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

Chemistry::Tutorial

Object oriented modules

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::XYZ

Chemistry::InternalCoords

Chemistry::Mok

Procedural modules

These are auxiliary modules for which object classes seemed overkill

Chemistry::Bond::Find

Chemistry::InternalCoords::Builder

Chemistry::Ring::Find

Chemistry::Canonicalize

Programs (scripts)

mok - an AWK for molecules

PerlMol bundle description and contents

PerlMol - This document

Publications

Publications

• F. Rosselló, G. Valiente. Chemical Graphs, Chemical Reaction Graphs, and Chemical Graph Transformation. To appear in Proc. 2nd Int. Workshop on Graph-Based Tools, Electronic Notes in Computer Science 2004 (abstract available at http://www.lsi.upc.es/%7Evaliente/abs-grabats-2004.html).

• Tubert-Brohman, I. Perl and Chemistry. The Perl Journal 2004-06 (subscription required)

VERSION INFORMATION

This is the PerlMol bundled release version 0.2600. It includes the following distributions:

Chemistry-Bond-Find             0.21
Chemistry-Canonicalize          0.10
Chemistry-File-MDLMol           0.17
Chemistry-File-Mopac            0.15
Chemistry-File-PDB              0.20
Chemistry-File-SLN              0.10
Chemistry-File-SMARTS           0.20
Chemistry-File-SMILES           0.42
Chemistry-File-XYZ              0.11
Chemistry-FormulaPattern        0.10
Chemistry-InternalCoords        0.17
Chemistry-MacroMol              0.06
Chemistry-MidasPattern          0.10
Chemistry-Mok                   0.23
Chemistry-Mol                   0.26
Chemistry-Pattern               0.25
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) 2004 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.

cpanm PerlMol

perl -MCPAN -e shell
install PerlMol