I don't know how many monks here are interested in chemistry, but I thought I might announce this project I've been working on.
The recently launched PerlMol project is a collection of Perl modules for chemoinformatics and computational chemistry. Version 0.2600 was just released today.
- an object model for molecules
- geometric functions
- read and write common file formats: MDL Mol, SDF, XYZ, Mopac, SMILES, SLN, PDB.
- ring perception
- substructure and formula pattern matching (SMARTS supported)
- automatic bond and bond order assignment from 3D coordinates
- Z-matrix builder
- atom selection in macromolecules using Midas/Chimera atom specifiers
- Mok: a concise AWK-like command-line language for "molecular munging".
See http://www.perlmol.org/features.html for more details. There was also an article about it in the June issue of The Perl Journal.