Skip to content

Instantly share code, notes, and snippets.

@siriusjack
Created March 15, 2015 12:49
Show Gist options
  • Save siriusjack/ae359025557d304de0e9 to your computer and use it in GitHub Desktop.
Save siriusjack/ae359025557d304de0e9 to your computer and use it in GitHub Desktop.
swig: openbabel-python.i
%module openbabel
%{
// used to set import/export for Cygwin DLLs
#ifdef WIN32
#define USING_OBDLL
#endif
#include <openbabel/obutil.h>
#include <openbabel/rand.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/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/atomclass.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>
%}
#ifdef HAVE_EIGEN
%{
#include <openbabel/conformersearch.h>
#include <openbabel/math/align.h>
%}
#else
%ignore OpenBabel::OBForceField::FastRotorSearch;
%ignore OpenBabel::OBForceField::DiverseConfGen;
#endif
%include "std_list.i"
%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(ULong, unsigned long)
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(AtomClassData)
CAST_GENERICDATA_TO(ChiralData)
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)
// This method is renamed to a valid Python method name, as otherwise
// it cannot be used from Python
%rename(inc) *::operator++;
%ignore *::operator=;
%ignore *::operator[];
%import <openbabel/babelconfig.h>
%include <openbabel/data.h>
%include <openbabel/rand.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>
//# 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/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>
%include <openbabel/obconversion.h>
%include <openbabel/residue.h>
%include <openbabel/internalcoord.h>
%include <openbabel/atom.h>
%include <openbabel/bond.h>
%include <openbabel/reaction.h>
// Remove C++ iterators
%pythoncode %{
def exceptionIter(*args):
raise Exception("""\nThis method can only be used from C++. To iterate from Python
use the Iter classes (OBMolAtomIter, etc.) as described at
http://openbabel.org/wiki/Python""")
%}
%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>
%pythoncode %{
OBMol.BeginAtoms = OBMol.EndAtoms = OBMol.BeginAtom = OBMol.EndAtom = exceptionIter
OBMol.BeginBonds = OBMol.EndBonds = OBMol.BeginBond = OBMol.EndBond = exceptionIter
OBMol.BeginResidues = OBMol.EndResidues = OBMol.BeginResidue = OBMol.EndResidue = exceptionIter
%}
%include <openbabel/ring.h>
%include <openbabel/parsmart.h>
%include <openbabel/alias.h>
%include <openbabel/atomclass.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>
%apply std::string& INPUT { std::string &start } // Required for OBChemTsfm.Init
%apply std::string& INPUT { std::string &end } // Required for OBChemTsfm.Init
%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>
%warnfilter(503) OpenBabel::OBBitVec; // Not wrapping any of the overloaded operators
%include <openbabel/bitvec.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_EIGEN
%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 &);
//# These classes are renamed so that they can be replaced by Python
//# classes of the same name which provide Pythonic iterators
//# (see %pythoncode section below)
%rename(_OBAtomAtomIter) OpenBabel::OBAtomAtomIter;
%rename(_OBAtomBondIter) OpenBabel::OBAtomBondIter;
%rename(_OBMolAngleIter) OpenBabel::OBMolAngleIter;
%rename(_OBMolAtomIter) OpenBabel::OBMolAtomIter;
%rename(_OBMolAtomBFSIter) OpenBabel::OBMolAtomBFSIter;
%rename(_OBMolAtomDFSIter) OpenBabel::OBMolAtomDFSIter;
%rename(_OBMolBondIter) OpenBabel::OBMolBondIter;
%rename(_OBMolPairIter) OpenBabel::OBMolPairIter;
%rename(_OBMolRingIter) OpenBabel::OBMolRingIter;
%rename(_OBMolTorsionIter) OpenBabel::OBMolTorsionIter;
%rename(_OBResidueIter) OpenBabel::OBResidueIter;
%rename(_OBResidueAtomIter) OpenBabel::OBResidueAtomIter;
%rename(_OBFingerprintIter) OpenBabel::PluginIter<OBFingerprint>;
%include <openbabel/obiter.h>
//# The following class, OBiter, is subclassed to provide Python iterators
//# equivalent to the C++ iterators in obiter.h and the plugin iterators
%pythoncode %{
class OBIter(object):
OBiterator = None # This is defined by the subclasses
def __init__(self, *params):
self.iter = self.OBiterator(*params)
self.finished = False
if not self.iter.__bool__():
self.finished = True
def __iter__(self):
return self
def next(self):
if not self.finished:
b = self.iter.__ref__()
self.iter.inc()
if not self.iter.__bool__():
# There is nothing left to iterate over
self.finished = True
return b
else:
raise StopIteration
__next__ = next
class OBIterWithDepth(OBIter):
def next(self):
if not self.finished:
b = self.iter.__ref__()
depth = self.iter.CurrentDepth()
self.iter.inc()
if not self.iter.__bool__():
# There is nothing left to iterate over
self.finished = True
return b, depth
else:
raise StopIteration
class OBAtomAtomIter(OBIter):
"""Iterator over the atoms attached to an atom."""
OBiterator = _OBAtomAtomIter
class OBAtomBondIter(OBIter):
"""Iterator over the bonds attached to an atom."""
OBiterator = _OBAtomBondIter
class OBMolAngleIter(OBIter):
"""Iterator over the angles in a molecule."""
OBiterator = _OBMolAngleIter
class OBMolAtomIter(OBIter):
"""Iterator over the atoms in a molecule."""
OBiterator = _OBMolAtomIter
class OBMolAtomBFSIter(OBIterWithDepth):
"""Iterator over the atoms in a molecule in a breadth-first manner."""
OBiterator = _OBMolAtomBFSIter
class OBMolAtomDFSIter(OBIter):
"""Iterator over the atoms in a molecule in a depth-first manner."""
OBiterator = _OBMolAtomDFSIter
class OBMolBondIter(OBIter):
"""Iterator over the bonds in a molecule."""
OBiterator = _OBMolBondIter
class OBMolPairIter(OBIter):
"""Iterator over pairs of atoms in a molecule."""
OBiterator = _OBMolPairIter
class OBMolRingIter(OBIter):
"""Iterator over the rings in a molecule."""
OBiterator = _OBMolRingIter
class OBMolTorsionIter(OBIter):
"""Iterator over the torsion angles in a molecule."""
OBiterator = _OBMolTorsionIter
class OBResidueIter(OBIter):
"""Iterator over the residues in a molecule."""
OBiterator = _OBResidueIter
class OBResidueAtomIter(OBIter):
"""Iterator over the atoms in a residue."""
OBiterator = _OBResidueAtomIter
%}
%include "carrays.i"
%array_class(double, doubleArray)
%pythoncode %{
def double_array(mylist):
"""Create a C array of doubles from a list."""
c = doubleArray(len(mylist))
for i,v in enumerate(mylist):
c[i] = v
return c
%}
//# Copy some of the global variables in cvar into the openbabel namespace
%pythoncode %{
obErrorLog = cvar.obErrorLog
ttab = cvar.ttab
etab = cvar.etab
isotab = cvar.isotab
atomtyper = cvar.atomtyper
aromtyper = cvar.aromtyper
%}
//# 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);
}
};
%pythoncode %{
def exception(*args):
raise Exception("Use OBMol.CloneData instead. OBMol.SetData is only for use from C++.")
OBMol.SetData = exception
%}
%include "stereo.i"
@siriusjack
Copy link
Author

swigでエラーを吐く部分(#から始まるコメント行)を//でコメントアウト
pip install openbabel
が死ぬのでsetup.pyを直接叩いてみた

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment