pygen-structures : A Python package to generate 3D molecular structures for simulations using the CHARMM forcefield

Hesketh, Travis (2020) pygen-structures : A Python package to generate 3D molecular structures for simulations using the CHARMM forcefield. Journal of Open Source Software, 5 (48). 2157. ISSN 2475-9066 (https://doi.org/10.21105/joss.02157)

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Abstract

pygen-structures is an open source (3-clause BSD license) Python library to generate 3 dimensional structures for molecules from the CHARMM forcefield. Coordinates are generated using an embedding method based on empirical data (Riniker & Landrum (2015), as implemented in the RDKit, The RDKit Contributors (n.d.)), and are written out as standard PSF and PDB files. The package contains convenience functions for generating molecules from a collection of CHARMM residues and patches, or from one letter amino acid codes (usable by calling pygen-structures as a command line application) and a series of classes and functions for representing and manipulating CHARMM data. The chirality of tetrahedral centres is set using internal coordinate data from the residue topology file. Classes provided by pygen-structures include representations of CHARMM residue topology files, which contain information about residues, their atoms and their connectivity; and parameter files, containing the relevant force constants involving sets of atoms. There are also classes which describe residues and patches from topology files, and representations of atoms and molecules. Residues from the forcefield (and molecules created from those residues) can be represented as RDKit Mols, enabling pattern matching of residues to molecules.

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