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Topoly: Python package to analyze topology of polymers

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dc.abstract.enThe increasing role of topology in (bio)physical properties of matter creates a need for an efficient method of detecting the topology of a (bio)polymer. However, the existing tools allow one to classify only the simplest knots and cannot be used in automated sample analysis. To answer this need, we created the Topoly Python package. This package enables the distinguishing of knots, slipknots, links and spatial graphs through the calculation of different topological polynomial invariants. It also enables one to create the minimal spanning surface on a given loop, e.g. to detect a lasso motif or to generate random closed polymers. It is capable of reading various file formats, including PDB. The extensive documentation along with test cases and the simplicity of the Python programming language make it a very simple to use yet powerful tool, suitable even for inexperienced users. Topoly can be obtained from https://topoly.cent.uw.edu.pl.
dc.affiliationUniwersytet Warszawski
dc.contributor.authorNiemyska, Wanda
dc.contributor.authorRubach, Pawel
dc.contributor.authorGren, Bartosz Ambrozy
dc.contributor.authorDabrowski-Tumanski, Pawel
dc.contributor.authorSułkowska, Joanna
dc.date.accessioned2024-01-26T10:54:38Z
dc.date.available2024-01-26T10:54:38Z
dc.date.copyright2020-07-29
dc.date.issued2020
dc.description.accesstimeAT_PUBLICATION
dc.description.financePublikacja bezkosztowa
dc.description.versionFINAL_PUBLISHED
dc.identifier.doi10.1093/BIB/BBAA196
dc.identifier.issn1467-5463
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/123498
dc.identifier.weblinkhttps://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbaa196/5906197#
dc.languageeng
dc.pbn.affiliationchemical sciences
dc.relation.ispartofBriefings in Bioinformatics
dc.rightsCC-BY-NC
dc.sciencecloudnosend
dc.subject.enknot
dc.subject.enlasso
dc.subject.engraph
dc.subject.encyclotide
dc.subject.enprotein
dc.subject.enDNA
dc.subject.plDNA
dc.subject.plwęzeł
dc.subject.pllasso
dc.subject.plwykres
dc.subject.plcyklotyd
dc.subject.plbiałko
dc.titleTopoly: Python package to analyze topology of polymers
dc.typeJournalArticle
dspace.entity.typePublication