ECFP4 Best First Clustering - Revision history

Jklyu at 15:51, 19 September 2017

2017-09-19T15:51:18Z

← Older revision		Revision as of 15:51, 19 September 2017
Line 18:		Line 18:
	Then run the command below		Then run the command below

	setenv BFCPATH = "/mnt/nfs/home/jklyu/zzz.github/ChemInfTools/utils/best_first_clustering_uint16/"		setenv BFCPATH "/mnt/nfs/home/jklyu/zzz.github/ChemInfTools/utils/best_first_clustering_uint16"
	${BFCPATH}/best_first_clustering_uint16 /path/fingerprint.file /path/count.file /path/smiles.file tc.thres.val max.num.val		${BFCPATH}/best_first_clustering_uint16 /path/fingerprint.file /path/count.file /path/smiles.file tc.thres.val max.num.val

Jklyu at 15:50, 19 September 2017

2017-09-19T15:50:08Z

← Older revision		Revision as of 15:50, 19 September 2017
Line 18:		Line 18:
	Then run the command below		Then run the command below

	/mnt/nfs/home/jklyu/zzz.github/ChemInfTools/utils/best_first_clustering_uint16/best_first_clustering_uint16 (1) fingerprint file (2) count file (3) smiles file (4) tanimoto coefficient threshold to define clustering (5) max number of clusters		setenv BFCPATH = "/mnt/nfs/home/jklyu/zzz.github/ChemInfTools/utils/best_first_clustering_uint16/"
			${BFCPATH}/best_first_clustering_uint16 /path/fingerprint.file /path/count.file /path/smiles.file tc.thres.val max.num.val

			syntax: best_first_clustering_uint16
			(1) fingerprint file
			(2) count file
			(3) smiles file
			(4) tanimoto coefficient threshold value to define clustering (must be between 0.0 and 1.0)
			(5) max number of clusters (must be an integer)

Jklyu at 05:35, 19 September 2017

2017-09-19T05:35:47Z

@@ Line 1: / Line 1: @@
 Written by Jiankun Lyu, 2017/09/13
 Run the script at where your extract_all.sort.uniq.txt locates
@@ Line 9: / Line 11: @@
 For clustering top1M molecules, it usually takes about 6 hours. Please do not cluster more than 1M molecules by this script.

TBalius at 23:16, 13 September 2017

2017-09-13T23:16:59Z

← Older revision		Revision as of 23:16, 13 September 2017
Line 6:		Line 6:
	Example:		Example:
	csh ~jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering.csh 1000000 0.5		csh ~jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering.csh 1000000 0.5
	so you will cluster top1M molecules from a docking run with tc cutoff 0.5.		so you will cluster top1M molecules from a docking run with tc cutoff 0.5.
	For clustering top1M molecules, it usually takes about 6 hours. Please do not cluster more than 1M molecules by this script.
			For clustering top1M molecules, it usually takes about 6 hours. Please do not cluster more than 1M molecules by this script.

Jklyu at 20:41, 13 September 2017

2017-09-13T20:41:40Z

← Older revision		Revision as of 20:41, 13 September 2017
Line 1:		Line 1:
			Written by Jiankun Lyu, 2017/09/13

	Run the script at where your extract_all.sort.uniq.txt locates		Run the script at where your extract_all.sort.uniq.txt locates

	cd where your extract_all.sort.uniq.txt locates		cd where your extract_all.sort.uniq.txt locates
	csh ~jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering.csh number_of_top_molecules_you_want_to_cluster TC_cutoff		csh ~jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering.csh number_of_top_molecules_you_want_to_cluster TC_cutoff
Line 6:		Line 7:
	csh ~jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering.csh 1000000 0.5		csh ~jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering.csh 1000000 0.5
	so you will cluster top1M molecules from a docking run with tc cutoff 0.5.		so you will cluster top1M molecules from a docking run with tc cutoff 0.5.
			For clustering top1M molecules, it usually takes about 6 hours. Please do not cluster more than 1M molecules by this script.

Jklyu: Created page with "Run the script at where your extract_all.sort.uniq.txt locates cd where your extract_all.sort.uniq.txt locates csh ~jklyu/zzz.script/large_scale_docking/cluster_analysis/be..."

2017-09-13T20:30:25Z

Created page with "Run the script at where your extract_all.sort.uniq.txt locates cd where your extract_all.sort.uniq.txt locates csh ~jklyu/zzz.script/large_scale_docking/cluster_analysis/be..."

New page

Run the script at where your extract_all.sort.uniq.txt locates

cd where your extract_all.sort.uniq.txt locates
csh ~jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering.csh number_of_top_molecules_you_want_to_cluster TC_cutoff
Example:
csh ~jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering.csh 1000000 0.5
so you will cluster top1M molecules from a docking run with tc cutoff 0.5.