OEChem TK 2.1.2¶
Minor bug fixes¶
OECounthas 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_OEMiniMolhave been fixed. Perception flags are now cleared correctly when deleting atoms or bonds. Coordinates are no longer lost when a molecule is swept.
OESubSearch.Initmethod now checks that the given query molecule is valid. In case of an invalid molecule a warning is thrown and the method returns
The message for the
ValueErrorexception raised when trying to attach an unrecognized type to an OpenEye object as generic data has been clarified.
OEBio TK 2.1.2¶
A new method,
OEInteractionHintContainer.DeleteInteraction, has been added.
The set of water orientations sampled by
OEPlaceHydrogensis now strictly based on local donor/acceptor interactions instead of the more generic quaternion sampling used previously.
The new method
OEPlaceHydrogensMoverNote.IsRestrainedindicates whether a given moveable functional group has been restrained.
Extended chelation interactions to cases where a protein is chelating a ligand metal.
For interaction hints between any two atoms, implement a perception precedence as follows:
Added chelation perception to protein intramolecular interaction hints. See
Major bug fixes¶
OEPlaceHydrogensresults have been significantly improved after fixing a bug related to the treatment of certain non-moving background atoms.
OEPlaceHydrogensno 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.
OEPlaceHydrogensnow uses a more concise definition of moveable groups and no longer fails due to matching atoms multiple times.
OEPlaceHydrogensnow generates correct hydrogen geometry on carboxylic acid (COOH) groups.
OEPlaceHydrogensno longer orients phenolic hydrogens at high angles to the ring plane.
OEPlaceHydrogensgenerates improved orientations for amines deprotonated upon chelating a metal.