OEB2DUReceptor

Overview

OEB2DUReceptor is a utility program to convert a molecule based receptor OEB or OEB.GZ file into a receptor inside OEDesignUnit, in OEDU file.

Note

The OEB2DUReceptor is not an utility to make a receptor. This is merely a converter for old receptor files, in OEB or OEB.GZ format, into a new OEDU format receptor.

To make a receptor, use the ReceptorInDU or the MakeReceptor.

Example Commands

Convert a receptor OEB.GZ file into an OEDU receptor

Converts the OEB.GZ receptor file into an OEDU receptor.

Input files

  • receptor.oeb.gz : OEB.GZ file to convert into an OEDU receptor.

Command line

prompt> oeb2dureceptor receptor.oeb.gz receptor.oedu

Output files

  • receptor.oedu : OEDU version of the receptor.

Command Line Help

A description of the command line interface can be obtained by executing OEB2DUReceptor with the --help option.

> oeb2dureceptor --help

will generate the following output:

Help functions:
  oeb2dureceptor --help simple      : Get a list of simple parameters
  oeb2dureceptor --help all         : Get a complete list of parameters
  oeb2dureceptor --help defaults    : List the defaults for all parameters
  oeb2dureceptor --help <parameter> : Get detailed help on a parameter
  oeb2dureceptor --help html        : Create an html help file for this program
  oeb2dureceptor --help versions    : List the toolkits and versions used in the application

Required Parameters

-in <filename>

An OEB or OEB.GZ file containing a receptor.

[keyless parameter 1]

Optional Parameters

Input Options

-molnames

This parameter specifies a text file containing a list of molecule names (one name per line in the file). If this parameter is set then only molecule in the input file(s) (see parameter -in) with names that match those in the text files will be read in.

The general purpose of this flag is to provide an easy mechanism for reading a few specific molecule(s) that are contained in a large database, without having to extract those molecules by hand from the database.

Output Options

-out <filename>

An OEDesignUnit file containing the receptor.

[keyless parameter 2]

-prefix

Prefix used to name output files.

-progress

Show progress on screen. Options are ‘none’, ‘dots’, ‘log’ and ‘percent’. The ‘dots’ options will displays dots on screen to show molecules completed. The ‘log’ option will duplicate the log file on screen. The ‘percent’ option will track progress through the input file. [default = none]