PerlMol - Perl modules for molecular chemistry


    # This is a bundle containing all of the modules
    # of the PerlMol Project and their dependencies.
    # This is not a real module; it is the main index
    # to the documentation of the PerlMol modules.


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.


What follows is an index of the relevant documentation.


Object oriented modules

The following modules are indented according to the class hierarchy:

Procedural modules

These are auxiliary modules for which object classes seemed overkill

Programs (scripts)

  • mok - an AWK for molecules

PerlMol bundle description and contents



The "examples" directory in the PerlMol distribution file has several sample scripts with lots of comments and a few input and output files that show how one can use PerlMol for common tasks. They can also be browsed online at Some of the examples are:

    * combinatorial_enumeration
    * file_conversion
    * molgrep
    * pdb_viewer
    * peptide_builder
    * polar_surface_area 


This is the PerlMol bundled release version 0.3500. It includes the following distributions:

    Chemistry-3DBuilder             0.10
    Chemistry-Bond-Find             0.21
    Chemistry-Canonicalize          0.10
    Chemistry-File-MDLMol           0.20
    Chemistry-File-Mopac            0.15
    Chemistry-File-PDB              0.21
    Chemistry-File-SLN              0.10
    Chemistry-File-SMARTS           0.22
    Chemistry-File-SMILES           0.44
    Chemistry-File-VRML             0.10
    Chemistry-File-XYZ              0.11
    Chemistry-FormulaPattern        0.10
    Chemistry-InternalCoords        0.18
    Chemistry-Isotope               0.11
    Chemistry-MacroMol              0.06
    Chemistry-MidasPattern          0.11
    Chemistry-Mok                   0.25
    Chemistry-Mol                   0.35
    Chemistry-Pattern               0.26
    Chemistry-Reaction              0.02
    Chemistry-Ring                  0.18
    Math-VectorReal                 1.02
    Parse-Yapp                      1.05
    Statistics-Regression           0.15

The version number of a PerlMol bundle is always the same as the version number of the included Chemistry-Mol distribution, plus two extra digits that distinguish between different bundles based on the same Chemistry-Mol distribution.


The PerlMol website


Ivan Tubert-Brohman <>


Copyright (c) 2005 Ivan Tubert-Brohman All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.