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 - A good place to start reading the documentation.
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
- Chemistry::3DBuilder
- 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
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).
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 0.15The 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.
1 POD Error
The following errors were encountered while parsing the POD:
- Around line 176:
Non-ASCII character seen before =encoding in 'Rosselló,'. Assuming CP1252