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.
Assuming a set of ROCS results for the previous chunker example are in a file called bar.list:
bar0000001_hits_01.sdf bar0000002_hits_01.sdf bar0000003_hits_01.sdf bar0000004_hits_01.sdf bar0000005_hits_01.sdf
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
- -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.