OEApplications 2023.1

Release Highlights 2023.1.1

The OEApplications 2023.1.1 is a bug-fix of the OEApplications 2023.1.0 release.

Release Highlights 2023.1.0

Supported Platforms

OS

Versions

Linux

RHEL8/9, Ubuntu20/22

Windows

Win10, Win11

macOS

11,12, 13

Detailed Release Notes 2023.1

AFITT 2.6.3

Minor internal improvements have been made.

BROOD 3.2.1

Minor bug fixes

  • The default for the -property parameter in BROOD has been changed to False, so it is consistent with vBROOD.

EON 2.4.1

Minor internal improvements have been made.

Zap TK 2.4.5

Minor internal improvements have been made.

OEDOCKING 4.2.1.1

  • An issue where the shape contour could extend out of the user-defined box has been fixed. The grid will fill the initial box adjusting for grid spacing, and the resulting re-drawn box will be slightly larger to sit at the edge of the generated grid.

  • The generate shape contour button can now only be clicked a subsequent time if a different user selection has been made that would cause the contour to change.

OEDOCKING 4.2.1.0

Major bug fixes

  • Posit now correctly provides only the nonclashing poses in the generated output file when running with -num_poses greater than one and results in a mix of clashed and nonclashed poses for a particular ligand.

  • Posit now provides three-dimensional structures in the clashed output file.

  • An issue in Posit that caused occasional relaxation of nonclashing poses when running with the -relax option set to clashed has been fixed.

  • Possible inconsistent behavior and/or crashes in MakeReceptor, while editing custom constraints or selecting a constraint from the list of created constraints, have been fixed.

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

OMEGA 4.2.2

Minor bug fixes

  • Defaults for -warts and -flipper_warts have been changed to False in OMEGA.

  • OMEGA now fails robustly when incorrectly attempting to use -fixsmarts without providing -fixfile or turning -fromCT to false.

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.

MolProp TK 2.6.2

Minor internal improvements have been made.

PICTO 5.0.0

New features

  • The ability to display all matches from a SMARTS query at once by checking the All Matches checkbox has been added. After that checkbox is toggled, the inverse checkbox is available to display the inverse of all matches.

  • A tab system was added to the SMARTS window to cycle between substructure search (SS), maximum common substructure search (MCS), and clique search (CS). SS and MCS include a Unique Search checkbox. MCS and CS include a scoring method and the ability to set the minimum atoms needed for a match. MCS also includes a search method.

  • Visual feedback for an invalid SMARTS query has been added. The text will turn red if the SMARTS query is invalid, and it will remain black if the SMARTS query is valid.

  • The ability to read and display multimolecule input files has been added.

  • The ability to cycle through the OpenEye, Daylight, Tripos, MDL, AND MMFF aromatic models when the aromatic view is set to either Circle or Dashed has been added.

  • A swapped matches dropbox with a spinbox has been added. Pressing the Enter key after entering a SMARTS query will set the focus to the spinbox. The spinbox can be cycled by using the arrows displayed in the application, changing the match number, or using the arrow keys when the spinbox has focus.

  • A display for an InChI output and InChI input that can be utilized to depict a molecule has been added.

  • The ability to export depicted molecules to different file formats has been added.

  • A tool to assign and delete AAMapping to an atom and atom-to-atom mapping when depicting a reaction-based SMILES has been added.

Major bug fixes

  • A selection will now display a “C” for any carbon that is not selected but has all of its bonds selected. Deleting an atom no longer deletes any other atom associated with the deleted atom’s bonds.

  • The Undo button now goes directly back to the previous depiction and does not cycle through the intermediate steps of setting up the molecule.

  • The ability to manipulate molecules in the main sketcher has been enabled so all tools in the toolbar can be used when the explicit hydrogens are retained. The Input text box and isomeric SMILES output will now reflect the depicted molecules dependent on the Retain Explicit Hydrogens checkbox.

  • Highlighting the isomeric SMILES output will now change the input to the isomeric SMILES of the depicted molecule to allow highlighting through the Input textbox.

OEDepict TK 2.5.2

Minor internal improvements have been made.

pKa-Prospector 1.2.1

Minor bug fixes

  • The status bar message now properly updates in cases when no results are found from a Search.

QUACPAC 2.2.2

Minor internal improvements have been made.

Quacpac TK 2.2.2

Minor internal improvements have been made.

ROCS 3.6.0

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 2.0.3

Minor internal improvements have been made.

Sitehopper TK 2.0.3

Minor internal improvements have been made.

SPRUCE 1.5.2.1

  • Legal values for the targetMask flag have been added to docs and command-line help.

SPRUCE 1.5.2.0

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 1.6.6

Minor internal improvements have been made.

Szmap TK 1.6.6

Minor internal improvements have been made.

SZYBKI 2.6.0

Minor bug fixes

  • OptLigandInDU no longer attempts to write an empty molecule in the output file when the optimization fails.

  • OptimizeDu now fails with an appropriate message when attempting to optimize an apo design unit.

Szybki TK 2.6.0.1

  • New constant OEForceFieldType::SAGE_OPENFF210 has been introduced that refers to the Sage 2.1.0 force field. The constant OEForceFieldType::SAGE_OPENFF now refers to this latest version of Sage force field.

Szybki TK 2.6.0.0

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.

VIDA 5.0.4

Minor internal improvements have been made.