OEToolkits 2021.1

Detailed Release Notes 2021.1

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 non-standard 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.

Major bug fixes

  • 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.

Minor bug fixes

  • 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.

Documentation changes

OEBio TK 3.1.1

New features

Minor bug fixes

  • 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

OESystem TK 3.1.1

Major bug fixes

  • 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.

OEPlatform TK 3.1.1

New features

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

OEGrid TK 3.1.1

Major bug fixes

OEMath TK 3.1.1

Minor internal improvements have been made.

OEDepict TK 2.4.6

July 2021

Minor internal improvements have been made.

OEDocking TK 4.1.0

July 2021

New features

Minor bug fixes

  • The default value for the OEMakeReceptorOptions::AddBox has been set to 0.0 in the OEMakeReceptorOptions class.

FastROCS TK 2.2.0

July 2021

New features

Minor bug fixes

  • An issue with custom weights in FastROCS custom color has been fixed.

Grapheme TK 1.4.3

July 2021

New features

  • Rendering of protein-ligand binding sites has been improved to handle new intramolecule types in the OEPerceiveInteractionHints function.

GraphSim TK 2.5.2

July 2021

Minor internal improvements have been made.

Lexichem TK 2.7.3

July 2021

New features

  • Support for input of many common drug names has been added.

  • Support for SMILES input of disubstituted alkenes when unknown subsituents are marked as * has been added. For example, SMILES input of *CCC* is now parsed and named as 1,3-disubstitutedpropylene.

Major bug fixes

  • An issue with naming of highly branched carbons structures has been fixed.

OEMedChem TK 1.1.4

July 2021

Minor bug fixes

MolProp TK 2.5.6

July 2021

Minor bug fixes

OEFF TK 2.3.1

July 2021

Minor internal improvements have been made.

Omega TK 4.1.1

July 2021

New features

Major bug fixes

Minor bug fixes

  • An issue with stereo specificity of the imino group (=NH) not being retained in a macrocycle has been fixed.

  • An issue with loss of relative stereo marked atoms in macrocycle mode has been fixed.

Quacpac TK 2.1.2

July 2021

Minor internal improvements have been made.

Shape TK 3.4.2

July 2021

Major bug fixes

  • A bug that caused some molecules to get a perfect Shape Tanimoto score of 1.0, even though their overlap was not optimal, has been fixed.

Spicoli TK 1.5.2

July 2021

Minor internal improvements have been made.

Spruce TK 1.3.0

July 2021

New features

More detailed changes are as follows:

Minor bug fixes

  • A bug that caused the loop modeling algorithm to crash in rare instances has been fixed.

  • Examples have been modified to use appropriate command-line arguments.

  • An issue that caused style on OEProtonateDesignUnit has been fixed.

  • An issue in OEMakeDesignUnitFromPocket that caused style to remain on both the previous binding site and the one defined from the pocket has been fixed.

  • An issue with the return value of superposition when two structures cannot be superposed has been fixed. It now properly returns a -1.00 RMSD.

  • A bug in superposition that resulted in a crash when using site residues that were not present on a design unit has been fixed.

  • A bug that kept the insert code from its anchor residue when there was an N-terminal cap has been fixed.

Documentation changes

  • Documentation has been added for the Iridium classification. Iridium.

Szmap TK 1.6.2

July 2021

Minor internal improvements have been made.

Szybki TK 2.3.1

July 2021

New features

Zap TK 2.4.1

July 2021

Minor internal improvements have been made.