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Release Notes

Release Highlights 2019.May

Windows Installer

The installer for Windows has been upgraded to a standard Windows MSI installer. This allows administrators to perform silent installation by executing the installer with the /quiet argument.

OEZ Compressed File Format

A new compressed file format, OEZ, has been introduced in OEChem TK. This format uses the zstd algorithm to efficiently compress individual multi-conformer molecules, making it well-suited to work with OEMolDatabase for fast read-only random access to molecules. Users can now use OEZ as the output format for OMEGA and as the input format for ROCS. For more details, see the Compressed Input and Output section of the OEChem TK documentation.

Note

This new file format is not backwards compatible. OpenEye applications and toolkits released before April 2019 will not be able to read or write this file format.

General Notices

  • MPI support for the applications on Linux and macOS is now based on Open MPI version 4.0.0.
  • GUI applications in the OpenEye applications bundle — vROCS, vBROOD, MakeReceptor, and pKa-Prospector — are not available on RHEL6. The RHEL6 package only includes command line tools.
  • All applications were ported to build using OEToolkits 2019.Apr. The previous versions were buiult using OEToolkits 2018.Oct.

Platform Support

  • This is the last release to support RHEL6
  • This is the last release to support Windows 7
  • Ubuntu 14 is no longer supported
  • macOS 10.11 and 10.12 are no longer supported

Detailed Release Notes

BROOD 3.1.1

May 2019

  • This version of BROOD has been built using OEToolkits 2019.Apr. The previous version was built using OEToolkits 2018.Oct.

Major bug fixes

  • BROOD now correctly finds analogs for queries that does not contain any color atoms.

EON 2.3.1

May 2019

  • This version of EON has been built using OEToolkits 2019.Apr. The previous version was built using OEToolkits 2018.Oct.

OEDocking 3.3.1

May 2019

  • This version of OEDocking has been built using OEToolkits 2019.Apr. The previous version was built using OEToolkits 2018.Oct.

Major bug fixes

  • POSIT now correctly uses the FRED method when there is no bound ligand in the receptor.
  • POSIT now correctly uses the FRED method when the similarity between the bound ligand and posed ligand is very low.

Minor bug fixes

  • The hybrid_Score.txt file now starts at 1 instead of 0 when labeling the poses, from a Hybrid calculation.

OMEGA 3.1.1

May 2019

  • This version of OMEGA has been built using OEToolkits 2019.Apr. The previous version was built using OEToolkits 2018.Oct.

New Features

Users can now use oez as the output format for OMEGA.

Major bug fixes

  • The default for -rotorOffsetCompress is set to true for all modes.
  • An issue that caused OMEGA to generate conformers with an occasional Coulombic collapse in the macrocycle mode for conformations of zwitterionic molecules has been fixed.

Minor bug fixes

  • The default for -enumNitrogen has been changed from true to unspecified so that any user-specified stereo information is not lost by default.
  • The flag -skip has been removed from MakeFraglib.
  • OMEGA calculations no longer repeat an error message.

pKa-Prospector 1.1.1

May 2019

  • This version of pKa-Prospector has been built using OEToolkits 2019.Apr. The previous version was built using OEToolkits 2018.Oct.

QUACPAC 2.0.1

May 2019

  • This version of QUACPAC has been built using OEToolkits 2019.Apr. The previous version was built using OEToolkits 2018.Oct.

New Features

  • New flag -wart added to pKaTyper to enable adding wart numbers with _ to each state.

Minor bug fixes

  • Failed molecules from a Tautomers run with .sdf.gz or .oeb.gz input are now written properly in a correspondiong .sdf.gz or .oeb.gz file.
  • Tautomers output now correctly adds wart to the molecule names, only when there are more than one tautomer.
  • Time required to generate an .sdf output from pKaTyper is now comparable to generating other formats of output.

ROCS 3.3.1

May 2019

  • This version of ROCS has been built using OEToolkits 2019.Apr. The previous version was built using OEToolkits 2018.Oct.

New Features

Users can now specify oez files as input to ROCS.

Major bug fixes

  • ROCS now properly handles empty query objects and queries consisting of only color atoms.
  • ROCS now properly handles molecules without coordinates.

Minor bug fixes

  • ROCS_ShapeQuery field now contains conformer ID when using -mcquery true.
  • ROCS no longer throws warning when used with a shape query that contains no molecule.

SZMAP 1.4.1

May 2019

  • This version of SZMAP has been built using OEToolkits 2019.Apr. The previous version was built using OEToolkits 2018.Oct.

Minor bug fixes

  • Output ligand box are now properly written in a .mol or .sdf file.

SZYBKI 1.10.1

May 2019

  • This version of SZYBKI has been built using OEToolkits 2019.Apr. The previous version was built using OEToolkits 2018.Oct.

Major bug fixes

  • freeform -calc solv has been fixed to properly calculate solvation energy when used with -solvcharges input.

Minor bug fixes

  • Occasional overflow of table contents in the freeform -calc conf generated report file has been eliminated.
  • Unreasonably high energy conformers information are clipped from the energy plots in the report generated from freeform -calc conf.
  • SZYBKI entropy calculation with -entropy AN no longer produces a crash.

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