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>
308 lines
9.4 KiB
OpenEdge ABL
308 lines
9.4 KiB
OpenEdge ABL
%module OpenBabel
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%include "std_string.i"
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// These fields are renamed to valid constant names
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%rename(U1MA) OpenBabel::OBResidueIndex::_1MA;
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%rename(U1MG) OpenBabel::OBResidueIndex::_1MG;
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%rename(U2MG) OpenBabel::OBResidueIndex::_2MG;
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%rename(U7MG) OpenBabel::OBResidueIndex::_7MG;
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%rename(U5MU) OpenBabel::OBResidueIndex::_5MU;
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%rename(U5MC) OpenBabel::OBResidueIndex::_5MC;
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%{
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// used to set import/export for Cygwin DLLs
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#ifdef WIN32
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#define USING_OBDLL
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#endif
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#include <openbabel/obutil.h>
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#include <openbabel/math/vector3.h>
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#include <openbabel/math/matrix3x3.h>
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#include <openbabel/math/transform3d.h>
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#include <openbabel/math/spacegroup.h>
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#include <openbabel/generic.h>
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#include <openbabel/griddata.h>
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#include <openbabel/base.h>
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#include <openbabel/elements.h>
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#include <openbabel/mol.h>
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#include <openbabel/atom.h>
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#include <openbabel/bond.h>
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#include <openbabel/reaction.h>
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#include <openbabel/residue.h>
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#include <openbabel/internalcoord.h>
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#include <openbabel/ring.h>
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#include <openbabel/obconversion.h>
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#include <openbabel/obfunctions.h>
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#include <openbabel/oberror.h>
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#include <openbabel/plugin.h>
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#include <openbabel/fingerprint.h>
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#include <openbabel/descriptor.h>
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#include <openbabel/format.h>
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#include <openbabel/forcefield.h>
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#include <openbabel/builder.h>
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#include <openbabel/op.h>
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#include <openbabel/bitvec.h>
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#include <openbabel/data.h>
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#include <openbabel/parsmart.h>
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#include <openbabel/alias.h>
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#include <openbabel/kinetics.h>
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#include <openbabel/rotor.h>
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#include <openbabel/rotamer.h>
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#include <openbabel/spectrophore.h>
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#include <openbabel/chargemodel.h>
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#include <openbabel/phmodel.h>
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#include <openbabel/graphsym.h>
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#include <openbabel/isomorphism.h>
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#include <openbabel/query.h>
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#include <openbabel/canon.h>
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#include <openbabel/stereo/tetrahedral.h>
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#include <openbabel/stereo/cistrans.h>
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#include <openbabel/stereo/squareplanar.h>
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#include <openbabel/stereo/bindings.h>
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#include <openbabel/chains.h>
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#include <openbabel/obiter.h>
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#include <openbabel/kekulize.h>
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%}
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%include "std_map.i"
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%include "std_vector.i"
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%include "std_list.i"
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%include "std_pair.i"
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namespace std {
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%define VVTEMPLATE_WRAP(name, T)
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%feature("ignore") vector< vector<T> >::append;
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%feature("ignore") vector< vector<T> >::assign;
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%feature("ignore") vector< vector<T> >::back;
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%feature("ignore") vector< vector<T> >::begin;
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%feature("ignore") vector< vector<T> >::capacity;
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%feature("ignore") vector< vector<T> >::clear;
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%feature("ignore") vector< vector<T> >::empty;
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%feature("ignore") vector< vector<T> >::end;
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%feature("ignore") vector< vector<T> >::erase;
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%feature("ignore") vector< vector<T> >::front;
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%feature("ignore") vector< vector<T> >::get_allocator;
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%feature("ignore") vector< vector<T> >::insert;
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%feature("ignore") vector< vector<T> >::pop;
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%feature("ignore") vector< vector<T> >::pop_back;
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%feature("ignore") vector< vector<T> >::push_back;
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%feature("ignore") vector< vector<T> >::rbegin;
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%feature("ignore") vector< vector<T> >::rend;
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%feature("ignore") vector< vector<T> >::reserve;
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%feature("ignore") vector< vector<T> >::resize;
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%feature("ignore") vector< vector<T> >::size;
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%feature("ignore") vector< vector<T> >::swap;
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%template(VectorV ## name) vector< vector<T> >;
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%enddef
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%define VECTORTEMPLATE_WRAP(vectorname, T)
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%feature("ignore") vector<T>::append;
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%feature("ignore") vector<T>::assign;
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%feature("ignore") vector<T>::back;
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%feature("ignore") vector<T>::begin;
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%feature("ignore") vector<T>::capacity;
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%feature("ignore") vector<T>::clear;
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%feature("ignore") vector<T>::empty;
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%feature("ignore") vector<T>::end;
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%feature("ignore") vector<T>::erase;
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%feature("ignore") vector<T>::front;
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%feature("ignore") vector<T>::get_allocator;
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%feature("ignore") vector<T>::insert;
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%feature("ignore") vector<T>::pop;
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%feature("ignore") vector<T>::pop_back;
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%feature("ignore") vector<T>::push_back;
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%feature("ignore") vector<T>::rbegin;
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%feature("ignore") vector<T>::rend;
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%feature("ignore") vector<T>::reserve;
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%feature("ignore") vector<T>::resize;
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%feature("ignore") vector<T>::size;
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%feature("ignore") vector<T>::swap;
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%template(Vector ## vectorname) vector<T>;
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%enddef
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VECTORTEMPLATE_WRAP(Int, int)
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VECTORTEMPLATE_WRAP(UnsignedInt, unsigned int)
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VVTEMPLATE_WRAP(Int, int)
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VECTORTEMPLATE_WRAP(Double, double)
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VECTORTEMPLATE_WRAP(String, std::string)
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VECTORTEMPLATE_WRAP(Vector3, OpenBabel::vector3)
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VECTORTEMPLATE_WRAP(OBMol, OpenBabel::OBMol)
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VECTORTEMPLATE_WRAP(OBBond, OpenBabel::OBBond)
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VECTORTEMPLATE_WRAP(OBResidue, OpenBabel::OBResidue)
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VECTORTEMPLATE_WRAP(OBRing, OpenBabel::OBRing)
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VECTORTEMPLATE_WRAP(pOBRing, OpenBabel::OBRing*)
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VECTORTEMPLATE_WRAP(pOBGenericData, OpenBabel::OBGenericData*)
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}
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%define CAST_GENERICDATA_TO(subclass)
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%inline %{
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OpenBabel::OB ## subclass *to ## subclass(OpenBabel::OBGenericData *data) {
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return (OpenBabel::OB ## subclass *) data;
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}
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%}
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%enddef
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CAST_GENERICDATA_TO(AngleData)
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CAST_GENERICDATA_TO(CommentData)
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CAST_GENERICDATA_TO(ConformerData)
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CAST_GENERICDATA_TO(ExternalBondData)
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CAST_GENERICDATA_TO(GridData)
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CAST_GENERICDATA_TO(MatrixData)
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CAST_GENERICDATA_TO(NasaThermoData)
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CAST_GENERICDATA_TO(PairData)
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// CAST_GENERICDATA_TO(PairTemplate)
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CAST_GENERICDATA_TO(RateData)
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CAST_GENERICDATA_TO(RotamerList)
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CAST_GENERICDATA_TO(RotationData)
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CAST_GENERICDATA_TO(SerialNums)
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CAST_GENERICDATA_TO(SetData)
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CAST_GENERICDATA_TO(SymmetryData)
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CAST_GENERICDATA_TO(TorsionData)
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CAST_GENERICDATA_TO(UnitCell)
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CAST_GENERICDATA_TO(VectorData)
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CAST_GENERICDATA_TO(VibrationData)
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CAST_GENERICDATA_TO(VirtualBond)
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CAST_GENERICDATA_TO(TetrahedralStereo)
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CAST_GENERICDATA_TO(CisTransStereo)
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CAST_GENERICDATA_TO(SquarePlanarStereo)
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// These methods are renamed to valid method names
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%rename(inc) *::operator++;
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%rename(good) *::operator bool;
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%rename(deref) *::operator->;
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%rename(add) *::operator+=;
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%rename(idx) *::operator[];
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%ignore *::DescribeBits;
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%ignore *::operator=;
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%ignore *::operator*=;
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%ignore *::operator/=;
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%ignore *::operator-=;
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%ignore *::operator!=;
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%ignore *::operator&=;
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%ignore *::operator^=;
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%ignore *::operator|=;
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%import <openbabel/babelconfig.h>
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%include <openbabel/data.h>
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%include <openbabel/obutil.h>
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%include <openbabel/math/vector3.h>
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%warnfilter(503) OpenBabel::matrix3x3; // Not wrapping any of the overloaded operators
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%include <openbabel/math/matrix3x3.h>
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%import <openbabel/math/spacegroup.h>
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%warnfilter(503) OpenBabel::OBBitVec; // Not wrapping any of the overloaded operators
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%include <openbabel/bitvec.h>
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// CloneData should be used instead of the following method
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%ignore OpenBabel::OBBase::SetData;
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%include <openbabel/base.h>
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%include <openbabel/generic.h>
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%include <openbabel/griddata.h>
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%import <openbabel/chains.h>
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%import <openbabel/typer.h>
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// To avoid warning in oberror.h about "Nothing known about std::binary_function"
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namespace std {
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template <T1, T2, T3>
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class binary_function {};
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}
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%template(Dummy) std::binary_function <const char *, const char *, bool>;
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%include <openbabel/plugin.h>
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// To avoid warning in oberror.h about "Nothing known about std::stringbuf"
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namespace std { class stringbuf {}; }
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%warnfilter(503) OpenBabel::OBError; // Not wrapping any of the overloaded operators
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%include <openbabel/oberror.h>
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%include <openbabel/format.h>
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%include <openbabel/obconversion.h>
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%include <openbabel/residue.h>
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%include <openbabel/internalcoord.h>
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%include <openbabel/elements.h>
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%include <openbabel/atom.h>
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%include <openbabel/bond.h>
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%include <openbabel/mol.h>
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%include <openbabel/ring.h>
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%include <openbabel/parsmart.h>
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%include <openbabel/alias.h>
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%ignore OpenBabel::FptIndex;
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%include <openbabel/fingerprint.h>
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%include <openbabel/descriptor.h>
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// Ignore shadowed methods
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%ignore OpenBabel::OBForceField::VectorSubtract(const double *const, const double *const, double *);
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%ignore OpenBabel::OBForceField::VectorMultiply(const double *const, const double, double *);
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#ifdef HAVE_EIGEN
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%{
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#include <openbabel/conformersearch.h>
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#include <openbabel/math/align.h>
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%}
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#else
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%ignore OpenBabel::OBForceField::FastRotorSearch;
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%ignore OpenBabel::OBForceField::DiverseConfGen;
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#endif
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%include <openbabel/forcefield.h>
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%include <openbabel/builder.h>
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%include <openbabel/op.h>
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%ignore OpenBabel::OBRotor::GetRotAtoms() const;
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%include <openbabel/rotor.h>
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%ignore OpenBabel::Swab;
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%include <openbabel/rotamer.h>
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// The following %ignores avoid warning messages due to shadowed classes.
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// This does not imply a loss of functionality as (in this case)
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// the shadowed class is identical (from the point of view of SWIG) to
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// the shadowing class.
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// This is because C++ references (&) are transformed by SWIG back into
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// pointers, so that OBAtomIter(OBMol &) would be treated the same as
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// OBAtomIter(OBMol *).
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%ignore OBAtomAtomIter(OBAtom &);
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%ignore OBAtomBondIter(OBAtom &);
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%ignore OBMolAngleIter(OBMol &);
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%ignore OBMolAtomIter(OBMol &);
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%ignore OBMolAtomBFSIter(OBMol &);
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%ignore OBMolAtomDFSIter(OBMol &);
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%ignore OBMolAtomBFSIter(OBMol &, int);
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%ignore OBMolAtomDFSIter(OBMol &, int);
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%ignore OBMolBondIter(OBMol &);
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%ignore OBMolBondBFSIter(OBMol &);
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%ignore OBMolBondBFSIter(OBMol &, int);
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%ignore OBMolPairIter(OBMol &);
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%ignore OBMolRingIter(OBMol &);
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%ignore OBMolTorsionIter(OBMol &);
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%ignore OBResidueIter(OBMol &);
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%ignore OBResidueAtomIter(OBResidue &);
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%ignore *::operator=;
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%include <openbabel/obiter.h>
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%include <openbabel/chargemodel.h>
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%include <openbabel/phmodel.h>
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%include <openbabel/graphsym.h>
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%include <openbabel/isomorphism.h>
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%include <openbabel/query.h>
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%include <openbabel/canon.h>
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%include <openbabel/stereo/stereo.h>
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%include <openbabel/kekulize.h>
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%include <openbabel/obfunctions.h>
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%include "stereo.i"
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