Topoly: Python package to analyze topology of polymers

• Published in: Briefings in bioinformatics Vol. 22; no. 3
• Main Authors: Dabrowski-Tumanski, Pawel, Rubach, Pawel, Niemyska, Wanda, Gren, Bartosz Ambrozy, Sulkowska, Joanna Ida
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 20.05.2021
• Subjects: Algorithms; Computational Biology - methods; Computer Graphics; Computer Simulation; Internet; Molecular Conformation; Polymers - chemistry; Problem Solving Protocol; Programming Languages; Reproducibility of Results; Software; knot; lasso; cyclotide; DNA; graph; protein
• ISSN: 1467-5463; 1477-4054; 1477-4054
• DOI: 10.1093/bib/bbaa196

The 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.