#molecular-dynamics #molecule #simulation #graph #algorithm #pdb #parser

molecules

A library for working with molecules and molecular dynamics simulations

8 releases

new 0.1.7 Apr 14, 2024
0.1.6 Apr 11, 2024
0.1.5 Mar 22, 2024

#197 in Science

Download history 171/week @ 2024-03-01 236/week @ 2024-03-08 229/week @ 2024-03-15 185/week @ 2024-03-22 13/week @ 2024-03-29 95/week @ 2024-04-05

565 downloads per month

MIT license

145KB
3K SLoC

Molecule

A library to work with molecules.

Features:

Efficient implementation of subgraph matching to find a mapping from Molecule A into Molecule B using the VF2 algorithm. Can parse xyz and smiles into the internal molecular graph representation. Determines connectivity automatically based on the molecular coordinates when parsing an xyz file.

To-Do: Implement parsing of planned additional formats: InChi mol sdf pdb Remove Openbabel in favor of a pure Rust canonicalisation algorithm.

Dependencies

~7–34MB
~483K SLoC