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::Domain
Chemistry::MacroMol
Chemistry::Ring (coming soon)
Chemistry::Atom
Chemistry::Pattern::Atom
Chemistry::Bond
Chemistry::Pattern::Bond
Chemistry::File
Chemistry::File::Formula
Chemistry::File::MDLMol
Chemistry::File::Mopac
Chemistry::File::PDB
Chemistry::File::SDF
Chemistry::File::SMILES
Chemistry::InternalCoords
Chemistry::Mok

Procedural modules

These are auxiliary modules for which object classes seemed overkill

Chemistry::Bond::Find
Chemistry::Ring::Find (coming soon)

Programs (scripts)

mok

VERSION INFORMATION

This is the PerlMol bundled release version 0.2300. It includes the following distributions:

Test-Simple                 0.47
Scalar-List-Utils           1.14
Storable                    2.12
Text-Balanced               1.95
Math-VectorReal             1.02
Chemistry-Mol               0.23
Chemistry-MacroMol          0.05
Chemistry-InternalCoords    0.11
Chemistry-File-MDLMol       0.15
Chemistry-File-SMILES       0.33
Chemistry-File-PDB          0.10
Chemistry-File-Mopac        0.10
Chemistry-Pattern           0.20
Chemistry-Bond-Find         0.20
Chemistry-Mok               0.20

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. Test-Simple, Scalar-List-Utils, Storable, and Text-Balanced are already included with perl distributions since version 5.7.3, but they are included here to simplify installation on perl 5.6.x distributions.

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.