OEChem TK 3.1.1¶

July 2021

New features¶

OEZ has been made the default file format for storing molecules in OERecord objects.
Two new functions, OECalcPMI and OEGetRadiusOfGyration, have been added. The first calculates the principal moment of inertia (PMI) for a molecule, and the second calculates the radius of gyration for that molecule using a previously calculated PMI.
InChI has been updated to v1.06. A new option to OEInChIOptions supports generation of nonstandard InChI strings with pseudoatoms present.
Atom/bond SMARTS expressions can now be used as generic data for SMARTS queries.
The function OEApplyStateFromRef now transfers stereo/chiral information from the reference state molecule.

The function OEPerceiveResidues has been enhanced to properly recognize ACE (acetyl) and NME (N-methyl) capping groups, which used to cause unexpected behaviors. Recognition of the NHE and FOR capping groups has also been improved.

An issue that caused a crash in the OEPDBOrderAtoms function when running with preserveResOrder=True and molecules that do not have chain IDs has been fixed.
An issue that caused OEApplyStateFromRef to return redundant matches when doing partial matching with long hydrocarbon chains has been fixed.
An issue that caused OEDetermineConnectivity to break all bonds between atoms with wrong valences (possibly resulting in a broken backbone) has been fixed. It now tries to break the bonds between non-adjacent residues first and, if the valences of involved atoms are still wrong, all bonds.

Two new constructors have been added to the OEDesignUnit class. These constructors are intended to be used with prepared molecules. The two APIs are for liganded or apo-structures, where in the latter case site-residues indicating the binding site are required.
Predicate versions of OEIsStandardProteinResidue and OEIsStandardNucleicAcidResidue have been added as OEIsStandardAminoAcid and OEIsStandardNucleicAcid, respectively.
The OEReceptor class now stores a predicate that can be used to subset an OEDesignUnit class component. For example, a specific water molecule in the solvent component that should be used when generating the receptor grid and during docking.
The function OESubsetDesignUnit and the method OEDesignUnit::GetComponents now take a predicate that will subset the component(s) they hit in the design unit.
The functions OESubsetDesignUnit and OEUpdateDesignUnit will now clear the stored OEReceptor if the targetMask and targetPredicate of the receptor match the content being updated or subsetted away.
Non-const methods for GetCustomConstraints, OEReceptor::GetProteinConstraints, and GetConstraintFeatures have been added giving access to edit constraint features.

Nitriles (C#N) are now recognized as hydrogen bond acceptors in interaction hint perception.
Hydrogen bonds to moeities that are also interacting as saltbridges are now properly perceived.
Amide NH atoms are now properly counted as as UnpairedLigandDonor when appropriate.
The default for GetMaxCationPiAngle was reduced to from 50 to 40 degrees.
The default for SetMaxNonIdealAcceptorAngle was increased from 70 to 90 degrees.
The default for GetMaxNonIdealDonorAngle was increased from 50 to 70 degrees.
Several intra molecular interaction types are now properly perceived with OEPerceiveInteractionHints

An issue that caused the string format method on the OEFieldType for double to be converted to int has been fixed. The format method now writes with a precision of 12.
An issue that caused the string format method on the OEFieldType for double to add a .0 after a NaN has been fixed.
An issue that caused the string format method on the OEFieldType for string and JSON to be elided if longer than 100 characters has been fixed.
An issue with metadata flags not getting properly updated when a field with new metadata was set on an existing field has been fixed.

ZSTD has been updated to version 1.4.9, resulting in improvements in compression and decompression performance for the OEZ file format.