PerlMol - Perl Modules for Molecular Chemistry

PerlMol is a collection of Perl modules for chemoinformatics and computational chemistry with the philosophy that "simple things should be simple". It should be possible to write one-liners that use this toolkit to do meaningful "molecular munging". The PerlMol toolkit provides objects and methods for representing molecules, atoms, and bonds in Perl; doing substructure matching; and reading and writing files in various formats. For a more detailed feature list, see the Features section.

Recent News

• 2009-05-10 Updated distributions: Chemistry-Mol-0.37, Chemistry-Pattern-0.27, Chemistry-Ring-0.20, Chemistry-Canonicalize-0.11, Chemistry-Bond-Find-0.23 Chemistry-File-MDLMol-0.21, Chemistry-File-PDB-0.23, Chemistry-File-SMILES-0.46,

Project status

The current status could be called "alpha", because there are still many missing or untested features, but there is enough for being useful for some real work. The Feature list shows how complete the current implementation for a given feature is.

The following CPAN distributions have been released:

• Chemistry-Mol
• Chemistry-Pattern
• Chemistry-FormulaPattern
• Chemistry-MidasPattern
• Chemistry-Reaction
• Chemistry-Bond-Find
• Chemistry-Canonicalize
• Chemistry-Ring
• Chemistry-InternalCoords
• Chemistry-3DBuilder
• Chemistry-File-SLN
• Chemistry-File-SMILES
• Chemistry-File-SMARTS
• Chemistry-File-MDLMol
• Chemistry-File-Mopac
• Chemistry-File-PDB
• Chemistry-MacroMol
• Chemistry-File-VRML
• Chemistry-File-XYZ
• Chemistry-Isotope
• Chemistry-Mok
• PerlMol

Authors

The PerlMol project was started and is being led and maintained by Ivan Tubert-Brohman. Other contributors include:

• Gabriel Valiente (Technical University of Catalonia) - Chemistry::Reaction module.
• Brent Gregersen - formula parsing patch for Chemistry::File::Formula.
• ... and many people that have sent helpful suggestions, questions, tests, and bug reports.

If anyone else would like to help, please send me an email.