Release Notes

EON v2.2.0 (June 2013)

New features

  • The default hitlist format has been changed from sdf to oeb for increased functionality and decreased filesize. The output format is adjustable with the -oformat parameter.
  • The -spacing parameter has been added. This parameter can be used to adjust the grid spacing of the Zap/PB calculations. [Case 16576]
  • An option has been added to allow hydrogen atoms in -OH, -SH, and amines to take part in conformational sampling. This new option can be enabled via the -sampleHydrogens parameter. By default, hydrogen atoms are not sampled.
  • Now SD tags are prefixed with EON_. The tags are optional with the -sdTags parameter. Additionally, any existing ROCS tags will not be removed because ROCS and EON tags no longer conflict. [Case 10096]

Bug fixes

  • A bug has been fixed where the multiconformer check was being applied to OEB format files. Additionally, the default for -scdbase has been changed from false to true to prevent inadvertent merging of molecules with other file formats. [Case 16393]
  • Warnings have been improved for charging failures. [Case 14433]
  • -writegrid will now write out a grid with the same spacing as the actual Zap/PB calculation. Previously the attached grid had tighter spacing which could lead to confusion. [Case 13651]

Other changes

  • PVM (parallel virtual machine) is no longer supported. OpenMPI version 1.6 is supported on all plafforms. The -mpi_np and -mpi_hostfile flags are now used to run EON in MPI mode. These new flags replace the oempirun script.
  • This will be the last release to support SuSe 10.

EON v2.1.0

June 2011


  • The command line flags for choosing which charges to use have been simplified. There is a single flag -charges. The default is still to calculate MMFF charges. To use charges you have precalculated outside EON, first make sure you have charges for both the query and the dbase molecules, then use -charges existing.


    To use existing charges you must provide input files in a format that can store charges. This means input should be in either OEB or MOL2.

  • This release adds EON to the set of applications that now use a common script in openeye/bin to determine the appropriate architecture and run the appropriate binary.

  • On Windows, there is now an installer that installs the documentation and sets up a command prompt to facilitate running the EON command line.

Bug Fixes

  • Fixed a bug to ensure that SD data present in the database is passed on to the EON hitlist. Note that this is specific to SD data other than ROCS scores. Since EON can modify the conformation, any ROCS scores would no longer be valid so they are removed from the output. Note that the score reported as EON_ShapeTanimoto is the final Shape Tanimoto calculated from the best conformation found inside EON.
  • Fixed a bug that caused a crash when trying to write an empty hitlist.
  • Fixed a bug that prevented -salt from working.
  • Adding better error checking and messages for input. All input must be molecules and cannot be shape queries.

EON v2.0.0

August 2007


This is a significant new release of EON. This release incorporates many internal changes in how Electrostatic Tanimoto is calculated compared to EON 1.1.

  • Salt in the PB calculation is now on by default to help moderate large, local charges. This should make EON 2.0 perform much better then 1.1 in the case of molecules with formal charges.
  • OpenEye’s neutral pH model has been incorporated allowing the setting of a pH model on both the query and database molecules. Since a significant use of EON is similarity searching, having a consistent model between the query and database molecules is very important. However, for the case where the states are well defined, this feature can be turned off.
  • Instead of the slow and buggy -spin model for searching terminal torsions, EON 2.0 uses technology from OMEGA to only search reasonable torsions and to prevent creation of bad structures while searching for better electrostatic overlap.
  • The hitlist is now sorted by default by a new score, ET_combo, which is the sum of the Shape Tanimoto (ST) and the Electrostatic Tanimoto (ET_pb).
  • To make visualization of results easier, EON can write out the actual ET grids to the hits file, attached to each hit. This file can be loaded into VIDA 3.0 or later and the grids can be visually compared.
  • There are also several changes to the mechanics of running the calculation including a new -progress feature and a more detailed PVM log output for PVM jobs.

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List of Selected EON Publications