Difference between revisions of "Another get poses.py"

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(Created page with "Another get_poses.py script modified on top of getposes_blazing_faster.py from Reed & Trent source /nfs/home/yingyang/.cshrc_opencadd python /nfs/home/yingyang/scripts/get_p...")
 
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Another get_poses.py script modified on top of getposes_blazing_faster.py from Reed & Trent
 
Another get_poses.py script modified on top of getposes_blazing_faster.py from Reed & Trent
  
source /nfs/home/yingyang/.cshrc_opencadd
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First, set environment variable
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source /nfs/home/yingyang/.cshrc_opencadd
  
python /nfs/home/yingyang/scripts/get_poses.py -h
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Get help information:
usage: get_poses.py [-h] [-d DIR] [-s SCORE] [-n NUM] [-f FILE] [-o OUT]
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python /nfs/home/yingyang/scripts/get_poses.py -h
                    [-z GZ_FILE]
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usage: get_poses.py [-h] [-d DIR] [-s SCORE] [-n NUM] [-f FILE] [-o OUT]
 
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                    [-z GZ_FILE]
optional arguments:
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optional arguments:
 
   -h, --help  show this help message and exit
 
   -h, --help  show this help message and exit
 
   -d DIR      path to where docking is located (default: )
 
   -d DIR      path to where docking is located (default: )
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   -o OUT      file name for poses (default: poses.mol2)
 
   -o OUT      file name for poses (default: poses.mol2)
 
   -z GZ_FILE  file name for input (default: test.mol2.gz)
 
   -z GZ_FILE  file name for input (default: test.mol2.gz)
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Example 1, get top 6k molecules from extract_all.sort.uniq.txt (in the docking directory). (getposes routine)
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  python /nfs/home/yingyangg/scripts/get_poses.py -s extract_all.sort.uniq.txt -n 6000 -o poses_top6k.mol2
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Example 2, only get molecules with names listed in a file, and cut at top 10k.
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  python /nfs/home/yingyangg/scripts/get_poses.py -s extract_all.sort.uniq.txt -n 10000 -f <zincid.txt> -o poses_interested.mol2

Revision as of 17:03, 24 March 2020

Another get_poses.py script modified on top of getposes_blazing_faster.py from Reed & Trent

First, set environment variable

source /nfs/home/yingyang/.cshrc_opencadd

Get help information:

python /nfs/home/yingyang/scripts/get_poses.py -h
usage: get_poses.py [-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:
             extract_all.sort.uniq.txt)
 -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/get_poses.py -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/get_poses.py -s extract_all.sort.uniq.txt -n 10000 -f <zincid.txt> -o poses_interested.mol2