Version 1.9.3

OEChem 1.9.3

New features

Major bug fixes

  • OECreateInChI now passes the following information to the InChI library when calling the OECreateInChI function:

    • atom coordinates
    • wedge/hash bond property for single bonds
    • “either” bond property read from MDL file formats for double bonds

    These changes have reduced the number of failure cases to 10 when reading the MDDR database in SDF format and testing the InChI strings generated by OECreateInChI against the strings generated by the stand-alone InChI application.

Minor bug fixes

  • The OEIsAtomHybridization.operator() method now checks whether the hybridization was perceived and calculates the hybridization of the atom on the fly by calling OEGetHybridization if necessary.
  • The previously release of OEChem, 1.9.2, started considering different isotopes of hydrogen for chirality perception. This incorrectly perceived the following molecules as chiral: “C[2H]”, “CC[2H]” and “C([2H])[3H]”. Atoms with one or two isotope hydrogen neighbors and at least two implicit hydrogens will no longer be considered chiral.
  • When reading MacroModel molecule files (.mmod, .mmd, and .dat), atom serial numbers and HETATM designations were not being set, and subsequently saving the molecules in PDB format resulted in poorly formed files. This has been corrected so that conversion from MacroModel to PDB files preserves residue information properly.
  • OESmilesToMol and OEInChIToMol will now call OEMolBase.Clear before parsing the string into the molecule.

Documentation fixes

  • The OEMMFF* functions are now properly documented.

OESystem 1.9.3

Major bug fixes

  • OEErrorHandlerStream.Msg now calls exit(EXIT_FAILURE) in case of OEErrorLevel_Fatal level and calls exit(EXIT_SUCCESS) in case of OEErrorLevel_Usage.
  • OEInterface will no longer strip trailing zero characters from parameters that are non-floating point types. For example, “-prefix 1.10” used to return “1.1”. This bug was introduced in OEChem 1.9.0.

OEPlatform 1.9.3

  • oeistream.gettoken will no longer improperly write a NULL character at buffer[max] location in memory in rare circumstances when the token is the exact same size as the buffer.

OEGrid 1.4.4

  • Fixed a rare crash when interpolating between grids. This affects many API points, including GridBabel, whenever converting a grid to another grid type.