3.1 Command Line Interface

A description of the commandline interface can be obtained by executing EON with the -help option.

prompt> eon --help

will generate the following output:

Help functions:
  eon --help simple      : Get a list of simple parameters
  eon --help all         : Get a complete list of parameters
  eon --help <parameter> : Get detailed help on a parameter
  eon --help html        : Create an html help file for this program

3.1.1 Required Parameters

-dbase

File containing one or more 3D molecules to score against a reference or query molecule. If only this flag is given, EON will use the first molecule in the dbase file as the query and score all the remaining molecules against it. This is most useful when scoring ROCS results when ROCS was run with -eon_input equal to true since the ROCS query and therefore EON query will be the first in the input file. The query or reference molecule can also be specified separately using the -query flag below.

File format for -dbase can be one of:

File type	Extension
SDF	`.sdf .mol .sdf.gz .mol.gz`
MOL2	`.mol2 .mol2.gz`
PDB	`.pdb .ent .pdb.gz .ent.gz`
MacroModel	`.mmod .mmod.gz`
OEBinary v2	`.oeb .oeb.gz`
Old OEBinary	`.bin`

3.1.2 Optional Parameters

3.1.2.1 Input Options

-query: File containing one 3D molecule to use as a query. File format can be any of the formats given in the table for -dbase above.
-query_charges: Specifies charges to be used on the query. Default is to calculate them internally with mmff. Specifying file uses charges found in the query file. [default = mmff]
-dbase_charges: Specifies charges to be used on the dbase molecules. Default is to calculate them internally with mmff. Specifying file uses charges found in the database file. [default = mmff]
-scdbase: Since EON reads multi-conformer input molecules, when reading from non-binary files, EON will compare consectutive molecules and if they are determined to be the same structure, they will be concatenated into a single, multi-conformer molecule. If the user desires to score each input conformation independently, then using this flag will turn off the conformer comparison step. [default = false]
-param: Defines the control parameter file. This file can contain a collection of parameters which can be used instead of writing each parameter to the command-line. In addition, the parameter file written by any EON run (see -prefix below), can be used with the -param flag in subsequent EON executions. Any command given explicitly on the command line will supercede any command found in a file specified with the -param parameter.

3.1.2.2 Output Options

-oformat: Format of output structure file(s). The default is sdf so that ET score can be included as tag data. The format for the file is determined by giving the extension. Valid values include all formats listed above for -query except old OEBinary (bin). [default = sdf]
-prefix: Defines a prefix used to name output files. Using -prefix FOO will create a hits structure file named like FOO_hits.sdf and a report file, FOO.rpt [default = EON]
-besthits: Process entire dbase file but only keep N best scores sorted by property specified by -rankby. Default value of 0 implies no hitlist will be maintained and structures will all be scored and output in input order. [default = 0]
-maxhits: Stop after finding first N hits. This option overrides any setting for -besthits [default=0]
-rankby: Property to use to sort hitlist. Values include ET_combo, ET_pb and ET_coul. [default = ET_combo]
-outputquery: Write the query to the top of the hits file. This make visualization of results much easier inside VIDA.
-scoreonly: Turn off the terminal torsion conformer search and just score each input conformation as-is.
-hitsfile FILE: Explicit filename for writing hits. Overrides the default filename created from -prefix.
-reportfile FILE: Explicit filename for writing hits. Overrides the default filename created from -prefix.
-nostructs: Giving this flag suppresses the generation of a structure output file. Useful if only numeric values in the report file are desired. [default = false]

3.1.2.3 Log Output Options

-logfile FILE

Filename for log file. Overrides log filename created from -prefix.

-progress

Method for showing job progress on the command line. Choices include:

percent - show a percent complete progress bar (DEFAULT)
log     - echo the log message for each molecule
dots    - show dots as in EON 1.1
none    - print nothing to console

-verbose

Give verbose output to console instead of simple progress. [default = false]

3.1.2.4 ZAP/PB Options

-fixpka_query: Apply a neutral pH model to the query molecule. [default = true]
-fixpka_dbase: Apply a neutral pH model to the database molecules. [default = true]
-salt: Add salt to the Zap calculation. To aid in moderating large, local charges, salt is added into the calculation. Legal values are between 0.0 and 0.1 (mM). [default = 0.04]
-writegrid: Write ET grid to output attached to each molecule. Useful for visualization in VIDA but this only works when writing hits to an OEB (.oeb or .oeb.gz) file. Note that while this feature is quite useful, grids do take a large amount of memory so care should be taken when using this feature for hit lists of more than 500 molecules. [default = false]

3.1.2.5 PVM Options

-pvmconf FILE: Causes ROCS to run in PVM mode using the hosts defined in FILE. A complete description of PVM setup is beyond the scope of this section, but more information can be found in chapter 4.3.
-pvmlog FILE: Actual filename for writing PVM log and status info during the run. This overrides the default PREFIX.pvmlog.
-pvmpass N: Determines number of molecules passed to each slave in a given message. Can be a useful tuning parameter, but for the most part this should be left at the default. [default = 20]