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Atomic ring invariant and Modified CANON extended connectivity algorithm for symmetry perception in molecular graphs and rigorous canonicalization of SMILES
We propose new invariant (the product of the corresponding primes for the ring size of each bond of an atom) as a simple unambiguous ring invariant of an atom that allows distinguishing symmetry classes in the highly symmetrical molecular graphs using traditional local and distance atom invariants....
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Springer International Publishing
2020
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7439248/ https://www.ncbi.nlm.nih.gov/pubmed/33431026 http://dx.doi.org/10.1186/s13321-020-00453-4 |
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author | Krotko, Dmytro G. |
author_facet | Krotko, Dmytro G. |
author_sort | Krotko, Dmytro G. |
collection | PubMed |
description | We propose new invariant (the product of the corresponding primes for the ring size of each bond of an atom) as a simple unambiguous ring invariant of an atom that allows distinguishing symmetry classes in the highly symmetrical molecular graphs using traditional local and distance atom invariants. Also, we propose modifications of Weininger’s CANON algorithm to avoid its ambiguities (swapping and leveling ranks, incorrect determination of symmetry classes in non-aromatic annulenes, arbitrary selection of atom for breaking ties). The atomic ring invariant and the Modified CANON algorithm allow us to create a rigorous procedure for the generation of canonical SMILES which can be used for accurate and fast structural searching in large chemical databases. |
format | Online Article Text |
id | pubmed-7439248 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Springer International Publishing |
record_format | MEDLINE/PubMed |
spelling | pubmed-74392482020-08-20 Atomic ring invariant and Modified CANON extended connectivity algorithm for symmetry perception in molecular graphs and rigorous canonicalization of SMILES Krotko, Dmytro G. J Cheminform Research Article We propose new invariant (the product of the corresponding primes for the ring size of each bond of an atom) as a simple unambiguous ring invariant of an atom that allows distinguishing symmetry classes in the highly symmetrical molecular graphs using traditional local and distance atom invariants. Also, we propose modifications of Weininger’s CANON algorithm to avoid its ambiguities (swapping and leveling ranks, incorrect determination of symmetry classes in non-aromatic annulenes, arbitrary selection of atom for breaking ties). The atomic ring invariant and the Modified CANON algorithm allow us to create a rigorous procedure for the generation of canonical SMILES which can be used for accurate and fast structural searching in large chemical databases. Springer International Publishing 2020-08-20 /pmc/articles/PMC7439248/ /pubmed/33431026 http://dx.doi.org/10.1186/s13321-020-00453-4 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Article Krotko, Dmytro G. Atomic ring invariant and Modified CANON extended connectivity algorithm for symmetry perception in molecular graphs and rigorous canonicalization of SMILES |
title | Atomic ring invariant and Modified CANON extended connectivity algorithm for symmetry perception in molecular graphs and rigorous canonicalization of SMILES |
title_full | Atomic ring invariant and Modified CANON extended connectivity algorithm for symmetry perception in molecular graphs and rigorous canonicalization of SMILES |
title_fullStr | Atomic ring invariant and Modified CANON extended connectivity algorithm for symmetry perception in molecular graphs and rigorous canonicalization of SMILES |
title_full_unstemmed | Atomic ring invariant and Modified CANON extended connectivity algorithm for symmetry perception in molecular graphs and rigorous canonicalization of SMILES |
title_short | Atomic ring invariant and Modified CANON extended connectivity algorithm for symmetry perception in molecular graphs and rigorous canonicalization of SMILES |
title_sort | atomic ring invariant and modified canon extended connectivity algorithm for symmetry perception in molecular graphs and rigorous canonicalization of smiles |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7439248/ https://www.ncbi.nlm.nih.gov/pubmed/33431026 http://dx.doi.org/10.1186/s13321-020-00453-4 |
work_keys_str_mv | AT krotkodmytrog atomicringinvariantandmodifiedcanonextendedconnectivityalgorithmforsymmetryperceptioninmoleculargraphsandrigorouscanonicalizationofsmiles |