Version 2.1.2

OEChem TK 2.1.2

New features

• 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:

  • OEMolBase.SetDimension

  • OEMolBase.GetDimension

  • OEMolBase.SetEnergy

  • OEMolBase.GetEnergy

• 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

• The documentation for the following APIs has been improved:

  • OEAddMols function

  • OEWriteConstMolecule function

  • OEWriteMolecule function

  • OEParseSmiles function

  • OESubsetMol function

  • OEPDBAtomName namespace

OEBio TK 2.1.2

New features

• 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:

  • SetBypassPredicate

  • SetFlipPredicate

  • SetNoFlipPredicate

  • GetBypassPredicate

  • GetFlipPredicate

  • GetNoFlipPredicate

• 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.

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.