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Man Pages


Manual Reference Pages  -  PERLMOL (3)

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NAME

PerlMol - Perl modules for molecular chemistry

CONTENTS

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:
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

    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

o Tubert-Brohman, I. Perl and Chemistry. The Perl Journal 2004-06 (subscription required)
o Cozens, S. Molecular Biology With Perl. The Perl Journal 2004, 8[8], 15-19 (<http://www.tpj.com/documents/s=7618/tpj0408/>; requires subscription)
o F. Rossello\k:'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>).
o Rossello\k:'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           0.15



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) 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.

POD ERRORS

Hey! <B>The above document had some coding errors, which are explained below:B>
Around line 176: Non-ASCII character seen before =encoding in ’Rossello\k:'Assuming ISO8859-1
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perl v5.20.3 PERLMOL (3) 2005-05-24

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