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

v1.6.0

• Added API/command-line options to generate StdInchiKeys
• Added support for the IUPAC recommended nomenclature for carbobohydrate lactones
• Added support for boronic acid pinacol esters
• Added basic support for specifying chalcogen acid tautomer form e.g. thioacetic S-acid
• Fused ring bridges are now numbered
• Names with Endo/Exo/Syn/Anti stereochemistry can now be partially interpreted if warnRatherThanFailOnUninterpretableStereochemistry is used
• The warnRatherThanFailOnUninterpretableStereochemistry option will now assign as much stereochemistry as OPSIN understands (All ignored stereochemistry terms are mentioned in the OpsinResult message)
• Many minor nomenclature support improvements e.g. succinic imide; hexaldehyde; phenyldiazonium, organotrifluoroborates etc.
• Added more trivial names that can be confused with systematic names e.g. Imidazolidinyl urea
• Fixed StackOverFlowError that could occur when processing molecules with over 5000 atoms
• Many minor bug fixes
• Minor vocabulary improvements
• Minor speed improvements
• NOTE: This is the last release to support Java 1.5

v1.5.0

• Command line interface now accepts files to read and write to as arguments
• Added option to allow interpretation of acids missing the word acid e.g. "acetic" (off by default)
• Added option to treat uninterpretable stereochemistry as a warning rather than a failure (off by default)
• Added support for nucleotide chains e.g. guanylyl(3'-5')uridine
• Added support for parabens, azetidides, morpholides, piperazides, piperidides and pyrrolidides
• Vocabulary improvements e.g. homo/beta amino acids
• Many minor bug fixes e.g. fulminic acid correctly interpreted

v1.4.0

• 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

v1.3.0

• Added option to output radicals as R groups (* in SMILES)
• Added support for carbolactone/dicarboximide/lactam/lactim/lactone/olide/sultam/sultim/sultine/sultone suffixes
• Resolved some cases of ambiguity in the grammar; the program's capability to handle longer peptide names is improved
• Allowed one (as in ketone) before yl e.g. indol-2-on-3-yl
• Allowed primed locants to be used as unprimed locants in a bracket e.g. 2-(4'-methylphenyl)pyridine
• Vocabulary improvements
• SMILES writer will no longer reuse ring closures on the same atom
• Fixed case where a name formed of many words that could be parsed ambiguously would cause OPSIN to run out of memory
• NameToStructure.getInstance() no longer throws a checked exception
• Many minor bug fixes

v1.2.0

• OPSIN is now available from Maven Central
• Basic support for cylised carbohydrates e.g. alpha-D-glucopyranose
• Basic support for systematic carbohydrate stems e.g. D-glycero-D-gluco-Heptose
• Added heuristic for correcting esters with omitted spaces
• Added support for xanthates/xanthic acid
• Minor vocabulary improvements
• Fixed a few minor bugs/limitations in the Cahn-Ingold-Prelog rules implementation and made more memory efficient
• Many minor improvements and bug fixes

v1.1.0

• Significant improvements to fused ring numbering code, specifically 3/4/5/7/8 member rings are no longer only allowed in chains of rings
• Added support for outputting to StdInChI
• Small improvements to fused ring building code
• Improvements to heuristics for disambiguating what group is being referred to by a locant
• Lower case indicated hydrogen is now recognised
• Improvements to parsing speed
• Many minor improvements and bug fixes

v1.0.0

• Added native isomeric SMILES output
• Improved command-line interface. The desired format i.e. CML/SMILES/InChI as well as options such as allowing radicals can now all be specified via flags
• Debugging is now performed using log4j rather than by passing a verbose flag
• Added traditional locants to carboxylic acids and alkanes e.g. beta-hydroxybutyric acid
• Added support for cis/trans indicating the relative stereochemistry of two substituents on rings and fused rings sytems
• Added support for stoichiometry ratios and mixture indicators
• Added support for alpha/beta stereochemistry on steroids
• Added support for the method for naming spiro systems described in the 1979 recommendations rule A-42
• Added detailedFailureAnalysis option to detect the part of a chemical name that fails to parse
• Added support for deoxy
• Added open-chain saccharides
• Improvements to CAS index name uninversion algorithm
• Added support for isotopes into the program allowing deuterio/tritio
• Added support for R/S stereochemistry indicated by a locant which is also used to indicate the point of substitution for a substituent
• Many minor improvements and bug fixes

v0.9.0

• Added transition metals/f-block elements and nobel gases
• Added support for specifying the charge or oxidation number on elements e.g. aluminium(3+), iron(II)
• Calculations based off a van Arkel diagram are now used to determine whether functional bonds to metals should be treated as ionic or covalent
• Improved support for prefix functional replacement e.g. hydrazono/amido/imido/hydrazido/nitrido/pseudohalides can now be used for functional replacement on appropriate acids
• Ortho/meta/para handling improved - can now only apply to six membered rings
• Added support for methylenedioxy
• Added support for simple bridge prefixes e.g. methano as in 2,3-methanoindene
• Added support for perfluoro/perchloro/perbromo/periodo
• Generalised alkane support to allow alkanes of lengths up to 9999 to be described without enumeration
• Updated dependency on JNI-InChI to 0.7, hence InChI 1.03 is now used.
• Improved algorithm for assigning unlocanted hydro terms
• Improved heuristic for determing meaning of oxido
• Improved charge balancing e.g. ionic substance of an implicit ratio 2:3 can now be handled rather than being represented as a net charged 1:1 mixture
• Grammar is a bit more lenient of placement of stereochemistry and multipliers
• Vocabulary improvements especially in the area of nucleosides and nucleotides
• Esters of biochemical compounds e.g. triphosphates are now supported
• Many minor improvements and bug fixes

v0.8.0

• NameToStructureConfig can now be used to configure whether radicals e.g. ethyl are output or not.
• Names like carbon tetrachloride are now supported
• glycol ethers e.g. ethylene glycol ethyl ether are now supported
• Prefix functional replacement support now includes halogens e.g. chlorophosphate
• Added support for epoxy/epithio/episeleno/epitelluro
• Added suport for hydrazides/fluorohydrins/chlorohydrins/bromohydrins/iodohydrins/cyanohydrins/acetals/ketals/hemiacetals/hemiketals/diketones/disulfones named using functional class nomenclature
• Improvements to algorithm for assigning and finding atoms corresponding to element symbol locants
• Added experimental right to left parser (ReverseParseRules.java)
• Vocabulary improvements
• Parsing is now even faster
• Various bug fixes and name intepretation fixes