Toolkit Version 2024.1

• OEToolkits 2024.1.3
• OEToolkits 2024.1.0
  • Release Highlights 2024.1.0
  • General Notices

Detailed Release Notes 2024.1

Bioisostere TK 4.0.0

This is the first commercial release of Bioisostere TK.

New features

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

• OEBroodBuildOptions

• OEBroodDBFilter

• OEBroodDBPacket

• OEBroodFragPrep

• OEBroodGeneralOptions

• OEBroodHit

• OEBroodHitlistOptions

• OEBroodOverlay

• OEBroodOverlayBase

• OEBroodQuery

• OEBroodScore

• OEBroodScoreOptions

• OEDBBuffer

• OEDBBuilder

• OEDBReader

• OEDBScreenOptions

• OEDBWriter

• OEFragConfReader

• OEFragmentOptions

• OEFragOverlay

• OEHitlistBuilder

• OEMolPropertyOptions

• OEIntrinsicPropOptions

• OEExtrinsicPropOptions

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

• OEBioisostereGetArch

• OEBioisostereGetLicensee

• OEBioisostereGetPlatform

• OEBioisostereGetRelease

• OEBioisostereGetSite

• OEBioisostereGetVersion

• OEBioisostereIsLicensed

• OECreateBroodQuery

• OEGenerateConformers

• OEGetBroodStatus

• OEGetDBIndices

• OEReadBroodQuery

• OEWriteBroodQuery

OEChem TK 4.1.0

New features

• We are now able to read and parse the Chem Comp section of mmCIF files.

• We can now force a deterministic sorted order to the enhanced stereo information in generated CXSMILES appendices.

• New overloads of the OESimpleAppOptions constructors have been added to enable their usage when an output parameter is not desired.

• A new value, OEFileStringType_BroodQMol, has been added to OEFileStringType to support molecule files containing BroodQuery.

• The following preliminary API classes have been made permanent.

  • OECreateSubSearchDatabaseOptions

  • OESubSearchDatabase

  • OESubSearchQuery

  • OESubSearchResult

  • OESubSearchScreen

  • OESubSearchScreenTypeBase

  • OEMolRecord

  • OEMolParameter

  • OEFileStringParameter

  • OEMolReaderParameter

  • OEMolWriterParameter

  • OEOutFileStringParameter

  • OEPredicateParameter

  • OEUnAtomPredParameter

  • OEUnBondPredParameter

  • OERefInputAppOptions

  • OESimpleAppOptions

• The following preliminary API functions have been made permanent.

  • OEReadCIFFile

  • OEWriteCIFFile

  • OECreateSubSearchDatabaseFile

  • OEGetSubSearchScreenType

  • OEIsComplementaryScreenType

  • OEIsValidSubSearchDatabase

  • OEIsValidSubSearchScreenString

  • OEMakeSubSearchQueryScreen

  • OEMakeSubSearchTargetScreen

  • OESameSubSearchScreenTypes

  • OEScreen

  • OESubSearchStatusToName

Major bug fixes

• The handling of OESMILESFlag_ExtBonds formatted fragments has been improved to better support explicit cis/trans parity information for the coupling bond.

• Parse multiply referenced enhanced stereogroups correctly from CXSMILES appendices.

• The mapping behavior of *atom and Rgroup atoms for both MDL and SMARTS queries is now synchronized. Rgroups and/or *atoms in queries are now equivalently supported for OEMakeSubSearchQueryScreen.

• Conversion of OERecord to CSV now writes CXSMILES instead of SMILES to ensure enhanced stereo is not dropped.

Minor bug fixes

• Null argument checks have been added to OESuppressHydrogens to avoid causing a crash.

• Any attempt to kekulize partial structures for OEUniMolecularRxn has been fully suppressed when specifically requested, which allows explicit nonaromatic/aromatic transformations for partial ring structures.

• .lst and .list no longer appear as viable input file types in the options in OESimpleAppOptions and OERefInputAppOptions.

OESystem TK 4.1.0

New features

• The following preliminary API classes have been made permanent.

  • OERecord

  • OEOptions

  • OEBoolParameter

  • OEConstParameter

  • OEDoubleParameter

  • OEFloatParameter

  • OEIntParameter

  • OEMultiParameter

  • OEPointerParameter

  • OEPODParameter

  • OEStringParameter

  • OEUIntParameter

• The following preliminary API functions have been made permanent.

  • OEConfigureItf

  • OEConfigureOpts

  • OEUpdateOpts

OEMath TK 4.1.0

New features

• The following preliminary API classes have been made permanent.

  • OEKernelPLS

  • OEMatrix

  • OESquareMatrix

OEBio TK 4.1.0

New features

• A new overload of OESubsetDesignUnit has been added to allow for in-place subsetting of a design unit to avoid generating a copy.

Major bug fixes

• Several issues in OEPlaceHydrogens have been added to address:

  • improved perception and geometry for sp³ secondary amines.

  • improved chelation rules for primary amines.

  • improved chelation rules for phosphate and borate groups.

  • improved chelation rules for sulfonamide groups.

  • improved chelation rules for hydroxamate moieties.

Minor bug fixes

• Null argument checks have been added to OEGetTorsion to avoid causing a crash.

OEGrid TK 4.1.0

Major bug fixes

• A problem in OEReadMTZ has been fixed.

OESystem TK 4.1.0

New features

• The following preliminary API classes have been made permanent.

  • OERecord

  • OEOptions

  • OEBoolParameter

  • OEConstParameter

  • OEDoubleParameter

  • OEFloatParameter

  • OEIntParameter

  • OEMultiParameter

  • OEPointerParameter

  • OEPODParameter

  • OEStringParameter

  • OEUIntParameter

• The following preliminary API functions have been made permanent.

  • OEConfigureItf

  • OEConfigureOpts

  • OEUpdateOpts

OEMath TK 4.1.0

New features

• The following preliminary API classes have been made permanent.

  • OEKernelPLS

  • OEMatrix

  • OESquareMatrix

OEDepict TK 2.5.4

Minor internal improvements have been made.

OEDocking TK 4.3.1.3

• An issue has been fixed in OEHasClash such that strong atom clashes are no longer mistakenly marked as covalent bonds causing failure to recognize those as actual clashes.

OEDocking TK 4.3.1.0

• An issue has been fixed that would occasionally cause segmentation faults when OEPosit would internally fail to generate conformers.

• New methods, GetPoseRelaxOptions and SetPoseRelaxOptions, have been added to OEPositOptions to allow more flexibility in relaxing the OEPosit generated poses.

• Internal algorithms have been improved in OEShapeFit to improve strain in generated poses.

FastROCS TK 2.2.6

Minor internal improvements have been made.

Grapheme TK 1.5.1.3

• Following new methods have been added to OEColorForceFieldDisplay to enable preserving user defined query colors.

  • Constructors (additional argument)

  • GetPreserveQueryColors

  • SetPreserveQueryColors

Grapheme TK 1.5.1.0

Minor internal improvements have been made.

GraphSim TK 2.6.0

Minor internal improvements have been made.

Lexichem TK 2.9.1

Minor internal improvements have been made.

OEMedChem TK 1.2.2

Minor internal improvements have been made.

MolProp TK 2.6.4

Minor internal improvements have been made.

OEFF TK 2.7.1.3

• The constant OESmirnoffType_SAGE_OPENFF now refers to the 2.2.0 version of the Sage-OpenFF force field.

OEFF TK 2.7.1

New features

• The following preliminary API classes have been made permanent.

  • OENonBondIntcsOptions

  • OEComplexFF

  • OEComplexFFParameter

  • OEFF14SBParsley

  • OEFF14SBParsleyComplex

  • OEFF14SBSage

  • OEFF14SBSageComplex

  • OEFF14SBSmirnoff

  • OEFF14SBSmirnoffComplex

  • OEForceFieldParameter

  • OEMMFFAmberComplex

  • OEMMFFComplex

  • OESmirnoffComplex

Minor bug fixes

• The Get and Set methods in OEInteractParams are now exposed properly in Python.

Omega TK 5.1.0

New features

• A new Flipper option has been added to enumerate internally perceived relative stereocenters (e.g., 1,4-disubstituted cyclohexanes). See SetEnumRelativeAtomStereo.

Minor bug fixes

• Stereochemistry of input molecules is now respected more consistently in OEMacrocycleBuilder.

• For SetMacroCycOptions in OEFragBuilderOptions, defaults for SetFragGen, SetFragKeep, and SetStartFactor have been changed to more appropriate values of 50000, 1024, and 20, respectively.

• An issue with the order of loading rules to an existing torsion library with AddTorsionLibrary has been fixed.

• A duplicate entry from the GUBA torsion library has been removed.

Quacpac TK 2.2.4

Minor internal improvements have been made.

Shape TK 3.6.2

New features

• The following preliminary API classes have been made permanent.

  • OEColorFFParameter

  • OEFlexiOverlapFunc

  • OEFlexiOverlapOptions

  • OEFlexiOverlapResults

  • OEFlexiOverlay

  • OEFlexiOverlayOptions

• New methods, SetAtomStrength and GetAtomStrength, have been added that allow multiplying the contribution of shape overlap for any atoms, without adding an additional atom or Gaussian.

SiteHopper TK 2.1.0

New features

• GPU-based SiteHopper is no longer used to prescreen but is enabled as a stand-alone search method.

Spicoli TK 1.6.0

Minor internal improvements have been made.

Spruce TK 1.6.0

New features

• The chemical components dictionary has been updated with latest structures from the wwPDB.

• A feature has been added to OEProtonateDesignUnit to detect acceptor–acceptor clashes, modify the protonation state of one of the moieties, and reoptimize the hydrogen bond network.

• The following preliminary API classes have been made permanent.

  • OECapBuilderOptions

  • OELoopBuilderOptions

  • OEPocket

  • OEPocketOptions

  • OESidechainBuilderOptions

  • OESpruceFilter

  • OESpruceFilterOptions

  • OEValidateDesignUnit

• The following preliminary API functions have been made permanent.

  • OEBuildLoops

  • OEBuildSingleLoop

  • OEFindPockets

  • OEMakeDesignUnitFromPocket

Major bug fixes

• A crash in OESpruceFilter has been fixed in relation to atoms that were cleaned up during the standardization process.

Minor bug fixes

• An issue has been fixed that ensures radii are assigned to all atoms in a design unit.

Documentation changes

• An example has been added showing how to convert FASTA files to structure metadata for structures missing the SEQRES information in the PDB metadata and MMCIF equivalent.

Szmap TK 1.7.0

Documentation changes

• Examples have been updated to use design units as inputs.

Szybki TK 2.7.1.3

• The constant SAGE_OPENFF refers to the 2.2.0 version of the Sage-OpenFF force field.

Szybki TK 2.7.1.0

• OEFixedProteinLigandOptimizer and OEFlexProteinLigandOptimizer now propagate error better when optimization fails.

Zap TK 2.4.7

Minor internal improvements have been made.

Recent Release History

• OEToolkits 2023.2
  • OEToolkits 2023.2.0
  • General Notices
• OEToolkits 2023.1
  • OEToolkits 2023.1.1
  • OEToolkits 2023.1.0
  • General Notices
• Release Highlights 2022.2
  • OEToolkits 2022.2.2
  • OEToolkits 2022.2.1
  • MCS based fix during OMEGA Conformer Generation
  • New ShapeFit Algorithm for Pose Prediction
  • Protein-ligand Optimization with ff14SB forcefield and PB solvent model
  • New BROOD Fragment Databases
• Release Highlights 2022.1
  • Enhanced Stereo Information Support
  • Sheffield Solvation Model for Proteins
  • Spruce Filter and Design Unit Validation
  • Multistate Heuristic pKa Model

Previous Release History

• 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