%module openbabel

%{
// used to set import/export for Cygwin DLLs
#ifdef WIN32
#define USING_OBDLL
#endif


#include <openbabel/obutil.h>
#include <openbabel/math/vector3.h>
#include <openbabel/math/matrix3x3.h>
#include <openbabel/math/transform3d.h>
#include <openbabel/math/spacegroup.h>

#include <openbabel/generic.h>
#include <openbabel/griddata.h>
#include <openbabel/kekulize.h>

#include <openbabel/base.h>
#include <openbabel/mol.h>
#include <openbabel/atom.h>
#include <openbabel/bond.h>
#include <openbabel/reaction.h>
#include <openbabel/residue.h>
#include <openbabel/internalcoord.h>

#include <openbabel/ring.h>
#include <openbabel/obconversion.h>
#include <openbabel/oberror.h>
#include <openbabel/plugin.h>
#include <openbabel/fingerprint.h>
#include <openbabel/descriptor.h>
#include <openbabel/format.h>

#include <openbabel/forcefield.h>
#include <openbabel/builder.h>
#include <openbabel/op.h>

#include <openbabel/bitvec.h>
#include <openbabel/data.h>
#include <openbabel/parsmart.h>
#include <openbabel/alias.h>

#include <openbabel/kinetics.h>
#include <openbabel/rotor.h>
#include <openbabel/rotamer.h>
#include <openbabel/spectrophore.h>

#include <openbabel/chargemodel.h>
#include <openbabel/graphsym.h>
#include <openbabel/isomorphism.h>
#include <openbabel/query.h>
#include <openbabel/canon.h>

#include <openbabel/chains.h>
#include <openbabel/obiter.h>
%}

#ifdef HAVE_EIGEN3
%{
#include <openbabel/conformersearch.h>
#include <openbabel/math/align.h>
%}
#endif

%include "std_map.i"
%include "std_vector.i"
%include "std_string.i"
%include "std_pair.i"

namespace std {

%define VVTEMPLATE_WRAP(name, T) 
%feature("ignore") vector< vector<T> >::append;
%feature("ignore") vector< vector<T> >::assign;
%feature("ignore") vector< vector<T> >::back;
%feature("ignore") vector< vector<T> >::begin;
%feature("ignore") vector< vector<T> >::capacity;
%feature("ignore") vector< vector<T> >::clear;
%feature("ignore") vector< vector<T> >::empty;
%feature("ignore") vector< vector<T> >::end;
%feature("ignore") vector< vector<T> >::erase;
%feature("ignore") vector< vector<T> >::front;
%feature("ignore") vector< vector<T> >::get_allocator;
%feature("ignore") vector< vector<T> >::insert;
%feature("ignore") vector< vector<T> >::pop;
%feature("ignore") vector< vector<T> >::pop_back;
%feature("ignore") vector< vector<T> >::push_back;
%feature("ignore") vector< vector<T> >::rbegin;
%feature("ignore") vector< vector<T> >::rend;
%feature("ignore") vector< vector<T> >::reserve;
%feature("ignore") vector< vector<T> >::resize;
//%feature("ignore") vector< vector<T> >::size;
%feature("ignore") vector< vector<T> >::swap;
%template(vectorv ## name) vector< vector<T> >;
%enddef

%define VECTORTEMPLATE_WRAP(vectorname, T) 
%feature("ignore") vector<T>::append;
%feature("ignore") vector<T>::assign;
%feature("ignore") vector<T>::back;
%feature("ignore") vector<T>::begin;
%feature("ignore") vector<T>::capacity;
%feature("ignore") vector<T>::clear;
%feature("ignore") vector<T>::empty;
%feature("ignore") vector<T>::end;
%feature("ignore") vector<T>::erase;
%feature("ignore") vector<T>::front;
%feature("ignore") vector<T>::get_allocator;
%feature("ignore") vector<T>::insert;
%feature("ignore") vector<T>::pop;
%feature("ignore") vector<T>::pop_back;
%feature("ignore") vector<T>::push_back;
%feature("ignore") vector<T>::rbegin;
%feature("ignore") vector<T>::rend;
%feature("ignore") vector<T>::reserve;
%feature("ignore") vector<T>::resize;
//%feature("ignore") vector<T>::size;
%feature("ignore") vector<T>::swap;
%template(vector ## vectorname) vector<T>;
%enddef

%define VECTORPAIRTEMPLATE_WRAP(vectorname, T1, T2) 
%feature("ignore") vector< pair<T1, T2> >::append;
%feature("ignore") vector< pair<T1, T2> >::assign;
%feature("ignore") vector< pair<T1, T2> >::back;
%feature("ignore") vector< pair<T1, T2> >::begin;
%feature("ignore") vector< pair<T1, T2> >::capacity;
%feature("ignore") vector< pair<T1, T2> >::clear;
%feature("ignore") vector< pair<T1, T2> >::empty;
%feature("ignore") vector< pair<T1, T2> >::end;
%feature("ignore") vector< pair<T1, T2> >::erase;
%feature("ignore") vector< pair<T1, T2> >::front;
%feature("ignore") vector< pair<T1, T2> >::get_allocator;
%feature("ignore") vector< pair<T1, T2> >::insert;
%feature("ignore") vector< pair<T1, T2> >::pop;
%feature("ignore") vector< pair<T1, T2> >::pop_back;
%feature("ignore") vector< pair<T1, T2> >::push_back;
%feature("ignore") vector< pair<T1, T2> >::rbegin;
%feature("ignore") vector< pair<T1, T2> >::rend;
%feature("ignore") vector< pair<T1, T2> >::reserve;
%feature("ignore") vector< pair<T1, T2> >::resize;
//%feature("ignore") vector< pair<T1, T2> >::size;
%feature("ignore") vector< pair<T1, T2> >::swap;
%template(vpair ## vectorname) vector< pair<T1, T2> >;
%enddef

VECTORTEMPLATE_WRAP(Int, int)
VECTORTEMPLATE_WRAP(UnsignedInt, unsigned int)
VVTEMPLATE_WRAP(Int, int)
VECTORTEMPLATE_WRAP(Double, double)
VECTORTEMPLATE_WRAP(String, std::string)
VECTORTEMPLATE_WRAP(Vector3, OpenBabel::vector3)
VVTEMPLATE_WRAP(Vector3, OpenBabel::vector3)
VECTORTEMPLATE_WRAP(OBMol, OpenBabel::OBMol)
VECTORTEMPLATE_WRAP(OBBond, OpenBabel::OBBond)
VECTORTEMPLATE_WRAP(OBResidue, OpenBabel::OBResidue)
VECTORTEMPLATE_WRAP(OBRing, OpenBabel::OBRing)
VECTORTEMPLATE_WRAP(pOBRing, OpenBabel::OBRing*)
VECTORTEMPLATE_WRAP(pOBGenericData, OpenBabel::OBGenericData*)
VECTORTEMPLATE_WRAP(pOBInternalCoord, OpenBabel::OBInternalCoord*)

%template(pairUIntUInt) pair<unsigned int, unsigned int>;
VECTORPAIRTEMPLATE_WRAP(UIntUInt, unsigned int, unsigned int);
%template(vvpairUIntUInt) vector< vector< pair<unsigned int, unsigned int> > >;
}

%define CAST_GENERICDATA_TO(subclass)
%inline %{
OpenBabel::OB ## subclass *to ## subclass(OpenBabel::OBGenericData *data) {
    return (OpenBabel::OB ## subclass *) data;
}
%}
%enddef
%inline %{ // can't use macro -- AliasData not OBAliasData
OpenBabel::AliasData *toAliasData(OpenBabel::OBGenericData *data) {
    return (OpenBabel::AliasData*) data;
}
%}
CAST_GENERICDATA_TO(AngleData)
CAST_GENERICDATA_TO(CommentData)
CAST_GENERICDATA_TO(ConformerData)
CAST_GENERICDATA_TO(ExternalBondData)
CAST_GENERICDATA_TO(GridData)
CAST_GENERICDATA_TO(MatrixData)
CAST_GENERICDATA_TO(NasaThermoData)
CAST_GENERICDATA_TO(PairData)
// CAST_GENERICDATA_TO(PairTemplate)
CAST_GENERICDATA_TO(RateData)
CAST_GENERICDATA_TO(RotamerList)
CAST_GENERICDATA_TO(RotationData)
CAST_GENERICDATA_TO(SerialNums)
CAST_GENERICDATA_TO(SetData)
CAST_GENERICDATA_TO(SymmetryData)
CAST_GENERICDATA_TO(TorsionData)
CAST_GENERICDATA_TO(UnitCell)
CAST_GENERICDATA_TO(VectorData)
CAST_GENERICDATA_TO(VibrationData)
CAST_GENERICDATA_TO(VirtualBond)

%rename(add)  *::operator+=;
%ignore *::operator=;
%ignore *::operator[];

%import <openbabel/babelconfig.h>

%include <openbabel/data.h>
%include <openbabel/obutil.h>
%include <openbabel/math/vector3.h>
%warnfilter(503) OpenBabel::matrix3x3; // Not wrapping any of the overloaded operators
%include <openbabel/math/matrix3x3.h>
%include <openbabel/math/transform3d.h>
%include <openbabel/math/spacegroup.h>
%warnfilter(503) OpenBabel::OBBitVec; // Not wrapping any of the overloaded operators
%include <openbabel/bitvec.h>

// CloneData should be used instead of the following method
%ignore OpenBabel::OBBase::SetData;
%include <openbabel/base.h>

%include <openbabel/generic.h>
%include <openbabel/griddata.h>
%include <openbabel/kekulize.h>


%include <openbabel/chains.h>
%include <openbabel/typer.h>
%include <openbabel/plugin.h>

// To avoid warning in oberror.h about "Nothing known about std::stringbuf"
namespace std { class stringbuf {}; }
%warnfilter(503) OpenBabel::OBError; // Not wrapping any of the overloaded operators
%include <openbabel/oberror.h>
%include <openbabel/format.h>
%include <openbabel/obconversion.h>
%include <openbabel/residue.h>
%include <openbabel/internalcoord.h>
%include <openbabel/atom.h>
%include <openbabel/bond.h>
%include <openbabel/reaction.h>

%define IGNORE_ITER(parent, iteree)
%ignore OpenBabel::parent::Begin ## iteree ## s;
%ignore OpenBabel::parent::End ## iteree ## s;
%ignore OpenBabel::parent::Begin ## iteree;
%ignore OpenBabel::parent::Next ## iteree;
%enddef
IGNORE_ITER(OBMol, Bond)
IGNORE_ITER(OBMol, Atom)
IGNORE_ITER(OBMol, Residue)
%include <openbabel/mol.h>

%include <openbabel/ring.h>
%include <openbabel/parsmart.h>
%include <openbabel/alias.h>
%ignore OpenBabel::FptIndex;
%include <openbabel/fingerprint.h>
%ignore OpenBabel::OBDescriptor::LessThan;
%include <openbabel/descriptor.h>

// Ignore shadowed methods
%ignore OpenBabel::OBForceField::VectorSubtract(const double *const, const double *const, double *);
%ignore OpenBabel::OBForceField::VectorMultiply(const double *const, const double, double *);
%include <openbabel/forcefield.h>

%include <openbabel/builder.h>
%include <openbabel/op.h>

%include <openbabel/chargemodel.h>
%include <openbabel/graphsym.h>
%include <openbabel/isomorphism.h>
%include <openbabel/query.h>
%include <openbabel/canon.h>
%include <openbabel/stereo/stereo.h>

// Ignore shadowed method
%ignore OpenBabel::OBRotor::GetRotAtoms() const;
%include <openbabel/rotor.h>
%ignore OpenBabel::Swab;
%include <openbabel/rotamer.h>
%include <openbabel/spectrophore.h>

#ifdef HAVE_EIGEN3
%include <openbabel/conformersearch.h>
%include <openbabel/math/align.h>
#endif

// The following %ignores avoid warning messages due to shadowed classes.
// This does not imply a loss of functionality as (in this case)
// the shadowed class is identical (from the point of view of SWIG) to
// the shadowing class.
// This is because C++ references (&) are transformed by SWIG back into
// pointers, so that OBAtomIter(OBMol &) would be treated the same as
// OBAtomIter(OBMol *).

%ignore OBAtomAtomIter(OBAtom &);
%ignore OBAtomBondIter(OBAtom &);
%ignore OBMolAngleIter(OBMol &);
%ignore OBMolAtomIter(OBMol &);
%ignore OBMolAtomBFSIter(OBMol &);
%ignore OBMolAtomDFSIter(OBMol &);
%ignore OBMolAtomBFSIter(OBMol &, int);
%ignore OBMolAtomDFSIter(OBMol &, int);
%ignore OBMolBondIter(OBMol &);
%ignore OBMolBondBFSIter(OBMol &);
%ignore OBMolBondBFSIter(OBMol &, int);
%ignore OBMolPairIter(OBMol &);
%ignore OBMolRingIter(OBMol &);
%ignore OBMolTorsionIter(OBMol &);
%ignore OBResidueIter(OBMol &);
%ignore OBResidueAtomIter(OBResidue &);

%include <openbabel/obiter.h>

// Functions to set the log file to std::cout and std::cerr
       
%ignore OBForceField::SetLogFile(std::ostream *pos);
%extend OpenBabel::OBForceField {
  void SetLogToStdOut() 
  {
    self->SetLogFile(&std::cout);
  }

  void SetLogToStdErr() 
  {
    self->SetLogFile(&std::cerr);
  }
};

%extend OpenBabel::OBMol {
  void SetTorsion(int i, int j, int k, int l, double ang) 
  {
    self->SetTorsion(self->GetAtom(i), self->GetAtom(j),
                     self->GetAtom(k), self->GetAtom(l), ang);
  }
};