PerlMol - Reference Manual

Here is the perldoc documentation for each module, converted to HTML. If you prefer, the whole thing is also available as one big (about 100 pages, 300 KB) PDF file: perlmol.pdf. Please note that this PDF file includes the documentation for the latest version of every module, which is not always the same as the version included in the latest PerlMol bundle. The contents of the latest PerlMol bundle are listed in the PerlMol chapter.

Tutorials

• Chemistry::Tutorial

Object oriented modules

These modules are indented according to the class hierarchy

• Chemistry::Obj
  • Chemistry::Mol
    • Chemistry::Pattern
      • Chemistry::FormulaPattern
      • Chemistry::MidasPattern
      • Chemistry::Reaction
    • Chemistry::Domain
    • Chemistry::MacroMol
    • Chemistry::Ring
  • Chemistry::Atom
    • Chemistry::Pattern::Atom
  • Chemistry::Bond
    • Chemistry::Pattern::Bond
• Chemistry::File
  • Chemistry::File::Dumper
  • Chemistry::File::Formula
  • Chemistry::File::FormulaPattern
  • Chemistry::File::MDLMol
  • Chemistry::File::MidasPattern
  • Chemistry::File::Mopac
  • Chemistry::File::PDB
  • Chemistry::File::QChemOut
  • 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::Bond::Find
• Chemistry::Canonicalize
• Chemistry::InternalCoords::Builder
• Chemistry::3DBuilder
• Chemistry::Ring::Find
• Chemistry::Isotope

Programs (scripts)

• mok

PerlMol bundle description and contents

• PerlMol

Publications

The following publications either describe, use, or cite PerlMol in some way.

• O'Donnel, T. J. Design and Use of Relational Databases in Chemistry CRC Press, 2008, ISBN 1420064428, p. 188.
• Mannhold, R. Molecular drug properties: measurement and prediction. Wiley-VCH, 2007 ISBN 3527317554, p. 120.
• Rosselló, F.; Valiente, G. Graph Transformation in Molecular Biology. (Full text).
• Rosselló, F.; Valiente, G. Chemical Graphs, Chemical Reaction Graphs, and Chemical Graph Transformation. Proc. 2nd Int. Workshop on Graph-Based Tools, Electronic Notes in Theoretical Computer Science 2005, 127, 157-166. doi: 10.1016/j.entcs.2004.12.033 (Abstract; Preprint full text).
• Cozens, S. Molecular Biology With Perl. The Perl Journal 2004, 8[8], 15-19 (Full text; requires subscription)
• Tubert-Brohman, I. Perl and Chemistry. The Perl Journal 2004, 8[6] 3-5 (Full text: requires subscription).