Substructure searching - Revision history

Jklyu at 19:14, 13 September 2017

2017-09-13T19:14:55Z

← Older revision		Revision as of 19:14, 13 September 2017
Line 44:		Line 44:
	NS(=O)(=O)c1cc([F,Cl,Br,I])ccc1[OD1] 2		NS(=O)(=O)c1cc([F,Cl,Br,I])ccc1[OD1] 2

	5) ~~split~~ the ZINC-downloader-2D-smi.database_index file into chunks		5) Split the ZINC-downloader-2D-smi.database_index file into chunks
	cd working		cd working
	python ../scripts/setup_substructure_searching_files.py . sub_searching_ ZINC-downloader-2D-smi.database_index number_of_chunks(change it to real number) count		python ../scripts/setup_substructure_searching_files.py . sub_searching_ ZINC-downloader-2D-smi.database_index number_of_chunks(change it to real number) count
	I suggest 3 SMILES files per chunk, so change the number_of_chunks based on your real size of tranches.		I suggest 3 SMILES files per chunk, so change the number_of_chunks based on your real size of tranches.

	6)		6) Submit substructure searching jobs
			csh ../scripts/submit.csh full_path_of_sub_pattern.smarts

			7) Collect results
			cat sub_searching_/.extract.output.smi > output.smi

Jklyu at 19:01, 13 September 2017

2017-09-13T19:01:05Z

← Older revision		Revision as of 19:01, 13 September 2017
Line 12:		Line 12:
	\|		\|
	------- scripts ------ submit.csh		------- scripts ------ submit.csh
	\|
	~~\|------ submit_sub_search.csh~~
	\|
	~~\|------ run_sub_search.csh~~
	\|
	~~\|------ search_multi_substructures.py~~
	\|		\|
	\|------ setup_substructure_searching_files.py		\|------ setup_substructure_searching_files.py
Line 43:		Line 37:
	cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/setup_substructure_searching_files.py .		cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/setup_substructure_searching_files.py .
	cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/multi_sub_searching/submit.csh .		cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/multi_sub_searching/submit.csh .
	~~cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/multi_sub_searching/run_sub_search.csh .~~
	~~cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/multi_sub_searching/submit_sub_search.csh .~~
	~~cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/multi_sub_searching/search_multi_substructures.py .~~
	cd ../		cd ../

Jklyu at 18:58, 13 September 2017

2017-09-13T18:58:36Z

← Older revision		Revision as of 18:58, 13 September 2017
Line 57:		Line 57:
	python ../scripts/setup_substructure_searching_files.py . sub_searching_ ZINC-downloader-2D-smi.database_index number_of_chunks(change it to real number) count		python ../scripts/setup_substructure_searching_files.py . sub_searching_ ZINC-downloader-2D-smi.database_index number_of_chunks(change it to real number) count
	I suggest 3 SMILES files per chunk, so change the number_of_chunks based on your real size of tranches.		I suggest 3 SMILES files per chunk, so change the number_of_chunks based on your real size of tranches.

			6)

Jklyu at 18:26, 13 September 2017

2017-09-13T18:26:00Z

← Older revision		Revision as of 18:26, 13 September 2017
Line 55:		Line 55:
	5) split the ZINC-downloader-2D-smi.database_index file into chunks		5) split the ZINC-downloader-2D-smi.database_index file into chunks
	cd working		cd working
	python ../scripts		python ../scripts/setup_substructure_searching_files.py . sub_searching_ ZINC-downloader-2D-smi.database_index number_of_chunks(change it to real number) count
			I suggest 3 SMILES files per chunk, so change the number_of_chunks based on your real size of tranches.

Jklyu at 18:21, 13 September 2017

2017-09-13T18:21:17Z

← Older revision		Revision as of 18:21, 13 September 2017
Line 11:		Line 11:
	\|		\|
	\|		\|
	------- ~~script~~ ------ submit.csh		------- scripts ------ submit.csh
	\|		\|
	\|------ submit_sub_search.csh		\|------ submit_sub_search.csh
Line 25:		Line 25:
	cd substructure_searching		cd substructure_searching
	mkdir working		mkdir working
	mkdir ~~script~~		mkdir scripts

	2) Download databases index from ZINC		2) Download databases index from ZINC
Line 36:		Line 36:
	2.3) download the databases index file		2.3) download the databases index file
	[[File:subsearching_fig2.png\|thumb\|center\|500px\|download the databases index file]]		[[File:subsearching_fig2.png\|thumb\|center\|500px\|download the databases index file]]

			2.4) download the file above and save it as ZINC-downloader-2D-smi.database_index, then upload the file to the working directory

	3) Copy scripts from my path.		3) Copy scripts from my path.
	cd ~~script~~		cd scripts
	cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/setup_substructure_searching_files.py .		cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/setup_substructure_searching_files.py .
	cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/multi_sub_searching/submit.csh .		cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/multi_sub_searching/submit.csh .
Line 44:		Line 46:
	cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/multi_sub_searching/submit_sub_search.csh .		cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/multi_sub_searching/submit_sub_search.csh .
	cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/multi_sub_searching/search_multi_substructures.py .		cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/multi_sub_searching/search_multi_substructures.py .
			cd ../

			4) Put SMARTS patterns you want to search in the sub_pattern.smarts file and give each SMARTS pattern a unique number or name
			Here is an example in the sub_pattern.smarts file
			NS(=O)(=O)c1cccc([F,Cl,Br,I])c1[OD1] 1
			NS(=O)(=O)c1cc([F,Cl,Br,I])ccc1[OD1] 2

			5) split the ZINC-downloader-2D-smi.database_index file into chunks
			cd working
			python ../scripts

Jklyu at 18:05, 13 September 2017

2017-09-13T18:05:08Z

← Older revision		Revision as of 18:05, 13 September 2017
Line 35:		Line 35:

	2.3) download the databases index file		2.3) download the databases index file
	~~fig2~~		[[File:subsearching_fig2.png\|thumb\|center\|500px\|download the databases index file]]

	3) Copy scripts from my path.		3) Copy scripts from my path.

Jklyu at 18:02, 13 September 2017

2017-09-13T18:02:51Z

← Older revision		Revision as of 18:02, 13 September 2017
Line 32:		Line 32:

	2.2) Choose the tranches you want to do substructure searching		2.2) Choose the tranches you want to do substructure searching
	~~fig1~~		[[File:subsearching_fig1.png\|thumb\|center\|500px\|Choose the tranches you want to do substructure searching]]

	2.3) download the databases index file		2.3) download the databases index file

Jklyu at 18:00, 13 September 2017

2017-09-13T18:00:34Z

← Older revision		Revision as of 18:00, 13 September 2017
Line 26:		Line 26:
	mkdir working		mkdir working
	mkdir script		mkdir script

			2) Download databases index from ZINC

			2.1) Go to ZINC http://zinc15.docking.org/tranches/home/#

			2.2) Choose the tranches you want to do substructure searching
			fig1

			2.3) download the databases index file
			fig2

			3) Copy scripts from my path.
			cd script
			cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/setup_substructure_searching_files.py .
			cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/multi_sub_searching/submit.csh .
			cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/multi_sub_searching/run_sub_search.csh .
			cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/multi_sub_searching/submit_sub_search.csh .
			cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/multi_sub_searching/search_multi_substructures.py .

Jklyu at 17:44, 13 September 2017

2017-09-13T17:44:49Z

← Older revision		Revision as of 17:44, 13 September 2017
Line 3:		Line 3:
	The hierarchy of the directories:		The hierarchy of the directories:

	~~thin_spheres_parameter_scanning~~----- working		substructure_searching----- working
	\|		\| \|
	\|------ ZINC-downloader-2D-smi.database_index		\| \|------ ZINC-downloader-2D-smi.database_index
	\| \|		\| \|
	\| \|------ sub_pattern.smarts		\| \|------ sub_pattern.smarts
	\|		\|
	\|		\|
Line 20:		Line 20:
	\|		\|
	\|------ setup_substructure_searching_files.py		\|------ setup_substructure_searching_files.py

			1) Make those directories above.
			mkdir substructure_searching
			cd substructure_searching
			mkdir working
			mkdir script

Jklyu: Created page with "Written by Jiankun Lyu, 2017/09/13 The hierarchy of the directories: thin_spheres_parameter_scanning----- working ..."

2017-09-13T17:39:44Z

Created page with "Written by Jiankun Lyu, 2017/09/13 The hierarchy of the directories: thin_spheres_parameter_scanning----- working ..."

New page

Written by Jiankun Lyu, 2017/09/13

The hierarchy of the directories:

thin_spheres_parameter_scanning----- working
|
|------ ZINC-downloader-2D-smi.database_index
| |
| |------ sub_pattern.smarts
|
|
|
------- script ------ submit.csh
|
|------ submit_sub_search.csh
|
|------ run_sub_search.csh
|
|------ search_multi_substructures.py
|
|------ setup_substructure_searching_files.py