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::MidasPattern

Chemistry::Domain

Chemistry::MacroMol

Chemistry::Ring

Chemistry::Atom

Chemistry::Pattern::Atom

Chemistry::Bond

Chemistry::Pattern::Bond

Chemistry::File

Chemistry::File::Formula

Chemistry::File::MDLMol

Chemistry::File::MidasPattern

Chemistry::File::Mopac

Chemistry::File::PDB

Chemistry::File::SDF

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

VERSION INFORMATION

This is the PerlMol bundled release version 0.2500. It includes the following distributions:

Math-VectorReal                1.02
Statistics-Regression          0.15
Chemistry-Mol                  0.25
Chemistry-MacroMol             0.06
Chemistry-InternalCoords       0.16
Chemistry-Ring                 0.15
Chemistry-Canonicalize         0.10
Chemistry-Pattern              0.21
Chemistry-Bond-Find            0.21
Chemistry-File-MDLMol          0.16
Chemistry-File-SMILES          0.41
Chemistry-File-PDB             0.20
Chemistry-MidasPattern         0.10
Chemistry-File-Mopac           0.15
Chemistry-File-SMARTS          0.11
Chemistry-File-XYZ             0.10
Chemistry-Mok                  0.22

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 <itub@cpan.org>

COPYRIGHT

Copyright (c) 2004 Ivan Tubert. All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.