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//
//
// Copyright (C) 2020 Schrödinger, 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.
//
#include <string>
#include <RDBoost/Wrap.h>
#include <RDBoost/python.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/CIPLabeler/CIPLabeler.h>
namespace python = boost::python;
using RDKit::CIPLabeler::assignCIPLabels;
void assignCIPLabelsWrapHelper(RDKit::ROMol &mol,
const python::object &atomsToLabel,
const python::object &bondsToLabel) {
auto atoms = pythonObjectToDynBitset(atomsToLabel, mol.getNumAtoms());
auto bonds = pythonObjectToDynBitset(bondsToLabel, mol.getNumBonds());
// If both atoms and bonds are None, assign all the mol.
if (!atomsToLabel && !bondsToLabel) {
atoms.set();
bonds.set();
}
assignCIPLabels(mol, atoms, bonds);
}
BOOST_PYTHON_MODULE(rdCIPLabeler) {
python::scope().attr("__doc__") =
"Module containing a function to assign stereochemical labels based "
"on an accurate CIP rules implementation. This algoritm is a port "
"of https://github.com/SiMolecule/centres, which was originally "
"written by John Mayfield. The original algorithm is described in:\n\n"
"Hanson, R. M., Musacchio, S., Mayfield, J. W., Vainio, M. J., Yerin, "
"A., Redkin, D.\nAlgorithmic Analysis of Cahn−Ingold−Prelog Rules of "
"Stereochemistry:\nProposals for Revised Rules and a Guide for Machine "
"Implementation.\nJ. Chem. Inf. Model. 2018, 58, 1755-1765.\n";
std::string docString =
"New implementation of Stereo assignment using a true CIP ranking";
python::def("AssignCIPLabels", assignCIPLabelsWrapHelper,
(python::arg("mol"),
python::arg("atomsToLabel") = python::object(),
python::arg("bondsToLabel") = python::object()),
docString.c_str());
}
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