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_EM_HAS_IMP_CGAL = _IMP_example.IMP_EM_HAS_IMP_CGAL
382 IMP_EM_HAS_IMP_CONTAINER = _IMP_example.IMP_EM_HAS_IMP_CONTAINER
383 IMP_EM_HAS_IMP_DISPLAY = _IMP_example.IMP_EM_HAS_IMP_DISPLAY
384 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_EM_HAS_IMP_SCORE_FUNCTOR
385 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_EM_HAS_BOOST_FILESYSTEM
386 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
387 IMP_EM_HAS_BOOST_RANDOM = _IMP_example.IMP_EM_HAS_BOOST_RANDOM
388 IMP_EM_HAS_BOOST_REGEX = _IMP_example.IMP_EM_HAS_BOOST_REGEX
389 IMP_EM_HAS_BOOST_SYSTEM = _IMP_example.IMP_EM_HAS_BOOST_SYSTEM
390 IMP_EM_HAS_CGAL = _IMP_example.IMP_EM_HAS_CGAL
391 IMP_EM_HAS_HDF5 = _IMP_example.IMP_EM_HAS_HDF5
392 IMP_EM_HAS_NUMPY = _IMP_example.IMP_EM_HAS_NUMPY
393 IMP_EM_HAS_PYTHON_IHM = _IMP_example.IMP_EM_HAS_PYTHON_IHM
394 IMPEM_SHOW_WARNINGS = _IMP_example.IMPEM_SHOW_WARNINGS
396 IMP_SAXS_HAS_IMP_CGAL = _IMP_example.IMP_SAXS_HAS_IMP_CGAL
397 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_example.IMP_SAXS_HAS_IMP_CONTAINER
398 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_example.IMP_SAXS_HAS_IMP_DISPLAY
399 IMP_SAXS_HAS_IMP_KERNEL = _IMP_example.IMP_SAXS_HAS_IMP_KERNEL
400 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
401 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_SAXS_HAS_BOOST_FILESYSTEM
402 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
403 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_example.IMP_SAXS_HAS_BOOST_RANDOM
404 IMP_SAXS_HAS_BOOST_REGEX = _IMP_example.IMP_SAXS_HAS_BOOST_REGEX
405 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_example.IMP_SAXS_HAS_BOOST_SYSTEM
406 IMP_SAXS_HAS_CGAL = _IMP_example.IMP_SAXS_HAS_CGAL
407 IMP_SAXS_HAS_HDF5 = _IMP_example.IMP_SAXS_HAS_HDF5
408 IMP_SAXS_HAS_NUMPY = _IMP_example.IMP_SAXS_HAS_NUMPY
409 IMP_SAXS_HAS_PYTHON_IHM = _IMP_example.IMP_SAXS_HAS_PYTHON_IHM
410 IMPSAXS_SHOW_WARNINGS = _IMP_example.IMPSAXS_SHOW_WARNINGS
412 IMP_ISD_HAS_IMP_CGAL = _IMP_example.IMP_ISD_HAS_IMP_CGAL
413 IMP_ISD_HAS_IMP_DISPLAY = _IMP_example.IMP_ISD_HAS_IMP_DISPLAY
414 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
415 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_ISD_HAS_BOOST_FILESYSTEM
416 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
417 IMP_ISD_HAS_BOOST_RANDOM = _IMP_example.IMP_ISD_HAS_BOOST_RANDOM
418 IMP_ISD_HAS_BOOST_REGEX = _IMP_example.IMP_ISD_HAS_BOOST_REGEX
419 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_example.IMP_ISD_HAS_BOOST_SYSTEM
420 IMP_ISD_HAS_CGAL = _IMP_example.IMP_ISD_HAS_CGAL
421 IMP_ISD_HAS_HDF5 = _IMP_example.IMP_ISD_HAS_HDF5
422 IMP_ISD_HAS_NUMPY = _IMP_example.IMP_ISD_HAS_NUMPY
423 IMP_ISD_HAS_PYTHON_IHM = _IMP_example.IMP_ISD_HAS_PYTHON_IHM
424 IMPISD_SHOW_WARNINGS = _IMP_example.IMPISD_SHOW_WARNINGS
426 IMP_RMF_HAS_IMP_CGAL = _IMP_example.IMP_RMF_HAS_IMP_CGAL
427 IMP_RMF_HAS_IMP_EM = _IMP_example.IMP_RMF_HAS_IMP_EM
428 IMP_RMF_HAS_IMP_SAXS = _IMP_example.IMP_RMF_HAS_IMP_SAXS
429 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
430 IMP_RMF_HAS_IMP_STATISTICS = _IMP_example.IMP_RMF_HAS_IMP_STATISTICS
431 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_RMF_HAS_BOOST_FILESYSTEM
432 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
433 IMP_RMF_HAS_BOOST_RANDOM = _IMP_example.IMP_RMF_HAS_BOOST_RANDOM
434 IMP_RMF_HAS_BOOST_REGEX = _IMP_example.IMP_RMF_HAS_BOOST_REGEX
435 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_example.IMP_RMF_HAS_BOOST_SYSTEM
436 IMP_RMF_HAS_CGAL = _IMP_example.IMP_RMF_HAS_CGAL
437 IMP_RMF_HAS_HDF5 = _IMP_example.IMP_RMF_HAS_HDF5
438 IMP_RMF_HAS_NUMPY = _IMP_example.IMP_RMF_HAS_NUMPY
439 IMP_RMF_HAS_PYTHON_IHM = _IMP_example.IMP_RMF_HAS_PYTHON_IHM
440 IMPRMF_SHOW_WARNINGS = _IMP_example.IMPRMF_SHOW_WARNINGS
443 IMP_DOMINO_HAS_IMP_ATOM = _IMP_example.IMP_DOMINO_HAS_IMP_ATOM
444 IMP_DOMINO_HAS_IMP_CGAL = _IMP_example.IMP_DOMINO_HAS_IMP_CGAL
445 IMP_DOMINO_HAS_IMP_EM = _IMP_example.IMP_DOMINO_HAS_IMP_EM
446 IMP_DOMINO_HAS_IMP_ISD = _IMP_example.IMP_DOMINO_HAS_IMP_ISD
447 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_example.IMP_DOMINO_HAS_IMP_KERNEL
448 IMP_DOMINO_HAS_IMP_RMF = _IMP_example.IMP_DOMINO_HAS_IMP_RMF
449 IMP_DOMINO_HAS_IMP_SAXS = _IMP_example.IMP_DOMINO_HAS_IMP_SAXS
450 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
451 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_DOMINO_HAS_BOOST_FILESYSTEM
452 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
453 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_example.IMP_DOMINO_HAS_BOOST_RANDOM
454 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_example.IMP_DOMINO_HAS_BOOST_REGEX
455 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_example.IMP_DOMINO_HAS_BOOST_SYSTEM
456 IMP_DOMINO_HAS_CGAL = _IMP_example.IMP_DOMINO_HAS_CGAL
457 IMP_DOMINO_HAS_HDF5 = _IMP_example.IMP_DOMINO_HAS_HDF5
458 IMP_DOMINO_HAS_NUMPY = _IMP_example.IMP_DOMINO_HAS_NUMPY
459 IMP_DOMINO_HAS_RMF = _IMP_example.IMP_DOMINO_HAS_RMF
460 IMP_DOMINO_HAS_PYTHON_IHM = _IMP_example.IMP_DOMINO_HAS_PYTHON_IHM
461 IMPDOMINO_SHOW_WARNINGS = _IMP_example.IMPDOMINO_SHOW_WARNINGS
464 IMP_EXAMPLE_HAS_IMP_ALGEBRA = _IMP_example.IMP_EXAMPLE_HAS_IMP_ALGEBRA
465 IMP_EXAMPLE_HAS_IMP_CGAL = _IMP_example.IMP_EXAMPLE_HAS_IMP_CGAL
466 IMP_EXAMPLE_HAS_IMP_DISPLAY = _IMP_example.IMP_EXAMPLE_HAS_IMP_DISPLAY
467 IMP_EXAMPLE_HAS_IMP_EM = _IMP_example.IMP_EXAMPLE_HAS_IMP_EM
468 IMP_EXAMPLE_HAS_IMP_ISD = _IMP_example.IMP_EXAMPLE_HAS_IMP_ISD
469 IMP_EXAMPLE_HAS_IMP_KERNEL = _IMP_example.IMP_EXAMPLE_HAS_IMP_KERNEL
470 IMP_EXAMPLE_HAS_IMP_RMF = _IMP_example.IMP_EXAMPLE_HAS_IMP_RMF
471 IMP_EXAMPLE_HAS_IMP_SAXS = _IMP_example.IMP_EXAMPLE_HAS_IMP_SAXS
472 IMP_EXAMPLE_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_EXAMPLE_HAS_IMP_SCORE_FUNCTOR
473 IMP_EXAMPLE_HAS_IMP_STATISTICS = _IMP_example.IMP_EXAMPLE_HAS_IMP_STATISTICS
474 IMP_EXAMPLE_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_FILESYSTEM
475 IMP_EXAMPLE_HAS_BOOST_GRAPH = _IMP_example.IMP_EXAMPLE_HAS_BOOST_GRAPH
476 IMP_EXAMPLE_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_EXAMPLE_HAS_BOOST_PROGRAMOPTIONS
477 IMP_EXAMPLE_HAS_BOOST_RANDOM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_RANDOM
478 IMP_EXAMPLE_HAS_BOOST_REGEX = _IMP_example.IMP_EXAMPLE_HAS_BOOST_REGEX
479 IMP_EXAMPLE_HAS_BOOST_SYSTEM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_SYSTEM
480 IMP_EXAMPLE_HAS_CGAL = _IMP_example.IMP_EXAMPLE_HAS_CGAL
481 IMP_EXAMPLE_HAS_HDF5 = _IMP_example.IMP_EXAMPLE_HAS_HDF5
482 IMP_EXAMPLE_HAS_NUMPY = _IMP_example.IMP_EXAMPLE_HAS_NUMPY
483 IMP_EXAMPLE_HAS_RMF = _IMP_example.IMP_EXAMPLE_HAS_RMF
484 IMP_EXAMPLE_HAS_PYTHON_IHM = _IMP_example.IMP_EXAMPLE_HAS_PYTHON_IHM
485 IMP_EXAMPLE_HAS_EXAMPLEDEPENDENCY = _IMP_example.IMP_EXAMPLE_HAS_EXAMPLEDEPENDENCY
486 IMPEXAMPLE_SHOW_WARNINGS = _IMP_example.IMPEXAMPLE_SHOW_WARNINGS
488 _object_types.append(
"ExampleRestraint")
491 def _object_cast_to_ExampleRestraint(o):
492 """_object_cast_to_ExampleRestraint(Object o) -> ExampleRestraint"""
493 return _IMP_example._object_cast_to_ExampleRestraint(o)
495 def ExampleDecorators(l=[]):
496 return [ExampleDecorator(x)
for x
in l]
497 _plural_types.append(
"ExampleDecorators")
500 _value_types.append(
"ExampleDecorator")
503 _object_types.append(
"ExampleUnaryFunction")
506 def _object_cast_to_ExampleUnaryFunction(o):
507 """_object_cast_to_ExampleUnaryFunction(Object o) -> ExampleUnaryFunction"""
508 return _IMP_example._object_cast_to_ExampleUnaryFunction(o)
510 _object_types.append(
"ExampleSingletonModifier")
513 def _object_cast_to_ExampleSingletonModifier(o):
514 """_object_cast_to_ExampleSingletonModifier(Object o) -> ExampleSingletonModifier"""
515 return _IMP_example._object_cast_to_ExampleSingletonModifier(o)
517 _object_types.append(
"ExamplePairScore")
520 def _object_cast_to_ExamplePairScore(o):
521 """_object_cast_to_ExamplePairScore(Object o) -> ExamplePairScore"""
522 return _IMP_example._object_cast_to_ExamplePairScore(o)
524 _object_types.append(
"ExampleSubsetFilterTable")
527 def _object_cast_to_ExampleSubsetFilterTable(o):
528 """_object_cast_to_ExampleSubsetFilterTable(Object o) -> ExampleSubsetFilterTable"""
529 return _IMP_example._object_cast_to_ExampleSubsetFilterTable(o)
531 _object_types.append(
"ExampleConstraint")
534 def _object_cast_to_ExampleConstraint(o):
535 """_object_cast_to_ExampleConstraint(Object o) -> ExampleConstraint"""
536 return _IMP_example._object_cast_to_ExampleConstraint(o)
538 _object_types.append(
"ExampleObject")
541 def _object_cast_to_ExampleObject(o):
542 """_object_cast_to_ExampleObject(Object o) -> ExampleObject"""
543 return _IMP_example._object_cast_to_ExampleObject(o)
545 ExampleTemplateClass3Ds=list
546 _plural_types.append(
"ExampleTemplateClass3Ds")
547 _value_types.append(
"ExampleTemplateClass3D")
550 def create_model_and_particles():
555 for i
in range(0,100):
556 p = m.add_particle(
"p")
560 d.set_coordinates_are_optimized(
True)
566 """An example restraint written in Python.
567 This should be functionally equivalent to the C++ ExampleRestraint.
569 def __init__(self, m, p, k):
570 IMP.Restraint.__init__(self, m,
"PythonExampleRestraint%1%")
571 self.p, self.k = p, k
575 score = .5 * self.k * d.get_z() * d.get_z()
576 if sa.get_derivative_accumulator():
577 deriv = self.k * d.get_z()
578 d.add_to_derivative(2, deriv, sa.get_derivative_accumulator())
582 return [self.
get_model().get_particle(self.p)]
588 """An example PairScore written in Python.
589 This should be functionally equivalent to the C++ ExamplePairScore.
591 def __init__(self, x0, k):
592 IMP.PairScore.__init__(self)
593 self.x0, self.k = x0, k
598 diff = (d0.get_coordinates()
599 - d1.get_coordinates()).get_magnitude() - self.x0
600 score = .5 * self.k * diff * diff
603 delta = d0.get_coordinates() - d1.get_coordinates()
604 udelta = delta.get_unit_vector()
606 d0.add_to_derivatives(udelta * dv, da)
607 d1.add_to_derivatives(-udelta * dv, da)
617 """An example UnaryFunction written in Python.
618 This should be functionally equivalent to the C++ ExampleUnaryFunction.
620 def __init__(self, center, k):
621 IMP.UnaryFunction.__init__(self)
622 self.center, self.k = center, k
625 return (self.
evaluate(feature), self.k * (feature - self.center))
628 return .5 * self.k * (feature - self.center) * (feature - self.center)
634 """An example Constraint written in Python.
635 This should be functionally equivalent to the C++ ExampleConstraint.
640 def __init__(self, p):
641 IMP.Constraint.__init__(self, p.get_model(),
"ExampleConstraint%1%")
644 PythonExampleConstraint.k =
IMP.IntKey(
"Constraint key")
645 if not p.has_attribute(self.k):
646 p.add_attribute(self.k, 0)
648 def do_update_attributes(self):
649 self.p.set_value(self.k, self.p.get_value(self.k) + 1)
651 def do_update_derivatives(self, da):
664 """An example SingletonModifier written in Python.
665 This should be functionally equivalent to the C++
666 ExampleSingletonModifier.
669 def __init__(self, bb):
670 IMP.SingletonModifier.__init__(self,
"ExampleSingletonModifier%1%")
677 while d.get_coordinate(i) < self.bb.get_corner(0)[i]:
678 d.set_coordinate(i,d.get_coordinate(i) + \
679 (self.bb.get_corner(1)[i] - self.bb.get_corner(0)[i]))
680 while d.get_coordinate(i) > self.bb.get_corner(1)[i]:
681 d.set_coordinate(i,d.get_coordinate(i) - \
682 (self.bb.get_corner(1)[i] - self.bb.get_corner(0)[i]))
692 """Proxy of C++ IMP::example::ExampleRestraint class."""
694 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
696 def __init__(self, m, p, k):
697 """__init__(IMP::example::ExampleRestraint self, Model m, ParticleIndex p, double k) -> ExampleRestraint"""
698 this = _IMP_example.new_ExampleRestraint(m, p, k)
700 self.this.append(this)
701 except __builtin__.Exception:
704 def do_add_score_and_derivatives(self, sa):
705 """do_add_score_and_derivatives(ExampleRestraint self, ScoreAccumulator sa)"""
706 return _IMP_example.ExampleRestraint_do_add_score_and_derivatives(self, sa)
710 """do_get_inputs(ExampleRestraint self) -> IMP::ModelObjectsTemp"""
711 return _IMP_example.ExampleRestraint_do_get_inputs(self)
715 """get_version_info(ExampleRestraint self) -> VersionInfo"""
716 return _IMP_example.ExampleRestraint_get_version_info(self)
720 """__str__(ExampleRestraint self) -> std::string"""
721 return _IMP_example.ExampleRestraint___str__(self)
725 """__repr__(ExampleRestraint self) -> std::string"""
726 return _IMP_example.ExampleRestraint___repr__(self)
731 return _object_cast_to_ExampleRestraint(o)
733 ExampleRestraint_swigregister = _IMP_example.ExampleRestraint_swigregister
734 ExampleRestraint_swigregister(ExampleRestraint)
737 """Proxy of C++ IMP::example::ExampleDecorator class."""
739 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
741 def get_decorator_name(self):
742 """get_decorator_name(ExampleDecorator self) -> std::string"""
743 return _IMP_example.ExampleDecorator_get_decorator_name(self)
746 def set_decorator_name(self, nm):
747 """set_decorator_name(ExampleDecorator self, std::string nm)"""
748 return _IMP_example.ExampleDecorator_set_decorator_name(self, nm)
751 def __init__(self, *args):
753 __init__(IMP::example::ExampleDecorator self) -> ExampleDecorator
754 __init__(IMP::example::ExampleDecorator self, Model m, ParticleIndex id) -> ExampleDecorator
755 __init__(IMP::example::ExampleDecorator self, _ParticleAdaptor d) -> ExampleDecorator
757 this = _IMP_example.new_ExampleDecorator(*args)
759 self.this.append(this)
760 except __builtin__.Exception:
763 def get_is_setup(*args):
765 get_is_setup(Model m, ParticleIndex pi) -> bool
766 get_is_setup(_ParticleAdaptor p) -> bool
768 return _IMP_example.ExampleDecorator_get_is_setup(*args)
770 get_is_setup = staticmethod(get_is_setup)
772 def show(self, *args):
774 show(ExampleDecorator self, _ostream out)
775 show(ExampleDecorator self)
777 return _IMP_example.ExampleDecorator_show(self, *args)
780 def setup_particle(*args):
782 setup_particle(Model m, ParticleIndex pi, std::string name) -> ExampleDecorator
783 setup_particle(_ParticleAdaptor decorator, std::string name) -> ExampleDecorator
785 return _IMP_example.ExampleDecorator_setup_particle(*args)
787 setup_particle = staticmethod(setup_particle)
789 def add_attribute(self, *args):
791 add_attribute(ExampleDecorator self, FloatKey k, IMP::Float v, bool opt)
792 add_attribute(ExampleDecorator self, FloatKey a0, IMP::Float a1)
793 add_attribute(ExampleDecorator self, IntKey a0, IMP::Int a1)
794 add_attribute(ExampleDecorator self, FloatsKey a0, IMP::Floats a1)
795 add_attribute(ExampleDecorator self, IntsKey a0, IMP::Ints a1)
796 add_attribute(ExampleDecorator self, StringKey a0, IMP::String a1)
797 add_attribute(ExampleDecorator self, ParticleIndexKey a0, Particle a1)
798 add_attribute(ExampleDecorator self, ObjectKey a0, Object a1)
800 return _IMP_example.ExampleDecorator_add_attribute(self, *args)
803 def get_value(self, *args):
805 get_value(ExampleDecorator self, FloatKey a0) -> IMP::Float
806 get_value(ExampleDecorator self, IntKey a0) -> IMP::Int
807 get_value(ExampleDecorator self, FloatsKey a0) -> IMP::Floats
808 get_value(ExampleDecorator self, IntsKey a0) -> IMP::Ints
809 get_value(ExampleDecorator self, StringKey a0) -> IMP::String
810 get_value(ExampleDecorator self, ParticleIndexKey a0) -> Particle
811 get_value(ExampleDecorator self, ObjectKey a0) -> Object
813 return _IMP_example.ExampleDecorator_get_value(self, *args)
816 def set_value(self, *args):
818 set_value(ExampleDecorator self, FloatKey a0, IMP::Float a1)
819 set_value(ExampleDecorator self, IntKey a0, IMP::Int a1)
820 set_value(ExampleDecorator self, FloatsKey a0, IMP::Floats a1)
821 set_value(ExampleDecorator self, IntsKey a0, IMP::Ints a1)
822 set_value(ExampleDecorator self, StringKey a0, IMP::String a1)
823 set_value(ExampleDecorator self, ParticleIndexKey a0, Particle a1)
824 set_value(ExampleDecorator self, ObjectKey a0, Object a1)
826 return _IMP_example.ExampleDecorator_set_value(self, *args)
829 def remove_attribute(self, *args):
831 remove_attribute(ExampleDecorator self, FloatKey a0)
832 remove_attribute(ExampleDecorator self, IntKey a0)
833 remove_attribute(ExampleDecorator self, FloatsKey a0)
834 remove_attribute(ExampleDecorator self, IntsKey a0)
835 remove_attribute(ExampleDecorator self, StringKey a0)
836 remove_attribute(ExampleDecorator self, ParticleIndexKey a0)
837 remove_attribute(ExampleDecorator self, ObjectKey a0)
839 return _IMP_example.ExampleDecorator_remove_attribute(self, *args)
842 def has_attribute(self, *args):
844 has_attribute(ExampleDecorator self, FloatKey a0) -> bool
845 has_attribute(ExampleDecorator self, IntKey a0) -> bool
846 has_attribute(ExampleDecorator self, FloatsKey a0) -> bool
847 has_attribute(ExampleDecorator self, IntsKey a0) -> bool
848 has_attribute(ExampleDecorator self, StringKey a0) -> bool
849 has_attribute(ExampleDecorator self, ParticleIndexKey a0) -> bool
850 has_attribute(ExampleDecorator self, ObjectKey a0) -> bool
852 return _IMP_example.ExampleDecorator_has_attribute(self, *args)
855 def get_derivative(self, a0):
856 """get_derivative(ExampleDecorator self, FloatKey a0) -> double"""
857 return _IMP_example.ExampleDecorator_get_derivative(self, a0)
861 """get_name(ExampleDecorator self) -> std::string"""
862 return _IMP_example.ExampleDecorator_get_name(self)
866 """clear_caches(ExampleDecorator self)"""
867 return _IMP_example.ExampleDecorator_clear_caches(self)
870 def set_name(self, a0):
871 """set_name(ExampleDecorator self, std::string a0)"""
872 return _IMP_example.ExampleDecorator_set_name(self, a0)
876 """set_check_level(ExampleDecorator self, IMP::CheckLevel a0)"""
877 return _IMP_example.ExampleDecorator_set_check_level(self, a0)
880 def add_to_derivative(self, a0, a1, a2):
881 """add_to_derivative(ExampleDecorator self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
882 return _IMP_example.ExampleDecorator_add_to_derivative(self, a0, a1, a2)
885 def set_is_optimized(self, a0, a1):
886 """set_is_optimized(ExampleDecorator self, FloatKey a0, bool a1)"""
887 return _IMP_example.ExampleDecorator_set_is_optimized(self, a0, a1)
890 def get_is_optimized(self, a0):
891 """get_is_optimized(ExampleDecorator self, FloatKey a0) -> bool"""
892 return _IMP_example.ExampleDecorator_get_is_optimized(self, a0)
895 def get_check_level(self):
896 """get_check_level(ExampleDecorator self) -> IMP::CheckLevel"""
897 return _IMP_example.ExampleDecorator_get_check_level(self)
900 def __eq__(self, *args):
902 __eq__(ExampleDecorator self, ExampleDecorator o) -> bool
903 __eq__(ExampleDecorator self, Particle d) -> bool
905 return _IMP_example.ExampleDecorator___eq__(self, *args)
908 def __ne__(self, *args):
910 __ne__(ExampleDecorator self, ExampleDecorator o) -> bool
911 __ne__(ExampleDecorator self, Particle d) -> bool
913 return _IMP_example.ExampleDecorator___ne__(self, *args)
916 def __le__(self, *args):
918 __le__(ExampleDecorator self, ExampleDecorator o) -> bool
919 __le__(ExampleDecorator self, Particle d) -> bool
921 return _IMP_example.ExampleDecorator___le__(self, *args)
924 def __lt__(self, *args):
926 __lt__(ExampleDecorator self, ExampleDecorator o) -> bool
927 __lt__(ExampleDecorator self, Particle d) -> bool
929 return _IMP_example.ExampleDecorator___lt__(self, *args)
932 def __ge__(self, *args):
934 __ge__(ExampleDecorator self, ExampleDecorator o) -> bool
935 __ge__(ExampleDecorator self, Particle d) -> bool
937 return _IMP_example.ExampleDecorator___ge__(self, *args)
940 def __gt__(self, *args):
942 __gt__(ExampleDecorator self, ExampleDecorator o) -> bool
943 __gt__(ExampleDecorator self, Particle d) -> bool
945 return _IMP_example.ExampleDecorator___gt__(self, *args)
949 """__hash__(ExampleDecorator self) -> std::size_t"""
950 return _IMP_example.ExampleDecorator___hash__(self)
954 """__str__(ExampleDecorator self) -> std::string"""
955 return _IMP_example.ExampleDecorator___str__(self)
959 """__repr__(ExampleDecorator self) -> std::string"""
960 return _IMP_example.ExampleDecorator___repr__(self)
962 __swig_destroy__ = _IMP_example.delete_ExampleDecorator
963 __del__ =
lambda self:
None
964 ExampleDecorator_swigregister = _IMP_example.ExampleDecorator_swigregister
965 ExampleDecorator_swigregister(ExampleDecorator)
967 def ExampleDecorator_get_is_setup(*args):
969 get_is_setup(Model m, ParticleIndex pi) -> bool
970 ExampleDecorator_get_is_setup(_ParticleAdaptor p) -> bool
972 return _IMP_example.ExampleDecorator_get_is_setup(*args)
974 def ExampleDecorator_setup_particle(*args):
976 setup_particle(Model m, ParticleIndex pi, std::string name) -> ExampleDecorator
977 ExampleDecorator_setup_particle(_ParticleAdaptor decorator, std::string name) -> ExampleDecorator
979 return _IMP_example.ExampleDecorator_setup_particle(*args)
982 def __lshift__(out, n):
983 """__lshift__(_ostream out, ExampleDecorator n) -> _ostream"""
984 return _IMP_example.__lshift__(out, n)
986 """Proxy of C++ IMP::example::ExampleUnaryFunction class."""
988 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
990 def __init__(self, center, k):
991 """__init__(IMP::example::ExampleUnaryFunction self, IMP::Float center, IMP::Float k) -> ExampleUnaryFunction"""
992 this = _IMP_example.new_ExampleUnaryFunction(center, k)
994 self.this.append(this)
995 except __builtin__.Exception:
999 """get_version_info(ExampleUnaryFunction self) -> VersionInfo"""
1000 return _IMP_example.ExampleUnaryFunction_get_version_info(self)
1004 """__str__(ExampleUnaryFunction self) -> std::string"""
1005 return _IMP_example.ExampleUnaryFunction___str__(self)
1009 """__repr__(ExampleUnaryFunction self) -> std::string"""
1010 return _IMP_example.ExampleUnaryFunction___repr__(self)
1015 return _object_cast_to_ExampleUnaryFunction(o)
1017 ExampleUnaryFunction_swigregister = _IMP_example.ExampleUnaryFunction_swigregister
1018 ExampleUnaryFunction_swigregister(ExampleUnaryFunction)
1021 """Proxy of C++ IMP::example::ExampleObject class."""
1023 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1025 def __init__(self, data):
1026 """__init__(IMP::example::ExampleObject self, IMP::Floats const & data) -> ExampleObject"""
1027 this = _IMP_example.new_ExampleObject(data)
1029 self.this.append(this)
1030 except __builtin__.Exception:
1033 def get_data(self, i):
1034 """get_data(ExampleObject self, unsigned int i) -> double"""
1035 return _IMP_example.ExampleObject_get_data(self, i)
1039 """get_version_info(ExampleObject self) -> VersionInfo"""
1040 return _IMP_example.ExampleObject_get_version_info(self)
1044 """__str__(ExampleObject self) -> std::string"""
1045 return _IMP_example.ExampleObject___str__(self)
1049 """__repr__(ExampleObject self) -> std::string"""
1050 return _IMP_example.ExampleObject___repr__(self)
1055 return _object_cast_to_ExampleObject(o)
1057 ExampleObject_swigregister = _IMP_example.ExampleObject_swigregister
1058 ExampleObject_swigregister(ExampleObject)
1061 """Proxy of C++ IMP::example::ExampleSingletonModifier class."""
1063 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1065 def __init__(self, bb):
1066 """__init__(IMP::example::ExampleSingletonModifier self, BoundingBox3D bb) -> ExampleSingletonModifier"""
1067 this = _IMP_example.new_ExampleSingletonModifier(bb)
1069 self.this.append(this)
1070 except __builtin__.Exception:
1074 """do_get_inputs(ExampleSingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1075 return _IMP_example.ExampleSingletonModifier_do_get_inputs(self, m, pis)
1079 """do_get_outputs(ExampleSingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1080 return _IMP_example.ExampleSingletonModifier_do_get_outputs(self, m, pis)
1084 """get_version_info(ExampleSingletonModifier self) -> VersionInfo"""
1085 return _IMP_example.ExampleSingletonModifier_get_version_info(self)
1089 """__str__(ExampleSingletonModifier self) -> std::string"""
1090 return _IMP_example.ExampleSingletonModifier___str__(self)
1094 """__repr__(ExampleSingletonModifier self) -> std::string"""
1095 return _IMP_example.ExampleSingletonModifier___repr__(self)
1100 return _object_cast_to_ExampleSingletonModifier(o)
1102 ExampleSingletonModifier_swigregister = _IMP_example.ExampleSingletonModifier_swigregister
1103 ExampleSingletonModifier_swigregister(ExampleSingletonModifier)
1106 """Proxy of C++ IMP::example::ExamplePairScore class."""
1108 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1110 def __init__(self, x0, k):
1111 """__init__(IMP::example::ExamplePairScore self, double x0, double k) -> ExamplePairScore"""
1112 this = _IMP_example.new_ExamplePairScore(x0, k)
1114 self.this.append(this)
1115 except __builtin__.Exception:
1119 """do_get_inputs(ExamplePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1120 return _IMP_example.ExamplePairScore_do_get_inputs(self, m, pis)
1124 """get_version_info(ExamplePairScore self) -> VersionInfo"""
1125 return _IMP_example.ExamplePairScore_get_version_info(self)
1129 """__str__(ExamplePairScore self) -> std::string"""
1130 return _IMP_example.ExamplePairScore___str__(self)
1134 """__repr__(ExamplePairScore self) -> std::string"""
1135 return _IMP_example.ExamplePairScore___repr__(self)
1140 return _object_cast_to_ExamplePairScore(o)
1142 ExamplePairScore_swigregister = _IMP_example.ExamplePairScore_swigregister
1143 ExamplePairScore_swigregister(ExamplePairScore)
1146 """Proxy of C++ IMP::example::ExampleSubsetFilterTable class."""
1148 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1150 def __init__(self, max_diff, pt):
1151 """__init__(IMP::example::ExampleSubsetFilterTable self, unsigned int max_diff, IMP::ParticlesTemp const & pt) -> ExampleSubsetFilterTable"""
1152 this = _IMP_example.new_ExampleSubsetFilterTable(max_diff, pt)
1154 self.this.append(this)
1155 except __builtin__.Exception:
1159 """get_version_info(ExampleSubsetFilterTable self) -> VersionInfo"""
1160 return _IMP_example.ExampleSubsetFilterTable_get_version_info(self)
1164 """__str__(ExampleSubsetFilterTable self) -> std::string"""
1165 return _IMP_example.ExampleSubsetFilterTable___str__(self)
1169 """__repr__(ExampleSubsetFilterTable self) -> std::string"""
1170 return _IMP_example.ExampleSubsetFilterTable___repr__(self)
1175 return _object_cast_to_ExampleSubsetFilterTable(o)
1177 ExampleSubsetFilterTable_swigregister = _IMP_example.ExampleSubsetFilterTable_swigregister
1178 ExampleSubsetFilterTable_swigregister(ExampleSubsetFilterTable)
1181 """Proxy of C++ IMP::example::ExampleConstraint class."""
1183 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1185 def __init__(self, p):
1186 """__init__(IMP::example::ExampleConstraint self, Particle p) -> ExampleConstraint"""
1187 this = _IMP_example.new_ExampleConstraint(p)
1189 self.this.append(this)
1190 except __builtin__.Exception:
1194 """do_get_inputs(ExampleConstraint self) -> IMP::ModelObjectsTemp"""
1195 return _IMP_example.ExampleConstraint_do_get_inputs(self)
1199 """do_get_outputs(ExampleConstraint self) -> IMP::ModelObjectsTemp"""
1200 return _IMP_example.ExampleConstraint_do_get_outputs(self)
1204 """get_key() -> IntKey"""
1205 return _IMP_example.ExampleConstraint_get_key()
1207 get_key = staticmethod(get_key)
1210 """get_version_info(ExampleConstraint self) -> VersionInfo"""
1211 return _IMP_example.ExampleConstraint_get_version_info(self)
1215 """__str__(ExampleConstraint self) -> std::string"""
1216 return _IMP_example.ExampleConstraint___str__(self)
1220 """__repr__(ExampleConstraint self) -> std::string"""
1221 return _IMP_example.ExampleConstraint___repr__(self)
1226 return _object_cast_to_ExampleConstraint(o)
1228 ExampleConstraint_swigregister = _IMP_example.ExampleConstraint_swigregister
1229 ExampleConstraint_swigregister(ExampleConstraint)
1231 def ExampleConstraint_get_key():
1232 """ExampleConstraint_get_key() -> IntKey"""
1233 return _IMP_example.ExampleConstraint_get_key()
1237 """create_serial_mover(Model m, IMP::ParticleIndexes const & pis) -> MonteCarloMover"""
1238 return _IMP_example.create_serial_mover(m, pis)
1242 optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs, IMP::PairPredicates const & excluded, IMP::OptimizerStates const & opt_states, IMP::LogLevel ll)
1243 optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs, IMP::PairPredicates const & excluded, IMP::OptimizerStates const & opt_states)
1244 optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs, IMP::PairPredicates const & excluded)
1245 optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs)
1246 optimize_balls(Model m, IMP::ParticleIndexes const & pis)
1248 return _IMP_example.optimize_balls(*args)
1252 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)
1253 optimize_assembly(Model m, IMP::ParticleIndexes const & components, IMP::RestraintsTemp const & interactions, IMP::RestraintsTemp const & other_restraints, BoundingBox3D bb, PairScore ev, double cutoff)
1255 return _IMP_example.optimize_assembly(*args)
1258 """get_number_of_incidences(IMP::ParticlesTemp const & psa, IMP::ParticlesTemp const & psb, double point_distance) -> unsigned int"""
1259 return _IMP_example.get_number_of_incidences(psa, psb, point_distance)
1262 """create_chain_restraint(Model m, IMP::ParticleIndexes const & ps, double length_factor, double k, std::string name) -> Restraint"""
1263 return _IMP_example.create_chain_restraint(m, ps, length_factor, k, name)
1266 """create_excluded_volume(Model m, IMP::ParticleIndexes const & ps, double k, std::string name) -> Restraint"""
1267 return _IMP_example.create_excluded_volume(m, ps, k, name)
1269 """Proxy of C++ IMP::example::ExampleTemplateClassD<(3)> class."""
1271 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1273 def __init__(self, *args):
1275 __init__(IMP::example::ExampleTemplateClassD<(3)> self) -> ExampleTemplateClass3D
1276 __init__(IMP::example::ExampleTemplateClassD<(3)> self, Vector3D a, Vector3D b) -> ExampleTemplateClass3D
1278 this = _IMP_example.new_ExampleTemplateClass3D(*args)
1280 self.this.append(this)
1281 except __builtin__.Exception:
1284 def get_point(self, i):
1285 """get_point(ExampleTemplateClass3D self, unsigned int i) -> Vector3D"""
1286 return _IMP_example.ExampleTemplateClass3D_get_point(self, i)
1289 def show(self, *args):
1291 show(ExampleTemplateClass3D self, _ostream out)
1292 show(ExampleTemplateClass3D self)
1294 return _IMP_example.ExampleTemplateClass3D_show(self, *args)
1298 """__str__(ExampleTemplateClass3D self) -> std::string"""
1299 return _IMP_example.ExampleTemplateClass3D___str__(self)
1303 """__repr__(ExampleTemplateClass3D self) -> std::string"""
1304 return _IMP_example.ExampleTemplateClass3D___repr__(self)
1306 __swig_destroy__ = _IMP_example.delete_ExampleTemplateClass3D
1307 __del__ =
lambda self:
None
1308 ExampleTemplateClass3D_swigregister = _IMP_example.ExampleTemplateClass3D_swigregister
1309 ExampleTemplateClass3D_swigregister(ExampleTemplateClass3D)
1313 """get_module_version() -> std::string const"""
1314 return _IMP_example.get_module_version()
1317 """get_example_path(std::string fname) -> std::string"""
1318 return _IMP_example.get_example_path(fname)
1321 """get_data_path(std::string fname) -> std::string"""
1322 return _IMP_example.get_data_path(fname)
1324 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.
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())
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.