This utility takes as input a single molecule file (SD or OEB) or list file containing one or more molecules files. It will re-rank these input files by a user-defined SD tag. The most common use is to create a single hitlist after running ROCS on the separate files created by chunker.

Example Commands

Assuming a set of ROCS results for the previous chunker example are in a file called bar.list:


To merge these, rank by Tanimoto Combo and then keep the top 200.

prompt> hlmerge -in bar.list -out bar_hits.sdf -rankby ROCS_TanimotoCombo -besthits 200

Command Line Help

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

> hlmerge --help

will generate the following output:

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

Required Parameters

-in <filename>

Name of input file to rank, or the name of a list file (.lst or .list) containing a collection of files to rank.

-out <filename>

Output structure file for sorted hits. Formats other than SDF or OEB will lose the SD tag data.

-rankby <SD tag>

SD tag containing a score (that can be converted to a floating point value) to use as the score to rank with.

Optional Parameters

-besthits N

Number of hits to keep. [ default = 500 ]


By default, hits are ranked with higher scores meaning better results. To rank by a score where the smaller value is better, use -biggerisbetter false. [ default = true ]