OSCAR Files

OPSIN - Open Parser for Systematic IUPAC Nomenclature
version 0.8.0 (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-0.8.0-jar-with-dependencies.jar will give you a command line interface to convert names to CML (Chemical Markup Language)
opsin-0.8.0-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-0.8.0-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>0.8.0</version>
		</dependency>
	If you need just CML output support

	or
		<dependency>
			 <groupId>opsin</groupId>
			 <artifactId>inchi</artifactId>
			 <version>0.8.0</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/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 CAS names

Currently UNsupported nomenclature includes:
Other less common stereochemical terms
Carbohydrates
Steroids
Nucleic acids
Non detachable bridge prefixes e.g. epoxymethano, 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: 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 SourceForge or you can email me directly (dl387@cam.ac.uk)