// needed to work around bug in SWIG -- can not completely override module from command-line
%module "Chemistry::OpenBabel"

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

// workaround perl namespace pollution - c++11 defines seed
#ifdef seed
  #undef seed
#endif

// workaround perl namespace pollution - handy.h defines Zero(d,n,t) which
// conflicts with Eigen's Zero() static method declarations
#ifdef Zero
  #undef Zero
#endif

#include <openbabel/obutil.h>
#include <openbabel/math/vector3.h>
#include <openbabel/math/matrix3x3.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/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/chains.h>
#include <openbabel/obiter.h>
%}

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

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)
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*)

}

%define CAST_GENERICDATA_TO(subclass)
%inline %{
OpenBabel::OB ## subclass *to ## subclass(OpenBabel::OBGenericData *data) {
    return (OpenBabel::OB ## subclass *) data;
}
%}
%enddef
%inline %{ // can not 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)

// These methods are renamed to valid method names
%rename(inc)   *::operator++;
%rename(good)  *::operator bool;
%rename(deref) *::operator->;
%rename(add)  *::operator+=;
%rename(idx)  *::operator[];
%ignore *::operator=;
%ignore *::operator*=;
%ignore *::operator/=;
%ignore *::operator-=;
%ignore *::operator!=;
%ignore *::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>

%import <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;
%rename(_local) OpenBabel::local;
%include <openbabel/base.h>
%include <openbabel/generic.h>
%include <openbabel/griddata.h>
%include <openbabel/kekulize.h>


%import <openbabel/chains.h>
%import <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/mol.h>
%include <openbabel/ring.h>
%include <openbabel/parsmart.h>
%include <openbabel/alias.h>

// %include <openbabel/fingerprint.h> // Causes an error (I do not know why)
%include <openbabel/descriptor.h>

#ifdef HAVE_EIGEN3
%{
#include <openbabel/conformersearch.h>
#include <openbabel/math/align.h>
%}
%include <openbabel/conformersearch.h>
%include <openbabel/math/align.h>
#else
%ignore OpenBabel::OBForceField::FastRotorSearch;
%ignore OpenBabel::OBForceField::DiverseConfGen;
#endif

// 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>

// Ignore shadowed method
%ignore OpenBabel::OBRotor::GetRotAtoms() const;
%warnfilter(314); // 'next' is a Perl keyword
%include <openbabel/rotor.h>
%ignore OpenBabel::Swab;
%include <openbabel/rotamer.h>

// 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 &);

%rename(_next) OpenBabel::OBMolAtomDFSIter::next;

%ignore *::operator=;

%perlcode %{
# http://www.perl.com/pub/a/2005/06/16/iterators.html
sub gen_iterator {
    my $iterator_function = shift;
    return sub {
        my $iter = new $iterator_function(shift);

        my ($current_state, $done);

        return sub {
            # code to calculate $next_state or $done;
            return undef if $done;
            my $next_state = $iter->deref();
            $iter->inc();
            if (!$iter->good()) {$done = 1;};
            return $current_state = $next_state;
        };
    };
}
%}

// Add some helper functions for C arrays
%inline %{
double *double_array(int size) {
   return (double *) malloc(sizeof(double)*size);
}
void double_destroy(int *a) {
   free(a);
}
void double_set(double *a, int i, double val) {
   a[i] = val;
}
double double_get(double *a, int i) {
   return a[i];
}

double (*rotation_matrix())[3] {
     return (double (*)[3]) malloc(9*sizeof(double));
}

void rotation_matrix_free(double (*m)[3]) {
    free(m);
}
%}


%define MAKE_ITER_CLASS(itername, renamediter)
%rename itername renamediter;
%perlcode %{
package Chemistry::OpenBabel::itername;

sub new {
   my $pkg = shift;
   my $self = Chemistry::OpenBabel::gen_iterator(Chemistry::OpenBabel::renamediter)->(shift);
   bless($self, $pkg);
}
%}
%enddef

MAKE_ITER_CLASS(OBAtomAtomIter, _OBAtomAtomIter)
MAKE_ITER_CLASS(OBAtomBondIter, _OBAtomBondIter)
MAKE_ITER_CLASS(OBMolAngleIter, _OBMolAngleIter)
MAKE_ITER_CLASS(OBMolAtomIter, _OBMolAtomIter)
MAKE_ITER_CLASS(OBMolAtomBFSIter, _OBMolAtomBFSIter)
MAKE_ITER_CLASS(OBMolAtomDFSIter, _OBMolAtomDFSIter)
MAKE_ITER_CLASS(OBMolBondIter, _OBMolBondIter)
MAKE_ITER_CLASS(OBMolPairIter, _OBMolPairIter)
MAKE_ITER_CLASS(OBMolRingIter, _OBMolRingIter)
MAKE_ITER_CLASS(OBMolTorsionIter, _OBMolTorsionIter)
MAKE_ITER_CLASS(OBResidueAtomIter, _OBResidueAtomIter)
MAKE_ITER_CLASS(OBFingerprintIter, _OBFingerprintIter)

%include <openbabel/obiter.h>
