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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.
//
#pragma once
#include <boost/dynamic_bitset.hpp>
#include <RDGeneral/export.h>
namespace RDKit {
class ROMol;
namespace CIPLabeler {
/**
* Calculate Stereochemical labels based on an accurate implementation
* of the CIP rules.
*
* This is a C++ port of https://github.com/SiMolecule/centres, which was
* originally written by John Mayfield in Java. The original algorithm was
* described in:
*
* Hanson, R. M., Musacchio, S., Mayfield, J. W., Vainio, M. J., Yerin, A.,
* Redkin, D. Algorithmic Analysis of Cahn−Ingold−Prelog Rules of
* Stereochemistry: Proposals for Revised Rules and a Guide for Machine
* Implementation. J. Chem. Inf. Model. 2018, 58, 1755-1765.
*
* \param mol - the molecule to be labelled.
*
* \note only atoms with chiral tags and double bonds with proper
* bond directions will be labelled.
* \note Labels will be stored under the common_properties::_CIPCode
* property of the relevant atoms/bonds.
*/
RDKIT_CIPLABELER_EXPORT void assignCIPLabels(ROMol &mol);
/**
* Overload that allows selecting which atoms and/or bonds will be labeled.
*
* \param mol - the molecule to be labelled.
*
* \param atoms - bitset with the atom indexes to be labeled.
*
* \param bonds - bitset with the bond indexes to be labeled.
*
*/
RDKIT_CIPLABELER_EXPORT void
assignCIPLabels(ROMol &mol, const boost::dynamic_bitset<> &atoms,
const boost::dynamic_bitset<> &bonds);
} // namespace CIPLabeler
} // namespace RDKit
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