Large-scale SMILES requesting - Revision history

Jklyu at 23:01, 18 September 2017

2017-09-18T23:01:04Z

← Older revision		Revision as of 23:01, 18 September 2017
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	\|		\|
	------- scripts/ ------ submit.csh		------- scripts/ ------ submit.csh
			\|
			\|------ make_chunks_for_file_new.py
	\|		\|
	\|------ setup_converting_fps_files.py		\|------ setup_converting_fps_files.py
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	cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering/converting_fps/submit.csh .		cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering/converting_fps/submit.csh .
	cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering/converting_fps/setup_converting_fps_files.py .		cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering/converting_fps/setup_converting_fps_files.py .
	cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering/converting_fps/combine_smi_and_fp.py		cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering/converting_fps/combine_smi_and_fp.py .
	cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering/converting_fps/check_outputs.csh		cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering/converting_fps/check_outputs.csh .
			cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering/converting_fps/make_chunks_for_file_new.py .
	cd ../		cd ../

Line 41:		Line 44:
	cd working/db_zincid		cd working/db_zincid
	head -(number) ../extract_all.sort.uniq.txt \| awk '{print $3" "$22}' > extract_all.top(number).sort.uniq.zincid.energy note: change number in the brackets		head -(number) ../extract_all.sort.uniq.txt \| awk '{print $3" "$22}' > extract_all.top(number).sort.uniq.zincid.energy note: change number in the brackets
	~~split -d -a 3 -l 36000~~ extract_all.top(number).sort.uniq.zincid.energy top(number).~~zincid_~~		python ../../scripts/make_chunks_for_file_new.py extract_all.top(number).sort.uniq.zincid.energy top(number).zincid 500 .
	cd ../		cd ../

Line 52:		Line 55:
	5) Submit requesting and converting jobs		5) Submit requesting and converting jobs
	csh ../scripts/submit.csh		csh ../scripts/submit.csh

			6) Check if every job finishes
			csh ../scripts/check_outputs.csh (number_of_jobs) (prefix)
			if you find any missing files, please edit dirlist in the working directory and resubmit them.

			6) Collect data from the compressed files
			cd db_zincid
			python ../../scripts/combine_smi_and_fp.py

Jklyu at 22:44, 18 September 2017

2017-09-18T22:44:43Z

← Older revision		Revision as of 22:44, 18 September 2017
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	ls /full/path/to/db_zincid/top(number).zincid_* > zincid.sdi		ls /full/path/to/db_zincid/top(number).zincid_* > zincid.sdi

	4) Set up		4) Set up requesting files and directories
			python ../scripts/setup_converting_fps_files.py . converting_fps_ zincid.sdi 500 count

			5) Submit requesting and converting jobs
			csh ../scripts/submit.csh

Jklyu at 22:39, 18 September 2017

2017-09-18T22:39:42Z

← Older revision		Revision as of 22:39, 18 September 2017
Line 41:		Line 41:
	cd working/db_zincid		cd working/db_zincid
	head -(number) ../extract_all.sort.uniq.txt \| awk '{print $3" "$22}' > extract_all.top(number).sort.uniq.zincid.energy note: change number in the brackets		head -(number) ../extract_all.sort.uniq.txt \| awk '{print $3" "$22}' > extract_all.top(number).sort.uniq.zincid.energy note: change number in the brackets
	split -d -l ~~300000~~ ../~~combined~~.~~smi combined~~.~~smi_~~		split -d -a 3 -l 36000 extract_all.top(number).sort.uniq.zincid.energy top(number).zincid_
			cd ../

			3) Create a zincid.sdi file
			ls /full/path/to/db_zincid/top(number).zincid_* > zincid.sdi

			4) Set up

Jklyu at 22:33, 18 September 2017

2017-09-18T22:33:57Z

← Older revision		Revision as of 22:33, 18 September 2017
Line 36:		Line 36:
	cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering/converting_fps/combine_smi_and_fp.py		cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering/converting_fps/combine_smi_and_fp.py
	cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering/converting_fps/check_outputs.csh		cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering/converting_fps/check_outputs.csh
			cd ../

	2) Get ZINC ID and energy columns from the extract_all.sort.uniq.txt file		2) Get ZINC ID and energy columns from the extract_all.sort.uniq.txt file
			cd working/db_zincid
			head -(number) ../extract_all.sort.uniq.txt \| awk '{print $3" "$22}' > extract_all.top(number).sort.uniq.zincid.energy note: change number in the brackets
	split -d -l 300000 ../combined.smi combined.smi_		split -d -l 300000 ../combined.smi combined.smi_

Jklyu at 22:25, 18 September 2017

2017-09-18T22:25:36Z

@@ Line 12: / Line 12: @@
+                |
                 ------- scripts/ ------ submit.csh
+                                |
                                 |------ setup_converting_fps_files.py
@@ Line 24: / Line 22: @@
 This tutorial is for requesting a large number of SMILES for docking results from ZINC server. Usually, the number is larger than 5M ZINC IDs.
-) Get ZINC ID and energy columns from the extract_all.sort.uniq.txt file
+) make directories and copy scripts
   split -d -l 300000 ../combined.smi combined.smi_

Jklyu at 22:19, 18 September 2017

2017-09-18T22:19:31Z

← Older revision		Revision as of 22:19, 18 September 2017
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	The hierarchy of the directories:		The hierarchy of the directories:

	smiles_requesting----- working		smiles_requesting/----- working/
	\| \|		\| \|
	\| \|------ extract_all.sort.uniq.txt file(soft link)		\| \|------ extract_all.sort.uniq.txt file(soft link)
	\| \|		\| \|
	\| \|------ db_zincid		\| \|------ db_zincid/
	\|		\|
	\|		\|
	\|		\|
	------- scripts ------ submit.csh		------- scripts/ ------ submit.csh
	\|		\|
	\|------ setup_substructure_searching_files.py		\|------ setup_substructure_searching_files.py
Line 17:		Line 17:
	\|------ setup_converting_fps_files.py		\|------ setup_converting_fps_files.py
	\|		\|
	\|------		\|------ combine_smi_and_fp.py
			\|
			\|------ check_outputs.csh

Jklyu at 22:18, 18 September 2017

2017-09-18T22:18:09Z

← Older revision		Revision as of 22:18, 18 September 2017
Line 1:		Line 1:
	Written by Jiankun Lyu, 20170918		Written by Jiankun Lyu, 20170918

			The hierarchy of the directories:

			smiles_requesting----- working
			\| \|
			\| \|------ extract_all.sort.uniq.txt file(soft link)
			\| \|
			\| \|------ db_zincid
			\|
			\|
			\|
			------- scripts ------ submit.csh
			\|
			\|------ setup_substructure_searching_files.py
			\|
			\|------ setup_converting_fps_files.py
			\|
			\|------


	This tutorial is for requesting a large number of SMILES for docking results from ZINC server. Usually, the number is larger than 5M ZINC IDs.		This tutorial is for requesting a large number of SMILES for docking results from ZINC server. Usually, the number is larger than 5M ZINC IDs.

			1) Get ZINC ID and energy columns from the extract_all.sort.uniq.txt file

			split -d -l 300000 ../combined.smi combined.smi_

Jklyu at 21:59, 18 September 2017

2017-09-18T21:59:27Z

← Older revision		Revision as of 21:59, 18 September 2017
Line 1:		Line 1:
	Written by Jiankun Lyu, 20170918		Written by Jiankun Lyu, 20170918

	This tutorial is for requesting a large number of SMILES from ZINC server. Usually, the number is larger than 5M ZINC IDs.		This tutorial is for requesting a large number of SMILES for docking results from ZINC server. Usually, the number is larger than 5M ZINC IDs.

Jklyu: Created page with "Written by Jiankun Lyu, 20170918 This tutorial is for requesting a large number of SMILES from ZINC server. Usually, the number is larger than 5M ZINC IDs."

2017-09-18T21:58:36Z

Created page with "Written by Jiankun Lyu, 20170918 This tutorial is for requesting a large number of SMILES from ZINC server. Usually, the number is larger than 5M ZINC IDs."

New page

Written by Jiankun Lyu, 20170918

This tutorial is for requesting a large number of SMILES from ZINC server. Usually, the number is larger than 5M ZINC IDs.