[Bioperl-l] PerlMol

Ivan Tubert-Brohman itubert at users.sourceforge.net
Tue Aug 3 16:46:02 EDT 2004

Dear bioperl-l subscribers,

The recent PerlMol project is a collection of Perl modules for 
chemoinformatics and computational chemistry. As such, I think it might 
be of interest to people using Perl for bioinformatics, considering the 
overlap between the (bio|chem)informatics fields.

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


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

Please note that this project has nothing to do (I hope) with an April 
fool's email sent to the CCP4 email list this year, and in fact it 
predates it.

Ivan Tubert-Brohman

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