mirror of
https://github.com/openbabel/openbabel.git
synced 2026-08-26 21:27:29 -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>
308 lines
9.4 KiB
OpenEdge ABL
308 lines
9.4 KiB
OpenEdge ABL
%module OpenBabel
|
|
%include "std_string.i"
|
|
|
|
// These fields are renamed to valid constant names
|
|
%rename(U1MA) OpenBabel::OBResidueIndex::_1MA;
|
|
%rename(U1MG) OpenBabel::OBResidueIndex::_1MG;
|
|
%rename(U2MG) OpenBabel::OBResidueIndex::_2MG;
|
|
%rename(U7MG) OpenBabel::OBResidueIndex::_7MG;
|
|
%rename(U5MU) OpenBabel::OBResidueIndex::_5MU;
|
|
%rename(U5MC) OpenBabel::OBResidueIndex::_5MC;
|
|
|
|
%{
|
|
// 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/obfunctions.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/phmodel.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>
|
|
#include <openbabel/kekulize.h>
|
|
%}
|
|
|
|
%include "std_map.i"
|
|
%include "std_vector.i"
|
|
%include "std_list.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
|
|
|
|
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
|
|
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)
|
|
CAST_GENERICDATA_TO(TetrahedralStereo)
|
|
CAST_GENERICDATA_TO(CisTransStereo)
|
|
CAST_GENERICDATA_TO(SquarePlanarStereo)
|
|
|
|
// 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 *::DescribeBits;
|
|
%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;
|
|
%include <openbabel/base.h>
|
|
%include <openbabel/generic.h>
|
|
%include <openbabel/griddata.h>
|
|
|
|
%import <openbabel/chains.h>
|
|
%import <openbabel/typer.h>
|
|
|
|
// To avoid warning in oberror.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>
|
|
%include <openbabel/obconversion.h>
|
|
%include <openbabel/residue.h>
|
|
%include <openbabel/internalcoord.h>
|
|
%include <openbabel/elements.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>
|
|
%ignore OpenBabel::FptIndex;
|
|
%include <openbabel/fingerprint.h>
|
|
%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 *);
|
|
#ifdef HAVE_EIGEN
|
|
%{
|
|
#include <openbabel/conformersearch.h>
|
|
#include <openbabel/math/align.h>
|
|
%}
|
|
#else
|
|
%ignore OpenBabel::OBForceField::FastRotorSearch;
|
|
%ignore OpenBabel::OBForceField::DiverseConfGen;
|
|
#endif
|
|
%include <openbabel/forcefield.h>
|
|
|
|
%include <openbabel/builder.h>
|
|
%include <openbabel/op.h>
|
|
|
|
%ignore OpenBabel::OBRotor::GetRotAtoms() const;
|
|
%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 &);
|
|
|
|
|
|
%ignore *::operator=;
|
|
|
|
%include <openbabel/obiter.h>
|
|
|
|
%include <openbabel/chargemodel.h>
|
|
%include <openbabel/phmodel.h>
|
|
%include <openbabel/graphsym.h>
|
|
%include <openbabel/isomorphism.h>
|
|
%include <openbabel/query.h>
|
|
%include <openbabel/canon.h>
|
|
|
|
%include <openbabel/stereo/stereo.h>
|
|
|
|
%include <openbabel/kekulize.h>
|
|
%include <openbabel/obfunctions.h>
|
|
|
|
%include "stereo.i"
|