Toolkit Version 2024.2

Detailed Release Notes 2024.2

Bioisostere TK 4.1.0

New features

  • A new algorithm, based on OEFlexiOverlay, has been adapted in Build for optimization of generated poses for molecules obtained from fragment replacement. The new algorithm is more robust for optimization of poses for all geometries, including cyclic peptides.

Major bug fixes

  • Query building algorithms in OECreateBroodQuery have been improved for robustness. The improved API automatically includes any associated hydrogen atoms as part of the query fragment. Behavior has also been improved to provide better error behavior against invalid selections.

  • The new methods SetSingleSourceMol and GetSingleSourceMol have been added to OEFragmentOptions to provide flexibility regarding source molecule storage during database building.

Minor bug fixes

  • Some memory management issues have been fixed in Build and Generate.

OEChem TK 4.1.1.1

Major bug fixes

  • An issue has been fixed where OEReadMolecule would fail to read a molecule from an mmCIF file if an invalid LINK record was present.

OEChem TK 4.1.1.0

New features

  • Support has been implemented for OEGroup information for OEMiniMol to support the return of enhanced stereogroup information from OEFastFPDatabase hits. Previously, enhanced stereogroup information on the indexed structures would be ignored during indexing and thus missed from returned hits.

  • LINK records in the PDB metadata are now parsed to improve perception of covalently bound heterogens. The equivalent _struct_conn metadata is also parsed from mmCIF files. The distance between the listed atoms is confirmed before applying the bond.

Minor bug fixes

  • If any parse error results from parsing a OEFormat::CXSMILES appendix specifically, the full appendix plus the molecule title are now returned in the molecule title to allow user inspection and corrective action.

  • OEFormat::SDF data parsing has been modified to ensure that >-prefixed data is properly captured. Since SDF data field name lines are >-prefixed as well, the new behavior explicitly requires a blank line delimiter to be present between data entries, including null data items, per the SDF file format specification. This allows unambiguous identification of data field name header lines versus data entry lines.

  • An issue has been fixed to avoid generating duplicate data tags from generic data that can result in invalid JSON output.

  • Titles returned from OEMolDatabase::GetTitle when OEFormat::CXSMILES files are indexed no longer contain the CXSMILES appendix unless there is a parse error with the appendix information itself.

  • An error has been fixed that sometimes resulted in missing atom parity information in output SDF format files when a nondefault oemolistream::SetConfTest was provided.

  • A line ending parse error has been fixed for OEFormat::FASTA files affecting windows files.

  • Propagation of perceived query aromaticity has been added for alternating single/double Kekulé forms so that alternate and equivalent s/d bond patterns are treated consistently.

  • Null pointer protections have been added to some internal search matching code that could cause a crash.

  • OEFileStringTypeFlavor::Default has been augmented to exclude file types that are not suggested for use. Accordingly, a new constant, OEFileStringTypeFlavor::Pretty, has been defined and is part of the new definition of OEFileStringTypeFlavor::Default. Removing OEFileStringTypeFlavor::Pretty from OEFileStringTypeFlavor::Default would provide the file types that include everything.

  • A new type, OEMMFFType::CION, has been added to define a generic type for counterions.

OEPlatform TK 4.1.1

New features

  • The ZSTD library has been updated from version 1.5.2 to 1.5.6.

OEBio TK 4.1.1

Major bug fixes

  • In the Iridium categorization of a design unit, a properly perceived, covalently bound ligand no longer triggers an HT to MT category transition. The rule flags atoms that are within what is considered a covalent bond distance, where a bond is not properly perceived.

  • An issue has been fixed so that ClearComponent can be used to clear user-defined components.

OEDepict TK 2.5.5

Minor internal improvements have been made.

OEDocking TK 4.3.2

New features

Major bug fixes

  • The method Optimize in OEPoseOptimizer is now more robust in optimizing a docked pose. Accordingly, Docking with relaxation in OEPosit is also now more robust.

  • The function OEHasClash now properly recognizes all clashes between a ligand and a protein that were previously mistaken because of some misidentification of covalent bonds.

Minor bug fixes

  • Selection of the best receptor has been improved in OEPosit, ensuring that the correct receptor will always be picked in case of a self-docking.

  • The internal algorithm has been optimized to improve time requirements for OEPosit when working with many receptors and a few ligands.

Eon TK 3.1.0

This is the first commercial release of Eon TK.

New features

The following classes are available as preliminary API with the first release of this toolkit.

The following functions are available as preliminary API with the first release of this toolkit.

FastROCS TK 2.2.7

New features

Grapheme TK 1.5.2

New features

Minor bug fixes

  • An issue has been fixed which incorrectly used the ligand density value for the active site density value when depicting the Iridium classification.

GraphSim TK 2.6.1

Minor bug fixes

Lexichem TK 2.9.2

Minor internal improvements have been made.

OEMedChem TK 1.2.3

Minor internal improvements have been made.

MolProp TK 2.6.5

Minor internal improvements have been made.

OEFF TK 2.8.0

New features

Minor Bug Fixes

  • Loading a SMIRNOFF set of parameters using OESmirnoffParams no longer picks up the library charges.

Omega TK 6.0.0

New features

Minor bug fixes

  • User-defined values passed through SetEnergyWindow, SetMaxConfs, and SetRMSThreshold are now properly accounted for, even when the corresponding defaults are range-based.

  • Molecule titles are retained when Build fails in OEOmega with fails to build structure from CT.

  • A verbose log is provided for fragments that fail when Build fails in OEOmega with fails to build structure from CT.

  • The OEOmegaIsGPUReady function has been safeguarded from a rare crash. The function has also been updated to check not only for device 0, but for devices from 0 to 100.

Quacpac TK 2.2.5

Minor bug fixes

Shape TK 3.7.0

New features

Minor bug fixes

SiteHopper TK 2.1.1

Minor bug fixes

Spicoli TK 1.6.1

Minor internal improvements have been made.

Spruce TK 1.6.1.1

Major bug fixes

  • An issue has been fixed where OEExtractBioUnits function would fail if there was a mismatch in author assigned chain names and PDB assigned chain names in the case where a molecule was extracted from an mmCIF file.

  • An issue was fixed in OEProtonateDesignUnit where a rule to flip clashing in-plane hydrogens on double bonded nitrogens was triggering incorrectly in specific instances.

Spruce TK 1.6.1

New features

  • OEBuildSidechains now minimizes target side chains by default. Minimization can be controlled by setting minimizeSidechains and minimizeSidechainsShell options in the OESidechainBuilderOptions class.

  • A feature has been added to support a next generation mmCIF feature, such that when an mmCIF file provides a connectivity record for the heterogens, Spruce will no longer look up the heterogen in the Chemical Component Dictionary but trust the input provided.

  • A feature has been added that allows in-plane flipping of a single hydrogen on a double bonded nitrogen, when a clash is detected as part of hydrogen bond network optimization.

Major bug fixes

  • An issue has been fixed related to using the OEHeterogenMetadata class, where the provided SMILES string was not respected for tautomer generation; when tautomers were not provided; and when the title (residue name) collided with existing residue names in the stored Chemical Component Dictionary.

  • An issue has been fixed related to covalently bound ligands, where the pre-reaction input SMILES and related tautomers were not adjusted properly when accounting for the formed covalent bond.

  • An issue has been fixed where the Spruce filter deleted single (disconnected) amino acid residues when they were marked HETATMs and were not real “floating” residues in part of the regular protein sequence.

Minor bug fixes

  • OEMutateResidues, OEMutateResidue, and OEBuildSidechains now reduce failures arising from clashes by using shell minimization by default.

  • An issue has been fixed that caused HEME-like molecules to be excluded from the stored chemical component database.

Documentation changes

  • Information has been added about setting and getting minimizeSidechains and minimizeSidechainsShell options in the OESidechainBuilderOptions class.

Szmap TK 1.7.1

Minor internal improvements have been made.

Szybki TK 2.8.0

New features

  • The constant SAGE_OPENFF refers to the latest version of the Sage OpenFF force field.

Zap TK 2.5.0

Minor internal improvements have been made.