Example CommandsΒΆ
The simplest way to run EON is to use the -eon_input
flag in
ROCS to create a set of ROCS-aligned structures with the ROCS query at the
top of the file. By default, if EON is only provided a dbase file, it will
assume the first molecule is the query.
prompt> eon -dbase rocs_eon_input.oeb.gz
Or you can provide a single molecule in a query file and a set of molecules in a dbase file. A common example would be to use a ROCS query as the EON query and the ROCS hits file as the dbase file for EON.
So for example:
prompt> eon -dbase rocs_hits_1.oeb -query rocsquery.sdf
will score all the structures in rocs_hits_1.oeb
against the
molecule in rocsquery.sdf
and place the structures in
EON_hits.oeb
(with ET scores in SD tag data) and a table of
results in EON.rpt
.
To keep only the best 100 hits, use:
prompt> eon -dbase rocs_hits_1.oeb -query rocsquery.sdf -besthits 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, use
-nostructs
to suppress the creation of an output structure
file.
prompt> eon -dbase rocs_hits_1.oeb -query rocsquery.sdf -nostructs
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:
prompt> eon -dbase rocs_hits_chgs.mol2 -query rocsquery_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 over-writing output files, the -prefix
flag
allows you to give unique names to these files.
prompt> eon -dbase rocs_hits_1.oeb -query rocsquery.sdf -prefix FOO
will write the hit structures into a file named FOO_hits.oeb
and the
numerical values will be in FOO.rpt
. The parameter file for this run
will likewise be named FOO.parm
.
To prevent EON for searching alternate terminal torsions, use the
-scoreonly
flag.
prompt> eon -dbase rocs_eon_input.oeb.gz -scoreonly
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.
prompt> eon -dbase rocs_eon_input.oeb.gz -oformat oeb.gz -writegrid