Lexichem TK 2.3.0

New features

  • Name generation for racemic structures when the ‘MDL AND’ group is present in the MDL V3000 format. Stereodescriptors ‘rac’, ‘RS’ and ‘SR’. (Section P-92.1.3 of the IUPAC Nomenclature of Organic Compounds, Draft 2004 - Racemates and meso compounds). Racemic stereogenic centers are labeled with ‘RS’ if the CIP stereo descriptor is ‘R’ and has the MDL AND group present, else ‘SR’ if the stereogenic center has the CIP stereo descriptor ‘S’ and an MDL AND group present. The prefix ‘rac’ is used in front of a set of descriptors or locants, if all stereogenic centers in the molecule are racemic.


Isotope Example Depictions

  • Support has been added for name generation for isotopic carbon atoms in chains (e.g. the SMILES: C[15CH2]C[13CH2]C[15CH2]CCC will generate the name (4^{13}C,2,6-^{15}C_{2})nonane), simple rings and simple suffixes (e.g. the SMILES: [13NH2]C(=[15O])C1=C[14CH]=CC=C1 will generate the name (3^{14}C)cyclohexatriene(^{13}N,^{15}O)carboxamide). The chemical structures generated from parsing the example SMILES strings into a molecule object are depicted in Figure: Isotope Example Depictions.

  • Support for simple rings and simple suffixes in isotopic name generation e.g. the SMILES: [13NH2]C(=[15O])C1=C[14CH]=CC=C1 will generate the name (3^{14}C)cyclohexatriene(^{13}N,^{15}O)carboxamide

Minor bug fixes

  • Fixed Lexichem’s thread safety. A global variable in Lexichem that has persisted since its first release in 2005, has been removed. This global variable affected the function OEParseIUPACName, used in name to structure conversion. Two thread safety issues used in structure to name conversion, namely: double bond (E/Z) CIP stereo (thread safety broken in the June 2012TK release) and enhanced relative stereochemistry (thread safety broken in the June 2013TK release), that affected the function OECreateIUPACName, have been resolved.

  • OEParseIUPACName will no longer access invalid memory for names of the form ‘(di/tri/tetra)BLAH (ester/hydrazone/oxime/selenoxime/telluroxime/thioxime)’.