5.6 Screen output

All screen output in FRED is sent to stderr.

The following is example screen output from a simple FRED run.

ninja:~/TESTING/FRED-docs> fred -rec rec1ppx.oeb.gz
          :jGf:                .o88o.                          .o8
        :jGDDDDf:              888 `'                         '888
      ,fDDDGjLDDDf,           o888oo  oooo d8b  .ooooo.   .oooo888
    ,fDDLt:   :iLDDL;          888    `888""8P d88' `88b d88' `888
  ;fDLt:         :tfDG;        888     888     888ooo888 888   888
,jft:   ,ijfffji,   :iff       888     888     888    .o 888   888
     .jGDDDDDDDDDGt.          o888o   d888b    `Y8bod8P' `Y8bod88P'
    ;GDDGt:''':tDDDG,
   .DDDG:       :GDDG.         Copyright (c) 2003,2004,2005,2006
   ;DDDj         tDDDi         OpenEye Scientific Software, Inc.
   ,DDDf         fDDD,         Licensed to OpenEye Scientific Software
    LDDDt.     .fDDDj          Version: 2.2 (Build date 20060810)
    .tDDDDfjtjfDDDGt           OEChem version: 1.4.2 debug 20060810
      :ifGDDDDDGfi.            Platform: linux-2.6-g++4.1-i586
          .:::.                Supported Run Modes:
  ......................         Single processor
  DDDDDDDDDDDDDDDDDDDDDD         PVM Multiprocessor (PVM Slavename : FRED)
  DDDDDDDDDDDDDDDDDDDDDD

----------------------------------------
#Interface settings

#Inputting Ligands :
    -dbase  ph_conf.oeb.gz

#Receptor Site :
    -rec  rec1azm.oeb.gz

Writing settings to : setup.txt
Run status will periodically be written to : status.txt

-----Receptor Information-----
  Site box volume      : 5579
  Outer contour volume : 1454
  Inner contour volume : 96
  Has bound ligand "_"
  Writing a copy of the receptor to receptor.oeb.gz

-----Ligand Database Information-----
Parsing ligands Done.
  1 molecules
  152 conformers

-----Docking Summary-----
  1) Exhaustive search will generate 100 using Chemgauss3
  2) Poses will be solid body optimized with Chemgauss3

-----Docked hitlists summary-----
  Sorted hitlists : TRUE
  Hitlist size : 1000

  --Structure files--
    Chemgauss3 : chemgauss3_docked.oeb.gz

  --Tab delimited score files--
    Chemgauss3 : chemgauss3_scores.txt

Note : Chemgauss3 scoring selected by default


Initializing docking
Exhaustive Search ..........Done.
Chemgauss3 ..........Done.
............x.x.............................x....x..............................
.....x.....................................x.....x......x......................
.................x.............................................................
................................x..........x.....................x.............
..x....x.x.....................xx....................................x.........
...............................x.....................x.........................
....................x..............x....................................x......
..x....x........x...x..........................................................
....x................................x...xx........x.x..................x......
........x......................................................................
...xx...............x......................x...x......x..........xx..x.........
..x..x...x..........x.............................x.........................x..
.......x...................x.......x..............

----------------------------------------
Outputing hitlists
Finished

The large block of .'s and x's are written to the screen as FRED docks molecules. Each . represents and sucessfully docked molecule, while each x represents a molecule that could not be docked and was sent to one of the undocked lists (see section 4.4.2). Any W characters that appear during docking indicate a warning was issued and sent to the warning log (see section 5.7.4). The remaining screen output is generally self explanatory.

				FRED Fast Rigid Exhaustive Docking

				FRED Fast Rigid Exhaustive Docking