OSCAR Files

OPSIN - Open Parser for Systematic IUPAC Nomenclature
version 0.7.0 (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
Source code: http://bitbucket.org/dan2097/opsin/

This is a Java 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.
OPSIN was formerly a component of OSCAR3 but is now a wholly standalone library.

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OPSIN is available as a standalone JAR from SourceForge(https://sourceforge.net/projects/oscar3-chem/) or Bitbucket (http://bitbucket.org/dan2097/opsin/)
It is also available as a dependency for use with Maven.
java -jar opsin-0.7.0-jar-with-dependencies.jar will give you a command line interface to convert names to CML (Chemical Markup Language)
opsin-0.7.0-jar-with-dependencies.jar includes InChI and CML output and all dependendencies
The main classes are uk.ac.cam.ch.wwmm.opsin.NameToStructure for CML and uk.ac.cam.ch.wwmm.opsin.NameToInchi for InChI

To use OPSIN as a library add opsin-0.7.0-jar-with-dependencies.jar to your classpath.

If you are using Maven then do the following:
	Add our repository:
		<repository>
			<id>ucc-repo</id>
			<url>https://maven.ch.cam.ac.uk/m2repo</url>
		</repository>

	Then add:
		<dependency>
			 <groupId>opsin</groupId>
			 <artifactId>core</artifactId>
			 <version>0.7.0</version>
		</dependency>
	If you need just CML output support

	or
		<dependency>
			 <groupId>opsin</groupId>
			 <artifactId>inchi</artifactId>
			 <version>0.7.0</version>
		</dependency>

	if you also need InChI output support.


Using OPSIN as a library:

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 the most efficient way to generate it is to use the InChI module and the corresponding parseToInChI method)

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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
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
Conjunctive nomenclature e.g. cyclohexaneethanol
Fused ring systems e.g. imidazo[4,5-d]pyridine. For a small number of fused ring systems numbering cannot be determined
Ring assemblies e.g. biphenyl
Most prefix and infix functional replacement nomenclature
The following functional classes: amides, anhydrides, esters, diesters, glycols, acids, azides, bromides, chlorides, cyanates, cyanides, fluorides, fulminates, hydrazones, hydroperoxides, imides,
iodides, isocyanates, isocyanides, isoselenocyanates, isothiocyanates, selenocyanates, thiocyanates, alcohols, selenols, thiols, ethers, ketones, oxides, oximes, peroxides, selenides,
selenones, selenoxides, selones, selenoketones, selenosemicarbazone, semicarbazones, sulfides, sulfones, sulfoxides, tellurides, telluroketones, tellurosemicarbazones, tellurones, telluroxides, thioketones and thiosemicarbazones
Greek letters
Lambda convention
E/Z/R/S stereochemistry
Amino Acids and derivatives
Structure-based polymer names e.g. poly(2,2'-diamino-5-hexadecylbiphenyl-3,3'-diyl)
Simple CAS names

Currently UNsupported nomenclature includes:
Other less common stereochemical terms
Carbohydrates
Steroids
Nucleic acids
Bridge prefixes e.g. epoxy, ethano
Fused ring systems involving non 6-membered rings which are not in a "chain" cannot be numbered e.g. indeno[2,1-c]pyridine can be numbered, benzo[cd]indole cannot

The following functional classes: Hydrazides, lactones, sultams, lactams, sultims, lactims, acetals, hemiacetals and ketals

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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)