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_gsl')).lstrip(
'.')
22 return importlib.import_module(mname)
24 return importlib.import_module(
'_IMP_gsl')
25 _IMP_gsl = 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_gsl', [dirname(__file__)])
39 _mod = imp.load_module(
'_IMP_gsl', fp, pathname, description)
43 _IMP_gsl = 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_GSL_SwigPyIterator(object):
114 """Proxy of C++ swig::IMP_GSL_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_gsl.delete_IMP_GSL_SwigPyIterator
122 __del__ =
lambda self:
None
125 """value(IMP_GSL_SwigPyIterator self) -> PyObject *"""
126 return _IMP_gsl.IMP_GSL_SwigPyIterator_value(self)
131 incr(IMP_GSL_SwigPyIterator self, size_t n=1) -> IMP_GSL_SwigPyIterator
132 incr(IMP_GSL_SwigPyIterator self) -> IMP_GSL_SwigPyIterator
134 return _IMP_gsl.IMP_GSL_SwigPyIterator_incr(self, n)
139 decr(IMP_GSL_SwigPyIterator self, size_t n=1) -> IMP_GSL_SwigPyIterator
140 decr(IMP_GSL_SwigPyIterator self) -> IMP_GSL_SwigPyIterator
142 return _IMP_gsl.IMP_GSL_SwigPyIterator_decr(self, n)
145 def distance(self, x):
146 """distance(IMP_GSL_SwigPyIterator self, IMP_GSL_SwigPyIterator x) -> ptrdiff_t"""
147 return _IMP_gsl.IMP_GSL_SwigPyIterator_distance(self, x)
151 """equal(IMP_GSL_SwigPyIterator self, IMP_GSL_SwigPyIterator x) -> bool"""
152 return _IMP_gsl.IMP_GSL_SwigPyIterator_equal(self, x)
156 """copy(IMP_GSL_SwigPyIterator self) -> IMP_GSL_SwigPyIterator"""
157 return _IMP_gsl.IMP_GSL_SwigPyIterator_copy(self)
161 """next(IMP_GSL_SwigPyIterator self) -> PyObject *"""
162 return _IMP_gsl.IMP_GSL_SwigPyIterator_next(self)
166 """__next__(IMP_GSL_SwigPyIterator self) -> PyObject *"""
167 return _IMP_gsl.IMP_GSL_SwigPyIterator___next__(self)
171 """previous(IMP_GSL_SwigPyIterator self) -> PyObject *"""
172 return _IMP_gsl.IMP_GSL_SwigPyIterator_previous(self)
175 def advance(self, n):
176 """advance(IMP_GSL_SwigPyIterator self, ptrdiff_t n) -> IMP_GSL_SwigPyIterator"""
177 return _IMP_gsl.IMP_GSL_SwigPyIterator_advance(self, n)
181 """__eq__(IMP_GSL_SwigPyIterator self, IMP_GSL_SwigPyIterator x) -> bool"""
182 return _IMP_gsl.IMP_GSL_SwigPyIterator___eq__(self, x)
186 """__ne__(IMP_GSL_SwigPyIterator self, IMP_GSL_SwigPyIterator x) -> bool"""
187 return _IMP_gsl.IMP_GSL_SwigPyIterator___ne__(self, x)
190 def __iadd__(self, n):
191 """__iadd__(IMP_GSL_SwigPyIterator self, ptrdiff_t n) -> IMP_GSL_SwigPyIterator"""
192 return _IMP_gsl.IMP_GSL_SwigPyIterator___iadd__(self, n)
195 def __isub__(self, n):
196 """__isub__(IMP_GSL_SwigPyIterator self, ptrdiff_t n) -> IMP_GSL_SwigPyIterator"""
197 return _IMP_gsl.IMP_GSL_SwigPyIterator___isub__(self, n)
200 def __add__(self, n):
201 """__add__(IMP_GSL_SwigPyIterator self, ptrdiff_t n) -> IMP_GSL_SwigPyIterator"""
202 return _IMP_gsl.IMP_GSL_SwigPyIterator___add__(self, n)
205 def __sub__(self, *args):
207 __sub__(IMP_GSL_SwigPyIterator self, ptrdiff_t n) -> IMP_GSL_SwigPyIterator
208 __sub__(IMP_GSL_SwigPyIterator self, IMP_GSL_SwigPyIterator x) -> ptrdiff_t
210 return _IMP_gsl.IMP_GSL_SwigPyIterator___sub__(self, *args)
214 IMP_GSL_SwigPyIterator_swigregister = _IMP_gsl.IMP_GSL_SwigPyIterator_swigregister
215 IMP_GSL_SwigPyIterator_swigregister(IMP_GSL_SwigPyIterator)
223 IMP_DEBUG = _IMP_gsl.IMP_DEBUG
224 IMP_RELEASE = _IMP_gsl.IMP_RELEASE
225 IMP_SILENT = _IMP_gsl.IMP_SILENT
226 IMP_PROGRESS = _IMP_gsl.IMP_PROGRESS
227 IMP_TERSE = _IMP_gsl.IMP_TERSE
228 IMP_VERBOSE = _IMP_gsl.IMP_VERBOSE
229 IMP_MEMORY = _IMP_gsl.IMP_MEMORY
230 IMP_NONE = _IMP_gsl.IMP_NONE
231 IMP_USAGE = _IMP_gsl.IMP_USAGE
232 IMP_INTERNAL = _IMP_gsl.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_gsl.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_gsl.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_gsl.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_gsl.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_gsl.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_gsl.IMP_KERNEL_HAS_GPERFTOOLS
239 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_gsl.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
240 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_gsl.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
241 IMPKERNEL_SHOW_WARNINGS = _IMP_gsl.IMPKERNEL_SHOW_WARNINGS
244 class _DirectorObjects(object):
245 """@internal Simple class to keep references to director objects
246 to prevent premature deletion."""
249 def register(self, obj):
250 """Take a reference to a director object; will only work for
251 refcounted C++ classes"""
252 if hasattr(obj,
'get_ref_count'):
253 self._objects.append(obj)
255 """Only drop our reference and allow cleanup by Python if no other
256 Python references exist (we hold 3 references: one in self._objects,
257 one in x, and one in the argument list for getrefcount) *and* no
258 other C++ references exist (the Python object always holds one)"""
259 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
260 or x.get_ref_count() > 1]
264 def get_object_count(self):
265 """Get number of director objects (useful for testing only)"""
266 return len(self._objects)
267 _director_objects = _DirectorObjects()
269 class _ostream(object):
270 """Proxy of C++ std::ostream class."""
272 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
274 def __init__(self, *args, **kwargs):
275 raise AttributeError(
"No constructor defined")
276 __repr__ = _swig_repr
278 def write(self, osa_buf):
279 """write(_ostream self, char const * osa_buf)"""
280 return _IMP_gsl._ostream_write(self, osa_buf)
282 _ostream_swigregister = _IMP_gsl._ostream_swigregister
283 _ostream_swigregister(_ostream)
285 IMP_COMPILER_HAS_OVERRIDE = _IMP_gsl.IMP_COMPILER_HAS_OVERRIDE
286 IMP_COMPILER_HAS_FINAL = _IMP_gsl.IMP_COMPILER_HAS_FINAL
287 IMP_HAS_NOEXCEPT = _IMP_gsl.IMP_HAS_NOEXCEPT
289 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_gsl.IMP_CGAL_HAS_BOOST_FILESYSTEM
290 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_gsl.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
291 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_gsl.IMP_CGAL_HAS_BOOST_RANDOM
292 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_gsl.IMP_CGAL_HAS_BOOST_SYSTEM
293 IMPCGAL_SHOW_WARNINGS = _IMP_gsl.IMPCGAL_SHOW_WARNINGS
295 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_gsl.IMP_ALGEBRA_HAS_IMP_CGAL
296 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_gsl.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
297 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_gsl.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
298 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_gsl.IMP_ALGEBRA_HAS_BOOST_RANDOM
299 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_gsl.IMP_ALGEBRA_HAS_BOOST_SYSTEM
300 IMP_ALGEBRA_HAS_CGAL = _IMP_gsl.IMP_ALGEBRA_HAS_CGAL
301 IMP_ALGEBRA_HAS_ANN = _IMP_gsl.IMP_ALGEBRA_HAS_ANN
302 IMPALGEBRA_SHOW_WARNINGS = _IMP_gsl.IMPALGEBRA_SHOW_WARNINGS
304 IMP_GSL_HAS_IMP_CGAL = _IMP_gsl.IMP_GSL_HAS_IMP_CGAL
305 IMP_GSL_HAS_BOOST_FILESYSTEM = _IMP_gsl.IMP_GSL_HAS_BOOST_FILESYSTEM
306 IMP_GSL_HAS_BOOST_PROGRAMOPTIONS = _IMP_gsl.IMP_GSL_HAS_BOOST_PROGRAMOPTIONS
307 IMP_GSL_HAS_BOOST_RANDOM = _IMP_gsl.IMP_GSL_HAS_BOOST_RANDOM
308 IMP_GSL_HAS_BOOST_SYSTEM = _IMP_gsl.IMP_GSL_HAS_BOOST_SYSTEM
309 IMP_GSL_HAS_CGAL = _IMP_gsl.IMP_GSL_HAS_CGAL
310 IMPGSL_SHOW_WARNINGS = _IMP_gsl.IMPGSL_SHOW_WARNINGS
312 _object_types.append(
"GSLOptimizer")
315 def _object_cast_to_GSLOptimizer(o):
316 """_object_cast_to_GSLOptimizer(Object o) -> GSLOptimizer"""
317 return _IMP_gsl._object_cast_to_GSLOptimizer(o)
319 _object_types.append(
"ConjugateGradients")
322 def _object_cast_to_ConjugateGradients(o):
323 """_object_cast_to_ConjugateGradients(Object o) -> ConjugateGradients"""
324 return _IMP_gsl._object_cast_to_ConjugateGradients(o)
326 _object_types.append(
"QuasiNewton")
329 def _object_cast_to_QuasiNewton(o):
330 """_object_cast_to_QuasiNewton(Object o) -> QuasiNewton"""
331 return _IMP_gsl._object_cast_to_QuasiNewton(o)
333 _object_types.append(
"Simplex")
336 def _object_cast_to_Simplex(o):
337 """_object_cast_to_Simplex(Object o) -> Simplex"""
338 return _IMP_gsl._object_cast_to_Simplex(o)
340 """Proxy of C++ IMP::gsl::GSLOptimizer class."""
342 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
344 def __init__(self, m):
345 """__init__(IMP::gsl::GSLOptimizer self, Model m) -> GSLOptimizer"""
346 if self.__class__ == GSLOptimizer:
350 this = _IMP_gsl.new_GSLOptimizer(_self, m)
352 self.this.append(this)
353 except __builtin__.Exception:
356 if self.__class__ != GSLOptimizer:
357 _director_objects.register(self)
361 __swig_destroy__ = _IMP_gsl.delete_GSLOptimizer
362 __del__ =
lambda self:
None
364 def set_stop_score(self, d):
365 """set_stop_score(GSLOptimizer self, double d)"""
366 return _IMP_gsl.GSLOptimizer_set_stop_score(self, d)
370 """__str__(GSLOptimizer self) -> std::string"""
371 return _IMP_gsl.GSLOptimizer___str__(self)
375 """__repr__(GSLOptimizer self) -> std::string"""
376 return _IMP_gsl.GSLOptimizer___repr__(self)
381 return _object_cast_to_GSLOptimizer(o)
384 def get_type_name(self):
385 return self.__class__.__name__
386 def do_show(self, out):
389 if"IMP::gsl" ==
"IMP":
390 return VersionInfo(self.__module__,
391 __import__(self.__module__).get_module_version())
394 __import__(self.__module__).get_module_version())
397 return _object_cast_to_GSLOptimizer(o)
399 def __disown__(self):
401 _IMP_gsl.disown_GSLOptimizer(self)
402 return weakref_proxy(self)
405 """do_destroy(GSLOptimizer self)"""
406 return _IMP_gsl.GSLOptimizer_do_destroy(self)
409 def handle_set_has_required_score_states(self, arg0):
410 """handle_set_has_required_score_states(GSLOptimizer self, bool arg0)"""
411 return _IMP_gsl.GSLOptimizer_handle_set_has_required_score_states(self, arg0)
415 """do_get_inputs(GSLOptimizer self) -> IMP::ModelObjectsTemp"""
416 return _IMP_gsl.GSLOptimizer_do_get_inputs(self)
420 """do_get_outputs(GSLOptimizer self) -> IMP::ModelObjectsTemp"""
421 return _IMP_gsl.GSLOptimizer_do_get_outputs(self)
424 def do_get_interactions(self):
425 """do_get_interactions(GSLOptimizer self) -> IMP::ModelObjectsTemps"""
426 return _IMP_gsl.GSLOptimizer_do_get_interactions(self)
429 def do_optimize(self, ns):
430 """do_optimize(GSLOptimizer self, unsigned int ns) -> double"""
431 return _IMP_gsl.GSLOptimizer_do_optimize(self, ns)
433 GSLOptimizer_swigregister = _IMP_gsl.GSLOptimizer_swigregister
434 GSLOptimizer_swigregister(GSLOptimizer)
436 class ConjugateGradients(GSLOptimizer):
437 """Proxy of C++ IMP::gsl::ConjugateGradients class."""
439 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
441 def __init__(self, m):
442 """__init__(IMP::gsl::ConjugateGradients self, Model m) -> ConjugateGradients"""
443 this = _IMP_gsl.new_ConjugateGradients(m)
445 self.this.append(this)
446 except __builtin__.Exception:
449 def set_threshold(self, mg):
450 """set_threshold(ConjugateGradients self, double mg)"""
451 return _IMP_gsl.ConjugateGradients_set_threshold(self, mg)
454 def do_optimize(self, max_steps):
455 """do_optimize(ConjugateGradients self, unsigned int max_steps) -> IMP::Float"""
456 return _IMP_gsl.ConjugateGradients_do_optimize(self, max_steps)
460 """get_version_info(ConjugateGradients self) -> VersionInfo"""
461 return _IMP_gsl.ConjugateGradients_get_version_info(self)
465 """__str__(ConjugateGradients self) -> std::string"""
466 return _IMP_gsl.ConjugateGradients___str__(self)
470 """__repr__(ConjugateGradients self) -> std::string"""
471 return _IMP_gsl.ConjugateGradients___repr__(self)
476 return _object_cast_to_ConjugateGradients(o)
478 ConjugateGradients_swigregister = _IMP_gsl.ConjugateGradients_swigregister
479 ConjugateGradients_swigregister(ConjugateGradients)
481 class QuasiNewton(GSLOptimizer):
482 """Proxy of C++ IMP::gsl::QuasiNewton class."""
484 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
486 def __init__(self, m):
487 """__init__(IMP::gsl::QuasiNewton self, Model m) -> QuasiNewton"""
488 this = _IMP_gsl.new_QuasiNewton(m)
490 self.this.append(this)
491 except __builtin__.Exception:
494 def set_initial_step(self, length):
495 """set_initial_step(QuasiNewton self, double length)"""
496 return _IMP_gsl.QuasiNewton_set_initial_step(self, length)
499 def set_line_step(self, d):
500 """set_line_step(QuasiNewton self, double d)"""
501 return _IMP_gsl.QuasiNewton_set_line_step(self, d)
504 def set_minimum_gradient(self, d):
505 """set_minimum_gradient(QuasiNewton self, double d)"""
506 return _IMP_gsl.QuasiNewton_set_minimum_gradient(self, d)
509 def do_optimize(self, max_steps):
510 """do_optimize(QuasiNewton self, unsigned int max_steps) -> IMP::Float"""
511 return _IMP_gsl.QuasiNewton_do_optimize(self, max_steps)
515 """get_version_info(QuasiNewton self) -> VersionInfo"""
516 return _IMP_gsl.QuasiNewton_get_version_info(self)
520 """__str__(QuasiNewton self) -> std::string"""
521 return _IMP_gsl.QuasiNewton___str__(self)
525 """__repr__(QuasiNewton self) -> std::string"""
526 return _IMP_gsl.QuasiNewton___repr__(self)
531 return _object_cast_to_QuasiNewton(o)
533 QuasiNewton_swigregister = _IMP_gsl.QuasiNewton_swigregister
534 QuasiNewton_swigregister(QuasiNewton)
536 class Simplex(GSLOptimizer):
537 """Proxy of C++ IMP::gsl::Simplex class."""
539 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
541 def __init__(self, m):
542 """__init__(IMP::gsl::Simplex self, Model m) -> Simplex"""
543 this = _IMP_gsl.new_Simplex(m)
545 self.this.append(this)
546 except __builtin__.Exception:
549 def set_initial_length(self, length):
550 """set_initial_length(Simplex self, double length)"""
551 return _IMP_gsl.Simplex_set_initial_length(self, length)
554 def set_minimum_size(self, d):
555 """set_minimum_size(Simplex self, double d)"""
556 return _IMP_gsl.Simplex_set_minimum_size(self, d)
559 def do_optimize(self, max_steps):
560 """do_optimize(Simplex self, unsigned int max_steps) -> IMP::Float"""
561 return _IMP_gsl.Simplex_do_optimize(self, max_steps)
565 """get_version_info(Simplex self) -> VersionInfo"""
566 return _IMP_gsl.Simplex_get_version_info(self)
570 """__str__(Simplex self) -> std::string"""
571 return _IMP_gsl.Simplex___str__(self)
575 """__repr__(Simplex self) -> std::string"""
576 return _IMP_gsl.Simplex___repr__(self)
581 return _object_cast_to_Simplex(o)
583 Simplex_swigregister = _IMP_gsl.Simplex_swigregister
584 Simplex_swigregister(Simplex)
587 def get_module_version():
588 """get_module_version() -> std::string const"""
589 return _IMP_gsl.get_module_version()
592 """get_example_path(std::string fname) -> std::string"""
593 return _IMP_gsl.get_example_path(fname)
596 """get_data_path(std::string fname) -> std::string"""
597 return _IMP_gsl.get_data_path(fname)
599 from .
import _version_check
600 _version_check.check_version(get_module_version())
601 __version__ = get_module_version()
Make CGAL functionality available to IMP.
virtual ModelObjectsTemp do_get_outputs(Model *m, const ParticleIndexes &pis) const =0
Overload this method to specify the outputs.
virtual void do_destroy()
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const =0
Overload this method to specify the inputs.
Version and module information for Objects.
Base class for optimizers that act on individual attributes.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
virtual VersionInfo get_version_info() const
Get information about the module and version of the object.
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.