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.
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.