Whole Library TC to Knowns Calculations - Revision history

Jklyu at 20:25, 9 June 2018

2018-06-09T20:25:52Z

← Older revision		Revision as of 20:25, 9 June 2018
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	cp /mnt/nfs/home/jklyu/zzz.script/TC_to_knowns/submit.csh .		cp /mnt/nfs/home/jklyu/zzz.script/TC_to_knowns/submit.csh .
	cp /mnt/nfs/home/jklyu/zzz.script/TC_to_knowns/setup_tc_calculations.py .		cp /mnt/nfs/home/jklyu/zzz.script/TC_to_knowns/setup_tc_calculations.py .
			cd ../

	4) Chunk combined SMILES file.		4) Chunk combined SMILES file.
			cd working
			mkdir db_smi
			cd db_smi
	python ../../scripts/make_chunks_for_file_new.py combined.smi combined.smi 100 .		python ../../scripts/make_chunks_for_file_new.py combined.smi combined.smi 100 .

2018-06-07T22:57:29Z

← Older revision		Revision as of 22:57, 7 June 2018
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	7) Submit jobs		7) Submit jobs
	csh ../scripts/submit.csh uint16.fp .smi uint16.count		csh ../scripts/submit.csh name.uint16.fp name.smi name.uint16.count

			name.uint16.fp, name.smi, name.uint16.count are a set of molecules from the bioactive molecules ( the like-molecules you want to look for in the sea of compounds).


	8) Check unfinished jobs		8) Check unfinished jobs

2018-06-07T22:16:57Z

← Older revision		Revision as of 22:16, 7 June 2018
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	6) Set up your TC calculations		6) Set up your TC calculations
	python ../scripts/~~setup_converting_fps_files~~.py . TC_cal_ smi.sdi 101 count		python ../scripts/setup_tc_calculations.py . TC_cal_ smi.sdi 101 count

	7) Submit jobs		7) Submit jobs

2018-05-24T20:47:10Z

← Older revision		Revision as of 20:47, 24 May 2018
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	6) Set up your TC calculations		6) Set up your TC calculations
	python ../scripts/setup_converting_fps_files.py . TC_cal_ smi.sdi 101 count		python ../scripts/setup_converting_fps_files.py . TC_cal_ smi.sdi 101 count

			7) Submit jobs
			csh ../scripts/submit.csh uint16.fp .smi uint16.count

			8) Check unfinished jobs
			cd db_smi
			csh ../../scripts/check_outputs.csh 101 combined

			9) Combine all the TC results
			python ../../scripts/combine_tc_matrix.py 101 combined

2018-05-24T20:43:48Z

← Older revision		Revision as of 20:43, 24 May 2018
Line 48:		Line 48:
	cp /mnt/nfs/home/jklyu/zzz.script/TC_to_knowns/submit.csh .		cp /mnt/nfs/home/jklyu/zzz.script/TC_to_knowns/submit.csh .
	cp /mnt/nfs/home/jklyu/zzz.script/TC_to_knowns/setup_tc_calculations.py .		cp /mnt/nfs/home/jklyu/zzz.script/TC_to_knowns/setup_tc_calculations.py .

			4) Chunk combined SMILES file.
			python ../../scripts/make_chunks_for_file_new.py combined.smi combined.smi 100 .

			5) Make sdi file.
			cd ../
			ls `pwd`/db_smi/combined_*.smi > smi.sdi

			6) Set up your TC calculations
			python ../scripts/setup_converting_fps_files.py . TC_cal_ smi.sdi 101 count

2018-05-24T20:27:59Z

@@ Line 28: / Line 28: @@
 ) Query SMILES from ZINC or prepare by yourself.
 .1) Query SMILES from ZINC
 See http://wiki.docking.org/index.php/Large-scale_SMILES_Requesting_and_Fingerprints_Converting
 .2) Prepare by yourself

2018-05-24T20:20:29Z

← Older revision		Revision as of 20:20, 24 May 2018
Line 7:		Line 7:
	\| \|------ smi.sdi		\| \|------ smi.sdi
	\| \|		\| \|
	\| \|------ db_smi		\| \|------ db_smi-------combined.smi
	\|		\|
	\|		\|
Line 20:		Line 20:
	\|		\|
	\|------ combine_tc_matrix.py		\|------ combine_tc_matrix.py

			1) Make those directories above.
			mkdir TC_calculations
			cd TC_calculations
			mkdir working
			mkdir scripts

			2) Query SMILES from ZINC or prepare by yourself.
			2.1) Query SMILES from ZINC
			See http://wiki.docking.org/index.php/Large-scale_SMILES_Requesting_and_Fingerprints_Converting
			2.2) Prepare by yourself

2018-05-24T19:53:08Z

← Older revision		Revision as of 19:53, 24 May 2018
Line 1:		Line 1:
	Written by Jiankun Lyu, 20180524		Written by Jiankun Lyu, 20180524

			The hierarchy of the directories:

			TC_calculations---------- working
			\| \|
			\| \|------ smi.sdi
			\| \|
			\| \|------ db_smi
			\|
			\|
			\|
			------- scripts ------ submit.csh
			\|
			\|------ check_outputs.csh
			\|
			\|------ setup_tc_calculations.py
			\|
			\|------ make_chunks_for_file_new.py
			\|
			\|------ combine_tc_matrix.py

2018-05-24T17:01:47Z

Created page with "Written by Jiankun Lyu, 20180524"

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Written by Jiankun Lyu, 20180524