History
During the development of OSCAR the need to have a program to convert identified chemical names to connection tables arose. Due to the absence of any open source efforts with broad coverage of organic nomenclature work was started by Peter Murray-Rust and Joe Townsend on such a program. This work was continued by Peter Corbett cumulating in the creation of a system broadly similar to the current incarnation (Corbett and Murray-Rust 2006). In 2008 Daniel Lowe took over development of the project as part of his PhD during which time the range of nomenclature supported as been expanded substantially, along with improvements to the parser to cope with the complexity of the grammar of chemical names.(Lowe et al. 2011)
Examples of Supported Nomenclature
![spiro[4.5]decane](opsin/spiro%5B4.5%5Ddecane.png){kind=link}
![pentaspiro[2.0.24.1.1.210.0.213.18.23]octadecane](opsin/pentaspiro%5B2.0.2%5E4.1.1.2%5E10.0.2%5E13.1%5E8.2%5E3%5Doctadecane.png){kind=link}
![1H,1'H-2,2'-spirobi[naphthalene]](opsin/1H%2C1'H-2%2C2'-spirobi%5Bnaphthalene%5D.png){kind=link}
![2λ6,2',2''-spiroter[[1,3,2]benzodioxathiole]](opsin/2%CE%BB6%2C2'%2C2''-spiroter%5B%5B1%2C3%2C2%5Dbenzodioxathiole%5D.png){kind=link}
![1'H,1''H,2H,8'H-1,2':7',2''-dispiroter[naphthalen]-1'-one](opsin/1'H%2C1''H%2C2H%2C8'H-1%2C2':7'%2C2''-dispiroter%5Bnaphthalen%5D-1'-one.png){kind=link}
![spiro[1,2-benzodithiole-3,2'-[1,3]benzodithiole]](opsin/spiro%5B1%2C2-benzodithiole-3%2C2'-%5B1%2C3%5Dbenzodithiole%5D.png){kind=link}
![pentacyclo[13.7.4.33,8.018,20.113,28]triacontane](opsin/pentacyclo%5B13.7.4.3%5E3%2C8.0%5E18%2C20.1%5E13%2C28%5Dtriacontane.png){kind=link}
-one.png){kind=link}
![3,3'-[ethane-1,2-diylbis(oxy)]bis{4-[2-(furan-3-yloxy)ethoxy]furan}](opsin/3%2C3'-%5Bethane-1%2C2-diylbis(oxy)%5Dbis%7B4-%5B2-(furan-3-yloxy)ethoxy%5Dfuran%7D.png){kind=link}
![imidazo[4,5-d]pyridine](opsin/imidazo%5B4%2C5-d%5Dpyridine.png){kind=link}
![phenothiazino[3',4':5,6][1,4]oxazino[2,3-i]benzo[5,6][1,4]thiazino[3,2-c]phenoxazine](opsin/phenothiazino%5B3'%2C4':5%2C6%5D%5B1%2C4%5Doxazino%5B2%2C3-i%5Dbenzo%5B5%2C6%5D%5B1%2C4%5Dthiazino%5B3%2C2-c%5Dphenoxazine.png){kind=link}
![phenanthro[4,5-bcd:1,2-c']difuran](opsin/phenanthro%5B4%2C5-bcd%3A1%2C2-c'%5Ddifuran.png){kind=link}
.png){kind=link}
-cholest-5-en-3-ol.png){kind=link}
%20chloride.png){kind=link}
%20chloride.png){kind=link}
-3-amino-3-methylcyclohexanecarboxylic%20acid.png){kind=link}
-but-2-ene.png){kind=link}
.png){kind=link}
References
[1] Peter Corbett and Peter Murray-Rust. High-Throughput Identification of Chemistry in Life Science Texts. Lecture Notes in Computer Science. 2006, 4216, pp107-118. DOI: 10.1007/11875741_11
[2] Daniel M. Lowe, Peter T. Corbett, Peter Murray-Rust, Robert C. Glen. Chemical Name to Structure: OPSIN, an Open Source Solution. Journal of Chemical Information and Modeling. 2011, 51 (3), 739-753 DOI: 10.1021/ci100384d
Libraries
OPSIN utilises dk.brics.automaton to provide a discrete finite state automaton to allow the parsing of chemical names. XOM is used as an XML framework for reading in resource files and for holding information about how a name was parsed. JNI-InChI is used to generate InChIs. Additionally for testing JUnit and Mockito are employed. The web interface is powered by Restlet with the Indigo toolkit being used for 2D coordinate generation and depiction.
License and Warranty
OPSIN is licensed under the Artistic License v2.0
OPSIN is made available in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.