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.

Homepage: http://www.perlmol.org/

Features:

• an object model for molecules
• geometric functions
• read and write common file formats: MDL Mol, SDF, XYZ, Mopac, SMILES, SLN, PDB.
• ring perception
• canonicalization
• 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.

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