Bringing sugars to OPSIN

cycleofsugarsupportI’m pleased to announce the release of OPSIN 1.4.0. This new release brings significant improvements to OPSIN’s coverage of carbohydrate nomenclature. It also complements NextMove Software’s Sugar & Splice project that aims to make the conversion between carbohydrate and small molecule representations effortless.

Below is the effect this improvement to OPSIN has had on the conversion of IUPAC names in ChEBI. (This is one of the data sets used in the OPSIN publication [free access])

Number of names convertible to InChI on IUPAC names from ChEBI (Sept 2010)
Number of names convertible to InChI on IUPAC names from ChEBI (Sept 2010)

Examples of new nomenclature supported (pictures generated by the OPSIN web service)

3-Deoxy-alpha-D-manno-oct-2-ulopyranosonic acid
3-Deoxy-alpha-D-manno-oct-2-ulopyranosonic acid

beta-D-Fructofuranosyl alpha-D-glucopyranoside
beta-D-Fructofuranosyl alpha-D-glucopyranoside

Methyl 2,3,4-tri-O-acetyl-alpha-D-glucopyranosyluronate bromide
Methyl 2,3,4-tri-O-acetyl-alpha-D-glucopyranosyluronate bromide

3-O-beta-D-galactosyl-sn-glycerol
3-O-beta-D-galactosyl-sn-glycerol

OPSIN 1.4.0 is available from Bitbucket and Maven Central. The full release notes are below:

  • Added support for dialdoses,diketoses,ketoaldoses,alditols,aldonic acids,uronic acids,aldaric acids,glycosides,oligosacchardides, named systematically or from trivial stems, in cyclic or acyclic form
  • Added support for ketoses named using dehydro
  • Added support for anhydro
  • Added more trivial carbohydrate names
  • Added support for sn-glcyerol
  • Improved heuristics for phospho substitution
  • Added hydrazido and anilate suffixes
  • Allowed more functional class nomenclature to apply to amino acids
  • Added support for inverting CAS names with substituted functional terms e.g. Acetaldehyde, O-methyloxime
  • Double substitution of a deoxy chiral centre now uses the CIP rules to decide which substituent replaced the hydroxy group
  • Unicode right arrows, superscripts and the soft hyphen are now recognised

Leave a Reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.