OEApplications 2023.2

Release Highlights 2023.2.3

  • Sage force field (Sage 2.1.0), from the Open Force Field Consortium, is now available in OMEGA as a complement to MMFF94.

  • The defaults for Sage force field from the Open Force Field Consortium have been updated to the latest 2.1.0 version, everywhere Sage is supported.

  • The built-in fragment library in OMEGA has been updated; expanding on 80 K fragments in the previous library, the new fragment library contains approximately 540 K fragments.

  • Stereo-enumeration options in Flipper have been improved to allow fine-grained control over enumerating different types of atom and bond stereocenters in an uncoupled manner.

  • The torsion scanning algorithm in SZYBKI has been improved by adding the ability to optimize in internal coordinate space.

  • Protein–ligand optimization with FF14SB-OpenFF in SZYBKI has been improved for performance and robustness.

  • Support for PDBx/mmCIF in OEChem TK has been improved, following the format updates to PDB entries by wwPDB. The MMCIF reader now runs on Gemmi version 0.6.2.

  • A preliminary API has been added to provide reaction automapping ability, based on the maximum common substructure, enhancing reaction support in OEChem TK.

  • Python toolkit packaging has been improved to use pyproject.toml to declare metadata and dependencies.

Supported Platforms

OS

Versions

Linux

RHEL8/9, Ubuntu20/22

Windows

Win10, Win11

macOS

12, 13

Detailed Release Notes 2023.2

AFITT 2.6.4

Minor internal improvements have been made.

BROOD 3.2.2

Minor bug fixes

  • BroodDBMerge can now merge databases built from any version of 3.x.

Minor internal improvements have been made.

EON 2.4.2

Minor internal improvements have been made.

Zap TK 2.4.6

New features

  • New overloads of GetArea have been added that return solvent accessible surface areas for specific residues.

OEDOCKING 4.3.0

Minor bug fixes

  • POSIT now correctly outputs the status of relaxation, indicating if flexible optimization was performed on the generated pose.

  • Closing out of the save dialog in MakeReceptor no longer causes a “Failed Save” message.

  • Constraint spheres now appear with appropriate colors when viewed in the Finish tab of MakeReceptor.

OEDocking TK 4.3.0

New features

Major bug fixes

  • An issue has been fixed where relaxation failed in OEPosit when the pose relaxation mode was set to either ALL or CLASHED.

  • An issue causing generation of bent ring structures and high strain poses when performing OEPosit has been fixed.

  • An issue has been fixed that caused flexible OEPosit with ALL relaxation mode to fail while generating nonclashing poses when NONE was successful.

Minor bug fixes

  • An issue where Dock passed too many conformers for flexible optimization with relaxation in OEPosit has been fixed. Now, OEShapeFit no longer passes too many conformers for flexible optimization that could occasionally cause a less accurate conformer to become the top predicted pose.

  • The Dock method with relaxation has been modified to be more aligned with other modes of failure when ligand charge assignments fail.

OMEGA 5.0.0

New Features

  • The default fragment library in OMEGA has been updated in Linux and OSX platforms. The new fragment library consists of over 580 K fragments, replacing the previous library of ~80 K fragments. OMEGA in Windows still uses the previous library as default, but the modified library, omega_fragment_lib_2023.oeb.gz, is available through the -addfraglib on the database downloads page.

  • A new parameter, -failed, has been added to OMEGA to allow reporting the failed molecules into a separate file.

Major bug fixes

  • Running OMEGA with -fixfile and -mpi_np now appropriately picks up the file for fixing part of molecule.

  • Output rpt.csv file from OMEGA now contains SMILES strings for most molecules. The entry is still blank for extremely large molecules that are beyond 400 atoms.

Minor bug fixes

  • Running OMEGA with one molecule in the classic/pose/dense/rocs/fastrocs modes and using -progress percent no longer causes the input molecule to be read twice.

Omega TK 5.0.0

New features

  • The default fragment library for OEOmega and OEMolBuilder has been updated. The new fragment library consists of over 580 K fragments, replacing the previous library with ~80 K fragments.

  • Three new force fields have been added and can be used with OEMolBuilder and OETorDriver in OEOmega:

  • The behavior of OEFlipperOptions has changed. New flags have been added to OEFlipperOptions, facilitating more complete decoupling of individual flags and more selective enumeration of specific stereocenter classes and environments than was previously possible.

  • A new option class, OEFlipperClassicOptions, has been added to allow a detailed comparison of the new flag behaviors with the previous OEFlipper enumeration behavior. This class will be deprecated in a future toolkit release.

  • The internal algorithm for storage and usage of torsion rules in OETorLib has been modified to improve performance when working with a library containing a large set of rules.

  • A new return code FailedCharges has been added to OEOmegaReturnCode to indicate failures due to partial charge assignment.

Minor bug fixes

  • The order of torsion rules in the default OETorLib has been changed to ensure that a specific rule is not ignored due to the presence of a more generic rule.

MolProp TK 2.6.3

Minor internal improvements have been made.

PICTO 5.1.0

New features

  • The inverse checkbox can now be toggled with individual matches, highlighting all atoms that were not a hit on a singular molecule.

  • A new chemistry drop-down menu adds support for reaction automapping of the reactants and products based on Maximum Common Substructure Search.

Major bug fixes

  • PICTO now properly handles reaction changes through the sketcher.

  • An issue where PICTO highlighted bonds that didn’t have matches with the substructure search was fixed.

Minor bug fixes

  • Minor changes were made to the pop-up window for a missing license file.

OEDepict TK 2.5.3

Minor internal improvements have been made.

pKa-Prospector 1.2.2

Minor internal improvements have been made.

QUACPAC 2.2.3

Quacpac TK 2.2.3

Minor internal improvements have been made.

ROCS 3.6.1

Minor bug fixes

  • Multiple successive runs of vROCS now correctly provide default job names.

Minor internal improvements have been made.

Shape TK 3.6.1

Major bug fixes

  • Memory consumption when initiating an OEColorForceField has been reduced by moving instantiation of internal OESubSearch-based colorer objects to a lazy instantiation mode.

SiteHopper 2.0.4

Sitehopper TK 2.0.4

Minor internal improvements have been made.

SPRUCE 1.5.3

Minor internal improvements have been made.

Spruce TK 1.5.3

New features

  • The chemical components dictionary was updated with latest data from the RCSB.

Major bug fixes

  • An issue that caused OESpruceFilter to segfault has been fixed and safeguarded.

Minor bug fixes

  • An issue has been fixed that caused incorrectly built loops when the protein structure contains nonstandard amino acids, particularly in the gap needing to be built or anchoring to it.

  • An issue with sequence mutation for cysteine residues, where an explicit hydrogen was left over after the mutation, has been fixed.

SZMAP 1.6.7

Szmap TK 1.6.7

Minor internal improvements have been made.

SZYBKI 2.7.0

Szybki TK 2.7.0

New features

Major bug fixes

Minor bug fixes

  • Validation of user-selected torsion in torsion scan has been added. If a torsion passed to function OETorsionScan or method Scan does not exist, the torsion scan code stops with a message that the torsion does not exist in the input molecule.

VIDA 5.0.5

Minor internal improvements have been made.