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.

Chemistry::Tutorial - A good place to start reading the documentation.

The following modules are indented according to the class hierarchy:

Chemistry::Obj

Chemistry::Mol

Chemistry::Pattern

Chemistry::FormulaPattern

Chemistry::MidasPattern

Chemistry::Domain

Chemistry::MacroMol

Chemistry::Ring

Chemistry::Atom

Chemistry::Pattern::Atom

Chemistry::Bond

Chemistry::Pattern::Bond

Chemistry::File

Chemistry::File::Formula

Chemistry::File::FormulaPattern

Chemistry::File::MDLMol

Chemistry::File::MidasPattern

Chemistry::File::Mopac

Chemistry::File::PDB

Chemistry::File::SDF

Chemistry::File::SLN

Chemistry::File::SMARTS

Chemistry::File::SMILES

Chemistry::File::VRML

Chemistry::File::XYZ

Chemistry::InternalCoords

Chemistry::Mok

These are auxiliary modules for which object classes seemed overkill

Chemistry::3DBuilder

Chemistry::Bond::Find

Chemistry::InternalCoords::Builder

Chemistry::Ring::Find

Chemistry::Canonicalize

mok - an AWK for molecules

PerlMol - This document

• Tubert-Brohman, I. Perl and Chemistry. The Perl Journal 2004-06 (subscription required)
• Cozens, S. Molecular Biology With Perl. The Perl Journal 2004, 8[8], 15-19 (http://www.tpj.com/documents/s=7618/tpj0408/; requires subscription)
• F. Rosselló, G. Valiente. Chemical Graphs, Chemical Reaction Graphs, and Chemical Graph Transformation. 2nd Int. Workshop on Graph-Based Tools, Electronic Notes in Computer Science 2005, 127, 157-166. (abstract: http://www.lsi.upc.es/%7Evaliente/abs-grabats-2004.html; preprint full text: http://tfs.cs.tu-berlin.de/grabats/Final04/valiente.pdf; published version: http://dx.doi.org/10.1016/j.entcs.2004.12.033).
• Rosselló, F.; Valiente, G. Graph Transformation in Molecular Biology. (Full text: http://bioinfo.uib.es/~cesc/recerca/he-paper.pdf).

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 

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 http://www.perlmol.org/

Ivan Tubert-Brohman <itub@cpan.org>

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.