mirror of
https://github.com/openbabel/openbabel.git
synced 2026-08-27 05:37:38 -05:00
David KoesandDavid Koes
4b5d4c426f
* IsElement implemention, make OBElements::Element enum * Fix php include. Consistent renaming. Resname all the single character residue constants. Do this instead of defining natively in python since the actual constants are arbitrary and so could change (unlike elements) Co-authored-by: David Koes <dkoes@beefy.dcb.private.net>
414 lines
14 KiB
OpenEdge ABL
414 lines
14 KiB
OpenEdge ABL
%module openbabel_java
|
|
|
|
%{
|
|
// 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/base.h>
|
|
#include <openbabel/elements.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/stereo/tetrahedral.h>
|
|
#include <openbabel/stereo/cistrans.h>
|
|
#include <openbabel/stereo/squareplanar.h>
|
|
#include <openbabel/stereo/bindings.h>
|
|
|
|
#include <openbabel/chains.h>
|
|
#include <openbabel/obiter.h>
|
|
%}
|
|
|
|
#ifdef HAVE_EIGEN
|
|
%{
|
|
#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> >::resize;
|
|
%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>::resize;
|
|
%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> >::resize;
|
|
%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 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)
|
|
|
|
%ignore *::operator=;
|
|
%ignore *::operator==;
|
|
%ignore *::operator!=;
|
|
%ignore *::operator<<;
|
|
%ignore *::operator();
|
|
%ignore *::operator*;
|
|
%ignore *::operator*=;
|
|
%ignore *::operator+;
|
|
%ignore *::operator+=;
|
|
%ignore *::operator-;
|
|
%ignore *::operator-=;
|
|
%ignore *::operator++;
|
|
%ignore *::operator--;
|
|
%ignore *::operator/;
|
|
%ignore *::operator/=;
|
|
%ignore *::operator bool;
|
|
%ignore *::operator[];
|
|
|
|
%import <openbabel/babelconfig.h>
|
|
|
|
%warnfilter(516) OpenBabel::OBElementTable; // Ignoring std::string methods in favour of char* ones
|
|
%include <openbabel/data.h>
|
|
%include <openbabel/obutil.h>
|
|
%warnfilter(516) OpenBabel::vector3; // Using the const x(), y() and z() in favour of the non-const
|
|
%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>
|
|
%warnfilter(516) OpenBabel::SpaceGroup; // Ignoring std::string methods in favour of char* ones
|
|
%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;
|
|
%ignore OpenBabel::OBBase::GetData(char const *);
|
|
%ignore OpenBabel::OBBase::HasData(char const *);
|
|
%include <openbabel/base.h>
|
|
|
|
%warnfilter(516) OpenBabel::OBPairData; // Ignoring std::string methods in favour of char* ones
|
|
%warnfilter(516) OpenBabel::OBSetData;
|
|
%warnfilter(516) OpenBabel::OBCommentData;
|
|
%warnfilter(516) OpenBabel::OBUnitCell; // Ignoring const methods in favour of non-const ones
|
|
%include <openbabel/generic.h>
|
|
%include <openbabel/griddata.h>
|
|
|
|
%include <openbabel/chains.h>
|
|
%include <openbabel/typer.h>
|
|
|
|
// To avoid warning in plugin.h about "Nothing known about std::binary_function"
|
|
namespace std {
|
|
template <T1, T2, T3>
|
|
class binary_function {};
|
|
}
|
|
%template(dummy) std::binary_function <const char *, const char *, bool>;
|
|
%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>
|
|
%ignore OpenBabel::OBConversion::FindFormat(const char *);
|
|
%ignore OpenBabel::OBConversion::FormatFromExt(const char *);
|
|
%include <openbabel/obconversion.h>
|
|
|
|
//avoid conflicts with OBElement
|
|
%rename(resC) OpenBabel::OBResidueIndex::C;
|
|
%rename(resI) OpenBabel::OBResidueIndex::I;
|
|
%rename(resU) OpenBabel::OBResidueIndex::U;
|
|
%include <openbabel/residue.h>
|
|
%include <openbabel/internalcoord.h>
|
|
%include <openbabel/elements.h>
|
|
|
|
%typemap(javacode) OpenBabel::OBAtom
|
|
%{
|
|
private int currentDepth = 0;
|
|
public void SetCurrentDepth(int d) {currentDepth = d;}
|
|
public int GetCurrentDepth() {return currentDepth;}
|
|
%}
|
|
%ignore OpenBabel::OBAtom::GetVector() const;
|
|
%ignore OpenBabel::OBAtom::IsHydrogen const;
|
|
%ignore OpenBabel::OBAtom::SetType(char const *);
|
|
%include <openbabel/atom.h>
|
|
%ignore OpenBabel::OBBond::GetBeginAtom() const;
|
|
%ignore OpenBabel::OBBond::GetEndAtom() const;
|
|
%include <openbabel/bond.h>
|
|
%include <openbabel/reaction.h>
|
|
|
|
// Remove C++ iterators
|
|
%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>
|
|
%warnfilter(516) OpenBabel::OBSmartsPattern; // Using non-const versions of GetSMARTS
|
|
%include <openbabel/parsmart.h>
|
|
%warnfilter(516) OpenBabel::AliasData; // Ignoring std::string methods in favour of char* ones
|
|
%include <openbabel/alias.h>
|
|
%ignore OpenBabel::FptIndex;
|
|
%include <openbabel/fingerprint.h>
|
|
%ignore OpenBabel::OBDescriptor::LessThan;
|
|
%include <openbabel/descriptor.h>
|
|
|
|
#ifdef HAVE_EIGEN
|
|
%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 *);
|
|
%warnfilter(516) OpenBabel::OBForceField; // Ignoring std::string methods in favour of char* ones
|
|
%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>
|
|
|
|
// 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 &);
|
|
|
|
%ignore SpaceGroup::RegisterSpaceGroup;
|
|
|
|
%define WRAPITERATOR(NAME, RETURNS, OPTIONAL)
|
|
%rename(_next) OpenBabel::NAME::next;
|
|
%rename(inc) OpenBabel::NAME::operator++;
|
|
%rename(HasMore) OpenBabel::NAME::operator bool;
|
|
%typemap(javainterfaces) OpenBabel::NAME "Iterable<RETURNS>, Iterator<RETURNS>";
|
|
%typemap(javaimports) OpenBabel::NAME " import org.openbabel.RETURNS;
|
|
import java.util.Iterator;"
|
|
%typemap(javacode) OpenBabel::NAME
|
|
%{
|
|
public Iterator<RETURNS> iterator() {
|
|
return this;
|
|
}
|
|
|
|
public boolean hasNext() {
|
|
return HasMore();
|
|
}
|
|
|
|
public RETURNS next() {
|
|
RETURNS atom = __ref__();
|
|
OPTIONAL
|
|
inc();
|
|
return atom;
|
|
}
|
|
|
|
public void remove() {
|
|
}
|
|
%}
|
|
%enddef
|
|
|
|
WRAPITERATOR(OBMolAtomIter, OBAtom, );
|
|
WRAPITERATOR(OBMolAtomDFSIter, OBAtom, );
|
|
WRAPITERATOR(OBMolAtomBFSIter, OBAtom, atom.SetCurrentDepth(CurrentDepth()););
|
|
WRAPITERATOR(OBMolBondIter, OBBond, );
|
|
WRAPITERATOR(OBMolAngleIter, vectorUnsignedInt, );
|
|
WRAPITERATOR(OBAtomAtomIter, OBAtom, )
|
|
WRAPITERATOR(OBAtomBondIter, OBBond, );
|
|
WRAPITERATOR(OBMolRingIter, OBRing, );
|
|
WRAPITERATOR(OBMolTorsionIter, vectorUnsignedInt, );
|
|
WRAPITERATOR(OBResidueIter, OBResidue, );
|
|
WRAPITERATOR(OBResidueAtomIter, OBAtom, );
|
|
WRAPITERATOR(OBMolPairIter, vectorUnsignedInt, );
|
|
|
|
%include <openbabel/obiter.h>
|
|
|
|
%include "stereo.i"
|