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PerlMol - Perl Modules for Molecular Chemistry

by itub (Priest)
on Aug 13, 2004 at 00:13 UTC ( #382510=perlnews: print w/replies, xml ) Need Help??

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
  • 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 for more details. There was also an article about it in the June issue of The Perl Journal.

  • Comment on PerlMol - Perl Modules for Molecular Chemistry

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Re: PerlMol - Perl Modules for Molecular Chemistry
by hv (Parson) on Aug 13, 2004 at 12:34 UTC

    Cool stuff. Does/will this support looking up molecule formula and structure given a name? While not dealing with chemistry from day to day I regularly come across a name and wonder what molecule it's talking about ...


      It depends. If you want to support trivial names (the ones that are used most of the time for interesting molecules), the logic is simple but you need a good database and that has to come from somewhere. If you want to parse systematic (IUPAC) names, you could in principle write code to do that, but it's not simple considering the large amount of rules involved. It would be neat to have that, but it's not in the near-term to-do list.
Re: PerlMol - Perl Modules for Molecular Chemistry
by jacques (Priest) on Aug 13, 2004 at 15:14 UTC
    The bioperl people would be interested in this. You should send them an announcement if you haven't done so already.
      I have, but thanks for the suggestion. I also intend to announce it to the Computational Chemistry List.

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