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703fe5a225
* remove include from headers * update implementation files * completely remove BOOST_FOREACH (#7) * convert those changes to use auto * get rid of all usage of BOOST_FOREACH Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
101 lines
3.8 KiB
C++
101 lines
3.8 KiB
C++
// $Id$
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//
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// Copyright (C) 2013 Greg Landrum
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#define PY_ARRAY_UNIQUE_SYMBOL rdreducedgraphs_array_API
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#include <RDBoost/python.h>
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#include <RDBoost/boost_numpy.h>
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#include <RDBoost/Wrap.h>
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#include <GraphMol/GraphMol.h>
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#include <RDBoost/import_array.h>
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#include <GraphMol/ReducedGraphs/ReducedGraphs.h>
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#include <Numerics/Vector.h>
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#include <vector>
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namespace python = boost::python;
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namespace {
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RDKit::ROMol *GenerateMolExtendedReducedGraphHelper(const RDKit::ROMol &mol,
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python::object atomTypes) {
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if (atomTypes) {
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throw_value_error("specification of atom types not yet supported");
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}
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RDKit::ROMol *res =
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RDKit::ReducedGraphs::generateMolExtendedReducedGraph(mol);
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return res;
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}
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PyObject *GenerateErGFingerprintForReducedGraphHelper(const RDKit::ROMol &mol,
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python::object atomTypes,
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double fuzzIncrement,
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int minPath,
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int maxPath) {
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if (atomTypes) {
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throw_value_error("specification of atom types not yet supported");
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}
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RDNumeric::DoubleVector *dv =
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RDKit::ReducedGraphs::generateErGFingerprintForReducedGraph(
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mol, nullptr, fuzzIncrement, minPath, maxPath);
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npy_intp dim = dv->size();
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auto *res = (PyArrayObject *)PyArray_SimpleNew(1, &dim, NPY_DOUBLE);
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memcpy(static_cast<void *>(PyArray_DATA(res)),
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static_cast<void *>(dv->getData()), dv->size() * sizeof(double));
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delete dv;
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return PyArray_Return(res);
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}
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PyObject *GetErGFingerprintHelper(const RDKit::ROMol &mol,
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python::object atomTypes,
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double fuzzIncrement, int minPath,
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int maxPath) {
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if (atomTypes) {
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throw_value_error("specification of atom types not yet supported");
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}
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RDNumeric::DoubleVector *dv = RDKit::ReducedGraphs::getErGFingerprint(
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mol, nullptr, fuzzIncrement, minPath, maxPath);
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npy_intp dim = dv->size();
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auto *res = (PyArrayObject *)PyArray_SimpleNew(1, &dim, NPY_DOUBLE);
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memcpy(static_cast<void *>(PyArray_DATA(res)),
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static_cast<void *>(dv->getData()), dv->size() * sizeof(double));
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delete dv;
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return PyArray_Return(res);
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}
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} // namespace
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BOOST_PYTHON_MODULE(rdReducedGraphs) {
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python::scope().attr("__doc__") =
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"Module containing functions to generate and work with reduced graphs";
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rdkit_import_array();
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std::string docString = "";
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docString = "Returns the reduced graph for a molecule";
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python::def(
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"GenerateMolExtendedReducedGraph", GenerateMolExtendedReducedGraphHelper,
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(python::arg("mol"), python::arg("atomTypes") = 0), docString.c_str(),
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python::return_value_policy<python::manage_new_object>());
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docString = "Returns the ErG fingerprint vector for a reduced graph";
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python::def("GenerateErGFingerprintForReducedGraph",
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GenerateErGFingerprintForReducedGraphHelper,
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(python::arg("mol"), python::arg("atomTypes") = 0,
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python::arg("fuzzIncrement") = 0.3, python::arg("minPath") = 1,
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python::arg("maxPath") = 15),
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docString.c_str());
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docString = "Returns the ErG fingerprint vector for a molecule";
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python::def("GetErGFingerprint", GetErGFingerprintHelper,
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(python::arg("mol"), python::arg("atomTypes") = 0,
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python::arg("fuzzIncrement") = 0.3, python::arg("minPath") = 1,
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python::arg("maxPath") = 15),
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docString.c_str());
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}
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