Toolkit Version 2025.1

• 2025.1 Highlights
  • OEToolkits 2025.1

Detailed Release Notes 2025.1

Bioisostere TK 4.2.0

New Features

• The new class OECPDDatabase has been added as a preliminary API, which can be used to perform 2D similarity comparisons between a Brood hit list and an external compound database.

• Eight new overloads have been added to the existing OECreateBroodQuery function. The new overloads extend the API for query generation in the presence of an active site protein and/or a selectivity protein. Additionally, there are new overloads to create a bridging query between two molecules.

• The following new methods have been added to OEHitlistBuilder:

  • GetRemovedHits

  • GetFailedCount

  • TrimHitlist

  • GetTrimmedCount

• The Build method in the OEHitlistBuilder has been expanded to accept an OETracerBase as an optional argument.

• The following new methods have been added to OEBroodHit:

  • GetBuildStatus

  • GetDeltaLocalStrain

Minor Bug Fixes

• Some memory management issues have been fixed in AddScores of the OEHitlistBuilder class.

• The OEBroodScore returned from the Overlay calculation now always contains the fragment, irrespective of whether the overlay was a success.

• The GetFrags method in the OEBroodDBPacket now properly returns an empty iterator if there are no fragments in a packet.

• The SetupRef method in OEFragOverlay is now substantially faster for subsequently initializing it with new reference fragments.

• The Init method in OEDBReader is now returning an unsigned int (instead of bool), reflecting the OEBioisostere OEBroodStatusCode Success or other error codes for database initialization.

OEChem TK 4.2.0

New Features

• If an mmCIF file with long residue names is written to PDB, it will first check whether the three-character version is unused and will use that if it is.

Major Bug Fixes

• An issue has been fixed that caused mmCIF files with long residue names to break the long residue names into multiple residues.

Minor Bug Fixes

• An issue has been fixed that ensures that missing mmCIF metadata relevant for Iridium classification of a structure does not cause problems.

• An issue has been fixed which ensures that LINK records are parsed only if formatted correctly.

Python-Specific Changes

• A couple of issues have been fixed that caused crashes using Python 3.12, related to using OEResidue objects in a dictionary and setting an OEBitVector (or classes derived from it) or an OEHalfFloat as generic data on a molecule.

OEBio TK 4.2.0

Minor Bug Fixes

• An issue has been fixed in the OEBio_OEIsNTerminalAtom predicate ensuring the NME capping group is not matched.

• OEProteinConstraintType constants are now properly wrapped in Python.

OEDepict TK 2.5.6

Minor internal improvements have been made.

OEDocking TK 4.3.3

Minor internal improvements have been made.

EON TK 3.1.1

Minor internal improvements have been made.

FastROCS TK 2.3.0

New Features

• FastROCS TK now supports shape grids in the input query, analogous to Shape TK.

Minor Bug Fixes

• A bug in the overlaid database pose has been fixed in the transformation from the inertial frame to the original one. FastROCS scores are unaffected. As a result, the CPU steps on top of FastROCS poses are no longer needed in SiteHopper.

Grapheme TK 1.5.3

Minor internal improvements have been made.

GraphSim TK 2.6.2

Minor internal improvements have been made.

Lexichem TK 2.9.3

Minor internal improvements have been made.

OEMedChem TK 1.2.4

Minor Bug Fixes

• A bug causing a crash on Windows builds has been fixed.

MolProp TK 2.6.6

Minor internal improvements have been made.

OEFF TK 2.9.0

New Features

• The new method GetLigandFF has been added to OEComplexFF that enables access to the underlying ligand force field.

• The following new classes have been introduced to enable accessing data associated with any OESmirnoffParams parameters:

  • OESmirnoffData

  • OESmirnoffStretchData

  • OESmirnoffBendData

  • OESmirnoffTorsionData

  • OESmirnoffImproperData

  • OESmirnoffVdWData

• The following new methods have been added to OESmirnoffParams to enable accessing data associated with various parameters:

  • AddBendData

  • AddImproperData

  • AddStretchData

  • AddTorsionData

  • AddVdWData

  • GetBendData

  • GetImproperData

  • GetStretchData

  • GetTorsionData

  • GetVdWData

  • SetBendData

  • SetImproperData

  • SetStretchData

  • SetTorsionData

  • SetVdWData

• The function OEIsValidMMFFMolecule has a new overload that allows it to ignore charges while checking if MMFF parameters are available for the specified molecule.

Minor Bug Fixes

• An issue that was causing an occasional segmentation fault in the SetHostFlex method in the OEFF14SBSageComplex class has been fixed.

• The method SetupConf in OEMolFunc is now properly wrapped in Python.

Omega TK 6.1.0

New Features

• The new methods SetOverlayRMS and GetOverlayRMS have been added to OESliceEnsembleOptions, enabling conformer slicing with in-place RMSD calculation between conformers, with OEConfSlicer and OESliceEnsemble.

Minor Bug Fixes

• OEOmega now properly places carboxylic acids in cis configuration when hydrogen sampling is not performed.

• All conformers generated with OEMacrocycleOmega now properly set the dimensionality of the conformers to 3.

Quacpac TK 2.2.6

Minor internal improvements have been made.

Shape TK 3.8.0

New Features

• A new method, AddShapeGaussians, has been added that allows adding shape Gaussians to the OEShapeQuery based on the intensity of values on a grid.

• A new class, OEShapeQueryOptions, has been added that allows modifying options that would be used in adding Gaussians using the AddColorGaussians and AddShapeGaussians. Subsequently, a new constructor for OEShapeQuery has been added that takes the OEShapeQueryOptions as an argument.

SiteHopper TK 2.1.2

Minor internal improvements have been made.

Spicoli TK 1.6.2

Minor internal improvements have been made.

Spruce TK 1.7.0

New Features

• The functions OEMakeDesignUnit and OEMakeBioDesignUnits will now use provided OEHeterogenMetadata in OEStructureMetadata as information for the splitting of a structure into a design unit, including such details as which parts should be considered cofactors.

Major Bug Fixes

• An issue has been fixed that caused charge and radii assignment to not happen, in paths where Spruce was also not allowed to protonate the structure.

• An issue has been fixed that caused radii to not be properly assigned to all atoms in the design unit.

Minor Bug Fixes

• An issue has been fixed which caused some mmCIF files to not be able to be prepared due to lack of missing metadata.

• An issue has been fixed where OEMutateResidues would crash if the structure contained the N-terminal capping group NME.

Szmap TK 1.7.2

Minor internal improvements have been made.

Szybki TK 2.9.0

New Features

• A new class, OEOELigandChargeOptions, has been added that provides options related to ligand charge assignment. The following classes now derive from OEOELigandChargeOptions, enabling greater flexibility in ligand charge assignment:

  • OEProteinLigandOptOptions

  • OETorsionScanOptions

  • OEBoundEntropyOptions

  • OELigandEntropyOptions

• The default optimization type has been changed to PoseCartesian in both OEFixedProteinLigandOptimizer and OEFlexProteinLigandOptimizer.

• The following two new constants have been added to the OESzybkiReturnCode namespace:

  • AromaticRingDev: refers to failure due to excessive aromatic distortion.

  • OptimizerFailed: refers to the optimizer failing to find a solution.

• The following class methods now take an optional predicate describing residues that should be considered as part of the protein target during optimization:

  • SetProtein in OEFixedProteinLigandOptimizer

  • Optimize in OEFlexProteinLigandOptimizer

  • Energy in OEFlexProteinLigandOptimizer

• The following new preliminary API classes have been added, enabling optimization of a ligand with torsion constraints:

  • OELigandEnergy

  • OELigandOptOptions

  • OELigandOptResults

  • OETorConstraintOptimizer

  • OETorConstraintOptOptions

Major Bug Fixes

• OEFixedProteinLigandOptimizer and OEFlexProteinLigandOptimizer no longer fail to optimize with the ExcessiveOverlap error code prematurely.

Minor Bug Fixes

• OEFreeFormConfOptions now sets the latest Sage force field as the default.

• An issue has been fixed in OETorsionScan where scanning using the option SetUseInternalCoord set to true would occasionally produce large unphysical energies at certain angles.

Zap TK 2.5.1

Minor internal improvements have been made.

Recent Release History

• OEToolkits 2024.2
  • OEToolkits 2024.2.1
  • OEToolkits 2024.2.0
• OEToolkits 2024.1
  • OEToolkits 2024.1.3
  • OEToolkits 2024.1.0
• OEToolkits 2023.2
  • OEToolkits 2023.2.0
  • General Notices
• OEToolkits 2023.1
  • OEToolkits 2023.1.1
  • OEToolkits 2023.1.0
  • General Notices

Previous Release History

• Release Highlights 2022.2
• Release Highlights 2022.1
• Release Highlights 2021.2
• Release Highlights 2021.1
• Release Highlights 2020.2
• Release Highlights 2020.1
• OEToolkits 2019.Oct
• OEToolkits 2019.Apr
• OEToolkits 2018.Oct
• OEToolkits 2018.Feb
• OEToolkits 2017.Oct
• OEToolkits 2017.Jun
• OEToolkits 2017.Feb
• OEToolkits 2016.Oct
• OEToolkits 2016.Jun
• OEToolkits 2016.Feb
• OEToolkits 2015.Oct
• OEToolkits 2015.Jun
• OEToolkits 2015.Feb
• OEToolkits 2014.Oct
• OEToolkits 2014.Jun
• OEToolkits 2014.Feb
• OEToolkits 2013.Oct
• OEToolkits 2013.Jun
• OEToolkits 2013.Feb
• OEToolkits 2012.Oct
• OEToolkits 2012.Jun
• OEToolkits 2012.Feb
• OEToolkits 2011.Oct
• OEToolkits 2011.1
• OEToolkits 1.7.4
• OEToolkits 1.7.2
• OEToolkits 1.7.1
• OEToolkits 1.7.0