gsl/__init__.py

# This file was automatically generated by SWIG (http://www.swig.org).
# Version 3.0.10
#
# Do not make changes to this file unless you know what you are doing--modify
# the SWIG interface file instead.

# This wrapper is part of IMP,
# Copyright 2007-2018 IMP Inventors. All rights reserved.

from __future__ import print_function, division, absolute_import




from sys import version_info as _swig_python_version_info
if _swig_python_version_info >= (2, 7, 0):
    def swig_import_helper():
        import importlib
        pkg = __name__.rpartition('.')[0]
        mname = '.'.join((pkg, '_IMP_gsl')).lstrip('.')
        try:
            return importlib.import_module(mname)
        except ImportError:
            return importlib.import_module('_IMP_gsl')
    _IMP_gsl = swig_import_helper()
    del swig_import_helper
elif _swig_python_version_info >= (2, 6, 0):
    def swig_import_helper():
        from os.path import dirname
        import imp
        fp = None
        try:
            fp, pathname, description = imp.find_module('_IMP_gsl', [dirname(__file__)])
        except ImportError:
            import _IMP_gsl
            return _IMP_gsl
        if fp is not None:
            try:
                _mod = imp.load_module('_IMP_gsl', fp, pathname, description)
            finally:
                fp.close()
            return _mod
    _IMP_gsl = swig_import_helper()
    del swig_import_helper
else:
    import _IMP_gsl
del _swig_python_version_info
try:
    _swig_property = property
except NameError:
    pass  # Python < 2.2 doesn't have 'property'.

try:
    import builtins as __builtin__
except ImportError:
    import __builtin__

def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
    if (name == "thisown"):
        return self.this.own(value)
    if (name == "this"):
        if type(value).__name__ == 'SwigPyObject':
            self.__dict__[name] = value
            return
    method = class_type.__swig_setmethods__.get(name, None)
    if method:
        return method(self, value)
    if (not static):
        object.__setattr__(self, name, value)
    else:
        raise AttributeError("You cannot add attributes to %s" % self)


def _swig_setattr(self, class_type, name, value):
    return _swig_setattr_nondynamic(self, class_type, name, value, 0)


def _swig_getattr(self, class_type, name):
    if (name == "thisown"):
        return self.this.own()
    method = class_type.__swig_getmethods__.get(name, None)
    if method:
        return method(self)
    raise AttributeError("'%s' object has no attribute '%s'" % (class_type.__name__, name))


def _swig_repr(self):
    try:
        strthis = "proxy of " + self.this.__repr__()
    except __builtin__.Exception:
        strthis = ""
    return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)


def _swig_setattr_nondynamic_method(set):
    def set_attr(self, name, value):
        if (name == "thisown"):
            return self.this.own(value)
        if hasattr(self, name) or (name == "this"):
            set(self, name, value)
        else:
            raise AttributeError("You cannot add attributes to %s" % self)
    return set_attr


try:
    import weakref
    weakref_proxy = weakref.proxy
except __builtin__.Exception:
    weakref_proxy = lambda x: x


class IMP_GSL_SwigPyIterator(object):
    """Proxy of C++ swig::IMP_GSL_SwigPyIterator class."""

    thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')

    def __init__(self, *args, **kwargs):
        raise AttributeError("No constructor defined - class is abstract")
    __repr__ = _swig_repr
    __swig_destroy__ = _IMP_gsl.delete_IMP_GSL_SwigPyIterator
    __del__ = lambda self: None

    def value(self):
        """value(IMP_GSL_SwigPyIterator self) -> PyObject *"""
        return _IMP_gsl.IMP_GSL_SwigPyIterator_value(self)


    def incr(self, n=1):
        """
        incr(IMP_GSL_SwigPyIterator self, size_t n=1) -> IMP_GSL_SwigPyIterator
        incr(IMP_GSL_SwigPyIterator self) -> IMP_GSL_SwigPyIterator
        """
        return _IMP_gsl.IMP_GSL_SwigPyIterator_incr(self, n)


    def decr(self, n=1):
        """
        decr(IMP_GSL_SwigPyIterator self, size_t n=1) -> IMP_GSL_SwigPyIterator
        decr(IMP_GSL_SwigPyIterator self) -> IMP_GSL_SwigPyIterator
        """
        return _IMP_gsl.IMP_GSL_SwigPyIterator_decr(self, n)


    def distance(self, x):
        """distance(IMP_GSL_SwigPyIterator self, IMP_GSL_SwigPyIterator x) -> ptrdiff_t"""
        return _IMP_gsl.IMP_GSL_SwigPyIterator_distance(self, x)


    def equal(self, x):
        """equal(IMP_GSL_SwigPyIterator self, IMP_GSL_SwigPyIterator x) -> bool"""
        return _IMP_gsl.IMP_GSL_SwigPyIterator_equal(self, x)


    def copy(self):
        """copy(IMP_GSL_SwigPyIterator self) -> IMP_GSL_SwigPyIterator"""
        return _IMP_gsl.IMP_GSL_SwigPyIterator_copy(self)


    def next(self):
        """next(IMP_GSL_SwigPyIterator self) -> PyObject *"""
        return _IMP_gsl.IMP_GSL_SwigPyIterator_next(self)


    def __next__(self):
        """__next__(IMP_GSL_SwigPyIterator self) -> PyObject *"""
        return _IMP_gsl.IMP_GSL_SwigPyIterator___next__(self)


    def previous(self):
        """previous(IMP_GSL_SwigPyIterator self) -> PyObject *"""
        return _IMP_gsl.IMP_GSL_SwigPyIterator_previous(self)


    def advance(self, n):
        """advance(IMP_GSL_SwigPyIterator self, ptrdiff_t n) -> IMP_GSL_SwigPyIterator"""
        return _IMP_gsl.IMP_GSL_SwigPyIterator_advance(self, n)


    def __eq__(self, x):
        """__eq__(IMP_GSL_SwigPyIterator self, IMP_GSL_SwigPyIterator x) -> bool"""
        return _IMP_gsl.IMP_GSL_SwigPyIterator___eq__(self, x)


    def __ne__(self, x):
        """__ne__(IMP_GSL_SwigPyIterator self, IMP_GSL_SwigPyIterator x) -> bool"""
        return _IMP_gsl.IMP_GSL_SwigPyIterator___ne__(self, x)


    def __iadd__(self, n):
        """__iadd__(IMP_GSL_SwigPyIterator self, ptrdiff_t n) -> IMP_GSL_SwigPyIterator"""
        return _IMP_gsl.IMP_GSL_SwigPyIterator___iadd__(self, n)


    def __isub__(self, n):
        """__isub__(IMP_GSL_SwigPyIterator self, ptrdiff_t n) -> IMP_GSL_SwigPyIterator"""
        return _IMP_gsl.IMP_GSL_SwigPyIterator___isub__(self, n)


    def __add__(self, n):
        """__add__(IMP_GSL_SwigPyIterator self, ptrdiff_t n) -> IMP_GSL_SwigPyIterator"""
        return _IMP_gsl.IMP_GSL_SwigPyIterator___add__(self, n)


    def __sub__(self, *args):
        """
        __sub__(IMP_GSL_SwigPyIterator self, ptrdiff_t n) -> IMP_GSL_SwigPyIterator
        __sub__(IMP_GSL_SwigPyIterator self, IMP_GSL_SwigPyIterator x) -> ptrdiff_t
        """
        return _IMP_gsl.IMP_GSL_SwigPyIterator___sub__(self, *args)

    def __iter__(self):
        return self
IMP_GSL_SwigPyIterator_swigregister = _IMP_gsl.IMP_GSL_SwigPyIterator_swigregister
IMP_GSL_SwigPyIterator_swigregister(IMP_GSL_SwigPyIterator)


_value_types=[]
_object_types=[]
_raii_types=[]
_plural_types=[]

IMP_DEBUG = _IMP_gsl.IMP_DEBUG
IMP_RELEASE = _IMP_gsl.IMP_RELEASE
IMP_SILENT = _IMP_gsl.IMP_SILENT
IMP_PROGRESS = _IMP_gsl.IMP_PROGRESS
IMP_TERSE = _IMP_gsl.IMP_TERSE
IMP_VERBOSE = _IMP_gsl.IMP_VERBOSE
IMP_MEMORY = _IMP_gsl.IMP_MEMORY
IMP_NONE = _IMP_gsl.IMP_NONE
IMP_USAGE = _IMP_gsl.IMP_USAGE
IMP_INTERNAL = _IMP_gsl.IMP_INTERNAL
IMP_KERNEL_HAS_LOG4CXX = _IMP_gsl.IMP_KERNEL_HAS_LOG4CXX
IMP_COMPILER_HAS_AUTO = _IMP_gsl.IMP_COMPILER_HAS_AUTO
IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_gsl.IMP_COMPILER_HAS_DEBUG_VECTOR
IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_gsl.IMP_COMPILER_HAS_UNIQUE_PTR
IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_gsl.IMP_KERNEL_HAS_BOOST_RANDOM
IMP_KERNEL_HAS_GPERFTOOLS = _IMP_gsl.IMP_KERNEL_HAS_GPERFTOOLS
IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_gsl.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_gsl.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
IMPKERNEL_SHOW_WARNINGS = _IMP_gsl.IMPKERNEL_SHOW_WARNINGS

import sys
class _DirectorObjects(object):
    """@internal Simple class to keep references to director objects
       to prevent premature deletion."""
    def __init__(self):
        self._objects = []
    def register(self, obj):
        """Take a reference to a director object; will only work for
           refcounted C++ classes"""
        if hasattr(obj, 'get_ref_count'):
            self._objects.append(obj)
    def cleanup(self):
        """Only drop our reference and allow cleanup by Python if no other
           Python references exist (we hold 3 references: one in self._objects,
           one in x, and one in the argument list for getrefcount) *and* no
           other C++ references exist (the Python object always holds one)"""
        objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
                                         or x.get_ref_count() > 1]
# Do in two steps so the references are kept until the end of the
# function (deleting references may trigger a fresh call to this method)
        self._objects = objs
    def get_object_count(self):
        """Get number of director objects (useful for testing only)"""
        return len(self._objects)
_director_objects = _DirectorObjects()

class _ostream(object):
    """Proxy of C++ std::ostream class."""

    thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')

    def __init__(self, *args, **kwargs):
        raise AttributeError("No constructor defined")
    __repr__ = _swig_repr

    def write(self, osa_buf):
        """write(_ostream self, char const * osa_buf)"""
        return _IMP_gsl._ostream_write(self, osa_buf)

_ostream_swigregister = _IMP_gsl._ostream_swigregister
_ostream_swigregister(_ostream)

IMP_COMPILER_HAS_OVERRIDE = _IMP_gsl.IMP_COMPILER_HAS_OVERRIDE
IMP_COMPILER_HAS_FINAL = _IMP_gsl.IMP_COMPILER_HAS_FINAL
IMP_HAS_NOEXCEPT = _IMP_gsl.IMP_HAS_NOEXCEPT
IMP_C_OPEN_BINARY = _IMP_gsl.IMP_C_OPEN_BINARY
import IMP
IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_gsl.IMP_CGAL_HAS_BOOST_FILESYSTEM
IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_gsl.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
IMP_CGAL_HAS_BOOST_RANDOM = _IMP_gsl.IMP_CGAL_HAS_BOOST_RANDOM
IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_gsl.IMP_CGAL_HAS_BOOST_SYSTEM
IMPCGAL_SHOW_WARNINGS = _IMP_gsl.IMPCGAL_SHOW_WARNINGS
import IMP.cgal
IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_gsl.IMP_ALGEBRA_HAS_IMP_CGAL
IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_gsl.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_gsl.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_gsl.IMP_ALGEBRA_HAS_BOOST_RANDOM
IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_gsl.IMP_ALGEBRA_HAS_BOOST_SYSTEM
IMP_ALGEBRA_HAS_CGAL = _IMP_gsl.IMP_ALGEBRA_HAS_CGAL
IMP_ALGEBRA_HAS_ANN = _IMP_gsl.IMP_ALGEBRA_HAS_ANN
IMPALGEBRA_SHOW_WARNINGS = _IMP_gsl.IMPALGEBRA_SHOW_WARNINGS
import IMP.algebra
IMP_GSL_HAS_IMP_CGAL = _IMP_gsl.IMP_GSL_HAS_IMP_CGAL
IMP_GSL_HAS_BOOST_FILESYSTEM = _IMP_gsl.IMP_GSL_HAS_BOOST_FILESYSTEM
IMP_GSL_HAS_BOOST_PROGRAMOPTIONS = _IMP_gsl.IMP_GSL_HAS_BOOST_PROGRAMOPTIONS
IMP_GSL_HAS_BOOST_RANDOM = _IMP_gsl.IMP_GSL_HAS_BOOST_RANDOM
IMP_GSL_HAS_BOOST_SYSTEM = _IMP_gsl.IMP_GSL_HAS_BOOST_SYSTEM
IMP_GSL_HAS_CGAL = _IMP_gsl.IMP_GSL_HAS_CGAL
IMPGSL_SHOW_WARNINGS = _IMP_gsl.IMPGSL_SHOW_WARNINGS

_object_types.append("GSLOptimizer")


def _object_cast_to_GSLOptimizer(o):
    """_object_cast_to_GSLOptimizer(Object o) -> GSLOptimizer"""
    return _IMP_gsl._object_cast_to_GSLOptimizer(o)

_object_types.append("ConjugateGradients")


def _object_cast_to_ConjugateGradients(o):
    """_object_cast_to_ConjugateGradients(Object o) -> ConjugateGradients"""
    return _IMP_gsl._object_cast_to_ConjugateGradients(o)

_object_types.append("QuasiNewton")


def _object_cast_to_QuasiNewton(o):
    """_object_cast_to_QuasiNewton(Object o) -> QuasiNewton"""
    return _IMP_gsl._object_cast_to_QuasiNewton(o)

_object_types.append("Simplex")


def _object_cast_to_Simplex(o):
    """_object_cast_to_Simplex(Object o) -> Simplex"""
    return _IMP_gsl._object_cast_to_Simplex(o)
class GSLOptimizer(IMP.AttributeOptimizer):
    """Proxy of C++ IMP::gsl::GSLOptimizer class."""

    thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')

    def __init__(self, m):
        """__init__(IMP::gsl::GSLOptimizer self, Model m) -> GSLOptimizer"""
        if self.__class__ == GSLOptimizer:
            _self = None
        else:
            _self = self
        this = _IMP_gsl.new_GSLOptimizer(_self, m)
        try:
            self.this.append(this)
        except __builtin__.Exception:
            self.this = this

        if self.__class__ != GSLOptimizer:
            _director_objects.register(self)



    __swig_destroy__ = _IMP_gsl.delete_GSLOptimizer
    __del__ = lambda self: None

    def set_stop_score(self, d):
        """set_stop_score(GSLOptimizer self, double d)"""
        return _IMP_gsl.GSLOptimizer_set_stop_score(self, d)


    def __str__(self):
        """__str__(GSLOptimizer self) -> std::string"""
        return _IMP_gsl.GSLOptimizer___str__(self)


    def __repr__(self):
        """__repr__(GSLOptimizer self) -> std::string"""
        return _IMP_gsl.GSLOptimizer___repr__(self)


    @staticmethod
    def get_from(o):
       return _object_cast_to_GSLOptimizer(o)


    def get_type_name(self):
        return self.__class__.__name__
    def do_show(self, out):
        pass
    def get_version_info(self):
        if"IMP::gsl" == "IMP":
          return VersionInfo(self.__module__,
                             __import__(self.__module__).get_module_version())
        else:
          return IMP.VersionInfo(self.__module__,
                             __import__(self.__module__).get_module_version())
    @staticmethod
    def get_from(o):
       return _object_cast_to_GSLOptimizer(o)

    def __disown__(self):
        self.this.disown()
        _IMP_gsl.disown_GSLOptimizer(self)
        return weakref_proxy(self)

    def do_destroy(self):
        """do_destroy(GSLOptimizer self)"""
        return _IMP_gsl.GSLOptimizer_do_destroy(self)


    def handle_set_has_required_score_states(self, arg0):
        """handle_set_has_required_score_states(GSLOptimizer self, bool arg0)"""
        return _IMP_gsl.GSLOptimizer_handle_set_has_required_score_states(self, arg0)


    def do_get_inputs(self):
        """do_get_inputs(GSLOptimizer self) -> IMP::ModelObjectsTemp"""
        return _IMP_gsl.GSLOptimizer_do_get_inputs(self)


    def do_get_outputs(self):
        """do_get_outputs(GSLOptimizer self) -> IMP::ModelObjectsTemp"""
        return _IMP_gsl.GSLOptimizer_do_get_outputs(self)


    def do_get_interactions(self):
        """do_get_interactions(GSLOptimizer self) -> IMP::ModelObjectsTemps"""
        return _IMP_gsl.GSLOptimizer_do_get_interactions(self)


    def do_optimize(self, ns):
        """do_optimize(GSLOptimizer self, unsigned int ns) -> double"""
        return _IMP_gsl.GSLOptimizer_do_optimize(self, ns)

GSLOptimizer_swigregister = _IMP_gsl.GSLOptimizer_swigregister
GSLOptimizer_swigregister(GSLOptimizer)

class ConjugateGradients(GSLOptimizer):
    """Proxy of C++ IMP::gsl::ConjugateGradients class."""

    thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')

    def __init__(self, m):
        """__init__(IMP::gsl::ConjugateGradients self, Model m) -> ConjugateGradients"""
        this = _IMP_gsl.new_ConjugateGradients(m)
        try:
            self.this.append(this)
        except __builtin__.Exception:
            self.this = this

    def set_threshold(self, mg):
        """set_threshold(ConjugateGradients self, double mg)"""
        return _IMP_gsl.ConjugateGradients_set_threshold(self, mg)


    def do_optimize(self, max_steps):
        """do_optimize(ConjugateGradients self, unsigned int max_steps) -> IMP::Float"""
        return _IMP_gsl.ConjugateGradients_do_optimize(self, max_steps)


    def get_version_info(self):
        """get_version_info(ConjugateGradients self) -> VersionInfo"""
        return _IMP_gsl.ConjugateGradients_get_version_info(self)


    def __str__(self):
        """__str__(ConjugateGradients self) -> std::string"""
        return _IMP_gsl.ConjugateGradients___str__(self)


    def __repr__(self):
        """__repr__(ConjugateGradients self) -> std::string"""
        return _IMP_gsl.ConjugateGradients___repr__(self)


    @staticmethod
    def get_from(o):
       return _object_cast_to_ConjugateGradients(o)

ConjugateGradients_swigregister = _IMP_gsl.ConjugateGradients_swigregister
ConjugateGradients_swigregister(ConjugateGradients)

class QuasiNewton(GSLOptimizer):
    """Proxy of C++ IMP::gsl::QuasiNewton class."""

    thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')

    def __init__(self, m):
        """__init__(IMP::gsl::QuasiNewton self, Model m) -> QuasiNewton"""
        this = _IMP_gsl.new_QuasiNewton(m)
        try:
            self.this.append(this)
        except __builtin__.Exception:
            self.this = this

    def set_initial_step(self, length):
        """set_initial_step(QuasiNewton self, double length)"""
        return _IMP_gsl.QuasiNewton_set_initial_step(self, length)


    def set_line_step(self, d):
        """set_line_step(QuasiNewton self, double d)"""
        return _IMP_gsl.QuasiNewton_set_line_step(self, d)


    def set_minimum_gradient(self, d):
        """set_minimum_gradient(QuasiNewton self, double d)"""
        return _IMP_gsl.QuasiNewton_set_minimum_gradient(self, d)


    def do_optimize(self, max_steps):
        """do_optimize(QuasiNewton self, unsigned int max_steps) -> IMP::Float"""
        return _IMP_gsl.QuasiNewton_do_optimize(self, max_steps)


    def get_version_info(self):
        """get_version_info(QuasiNewton self) -> VersionInfo"""
        return _IMP_gsl.QuasiNewton_get_version_info(self)


    def __str__(self):
        """__str__(QuasiNewton self) -> std::string"""
        return _IMP_gsl.QuasiNewton___str__(self)


    def __repr__(self):
        """__repr__(QuasiNewton self) -> std::string"""
        return _IMP_gsl.QuasiNewton___repr__(self)


    @staticmethod
    def get_from(o):
       return _object_cast_to_QuasiNewton(o)

QuasiNewton_swigregister = _IMP_gsl.QuasiNewton_swigregister
QuasiNewton_swigregister(QuasiNewton)

class Simplex(GSLOptimizer):
    """Proxy of C++ IMP::gsl::Simplex class."""

    thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')

    def __init__(self, m):
        """__init__(IMP::gsl::Simplex self, Model m) -> Simplex"""
        this = _IMP_gsl.new_Simplex(m)
        try:
            self.this.append(this)
        except __builtin__.Exception:
            self.this = this

    def set_initial_length(self, length):
        """set_initial_length(Simplex self, double length)"""
        return _IMP_gsl.Simplex_set_initial_length(self, length)


    def set_minimum_size(self, d):
        """set_minimum_size(Simplex self, double d)"""
        return _IMP_gsl.Simplex_set_minimum_size(self, d)


    def do_optimize(self, max_steps):
        """do_optimize(Simplex self, unsigned int max_steps) -> IMP::Float"""
        return _IMP_gsl.Simplex_do_optimize(self, max_steps)


    def get_version_info(self):
        """get_version_info(Simplex self) -> VersionInfo"""
        return _IMP_gsl.Simplex_get_version_info(self)


    def __str__(self):
        """__str__(Simplex self) -> std::string"""
        return _IMP_gsl.Simplex___str__(self)


    def __repr__(self):
        """__repr__(Simplex self) -> std::string"""
        return _IMP_gsl.Simplex___repr__(self)


    @staticmethod
    def get_from(o):
       return _object_cast_to_Simplex(o)

Simplex_swigregister = _IMP_gsl.Simplex_swigregister
Simplex_swigregister(Simplex)


def get_module_version():
    """get_module_version() -> std::string const"""
    return _IMP_gsl.get_module_version()

def get_example_path(fname):
    """get_example_path(std::string fname) -> std::string"""
    return _IMP_gsl.get_example_path(fname)

def get_data_path(fname):
    """get_data_path(std::string fname) -> std::string"""
    return _IMP_gsl.get_data_path(fname)

from . import _version_check
_version_check.check_version(get_module_version())
__version__ = get_module_version()