NAME

PerlMol - Perl modules for molecular chemistry

SYNOPSIS

    # 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.

DESCRIPTION

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.

DOCUMENTATION

What follows is an index of the relevant documentation.

Tutorial

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

Publications

EXAMPLES

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 http://www.perlmol.org/examples/. Some of the examples are:

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

VERSION INFORMATION

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.

SEE ALSO

The PerlMol website http://www.perlmol.org/

AUTHOR

Ivan Tubert-Brohman <itub@cpan.org>

COPYRIGHT

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.