OpenSMILES Specification

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7. APPENDIX 1: References and Citations

7.1 Groups

Blue Obelisk
  http://blueobelisk.sourceforge.net/

7.2 Documentation

Daylight
  http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html
     The most-referenced definition of SMILES on the web.

  http://www.daylight.com/meetings/mug01/Sayle/m4xbondage.html
     Article by Roger Sayle about converting PDB files to SMILES with a
     thorough treatment of aromaticity.

OpenEye
  http://www.eyesopen.com/docs/html/pyprog/TheSMILESLineNotation.html
  http://www.eyesopen.com/docs/html/pyprog/DaylightSMILES.html

OpenBabel
  http://openbabel.sourceforge.net/wiki/Radicals_and_SMILES_extensions
  http://openbabel.sourceforge.net/wiki/SMILES

Wikipedia
  http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification

7.3 Toolkits

OpenBabel
  http://openbabel.sourceforge.net/wiki/Main_Page

The Chemistry Development Kit
  http://cdk.sourceforge.net/

Marvin
  http://www.chemaxon.com/marvin/doc/user/smiles-doc.html

RDKit
  http://www.rdkit.org/

Frowns
  http://frowns.sourceforge.net/frowns.html

PerlMol.org
  http://search.cpan.org/~itub/Chemistry-File-SMILES-0.45/SMILES.pm

InChI
  http://www.iupac.org/inchi/
  http://inchi.info/
  http://en.wikipedia.org/wiki/International_Chemical_Identifier

7.3 Some Key Scientific Papers

  David Weininger  (1988)
  SMILES, a Chemical Language and Information System. 1. Introduction to Methodology and Encoding Rules,
  Journal of Chemical Information and Computer Sciences 28:31-36.

  David Weininger, Arthur Weininger, and Joseph L Weininger  (1989)
  SMILES 2. Algorithm for Generation of Unique SMILES Notation
  Journal of Chemical Information and Computer Sciences 29:97-101.

  Morgan's original canonicalization paper:
  Morgan, H.L. J.Chem.Doc. 1965, 5, 107

  Review of Ring Perception Algorithms for Chemical Graphs,
  G. M. Downs et al, J. Chem. Inf. Comput. Cci. 1989, 29, 172-187

  Novel Algorithms for the Rapid Perception of a Unique Optimal Set of
  Rings, R. Balducci and R. Pearlman, J. Am. Chem. Soc. (date?)

7.5 Molecule Editors that can produce SMILES

  ChemWriter
  JME
  CACTVS
  ISISDraw?
  ChemDraw
  ACD/ChemSketch
  MarvinSketch

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