Another getposes.py - Revision history

Yingyang at 05:45, 6 October 2020

2020-10-06T05:45:47Z

← Older revision		Revision as of 05:45, 6 October 2020
Line 1:		Line 1:
	10/5/2020 Ying		10/5/2020 Ying
	~~Csh script~~ to run getposes.py strainfilter.py interfilter.py in parallel (on wynton):
			Script to run getposes.py strainfilter.py interfilter.py in parallel (on wynton):
	cd <path chunk folders from LSD>		cd <path chunk folders from LSD>
	cp ~yingyang/scripts/getposes_inter_strain.csh .		cp ~yingyang/scripts/getposes_inter_strain.csh .

	Edit the getposes_inter_strain.csh file to change the input to interfilter.py (http://wiki.bkslab.org/index.php/Interaction_Filtering):		Edit the getposes_inter_strain.csh file to change the input to interfilter.py (http://wiki.bkslab.org/index.php/Interaction_Filtering):

	- line 67: change to key residue		- line 67: change to key residue

	- line 68: change to path to rec.crg.pdb		- line 68: change to path to rec.crg.pdb

	Finally, run the script:		Finally, run the script:
	csh getposes_inter_strain.csh <absolute path to extract_all.sort.uniq.txt>		csh getposes_inter_strain.csh <absolute path to extract_all.sort.uniq.txt>

Yingyang at 05:44, 6 October 2020

2020-10-06T05:44:46Z

← Older revision		Revision as of 05:44, 6 October 2020
Line 1:		Line 1:
			10/5/2020 Ying
			Csh script to run getposes.py strainfilter.py interfilter.py in parallel (on wynton):
			cd <path chunk folders from LSD>
			cp ~yingyang/scripts/getposes_inter_strain.csh .

			Edit the getposes_inter_strain.csh file to change the input to interfilter.py (http://wiki.bkslab.org/index.php/Interaction_Filtering):
			- line 67: change to key residue
			- line 68: change to path to rec.crg.pdb
			Finally, run the script:
			csh getposes_inter_strain.csh <absolute path to extract_all.sort.uniq.txt>



	5/8/2020 Ying		5/8/2020 Ying

Yingyang at 04:47, 9 May 2020

2020-05-09T04:47:53Z

← Older revision		Revision as of 04:47, 9 May 2020
Line 1:		Line 1:
	5/8/2020 Ying		5/8/2020 Ying
	Getting more than one pose
			Getting more than one pose...

	Example of getting 3 poses for the top scored 6k molecules:		Example of getting 3 poses for the top scored 6k molecules:
	/nfs/home/yingyang/programs/miniconda3/envs/teachopencadd/bin/python \		/nfs/home/yingyang/programs/miniconda3/envs/teachopencadd/bin/python \

Yingyang at 04:42, 9 May 2020

2020-05-09T04:42:34Z

← Older revision		Revision as of 04:42, 9 May 2020
Line 1:		Line 1:
			5/8/2020 Ying
			Getting more than one pose
			Example of getting 3 poses for the top scored 6k molecules:
			/nfs/home/yingyang/programs/miniconda3/envs/teachopencadd/bin/python \
			/nfs/home/yingyangg/scripts/get_poses_multi.py -s extract_all.sort.uniq.txt -n 6000 -p 3 -o pose_top6k_x3.mol2



	4/20/2020 Ying		4/20/2020 Ying

Yingyang at 07:03, 20 April 2020

2020-04-20T07:03:15Z

@@ Line 1: / Line 1: @@
 /25/2020 Ying
@@ Line 27: / Line 35: @@
 Example 2, only get molecules with names listed in a file (for example, zincids of cluster heads), and cut at top 100k.
    python /nfs/home/yingyangg/scripts/get_poses.py -s extract_all.sort.uniq.txt -n 100000 -f <zincid.txt> -o poses_interested.mol2

Yingyang at 02:37, 20 April 2020

2020-04-20T02:37:40Z

← Older revision		Revision as of 02:37, 20 April 2020
Line 29:		Line 29:

	Directly call python also works...		Directly call python also works...
	/nfs/home/yingyang/programs/miniconda3/envs/teachopencadd/bin/python /nfs/home/yingyangg/scripts/get_poses.py -s extract_all.sort.uniq.txt -n 6000 -o pose_top6k.mol2		/nfs/home/yingyang/programs/miniconda3/envs/teachopencadd/bin/python /nfs/home/yingyangg/scripts/get_poses.py -s extract_all.sort.uniq.txt -n 6000 -o pose_top6k.mol2

Yingyang at 02:37, 20 April 2020

2020-04-20T02:37:11Z

← Older revision		Revision as of 02:37, 20 April 2020
Line 27:		Line 27:
	Example 2, only get molecules with names listed in a file (for example, zincids of cluster heads), and cut at top 100k.		Example 2, only get molecules with names listed in a file (for example, zincids of cluster heads), and cut at top 100k.
	python /nfs/home/yingyangg/scripts/get_poses.py -s extract_all.sort.uniq.txt -n 100000 -f <zincid.txt> -o poses_interested.mol2		python /nfs/home/yingyangg/scripts/get_poses.py -s extract_all.sort.uniq.txt -n 100000 -f <zincid.txt> -o poses_interested.mol2

			Directly call python also works...
			/nfs/home/yingyang/programs/miniconda3/envs/teachopencadd/bin/python /nfs/home/yingyangg/scripts/get_poses.py -s extract_all.sort.uniq.txt -n 6000 -o pose_top6k.mol2

Yingyang at 21:26, 31 March 2020

2020-03-31T21:26:53Z

← Older revision		Revision as of 21:26, 31 March 2020
Line 25:		Line 25:
	python /nfs/home/yingyangg/scripts/get_poses.py -s extract_all.sort.uniq.txt -n 6000 -o poses_top6k.mol2		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~~.		Example 2, only get molecules with names listed in a file (for example, zincids of cluster heads), and cut at top 100k.
	python /nfs/home/yingyangg/scripts/get_poses.py -s extract_all.sort.uniq.txt -n ~~10000~~ -f <zincid.txt> -o poses_interested.mol2		python /nfs/home/yingyangg/scripts/get_poses.py -s extract_all.sort.uniq.txt -n 100000 -f <zincid.txt> -o poses_interested.mol2

Yingyang: Created page with "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..."

2020-03-31T21:24:41Z

Created page with "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..."

New page

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
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

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Comparing the computation time:
[[File:runtime_getposes.png|thumb|center|375px]]