Toolkit Version 2025.2

Detailed Release Notes 2025.2

OEBioisostere TK 4.2.1

New Features

  • A new overload has been added to the SetSmartsFile method in OEFragmentOptions, enabling the ability to pass in a file name directly.

  • A new overload has been added to the OEGenerateConformers, enabling the option for rotorOffset compression during conformer generation. The existing overload no longer performs rotorOffset compression.

  • A new method, HasProteinSelect, has been added to the OEBroodQuery class that can be called on a query to check whether it has a selectivity protein.

Minor Bug Fixes

OEChem TK 4.3.0

New Features

  • A new function, OESweepMDLStereoGroups, has been added to strip nonstereo atoms from existing enhanced stereogroups, which can be used to reconcile the stereogroup information with the existing atom stereo parities.

  • A new function, OESameAlternateLocation, has been added to determine whether two atoms have the same alternate location set. It optionally allows for one of the states to be blank or unspecified, similar to the predicate OEHasAlternateLocation.

  • A new function, OEClearFormalCharges, has been added that resets all formal charges to zero.

  • A new OECIFData object has been added for easier access, coordination, validation, and updates to CIF header data. The full list of new features related to this object can be found on the OECIFData API page. Data available in this object reflects what is contained in the CIF data_ section.

  • A new OECIFCategory object holds CIF category data and acts as an interface to interact with this header data. The full list of new features related to this object can be found on the OECIFCategory API page. Data available in this object reflects what is contained in CIF pair or loop sections.

  • A new OECIFOptions object is used during CIF update functions and informs what categories and data items in the CIF header will be updated.

  • The OESetCIFData function can also take an OECIFData object as an input to save data stored in the object on the input molecule.

  • The new function OEUpdateCIFData will update the molecule’s CIF header data based on the molecule’s current structure.

  • The new function OESetMMCIFChemCompData was created to override mmCIF chemical component data on the molecule’s CIF header data.

  • The new function OEIsCIFHeaderCompliant takes the RCSB’s PDB Exchange Dictionary as input and checks if the CIF categories stored on the molecule are supported by the RCSB.

  • A new OEOFlavor for mmCIF, PerceiveMetadata, can be used to perceive all CIF header metadata at write time, based on the molecule’s structure.

  • Improvements have been made to CIF file reads that utilize chemical component header sections.

  • The OEIsDisulfideBridgeBond functor identifies inter-residue disulfide bridge bonds and follows the same bond identification criteria that was in the OEBio OEIsDisulfideBond functor.

  • The new OEIsAmideBond functor identifies inter-residue amide bonds.

  • The new OEIsIntraResidueBond functor identifies inter-residue bonds.

Major Bug Fixes

  • Improvements have been made to mmCIF file writes for stability to minimize overwriting data stored in the header.

  • Improved mmCIF file write stability has been added.

Minor Bug Fixes

  • A coding error in the assignment operator for OEMiniMol has been fixed.

  • An issue with invalid object pointers returned from OEGetAutomorphs has been fixed.

  • Various stability improvements to CIF header writes have been made.

  • An issue reading certain LINK records from PDB files has been fixed

OEBio TK 4.3.0

New Features

Major Bug Fixes

Minor Bug Fixes

  • The following were removed from the polymers category in the residue database: ZYA, R99, RL2, VSC, ZU5, S89, 0I5, 0D6, 0E6, ZRA, I0Y, and K36.

  • The OEIsDisulfideBond functor now uses the OEChem OEIsDisulfideBridgeBond functor for its implementation.

  • The covalent perception distance in design unit splitting to components has been relaxed.

OEGrid 4.3.0

New Features

OEDepict TK 2.6.0

Minor internal improvements have been made.

OEDocking TK 4.3.4

Minor Bug Fixes

  • An issue has been fixed where a receptor grid could not be constructed for covalently bonded ligands.

Eon TK 3.1.2

Minor internal improvements have been made.

FastROCS TK 2.3.1

Minor internal improvements have been made.

Grapheme TK 1.5.4

Minor internal improvements have been made.

GraphSim TK 2.7.0

New Features

  • New API functions have been added to explicitly provide access to virtual screening fingerprints which were previously generated with a subtle boolean function argument. See OEMakeVSFP and OEGetVSFPType.

  • New Python function has been added to create a NumPy Array from the bits stored in an OEFingerPrint. See OEFPToNumpyArray.

Minor Bug Fixes

Lexichem TK 2.9.4

Minor Bug Fixes

  • An issue has been fixed relating to IUPAC name generation where the term substituted was incorrectly inserted in certain cases.

  • A round-trip conversion issue between SMILES and IUPAC names has been resolved for cases where a SMILES string contained a single asterisk.

OEMedChem TK 1.2.5

Minor internal improvements have been made.

MolProp TK 2.6.7

Minor internal improvements have been made.

OEFF TK 2.9.1

Minor internal improvements have been made.

Omega TK 6.1.1

Minor Bug Fixes

Quacpac TK 2.2.7

Minor Bug Fixes

  • An issue that retained MDL-enhanced stereogroup information on stereocenters that are destroyed by protonation or bond order changes has been repaired.

Saiph TK 1.0.0

This is the first release of Saiph TK in C++ and Python.

New Features

Shape TK 3.9.0

New Features

  • The SetupRef method in OEOverlay now accepts molecules containing only color atoms. Accordingly, any molecule containing only color atoms or an OEShapeQuery containing only color Gaussians can now be used as a reference for overlay optimization.

  • The SetupRef method in OEOverlapFunc now accepts molecules and OEShapeQuery containing just color components.

  • A new class, OEHermiteOverlay, and a corresponding options class, OEHermiteOverlayOptions, are introduced, enabling overlays using the Hermite expansion approach. Three types of reference and database molecule representations are supported: Hermite vector, molecule, and scalar grid. Consequently, grid/grid overlays are enabled by using these classes.

  • The grid-to-Gaussians fit algorithm, to add Gaussians in an OEShapeQuery using AddShapeGaussians and AddColorGaussians, has been improved for better representation of the grid by the generated Gaussians. With the introduction of the modified algorithm, some of the associated options in OEShapeQueryOptions are no longer relevant and have been removed from the class API. The following functions have been removed:

    • GetDuplicateDistance and SetDuplicateDistance

    • GetMaxNumGaussians and SetMaxNumGaussians

  • A new overload has been added for Transform that enables transformation of a scalar grid by the rigid transformation in OEBestOverlayScore.

  • A new overload has been added for Setup that enables setting up OEStarts with known fit symmetry.

  • The following new methods have been added to OEHermite to enhance usability:

Minor Bug Fixes

  • An issue related to Init was causing intermittent slowdown in some API calls, especially in CUDA-enabled builds. This has been fixed.

Sitehopper TK 2.1.3

Minor internal improvements have been made.

Spicoli TK 1.6.3

Minor internal improvements have been made.

Spruce TK 1.8.0

New Features

  • The function OEBuildSingleLoop now checks for loop clashes after minimization. The option can be set using SetRejectClashingLoopsPostMinimization.

  • The function OEBuildSingleLoop can now delete residues already present at sites where a new loop needs to be built. The option can be set using SetDeleteExistingResidues.

  • The function OEBuildSidechains can now partially build target residues in the event that some targets fail.

  • Improved loop modeling has been added involving disulfide bridge creation by adding a bond length check.

  • When running with OESpruceFilter.FixResStates set to true, if the input molecule contains CIF header data, the filter will utilize the chemical component header section to inform a residue’s bond order and subsequent formal charge.

  • A new method, OESuperposeOptions.SetUseSeqScoreChainMatching, has been added to OESuperposeOptions that, when enabled, optimizes the sequence score over the overall RMSD when matching on multiple protein chains.

Major Bug Fixes

  • An issue has been fixed where gaps in the protein structure were misidentified due to unconventional insert code usage.

Minor Bug Fixes

  • Loop modeling results have been improved by setting OELoopBuilderOptions StrictProlineMatch to False by default. The updated default is due to an improved side chain building routine in a prior toolkit release.

  • An issue has been fixed to ensure loops extracted from the loop database had the desired structural properties.

  • When truncating a residue or converting a residue to a capping group, if that residue had a crosslink bond, the residue opposite would retain an atom in a bad valence state. That issue has been fixed.

  • An issue has been fixed in the routine to reassign ambiguous water and metals from packing residues to the protein chain of interest. The issue caused HEME-analogs and connected amino acids to be soaked into a given chain ID.

  • An issue has been fixed causing loop-relevant information with insert codes in an mmCIF header to be incorrectly read.

  • The OECapCTermini, OECapNTermini, and OECapTermini functions address an issue that could result in an incorrectly labeled cap residue SequenceID.

  • Several improvements were made to address performance issues in the OESpruceFilter.

Documentation Changes

  • Several examples have been added, and the advanced protein preparation tutorial has been expanded.

Szmap TK 1.7.3

Minor internal improvements have been made.

Szybki TK 2.9.1

Minor internal improvements have been made.

Zap TK 2.5.2

Minor internal improvements have been made.

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