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// $Id$
//
// Copyright (C) 2004-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#define NO_IMPORT_ARRAY
#include <RDBoost/python.h>
#include <RDGeneral/types.h>
#include <RDBoost/pyint_api.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/MolChemicalFeatures/MolChemicalFeature.h>
#include <GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h>
namespace python = boost::python;
namespace RDKit {
PyObject *getFeatAtomIds(const MolChemicalFeature &feat) {
const MolChemicalFeature::AtomPtrContainer &atoms = feat.getAtoms();
PyObject *res = PyTuple_New(atoms.size());
MolChemicalFeature::AtomPtrContainer_CI aci;
int idx = 0;
for (aci = atoms.begin(); aci != atoms.end(); ++aci) {
PyTuple_SetItem(res, idx, PyInt_FromLong((*aci)->getIdx()));
idx++;
}
return res;
}
std::string featClassDoc =
"Class to represent a chemical feature.\n\
These chemical features may or may not have been derived from molecule object;\n\
i.e. it is possible to have a chemical feature that was created just from its type\n\
and location.\n";
struct feat_wrapper {
static void wrap() {
python::class_<MolChemicalFeature, FeatSPtr>(
"MolChemicalFeature", featClassDoc.c_str(), python::no_init)
.def("GetId", &MolChemicalFeature::getId,
"Returns the identifier of the feature\n")
.def("GetFamily", &MolChemicalFeature::getFamily,
"Get the family to which the feature belongs; donor, acceptor, "
"etc.",
python::return_value_policy<python::copy_const_reference>())
.def("GetType", &MolChemicalFeature::getType,
"Get the specific type for the feature",
python::return_value_policy<python::copy_const_reference>())
.def("GetPos",
(RDGeom::Point3D(MolChemicalFeature::*)(int) const) &
MolChemicalFeature::getPos,
(python::arg("self"), python::arg("confId") = -1),
"Get the location of the chemical feature")
.def("GetAtomIds", getFeatAtomIds,
"Get the IDs of the atoms that participate in the feature")
.def("GetMol", &MolChemicalFeature::getMol,
"Get the molecule used to derive the features",
python::return_value_policy<python::reference_existing_object>())
.def("GetFactory", &MolChemicalFeature::getFactory,
"Get the factory used to generate this feature",
python::return_value_policy<python::reference_existing_object>())
.def("ClearCache", &MolChemicalFeature::clearCache,
"Clears the cache used to store position information.")
.def("SetActiveConformer", &MolChemicalFeature::setActiveConformer,
"Sets the conformer to use (must be associated with a molecule).")
.def("GetActiveConformer", &MolChemicalFeature::getActiveConformer,
"Gets the conformer to use.");
};
};
} // namespace RDKit
void wrap_MolChemicalFeat() { RDKit::feat_wrapper::wrap(); }
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