OSCAR Files

OPSIN - Open Parser for Systematic IUPAC Nomenclature
version 0.9.0 (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 Bitbucket (http://bitbucket.org/dan2097/opsin/) or SourceForge(https://sourceforge.net/projects/oscar3-chem/)
It is also available as a dependency for use with Maven.
opsin-0.9.0-jar-with-dependencies.jar includes CML (Chemical Markup Language) and InChI (IUPAC International Chemical Identifier) 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-0.9.0-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>0.9.0</version>
		</dependency>
	If you need just CML output support

	or
		<dependency>
			 <groupId>opsin</groupId>
			 <artifactId>inchi</artifactId>
			 <version>0.9.0</version>
		</dependency>

	if you also need InChI output support.

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Using OPSIN as a commandline utility:
	java -jar opsin-0.9.0-jar-with-dependencies.jar will give you a command line interface to convert names to CML
	java -cp opsin-0.9.0-jar-with-dependencies.jar uk.ac.cam.ch.wwmm.opsin.NameToInchi will give you a command line interface to convert names to InChI

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)

OPSIN's API also support limited configurability and a mechanism to return the reason for failure e.g.:
	NameToStructure nts = NameToStructure.getInstance();
	NameToStructureConfig n2sconfig = new NameToStructureConfig();
	n2sconfig.setAllowRadicals(true);
	OpsinResult result = nts.parseChemicalName("acetonitrile", n2sconfig);
	if (result.getStatus() != OpsinResult.OPSIN_RESULT_STATUS.FAILURE){
		Element cml = result.getCml();
		String inchi = NameToInchi.convertResultToInChI(result, false);
	}
	else{
		System.out.println(result.getMessage());
	}

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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.

A paper describing the current operation of OPSIN is currently being reviewed.

The following list broadly summarises 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/dehydro e.g. 2,3-dihydropyridine
Indicated hydrogen e.g. 1H-benzoimidazole
Heteroatom replacement
Specification of charge e.g. ium/ide/ylium/uide
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: acids, acetals, alcohols, amides, anhydrides, azides, bromides, chlorides, cyanates, cyanides, esters, di/tri/tetra esters
ethers, fluorides, fulminates, glycols, glycol ethers, hemiacetals, hemiketal, hydrazones, hydroperoxides, hydrazides, imides, iodides, isocyanates,
isocyanides, isoselenocyanates, isothiocyanates, ketals, ketones, selenocyanates, thiocyanates, selenols, thiols, 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 bridge prefixes e.g. methano
Nucleosides, nucleotides and their esters
Specification of oxidation numbers and charge on elements
Perhalogeno terms
Simple CAS names

Currently UNsupported nomenclature includes:
Other less common stereochemical terms
Carbohydrates
Natural Products
Specification of stereochemistry on steroids
Subtractive nomenclature
Composite and multiplied bridge prefixes e.g. epoxymethano
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: Lactones, sultams, lactams, sultims and lactims

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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 Bitbucket or you can email me directly (dl387@cam.ac.uk)