inefable12/opsin

Open Parser for Systematic IUPAC Nomenclature. Chemical name to structure conversion

OPSIN - Open Parser for Systematic IUPAC Nomenclature

Version 2.6.0 (see ReleaseNotes.txt for what's new in this version)
Source code: https://github.com/dan2097/opsin
Web interface and informational site: https://opsin.ch.cam.ac.uk/
License: MIT License

OPSIN is a Java library for IUPAC name-to-structure conversion offering high recall and precision on organic chemical nomenclature.

Java 8 (or higher) is required for OPSIN 2.6.0

Supported outputs are SMILES, CML (Chemical Markup Language) and InChI (IUPAC International Chemical Identifier)

Simple Usage Examples

Convert a chemical name to SMILES

java -jar opsin-cli-2.6.0-jar-with-dependencies.jar -osmi input.txt output.txt
where input.txt contains chemical name/s, one per line

NameToStructure nts = NameToStructure.getInstance();
String smiles = nts.parseToSmiles("acetamide");

Convert a chemical name to CML

java -jar opsin-cli-2.6.0-jar-with-dependencies.jar -ocml input.txt output.txt
where input.txt contains chemical name/s, one per line

NameToStructure nts = NameToStructure.getInstance();
String cml = nts.parseToCML("acetamide");

Convert a chemical name to StdInChI/StdInChIKey/InChI with FixedH

java -jar opsin-cli-2.6.0-jar-with-dependencies.jar -ostdinchi input.txt output.txt
java -jar opsin-cli-2.6.0-jar-with-dependencies.jar -ostdinchikey input.txt output.txt
java -jar opsin-cli-2.6.0-jar-with-dependencies.jar -oinchi input.txt output.txt
where input.txt contains chemical name/s, one per line

NameToInchi nti = new NameToInchi()
String stdInchi = nti.parseToStdInchi("acetamide");
String stdInchiKey = nti.parseToStdInchiKey("acetamide");
String inchi = nti.parseToInchi("acetamide");

NOTE: OPSIN's non-standard InChI includes an additional layer (FixedH) that indicates which tautomer the chemical name described. StdInChI aims to be tautomer independent.

Advanced Usage

OPSIN 2.6.0 allows enabling of the following options:

• allowRadicals: Allows substituents to be interpretable e.g. allows interpretation of "ethyl"
• wildcardRadicals: If allowRadicals is enabled, this option uses atoms in the output to represent radicals: 'R' in CML and '*' in SMILES e.g. changes the output of ethyl from C[CH2] to CC*
• detailedFailureAnalysis: Provides a potentially more accurate reason as to why a chemical name could not be parsed. This is done by parsing the chemical name from right to left. The trade-off for enabling this is slightly increased memory usage.
• allowAcidsWithoutAcid: Allows interpretation of acids without the word acid e.g. "acetic"
• allowUninterpretableStereo: Allows stereochemistry uninterpretable by OPSIN to be ignored (When used as a library the OpsinResult has a status of WARNING if stereochemistry was ignored)
• verbose: Enables debugging output (command-line only). This option has the effect of lowering the logging threshold on the uk.ac.cam.ch.wwmm.opsin package to DEBUG.

The usage of these options on the command line is described in the command line's help dialog accessible via: java -jar opsin-cli-2.6.0-jar-with-dependencies.jar -h

These options may be controlled using the following code:

NameToStructure nts = NameToStructure.getInstance();
NameToStructureConfig ntsconfig = new NameToStructureConfig();
//a new NameToStructureConfig starts as a copy of OPSIN's default configuration
ntsconfig.setAllowRadicals(true);
OpsinResult result = nts.parseChemicalName("acetamide", ntsconfig);
String cml = result.getCml();
String smiles = result.getSmiles();
String stdinchi = NameToInchi.convertResultToStdInChI(result);

result.getStatus() may be checked to see if the conversion was successful. If a structure was generated but OPSIN believes there may be a problem a status of WARNING is returned. Currently this may occur if the name appeared to be ambiguous or stereochemistry was ignored. By default only optical rotation specification is ignored (this cannot be converted to stereo-configuration algorithmically).

Convenience methods like result.nameAppearsToBeAmbiguous() may be used to check the cause of the warning.

NOTE: (Std)InChI cannot be generated for polymers or radicals generated in combination with the wildcardRadicals option

Availability

OPSIN is available as a standalone JAR from GitHub, https://github.com/dan2097/opsin/releases

• opsin-cli-2.6.0-jar-with-dependencies.jar can be executed as a command-line application. It includes SMILES/CML/InChI support and bundles a logging implementation.
• opsin-core-2.6.0-jar-with-dependencies.jar includes just SMILES/CML support.

OPSIN is also available from the Maven Central Repository. For SMILES/CML output support you would include:

<dependency>
   <groupId>uk.ac.cam.ch.opsin</groupId>
   <artifactId>opsin-core</artifactId>
   <version>2.6.0</version>
</dependency>

or if you also need InChI output support:

<dependency>
   <groupId>uk.ac.cam.ch.opsin</groupId>
   <artifactId>opsin-inchi</artifactId>
   <version>2.6.0</version>
</dependency>

Building from source

To build OPSIN from source, download Maven 3 and OPSIN's source code.

Running mvn package in the root of OPSIN's source will build:

Artifact	Location	Description
opsin-cli-<version>-jar-with-dependencies.jar	opsin-cli/target	Standalone command-line application with SMILES/CML/InChI support
opsin-core-<version>-jar-with-dependencies.jar	opsin-core/target	Library with SMILES/CML support
opsin-inchi-<version>-jar-with-dependencies.jar	opsin-inchi/target	Library with SMILES/CML/InChI support

About OPSIN

The workings of OPSIN are more fully described in:

Chemical Name to Structure: OPSIN, an Open Source Solution
Daniel M. Lowe, Peter T. Corbett, Peter Murray-Rust, Robert C. Glen
Journal of Chemical Information and Modeling 2011 51 (3), 739-753

If you use OPSIN in your work, then it would be great if you could cite us.

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 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
• Ring assemblies e.g. biphenyl
• Most prefix and infix functional replacement nomenclature
• The following functional classes: acetals, acids, alcohols, amides, anhydrides, anilides, azetidides, azides, bromides, chlorides, cyanates, cyanides, esters, di/tri/tetra esters, ethers, fluorides, fulminates, glycol ethers, glycols, hemiacetals, hemiketal, hydrazides, hydrazones, hydrides, hydroperoxides, hydroxides, imides, iodides, isocyanates, isocyanides, isoselenocyanates, isothiocyanates, ketals, ketones, lactams, lactims, lactones, mercaptans, morpholides, oxides, oximes, peroxides, piperazides, piperidides, pyrrolidides, selenides, selenocyanates, selenoketones, selenolsselenosemicarbazones, selenones, selenoxides, selones, semicarbazones, sulfides, sulfones, sulfoxides, sultams, sultims, sultines, sultones, tellurides, telluroketones, tellurones, tellurosemicarbazones, telluroxides, thiocyanates, thioketones, thiols, thiosemicarbazones
• Greek letters
• Lambda convention
• Amino Acids and derivatives
• Structure-based polymer names e.g. poly(2,2'-diamino-5-hexadecylbiphenyl-3,3'-diyl)
• Bridge prefixes e.g. methano
• Specification of oxidation numbers and charge on elements
• Perhalogeno terms
• Subtractive prefixes: deoxy, dehydro, anhydro, demethyl, deamino
• Stoichiometry ratios and mixture indicators
• Nucleosides, (oligo)nucleotides and their esters
• Carbohydrate nomenclature
• Simple CAS names including inverted CAS names
• Steroids including alpha/beta stereochemistry
• Isotopic labelling
• E/Z/R/S stereochemistry
• cis/trans indicating relative stereochemistry on rings and as a synonym of E/Z

Currently UNsupported nomenclature includes:

• Other less common stereochemical terms
• Most alkaloids/terpenoids
• Natural product specific nomenclature operations

Developers and Contributors

• Rich Apodaca
• Albina Asadulina
• Peter Corbett
• Daniel Lowe (Current maintainer)
• John Mayfield
• Peter Murray-Rust
• Noel O'Boyle
• Mark Williamson

Thanks also to the many users who have contributed through suggestions and bug reporting.

OPSIN's developers use YourKit to profile and optimise code.

YourKit supports open source projects with its full-featured Java Profiler. YourKit, LLC is the creator of YourKit Java Profiler and YourKit .NET Profiler, innovative and intelligent tools for profiling Java and .NET applications.

Good Luck and let us know if you have problems, comments or suggestions! Bugs may be reported on the project's issue tracker.