OSCAR Files

OPSIN - Open Parser for Structural IUPAC Nomenclature
version 0.5.3 (see ReleaseNotes.txt for what's new in this version)

Daniel Lowe(Current maintainer), Dr. Peter Corbett and Prof. Peter Murray-Rust

Contact address: dl387@cam.ac.uk

Factored out of OSCAR3 (again) by Daniel Lowe. Thanks to Richard Apodaca for doing this previously.

***NB*** OPSIN is not OSCAR3. OPSIN was developed as an OSCAR3
   component but can also standalone - hence this package.

This is a library for IUPAC name-to-structure conversion. Currently it
should be considered to be under development although the interface for using it will remain constant.

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The easiest way to use OPSIN is to use the standalone jar available from sourceforge.
java -jar opsin-0.5.3.jar will give you a command line interface to convert names to CML (Chemical Markup Language)
opsinToInChI-0.5.3.jar is also available if InChI is your preferred format

To use OPSIN as a library within Java add opsin-0.5.3.jar to your classpath then:

1) Learn about XOM (http://xom.nu), the XML processing framework used
   by OPSIN
2) Create an OPSIN instance, by calling the following static method

NameToStructure nameToStructure = NameToStructure.getInstance();

3) Get CML (as XOM Elements):

Element cmlElement = nameToStructure.parseToCML("acetonitrile");

4) Whatever you like. Maybe print it out, thus:

System.out.println(cmlElement.toXML());

parseToCML will typically take 5-10ms to convert a name to CML making OPSIN suitable for use on a large number of names.

CML can, if desired, be converted to other format such as SD, SMILES, InChI etc. by toolkits such as CDK, OpenBabel and JUMBO.
(NOTE: if you want InChI you can get it directly by using opsinToInChI-0.5.3.jar on your classpath and instantiating a NameToInchi instead of a NameToStructure)

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The workings of OPSIN are more fully described in:

Peter Corbett, Peter Murray-Rust High-throughput identification of
chemistry in life science texts. Proceedings of Computational Life
Sciences (CompLife) 2006, Cambridge, UK, pp. 107-118.

The following lists broadly summarise what OPSIN can currently do and what will be worked on in the future.

Supported nomenclature includes:
alkanes/alkenes/alkynes/heteroatom chains e.g. hexane, hex-1-ene, tetrasiloxane and their cyclic analogues e.g. cyclopropane
All IUPAC 1993 recommended rings
Trivial acids
Hantzsch-Widman e.g. 1,3-oxazole
Spiro systems (using Von baeyer brackets)
All von Baeyer rings e.g. bicyclo[2.2.2]octane
Hydro e.g. 2,3-dihydropyridine
Indicated hydrogen e.g. 1H-benzoimidazole
Heteroatom replacement
Specification of charge e.g. ium/ide
Multiplicative nomenclature e.g. ethylenediaminetetraacetic acid
Fused ring systems with some exceptions e.g. imidazo[4,5-d]pyridine
Ring assemblies e.g. biphenyl
Most prefix and infix functional replacement nomenclature
The following functional classes: amide, esters, diesters, glycols, acids, azides, bromides, chlorides, cyanates, cyanides, fluorides, fulminates, hydroperoxides, iodides, isocyanates, isocyanides, isoselenocyanates, isothiocyanates, selenocyanates, thiocyanates, alcohols, selenols, thiols, ethers, ketones, peroxides, selenides, selenones, selenoxides, selones, selenoketones, sulfides, sulfones, sulfoxides, tellurides, telluroketones, tellurones, telluroxides and thioketones
Locanted E/Z/R/S stereochemistry

Currently UNsupported nomenclature includes:
Any stereochemistry other than locanted E/Z/R/S stereochemistry
Greek letters
Lambda convention
Amino Acids (simple substitutive operations are allowed)
Carbohydrates
Steroids
Nucleic acids
Bridged rings 
Fused ring systems built from more than one fusion or that involve non 6-membered rings AND are not in a chain
Some conjunctive operations e.g. cyclohexaneethanol
Some functional replacement nomenclature
The following functional classes: Hydrazides, lactones, lactams, acetals, hemiacetals, oxime, oxides, ketals, hydrazones, anhydrides and semicarbazones

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Good Luck and let us know if you have problems, comments or suggestions!
You can contact us by posting a message on SourceForge or you can email me directly (dl387@cam.ac.uk)