Version 2.1.2

OEChem TK 2.1.2

New features

Minor bug fixes

  • The function OECount has been fixed to return the number of substructure search matches. An extra parameter has been added to control whether the count of unique or non-unique matches is returned.

  • The following functions have been fixed to properly handle multi-conformer molecules with no active conformation:

  • Several problems with the internal implementation of OEMolBaseType.OEMiniMol have been fixed. Perception flags are now cleared correctly when deleting atoms or bonds. Coordinates are no longer lost when a molecule is swept.

  • The OEGenerate2DCoordinates function now clears MDL bond stereo that can be re-perceived by calling the OEMDLPerceiveBondStereo function.

  • The OESubSearch.Init method now checks that the given query molecule is valid. In case of an invalid molecule a warning is thrown and the method returns false.

Python-specific changes

  • The message for the ValueError exception raised when trying to attach an unrecognized type to an OpenEye object as generic data has been clarified.

Documentation changes

OEBio TK 2.1.2

New features

Major bug fixes

  • OEPlaceHydrogens results have been significantly improved after fixing a bug related to the treatment of certain non-moving background atoms.

  • OEPlaceHydrogens no longer fails with a segmentation fault when encountering an H-bond where there is a missing covalent bond. It also no longer fails in certain cases when adding explicit hydrogens.

  • OEPlaceHydrogens now uses a more concise definition of moveable groups and no longer fails due to matching atoms multiple times.

  • The MMFF-NIE scoring system used by OEPlaceHydrogens now works with elements such as Mn that are not parameterized in the MMFF94 force field.

  • OEPlaceHydrogens now generates correct hydrogen geometry on carboxylic acid (COOH) groups.

  • OEPlaceHydrogens no longer orients phenolic hydrogens at high angles to the ring plane.

  • OEPlaceHydrogens generates improved orientations for amines deprotonated upon chelating a metal.

Minor bug fixes

  • The ordering of moveable groups associated with a cluster in an OEPlaceHydrogensDetails object is now consistent across operating systems and platforms.

  • OEPlaceHydrogens now produces fewer warning messages.

  • Improved specificity of OEAcceptor definitions for interaction hint perception.