Generating extrema set - Revision history

Rstein at 17:13, 27 May 2020

2020-05-27T17:13:23Z

2020-05-27T17:12:16Z

← Older revision		Revision as of 17:12, 27 May 2020
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	Then run:		Then run:

	python ~rstein/zzz.scripts/TLDR_DUDE/~~0001_map_tranche_collect_db2_gz~~.py {~~SMILES_FILE} {NUM_MOLS~~}		python ~rstein/zzz.scripts/TLDR_DUDE/0001_db2_map_tranche_collect_db2_gz.py -s {SMILES_FILES}

	~~A good~~ number of molecules is 1-2K		You can also specify number of molecules to return. The default is 500.

			python ~rstein/zzz.scripts/TLDR_DUDE/0001_db2_map_tranche_collect_db2_gz.py -s {SMILES_FILES} -n 1000

	This script will find the interquartile range of molecular weight/cLogP properties of your input SMILES ligands. Then it will retrieve db2.gz files for all -2, -1, 0, +1, +2 charges for each MWT/cLogP tranche.		This script will find the interquartile range of molecular weight/cLogP properties of your input SMILES ligands. Then it will retrieve db2.gz files for all -2, -1, 0, +1, +2 charges for each MWT/cLogP tranche.

2020-05-21T20:47:07Z

← Older revision		Revision as of 20:47, 21 May 2020
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	Written by Reed Stein.		Written by Reed Stein.

	A wrapper script that performs everything below requires a SMILES file and the number of molecules you would like from each molecular weight/cLogP tranche. Make sure to source python3		This is a wrapper script that performs everything below including JK's "gen_extrema.py" script.
			It requires a SMILES file and the number of molecules you would like from each molecular weight/cLogP tranche. Make sure to source python3

	source /nfs/soft/python/current/env.csh		source /nfs/soft/python/current/env.csh
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	python ~rstein/zzz.scripts/TLDR_DUDE/0001_map_tranche_collect_db2_gz.py {SMILES_FILE} {NUM_MOLS}		python ~rstein/zzz.scripts/TLDR_DUDE/0001_map_tranche_collect_db2_gz.py {SMILES_FILE} {NUM_MOLS}

			A good number of molecules is 1-2K

	This script will find the interquartile range of molecular weight/cLogP properties of your input SMILES ligands. Then it will retrieve db2.gz files for all -2, -1, 0, +1, +2 charges for each MWT/cLogP tranche.		This script will find the interquartile range of molecular weight/cLogP properties of your input SMILES ligands. Then it will retrieve db2.gz files for all -2, -1, 0, +1, +2 charges for each MWT/cLogP tranche.

2020-05-21T19:41:04Z

← Older revision		Revision as of 19:41, 21 May 2020
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	cat *_charge_tranches.list > extrema_set.list		cat *_charge_tranches.list > extrema_set.list

			which is the split_database_index you would then use for docking.

2020-05-21T19:40:25Z

← Older revision		Revision as of 19:40, 21 May 2020
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	This script will find the interquartile range of molecular weight/cLogP properties of your input SMILES ligands. Then it will retrieve db2.gz files for all -2, -1, 0, +1, +2 charges for each MWT/cLogP tranche.		This script will find the interquartile range of molecular weight/cLogP properties of your input SMILES ligands. Then it will retrieve db2.gz files for all -2, -1, 0, +1, +2 charges for each MWT/cLogP tranche.

			Once this finishes running, as below:

			cat *_charge_tranches.list > extrema_set.list

2020-05-21T19:38:51Z

← Older revision		Revision as of 19:38, 21 May 2020
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			Updated 5/21/2020

			Written by Reed Stein.

			A wrapper script that performs everything below requires a SMILES file and the number of molecules you would like from each molecular weight/cLogP tranche. Make sure to source python3

			source /nfs/soft/python/current/env.csh

			Then run:

			python ~rstein/zzz.scripts/TLDR_DUDE/0001_map_tranche_collect_db2_gz.py {SMILES_FILE} {NUM_MOLS}

			This script will find the interquartile range of molecular weight/cLogP properties of your input SMILES ligands. Then it will retrieve db2.gz files for all -2, -1, 0, +1, +2 charges for each MWT/cLogP tranche.



	Written by Jiankun Lyu, 2019/10/12		Written by Jiankun Lyu, 2019/10/12

2019-10-12T21:49:03Z

← Older revision		Revision as of 21:49, 12 October 2019
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	3) Run extrema set generation on 5 different charge types		3) Run extrema set generation on 5 different charge types

			python /mnt/nfs/ex5/work/jklyu/sigma2/gen_extrema/script/gen_extrema.py
			First input: the DB index from ZINC15
			Second input: the prefix of the ligand charge
			Third input: the lower bound of number of molecules for each tranche

	python /mnt/nfs/ex5/work/jklyu/sigma2/gen_extrema/script/gen_extrema.py ZINC-downloader-3D-plus2.database_index 'plus2' 100 > log_plus2 &		python /mnt/nfs/ex5/work/jklyu/sigma2/gen_extrema/script/gen_extrema.py ZINC-downloader-3D-plus2.database_index 'plus2' 100 > log_plus2 &
	python /mnt/nfs/ex5/work/jklyu/sigma2/gen_extrema/script/gen_extrema.py ZINC-downloader-3D-plus1.database_index 'plus1' 100 > log_plus1 &		python /mnt/nfs/ex5/work/jklyu/sigma2/gen_extrema/script/gen_extrema.py ZINC-downloader-3D-plus1.database_index 'plus1' 100 > log_plus1 &

2019-10-12T21:38:58Z

← Older revision		Revision as of 21:38, 12 October 2019
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	1994		1994

	4.2) (charge-type)_charge_tranches.list. The file contains the db2 ~~index~~ that ~~has~~ been selected from the extrema generation.		4.2) (charge-type)_charge_tranches.list. The file contains all the db2 indexes that have been selected from the extrema generation.

	5) Combine all the db2 indexes generated by the script.		5) Combine all the db2 indexes generated by the script.

2019-10-12T21:38:20Z

← Older revision		Revision as of 21:38, 12 October 2019
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	5) Combine all the db2 indexes generated by the script.		5) Combine all the db2 indexes generated by the script.
	cat *_charge_tranches.list > extrema_set.list		cat *_charge_tranches.list > extrema_set.list
	~~Then use~~ the extrema_set.list as .sdi to set up your docking screen ~~and~~ run it.
			6) Use the extrema_set.list as .sdi to set up your docking screen then run it.

2019-10-12T21:34:38Z

← Older revision		Revision as of 21:34, 12 October 2019
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	Written by Jiankun Lyu, 2019/10/12		Written by Jiankun Lyu, 2019/10/12

			The main purpose of the extrema set is to test the charge preference of your docking setup and to make sure that you don't over-optimize your docking setup with property-matched(charged-matched) decoys generated by DUDE. This is also a sanity check of your docking setup, put it on your checklist!

	extrema_set_gen------- working		extrema_set_gen------- working