Example CommandsΒΆ
EON needs an input for a query file and a set of molecules in the database file.
So for example:
eon -in database_molecules.oeb.gz -query query.sdf -out EON_hits.oeb
will overlay and score all the structures in database_molecules.oeb.gz against the molecule in query.sdf and place the structures in
EON_hits.oeb (with ET scores in SD tag data) and a table of
results in eon_hitlist_rpt.csv.
To keep only the best 100 hits, use:
eon -in database_molecules.oeb.gz -query query.sdf -out EON_hits.oeb -maxhits 100
Note that the use of an output structure file is mostly for generation
of a single file containing structures and tag data such that loading
this single file into VIDA provides easy analysis of the results. If
however, the only real desire is for the numerical scores, simply do not use -out command line flag.
eon -in database_molecules.oeb.gz -query query.sdf
By default, EON calculates partial charges using MMFF94. However, if you have structure files that already contain good partial charges in both your dbase file and query file, you can tell EON to use them instead:
eon -in database_with_charges.mol2 -query query_chg.mol2 -charges existing -fixpka_query false -fixpka_dbase false
Please note that both -fixpka_query and -fixpka_dbase should
be set to false if -charges is set to existing; otherwise EON
will fail.
To prevent continually overwriting output files, the -prefix flag
allows you to give unique names to these files.
eon -in database_molecules.oeb.gz -query query.sdf -prefix FOO
will write the hit structures into a file named FOO_eon.oeb.gz and the
numerical values will be in FOO_hitlist_rpt.csv. The parameter file for this run will likewise be named FOO_parm.txt and the log file FOO_log.txt.
Finally, to create ET grids as used in the calculation and attach them to each output molecule. Note, this only works for OEB output and can be very memory intensive.
eon -in database_molecules.oeb.gz -query query.sdf -writegrid true -out EON_results_with_ET_grids.oeb