Added support for reading the
V3000file format for molecules, queries, and reactions. By default, whether to read the
V3000format will be detected automatically from the header inside
OEGroupBaseclass added as a container of atoms and bonds inside a
OEMolBaseto store MDL enhanced stereo information. See the
OEGroupTypenamespace for the different types of enhanced stereo information that can be processed. Only the following subset of OEChem functions handle
OEGroupBaseinformation at this time:
Adding the following predicates for handling
OEGroupBaseobjects on molecules.
OEAssignZap9Radiihas been updated to use the method published in the 2010 Journal of Computer-Aided Molecular Design by Nicholls, Wlodek, and Grant. The old behavior can be accessed by passing constants found in the
oemolithreadnow works with
OEIFlavor.PDB.FORMALCHARGEinput flavor for PDB file reading added. This flavor is provided for advanced users who wish to read the formal charge from the file and do their own bond and hydrogen perception. It is not yet turned on by default.
SD data tags and value in
SDFfiles can now be up to 64 kilobytes in length, up from the previous limit of just 4 kilobytes.
OEMolecularFormulaextended to include hydrogen isotopes deuterium (
D) and tritium (
T) in the molecular formula output. Note, the default behavior has not changed, the user is required to pass an additional parameter to enable this feature.
The Amber C-terminal capping residue
OEResidueIndex.NMEis now supported. Support for the Amber C-terminal capping residue OEChem::OEResidueIndex::NMH is incomplete.
Major bug fixes¶
OESubsetMolwill no longer crash non-deterministically when setting the
OEInterfacehad a rare one time initialization thread safety bug when dealing with molecule parameters that has been fixed.
OEMCSType.Approximatesearch method will now terminate once the
OEMCSSearch.GetMaxMatcheslimit has been reached. The previous behavior was to keep enumerating all possible matches, then choose the first matches up to the limit. This significantly speeds up
OEMCSType.Approximatesearches that results in a lot of matches, e.g., matching a molecule onto itself.
It is highly recommended to call
OESuppressHydrogensbefore trying to perform a self match on a molecule.