A. Param Files

Omega's command-line interface can be efficiently run using the -param command line parameter followed by the name of a .param-file. Param files are simply files that contain one command-line parameter on each line. Every execution of omega generates a .param file called prefix.param. This file contains all of the parameters used by Omega. Further, this file can be used in subsequent Omega runs with the -param flag either with or without user modifications.

The following execution will generate a .parm file called "omega.parm" which is listed below. This file could be edited and used with subsequent Omega runs.

prompt> omega2 -in drugs.smi -out drugs.oeb.gz

Listing of "omega.parm":

#Interface settings
#File Options :
    -commentEnergy  false (default)
    -in  drugs.smi
    -includeInput  false (default)
    #-log (Not set, no default)
    -out  drugs.oeb.gz
    #-param (Not set, no default)
    -prefix  omega2 (default)
    -rotorOffsetCompress  true (default)
    -sdEnergy  false (default)
    #-status (Not set, no default)
    -verbose  false (default)
    -warts  false (default)

#3D Construction Parameters :
    #-addfraglib (Not set, no default)
    -buildff  mmff94s_NoEstat (default)
    -canonOrder  true (default)
    -deleteFixHydrogens  true (default)
    #-dielectric (Not set, no default)
    #-exponent (Not set, no default)
    #-fixfile (Not set, no default)
    -fixrms  0.150000 (default)
    -fromCT  true (default)
    -maxmatch  10 (default)
    #-setfraglib (Not set, no default)
    -umatch  true (default)

#Structure Enumeration :
    -enumNitrogen  true (default)
    -enumRing  true (default)

#Torsion Driving Parameters :
    #-erange (Not set, no default)
    -ewindow  10.000000 (default)
    #-maxConfRange (Not set, no default)
    -maxconfgen  50000 (default)
    -maxconfs  400 (default)
    -maxrot  -1 (default)
    -maxtime  120.000000 (default)
    -rangeIncrement  5 (default)
    -rms  0.800000 (default)
    #-rmsrange (Not set, no default)
    -searchff  mmff94s_Trunc (default)
    #-torlib (Not set, no default)

#PVM Parameters :
    #-pvmconf (Not set, no default)
    -pvmdebug  false (default)
    #-pvmlog (Not set, no default)
    -pvmpass  10 (default)

				OMEGA C++ Toolkit

				OMEGA C++ Toolkit