#molecular-dynamics #molecule #pdb #parser #coordinates #subgraph #smiles #simulation #graph

molecules

A library for working with molecules and molecular dynamics simulations

8 releases

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

#1006 in Math

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

~8–26MB
~439K SLoC