Another get poses.py - Revision history

Yingyang at 01:19, 26 March 2020

2020-03-26T01:19:57Z

← Older revision		Revision as of 01:19, 26 March 2020
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	Poses are needed for Shuo's interaction filter and strain filter, sometimes we need to get poses pre-clustering. Owing to the need, here's another get_poses.py script modified on top of getposes_blazing_faster.py from Reed & Trent.		Poses are needed for Shuo's interaction filter and strain filter, sometimes we need to get poses pre-clustering. Owing to the need, here's another get_poses.py script modified on top of getposes_blazing_faster.py from Reed & Trent.

	The idea is that we only want to get one pose per zincid with the best dock score. So the script read extract_all.sort.uniq.txt file, and store the min_score for each zincid. When processing mol2.gz file, check if this molecule's mol2 with zincid matches the min_score, otherwise, skip to the next molecule.		The idea is that we only want to get one pose per zincid with the best dock score. So the script read extract_all.sort.uniq.txt file, and store the min_score for each zincid. When processing mol2.gz file, check if this molecule's mol2 with zincid matches the min_score, otherwise, skip to the next molecule.

Yingyang at 00:16, 25 March 2020

2020-03-25T00:16:27Z

← Older revision		Revision as of 00:16, 25 March 2020
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	~~Another~~ get_poses.py script modified on top of getposes_blazing_faster.py from Reed & Trent		3/25/2020 Ying

			Poses are needed for Shuo's interaction filter and strain filter, sometimes we need to get poses pre-clustering. Owing to the need, here's another get_poses.py script modified on top of getposes_blazing_faster.py from Reed & Trent.
			The idea is that we only want to get one pose per zincid with the best dock score. So the script read extract_all.sort.uniq.txt file, and store the min_score for each zincid. When processing mol2.gz file, check if this molecule's mol2 with zincid matches the min_score, otherwise, skip to the next molecule.

	First, set environment variable		First, set environment variable

Yingyang at 00:03, 25 March 2020

2020-03-25T00:03:50Z

← Older revision		Revision as of 00:03, 25 March 2020
Line 1:		Line 1:
	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		First, set environment variable
			source /nfs/home/yingyang/.cshrc_opencadd

	python /nfs/home/yingyang/scripts/get_poses.py -h		Get help information:
	usage: get_poses.py [-h] [-d DIR] [-s SCORE] [-n NUM] [-f FILE] [-o OUT]		python /nfs/home/yingyang/scripts/get_poses.py -h
	[-z GZ_FILE]		usage: get_poses.py [-h] [-d DIR] [-s SCORE] [-n NUM] [-f FILE] [-o OUT]
			[-z GZ_FILE]
	optional arguments:		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)

			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

Yingyang: 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..."

2020-03-24T23:55:43Z

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

source /nfs/home/yingyang/.cshrc_opencadd

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)