Toolkit Version 2023.1

Detailed Release Notes 2023.1

OEChem TK 3.4.0

New features

Minor bug fixes

  • Reaction mapping semantics for SMARTS queries which force the query mapping to the respective reactants or products in the target have been activated. Previously, reaction SMIRKS queries would hit either reactants or products regardless of the presence of the >>. To restore the old behavior, remove the >> from query patterns.

  • An issue with the OEIsTermHeavyAtom predicate, which did not properly account for atom type and implicit or explicit hydrogen environments of the interrogated atom, has been fixed.

  • An issue in which the status of double ether bonds was not maintained when exported in V3000 format has been fixed.

  • An issue in which the nondefault output flavor flags could not be used with the OEFormat::CXSMILES format has been fixed.

  • An issue with buffer overrun for V2000 SDF parsing that could result in erroneous application of properties from prior parsed lines has been fixed.

  • An issue with stale OEGroup pointers that could result in a crash for molecule copy operations has been fixed.

Python-specific changes

  • An option has been added to the molcount.py example that allows use of an Omega-specific ContTest handling for Omega generated conformer inputs.

OESystem TK 3.3.1

Minor internal improvements have been made.

OEPlatform TK 3.3.1

Minor internal improvements have been made.

C++-specific changes

  • The code has been changed to define the statement “NOMINMAX” to trigger only if not already set.

OEDepict TK 2.5.2

Minor internal improvements have been made.

OEDocking TK 4.2.1

New features

Major bug fixes

  • The Dock method in OEPosit now returns poses instead of a failure, if there is a failure during flexible optimization.

  • An issue that caused intermittent crash for specific calculations on specific platforms when working with OEPosit has been fixed.

  • OEPosit now accurately returns NoValidNonClashPoses as status when the predicted pose contains clashes based on the defined clash allowed type. Note that the clashed poses can still be retrieved from the resulting OESinglePoseResult if desired.

Minor bug fixes

Documentation changes

FastROCS TK 2.2.4

Minor internal improvements have been made.

Grapheme TK 1.4.7

Minor internal improvements have been made.

GraphSim TK 2.5.6

Minor internal improvements have been made.

Lexichem TK 2.8.1

Minor internal improvements have been made.

OEMedChem TK 1.2.0

Internal changes

MolProp TK 2.6.2

Minor internal improvements have been made.

OEFF TK 2.5.2

Major bug fixes

  • The OEComplexFF class is now derived from OEMolFunc2 and has limited support for second derivatives when the protein is fixed.

Omega TK 4.2.2

Minor bug fixes

  • The OEOmega method Build will now fail when MCS matching is requested but a corresponding FixMol has not been set.

Quacpac TK 2.2.2

Minor internal improvements have been made.

Shape TK 3.6.0

New features

  • OEFlexiOverlapFunc and OEFlexiOverlay have been updated to allow users to use a Shape Query as the reference system. This allows OEFlexiOverlapFunc SetupRef and OEFlexiOverlay SetupRef to accept a Shape Query.

  • A new method, SetupFlex, has been added. This method can be used to set up overlap calculation functions when molecules are expected to be flexible and their self overlaps are not fixed to the initial value.

  • A new method, SortedOverlay, has been added as an alternative to Overlay. This method provides a desired number of top hit results instead of all of the hits and is especially suitable when working with molecules with excessive numbers of conformers.

  • Two additional control flags, GetRigidOverlay and SetRigidOverlay, have been added to the OEFlexiOverlayOptions class. These flags indicate if rigid overlay optimization between the fit molecule conformers and the reference system should be performed prior to the flexible optimization.

Major bug fixes

  • An issue in OEFlexiOverlay that caused a TanimotoCombo value greater than 2.0 when a molecule was flexibly fitted against itself has been fixed.

Minor bug fixes

  • The default value for the color function in OEFlexiOverlapOptions during OEFlexiOverlay has been changed from none to exact. This ensures that color overlaps are reported when flexible optimization is performed with default parameters.

  • An issue has been fixed with OEFlexiOverlay that was causing shape Tanimoto to be occasionally reported as larger than 1.0 after a flexible optimization.

  • The legal range of values for the color score multiplier has been added to the OEFlexiOverlapOptions and OEOverlayOptions option classes.

  • OEColorFFParameter now allows users to select explicitmillsdeannorings properly as the color force field.

  • The acceptable ranges for the number of optimization iteration steps have been defined for OEFlexiOverlayOptions and OEOverlayOptions.

  • Newer implementation of Hermite code had limits on lambda parameters of the expansion. In rare cases, these were affecting the lambda parameter search (Newton optimization stepping outside the limits). Removing the limits fixed the previous problems with finding lambda parameters.

Sitehopper TK 2.0.3

Minor internal improvements have been made.

Spicoli TK 1.5.6

Minor internal improvements have been made.

Spruce TK 1.5.2

New features

  • OESpruceFilterOptions has an option to automatically assign chain IDs (default is true) when they are missing either completely or partially in the structure for a structure processed by OESpruceFilter.

  • The built-in heterogen database has been updated with the latest structures from the ligand-expo at the RCSB.

Major bug fixes

  • An issue where tautomers passed using metadata were not respected has been fixed.

  • An issue has been fixed where, in a small fraction of cases, an OXT atom was not correctly built out when needed at the protein C-terminals.

  • An issue has been fixed where the option to fix the state of backbone atoms and bonds in OESpruceFilterOptions was sometimes not respected in OESpruceFilter, which led to issues such as OXT atoms being built even if the option was disabled.

Minor bug fixes

  • An issue was fixed in filter options to not accept the disallowed residue names UNL and UNK. Instead, they are renamed to LIG, which is a change filter that applies in the structure upon standardization.

  • An issue where the maximum number of atoms in the biological unit was not being respected has been fixed.

Documentation changes

  • Minor documentation and example improvements have been fixed.

Szmap TK 1.6.6

Minor internal improvements have been made.

Szybki TK 2.6.0

New features

Major bug fixes

  • An issue with the torsion scan (OETorsionScan) in solution with PB solvation has been fixed. It no longer incorrectly uses the MMFF94S potential even when scanning is done with the OpenFF force field.

  • An issue with hysteresis that in certain cases caused asymmetric torsion scans has been addressed by resetting to the starting angle before starting reverse scans.

Minor bug fixes

  • Better diagnostics have been added to OEFixedProteinLigandOptimizer when the optimization of a ligand in a fixed protein receptor fails due to an initial clash. An appropriate error code is now returned for such cases.

  • OEFlexProteinLigandOptimizer now provides an appropriate error code when asked to optimize a design unit that does not contain a ligand.

Zap TK 2.4.5

Minor internal improvements have been made.