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90 lines
2.8 KiB
C++
90 lines
2.8 KiB
C++
//
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//
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// Copyright (C) 2020 Schrödinger, LLC
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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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#pragma once
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#include <RDGeneral/BoostStartInclude.h>
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#include <boost/dynamic_bitset.hpp>
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#include <RDGeneral/BoostEndInclude.h>
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#include <RDGeneral/export.h>
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namespace RDKit {
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class ROMol;
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namespace CIPLabeler_detail {
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RDKIT_CIPLABELER_EXPORT bool decrementRemainingCallCountAndCheck();
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}
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namespace CIPLabeler {
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/*
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Some very symmetrical mols can cause pseudo infinite processing
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(e.g. dodecahedrane)
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To avoid this a maxinum number of iterations can be set by the caller as a
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parameter to assignCIPLabels.
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If that maximum value is exceeded, the following error is thrown
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*/
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class RDKIT_CIPLABELER_EXPORT MaxIterationsExceeded
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: public std::runtime_error {
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public:
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explicit MaxIterationsExceeded()
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: std::runtime_error("Max Iterations Exceeded in CIP label calculation") {
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};
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};
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/**
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* Calculate Stereochemical labels based on an accurate implementation
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* of the CIP rules.
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*
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* This is a C++ port of https://github.com/SiMolecule/centres, which was
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* originally written by John Mayfield in Java. The original algorithm was
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* described in:
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*
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* Hanson, R. M., Musacchio, S., Mayfield, J. W., Vainio, M. J., Yerin, A.,
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* Redkin, D. Algorithmic Analysis of Cahn--Ingold--Prelog Rules of
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* Stereochemistry: Proposals for Revised Rules and a Guide for Machine
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* Implementation. J. Chem. Inf. Model. 2018, 58, 1755-1765.
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*
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* \param mol - the molecule to be labelled.
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*
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* \note only atoms with chiral tags and double bonds with proper
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* bond directions will be labelled.
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* \note Labels will be stored under the common_properties::_CIPCode
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* property of the relevant atoms/bonds.
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*/
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RDKIT_CIPLABELER_EXPORT void assignCIPLabels(
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ROMol &mol, unsigned int maxRecursiveIterations = 0);
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/**
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* Overload that allows selecting which atoms and/or bonds will be labeled.
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*
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* \param mol - the molecule to be labelled.
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*
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* \param atoms - bitset with the atom indexes to be labeled.
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*
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* \param bonds - bitset with the bond indexes to be labeled.
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*
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* \param maxRecursiveIterations - maximum number of iterations
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* A value of 1,250,000 take about 1 second. Most structures requires
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* less than 10,000 iterations. A peptide with MW~3000 took about
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* 100 iterations, and a 20,000 mw protein took about 600 iterations.
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*
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*/
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RDKIT_CIPLABELER_EXPORT void assignCIPLabels(
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ROMol &mol, const boost::dynamic_bitset<> &atoms,
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const boost::dynamic_bitset<> &bonds,
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unsigned int maxRecursiveIterations = 0);
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} // namespace CIPLabeler
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} // namespace RDKit
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