14 from sys
import version_info
as _swig_python_version_info
18 import builtins
as __builtin__
24 strthis =
"proxy of " + self.this.__repr__()
25 except __builtin__.Exception:
27 return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
30 def _swig_setattr_nondynamic_instance_variable(set):
31 def set_instance_attr(self, name, value):
33 set(self, name, value)
34 elif name ==
"thisown":
36 elif hasattr(self, name)
and isinstance(getattr(type(self), name), property):
37 set(self, name, value)
39 raise AttributeError(
"You cannot add instance attributes to %s" % self)
40 return set_instance_attr
43 def _swig_setattr_nondynamic_class_variable(set):
44 def set_class_attr(cls, name, value):
45 if hasattr(cls, name)
and not isinstance(getattr(cls, name), property):
48 raise AttributeError(
"You cannot add class attributes to %s" % cls)
52 def _swig_add_metaclass(metaclass):
53 """Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""
55 return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
59 class _SwigNonDynamicMeta(type):
60 """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
61 __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
66 class IMP_EXAMPLE_SwigPyIterator(object):
67 r"""Proxy of C++ swig::IMP_EXAMPLE_SwigPyIterator class."""
69 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
71 def __init__(self, *args, **kwargs):
72 raise AttributeError(
"No constructor defined - class is abstract")
74 __swig_destroy__ = _IMP_example.delete_IMP_EXAMPLE_SwigPyIterator
77 r"""value(IMP_EXAMPLE_SwigPyIterator self) -> PyObject *"""
78 return _IMP_example.IMP_EXAMPLE_SwigPyIterator_value(self)
81 r"""incr(IMP_EXAMPLE_SwigPyIterator self, size_t n=1) -> IMP_EXAMPLE_SwigPyIterator"""
82 return _IMP_example.IMP_EXAMPLE_SwigPyIterator_incr(self, n)
85 r"""decr(IMP_EXAMPLE_SwigPyIterator self, size_t n=1) -> IMP_EXAMPLE_SwigPyIterator"""
86 return _IMP_example.IMP_EXAMPLE_SwigPyIterator_decr(self, n)
88 def distance(self, x):
89 r"""distance(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> ptrdiff_t"""
90 return _IMP_example.IMP_EXAMPLE_SwigPyIterator_distance(self, x)
93 r"""equal(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> bool"""
94 return _IMP_example.IMP_EXAMPLE_SwigPyIterator_equal(self, x)
97 r"""copy(IMP_EXAMPLE_SwigPyIterator self) -> IMP_EXAMPLE_SwigPyIterator"""
98 return _IMP_example.IMP_EXAMPLE_SwigPyIterator_copy(self)
101 r"""next(IMP_EXAMPLE_SwigPyIterator self) -> PyObject *"""
102 return _IMP_example.IMP_EXAMPLE_SwigPyIterator_next(self)
105 r"""__next__(IMP_EXAMPLE_SwigPyIterator self) -> PyObject *"""
106 return _IMP_example.IMP_EXAMPLE_SwigPyIterator___next__(self)
109 r"""previous(IMP_EXAMPLE_SwigPyIterator self) -> PyObject *"""
110 return _IMP_example.IMP_EXAMPLE_SwigPyIterator_previous(self)
112 def advance(self, n):
113 r"""advance(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator"""
114 return _IMP_example.IMP_EXAMPLE_SwigPyIterator_advance(self, n)
117 r"""__eq__(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> bool"""
118 return _IMP_example.IMP_EXAMPLE_SwigPyIterator___eq__(self, x)
121 r"""__ne__(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> bool"""
122 return _IMP_example.IMP_EXAMPLE_SwigPyIterator___ne__(self, x)
124 def __iadd__(self, n):
125 r"""__iadd__(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator"""
126 return _IMP_example.IMP_EXAMPLE_SwigPyIterator___iadd__(self, n)
128 def __isub__(self, n):
129 r"""__isub__(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator"""
130 return _IMP_example.IMP_EXAMPLE_SwigPyIterator___isub__(self, n)
132 def __add__(self, n):
133 r"""__add__(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator"""
134 return _IMP_example.IMP_EXAMPLE_SwigPyIterator___add__(self, n)
136 def __sub__(self, *args):
138 __sub__(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator
139 __sub__(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> ptrdiff_t
141 return _IMP_example.IMP_EXAMPLE_SwigPyIterator___sub__(self, *args)
146 _IMP_example.IMP_EXAMPLE_SwigPyIterator_swigregister(IMP_EXAMPLE_SwigPyIterator)
153 IMP_DEBUG = _IMP_example.IMP_DEBUG
155 IMP_RELEASE = _IMP_example.IMP_RELEASE
157 IMP_SILENT = _IMP_example.IMP_SILENT
159 IMP_PROGRESS = _IMP_example.IMP_PROGRESS
161 IMP_TERSE = _IMP_example.IMP_TERSE
163 IMP_VERBOSE = _IMP_example.IMP_VERBOSE
165 IMP_MEMORY = _IMP_example.IMP_MEMORY
167 IMP_NONE = _IMP_example.IMP_NONE
169 IMP_USAGE = _IMP_example.IMP_USAGE
171 IMP_INTERNAL = _IMP_example.IMP_INTERNAL
173 IMP_KERNEL_HAS_LOG4CXX = _IMP_example.IMP_KERNEL_HAS_LOG4CXX
175 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_example.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
177 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_example.IMP_COMPILER_HAS_DEBUG_VECTOR
179 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_example.IMP_COMPILER_HAS_RANDOM_SHUFFLE
181 IMP_COMPILER_HAS_THREE_WAY = _IMP_example.IMP_COMPILER_HAS_THREE_WAY
183 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_example.IMP_KERNEL_HAS_BOOST_RANDOM
185 IMP_KERNEL_HAS_NUMPY = _IMP_example.IMP_KERNEL_HAS_NUMPY
187 IMP_KERNEL_HAS_BOOST_SYSTEM = _IMP_example.IMP_KERNEL_HAS_BOOST_SYSTEM
189 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_example.IMP_KERNEL_HAS_GPERFTOOLS
191 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_example.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
193 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_example.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
195 IMPKERNEL_SHOW_WARNINGS = _IMP_example.IMPKERNEL_SHOW_WARNINGS
199 class _DirectorObjects:
200 """@internal Simple class to keep references to director objects
201 to prevent premature deletion."""
204 def register(self, obj):
205 """Take a reference to a director object; will only work for
206 refcounted C++ classes"""
207 if hasattr(obj,
'get_ref_count'):
208 self._objects.append(obj)
210 """Only drop our reference and allow cleanup by Python if no other
211 Python references exist (we hold 3 references: one in self._objects,
212 one in x, and one in the argument list for getrefcount) *and* no
213 other C++ references exist (the Python object always holds one)"""
214 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
215 or x.get_ref_count() > 1]
219 def get_object_count(self):
220 """Get number of director objects (useful for testing only)"""
221 return len(self._objects)
222 _director_objects = _DirectorObjects()
224 class _ostream(object):
225 r"""Proxy of C++ std::ostream class."""
227 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
229 def __init__(self, *args, **kwargs):
230 raise AttributeError(
"No constructor defined")
231 __repr__ = _swig_repr
233 def write(self, osa_buf):
234 r"""write(_ostream self, char const * osa_buf)"""
235 return _IMP_example._ostream_write(self, osa_buf)
238 _IMP_example._ostream_swigregister(_ostream)
239 IMP_C_OPEN_BINARY = _IMP_example.IMP_C_OPEN_BINARY
242 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CGAL_HAS_BOOST_FILESYSTEM
244 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
246 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_example.IMP_CGAL_HAS_BOOST_RANDOM
248 IMP_CGAL_HAS_NUMPY = _IMP_example.IMP_CGAL_HAS_NUMPY
250 IMPCGAL_SHOW_WARNINGS = _IMP_example.IMPCGAL_SHOW_WARNINGS
253 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_example.IMP_ALGEBRA_HAS_IMP_CGAL
255 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
257 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
259 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_example.IMP_ALGEBRA_HAS_BOOST_RANDOM
261 IMP_ALGEBRA_HAS_CGAL = _IMP_example.IMP_ALGEBRA_HAS_CGAL
263 IMP_ALGEBRA_HAS_NUMPY = _IMP_example.IMP_ALGEBRA_HAS_NUMPY
265 IMP_ALGEBRA_HAS_ANN = _IMP_example.IMP_ALGEBRA_HAS_ANN
267 IMPALGEBRA_SHOW_WARNINGS = _IMP_example.IMPALGEBRA_SHOW_WARNINGS
270 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_example.IMP_DISPLAY_HAS_IMP_CGAL
272 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
274 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
276 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_example.IMP_DISPLAY_HAS_BOOST_RANDOM
278 IMP_DISPLAY_HAS_CGAL = _IMP_example.IMP_DISPLAY_HAS_CGAL
280 IMP_DISPLAY_HAS_NUMPY = _IMP_example.IMP_DISPLAY_HAS_NUMPY
282 IMPDISPLAY_SHOW_WARNINGS = _IMP_example.IMPDISPLAY_SHOW_WARNINGS
285 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_example.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
287 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
289 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
291 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
293 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_example.IMP_SCORE_FUNCTOR_HAS_CGAL
295 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_example.IMP_SCORE_FUNCTOR_HAS_HDF5
297 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_example.IMP_SCORE_FUNCTOR_HAS_NUMPY
299 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_example.IMPSCOREFUNCTOR_SHOW_WARNINGS
302 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_example.IMP_STATISTICS_HAS_IMP_CGAL
304 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
306 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
308 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_example.IMP_STATISTICS_HAS_BOOST_RANDOM
310 IMP_STATISTICS_HAS_CGAL = _IMP_example.IMP_STATISTICS_HAS_CGAL
312 IMP_STATISTICS_HAS_NUMPY = _IMP_example.IMP_STATISTICS_HAS_NUMPY
314 IMPSTATISTICS_SHOW_WARNINGS = _IMP_example.IMPSTATISTICS_SHOW_WARNINGS
317 IMP_CORE_HAS_IMP_CGAL = _IMP_example.IMP_CORE_HAS_IMP_CGAL
319 IMP_CORE_HAS_IMP_KERNEL = _IMP_example.IMP_CORE_HAS_IMP_KERNEL
321 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CORE_HAS_BOOST_FILESYSTEM
323 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
325 IMP_CORE_HAS_BOOST_RANDOM = _IMP_example.IMP_CORE_HAS_BOOST_RANDOM
327 IMP_CORE_HAS_CGAL = _IMP_example.IMP_CORE_HAS_CGAL
329 IMP_CORE_HAS_HDF5 = _IMP_example.IMP_CORE_HAS_HDF5
331 IMP_CORE_HAS_NUMPY = _IMP_example.IMP_CORE_HAS_NUMPY
333 IMPCORE_SHOW_WARNINGS = _IMP_example.IMPCORE_SHOW_WARNINGS
336 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_example.IMP_CONTAINER_HAS_IMP_ALGEBRA
338 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_example.IMP_CONTAINER_HAS_IMP_CGAL
340 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_example.IMP_CONTAINER_HAS_IMP_DISPLAY
342 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_example.IMP_CONTAINER_HAS_IMP_KERNEL
344 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
346 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
348 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
350 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_example.IMP_CONTAINER_HAS_BOOST_RANDOM
352 IMP_CONTAINER_HAS_CGAL = _IMP_example.IMP_CONTAINER_HAS_CGAL
354 IMP_CONTAINER_HAS_HDF5 = _IMP_example.IMP_CONTAINER_HAS_HDF5
356 IMP_CONTAINER_HAS_NUMPY = _IMP_example.IMP_CONTAINER_HAS_NUMPY
358 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
362 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_example.IMP_CONTAINER_HAS_ROBIN_MAP
364 IMPCONTAINER_SHOW_WARNINGS = _IMP_example.IMPCONTAINER_SHOW_WARNINGS
367 IMP_ATOM_HAS_IMP_CGAL = _IMP_example.IMP_ATOM_HAS_IMP_CGAL
369 IMP_ATOM_HAS_IMP_KERNEL = _IMP_example.IMP_ATOM_HAS_IMP_KERNEL
371 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
373 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
375 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_example.IMP_ATOM_HAS_BOOST_RANDOM
377 IMP_ATOM_HAS_BOOST_REGEX = _IMP_example.IMP_ATOM_HAS_BOOST_REGEX
379 IMP_ATOM_HAS_CGAL = _IMP_example.IMP_ATOM_HAS_CGAL
381 IMP_ATOM_HAS_HDF5 = _IMP_example.IMP_ATOM_HAS_HDF5
383 IMP_ATOM_HAS_NUMPY = _IMP_example.IMP_ATOM_HAS_NUMPY
385 IMP_ATOM_HAS_PYTHON_IHM = _IMP_example.IMP_ATOM_HAS_PYTHON_IHM
387 IMPATOM_SHOW_WARNINGS = _IMP_example.IMPATOM_SHOW_WARNINGS
389 IMP_ATOM_TYPE_INDEX = _IMP_example.IMP_ATOM_TYPE_INDEX
391 IMP_RESIDUE_TYPE_INDEX = _IMP_example.IMP_RESIDUE_TYPE_INDEX
393 IMP_HIERARCHY_TYPE_INDEX = _IMP_example.IMP_HIERARCHY_TYPE_INDEX
395 IMP_CHAIN_TYPE_INDEX = _IMP_example.IMP_CHAIN_TYPE_INDEX
398 IMP_EM_HAS_IMP_CGAL = _IMP_example.IMP_EM_HAS_IMP_CGAL
400 IMP_EM_HAS_IMP_CONTAINER = _IMP_example.IMP_EM_HAS_IMP_CONTAINER
402 IMP_EM_HAS_IMP_DISPLAY = _IMP_example.IMP_EM_HAS_IMP_DISPLAY
404 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_EM_HAS_IMP_SCORE_FUNCTOR
406 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_EM_HAS_BOOST_FILESYSTEM
408 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
410 IMP_EM_HAS_BOOST_RANDOM = _IMP_example.IMP_EM_HAS_BOOST_RANDOM
412 IMP_EM_HAS_BOOST_REGEX = _IMP_example.IMP_EM_HAS_BOOST_REGEX
414 IMP_EM_HAS_CGAL = _IMP_example.IMP_EM_HAS_CGAL
416 IMP_EM_HAS_HDF5 = _IMP_example.IMP_EM_HAS_HDF5
418 IMP_EM_HAS_NUMPY = _IMP_example.IMP_EM_HAS_NUMPY
420 IMP_EM_HAS_PYTHON_IHM = _IMP_example.IMP_EM_HAS_PYTHON_IHM
422 IMPEM_SHOW_WARNINGS = _IMP_example.IMPEM_SHOW_WARNINGS
425 IMP_SAXS_HAS_IMP_CGAL = _IMP_example.IMP_SAXS_HAS_IMP_CGAL
427 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_example.IMP_SAXS_HAS_IMP_CONTAINER
429 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_example.IMP_SAXS_HAS_IMP_DISPLAY
431 IMP_SAXS_HAS_IMP_KERNEL = _IMP_example.IMP_SAXS_HAS_IMP_KERNEL
433 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
435 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_SAXS_HAS_BOOST_FILESYSTEM
437 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
439 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_example.IMP_SAXS_HAS_BOOST_RANDOM
441 IMP_SAXS_HAS_BOOST_REGEX = _IMP_example.IMP_SAXS_HAS_BOOST_REGEX
443 IMP_SAXS_HAS_CGAL = _IMP_example.IMP_SAXS_HAS_CGAL
445 IMP_SAXS_HAS_HDF5 = _IMP_example.IMP_SAXS_HAS_HDF5
447 IMP_SAXS_HAS_NUMPY = _IMP_example.IMP_SAXS_HAS_NUMPY
449 IMP_SAXS_HAS_PYTHON_IHM = _IMP_example.IMP_SAXS_HAS_PYTHON_IHM
451 IMPSAXS_SHOW_WARNINGS = _IMP_example.IMPSAXS_SHOW_WARNINGS
454 IMP_ISD_HAS_IMP_CGAL = _IMP_example.IMP_ISD_HAS_IMP_CGAL
456 IMP_ISD_HAS_IMP_DISPLAY = _IMP_example.IMP_ISD_HAS_IMP_DISPLAY
458 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
460 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_ISD_HAS_BOOST_FILESYSTEM
462 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
464 IMP_ISD_HAS_BOOST_RANDOM = _IMP_example.IMP_ISD_HAS_BOOST_RANDOM
466 IMP_ISD_HAS_BOOST_REGEX = _IMP_example.IMP_ISD_HAS_BOOST_REGEX
468 IMP_ISD_HAS_CGAL = _IMP_example.IMP_ISD_HAS_CGAL
470 IMP_ISD_HAS_HDF5 = _IMP_example.IMP_ISD_HAS_HDF5
472 IMP_ISD_HAS_NUMPY = _IMP_example.IMP_ISD_HAS_NUMPY
474 IMP_ISD_HAS_PYTHON_IHM = _IMP_example.IMP_ISD_HAS_PYTHON_IHM
476 IMPISD_SHOW_WARNINGS = _IMP_example.IMPISD_SHOW_WARNINGS
479 IMP_RMF_HAS_IMP_CGAL = _IMP_example.IMP_RMF_HAS_IMP_CGAL
481 IMP_RMF_HAS_IMP_EM = _IMP_example.IMP_RMF_HAS_IMP_EM
483 IMP_RMF_HAS_IMP_SAXS = _IMP_example.IMP_RMF_HAS_IMP_SAXS
485 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
487 IMP_RMF_HAS_IMP_STATISTICS = _IMP_example.IMP_RMF_HAS_IMP_STATISTICS
489 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_RMF_HAS_BOOST_FILESYSTEM
491 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
493 IMP_RMF_HAS_BOOST_RANDOM = _IMP_example.IMP_RMF_HAS_BOOST_RANDOM
495 IMP_RMF_HAS_BOOST_REGEX = _IMP_example.IMP_RMF_HAS_BOOST_REGEX
497 IMP_RMF_HAS_CGAL = _IMP_example.IMP_RMF_HAS_CGAL
499 IMP_RMF_HAS_HDF5 = _IMP_example.IMP_RMF_HAS_HDF5
501 IMP_RMF_HAS_NUMPY = _IMP_example.IMP_RMF_HAS_NUMPY
503 IMP_RMF_HAS_PYTHON_IHM = _IMP_example.IMP_RMF_HAS_PYTHON_IHM
505 IMPRMF_SHOW_WARNINGS = _IMP_example.IMPRMF_SHOW_WARNINGS
509 IMP_DOMINO_HAS_IMP_ATOM = _IMP_example.IMP_DOMINO_HAS_IMP_ATOM
511 IMP_DOMINO_HAS_IMP_CGAL = _IMP_example.IMP_DOMINO_HAS_IMP_CGAL
513 IMP_DOMINO_HAS_IMP_EM = _IMP_example.IMP_DOMINO_HAS_IMP_EM
515 IMP_DOMINO_HAS_IMP_ISD = _IMP_example.IMP_DOMINO_HAS_IMP_ISD
517 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_example.IMP_DOMINO_HAS_IMP_KERNEL
519 IMP_DOMINO_HAS_IMP_RMF = _IMP_example.IMP_DOMINO_HAS_IMP_RMF
521 IMP_DOMINO_HAS_IMP_SAXS = _IMP_example.IMP_DOMINO_HAS_IMP_SAXS
523 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
525 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_DOMINO_HAS_BOOST_FILESYSTEM
527 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
529 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_example.IMP_DOMINO_HAS_BOOST_RANDOM
531 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_example.IMP_DOMINO_HAS_BOOST_REGEX
533 IMP_DOMINO_HAS_CGAL = _IMP_example.IMP_DOMINO_HAS_CGAL
535 IMP_DOMINO_HAS_HDF5 = _IMP_example.IMP_DOMINO_HAS_HDF5
537 IMP_DOMINO_HAS_NUMPY = _IMP_example.IMP_DOMINO_HAS_NUMPY
539 IMP_DOMINO_HAS_RMF = _IMP_example.IMP_DOMINO_HAS_RMF
541 IMP_DOMINO_HAS_PYTHON_IHM = _IMP_example.IMP_DOMINO_HAS_PYTHON_IHM
543 IMPDOMINO_SHOW_WARNINGS = _IMP_example.IMPDOMINO_SHOW_WARNINGS
547 IMP_EXAMPLE_HAS_IMP_ALGEBRA = _IMP_example.IMP_EXAMPLE_HAS_IMP_ALGEBRA
549 IMP_EXAMPLE_HAS_IMP_CGAL = _IMP_example.IMP_EXAMPLE_HAS_IMP_CGAL
551 IMP_EXAMPLE_HAS_IMP_DISPLAY = _IMP_example.IMP_EXAMPLE_HAS_IMP_DISPLAY
553 IMP_EXAMPLE_HAS_IMP_EM = _IMP_example.IMP_EXAMPLE_HAS_IMP_EM
555 IMP_EXAMPLE_HAS_IMP_ISD = _IMP_example.IMP_EXAMPLE_HAS_IMP_ISD
557 IMP_EXAMPLE_HAS_IMP_KERNEL = _IMP_example.IMP_EXAMPLE_HAS_IMP_KERNEL
559 IMP_EXAMPLE_HAS_IMP_RMF = _IMP_example.IMP_EXAMPLE_HAS_IMP_RMF
561 IMP_EXAMPLE_HAS_IMP_SAXS = _IMP_example.IMP_EXAMPLE_HAS_IMP_SAXS
563 IMP_EXAMPLE_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_EXAMPLE_HAS_IMP_SCORE_FUNCTOR
565 IMP_EXAMPLE_HAS_IMP_STATISTICS = _IMP_example.IMP_EXAMPLE_HAS_IMP_STATISTICS
567 IMP_EXAMPLE_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_FILESYSTEM
569 IMP_EXAMPLE_HAS_BOOST_GRAPH = _IMP_example.IMP_EXAMPLE_HAS_BOOST_GRAPH
571 IMP_EXAMPLE_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_EXAMPLE_HAS_BOOST_PROGRAMOPTIONS
573 IMP_EXAMPLE_HAS_BOOST_RANDOM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_RANDOM
575 IMP_EXAMPLE_HAS_BOOST_REGEX = _IMP_example.IMP_EXAMPLE_HAS_BOOST_REGEX
577 IMP_EXAMPLE_HAS_CGAL = _IMP_example.IMP_EXAMPLE_HAS_CGAL
579 IMP_EXAMPLE_HAS_HDF5 = _IMP_example.IMP_EXAMPLE_HAS_HDF5
581 IMP_EXAMPLE_HAS_NUMPY = _IMP_example.IMP_EXAMPLE_HAS_NUMPY
583 IMP_EXAMPLE_HAS_RMF = _IMP_example.IMP_EXAMPLE_HAS_RMF
585 IMP_EXAMPLE_HAS_PYTHON_IHM = _IMP_example.IMP_EXAMPLE_HAS_PYTHON_IHM
587 IMP_EXAMPLE_HAS_EXAMPLEDEPENDENCY = _IMP_example.IMP_EXAMPLE_HAS_EXAMPLEDEPENDENCY
589 IMPEXAMPLE_SHOW_WARNINGS = _IMP_example.IMPEXAMPLE_SHOW_WARNINGS
592 _object_types.append(
"ExampleRestraint")
595 def _object_cast_to_ExampleRestraint(o):
596 r"""_object_cast_to_ExampleRestraint(Object o) -> ExampleRestraint"""
597 return _IMP_example._object_cast_to_ExampleRestraint(o)
599 def ExampleDecorators(l=[]):
600 return [ExampleDecorator(x)
for x
in l]
601 _plural_types.append(
"ExampleDecorators")
604 _value_types.append(
"ExampleDecorator")
607 _object_types.append(
"ExampleUnaryFunction")
610 def _object_cast_to_ExampleUnaryFunction(o):
611 r"""_object_cast_to_ExampleUnaryFunction(Object o) -> ExampleUnaryFunction"""
612 return _IMP_example._object_cast_to_ExampleUnaryFunction(o)
614 _object_types.append(
"ExampleSingletonModifier")
617 def _object_cast_to_ExampleSingletonModifier(o):
618 r"""_object_cast_to_ExampleSingletonModifier(Object o) -> ExampleSingletonModifier"""
619 return _IMP_example._object_cast_to_ExampleSingletonModifier(o)
621 _object_types.append(
"ExamplePairScore")
624 def _object_cast_to_ExamplePairScore(o):
625 r"""_object_cast_to_ExamplePairScore(Object o) -> ExamplePairScore"""
626 return _IMP_example._object_cast_to_ExamplePairScore(o)
628 _object_types.append(
"ExampleSubsetFilterTable")
631 def _object_cast_to_ExampleSubsetFilterTable(o):
632 r"""_object_cast_to_ExampleSubsetFilterTable(Object o) -> ExampleSubsetFilterTable"""
633 return _IMP_example._object_cast_to_ExampleSubsetFilterTable(o)
635 _object_types.append(
"ExampleConstraint")
638 def _object_cast_to_ExampleConstraint(o):
639 r"""_object_cast_to_ExampleConstraint(Object o) -> ExampleConstraint"""
640 return _IMP_example._object_cast_to_ExampleConstraint(o)
642 _object_types.append(
"ExampleObject")
645 def _object_cast_to_ExampleObject(o):
646 r"""_object_cast_to_ExampleObject(Object o) -> ExampleObject"""
647 return _IMP_example._object_cast_to_ExampleObject(o)
649 ExampleTemplateClass3Ds=list
650 _plural_types.append(
"ExampleTemplateClass3Ds")
651 _value_types.append(
"ExampleTemplateClass3D")
654 def create_model_and_particles():
659 for i
in range(0,100):
660 p = m.add_particle(
"p")
664 d.set_coordinates_are_optimized(
True)
670 """An example restraint written in Python.
671 This should be functionally equivalent to the C++ ExampleRestraint.
673 def __init__(self, m, p, k):
674 IMP.Restraint.__init__(self, m,
"PythonExampleRestraint%1%")
675 self.p, self.k = p, k
677 def do_add_score_and_derivatives(self, sa):
679 score = .5 * self.k * d.get_z() * d.get_z()
680 if sa.get_derivative_accumulator():
681 deriv = self.k * d.get_z()
682 d.add_to_derivative(2, deriv, sa.get_derivative_accumulator())
686 return [self.
get_model().get_particle(self.p)]
692 """An example PairScore written in Python.
693 This should be functionally equivalent to the C++ ExamplePairScore.
695 def __init__(self, x0, k):
696 IMP.PairScore.__init__(self)
697 self.x0, self.k = x0, k
702 diff = (d0.get_coordinates()
703 - d1.get_coordinates()).get_magnitude() - self.x0
704 score = .5 * self.k * diff * diff
707 delta = d0.get_coordinates() - d1.get_coordinates()
708 udelta = delta.get_unit_vector()
710 d0.add_to_derivatives(udelta * dv, da)
711 d1.add_to_derivatives(-udelta * dv, da)
721 """An example UnaryFunction written in Python.
722 This should be functionally equivalent to the C++ ExampleUnaryFunction.
724 def __init__(self, center, k):
725 IMP.UnaryFunction.__init__(self)
726 self.center, self.k = center, k
729 return (self.
evaluate(feature), self.k * (feature - self.center))
732 return .5 * self.k * (feature - self.center) * (feature - self.center)
738 """An example Constraint written in Python.
739 This should be functionally equivalent to the C++ ExampleConstraint.
744 def __init__(self, p):
745 IMP.Constraint.__init__(self, p.get_model(),
"ExampleConstraint%1%")
748 PythonExampleConstraint.k =
IMP.IntKey(
"Constraint key")
749 if not p.has_attribute(self.k):
750 p.add_attribute(self.k, 0)
752 def do_update_attributes(self):
753 self.p.set_value(self.k, self.p.get_value(self.k) + 1)
755 def do_update_derivatives(self, da):
768 """An example SingletonModifier written in Python.
769 This should be functionally equivalent to the C++
770 ExampleSingletonModifier.
773 def __init__(self, bb):
774 IMP.SingletonModifier.__init__(self,
"ExampleSingletonModifier%1%")
781 while d.get_coordinate(i) < self.bb.get_corner(0)[i]:
782 d.set_coordinate(i,d.get_coordinate(i) + \
783 (self.bb.get_corner(1)[i] - self.bb.get_corner(0)[i]))
784 while d.get_coordinate(i) > self.bb.get_corner(1)[i]:
785 d.set_coordinate(i,d.get_coordinate(i) - \
786 (self.bb.get_corner(1)[i] - self.bb.get_corner(0)[i]))
796 r"""Proxy of C++ IMP::example::ExampleRestraint class."""
798 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
800 def __init__(self, *args):
802 __init__(ExampleRestraint self, Model m, ParticleIndex p, double k) -> ExampleRestraint
803 __init__(ExampleRestraint self) -> ExampleRestraint
805 _IMP_example.ExampleRestraint_swiginit(self, _IMP_example.new_ExampleRestraint(*args))
807 def do_add_score_and_derivatives(self, sa):
808 r"""do_add_score_and_derivatives(ExampleRestraint self, ScoreAccumulator sa)"""
809 return _IMP_example.ExampleRestraint_do_add_score_and_derivatives(self, sa)
812 r"""do_get_inputs(ExampleRestraint self) -> IMP::ModelObjectsTemp"""
813 return _IMP_example.ExampleRestraint_do_get_inputs(self)
816 r"""get_version_info(ExampleRestraint self) -> VersionInfo"""
817 return _IMP_example.ExampleRestraint_get_version_info(self)
818 __swig_destroy__ = _IMP_example.delete_ExampleRestraint
821 r"""__str__(ExampleRestraint self) -> std::string"""
822 return _IMP_example.ExampleRestraint___str__(self)
825 r"""__repr__(ExampleRestraint self) -> std::string"""
826 return _IMP_example.ExampleRestraint___repr__(self)
830 return _object_cast_to_ExampleRestraint(o)
833 def _get_as_binary(self):
834 r"""_get_as_binary(ExampleRestraint self) -> PyObject *"""
835 return _IMP_example.ExampleRestraint__get_as_binary(self)
837 def _set_from_binary(self, p):
838 r"""_set_from_binary(ExampleRestraint self, PyObject * p)"""
839 return _IMP_example.ExampleRestraint__set_from_binary(self, p)
841 def __getstate__(self):
842 p = self._get_as_binary()
843 if len(self.__dict__) > 1:
844 d = self.__dict__.copy()
849 def __setstate__(self, p):
850 if not hasattr(self,
'this'):
852 if isinstance(p, tuple):
854 self.__dict__.update(d)
855 return self._set_from_binary(p)
859 _IMP_example.ExampleRestraint_swigregister(ExampleRestraint)
861 r"""Proxy of C++ IMP::example::ExampleDecorator class."""
863 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
865 def get_decorator_name(self):
866 r"""get_decorator_name(ExampleDecorator self) -> std::string"""
867 return _IMP_example.ExampleDecorator_get_decorator_name(self)
869 def set_decorator_name(self, nm):
870 r"""set_decorator_name(ExampleDecorator self, std::string nm)"""
871 return _IMP_example.ExampleDecorator_set_decorator_name(self, nm)
873 def __init__(self, *args):
875 __init__(ExampleDecorator self) -> ExampleDecorator
876 __init__(ExampleDecorator self, Model m, ParticleIndex id) -> ExampleDecorator
877 __init__(ExampleDecorator self, _ParticleAdaptor d) -> ExampleDecorator
879 _IMP_example.ExampleDecorator_swiginit(self, _IMP_example.new_ExampleDecorator(*args))
882 def get_is_setup(*args):
884 get_is_setup(Model m, ParticleIndex pi) -> bool
885 get_is_setup(_ParticleAdaptor p) -> bool
887 return _IMP_example.ExampleDecorator_get_is_setup(*args)
889 def show(self, *args):
890 r"""show(ExampleDecorator self, _ostream out=std::cout)"""
891 return _IMP_example.ExampleDecorator_show(self, *args)
894 def setup_particle(*args):
896 setup_particle(Model m, ParticleIndex pi, std::string name) -> ExampleDecorator
897 setup_particle(_ParticleAdaptor pa, std::string name) -> ExampleDecorator
899 return _IMP_example.ExampleDecorator_setup_particle(*args)
901 def add_attribute(self, *args):
903 add_attribute(ExampleDecorator self, FloatKey k, IMP::Float v, bool opt)
904 add_attribute(ExampleDecorator self, FloatKey a0, IMP::Float a1)
905 add_attribute(ExampleDecorator self, IntKey a0, IMP::Int a1)
906 add_attribute(ExampleDecorator self, FloatsKey a0, IMP::Floats a1)
907 add_attribute(ExampleDecorator self, IntsKey a0, IMP::Ints a1)
908 add_attribute(ExampleDecorator self, StringKey a0, IMP::String a1)
909 add_attribute(ExampleDecorator self, ParticleIndexKey a0, Particle a1)
910 add_attribute(ExampleDecorator self, ObjectKey a0, Object a1)
911 add_attribute(ExampleDecorator self, SparseFloatKey a0, IMP::Float a1)
912 add_attribute(ExampleDecorator self, SparseIntKey a0, IMP::Int a1)
913 add_attribute(ExampleDecorator self, SparseStringKey a0, IMP::String a1)
914 add_attribute(ExampleDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
916 return _IMP_example.ExampleDecorator_add_attribute(self, *args)
918 def get_value(self, *args):
920 get_value(ExampleDecorator self, FloatKey a0) -> IMP::Float
921 get_value(ExampleDecorator self, IntKey a0) -> IMP::Int
922 get_value(ExampleDecorator self, FloatsKey a0) -> IMP::Floats
923 get_value(ExampleDecorator self, IntsKey a0) -> IMP::Ints
924 get_value(ExampleDecorator self, StringKey a0) -> IMP::String
925 get_value(ExampleDecorator self, ParticleIndexKey a0) -> Particle
926 get_value(ExampleDecorator self, ObjectKey a0) -> Object
927 get_value(ExampleDecorator self, SparseFloatKey a0) -> IMP::Float
928 get_value(ExampleDecorator self, SparseIntKey a0) -> IMP::Int
929 get_value(ExampleDecorator self, SparseStringKey a0) -> IMP::String
930 get_value(ExampleDecorator self, SparseParticleIndexKey a0) -> ParticleIndex
932 return _IMP_example.ExampleDecorator_get_value(self, *args)
934 def set_value(self, *args):
936 set_value(ExampleDecorator self, FloatKey a0, IMP::Float a1)
937 set_value(ExampleDecorator self, IntKey a0, IMP::Int a1)
938 set_value(ExampleDecorator self, FloatsKey a0, IMP::Floats a1)
939 set_value(ExampleDecorator self, IntsKey a0, IMP::Ints a1)
940 set_value(ExampleDecorator self, StringKey a0, IMP::String a1)
941 set_value(ExampleDecorator self, ParticleIndexKey a0, Particle a1)
942 set_value(ExampleDecorator self, ObjectKey a0, Object a1)
943 set_value(ExampleDecorator self, SparseFloatKey a0, IMP::Float a1)
944 set_value(ExampleDecorator self, SparseIntKey a0, IMP::Int a1)
945 set_value(ExampleDecorator self, SparseStringKey a0, IMP::String a1)
946 set_value(ExampleDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
948 return _IMP_example.ExampleDecorator_set_value(self, *args)
950 def remove_attribute(self, *args):
952 remove_attribute(ExampleDecorator self, FloatKey a0)
953 remove_attribute(ExampleDecorator self, IntKey a0)
954 remove_attribute(ExampleDecorator self, FloatsKey a0)
955 remove_attribute(ExampleDecorator self, IntsKey a0)
956 remove_attribute(ExampleDecorator self, StringKey a0)
957 remove_attribute(ExampleDecorator self, ParticleIndexKey a0)
958 remove_attribute(ExampleDecorator self, ObjectKey a0)
959 remove_attribute(ExampleDecorator self, SparseFloatKey a0)
960 remove_attribute(ExampleDecorator self, SparseIntKey a0)
961 remove_attribute(ExampleDecorator self, SparseStringKey a0)
962 remove_attribute(ExampleDecorator self, SparseParticleIndexKey a0)
964 return _IMP_example.ExampleDecorator_remove_attribute(self, *args)
966 def has_attribute(self, *args):
968 has_attribute(ExampleDecorator self, FloatKey a0) -> bool
969 has_attribute(ExampleDecorator self, IntKey a0) -> bool
970 has_attribute(ExampleDecorator self, FloatsKey a0) -> bool
971 has_attribute(ExampleDecorator self, IntsKey a0) -> bool
972 has_attribute(ExampleDecorator self, StringKey a0) -> bool
973 has_attribute(ExampleDecorator self, ParticleIndexKey a0) -> bool
974 has_attribute(ExampleDecorator self, ObjectKey a0) -> bool
975 has_attribute(ExampleDecorator self, SparseFloatKey a0) -> bool
976 has_attribute(ExampleDecorator self, SparseIntKey a0) -> bool
977 has_attribute(ExampleDecorator self, SparseStringKey a0) -> bool
978 has_attribute(ExampleDecorator self, SparseParticleIndexKey a0) -> bool
980 return _IMP_example.ExampleDecorator_has_attribute(self, *args)
982 def get_derivative(self, a0):
983 r"""get_derivative(ExampleDecorator self, FloatKey a0) -> double"""
984 return _IMP_example.ExampleDecorator_get_derivative(self, a0)
987 r"""get_name(ExampleDecorator self) -> std::string"""
988 return _IMP_example.ExampleDecorator_get_name(self)
991 r"""clear_caches(ExampleDecorator self)"""
992 return _IMP_example.ExampleDecorator_clear_caches(self)
994 def set_name(self, a0):
995 r"""set_name(ExampleDecorator self, std::string a0)"""
996 return _IMP_example.ExampleDecorator_set_name(self, a0)
999 r"""set_check_level(ExampleDecorator self, IMP::CheckLevel a0)"""
1000 return _IMP_example.ExampleDecorator_set_check_level(self, a0)
1002 def add_to_derivative(self, a0, a1, a2):
1003 r"""add_to_derivative(ExampleDecorator self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1004 return _IMP_example.ExampleDecorator_add_to_derivative(self, a0, a1, a2)
1006 def set_is_optimized(self, a0, a1):
1007 r"""set_is_optimized(ExampleDecorator self, FloatKey a0, bool a1)"""
1008 return _IMP_example.ExampleDecorator_set_is_optimized(self, a0, a1)
1010 def get_is_optimized(self, a0):
1011 r"""get_is_optimized(ExampleDecorator self, FloatKey a0) -> bool"""
1012 return _IMP_example.ExampleDecorator_get_is_optimized(self, a0)
1014 def get_check_level(self):
1015 r"""get_check_level(ExampleDecorator self) -> IMP::CheckLevel"""
1016 return _IMP_example.ExampleDecorator_get_check_level(self)
1018 def __eq__(self, *args):
1020 __eq__(ExampleDecorator self, ExampleDecorator o) -> bool
1021 __eq__(ExampleDecorator self, Particle d) -> bool
1023 return _IMP_example.ExampleDecorator___eq__(self, *args)
1025 def __ne__(self, *args):
1027 __ne__(ExampleDecorator self, ExampleDecorator o) -> bool
1028 __ne__(ExampleDecorator self, Particle d) -> bool
1030 return _IMP_example.ExampleDecorator___ne__(self, *args)
1032 def __le__(self, *args):
1034 __le__(ExampleDecorator self, ExampleDecorator o) -> bool
1035 __le__(ExampleDecorator self, Particle d) -> bool
1037 return _IMP_example.ExampleDecorator___le__(self, *args)
1039 def __lt__(self, *args):
1041 __lt__(ExampleDecorator self, ExampleDecorator o) -> bool
1042 __lt__(ExampleDecorator self, Particle d) -> bool
1044 return _IMP_example.ExampleDecorator___lt__(self, *args)
1046 def __ge__(self, *args):
1048 __ge__(ExampleDecorator self, ExampleDecorator o) -> bool
1049 __ge__(ExampleDecorator self, Particle d) -> bool
1051 return _IMP_example.ExampleDecorator___ge__(self, *args)
1053 def __gt__(self, *args):
1055 __gt__(ExampleDecorator self, ExampleDecorator o) -> bool
1056 __gt__(ExampleDecorator self, Particle d) -> bool
1058 return _IMP_example.ExampleDecorator___gt__(self, *args)
1061 r"""__hash__(ExampleDecorator self) -> std::size_t"""
1062 return _IMP_example.ExampleDecorator___hash__(self)
1065 r"""__str__(ExampleDecorator self) -> std::string"""
1066 return _IMP_example.ExampleDecorator___str__(self)
1069 r"""__repr__(ExampleDecorator self) -> std::string"""
1070 return _IMP_example.ExampleDecorator___repr__(self)
1072 def _get_as_binary(self):
1073 r"""_get_as_binary(ExampleDecorator self) -> PyObject *"""
1074 return _IMP_example.ExampleDecorator__get_as_binary(self)
1076 def _set_from_binary(self, p):
1077 r"""_set_from_binary(ExampleDecorator self, PyObject * p)"""
1078 return _IMP_example.ExampleDecorator__set_from_binary(self, p)
1080 def __getstate__(self):
1081 p = self._get_as_binary()
1082 if len(self.__dict__) > 1:
1083 d = self.__dict__.copy()
1088 def __setstate__(self, p):
1089 if not hasattr(self,
'this'):
1091 if isinstance(p, tuple):
1093 self.__dict__.update(d)
1094 return self._set_from_binary(p)
1096 __swig_destroy__ = _IMP_example.delete_ExampleDecorator
1099 _IMP_example.ExampleDecorator_swigregister(ExampleDecorator)
1101 def __lshift__(out, n):
1102 r"""__lshift__(_ostream out, ExampleDecorator n) -> _ostream"""
1103 return _IMP_example.__lshift__(out, n)
1105 r"""Proxy of C++ IMP::example::ExampleUnaryFunction class."""
1107 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1109 def __init__(self, *args):
1111 __init__(ExampleUnaryFunction self, IMP::Float center, IMP::Float k) -> ExampleUnaryFunction
1112 __init__(ExampleUnaryFunction self) -> ExampleUnaryFunction
1114 _IMP_example.ExampleUnaryFunction_swiginit(self, _IMP_example.new_ExampleUnaryFunction(*args))
1117 r"""get_version_info(ExampleUnaryFunction self) -> VersionInfo"""
1118 return _IMP_example.ExampleUnaryFunction_get_version_info(self)
1119 __swig_destroy__ = _IMP_example.delete_ExampleUnaryFunction
1122 r"""__str__(ExampleUnaryFunction self) -> std::string"""
1123 return _IMP_example.ExampleUnaryFunction___str__(self)
1126 r"""__repr__(ExampleUnaryFunction self) -> std::string"""
1127 return _IMP_example.ExampleUnaryFunction___repr__(self)
1131 return _object_cast_to_ExampleUnaryFunction(o)
1134 def _get_as_binary(self):
1135 r"""_get_as_binary(ExampleUnaryFunction self) -> PyObject *"""
1136 return _IMP_example.ExampleUnaryFunction__get_as_binary(self)
1138 def _set_from_binary(self, p):
1139 r"""_set_from_binary(ExampleUnaryFunction self, PyObject * p)"""
1140 return _IMP_example.ExampleUnaryFunction__set_from_binary(self, p)
1142 def __getstate__(self):
1143 p = self._get_as_binary()
1144 if len(self.__dict__) > 1:
1145 d = self.__dict__.copy()
1150 def __setstate__(self, p):
1151 if not hasattr(self,
'this'):
1153 if isinstance(p, tuple):
1155 self.__dict__.update(d)
1156 return self._set_from_binary(p)
1160 _IMP_example.ExampleUnaryFunction_swigregister(ExampleUnaryFunction)
1162 r"""Proxy of C++ IMP::example::ExampleObject class."""
1164 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1166 def __init__(self, *args):
1168 __init__(ExampleObject self, IMP::Floats const & data) -> ExampleObject
1169 __init__(ExampleObject self) -> ExampleObject
1171 _IMP_example.ExampleObject_swiginit(self, _IMP_example.new_ExampleObject(*args))
1173 def get_data(self, i):
1174 r"""get_data(ExampleObject self, unsigned int i) -> double"""
1175 return _IMP_example.ExampleObject_get_data(self, i)
1178 r"""get_version_info(ExampleObject self) -> VersionInfo"""
1179 return _IMP_example.ExampleObject_get_version_info(self)
1180 __swig_destroy__ = _IMP_example.delete_ExampleObject
1183 r"""__str__(ExampleObject self) -> std::string"""
1184 return _IMP_example.ExampleObject___str__(self)
1187 r"""__repr__(ExampleObject self) -> std::string"""
1188 return _IMP_example.ExampleObject___repr__(self)
1192 return _object_cast_to_ExampleObject(o)
1195 def _get_as_binary(self):
1196 r"""_get_as_binary(ExampleObject self) -> PyObject *"""
1197 return _IMP_example.ExampleObject__get_as_binary(self)
1199 def _set_from_binary(self, p):
1200 r"""_set_from_binary(ExampleObject self, PyObject * p)"""
1201 return _IMP_example.ExampleObject__set_from_binary(self, p)
1203 def __getstate__(self):
1204 p = self._get_as_binary()
1205 if len(self.__dict__) > 1:
1206 d = self.__dict__.copy()
1211 def __setstate__(self, p):
1212 if not hasattr(self,
'this'):
1214 if isinstance(p, tuple):
1216 self.__dict__.update(d)
1217 return self._set_from_binary(p)
1221 _IMP_example.ExampleObject_swigregister(ExampleObject)
1223 r"""Proxy of C++ IMP::example::ExampleSingletonModifier class."""
1225 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1227 def __init__(self, *args):
1229 __init__(ExampleSingletonModifier self, BoundingBox3D bb) -> ExampleSingletonModifier
1230 __init__(ExampleSingletonModifier self) -> ExampleSingletonModifier
1232 _IMP_example.ExampleSingletonModifier_swiginit(self, _IMP_example.new_ExampleSingletonModifier(*args))
1235 r"""do_get_inputs(ExampleSingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1236 return _IMP_example.ExampleSingletonModifier_do_get_inputs(self, m, pis)
1239 r"""do_get_outputs(ExampleSingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1240 return _IMP_example.ExampleSingletonModifier_do_get_outputs(self, m, pis)
1243 r"""get_version_info(ExampleSingletonModifier self) -> VersionInfo"""
1244 return _IMP_example.ExampleSingletonModifier_get_version_info(self)
1245 __swig_destroy__ = _IMP_example.delete_ExampleSingletonModifier
1248 r"""__str__(ExampleSingletonModifier self) -> std::string"""
1249 return _IMP_example.ExampleSingletonModifier___str__(self)
1252 r"""__repr__(ExampleSingletonModifier self) -> std::string"""
1253 return _IMP_example.ExampleSingletonModifier___repr__(self)
1257 return _object_cast_to_ExampleSingletonModifier(o)
1260 def _get_as_binary(self):
1261 r"""_get_as_binary(ExampleSingletonModifier self) -> PyObject *"""
1262 return _IMP_example.ExampleSingletonModifier__get_as_binary(self)
1264 def _set_from_binary(self, p):
1265 r"""_set_from_binary(ExampleSingletonModifier self, PyObject * p)"""
1266 return _IMP_example.ExampleSingletonModifier__set_from_binary(self, p)
1268 def __getstate__(self):
1269 p = self._get_as_binary()
1270 if len(self.__dict__) > 1:
1271 d = self.__dict__.copy()
1276 def __setstate__(self, p):
1277 if not hasattr(self,
'this'):
1279 if isinstance(p, tuple):
1281 self.__dict__.update(d)
1282 return self._set_from_binary(p)
1286 _IMP_example.ExampleSingletonModifier_swigregister(ExampleSingletonModifier)
1288 r"""Proxy of C++ IMP::example::ExamplePairScore class."""
1290 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1292 def __init__(self, *args):
1294 __init__(ExamplePairScore self, double x0, double k) -> ExamplePairScore
1295 __init__(ExamplePairScore self) -> ExamplePairScore
1297 _IMP_example.ExamplePairScore_swiginit(self, _IMP_example.new_ExamplePairScore(*args))
1300 r"""do_get_inputs(ExamplePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1301 return _IMP_example.ExamplePairScore_do_get_inputs(self, m, pis)
1303 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
1304 r"""evaluate_indexes(ExamplePairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
1305 return _IMP_example.ExamplePairScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
1307 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
1308 r"""evaluate_indexes_scores(ExamplePairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, DistBase score, bool all_indexes_checked=False) -> double"""
1309 return _IMP_example.ExamplePairScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
1311 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
1312 r"""evaluate_indexes_delta(ExamplePairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, DistBase score, bool all_indexes_checked=False) -> double"""
1313 return _IMP_example.ExamplePairScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
1315 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
1316 r"""evaluate_if_good_indexes(ExamplePairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
1317 return _IMP_example.ExamplePairScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
1320 r"""get_version_info(ExamplePairScore self) -> VersionInfo"""
1321 return _IMP_example.ExamplePairScore_get_version_info(self)
1322 __swig_destroy__ = _IMP_example.delete_ExamplePairScore
1325 r"""__str__(ExamplePairScore self) -> std::string"""
1326 return _IMP_example.ExamplePairScore___str__(self)
1329 r"""__repr__(ExamplePairScore self) -> std::string"""
1330 return _IMP_example.ExamplePairScore___repr__(self)
1334 return _object_cast_to_ExamplePairScore(o)
1337 def _get_as_binary(self):
1338 r"""_get_as_binary(ExamplePairScore self) -> PyObject *"""
1339 return _IMP_example.ExamplePairScore__get_as_binary(self)
1341 def _set_from_binary(self, p):
1342 r"""_set_from_binary(ExamplePairScore self, PyObject * p)"""
1343 return _IMP_example.ExamplePairScore__set_from_binary(self, p)
1345 def __getstate__(self):
1346 p = self._get_as_binary()
1347 if len(self.__dict__) > 1:
1348 d = self.__dict__.copy()
1353 def __setstate__(self, p):
1354 if not hasattr(self,
'this'):
1356 if isinstance(p, tuple):
1358 self.__dict__.update(d)
1359 return self._set_from_binary(p)
1363 _IMP_example.ExamplePairScore_swigregister(ExamplePairScore)
1365 r"""Proxy of C++ IMP::example::ExampleSubsetFilterTable class."""
1367 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1369 def __init__(self, max_diff, pt):
1370 r"""__init__(ExampleSubsetFilterTable self, unsigned int max_diff, IMP::ParticlesTemp const & pt) -> ExampleSubsetFilterTable"""
1371 _IMP_example.ExampleSubsetFilterTable_swiginit(self, _IMP_example.new_ExampleSubsetFilterTable(max_diff, pt))
1374 r"""get_version_info(ExampleSubsetFilterTable self) -> VersionInfo"""
1375 return _IMP_example.ExampleSubsetFilterTable_get_version_info(self)
1376 __swig_destroy__ = _IMP_example.delete_ExampleSubsetFilterTable
1379 r"""__str__(ExampleSubsetFilterTable self) -> std::string"""
1380 return _IMP_example.ExampleSubsetFilterTable___str__(self)
1383 r"""__repr__(ExampleSubsetFilterTable self) -> std::string"""
1384 return _IMP_example.ExampleSubsetFilterTable___repr__(self)
1388 return _object_cast_to_ExampleSubsetFilterTable(o)
1392 _IMP_example.ExampleSubsetFilterTable_swigregister(ExampleSubsetFilterTable)
1394 r"""Proxy of C++ IMP::example::ExampleConstraint class."""
1396 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1398 def __init__(self, *args):
1400 __init__(ExampleConstraint self, Particle p) -> ExampleConstraint
1401 __init__(ExampleConstraint self) -> ExampleConstraint
1403 _IMP_example.ExampleConstraint_swiginit(self, _IMP_example.new_ExampleConstraint(*args))
1406 r"""do_get_inputs(ExampleConstraint self) -> IMP::ModelObjectsTemp"""
1407 return _IMP_example.ExampleConstraint_do_get_inputs(self)
1410 r"""do_get_outputs(ExampleConstraint self) -> IMP::ModelObjectsTemp"""
1411 return _IMP_example.ExampleConstraint_do_get_outputs(self)
1415 r"""get_key() -> IntKey"""
1416 return _IMP_example.ExampleConstraint_get_key()
1419 r"""get_version_info(ExampleConstraint self) -> VersionInfo"""
1420 return _IMP_example.ExampleConstraint_get_version_info(self)
1421 __swig_destroy__ = _IMP_example.delete_ExampleConstraint
1424 r"""__str__(ExampleConstraint self) -> std::string"""
1425 return _IMP_example.ExampleConstraint___str__(self)
1428 r"""__repr__(ExampleConstraint self) -> std::string"""
1429 return _IMP_example.ExampleConstraint___repr__(self)
1433 return _object_cast_to_ExampleConstraint(o)
1436 def _get_as_binary(self):
1437 r"""_get_as_binary(ExampleConstraint self) -> PyObject *"""
1438 return _IMP_example.ExampleConstraint__get_as_binary(self)
1440 def _set_from_binary(self, p):
1441 r"""_set_from_binary(ExampleConstraint self, PyObject * p)"""
1442 return _IMP_example.ExampleConstraint__set_from_binary(self, p)
1444 def __getstate__(self):
1445 p = self._get_as_binary()
1446 if len(self.__dict__) > 1:
1447 d = self.__dict__.copy()
1452 def __setstate__(self, p):
1453 if not hasattr(self,
'this'):
1455 if isinstance(p, tuple):
1457 self.__dict__.update(d)
1458 return self._set_from_binary(p)
1462 _IMP_example.ExampleConstraint_swigregister(ExampleConstraint)
1465 r"""get_number_of_incidences(IMP::ParticlesTemp const & psa, IMP::ParticlesTemp const & psb, double point_distance) -> unsigned int"""
1466 return _IMP_example.get_number_of_incidences(psa, psb, point_distance)
1469 r"""create_chain_restraint(Model m, IMP::ParticleIndexes const & ps, double length_factor, double k, std::string name) -> Restraint"""
1470 return _IMP_example.create_chain_restraint(m, ps, length_factor, k, name)
1473 r"""create_excluded_volume(Model m, IMP::ParticleIndexes const & ps, double k, std::string name) -> Restraint"""
1474 return _IMP_example.create_excluded_volume(m, ps, k, name)
1476 r"""Proxy of C++ IMP::example::ExampleTemplateClassD< 3 > class."""
1478 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1480 def __init__(self, *args):
1482 __init__(ExampleTemplateClass3D self) -> ExampleTemplateClass3D
1483 __init__(ExampleTemplateClass3D self, Vector3D a, Vector3D b) -> ExampleTemplateClass3D
1485 _IMP_example.ExampleTemplateClass3D_swiginit(self, _IMP_example.new_ExampleTemplateClass3D(*args))
1487 def get_point(self, i):
1488 r"""get_point(ExampleTemplateClass3D self, unsigned int i) -> Vector3D"""
1489 return _IMP_example.ExampleTemplateClass3D_get_point(self, i)
1491 def show(self, *args):
1492 r"""show(ExampleTemplateClass3D self, _ostream out=std::cout)"""
1493 return _IMP_example.ExampleTemplateClass3D_show(self, *args)
1496 r"""__str__(ExampleTemplateClass3D self) -> std::string"""
1497 return _IMP_example.ExampleTemplateClass3D___str__(self)
1500 r"""__repr__(ExampleTemplateClass3D self) -> std::string"""
1501 return _IMP_example.ExampleTemplateClass3D___repr__(self)
1502 __swig_destroy__ = _IMP_example.delete_ExampleTemplateClass3D
1505 _IMP_example.ExampleTemplateClass3D_swigregister(ExampleTemplateClass3D)
1507 def get_module_name():
1508 r"""get_module_name() -> std::string const"""
1509 return _IMP_example.get_module_name()
1512 r"""get_module_version() -> std::string const"""
1513 return _IMP_example.get_module_version()
1516 r"""get_example_path(std::string fname) -> std::string"""
1517 return _IMP_example.get_example_path(fname)
1520 r"""get_data_path(std::string fname) -> std::string"""
1521 return _IMP_example.get_data_path(fname)
1523 from .
import _version_check
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.
Make CGAL functionality available to IMP.
A line segment templated on the dimension.
ParticlesTemp get_particles(Model *m, const ParticleIndexes &ps)
Get the particles from a list of indexes.
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.
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.
Restrain a particle to be in the x,y plane.
Basic utilities for handling cryo-electron microscopy 3D density maps.
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
std::string get_module_version()
Return the version of this module, as a string.
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.
Support for small angle X-ray scattering (SAXS) data.
Inferential scoring building on methods developed as part of the Inferential Structure Determination ...
A restraint is a term in an IMP ScoringFunction.