cnmultifit/__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 2007-2017 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_cnmultifit')).lstrip('.')
        try:
            return importlib.import_module(mname)
        except ImportError:
            return importlib.import_module('_IMP_cnmultifit')
    _IMP_cnmultifit = 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_cnmultifit', [dirname(__file__)])
        except ImportError:
            import _IMP_cnmultifit
            return _IMP_cnmultifit
        if fp is not None:
            try:
                _mod = imp.load_module('_IMP_cnmultifit', fp, pathname, description)
            finally:
                fp.close()
            return _mod
    _IMP_cnmultifit = swig_import_helper()
    del swig_import_helper
else:
    import _IMP_cnmultifit
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_CNMULTIFIT_SwigPyIterator(object):
    """Proxy of C++ swig::IMP_CNMULTIFIT_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_cnmultifit.delete_IMP_CNMULTIFIT_SwigPyIterator
    __del__ = lambda self: None

    def value(self):
        """value(IMP_CNMULTIFIT_SwigPyIterator self) -> PyObject *"""
        return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_value(self)


    def incr(self, n=1):
        """
        incr(IMP_CNMULTIFIT_SwigPyIterator self, size_t n=1) -> IMP_CNMULTIFIT_SwigPyIterator
        incr(IMP_CNMULTIFIT_SwigPyIterator self) -> IMP_CNMULTIFIT_SwigPyIterator
        """
        return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_incr(self, n)


    def decr(self, n=1):
        """
        decr(IMP_CNMULTIFIT_SwigPyIterator self, size_t n=1) -> IMP_CNMULTIFIT_SwigPyIterator
        decr(IMP_CNMULTIFIT_SwigPyIterator self) -> IMP_CNMULTIFIT_SwigPyIterator
        """
        return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_decr(self, n)


    def distance(self, x):
        """distance(IMP_CNMULTIFIT_SwigPyIterator self, IMP_CNMULTIFIT_SwigPyIterator x) -> ptrdiff_t"""
        return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_distance(self, x)


    def equal(self, x):
        """equal(IMP_CNMULTIFIT_SwigPyIterator self, IMP_CNMULTIFIT_SwigPyIterator x) -> bool"""
        return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_equal(self, x)


    def copy(self):
        """copy(IMP_CNMULTIFIT_SwigPyIterator self) -> IMP_CNMULTIFIT_SwigPyIterator"""
        return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_copy(self)


    def next(self):
        """next(IMP_CNMULTIFIT_SwigPyIterator self) -> PyObject *"""
        return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_next(self)


    def __next__(self):
        """__next__(IMP_CNMULTIFIT_SwigPyIterator self) -> PyObject *"""
        return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___next__(self)


    def previous(self):
        """previous(IMP_CNMULTIFIT_SwigPyIterator self) -> PyObject *"""
        return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_previous(self)


    def advance(self, n):
        """advance(IMP_CNMULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_CNMULTIFIT_SwigPyIterator"""
        return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_advance(self, n)


    def __eq__(self, x):
        """__eq__(IMP_CNMULTIFIT_SwigPyIterator self, IMP_CNMULTIFIT_SwigPyIterator x) -> bool"""
        return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___eq__(self, x)


    def __ne__(self, x):
        """__ne__(IMP_CNMULTIFIT_SwigPyIterator self, IMP_CNMULTIFIT_SwigPyIterator x) -> bool"""
        return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___ne__(self, x)


    def __iadd__(self, n):
        """__iadd__(IMP_CNMULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_CNMULTIFIT_SwigPyIterator"""
        return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___iadd__(self, n)


    def __isub__(self, n):
        """__isub__(IMP_CNMULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_CNMULTIFIT_SwigPyIterator"""
        return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___isub__(self, n)


    def __add__(self, n):
        """__add__(IMP_CNMULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_CNMULTIFIT_SwigPyIterator"""
        return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___add__(self, n)


    def __sub__(self, *args):
        """
        __sub__(IMP_CNMULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_CNMULTIFIT_SwigPyIterator
        __sub__(IMP_CNMULTIFIT_SwigPyIterator self, IMP_CNMULTIFIT_SwigPyIterator x) -> ptrdiff_t
        """
        return _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator___sub__(self, *args)

    def __iter__(self):
        return self
IMP_CNMULTIFIT_SwigPyIterator_swigregister = _IMP_cnmultifit.IMP_CNMULTIFIT_SwigPyIterator_swigregister
IMP_CNMULTIFIT_SwigPyIterator_swigregister(IMP_CNMULTIFIT_SwigPyIterator)


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

IMP_DEBUG = _IMP_cnmultifit.IMP_DEBUG
IMP_RELEASE = _IMP_cnmultifit.IMP_RELEASE
IMP_SILENT = _IMP_cnmultifit.IMP_SILENT
IMP_PROGRESS = _IMP_cnmultifit.IMP_PROGRESS
IMP_TERSE = _IMP_cnmultifit.IMP_TERSE
IMP_VERBOSE = _IMP_cnmultifit.IMP_VERBOSE
IMP_MEMORY = _IMP_cnmultifit.IMP_MEMORY
IMP_NONE = _IMP_cnmultifit.IMP_NONE
IMP_USAGE = _IMP_cnmultifit.IMP_USAGE
IMP_INTERNAL = _IMP_cnmultifit.IMP_INTERNAL
IMP_KERNEL_HAS_LOG4CXX = _IMP_cnmultifit.IMP_KERNEL_HAS_LOG4CXX
IMP_COMPILER_HAS_AUTO = _IMP_cnmultifit.IMP_COMPILER_HAS_AUTO
IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_cnmultifit.IMP_COMPILER_HAS_DEBUG_VECTOR
IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_cnmultifit.IMP_COMPILER_HAS_UNIQUE_PTR
IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_KERNEL_HAS_BOOST_RANDOM
IMP_KERNEL_HAS_GPERFTOOLS = _IMP_cnmultifit.IMP_KERNEL_HAS_GPERFTOOLS
IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_cnmultifit.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_cnmultifit.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
IMPKERNEL_SHOW_WARNINGS = _IMP_cnmultifit.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_cnmultifit._ostream_write(self, osa_buf)

_ostream_swigregister = _IMP_cnmultifit._ostream_swigregister
_ostream_swigregister(_ostream)

IMP_COMPILER_HAS_OVERRIDE = _IMP_cnmultifit.IMP_COMPILER_HAS_OVERRIDE
IMP_COMPILER_HAS_FINAL = _IMP_cnmultifit.IMP_COMPILER_HAS_FINAL
IMP_HAS_NOEXCEPT = _IMP_cnmultifit.IMP_HAS_NOEXCEPT
import IMP
IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_CGAL_HAS_BOOST_FILESYSTEM
IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
IMP_CGAL_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_CGAL_HAS_BOOST_RANDOM
IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_CGAL_HAS_BOOST_SYSTEM
IMPCGAL_SHOW_WARNINGS = _IMP_cnmultifit.IMPCGAL_SHOW_WARNINGS
import IMP.cgal
IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_ALGEBRA_HAS_IMP_CGAL
IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_ALGEBRA_HAS_BOOST_RANDOM
IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_ALGEBRA_HAS_BOOST_SYSTEM
IMP_ALGEBRA_HAS_CGAL = _IMP_cnmultifit.IMP_ALGEBRA_HAS_CGAL
IMP_ALGEBRA_HAS_ANN = _IMP_cnmultifit.IMP_ALGEBRA_HAS_ANN
IMPALGEBRA_SHOW_WARNINGS = _IMP_cnmultifit.IMPALGEBRA_SHOW_WARNINGS
import IMP.algebra
IMP_DISPLAY_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_DISPLAY_HAS_IMP_CGAL
IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_DISPLAY_HAS_BOOST_RANDOM
IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_DISPLAY_HAS_BOOST_SYSTEM
IMP_DISPLAY_HAS_CGAL = _IMP_cnmultifit.IMP_DISPLAY_HAS_CGAL
IMPDISPLAY_SHOW_WARNINGS = _IMP_cnmultifit.IMPDISPLAY_SHOW_WARNINGS
import IMP.display
IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_CGAL
IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_cnmultifit.IMP_SCORE_FUNCTOR_HAS_HDF5
IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_cnmultifit.IMPSCOREFUNCTOR_SHOW_WARNINGS
import IMP.score_functor
IMP_STATISTICS_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_STATISTICS_HAS_IMP_CGAL
IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_STATISTICS_HAS_BOOST_RANDOM
IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_STATISTICS_HAS_BOOST_SYSTEM
IMP_STATISTICS_HAS_CGAL = _IMP_cnmultifit.IMP_STATISTICS_HAS_CGAL
IMPSTATISTICS_SHOW_WARNINGS = _IMP_cnmultifit.IMPSTATISTICS_SHOW_WARNINGS
import IMP.statistics
IMP_CORE_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_CORE_HAS_IMP_CGAL
IMP_CORE_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_CORE_HAS_IMP_KERNEL
IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_CORE_HAS_BOOST_FILESYSTEM
IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
IMP_CORE_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_CORE_HAS_BOOST_RANDOM
IMP_CORE_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_CORE_HAS_BOOST_SYSTEM
IMP_CORE_HAS_CGAL = _IMP_cnmultifit.IMP_CORE_HAS_CGAL
IMP_CORE_HAS_HDF5 = _IMP_cnmultifit.IMP_CORE_HAS_HDF5
IMPCORE_SHOW_WARNINGS = _IMP_cnmultifit.IMPCORE_SHOW_WARNINGS
import IMP.core
IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_ALGEBRA
IMP_CONTAINER_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_CGAL
IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_DISPLAY
IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_KERNEL
IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_CONTAINER_HAS_BOOST_RANDOM
IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_CONTAINER_HAS_BOOST_SYSTEM
IMP_CONTAINER_HAS_CGAL = _IMP_cnmultifit.IMP_CONTAINER_HAS_CGAL
IMP_CONTAINER_HAS_HDF5 = _IMP_cnmultifit.IMP_CONTAINER_HAS_HDF5
IMPCONTAINER_SHOW_WARNINGS = _IMP_cnmultifit.IMPCONTAINER_SHOW_WARNINGS
import IMP.container
IMP_ATOM_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_ATOM_HAS_IMP_CGAL
IMP_ATOM_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_ATOM_HAS_IMP_KERNEL
IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
IMP_ATOM_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_ATOM_HAS_BOOST_RANDOM
IMP_ATOM_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_ATOM_HAS_BOOST_REGEX
IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_ATOM_HAS_BOOST_SYSTEM
IMP_ATOM_HAS_CGAL = _IMP_cnmultifit.IMP_ATOM_HAS_CGAL
IMP_ATOM_HAS_HDF5 = _IMP_cnmultifit.IMP_ATOM_HAS_HDF5
IMPATOM_SHOW_WARNINGS = _IMP_cnmultifit.IMPATOM_SHOW_WARNINGS
IMP_ATOM_TYPE_INDEX = _IMP_cnmultifit.IMP_ATOM_TYPE_INDEX
IMP_RESIDUE_TYPE_INDEX = _IMP_cnmultifit.IMP_RESIDUE_TYPE_INDEX
IMP_HIERARCHY_TYPE_INDEX = _IMP_cnmultifit.IMP_HIERARCHY_TYPE_INDEX
import IMP.atom
IMP_EM_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_EM_HAS_IMP_CGAL
IMP_EM_HAS_IMP_CONTAINER = _IMP_cnmultifit.IMP_EM_HAS_IMP_CONTAINER
IMP_EM_HAS_IMP_DISPLAY = _IMP_cnmultifit.IMP_EM_HAS_IMP_DISPLAY
IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_EM_HAS_IMP_SCORE_FUNCTOR
IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_EM_HAS_BOOST_FILESYSTEM
IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
IMP_EM_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_EM_HAS_BOOST_RANDOM
IMP_EM_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_EM_HAS_BOOST_REGEX
IMP_EM_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_EM_HAS_BOOST_SYSTEM
IMP_EM_HAS_CGAL = _IMP_cnmultifit.IMP_EM_HAS_CGAL
IMP_EM_HAS_HDF5 = _IMP_cnmultifit.IMP_EM_HAS_HDF5
IMPEM_SHOW_WARNINGS = _IMP_cnmultifit.IMPEM_SHOW_WARNINGS
import IMP.em
IMP_RMF_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_RMF_HAS_IMP_CGAL
IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_FILESYSTEM
IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
IMP_RMF_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_RANDOM
IMP_RMF_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_REGEX
IMP_RMF_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_RMF_HAS_BOOST_SYSTEM
IMP_RMF_HAS_CGAL = _IMP_cnmultifit.IMP_RMF_HAS_CGAL
IMP_RMF_HAS_HDF5 = _IMP_cnmultifit.IMP_RMF_HAS_HDF5
IMPRMF_SHOW_WARNINGS = _IMP_cnmultifit.IMPRMF_SHOW_WARNINGS
import IMP.rmf
import RMF
IMP_DOMINO_HAS_IMP_ATOM = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_ATOM
IMP_DOMINO_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_CGAL
IMP_DOMINO_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_KERNEL
IMP_DOMINO_HAS_IMP_RMF = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_RMF
IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_FILESYSTEM
IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_RANDOM
IMP_DOMINO_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_REGEX
IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_DOMINO_HAS_BOOST_SYSTEM
IMP_DOMINO_HAS_CGAL = _IMP_cnmultifit.IMP_DOMINO_HAS_CGAL
IMP_DOMINO_HAS_HDF5 = _IMP_cnmultifit.IMP_DOMINO_HAS_HDF5
IMP_DOMINO_HAS_RMF = _IMP_cnmultifit.IMP_DOMINO_HAS_RMF
IMPDOMINO_SHOW_WARNINGS = _IMP_cnmultifit.IMPDOMINO_SHOW_WARNINGS
import RMF_HDF5
import IMP.domino
IMP_MULTIFIT_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_CGAL
IMP_MULTIFIT_HAS_IMP_CONTAINER = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_CONTAINER
IMP_MULTIFIT_HAS_IMP_DISPLAY = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_DISPLAY
IMP_MULTIFIT_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_KERNEL
IMP_MULTIFIT_HAS_IMP_RMF = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_RMF
IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR
IMP_MULTIFIT_HAS_BOOST_GRAPH = _IMP_cnmultifit.IMP_MULTIFIT_HAS_BOOST_GRAPH
IMP_MULTIFIT_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_MULTIFIT_HAS_BOOST_RANDOM
IMP_MULTIFIT_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_MULTIFIT_HAS_BOOST_REGEX
IMP_MULTIFIT_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_MULTIFIT_HAS_BOOST_SYSTEM
IMP_MULTIFIT_HAS_CGAL = _IMP_cnmultifit.IMP_MULTIFIT_HAS_CGAL
IMP_MULTIFIT_HAS_HDF5 = _IMP_cnmultifit.IMP_MULTIFIT_HAS_HDF5
IMP_MULTIFIT_HAS_RMF = _IMP_cnmultifit.IMP_MULTIFIT_HAS_RMF
IMPMULTIFIT_SHOW_WARNINGS = _IMP_cnmultifit.IMPMULTIFIT_SHOW_WARNINGS
import IMP.multifit
IMP_CNMULTIFIT_HAS_IMP_CGAL = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_CGAL
IMP_CNMULTIFIT_HAS_IMP_CONTAINER = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_CONTAINER
IMP_CNMULTIFIT_HAS_IMP_DISPLAY = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_DISPLAY
IMP_CNMULTIFIT_HAS_IMP_DOMINO = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_DOMINO
IMP_CNMULTIFIT_HAS_IMP_KERNEL = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_KERNEL
IMP_CNMULTIFIT_HAS_IMP_RMF = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_RMF
IMP_CNMULTIFIT_HAS_IMP_SCORE_FUNCTOR = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_IMP_SCORE_FUNCTOR
IMP_CNMULTIFIT_HAS_BOOST_GRAPH = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_BOOST_GRAPH
IMP_CNMULTIFIT_HAS_BOOST_RANDOM = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_BOOST_RANDOM
IMP_CNMULTIFIT_HAS_BOOST_REGEX = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_BOOST_REGEX
IMP_CNMULTIFIT_HAS_BOOST_SYSTEM = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_BOOST_SYSTEM
IMP_CNMULTIFIT_HAS_CGAL = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_CGAL
IMP_CNMULTIFIT_HAS_FFTW3 = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_FFTW3
IMP_CNMULTIFIT_HAS_HDF5 = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_HDF5
IMP_CNMULTIFIT_HAS_RMF = _IMP_cnmultifit.IMP_CNMULTIFIT_HAS_RMF
IMPCNMULTIFIT_SHOW_WARNINGS = _IMP_cnmultifit.IMPCNMULTIFIT_SHOW_WARNINGS

AlignSymmetrics=list
_plural_types.append("AlignSymmetrics")
_value_types.append("AlignSymmetric")


CnSymmAxisDetectors=list
_plural_types.append("CnSymmAxisDetectors")
_value_types.append("CnSymmAxisDetector")


MolCnSymmAxisDetectors=list
_plural_types.append("MolCnSymmAxisDetectors")
_value_types.append("MolCnSymmAxisDetector")

class CnSymmAxisDetector(object):
    """Proxy of C++ IMP::cnmultifit::CnSymmAxisDetector class."""

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

    def __init__(self, *args):
        """
        __init__(IMP::cnmultifit::CnSymmAxisDetector self, int symm_deg, DensityMap dmap, float density_threshold, float top_p=0.8) -> CnSymmAxisDetector
        __init__(IMP::cnmultifit::CnSymmAxisDetector self, int symm_deg, DensityMap dmap, float density_threshold) -> CnSymmAxisDetector
        __init__(IMP::cnmultifit::CnSymmAxisDetector self, int symm_deg, IMP::atom::Hierarchies const & mhs) -> CnSymmAxisDetector
        """
        this = _IMP_cnmultifit.new_CnSymmAxisDetector(*args)
        try:
            self.this.append(this)
        except __builtin__.Exception:
            self.this = this

    def get_pca(self):
        """get_pca(CnSymmAxisDetector self) -> PrincipalComponentAnalysis3D"""
        return _IMP_cnmultifit.CnSymmAxisDetector_get_pca(self)


    def calc_symm_score(self, symm_axis_ind):
        """calc_symm_score(CnSymmAxisDetector self, int symm_axis_ind) -> float"""
        return _IMP_cnmultifit.CnSymmAxisDetector_calc_symm_score(self, symm_axis_ind)


    def get_symmetry_axis(self):
        """get_symmetry_axis(CnSymmAxisDetector self) -> Vector3D"""
        return _IMP_cnmultifit.CnSymmAxisDetector_get_symmetry_axis(self)


    def get_symmetry_axis_index(self):
        """get_symmetry_axis_index(CnSymmAxisDetector self) -> int"""
        return _IMP_cnmultifit.CnSymmAxisDetector_get_symmetry_axis_index(self)


    def get_non_symmetry_axis_length(self):
        """get_non_symmetry_axis_length(CnSymmAxisDetector self) -> int"""
        return _IMP_cnmultifit.CnSymmAxisDetector_get_non_symmetry_axis_length(self)


    def show(self, *args):
        """
        show(CnSymmAxisDetector self, _ostream out)
        show(CnSymmAxisDetector self)
        """
        return _IMP_cnmultifit.CnSymmAxisDetector_show(self, *args)


    def __str__(self):
        """__str__(CnSymmAxisDetector self) -> std::string"""
        return _IMP_cnmultifit.CnSymmAxisDetector___str__(self)


    def __repr__(self):
        """__repr__(CnSymmAxisDetector self) -> std::string"""
        return _IMP_cnmultifit.CnSymmAxisDetector___repr__(self)

    __swig_destroy__ = _IMP_cnmultifit.delete_CnSymmAxisDetector
    __del__ = lambda self: None
CnSymmAxisDetector_swigregister = _IMP_cnmultifit.CnSymmAxisDetector_swigregister
CnSymmAxisDetector_swigregister(CnSymmAxisDetector)

class MolCnSymmAxisDetector(object):
    """Proxy of C++ IMP::cnmultifit::MolCnSymmAxisDetector class."""

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

    def __init__(self, symm_deg, mhs):
        """__init__(IMP::cnmultifit::MolCnSymmAxisDetector self, int symm_deg, IMP::atom::Hierarchies const & mhs) -> MolCnSymmAxisDetector"""
        this = _IMP_cnmultifit.new_MolCnSymmAxisDetector(symm_deg, mhs)
        try:
            self.this.append(this)
        except __builtin__.Exception:
            self.this = this

    def get_pca(self):
        """get_pca(MolCnSymmAxisDetector self) -> PrincipalComponentAnalysis3D"""
        return _IMP_cnmultifit.MolCnSymmAxisDetector_get_pca(self)


    def get_symmetry_axis(self):
        """get_symmetry_axis(MolCnSymmAxisDetector self) -> Vector3D"""
        return _IMP_cnmultifit.MolCnSymmAxisDetector_get_symmetry_axis(self)


    def get_symmetry_axis_index(self):
        """get_symmetry_axis_index(MolCnSymmAxisDetector self) -> int"""
        return _IMP_cnmultifit.MolCnSymmAxisDetector_get_symmetry_axis_index(self)


    def show(self, *args):
        """
        show(MolCnSymmAxisDetector self, _ostream out)
        show(MolCnSymmAxisDetector self)
        """
        return _IMP_cnmultifit.MolCnSymmAxisDetector_show(self, *args)


    def calc_symm_score(self, symm_axis_ind):
        """calc_symm_score(MolCnSymmAxisDetector self, int symm_axis_ind) -> float"""
        return _IMP_cnmultifit.MolCnSymmAxisDetector_calc_symm_score(self, symm_axis_ind)


    def __str__(self):
        """__str__(MolCnSymmAxisDetector self) -> std::string"""
        return _IMP_cnmultifit.MolCnSymmAxisDetector___str__(self)


    def __repr__(self):
        """__repr__(MolCnSymmAxisDetector self) -> std::string"""
        return _IMP_cnmultifit.MolCnSymmAxisDetector___repr__(self)

    __swig_destroy__ = _IMP_cnmultifit.delete_MolCnSymmAxisDetector
    __del__ = lambda self: None
MolCnSymmAxisDetector_swigregister = _IMP_cnmultifit.MolCnSymmAxisDetector_swigregister
MolCnSymmAxisDetector_swigregister(MolCnSymmAxisDetector)

class AlignSymmetric(object):
    """Proxy of C++ IMP::cnmultifit::AlignSymmetric class."""

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

    def __init__(self, dmap, threshold, cn_symm_deg):
        """__init__(IMP::cnmultifit::AlignSymmetric self, DensityMap dmap, float threshold, int cn_symm_deg) -> AlignSymmetric"""
        this = _IMP_cnmultifit.new_AlignSymmetric(dmap, threshold, cn_symm_deg)
        try:
            self.this.append(this)
        except __builtin__.Exception:
            self.this = this

    def get_sorted_principal_values(self):
        """get_sorted_principal_values(AlignSymmetric self) -> IMP::Floats"""
        return _IMP_cnmultifit.AlignSymmetric_get_sorted_principal_values(self)


    def score_alignment(self, mhs, max_allowed_diff):
        """score_alignment(AlignSymmetric self, IMP::atom::Hierarchies mhs, float max_allowed_diff) -> int"""
        return _IMP_cnmultifit.AlignSymmetric_score_alignment(self, mhs, max_allowed_diff)


    def get_symm_axis_alignments_from_model_to_density(self, mhs, sample_translation, fine_rotation_sampling=True):
        """
        get_symm_axis_alignments_from_model_to_density(AlignSymmetric self, IMP::atom::Hierarchies mhs, bool sample_translation, bool fine_rotation_sampling=True) -> IMP::algebra::Transformation3Ds
        get_symm_axis_alignments_from_model_to_density(AlignSymmetric self, IMP::atom::Hierarchies mhs, bool sample_translation) -> IMP::algebra::Transformation3Ds
        """
        return _IMP_cnmultifit.AlignSymmetric_get_symm_axis_alignments_from_model_to_density(self, mhs, sample_translation, fine_rotation_sampling)


    def show(self, *args):
        """
        show(AlignSymmetric self, _ostream out)
        show(AlignSymmetric self)
        """
        return _IMP_cnmultifit.AlignSymmetric_show(self, *args)


    def __str__(self):
        """__str__(AlignSymmetric self) -> std::string"""
        return _IMP_cnmultifit.AlignSymmetric___str__(self)


    def __repr__(self):
        """__repr__(AlignSymmetric self) -> std::string"""
        return _IMP_cnmultifit.AlignSymmetric___repr__(self)

    __swig_destroy__ = _IMP_cnmultifit.delete_AlignSymmetric
    __del__ = lambda self: None
AlignSymmetric_swigregister = _IMP_cnmultifit.AlignSymmetric_swigregister
AlignSymmetric_swigregister(AlignSymmetric)


def generate_cn_transformations(mhs, symm_deg):
    """generate_cn_transformations(IMP::atom::Hierarchies mhs, int symm_deg) -> IMP::algebra::Transformation3Ds"""
    return _IMP_cnmultifit.generate_cn_transformations(mhs, symm_deg)

def generate_translations_along_symm_axis(mhs, symm_deg):
    """generate_translations_along_symm_axis(IMP::atom::Hierarchies mhs, int symm_deg) -> IMP::algebra::Transformation3Ds"""
    return _IMP_cnmultifit.generate_translations_along_symm_axis(mhs, symm_deg)

def symmetry_local_fitting(mhs, cn_symm_deg, dn_symm_deg, dmap, num_of_trans_to_consider):
    """symmetry_local_fitting(IMP::atom::Hierarchies mhs, int cn_symm_deg, int dn_symm_deg, DensityMap dmap, int num_of_trans_to_consider) -> FittingSolutions"""
    return _IMP_cnmultifit.symmetry_local_fitting(mhs, cn_symm_deg, dn_symm_deg, dmap, num_of_trans_to_consider)

def build_cn_dens_assembly(subunit_dens, asmb_dens_header, monomer_t, symm_deg):
    """build_cn_dens_assembly(DensityMap subunit_dens, DensityHeader asmb_dens_header, Transformation3D monomer_t, int symm_deg) -> DensityMap"""
    return _IMP_cnmultifit.build_cn_dens_assembly(subunit_dens, asmb_dens_header, monomer_t, symm_deg)

def transform_cn_assembly(mhs, monomer_t):
    """transform_cn_assembly(IMP::atom::Hierarchies mhs, Transformation3D monomer_t)"""
    return _IMP_cnmultifit.transform_cn_assembly(mhs, monomer_t)

def fit_cn_assembly(*args):
    """
    fit_cn_assembly(IMP::atom::Hierarchies mhs, int dn_symm_deg, DensityMap dmap, float threshold, AlignSymmetric aligner, bool sample_translation=False, bool fine_rotational_sampling=True) -> FittingSolutions
    fit_cn_assembly(IMP::atom::Hierarchies mhs, int dn_symm_deg, DensityMap dmap, float threshold, AlignSymmetric aligner, bool sample_translation=False) -> FittingSolutions
    fit_cn_assembly(IMP::atom::Hierarchies mhs, int dn_symm_deg, DensityMap dmap, float threshold, AlignSymmetric aligner) -> FittingSolutions
    fit_cn_assembly(DensityMap asmb_map, MolCnSymmAxisDetector symm_mol, DensityMap dmap, CnSymmAxisDetector symm_map, int symm_deg, float threshold) -> FittingSolutions
    """
    return _IMP_cnmultifit.fit_cn_assembly(*args)

def pca_matching(pca1, pca2, resolution):
    """pca_matching(PrincipalComponentAnalysis3D pca1, PrincipalComponentAnalysis3D pca2, float resolution) -> bool"""
    return _IMP_cnmultifit.pca_matching(pca1, pca2, resolution)

def cn_symm_score(mhs, center, direction, symm_deg):
    """cn_symm_score(IMP::atom::Hierarchies mhs, Vector3D center, Vector3D direction, int symm_deg) -> float"""
    return _IMP_cnmultifit.cn_symm_score(mhs, center, direction, symm_deg)

def prune_by_pca(param_fn, sols, dn=1):
    """
    prune_by_pca(std::string const & param_fn, IMP::multifit::FittingSolutionRecords const & sols, int dn=1) -> IMP::multifit::FittingSolutionRecords
    prune_by_pca(std::string const & param_fn, IMP::multifit::FittingSolutionRecords const & sols) -> IMP::multifit::FittingSolutionRecords
    """
    return _IMP_cnmultifit.prune_by_pca(param_fn, sols, dn)

def calc_transformation_around_axis(a, b, angle_rad):
    """calc_transformation_around_axis(Vector3D a, Vector3D b, float angle_rad) -> Transformation3D"""
    return _IMP_cnmultifit.calc_transformation_around_axis(a, b, angle_rad)

def get_cn_rmsd(mh1, mh2):
    """get_cn_rmsd(IMP::atom::Hierarchies mh1, IMP::atom::Hierarchies mh2) -> float"""
    return _IMP_cnmultifit.get_cn_rmsd(mh1, mh2)

def do_all_fitting(*args):
    """
    do_all_fitting(std::string const param_filename, std::string const chimera_filename)
    do_all_fitting(std::string const param_filename)
    """
    return _IMP_cnmultifit.do_all_fitting(*args)

def get_rmsd_for_models(param_filename, trans_filename, ref_filename, start_model=0, end_model=-1):
    """
    get_rmsd_for_models(std::string const param_filename, std::string const trans_filename, std::string const ref_filename, int start_model=0, int end_model=-1) -> IMP::Floats
    get_rmsd_for_models(std::string const param_filename, std::string const trans_filename, std::string const ref_filename, int start_model=0) -> IMP::Floats
    get_rmsd_for_models(std::string const param_filename, std::string const trans_filename, std::string const ref_filename) -> IMP::Floats
    """
    return _IMP_cnmultifit.get_rmsd_for_models(param_filename, trans_filename, ref_filename, start_model, end_model)

_all_commands = ["build", "rmsd", "surface",
                 "param", "chimera_models"]


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

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

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

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