL = _IMP_example.IMP_ATOM_HAS_IMP_CGAL
365 IMP_ATOM_HAS_IMP_KERNEL = _IMP_example.IMP_ATOM_HAS_IMP_KERNEL
366 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
367 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
368 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_example.IMP_ATOM_HAS_BOOST_RANDOM
369 IMP_ATOM_HAS_BOOST_REGEX = _IMP_example.IMP_ATOM_HAS_BOOST_REGEX
370 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_example.IMP_ATOM_HAS_BOOST_SYSTEM
371 IMP_ATOM_HAS_CGAL = _IMP_example.IMP_ATOM_HAS_CGAL
372 IMP_ATOM_HAS_HDF5 = _IMP_example.IMP_ATOM_HAS_HDF5
373 IMP_ATOM_HAS_NUMPY = _IMP_example.IMP_ATOM_HAS_NUMPY
374 IMP_ATOM_HAS_PYTHON_IHM = _IMP_example.IMP_ATOM_HAS_PYTHON_IHM
375 IMPATOM_SHOW_WARNINGS = _IMP_example.IMPATOM_SHOW_WARNINGS
376 IMP_ATOM_TYPE_INDEX = _IMP_example.IMP_ATOM_TYPE_INDEX
377 IMP_RESIDUE_TYPE_INDEX = _IMP_example.IMP_RESIDUE_TYPE_INDEX
378 IMP_HIERARCHY_TYPE_INDEX = _IMP_example.IMP_HIERARCHY_TYPE_INDEX
379 IMP_CHAIN_TYPE_INDEX = _IMP_example.IMP_CHAIN_TYPE_INDEX
381 IMP_RMF_HAS_IMP_CGAL = _IMP_example.IMP_RMF_HAS_IMP_CGAL
382 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
383 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_RMF_HAS_BOOST_FILESYSTEM
384 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
385 IMP_RMF_HAS_BOOST_RANDOM = _IMP_example.IMP_RMF_HAS_BOOST_RANDOM
386 IMP_RMF_HAS_BOOST_REGEX = _IMP_example.IMP_RMF_HAS_BOOST_REGEX
387 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_example.IMP_RMF_HAS_BOOST_SYSTEM
388 IMP_RMF_HAS_CGAL = _IMP_example.IMP_RMF_HAS_CGAL
389 IMP_RMF_HAS_HDF5 = _IMP_example.IMP_RMF_HAS_HDF5
390 IMP_RMF_HAS_NUMPY = _IMP_example.IMP_RMF_HAS_NUMPY
391 IMP_RMF_HAS_PYTHON_IHM = _IMP_example.IMP_RMF_HAS_PYTHON_IHM
392 IMPRMF_SHOW_WARNINGS = _IMP_example.IMPRMF_SHOW_WARNINGS
395 IMP_DOMINO_HAS_IMP_ATOM = _IMP_example.IMP_DOMINO_HAS_IMP_ATOM
396 IMP_DOMINO_HAS_IMP_CGAL = _IMP_example.IMP_DOMINO_HAS_IMP_CGAL
397 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_example.IMP_DOMINO_HAS_IMP_KERNEL
398 IMP_DOMINO_HAS_IMP_RMF = _IMP_example.IMP_DOMINO_HAS_IMP_RMF
399 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
400 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_DOMINO_HAS_BOOST_FILESYSTEM
401 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
402 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_example.IMP_DOMINO_HAS_BOOST_RANDOM
403 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_example.IMP_DOMINO_HAS_BOOST_REGEX
404 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_example.IMP_DOMINO_HAS_BOOST_SYSTEM
405 IMP_DOMINO_HAS_CGAL = _IMP_example.IMP_DOMINO_HAS_CGAL
406 IMP_DOMINO_HAS_HDF5 = _IMP_example.IMP_DOMINO_HAS_HDF5
407 IMP_DOMINO_HAS_NUMPY = _IMP_example.IMP_DOMINO_HAS_NUMPY
408 IMP_DOMINO_HAS_RMF = _IMP_example.IMP_DOMINO_HAS_RMF
409 IMP_DOMINO_HAS_PYTHON_IHM = _IMP_example.IMP_DOMINO_HAS_PYTHON_IHM
410 IMPDOMINO_SHOW_WARNINGS = _IMP_example.IMPDOMINO_SHOW_WARNINGS
413 IMP_EXAMPLE_HAS_IMP_ALGEBRA = _IMP_example.IMP_EXAMPLE_HAS_IMP_ALGEBRA
414 IMP_EXAMPLE_HAS_IMP_CGAL = _IMP_example.IMP_EXAMPLE_HAS_IMP_CGAL
415 IMP_EXAMPLE_HAS_IMP_DISPLAY = _IMP_example.IMP_EXAMPLE_HAS_IMP_DISPLAY
416 IMP_EXAMPLE_HAS_IMP_KERNEL = _IMP_example.IMP_EXAMPLE_HAS_IMP_KERNEL
417 IMP_EXAMPLE_HAS_IMP_RMF = _IMP_example.IMP_EXAMPLE_HAS_IMP_RMF
418 IMP_EXAMPLE_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_EXAMPLE_HAS_IMP_SCORE_FUNCTOR
419 IMP_EXAMPLE_HAS_IMP_STATISTICS = _IMP_example.IMP_EXAMPLE_HAS_IMP_STATISTICS
420 IMP_EXAMPLE_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_FILESYSTEM
421 IMP_EXAMPLE_HAS_BOOST_GRAPH = _IMP_example.IMP_EXAMPLE_HAS_BOOST_GRAPH
422 IMP_EXAMPLE_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_EXAMPLE_HAS_BOOST_PROGRAMOPTIONS
423 IMP_EXAMPLE_HAS_BOOST_RANDOM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_RANDOM
424 IMP_EXAMPLE_HAS_BOOST_REGEX = _IMP_example.IMP_EXAMPLE_HAS_BOOST_REGEX
425 IMP_EXAMPLE_HAS_BOOST_SYSTEM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_SYSTEM
426 IMP_EXAMPLE_HAS_CGAL = _IMP_example.IMP_EXAMPLE_HAS_CGAL
427 IMP_EXAMPLE_HAS_HDF5 = _IMP_example.IMP_EXAMPLE_HAS_HDF5
428 IMP_EXAMPLE_HAS_NUMPY = _IMP_example.IMP_EXAMPLE_HAS_NUMPY
429 IMP_EXAMPLE_HAS_RMF = _IMP_example.IMP_EXAMPLE_HAS_RMF
430 IMP_EXAMPLE_HAS_PYTHON_IHM = _IMP_example.IMP_EXAMPLE_HAS_PYTHON_IHM
431 IMP_EXAMPLE_HAS_EXAMPLEDEPENDENCY = _IMP_example.IMP_EXAMPLE_HAS_EXAMPLEDEPENDENCY
432 IMPEXAMPLE_SHOW_WARNINGS = _IMP_example.IMPEXAMPLE_SHOW_WARNINGS
434 _object_types.append(
"ExampleRestraint")
437 def _object_cast_to_ExampleRestraint(o):
438 """_object_cast_to_ExampleRestraint(Object o) -> ExampleRestraint"""
439 return _IMP_example._object_cast_to_ExampleRestraint(o)
441 def ExampleDecorators(l=[]):
442 return [ExampleDecorator(x)
for x
in l]
443 _plural_types.append(
"ExampleDecorators")
446 _value_types.append(
"ExampleDecorator")
449 _object_types.append(
"ExampleUnaryFunction")
452 def _object_cast_to_ExampleUnaryFunction(o):
453 """_object_cast_to_ExampleUnaryFunction(Object o) -> ExampleUnaryFunction"""
454 return _IMP_example._object_cast_to_ExampleUnaryFunction(o)
456 _object_types.append(
"ExampleSingletonModifier")
459 def _object_cast_to_ExampleSingletonModifier(o):
460 """_object_cast_to_ExampleSingletonModifier(Object o) -> ExampleSingletonModifier"""
461 return _IMP_example._object_cast_to_ExampleSingletonModifier(o)
463 _object_types.append(
"ExamplePairScore")
466 def _object_cast_to_ExamplePairScore(o):
467 """_object_cast_to_ExamplePairScore(Object o) -> ExamplePairScore"""
468 return _IMP_example._object_cast_to_ExamplePairScore(o)
470 _object_types.append(
"ExampleSubsetFilterTable")
473 def _object_cast_to_ExampleSubsetFilterTable(o):
474 """_object_cast_to_ExampleSubsetFilterTable(Object o) -> ExampleSubsetFilterTable"""
475 return _IMP_example._object_cast_to_ExampleSubsetFilterTable(o)
477 _object_types.append(
"ExampleConstraint")
480 def _object_cast_to_ExampleConstraint(o):
481 """_object_cast_to_ExampleConstraint(Object o) -> ExampleConstraint"""
482 return _IMP_example._object_cast_to_ExampleConstraint(o)
484 _object_types.append(
"ExampleObject")
487 def _object_cast_to_ExampleObject(o):
488 """_object_cast_to_ExampleObject(Object o) -> ExampleObject"""
489 return _IMP_example._object_cast_to_ExampleObject(o)
491 ExampleTemplateClass3Ds=list
492 _plural_types.append(
"ExampleTemplateClass3Ds")
493 _value_types.append(
"ExampleTemplateClass3D")
496 def create_model_and_particles():
501 for i
in range(0,100):
502 p = m.add_particle(
"p")
506 d.set_coordinates_are_optimized(
True)
512 """An example restraint written in Python.
513 This should be functionally equivalent to the C++ ExampleRestraint.
515 def __init__(self, m, p, k):
516 IMP.Restraint.__init__(self, m,
"PythonExampleRestraint%1%")
517 self.p, self.k = p, k
521 score = .5 * self.k * d.get_z() * d.get_z()
522 if sa.get_derivative_accumulator():
523 deriv = self.k * d.get_z()
524 d.add_to_derivative(2, deriv, sa.get_derivative_accumulator())
528 return [self.
get_model().get_particle(self.p)]
534 """An example PairScore written in Python.
535 This should be functionally equivalent to the C++ ExamplePairScore.
537 def __init__(self, x0, k):
538 IMP.PairScore.__init__(self)
539 self.x0, self.k = x0, k
544 diff = (d0.get_coordinates()
545 - d1.get_coordinates()).get_magnitude() - self.x0
546 score = .5 * self.k * diff * diff
549 delta = d0.get_coordinates() - d1.get_coordinates()
550 udelta = delta.get_unit_vector()
552 d0.add_to_derivatives(udelta * dv, da)
553 d1.add_to_derivatives(-udelta * dv, da)
563 """An example UnaryFunction written in Python.
564 This should be functionally equivalent to the C++ ExampleUnaryFunction.
566 def __init__(self, center, k):
567 IMP.UnaryFunction.__init__(self)
568 self.center, self.k = center, k
571 return (self.
evaluate(feature), self.k * (feature - self.center))
574 return .5 * self.k * (feature - self.center) * (feature - self.center)
580 """An example Constraint written in Python.
581 This should be functionally equivalent to the C++ ExampleConstraint.
586 def __init__(self, p):
587 IMP.Constraint.__init__(self, p.get_model(),
"ExampleConstraint%1%")
590 PythonExampleConstraint.k =
IMP.IntKey(
"Constraint key")
591 if not p.has_attribute(self.k):
592 p.add_attribute(self.k, 0)
594 def do_update_attributes(self):
595 self.p.set_value(self.k, self.p.get_value(self.k) + 1)
597 def do_update_derivatives(self, da):
610 """An example SingletonModifier written in Python.
611 This should be functionally equivalent to the C++
612 ExampleSingletonModifier.
615 def __init__(self, bb):
616 IMP.SingletonModifier.__init__(self,
"ExampleSingletonModifier%1%")
623 while d.get_coordinate(i) < self.bb.get_corner(0)[i]:
624 d.set_coordinate(i,d.get_coordinate(i) + \
625 (self.bb.get_corner(1)[i] - self.bb.get_corner(0)[i]))
626 while d.get_coordinate(i) > self.bb.get_corner(1)[i]:
627 d.set_coordinate(i,d.get_coordinate(i) - \
628 (self.bb.get_corner(1)[i] - self.bb.get_corner(0)[i]))
638 """Proxy of C++ IMP::example::ExampleRestraint class."""
640 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
642 def __init__(self, m, p, k):
643 """__init__(IMP::example::ExampleRestraint self, Model m, ParticleIndex p, double k) -> ExampleRestraint"""
644 this = _IMP_example.new_ExampleRestraint(m, p, k)
646 self.this.append(this)
647 except __builtin__.Exception:
650 def do_add_score_and_derivatives(self, sa):
651 """do_add_score_and_derivatives(ExampleRestraint self, ScoreAccumulator sa)"""
652 return _IMP_example.ExampleRestraint_do_add_score_and_derivatives(self, sa)
656 """do_get_inputs(ExampleRestraint self) -> IMP::ModelObjectsTemp"""
657 return _IMP_example.ExampleRestraint_do_get_inputs(self)
661 """get_version_info(ExampleRestraint self) -> VersionInfo"""
662 return _IMP_example.ExampleRestraint_get_version_info(self)
666 """__str__(ExampleRestraint self) -> std::string"""
667 return _IMP_example.ExampleRestraint___str__(self)
671 """__repr__(ExampleRestraint self) -> std::string"""
672 return _IMP_example.ExampleRestraint___repr__(self)
677 return _object_cast_to_ExampleRestraint(o)
679 ExampleRestraint_swigregister = _IMP_example.ExampleRestraint_swigregister
680 ExampleRestraint_swigregister(ExampleRestraint)
683 """Proxy of C++ IMP::example::ExampleDecorator class."""
685 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
687 def get_decorator_name(self):
688 """get_decorator_name(ExampleDecorator self) -> std::string"""
689 return _IMP_example.ExampleDecorator_get_decorator_name(self)
692 def set_decorator_name(self, nm):
693 """set_decorator_name(ExampleDecorator self, std::string nm)"""
694 return _IMP_example.ExampleDecorator_set_decorator_name(self, nm)
697 def __init__(self, *args):
699 __init__(IMP::example::ExampleDecorator self) -> ExampleDecorator
700 __init__(IMP::example::ExampleDecorator self, Model m, ParticleIndex id) -> ExampleDecorator
701 __init__(IMP::example::ExampleDecorator self, _ParticleAdaptor d) -> ExampleDecorator
703 this = _IMP_example.new_ExampleDecorator(*args)
705 self.this.append(this)
706 except __builtin__.Exception:
709 def get_is_setup(*args):
711 get_is_setup(Model m, ParticleIndex pi) -> bool
712 get_is_setup(_ParticleAdaptor p) -> bool
714 return _IMP_example.ExampleDecorator_get_is_setup(*args)
716 get_is_setup = staticmethod(get_is_setup)
718 def show(self, *args):
720 show(ExampleDecorator self, _ostream out)
721 show(ExampleDecorator self)
723 return _IMP_example.ExampleDecorator_show(self, *args)
726 def setup_particle(*args):
728 setup_particle(Model m, ParticleIndex pi, std::string name) -> ExampleDecorator
729 setup_particle(_ParticleAdaptor decorator, std::string name) -> ExampleDecorator
731 return _IMP_example.ExampleDecorator_setup_particle(*args)
733 setup_particle = staticmethod(setup_particle)
735 def add_attribute(self, *args):
737 add_attribute(ExampleDecorator self, FloatKey k, IMP::Float v, bool opt)
738 add_attribute(ExampleDecorator self, FloatKey a0, IMP::Float a1)
739 add_attribute(ExampleDecorator self, IntKey a0, IMP::Int a1)
740 add_attribute(ExampleDecorator self, StringKey a0, IMP::String a1)
741 add_attribute(ExampleDecorator self, ParticleIndexKey a0, Particle a1)
742 add_attribute(ExampleDecorator self, ObjectKey a0, Object a1)
744 return _IMP_example.ExampleDecorator_add_attribute(self, *args)
747 def get_value(self, *args):
749 get_value(ExampleDecorator self, FloatKey a0) -> IMP::Float
750 get_value(ExampleDecorator self, IntKey a0) -> IMP::Int
751 get_value(ExampleDecorator self, StringKey a0) -> IMP::String
752 get_value(ExampleDecorator self, ParticleIndexKey a0) -> Particle
753 get_value(ExampleDecorator self, ObjectKey a0) -> Object
755 return _IMP_example.ExampleDecorator_get_value(self, *args)
758 def set_value(self, *args):
760 set_value(ExampleDecorator self, FloatKey a0, IMP::Float a1)
761 set_value(ExampleDecorator self, IntKey a0, IMP::Int a1)
762 set_value(ExampleDecorator self, StringKey a0, IMP::String a1)
763 set_value(ExampleDecorator self, ParticleIndexKey a0, Particle a1)
764 set_value(ExampleDecorator self, ObjectKey a0, Object a1)
766 return _IMP_example.ExampleDecorator_set_value(self, *args)
769 def remove_attribute(self, *args):
771 remove_attribute(ExampleDecorator self, FloatKey a0)
772 remove_attribute(ExampleDecorator self, IntKey a0)
773 remove_attribute(ExampleDecorator self, StringKey a0)
774 remove_attribute(ExampleDecorator self, ParticleIndexKey a0)
775 remove_attribute(ExampleDecorator self, ObjectKey a0)
777 return _IMP_example.ExampleDecorator_remove_attribute(self, *args)
780 def has_attribute(self, *args):
782 has_attribute(ExampleDecorator self, FloatKey a0) -> bool
783 has_attribute(ExampleDecorator self, IntKey a0) -> bool
784 has_attribute(ExampleDecorator self, StringKey a0) -> bool
785 has_attribute(ExampleDecorator self, ParticleIndexKey a0) -> bool
786 has_attribute(ExampleDecorator self, ObjectKey a0) -> bool
788 return _IMP_example.ExampleDecorator_has_attribute(self, *args)
791 def get_derivative(self, a0):
792 """get_derivative(ExampleDecorator self, FloatKey a0) -> double"""
793 return _IMP_example.ExampleDecorator_get_derivative(self, a0)
797 """get_name(ExampleDecorator self) -> std::string"""
798 return _IMP_example.ExampleDecorator_get_name(self)
802 """clear_caches(ExampleDecorator self)"""
803 return _IMP_example.ExampleDecorator_clear_caches(self)
806 def set_name(self, a0):
807 """set_name(ExampleDecorator self, std::string a0)"""
808 return _IMP_example.ExampleDecorator_set_name(self, a0)
812 """set_check_level(ExampleDecorator self, IMP::CheckLevel a0)"""
813 return _IMP_example.ExampleDecorator_set_check_level(self, a0)
816 def add_to_derivative(self, a0, a1, a2):
817 """add_to_derivative(ExampleDecorator self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
818 return _IMP_example.ExampleDecorator_add_to_derivative(self, a0, a1, a2)
821 def set_is_optimized(self, a0, a1):
822 """set_is_optimized(ExampleDecorator self, FloatKey a0, bool a1)"""
823 return _IMP_example.ExampleDecorator_set_is_optimized(self, a0, a1)
826 def get_is_optimized(self, a0):
827 """get_is_optimized(ExampleDecorator self, FloatKey a0) -> bool"""
828 return _IMP_example.ExampleDecorator_get_is_optimized(self, a0)
831 def get_check_level(self):
832 """get_check_level(ExampleDecorator self) -> IMP::CheckLevel"""
833 return _IMP_example.ExampleDecorator_get_check_level(self)
836 def __eq__(self, *args):
838 __eq__(ExampleDecorator self, ExampleDecorator o) -> bool
839 __eq__(ExampleDecorator self, Particle d) -> bool
841 return _IMP_example.ExampleDecorator___eq__(self, *args)
844 def __ne__(self, *args):
846 __ne__(ExampleDecorator self, ExampleDecorator o) -> bool
847 __ne__(ExampleDecorator self, Particle d) -> bool
849 return _IMP_example.ExampleDecorator___ne__(self, *args)
852 def __le__(self, *args):
854 __le__(ExampleDecorator self, ExampleDecorator o) -> bool
855 __le__(ExampleDecorator self, Particle d) -> bool
857 return _IMP_example.ExampleDecorator___le__(self, *args)
860 def __lt__(self, *args):
862 __lt__(ExampleDecorator self, ExampleDecorator o) -> bool
863 __lt__(ExampleDecorator self, Particle d) -> bool
865 return _IMP_example.ExampleDecorator___lt__(self, *args)
868 def __ge__(self, *args):
870 __ge__(ExampleDecorator self, ExampleDecorator o) -> bool
871 __ge__(ExampleDecorator self, Particle d) -> bool
873 return _IMP_example.ExampleDecorator___ge__(self, *args)
876 def __gt__(self, *args):
878 __gt__(ExampleDecorator self, ExampleDecorator o) -> bool
879 __gt__(ExampleDecorator self, Particle d) -> bool
881 return _IMP_example.ExampleDecorator___gt__(self, *args)
885 """__hash__(ExampleDecorator self) -> std::size_t"""
886 return _IMP_example.ExampleDecorator___hash__(self)
890 """__str__(ExampleDecorator self) -> std::string"""
891 return _IMP_example.ExampleDecorator___str__(self)
895 """__repr__(ExampleDecorator self) -> std::string"""
896 return _IMP_example.ExampleDecorator___repr__(self)
898 __swig_destroy__ = _IMP_example.delete_ExampleDecorator
899 __del__ =
lambda self:
None
900 ExampleDecorator_swigregister = _IMP_example.ExampleDecorator_swigregister
901 ExampleDecorator_swigregister(ExampleDecorator)
903 def ExampleDecorator_get_is_setup(*args):
905 get_is_setup(Model m, ParticleIndex pi) -> bool
906 ExampleDecorator_get_is_setup(_ParticleAdaptor p) -> bool
908 return _IMP_example.ExampleDecorator_get_is_setup(*args)
910 def ExampleDecorator_setup_particle(*args):
912 setup_particle(Model m, ParticleIndex pi, std::string name) -> ExampleDecorator
913 ExampleDecorator_setup_particle(_ParticleAdaptor decorator, std::string name) -> ExampleDecorator
915 return _IMP_example.ExampleDecorator_setup_particle(*args)
918 def __lshift__(out, n):
919 """__lshift__(_ostream out, ExampleDecorator n) -> _ostream"""
920 return _IMP_example.__lshift__(out, n)
922 """Proxy of C++ IMP::example::ExampleUnaryFunction class."""
924 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
926 def __init__(self, center, k):
927 """__init__(IMP::example::ExampleUnaryFunction self, IMP::Float center, IMP::Float k) -> ExampleUnaryFunction"""
928 this = _IMP_example.new_ExampleUnaryFunction(center, k)
930 self.this.append(this)
931 except __builtin__.Exception:
935 """get_version_info(ExampleUnaryFunction self) -> VersionInfo"""
936 return _IMP_example.ExampleUnaryFunction_get_version_info(self)
940 """__str__(ExampleUnaryFunction self) -> std::string"""
941 return _IMP_example.ExampleUnaryFunction___str__(self)
945 """__repr__(ExampleUnaryFunction self) -> std::string"""
946 return _IMP_example.ExampleUnaryFunction___repr__(self)
951 return _object_cast_to_ExampleUnaryFunction(o)
953 ExampleUnaryFunction_swigregister = _IMP_example.ExampleUnaryFunction_swigregister
954 ExampleUnaryFunction_swigregister(ExampleUnaryFunction)
957 """Proxy of C++ IMP::example::ExampleObject class."""
959 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
961 def __init__(self, data):
962 """__init__(IMP::example::ExampleObject self, IMP::Floats const & data) -> ExampleObject"""
963 this = _IMP_example.new_ExampleObject(data)
965 self.this.append(this)
966 except __builtin__.Exception:
969 def get_data(self, i):
970 """get_data(ExampleObject self, unsigned int i) -> double"""
971 return _IMP_example.ExampleObject_get_data(self, i)
975 """get_version_info(ExampleObject self) -> VersionInfo"""
976 return _IMP_example.ExampleObject_get_version_info(self)
980 """__str__(ExampleObject self) -> std::string"""
981 return _IMP_example.ExampleObject___str__(self)
985 """__repr__(ExampleObject self) -> std::string"""
986 return _IMP_example.ExampleObject___repr__(self)
991 return _object_cast_to_ExampleObject(o)
993 ExampleObject_swigregister = _IMP_example.ExampleObject_swigregister
994 ExampleObject_swigregister(ExampleObject)
997 """Proxy of C++ IMP::example::ExampleSingletonModifier class."""
999 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1001 def __init__(self, bb):
1002 """__init__(IMP::example::ExampleSingletonModifier self, BoundingBox3D bb) -> ExampleSingletonModifier"""
1003 this = _IMP_example.new_ExampleSingletonModifier(bb)
1005 self.this.append(this)
1006 except __builtin__.Exception:
1010 """do_get_inputs(ExampleSingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1011 return _IMP_example.ExampleSingletonModifier_do_get_inputs(self, m, pis)
1015 """do_get_outputs(ExampleSingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1016 return _IMP_example.ExampleSingletonModifier_do_get_outputs(self, m, pis)
1020 """get_version_info(ExampleSingletonModifier self) -> VersionInfo"""
1021 return _IMP_example.ExampleSingletonModifier_get_version_info(self)
1025 """__str__(ExampleSingletonModifier self) -> std::string"""
1026 return _IMP_example.ExampleSingletonModifier___str__(self)
1030 """__repr__(ExampleSingletonModifier self) -> std::string"""
1031 return _IMP_example.ExampleSingletonModifier___repr__(self)
1036 return _object_cast_to_ExampleSingletonModifier(o)
1038 ExampleSingletonModifier_swigregister = _IMP_example.ExampleSingletonModifier_swigregister
1039 ExampleSingletonModifier_swigregister(ExampleSingletonModifier)
1042 """Proxy of C++ IMP::example::ExamplePairScore class."""
1044 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1046 def __init__(self, x0, k):
1047 """__init__(IMP::example::ExamplePairScore self, double x0, double k) -> ExamplePairScore"""
1048 this = _IMP_example.new_ExamplePairScore(x0, k)
1050 self.this.append(this)
1051 except __builtin__.Exception:
1055 """do_get_inputs(ExamplePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1056 return _IMP_example.ExamplePairScore_do_get_inputs(self, m, pis)
1060 """get_version_info(ExamplePairScore self) -> VersionInfo"""
1061 return _IMP_example.ExamplePairScore_get_version_info(self)
1065 """__str__(ExamplePairScore self) -> std::string"""
1066 return _IMP_example.ExamplePairScore___str__(self)
1070 """__repr__(ExamplePairScore self) -> std::string"""
1071 return _IMP_example.ExamplePairScore___repr__(self)
1076 return _object_cast_to_ExamplePairScore(o)
1078 ExamplePairScore_swigregister = _IMP_example.ExamplePairScore_swigregister
1079 ExamplePairScore_swigregister(ExamplePairScore)
1082 """Proxy of C++ IMP::example::ExampleSubsetFilterTable class."""
1084 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1086 def __init__(self, max_diff, pt):
1087 """__init__(IMP::example::ExampleSubsetFilterTable self, unsigned int max_diff, IMP::ParticlesTemp const & pt) -> ExampleSubsetFilterTable"""
1088 this = _IMP_example.new_ExampleSubsetFilterTable(max_diff, pt)
1090 self.this.append(this)
1091 except __builtin__.Exception:
1095 """get_version_info(ExampleSubsetFilterTable self) -> VersionInfo"""
1096 return _IMP_example.ExampleSubsetFilterTable_get_version_info(self)
1100 """__str__(ExampleSubsetFilterTable self) -> std::string"""
1101 return _IMP_example.ExampleSubsetFilterTable___str__(self)
1105 """__repr__(ExampleSubsetFilterTable self) -> std::string"""
1106 return _IMP_example.ExampleSubsetFilterTable___repr__(self)
1111 return _object_cast_to_ExampleSubsetFilterTable(o)
1113 ExampleSubsetFilterTable_swigregister = _IMP_example.ExampleSubsetFilterTable_swigregister
1114 ExampleSubsetFilterTable_swigregister(ExampleSubsetFilterTable)
1117 """Proxy of C++ IMP::example::ExampleConstraint class."""
1119 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1121 def __init__(self, p):
1122 """__init__(IMP::example::ExampleConstraint self, Particle p) -> ExampleConstraint"""
1123 this = _IMP_example.new_ExampleConstraint(p)
1125 self.this.append(this)
1126 except __builtin__.Exception:
1130 """do_get_inputs(ExampleConstraint self) -> IMP::ModelObjectsTemp"""
1131 return _IMP_example.ExampleConstraint_do_get_inputs(self)
1135 """do_get_outputs(ExampleConstraint self) -> IMP::ModelObjectsTemp"""
1136 return _IMP_example.ExampleConstraint_do_get_outputs(self)
1140 """get_key() -> IntKey"""
1141 return _IMP_example.ExampleConstraint_get_key()
1143 get_key = staticmethod(get_key)
1146 """get_version_info(ExampleConstraint self) -> VersionInfo"""
1147 return _IMP_example.ExampleConstraint_get_version_info(self)
1151 """__str__(ExampleConstraint self) -> std::string"""
1152 return _IMP_example.ExampleConstraint___str__(self)
1156 """__repr__(ExampleConstraint self) -> std::string"""
1157 return _IMP_example.ExampleConstraint___repr__(self)
1162 return _object_cast_to_ExampleConstraint(o)
1164 ExampleConstraint_swigregister = _IMP_example.ExampleConstraint_swigregister
1165 ExampleConstraint_swigregister(ExampleConstraint)
1167 def ExampleConstraint_get_key():
1168 """ExampleConstraint_get_key() -> IntKey"""
1169 return _IMP_example.ExampleConstraint_get_key()
1173 """create_serial_mover(Model m, IMP::ParticleIndexes const & pis) -> MonteCarloMover"""
1174 return _IMP_example.create_serial_mover(m, pis)
1178 optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs, IMP::PairPredicates const & excluded, IMP::OptimizerStates const & opt_states, IMP::LogLevel ll)
1179 optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs, IMP::PairPredicates const & excluded, IMP::OptimizerStates const & opt_states)
1180 optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs, IMP::PairPredicates const & excluded)
1181 optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs)
1182 optimize_balls(Model m, IMP::ParticleIndexes const & pis)
1184 return _IMP_example.optimize_balls(*args)
1188 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)
1189 optimize_assembly(Model m, IMP::ParticleIndexes const & components, IMP::RestraintsTemp const & interactions, IMP::RestraintsTemp const & other_restraints, BoundingBox3D bb, PairScore ev, double cutoff)
1191 return _IMP_example.optimize_assembly(*args)
1194 """get_number_of_incidences(IMP::ParticlesTemp const & psa, IMP::ParticlesTemp const & psb, double point_distance) -> unsigned int"""
1195 return _IMP_example.get_number_of_incidences(psa, psb, point_distance)
1198 """create_chain_restraint(Model m, IMP::ParticleIndexes const & ps, double length_factor, double k, std::string name) -> Restraint"""
1199 return _IMP_example.create_chain_restraint(m, ps, length_factor, k, name)
1202 """create_excluded_volume(Model m, IMP::ParticleIndexes const & ps, double k, std::string name) -> Restraint"""
1203 return _IMP_example.create_excluded_volume(m, ps, k, name)
1205 """Proxy of C++ IMP::example::ExampleTemplateClassD<(3)> class."""
1207 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1209 def __init__(self, *args):
1211 __init__(IMP::example::ExampleTemplateClassD<(3)> self) -> ExampleTemplateClass3D
1212 __init__(IMP::example::ExampleTemplateClassD<(3)> self, Vector3D a, Vector3D b) -> ExampleTemplateClass3D
1214 this = _IMP_example.new_ExampleTemplateClass3D(*args)
1216 self.this.append(this)
1217 except __builtin__.Exception:
1220 def get_point(self, i):
1221 """get_point(ExampleTemplateClass3D self, unsigned int i) -> Vector3D"""
1222 return _IMP_example.ExampleTemplateClass3D_get_point(self, i)
1225 def show(self, *args):
1227 show(ExampleTemplateClass3D self, _ostream out)
1228 show(ExampleTemplateClass3D self)
1230 return _IMP_example.ExampleTemplateClass3D_show(self, *args)
1234 """__str__(ExampleTemplateClass3D self) -> std::string"""
1235 return _IMP_example.ExampleTemplateClass3D___str__(self)
1239 """__repr__(ExampleTemplateClass3D self) -> std::string"""
1240 return _IMP_example.ExampleTemplateClass3D___repr__(self)
1242 __swig_destroy__ = _IMP_example.delete_ExampleTemplateClass3D
1243 __del__ =
lambda self:
None
1244 ExampleTemplateClass3D_swigregister = _IMP_example.ExampleTemplateClass3D_swigregister
1245 ExampleTemplateClass3D_swigregister(ExampleTemplateClass3D)
1248 def get_module_version():
1249 """get_module_version() -> std::string const"""
1250 return _IMP_example.get_module_version()
1253 """get_example_path(std::string fname) -> std::string"""
1254 return _IMP_example.get_example_path(fname)
1257 """get_data_path(std::string fname) -> std::string"""
1258 return _IMP_example.get_data_path(fname)
1260 from .
import _version_check
1261 _version_check.check_version(get_module_version())
1262 __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.