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Release Notes

Release Highlights 2018.Nov

First release of all OpenEye Applications as a single package

This is the first release of OpenEye Applications as a single package. It includes all the OpenEye Applications suites except for VIDA and AFITT. The applications are built on top of the 2018.Oct release of the OpenEye Toolkits.

The application suites available as part of the package are:

  • BROOD
  • EON
  • OEDocking
  • OMEGA
  • pKa-Prospector
  • QUACPAC
  • ROCS
  • SZMAP
  • SZYBKI

ROCS: ROCS

Shape TK has gone through a major re-engineering in the OpenEye Toolkits v2017.Oct release. This release brings the new technology to ROCS. One consequence is that overlay optimization in ROCS is now approximately 10% faster than in its previous release. Feature improvements of future versions of ROCS will be derived from this new foundation.

QUACPAC: Tautomers

This release adds several improvements to the Tautomers application in QUACPAC. Tautomer handling in molecular modeling and cheminformatics usually includes three important functions:

  • Generating a canonical protomer representation for duplicate-free storage
  • Generating a single tautomer suitable for visualization by chemists and modelers
  • Generating an ensemble of aqueous-phase tautomers suitable for molecular modeling
../../_images/tautomer-enumeration.png

Example of generating an ensemble of biologically relevant tautomers

Following the Quacpac TK 2.0 release in OpenEye Toolkits v2018.Oct , this release provides new APIs to cover each of these use-cases. Memory usage in cases where there are many possible tautomeric forms has been significantly improved.

General Notices

  • MPI support for the applications on Windows is now based on Microsoft’s implementation of MPI. For Linux and macOS, MPI support is still based on Open MPI.

Platform Support

  • RHEL6 (x64), RHEL7 (x64)
  • Ubuntu 14.04, Ubuntu16.04 (x64) LTS
  • macOS 10.11, 10.12, 10.13, 10.14
  • Windows 7/8.1/10 (64 bit)

Detailed Release Notes

BROOD 3.1.0

November 2018

  • This version of BROOD has been built using OEToolkits 2018.Oct. The previous version was built using OEToolkits 2015.Jun.

Minor bug fixes

  • The Documentation sub-menu of vBROOD now correctly points to the online documentation.

EON 2.3.0

November 2018

  • This version of EON has been built using OEToolkits 2018.Oct. The previous version was built using OEToolkits 2012.Oct.

OEDocking 3.3.0

November 2018

  • This version of OEDocking has been built using OEToolkits 2018.Oct. The previous version was built using OEToolkits 2015.Jun.

Major bug fixes

  • ScorePose no longer requires an OEChem TK license.

Minor bug fixes

  • The -force_planar_aromatic flag has been removed from POSIT.

OMEGA 3.1.0

November 2018

  • This version of OMEGA has been built using OEToolkits 2018.Oct. The previous version was built using OEToolkits 2017.Feb.

New features

  • A new fastrocs mode has been added to generate conformers for use in FastROCS.
  • All available options in OMEGA classic mode are now also available in the pose, rocs, fastrocs, and dense modes.
  • Four new options, mmff94smod, mmff94smod_NoEstat, mmff94smod_Trunc, and mmff94smod_Sheff, have been added to the -buildff flag of MakeFraglib. mmff94smod modifies the torsion interaction parameters of mmff94s to produce the desired equatorial conformers for monosubstituted cyclohexanes. mmff94smod_NoEstat includes all mmff94smod terms except Coulomb interactions. mmff94smod_Trunc excludes both Coulomb interactions and the attractive part of Van der Waals interactions. mmff94smod_Sheff includes all mmff94smod terms along with the Sheffield solvation model for calculation of energies.

Major bug fixes

  • Except for macrocycle, all OMEGA modes are now driven by the same executable. Previously, each mode had its own executable.

Minor bug fixes

  • An issue that caused the -maxtime option to be not honoured during torsion search has been fixed.
  • An issue that caused the -strictatomtyping option to fail to return False has been fixed.
  • An issue related to how the number of newly generated conformers per cycle is calculated for the macrocycle mode has been fixed.

pKa-Prospector 1.1.0

November 2018

  • This version of pKa-Prospector has been built using OEToolkits 2018.Oct. The previous version was built using OEToolkits 2013.Jun.

Minor bug fixes

  • Fixed the application so that the Visual C++ 2008 redistributable package (x86) is no longer required to run pKa-Prospector in Windows 10.

QUACPAC 2.0.0

November 2018

  • This version of QUACPAC has been built using OEToolkits 2018.Oct. The previous version was built using OEToolkits 2016.Feb.

New features

  • The tautomers functionality has gone through major improvements, and the Tautomer application options have been redesigned to take advantage of these improvements.
  • Keto-enol tautomerization has been added to improve the canonical grouping of unique molecules by their representative tautomers.

Major bug fixes

The following issues has been fixed in Tautomers:

  • The handling of keto-enol tautomerization by default has been improved. The improvement extends to include imine-enamine tautomerization and related analogs. The keto and imine forms are favored except in the case of 1,3 diketones, where the internal hydrogen bond can be formed.
  • The process for generating reasonable tautomers for many simple and complex pyridone analogs, pyrrole analogs, and pyridine analogs have been improved.
  • An issue that caused double bonds and hydrogens to move too far through a series of sp3 centers has been fixed.
  • The default behavior of peptide tautomers and peptide stereochemistry have been improved.

Minor bug fixes

  • pKaTyper‘s output now includes neutral species.

ROCS 3.3.0

November 2018

  • This version of ROCS has been built using OEToolkits 2018.Oct. The previous version was built using OEToolkits 2016.Oct.
  • The engine behind ROCS, Shape TK, has gone through a major re-engineering in the OpenEye Toolkits v2017.Oct release. With the introduction of Shape TK 2.0, overlay optimization in ROCS is now approximately 10% faster than in the previous release.

Major bug fixes

  • An issue that caused ROCS to crash when a shape query from Shape TK was used as a ROCS query has been fixed.
  • The Ligand Model Builder in vROCS now properly handles queries that contain no heavy atoms.

Minor bug fixes

  • The Documentation sub-menu of vROCS now correctly points to the online documentation.
  • Negative values and values larger than 1.0 for color Tanimoto are no longer reported.
  • The Rank by drop-down menu of the Options tab in vROCS validation has been modified to use the same score names as those used in the ROCS application.

SZMAP 1.4.0

November 2018

  • This version of SZMAP has been built using OEToolkits 2018.Oct. The previous version was built using OEToolkits 2013.Oct.

Major bug fixes

  • An issue related to running GamePlan in MPI mode has been fixed.

Minor bug fixes

  • Finding the location of the SZMAP application in GamePlan is no longer platform-dependent.

SZYBKI 1.10.0

November 2018

  • This version of SZYBKI has been built using OEToolkits 2018.Oct. The previous version was built using OEToolkits 2015.Oct.

New features

  • The Freeform application has been re-implemented to take advantage of the re-engineered functionality in Szybki TK.
  • The PDF report generated with Freeform has been improved for clarity.

Minor bug fixes

  • An issue that caused a SZYBKI entropy job to terminate if a molecule in a multi-molecule input file failed to process successfully has been fixed. If the entropy calculation fails on a particular molecule, the next molecule is now processed.