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// $Id$
//
// Copyright (C) 2013 Greg Landrum
//
// @@ 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 PY_ARRAY_UNIQUE_SYMBOL rdreducedgraphs_array_API
#include <RDBoost/python.h>
#include <RDBoost/boost_numpy.h>
#include <RDBoost/Wrap.h>
#include <GraphMol/GraphMol.h>
#include <boost/foreach.hpp>
#include <RDBoost/import_array.h>
#include <GraphMol/ReducedGraphs/ReducedGraphs.h>
#include <Numerics/Vector.h>
#include <vector>
namespace python = boost::python;
namespace {
RDKit::ROMol *GenerateMolExtendedReducedGraphHelper(const RDKit::ROMol &mol,
python::object atomTypes) {
if (atomTypes) {
throw_value_error("specification of atom types not yet supported");
}
RDKit::ROMol *res =
RDKit::ReducedGraphs::generateMolExtendedReducedGraph(mol);
return res;
}
PyObject *GenerateErGFingerprintForReducedGraphHelper(const RDKit::ROMol &mol,
python::object atomTypes,
double fuzzIncrement,
int minPath,
int maxPath) {
if (atomTypes) {
throw_value_error("specification of atom types not yet supported");
}
RDNumeric::DoubleVector *dv =
RDKit::ReducedGraphs::generateErGFingerprintForReducedGraph(
mol, nullptr, fuzzIncrement, minPath, maxPath);
npy_intp dim = dv->size();
PyArrayObject *res = (PyArrayObject *)PyArray_SimpleNew(1, &dim, NPY_DOUBLE);
memcpy(static_cast<void *>(PyArray_DATA(res)),
static_cast<void *>(dv->getData()), dv->size() * sizeof(double));
delete dv;
return PyArray_Return(res);
}
PyObject *GetErGFingerprintHelper(const RDKit::ROMol &mol,
python::object atomTypes,
double fuzzIncrement, int minPath,
int maxPath) {
if (atomTypes) {
throw_value_error("specification of atom types not yet supported");
}
RDNumeric::DoubleVector *dv = RDKit::ReducedGraphs::getErGFingerprint(
mol, nullptr, fuzzIncrement, minPath, maxPath);
npy_intp dim = dv->size();
PyArrayObject *res = (PyArrayObject *)PyArray_SimpleNew(1, &dim, NPY_DOUBLE);
memcpy(static_cast<void *>(PyArray_DATA(res)),
static_cast<void *>(dv->getData()), dv->size() * sizeof(double));
delete dv;
return PyArray_Return(res);
}
}
BOOST_PYTHON_MODULE(rdReducedGraphs) {
python::scope().attr("__doc__") =
"Module containing functions to generate and work with reduced graphs";
rdkit_import_array();
std::string docString = "";
docString = "Returns the reduced graph for a molecule";
python::def(
"GenerateMolExtendedReducedGraph", GenerateMolExtendedReducedGraphHelper,
(python::arg("mol"), python::arg("atomTypes") = 0), docString.c_str(),
python::return_value_policy<python::manage_new_object>());
docString = "Returns the ErG fingerprint vector for a reduced graph";
python::def("GenerateErGFingerprintForReducedGraph",
GenerateErGFingerprintForReducedGraphHelper,
(python::arg("mol"), python::arg("atomTypes") = 0,
python::arg("fuzzIncrement") = 0.3, python::arg("minPath") = 1,
python::arg("maxPath") = 15),
docString.c_str());
docString = "Returns the ErG fingerprint vector for a molecule";
python::def("GetErGFingerprint", GetErGFingerprintHelper,
(python::arg("mol"), python::arg("atomTypes") = 0,
python::arg("fuzzIncrement") = 0.3, python::arg("minPath") = 1,
python::arg("maxPath") = 15),
docString.c_str());
}
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