3.1 Command Line Interface

Executing Filter with no arguments will result in:

prompt> filter

Filter version 2.0.1
  OEChem version 1.4.2, 20070115
  Platform: microsoft-win32-g++3.3-i586
  OpenEye Scientific Software, Inc.

No argument specified on the command line
Required parameters:
    -in : Input filename
    -out : Output filename
For more help type:
  filter --help'

A description of the command line interface can be obtained by executing filter with the -help option.

prompt> filter --help

will generate the following output:

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

If you desire to see all of the command-line options use -help all.

prompt> filter --help all

will generate the following output:

Filter version 2.0.1, 20070115
  OEChem version 1.4.2, 20070115
  Platform: microsoft-win32-g++3.3-i586
  OpenEye Scientific Software, Inc.

Complete parameter list
    filter
      -dots : Write a dot to the terminal for every 500 cpds processed
      -fail : Write failed molecules to file
      -filter : Filter to use in filtering
      -in : Input filename
      -info : Write to specified info file (overrides -prefix)
      -interval : Update info file every N molecules
      -log : Write to log file
      -newrule : File listing additional filter rules and SMARTS
      -normalize : SMIRKS file for normalization of molecules
      -out : Output filename
      -param : Filter control parameter file
      -pkanorm : Apply a neutral pH model
      -prefix : Prefix all generic file output with this string
      -salt : Molecule file of salts to remove instead of calling strip salts
      -sdtag : Add all filter parameters as SD Tags
      -select : Smarts pattern to select for groups
      -table : Write complete output in table form
      -tableFlag : Flag failure values in table form with an asterix
      -typecheck : Check for broken molecules (impossible valence states)

Subsections

				FILTER Database preparation Property calculation

				FILTER Database preparation Property calculation