OEGetPathLength function’s performance has been significantly improved.
The APIs of the functions for accessing anisotropic B-factor parameters OEGetAnisou and OESetAnisou have been expanded for easier use in wrapped languages. The predicate OEHasAnisou and the container object OEAnisoUij have been added to support this functionality.
The ability to request bond stereomark corrections to reduce the number of stereo-center correction warnings when reading MDL format files has been added. For more information, see OEMDLStereoFromBondStereo function, OEIFlavor.SDF.FixBondMarks, OEIFlavor.MDL.FixBondMarks, and OEIFlavor.RDF.FixBondMarks constants.
41 new ring templates have been added to the built-in ring dictionary.
The following problems have been fixed for reading V3000 MDL files:
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.
OEPerceiveInteractionHints function has been added to perceive possible ligand-protein interactions (contact, clash, hydrogen bond, salt-bridge, chelator, and aromatic ring stacking).
The following classes and namespaces have been introduced to handle the new interaction types:
OECrystalSymmetryParams class has been added, along with overloaded versions of OEGetCrystalSymmetry and OESetCrystalSymmetry functions taking an OECrystalSymmetryParams object. This is the recommended API to use in the wrapped languages.
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.