Another get

Revision as of 17:03, 24 March 2020 by Yingyang (Talk | contribs)

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Another script modified on top of from Reed & Trent

First, set environment variable

source /nfs/home/yingyang/.cshrc_opencadd

Get help information:

python /nfs/home/yingyang/scripts/ -h
usage: [-h] [-d DIR] [-s SCORE] [-n NUM] [-f FILE] [-o OUT]
                    [-z GZ_FILE]
optional arguments:
 -h, --help  show this help message and exit
 -d DIR      path to where docking is located (default: )
 -s SCORE    path to where the extract all file is (default:
 -n NUM      number of molecules (poses) to get. (default: 500)
 -f FILE     file contained ligand names to extract (default: None)
 -o OUT      file name for poses (default: poses.mol2)
 -z GZ_FILE  file name for input (default: test.mol2.gz)

Example 1, get top 6k molecules from extract_all.sort.uniq.txt (in the docking directory). (getposes routine)

 python /nfs/home/yingyangg/scripts/ -s extract_all.sort.uniq.txt -n 6000 -o poses_top6k.mol2

Example 2, only get molecules with names listed in a file, and cut at top 10k.

 python /nfs/home/yingyangg/scripts/ -s extract_all.sort.uniq.txt -n 10000 -f <zincid.txt> -o poses_interested.mol2