DU2OEBReceptor

Overview

DU2OEBReceptor is a utility program to convert a design unit, OEDU file, containing a receptor into a molecule based receptor, in OEB or OEB.GZ file.

Note

The molecule based OEB or OEB.GZ receptors are no longer the preferred form of receptor, and instead receptors inside design unit in OEDU are desired. The DU2OEBReceptor is provided for a handful of cases where receptors inside design units in OEDU format cannot still be used.

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

Example Commands

Convert a receptor OEDU file into an OEB.GZ receptor

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

Input files

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

Command line

prompt> DU2OEBReceptor receptor.oedu receptor.oeb.gz

Output files

• receptor.oeb.gz : OEB.GZ version of the receptor.

Command Line Help

A description of the command line interface can be obtained by executing DU2OEBReceptor with the –help option.

> du2oebreceptor --help

will generate the following output:

Help functions:
  du2oebreceptor --help simple      : Get a list of simple parameters
  du2oebreceptor --help all         : Get a complete list of parameters
  du2oebreceptor --help defaults    : List the defaults for all parameters
  du2oebreceptor --help <parameter> : Get detailed help on a parameter
  du2oebreceptor --help html        : Create an html help file for this program
  du2oebreceptor --help versions    : List the toolkits and versions used in the application

Required Parameters

-in <filename>

An OEDU 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 OEB or OEB.GZ file containing 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]