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
- 2006-10-04 New distribution: Chemistry-File-QChemOut
- 2005-09-20 Updated distribution: Chemistry-Mol-0.36
- 2005-09-02 Mok poster (PDF, 352k). Presented at the American Chemical Society national meeting in Washington, DC.
- 2005-05-24 New PerlMol Bundle! - PerlMol-0.3500 released, both as a standard .tar.gz distribution and as an PPM package.
- 2005-05-23 Added the Examples section to the website.
- 2005-05-20 Updated distributions: Chemistry-Mol-0.35, Chemistry-File-MDLMol-0.20
- 2005-05-16 Updated distributions: Chemistry-Isotope-0.11
- 2005-05-16 Updated distributions: Chemistry-Mol-0.34, Chemistry-Mok-0.25, Chemistry-Pattern-0.26, Chemistry-File-PDB-0.21, Chemistry-MidasPattern-0.11, Chemistry-File-SMARTS-0.22
- 2005-05-16 Chemistry-File-VRML-0.10 released (new distribution!)
- 2005-05-06 Chemistry-3DBuilder-0.10 released (new distribution!) Chemistry-File-SMILES-0.44, and Chemistry-Ring-0.19 released
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, a graduate student at Yale University. 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.