PerturbableOpenMMMolecule.pypp.cpp

// This file has been generated by Py++.

// (C) Christopher Woods, GPL >= 3 License

#include "boost/python.hpp"
#include "PerturbableOpenMMMolecule.pypp.hpp"

namespace bp = boost::python;

#include "SireBase/parallel.h"

#include "SireBase/propertylist.h"

#include "SireError/errors.h"

#include "SireMM/amberparams.h"

#include "SireMM/atomljs.h"

#include "SireMM/selectorbond.h"

#include "SireMM/twoatomfunctions.h"

#include "SireMaths/vector.h"

#include "SireMol/atomcharges.h"

#include "SireMol/atomcoords.h"

#include "SireMol/atomelements.h"

#include "SireMol/atommasses.h"

#include "SireMol/atomproperty.hpp"

#include "SireMol/atomvelocities.h"

#include "SireMol/bondid.h"

#include "SireMol/bondorder.h"

#include "SireMol/connectivity.h"

#include "SireMol/core.h"

#include "SireMol/moleditor.h"

#include "SireUnits/units.h"

#include "openmmmolecule.h"

#include "tostring.h"

#include <QDebug>

#include <QReadWriteLock>

#include <QSet>

#include <boost/tuple/tuple_comparison.hpp>

#include "SireBase/parallel.h"

#include "SireBase/propertylist.h"

#include "SireError/errors.h"

#include "SireMM/amberparams.h"

#include "SireMM/atomljs.h"

#include "SireMM/selectorbond.h"

#include "SireMM/twoatomfunctions.h"

#include "SireMaths/vector.h"

#include "SireMol/atomcharges.h"

#include "SireMol/atomcoords.h"

#include "SireMol/atomelements.h"

#include "SireMol/atommasses.h"

#include "SireMol/atomproperty.hpp"

#include "SireMol/atomvelocities.h"

#include "SireMol/bondid.h"

#include "SireMol/bondorder.h"

#include "SireMol/connectivity.h"

#include "SireMol/core.h"

#include "SireMol/moleditor.h"

#include "SireUnits/units.h"

#include "openmmmolecule.h"

#include "tostring.h"

#include <QDebug>

#include <QReadWriteLock>

#include <QSet>

#include <boost/tuple/tuple_comparison.hpp>

SireOpenMM::PerturbableOpenMMMolecule __copy__(const SireOpenMM::PerturbableOpenMMMolecule &other){ return SireOpenMM::PerturbableOpenMMMolecule(other); }

#include "Helpers/copy.hpp"

#include "Helpers/str.hpp"

#include "Helpers/release_gil_policy.hpp"

void register_PerturbableOpenMMMolecule_class(){

    { //::SireOpenMM::PerturbableOpenMMMolecule
        typedef bp::class_< SireOpenMM::PerturbableOpenMMMolecule > PerturbableOpenMMMolecule_exposer_t;
        PerturbableOpenMMMolecule_exposer_t PerturbableOpenMMMolecule_exposer = PerturbableOpenMMMolecule_exposer_t( "PerturbableOpenMMMolecule", "This class holds all of the information of an OpenMM molecule\nthat can be perturbed using a LambdaSchedule. The data is held\nin easy-to-access arrays, with guarantees that the arrays are\ncompatible and the data is aligned.\n", bp::init< >("Null constructor") );
        bp::scope PerturbableOpenMMMolecule_scope( PerturbableOpenMMMolecule_exposer );
        PerturbableOpenMMMolecule_exposer.def( bp::init< SireOpenMM::OpenMMMolecule const &, bp::optional< SireBase::PropertyMap const & > >(( bp::arg("mol"), bp::arg("map")=SireBase::PropertyMap() ), "Construct from the passed OpenMMMolecule") );
        PerturbableOpenMMMolecule_exposer.def( bp::init< SireMol::Molecule const &, int, bp::optional< SireBase::PropertyMap const & > >(( bp::arg("mol"), bp::arg("map")=SireBase::PropertyMap() ), "Construct from a passed molecule and map") );
        PerturbableOpenMMMolecule_exposer.def( bp::init< SireOpenMM::PerturbableOpenMMMolecule const & >(( bp::arg("other") ), "Copy constructor") );
        { //::SireOpenMM::PerturbableOpenMMMolecule::angles
        
            typedef ::QList< SireMM::Angle > ( ::SireOpenMM::PerturbableOpenMMMolecule::*angles_function_type)(  ) const;
            angles_function_type angles_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::angles );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "angles"
                , angles_function_value
                , bp::release_gil_policy()
                , "Return the angles which are perturbed, in the order they are\n  set in this perturbation\n" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::atoms
        
            typedef ::QList< SireMol::Atom > ( ::SireOpenMM::PerturbableOpenMMMolecule::*atoms_function_type)(  ) const;
            atoms_function_type atoms_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::atoms );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "atoms"
                , atoms_function_value
                , bp::release_gil_policy()
                , "Return the atoms which are perturbed, in the order they are\n  set in this perturbation\n" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::bonds
        
            typedef ::QList< SireMM::Bond > ( ::SireOpenMM::PerturbableOpenMMMolecule::*bonds_function_type)(  ) const;
            bonds_function_type bonds_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::bonds );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "bonds"
                , bonds_function_value
                , bp::release_gil_policy()
                , "Return the bonds which are perturbed, in the order they are\n  set in this perturbation\n" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getAlphas0
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getAlphas0_function_type)(  ) const;
            getAlphas0_function_type getAlphas0_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getAlphas0 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getAlphas0"
                , getAlphas0_function_value
                , bp::release_gil_policy()
                , "Return the alpha parameters of the reference state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getAlphas1
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getAlphas1_function_type)(  ) const;
            getAlphas1_function_type getAlphas1_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getAlphas1 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getAlphas1"
                , getAlphas1_function_value
                , bp::release_gil_policy()
                , "Return the alpha parameters of the perturbed state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getAngleKs0
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getAngleKs0_function_type)(  ) const;
            getAngleKs0_function_type getAngleKs0_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getAngleKs0 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getAngleKs0"
                , getAngleKs0_function_value
                , bp::release_gil_policy()
                , "Return the angle k parameters of the reference state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getAngleKs1
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getAngleKs1_function_type)(  ) const;
            getAngleKs1_function_type getAngleKs1_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getAngleKs1 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getAngleKs1"
                , getAngleKs1_function_value
                , bp::release_gil_policy()
                , "Return the angle k parameters of the perturbed state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getAngleSizes0
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getAngleSizes0_function_type)(  ) const;
            getAngleSizes0_function_type getAngleSizes0_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getAngleSizes0 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getAngleSizes0"
                , getAngleSizes0_function_value
                , bp::release_gil_policy()
                , "Return the angle size parameters of the reference state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getAngleSizes1
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getAngleSizes1_function_type)(  ) const;
            getAngleSizes1_function_type getAngleSizes1_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getAngleSizes1 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getAngleSizes1"
                , getAngleSizes1_function_value
                , bp::release_gil_policy()
                , "Return the angle size parameters of the perturbed state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getBondKs0
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getBondKs0_function_type)(  ) const;
            getBondKs0_function_type getBondKs0_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getBondKs0 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getBondKs0"
                , getBondKs0_function_value
                , bp::release_gil_policy()
                , "Return the bond k parameters of the reference state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getBondKs1
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getBondKs1_function_type)(  ) const;
            getBondKs1_function_type getBondKs1_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getBondKs1 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getBondKs1"
                , getBondKs1_function_value
                , bp::release_gil_policy()
                , "Return the bond k parameters of the perturbed state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getBondLengths0
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getBondLengths0_function_type)(  ) const;
            getBondLengths0_function_type getBondLengths0_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getBondLengths0 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getBondLengths0"
                , getBondLengths0_function_value
                , bp::release_gil_policy()
                , "Return the bond length parameters of the reference state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getBondLengths1
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getBondLengths1_function_type)(  ) const;
            getBondLengths1_function_type getBondLengths1_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getBondLengths1 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getBondLengths1"
                , getBondLengths1_function_value
                , bp::release_gil_policy()
                , "Return the bond length parameters of the perturbed state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getChargeScales0
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getChargeScales0_function_type)(  ) const;
            getChargeScales0_function_type getChargeScales0_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getChargeScales0 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getChargeScales0"
                , getChargeScales0_function_value
                , bp::release_gil_policy()
                , "Return the coulomb intramolecular scale factors of the reference state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getChargeScales1
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getChargeScales1_function_type)(  ) const;
            getChargeScales1_function_type getChargeScales1_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getChargeScales1 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getChargeScales1"
                , getChargeScales1_function_value
                , bp::release_gil_policy()
                , "Return the coulomb intramolecular scale factors of the perturbed state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getCharges0
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getCharges0_function_type)(  ) const;
            getCharges0_function_type getCharges0_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getCharges0 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getCharges0"
                , getCharges0_function_value
                , bp::release_gil_policy()
                , "Return the atom charges of the reference state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getCharges1
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getCharges1_function_type)(  ) const;
            getCharges1_function_type getCharges1_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getCharges1 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getCharges1"
                , getCharges1_function_value
                , bp::release_gil_policy()
                , "Return the atom charges of the perturbed state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getConstraintIndicies
        
            typedef ::QVector< int > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getConstraintIndicies_function_type)(  ) const;
            getConstraintIndicies_function_type getConstraintIndicies_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getConstraintIndicies );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getConstraintIndicies"
                , getConstraintIndicies_function_value
                , bp::release_gil_policy()
                , "Return the indicies of the perturbable constraints" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getEpsilons0
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getEpsilons0_function_type)(  ) const;
            getEpsilons0_function_type getEpsilons0_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getEpsilons0 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getEpsilons0"
                , getEpsilons0_function_value
                , bp::release_gil_policy()
                , "Return the LJ epsilon parameters of the reference state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getEpsilons1
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getEpsilons1_function_type)(  ) const;
            getEpsilons1_function_type getEpsilons1_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getEpsilons1 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getEpsilons1"
                , getEpsilons1_function_value
                , bp::release_gil_policy()
                , "Return the LJ epsilon parameters of the perturbed state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getExceptionAtoms
        
            typedef ::QVector< boost::tuples::tuple< int, int, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getExceptionAtoms_function_type)(  ) const;
            getExceptionAtoms_function_type getExceptionAtoms_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getExceptionAtoms );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getExceptionAtoms"
                , getExceptionAtoms_function_value
                , bp::release_gil_policy()
                , "Return the indices of the atoms in the exceptions" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getExceptionIndicies
        
            typedef ::QVector< boost::tuples::tuple< int, int, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getExceptionIndicies_function_type)( ::QString const & ) const;
            getExceptionIndicies_function_type getExceptionIndicies_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getExceptionIndicies );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getExceptionIndicies"
                , getExceptionIndicies_function_value
                , ( bp::arg("name") )
                , bp::release_gil_policy()
                , "Return the global indexes of the exceptions in the non-bonded and\n  ghost-14 forces\n" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getFromGhostIdxs
        
            typedef ::QSet< int > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getFromGhostIdxs_function_type)(  ) const;
            getFromGhostIdxs_function_type getFromGhostIdxs_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getFromGhostIdxs );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getFromGhostIdxs"
                , getFromGhostIdxs_function_value
                , bp::release_gil_policy()
                , "Return the indexes of the atoms that were ghosts in the\n  reference state\n" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getKappas0
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getKappas0_function_type)(  ) const;
            getKappas0_function_type getKappas0_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getKappas0 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getKappas0"
                , getKappas0_function_value
                , bp::release_gil_policy()
                , "Return the kappa parameters of the reference state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getKappas1
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getKappas1_function_type)(  ) const;
            getKappas1_function_type getKappas1_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getKappas1 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getKappas1"
                , getKappas1_function_value
                , bp::release_gil_policy()
                , "Return the kappa parameters of the perturbed state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getLJScales0
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getLJScales0_function_type)(  ) const;
            getLJScales0_function_type getLJScales0_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getLJScales0 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getLJScales0"
                , getLJScales0_function_value
                , bp::release_gil_policy()
                , "Return the LJ intramolecular scale factors of the reference state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getLJScales1
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getLJScales1_function_type)(  ) const;
            getLJScales1_function_type getLJScales1_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getLJScales1 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getLJScales1"
                , getLJScales1_function_value
                , bp::release_gil_policy()
                , "Return the LJ intramolecular scale factors of the perturbed state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getPerturbableConstraints
        
            typedef ::boost::tuples::tuple< QVector< int >, QVector< double >, QVector< double >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getPerturbableConstraints_function_type)(  ) const;
            getPerturbableConstraints_function_type getPerturbableConstraints_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getPerturbableConstraints );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getPerturbableConstraints"
                , getPerturbableConstraints_function_value
                , bp::release_gil_policy()
                , "Return three arrays containing the constraint indexes, and the\n  reference and perturbed values of the constraint lengths\n" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getPerturbableConstraintsWithAtoms
        
            typedef ::QVector< boost::tuples::tuple< int, int, double, double, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getPerturbableConstraintsWithAtoms_function_type)(  ) const;
            getPerturbableConstraintsWithAtoms_function_type getPerturbableConstraintsWithAtoms_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getPerturbableConstraintsWithAtoms );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getPerturbableConstraintsWithAtoms"
                , getPerturbableConstraintsWithAtoms_function_value
                , bp::release_gil_policy()
                , "Return the atom indexes of all of the constraints, with\n  the constraint lengths at the two end states, in the order\n  they appear in this molecule\n" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getSigmas0
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getSigmas0_function_type)(  ) const;
            getSigmas0_function_type getSigmas0_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getSigmas0 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getSigmas0"
                , getSigmas0_function_value
                , bp::release_gil_policy()
                , "Return the LJ sigma parameters of the reference state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getSigmas1
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getSigmas1_function_type)(  ) const;
            getSigmas1_function_type getSigmas1_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getSigmas1 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getSigmas1"
                , getSigmas1_function_value
                , bp::release_gil_policy()
                , "Return the LJ sigma parameters of the perturbed state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getToGhostIdxs
        
            typedef ::QSet< int > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getToGhostIdxs_function_type)(  ) const;
            getToGhostIdxs_function_type getToGhostIdxs_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getToGhostIdxs );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getToGhostIdxs"
                , getToGhostIdxs_function_value
                , bp::release_gil_policy()
                , "Return the indexes of the atoms that are to be ghosted in the\n  perturbed state\n" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getTorsionKs0
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getTorsionKs0_function_type)(  ) const;
            getTorsionKs0_function_type getTorsionKs0_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getTorsionKs0 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getTorsionKs0"
                , getTorsionKs0_function_value
                , bp::release_gil_policy()
                , "Return the torsion k parameters of the reference state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getTorsionKs1
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getTorsionKs1_function_type)(  ) const;
            getTorsionKs1_function_type getTorsionKs1_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getTorsionKs1 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getTorsionKs1"
                , getTorsionKs1_function_value
                , bp::release_gil_policy()
                , "Return the torsion k parameters of the perturbed state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getTorsionPeriodicities0
        
            typedef ::QVector< signed char > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getTorsionPeriodicities0_function_type)(  ) const;
            getTorsionPeriodicities0_function_type getTorsionPeriodicities0_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getTorsionPeriodicities0 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getTorsionPeriodicities0"
                , getTorsionPeriodicities0_function_value
                , bp::release_gil_policy()
                , "Return the torsion periodicity parameters of the reference state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getTorsionPeriodicities1
        
            typedef ::QVector< signed char > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getTorsionPeriodicities1_function_type)(  ) const;
            getTorsionPeriodicities1_function_type getTorsionPeriodicities1_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getTorsionPeriodicities1 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getTorsionPeriodicities1"
                , getTorsionPeriodicities1_function_value
                , bp::release_gil_policy()
                , "Return the torsion periodicity parameters of the perturbed state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getTorsionPhases0
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getTorsionPhases0_function_type)(  ) const;
            getTorsionPhases0_function_type getTorsionPhases0_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getTorsionPhases0 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getTorsionPhases0"
                , getTorsionPhases0_function_value
                , bp::release_gil_policy()
                , "Return the torsion phase parameters of the reference state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getTorsionPhases1
        
            typedef ::QVector< double > ( ::SireOpenMM::PerturbableOpenMMMolecule::*getTorsionPhases1_function_type)(  ) const;
            getTorsionPhases1_function_type getTorsionPhases1_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getTorsionPhases1 );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "getTorsionPhases1"
                , getTorsionPhases1_function_value
                , bp::release_gil_policy()
                , "Return the torsion phase parameters of the perturbed state" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getCMAPGrids0

            typedef ::QVector< double > const & ( ::SireOpenMM::PerturbableOpenMMMolecule::*getCMAPGrids0_function_type)(  ) const;
            getCMAPGrids0_function_type getCMAPGrids0_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getCMAPGrids0 );

            PerturbableOpenMMMolecule_exposer.def(
                "getCMAPGrids0"
                , getCMAPGrids0_function_value
                , bp::return_value_policy< bp::copy_const_reference >()
                , "Return the flat concatenated CMAP grid values (column-major, kJ/mol) "
                  "for the reference state. Grid k has getCMAPGridSizes()[k]^2 entries." );

        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getCMAPGrids1

            typedef ::QVector< double > const & ( ::SireOpenMM::PerturbableOpenMMMolecule::*getCMAPGrids1_function_type)(  ) const;
            getCMAPGrids1_function_type getCMAPGrids1_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getCMAPGrids1 );

            PerturbableOpenMMMolecule_exposer.def(
                "getCMAPGrids1"
                , getCMAPGrids1_function_value
                , bp::return_value_policy< bp::copy_const_reference >()
                , "Return the flat concatenated CMAP grid values (column-major, kJ/mol) "
                  "for the perturbed state. Grid k has getCMAPGridSizes()[k]^2 entries." );

        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getCMAPGridSizes

            typedef ::QVector< int > const & ( ::SireOpenMM::PerturbableOpenMMMolecule::*getCMAPGridSizes_function_type)(  ) const;
            getCMAPGridSizes_function_type getCMAPGridSizes_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getCMAPGridSizes );

            PerturbableOpenMMMolecule_exposer.def(
                "getCMAPGridSizes"
                , getCMAPGridSizes_function_value
                , bp::return_value_policy< bp::copy_const_reference >()
                , "Return the grid dimension N for each CMAP torsion (grid is N x N). "
                  "Entries correspond to the grids in getCMAPGrids0/1." );

        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::getCMAPAtoms

            typedef ::QVector< boost::tuples::tuple< int, int, int, int, int,
                boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type,
                boost::tuples::null_type, boost::tuples::null_type > >
                ( ::SireOpenMM::PerturbableOpenMMMolecule::*getCMAPAtoms_function_type)(  ) const;
            getCMAPAtoms_function_type getCMAPAtoms_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::getCMAPAtoms );

            PerturbableOpenMMMolecule_exposer.def(
                "getCMAPAtoms"
                , getCMAPAtoms_function_value
                , bp::release_gil_policy()
                , "Return the molecule-local 5-atom indices for each CMAP torsion, "
                  "in the same order as getCMAPGridSizes(). Used for REST2 scaling." );

        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::isGhostAtom

            typedef bool ( ::SireOpenMM::PerturbableOpenMMMolecule::*isGhostAtom_function_type)( int ) const;
            isGhostAtom_function_type isGhostAtom_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::isGhostAtom );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "isGhostAtom"
                , isGhostAtom_function_value
                , ( bp::arg("atom") )
                , bp::release_gil_policy()
                , "Return true if the atom is a ghost atom in the\n  referenece or perturbed states" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::isNull
        
            typedef bool ( ::SireOpenMM::PerturbableOpenMMMolecule::*isNull_function_type)(  ) const;
            isNull_function_type isNull_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::isNull );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "isNull"
                , isNull_function_value
                , bp::release_gil_policy()
                , "Return whether or not this is null" );
        
        }
        PerturbableOpenMMMolecule_exposer.def( bp::self != bp::self );
        { //::SireOpenMM::PerturbableOpenMMMolecule::operator=
        
            typedef ::SireOpenMM::PerturbableOpenMMMolecule & ( ::SireOpenMM::PerturbableOpenMMMolecule::*assign_function_type)( ::SireOpenMM::PerturbableOpenMMMolecule const & ) ;
            assign_function_type assign_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::operator= );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "assign"
                , assign_function_value
                , ( bp::arg("other") )
                , bp::return_self< >()
                , "" );
        
        }
        PerturbableOpenMMMolecule_exposer.def( bp::self == bp::self );
        { //::SireOpenMM::PerturbableOpenMMMolecule::setConstraintIndicies
        
            typedef void ( ::SireOpenMM::PerturbableOpenMMMolecule::*setConstraintIndicies_function_type)( ::QVector< int > const & ) ;
            setConstraintIndicies_function_type setConstraintIndicies_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::setConstraintIndicies );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "setConstraintIndicies"
                , setConstraintIndicies_function_value
                , ( bp::arg("constraint_idxs") )
                , bp::release_gil_policy()
                , "Set the indexes of perturbable constraints in the System" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::setExceptionIndicies
        
            typedef void ( ::SireOpenMM::PerturbableOpenMMMolecule::*setExceptionIndicies_function_type)( ::QString const &,::QVector< boost::tuples::tuple< int, int, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > > const & ) ;
            setExceptionIndicies_function_type setExceptionIndicies_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::setExceptionIndicies );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "setExceptionIndicies"
                , setExceptionIndicies_function_value
                , ( bp::arg("name"), bp::arg("exception_idxs") )
                , bp::release_gil_policy()
                , "Set the global indexes of the exceptions in the non-bonded and\n  ghost-14 forces\n" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::toString
        
            typedef ::QString ( ::SireOpenMM::PerturbableOpenMMMolecule::*toString_function_type)(  ) const;
            toString_function_type toString_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::toString );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "toString"
                , toString_function_value
                , bp::release_gil_policy()
                , "" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::torsions
        
            typedef ::QList< SireMM::Dihedral > ( ::SireOpenMM::PerturbableOpenMMMolecule::*torsions_function_type)(  ) const;
            torsions_function_type torsions_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::torsions );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "torsions"
                , torsions_function_value
                , bp::release_gil_policy()
                , "Return the torsions which are perturbed, in the order they are\n  set in this perturbation. Note that this include both the\n  normal dihedrals and the improper torsions (openmm internally\n  treats them the same)\n" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::typeName
        
            typedef char const * ( *typeName_function_type )(  );
            typeName_function_type typeName_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::typeName );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "typeName"
                , typeName_function_value
                , bp::release_gil_policy()
                , "" );
        
        }
        { //::SireOpenMM::PerturbableOpenMMMolecule::what
        
            typedef char const * ( ::SireOpenMM::PerturbableOpenMMMolecule::*what_function_type)(  ) const;
            what_function_type what_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::what );
            
            PerturbableOpenMMMolecule_exposer.def( 
                "what"
                , what_function_value
                , bp::release_gil_policy()
                , "" );
        
        }
        PerturbableOpenMMMolecule_exposer.staticmethod( "typeName" );
        PerturbableOpenMMMolecule_exposer.def( "__copy__", &__copy__<SireOpenMM::PerturbableOpenMMMolecule>);
        PerturbableOpenMMMolecule_exposer.def( "__deepcopy__", &__copy__<SireOpenMM::PerturbableOpenMMMolecule>);
        PerturbableOpenMMMolecule_exposer.def( "clone", &__copy__<SireOpenMM::PerturbableOpenMMMolecule>);
        PerturbableOpenMMMolecule_exposer.def( "__str__", &__str__< ::SireOpenMM::PerturbableOpenMMMolecule > );
        PerturbableOpenMMMolecule_exposer.def( "__repr__", &__str__< ::SireOpenMM::PerturbableOpenMMMolecule > );
    }

}