Version 2.0.7

OEChem 2.0.7

New features

Major bug fixes

Minor bug fixes

  • The following problems have been fixed for reading V3000 MDL files:

    • OEReadMDLQueryFile function has been generalized to more reliably identify a V3000 header and dispatch to the correct reader.
    • A parsing error for V3000 MDL files with an atom list has been fixed.
    • An issue with atom lists in V3000 format that resulted in the export of invalid atom symbols has been fixed. Atom lists will now export as “L” but will lose the original atom list information. Query features are not yet supported for molecule writing.
  • A new warning will be issued for any V3000 MDL files that contain SCSR template information. This information is currently ignored.

  • A new warning will be issued for any MDL files that contain Sgroup information or Rgroup definition. This information is currently ignored.

  • An issue that occurred when valid cis/trans bond stereo were being converted to double either bonds in MDL reaction files has been corrected. This problem was introduced in the 2015.Oct release.

  • The function to access anisotropic B-factor parameters OEGetAnisou now sets all the parameters to 0 if no data is associated with the given atom, rather than leaving the parameters in an uninitialized state. The new predicate OEHasAnisou can be used to determine if an atom has these parameters.

  • OEMCSSearch constructor no longer throws a warning when initialized with a molecule that has up-to-date ring perception information.

  • OEAssignAromaticFlags function now invalidates the hybridization perception flag since different aromaticity models affect the recorded hybridization values.

  • Atom stereochemistry is more thoroughly examined and may result in multiple marks to the stereocenter(s) and/or marks to ring bond(s) for OEMDLStereoFromBondStereo activity to reduce the number of Stereochemistry corrected ... warnings on re-read of the exported structure.

    ../../_images/OEMDLStereoFromBondStereo-2.png

Documentation changes

  • Minor corrections to the OEPerceived namespace have been made.

OEBio 2.0.7

New features

Minor bug fixes

Documentation changes

OESystem 2.0.7

New features

OEPlatform 2.0.7

New features

  • OELIMITEDSTACK macro define value can now be controlled from compiler flags like -DOELIMITEDSTACK=0. This allows projects to use the C++ header files when compiling OpenEye C++ code for use with OpenEye Java toolkits.

    For more information on compiling custom OpenEye C++ code for use by OpenEye Java toolkit projects, see https://github.com/oess/oejava_extension.