OEChem TK 2.1.4¶
A new class,
OE2DRingDictionaryCreatorOptions, has been added to customize generating user-defined ring template dictionaries.
A new function,
OEClear2DRingDictionary, has been added to clear the global user-defined ring dictionary used for 2D coordinate generation.
A new function,
OESet2DHydrogenGeom, has been added to assign approximate 2D coordinates to explicit hydrogen atoms.
Major bug fixes¶
OEChem::OEWriteMolToStringfunctions use internal buffers for the encoding or decoding of molecules from bytes. Previously, depending on library load order, internal buffers could be initialized without the complete set of binary input/output handlers. This could result in the loss of custom datatypes when translating to or from bytes. These internal buffers now are updated during subsequent loads of OpenEye libraries to ensure that the complete set of custom datatypes is handled correctly.
The implementations of
OEChem::OEMiniMolhave been corrected to avoid a potential crash after an
OEMolBase::UnCompresscall sequence when the molecule contains
OEGroupBaseobjects (e.g., reaction component information or V3000 enhanced stereo information). While the
OEGroupBaseobjects, it cannot save and restore following
OEMolBase::UnCompresscalls, so this class must never be used if
OEGroupBaseinformation is to be maintained. The
OEChem::OEDBMolimplementation is the preferred class for low memory footprint applications when
OEGroupBasemay be present.
When writing a 2D molecule with explicit hydrogens to an MDL file, the coordinates of the stereo hydrogens are now reassigned by calling the
OESet2DHydrogenGeomfunction if they are identical to their parent heavy atom coordinates. This ensures that reinterpretation of the MDL file does not inadvertently flip stereo configurations.
Minor bug fixes¶
The algorithm used by
OEGenerate2DCoordinatesto detect and resolve atom clashes when generating 2D coordinates has been improved.
When calling the
OERMSDfunction for a multi conformer fit molecule, the returned RMSD array will now have a -1.0 value for conformation indices that are not valid for the fit molecule.
OEAssignAromaticFlagsfunction now limits the search path to 30 bonds when the bond/atom ratio is higher than 1.3. As a result, buckyball-like molecules can be processed in reasonable time.
A crash in the Python interpreter due to malformed UTF-8 input character sequences has been fixed.
Binary data now can be safely attached to objects as generic data without being truncated at a
A minor issue with the C#
verify.pyscript that caused the validation to halt if one or more toolkit licenses was missing from the active license file has been fixed.
OESystem TK 2.1.4¶
OEBio TK 2.1.4¶
Minor bug fixes¶
OEIsChelatorInteractionHintpredicate has been fixed to recognize the
OESaltBridgeInteractionHintType::UnpairedLigandtype has been deprecated and replaced with
OESaltBridgeInteractionHintType::UnpairedProteintype has been deprecated and replaced with
The implementation of
OEHBondInteractionHintType::Clashhas been corrected to use proper geometric constraints in determining these unfavorable interactions. In addition,
OEHBondInteractionHintType::Clashhas been split into
OEHBondInteractionHintType::ClashAcceptorAcceptorto provide more specificity. These interactions are assigned only after other stronger or more favorable interactions have been assessed. Finally, hydrogen-bonding interaction clashes will not be assigned to groups that could avoid the interaction with a simple hydrogen rotation.