v2.8.0

• Support for undecahectane/undecadictane (previously only hendeca was supported)
• Support for dicarboximido
• Improved support for lysergic acid derivatives
• Added a few more sugars e.g. digitalose
• Added borodeuteride and hydro contractions of pharmaceutical salts e.g. hydromethanesulfonate
• Support substitution on glyceric acid
• Corrected interpretation of imidazolium, trioxane and phthalhydrazide

v2.7.0

• Improved coverage of flavonoid parent structures
• Support for apiofuranosyl, added 5 locant to apiose
• Improved support for n-amyl
• Superscripted numbers in poly spiro systems are now intelligently determined if the input lacks superscript indication
• Support for annulynes
• Fixed issues where amino acid salts were being interpreted as functionalisation of the amino acid
• Fixed bug where annulene parsing was case sensitive
• Chalcone, in accordance with current IUPAC recommendations, is now interpreted as specifically the trans isomer
• Minor dependency updates

v2.6.0

• OPSIN now requires Java 8 (or higher)
• OPSIN command-line functionality moved to opsin-cli module
• OPSIN standalone jars are now built with mvn package
• Updated from InChI 1.03 to InChI 1.06
• Support for capturing relative/racemic stereochemistry (output via CxSmiles) [contributed by John Mayfield]
• Support for deaza/dethia
• Support nitrile as a suffix on amino acids [contributed by John Mayfield]
• Support more glycero-n-phospho substituents
• Support for chloroxime and other haloximes
• Support cis/trans on rings where a stereocenter has two non-hydrogen substituents, using Cahn-Ingold-Prelog rules to determine which are relative
• Multiple improvements to implicit bracketting logic
• Corrected interpretation of methylselenopyruvate
• Added group 1/2 nitrides e.g. magnesium nitride
• Added molecular diatomics e.g. molecular hydrogen (or dihydrogen)
• Fixed out of memory error if a fusion bracket referenced an interior atom instead of a peripheral atom
• Fixed out of memory error while parsing very long ambiguous input, by switching parsing algorithm from breadth-first to depth-first

Dependency changes:

• Updated logging from Log4J v1.2.17 to the latest Log4J2 (v2.17.0). Neither OPSIN 2.5.0 nor 2.6.0 are vulnerable to Log4Shell. The logging implementation is only included in the opsin-cli module
• opsin-inchi now uses JNA-InChI rather than JNI-InChI. This supports the latest version of InChI and also support new Macs with ARM64 processors
• Woodstox now uses groupid com.fasterxml.woodstox (the groupid change did not signify a break in API compatibility)
• dk.brics.automaton now uses groupid dk.brics (the groupid change did not signify a break in API compatibility)
• commons-cli is only used by the opsin-cli module

v2.5.0

• OPSIN now requires Java 7 (or higher)
• Support for traditional oxidation state names e.g. ferric
• Added support for defining the stereochemistry of phosphines/arsines
• Added newly discovered elements
• Improved algorithm for correctly interpreting ester names with a missing space e.g. 3-aminophenyl-4-aminobenzenesulfonate
• Fixed structure of canavanine
• Corrected interpretation of silver oxide
• Vocabulary improvements
• Minor improvements/bug fixes

Internal XML Changes:

• tokenList files now all use the same schema (tokenLists.dtd)

v2.4.0

• OPSIN is now licensed under the MIT License
• Locant labels included in extended SMILES output
• Command-line now has a name flag to include the input name in SMILES/InChI output (tab delimited)
• Added support for carotenoids
• Added support for Vitamin B-6 related compounds
• Added support for more fused ring system bridge prefixes
• Added support for anilide as a functional replacement group
• Allow heteroatom replacement as a detachable prefix e.g. 3,6,9-triaza-2-(4-phenylbutyl)undecanoic acid
• Support Boughton system isotopic suffixes for 13C/14C/15N/17O/18O
• Support salts of acids in CAS inverted names
• Improved support for implicitly positively charged purine nucleosides/nucleotides
• Added various biochemical groups/substituents
• Improved logic for determining intended substitution in names with too few brackets
• Incorrectly capitalized locants can now be used to reference ring fusion atoms
• Some names no longer allow substitution e.g. water, hydrochloride
• Many minor precision/recall improvements

v2.3.1

• Fixed fused ring numbering algorithm incorrectly numbering some ortho- and peri-fused fused systems involving 7-membered rings
• Support P-thio to indicate thiophosphate linkage
• Count of isotopic replacements no longer required if locants given
• Fixed bug where CIP algorithm could assign priorities to identical substituents
• Fixed "DL" before a substituent not assigning the substituted alpha-carbon as racemic stereo
• L-stereochemistry no longer assumed on semi-systematic glycine derivatives e.g. phenylglycine
• Fixed some cases where substituents like carbonyl should have been part of an implicitly bracketed section
• Fixed interpretation of leucinic acid and 3/4/5-pyrazolone

v2.3.0

• D/L stereochemistry can now be assigned algorithmically e.g. L-2-aminobutyric acid
• Other minor improvements to amino acid support e.g. homoproline added
• Extended SMILES added to command-line interface
• Names intended to include the triiodide/tribromide anion no longer erroneously have three monohalides
• Ambiguity detected when applying unlocanted subtractive prefixes
• Better support for adjacent multipliers e.g. ditrifluoroacetic acid
• deoxynucleosides are now implicitly 2'-deoxynucleosides
• Added support for <number> as a syntax for a superscripted number
• Added support for amidrazones
• Aluminium hydrides/chlorides/bromides/iodides are now covalently bonded
• Fixed names with isotopes less than 10 not being supported
• Fixed interpretation of some trivial names that clash with systematic names

v2.2.0

• Added support for IUPAC system for isotope specification e.g. (3-14C,2,2-2H2)butane
• Added support for specifying deuteration using the Boughton system e.g. butane-2,2-d2
• Added support for multiplied bridges e.g. 1,2:3,4-diepoxy
• Front locants after a von baeyer descriptor are now supported e.g. bicyclo[2.2.2]-7-octene
• onosyl substituents now supported e.g. glucuronosyl
• More sugar substituents e.g. glucosaminyl
• Improved support for malformed polycyclic spiro names
• Support for oximino as a suffix
• Added method [NameToStructure.getVersion()] to retrieve OPSIN version number
• Allowed bridges to be used as detachable prefixes
• Allow odd numbers of hydro to be added e.g. trihydro
• Added support for unbracketed R stereochemistry (but not S, for the moment, due to the ambiguity with sulfur locants)
• Various minor bug fixes e.g. stereochemistry was incorrect for isovaline
• Minor vocabulary improvements

v2.1.0

• Added support for fractional multipliers e.g. hemihydrochloride
• Added support for abbreviated common salts e.g. HCl
• Added support for sandwich compounds e.g. ferrocene
• Improved recognition of names missing the last 'e' (common in German)
• Support for E/Z directly before double bond indication e.g. 2Z-ylidene, 2Z-ene
• Improved support for functional class ethers e.g. "glycerol triglycidyl ether"
• Added general support for names involving an ester formed from an alcohol and an ate group
• Grignards reagents and certain compounds (e.g. uranium hexafluoride), are now treated as covalent rather than ionic
• Added experimental support for outputting extended SMILES. Polymers and attachment points are annotated explicitly
• Polymers when output as SMILES now have atom classes to indicate which end of the repeat unit is which
• Support * as a superscript indicator e.g. 6 to mean superscript 6
• Improved recognition of racemic stereochemistry terms
• Added general support for names like "beta-alanine N,N-diacetic acid"
• Allowed "one" and "ol" suffixes to be used in more cases where another suffix is also present
• "ic acid halide" is not interpreted the same as "ic halide"
• Fixed some cases where ambiguous operations were not considered ambiguous e.g. monosubstitututed phenyl
• Improvements/bug fixes to heuristics for detecting when spaces are omitted from ether/ester names
• Improved support for stereochemistry in older CAS index names
• Many precision improvements e.g. cyclotriphosphazene, thiazoline, TBDMS/TBDPS protecting groups, S-substituted-methionine
• Various minor bug fixes e.g. names containing "SULPH" not recognized
• Minor vocabulary improvements

Internal XML Changes:

• Synonymns of the same concept are now or-ed rather being seperate entities e.g. <token>tertiary|tert-|t-</token>

v2.0.0

MAJOR CHANGES

• Requires Java 1.6 or higher

• CML (Chemical Markup Language) is now returned as a String rather than a XOM Element

• OPSIN now attempts to identify if a chemical name is ambiguous. Names that appear ambiguous return with a status of WARNING with the structure provided being one interpretation of the name

• Added support for "alcohol esters" e.g. phenol acetate [meaning phenyl acetate]

• Multiplied unlocanted substitution is now more intelligent e.g. all substituents must connect to same group, and degeneracy of atom environments is taken into account

• The ester interpretation is now preferred in more cases where a name does not contain a space but the parent is methanoate/ethanoate/formate/acetate/carbamate

• Inorganic oxides are now interpreted, yielding structures with [O-2] ions

• Added more trivial names of simple molecules

• Support for nitrolic acids

• Fixed parsing issue where a directly substituted acetal was not interpretable

• Fixed certain groups e.g. phenethyl, not having their suffix attached to a specific location

• Corrected interpretation of xanthyl, and various trivial names that look systematic

• Name to structure is now ~20% faster

• Initialisation time reduced by a third

• InChI generation is now ~20% faster

• XML processing dependency changed from XOM to Woodstox

• Significant internal refactoring

• Utility functions designed for internal use are no longer on the public API

• Various minor bug fixes

Internal XML Changes:

• Groups lacking a labels attribute now have no locants (previously had ascending numeric locants)
• Syntax for addGroup/addHeteroAtom/addBond attributes changed to be easier to parse and allow specification of whether the name is ambiguous if a locant is not provided