OEChem TK 2.1.2¶
- A new function, OEGetSmiStringOrder, has been added to retrieve the atoms of a molecule in the order that they are encoded in the SMILES string for that molecule.
- New methods OELibraryGen.SetClearCoordinates and OEUniMolecularRxn.SetClearCoordinates have been added to clear the coordinates of generated products.
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.
- The message for the ValueError exception 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 OEPlaceHydrogens is now strictly based on local donor/acceptor interactions instead of the more generic quaternion sampling used previously.
- The following methods have been added to OEPlaceHydrogensOptions to control the optimization of conformations of moveable functional groups by OEPlaceHydrogens:
- The new method OEPlaceHydrogensMoverNote.IsRestrained indicates 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: Chelation > Charge > Hydrogen-bonding.
- Added chelation perception to protein intramolecular interaction hints. See OEChelatorInteractionHintType.IntramolecularProtein.
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.