Generating decoys (Reed's way) - Revision history

Sevigneron at 18:59, 30 July 2024

2024-07-30T18:59:39Z

← Older revision		Revision as of 18:59, 30 July 2024
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	source /nfs/home/bwhall61/.python_envs/pulp/bin/activate		source /nfs/home/bwhall61/.python_envs/pulp/bin/activate
	python /nfs/home/bwhall61/work/decoy_gen_improvement/filter_decoys.py		python /nfs/home/bwhall61/work/decoy_gen_improvement/filter_decoys.py

	this may take some time to run, so it is recommended to run in a screen.		this may take some time to run, so it is recommended to run in a screen.

Sevigneron at 18:58, 30 July 2024

2024-07-30T18:58:30Z

← Older revision		Revision as of 18:58, 30 July 2024
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	Jobs will run for 15 minutes to 1-2 hours depending on how many ligands you input.		Jobs will run for 15 minutes to 1-2 hours depending on how many ligands you input.

			***There was a new bug in Reed's original script that Brendan Hall was able to fix (July 30, 2024), run this script instead:

			python /nfs/home/bwhall61/work/decoy_gen_improvement/0001_qsub_generate_decoys.py {NEW_DIR_NAME}

	=== Step 3) Assigning decoys to ligands ===		=== Step 3) Assigning decoys to ligands ===

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	python /mnt/nfs/home/rstein/zzz.scripts/new_DUDE_SCRIPTS/0002_qsub_filter_decoys.py {NEW_DIR_NAME}		python /mnt/nfs/home/rstein/zzz.scripts/new_DUDE_SCRIPTS/0002_qsub_filter_decoys.py {NEW_DIR_NAME}

			*** Again Brendan Hall was able to fix the errors in the above script, run this instead:
			cd {NEW_DIR_NAME}
			source /nfs/home/bwhall61/.python_envs/pulp/bin/activate
			python /nfs/home/bwhall61/work/decoy_gen_improvement/filter_decoys.py

			this may take some time to run, so it is recommended to run in a screen.


	This will run on the queue. As with "Querying ZINC for Protomers":		This will run on the queue. As with "Querying ZINC for Protomers":

Khtang: Reverted edits by Jklyu (talk) to last revision by Fliu

2022-09-23T07:49:10Z

Reverted edits by Jklyu (talk) to last revision by Fliu

← Older revision		Revision as of 07:49, 23 September 2022
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	If you have edited the "decoy_generation.in" file which is now located in {NEW_DIR_NAME} as you want, you can run the following command:		If you have edited the "decoy_generation.in" file which is now located in {NEW_DIR_NAME} as you want, you can run the following command:

	python /mnt/nfs/~~ex9~~/~~work~~/~~stefan~~/~~Covid-19/20210804_Mpro_CUBS/decoys_larger_SMILES/test-code~~/0001_qsub_generate_decoys.py {NEW_DIR_NAME}		python /mnt/nfs/home/rstein/zzz.scripts/new_DUDE_SCRIPTS/0001_qsub_generate_decoys.py {NEW_DIR_NAME}

	Jobs will run for 15 minutes to 1-2 hours depending on how many ligands you input.		Jobs will run for 15 minutes to 1-2 hours depending on how many ligands you input.

Jklyu: /* Step 2) Retrieving SMILES decoys from ZINC15 */

2022-09-22T23:41:08Z

Step 2) Retrieving SMILES decoys from ZINC15

← Older revision		Revision as of 23:41, 22 September 2022
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	If you have edited the "decoy_generation.in" file which is now located in {NEW_DIR_NAME} as you want, you can run the following command:		If you have edited the "decoy_generation.in" file which is now located in {NEW_DIR_NAME} as you want, you can run the following command:

	python /mnt/nfs/~~home~~/~~rstein~~/~~zzz.scripts~~/~~new_DUDE_SCRIPTS~~/0001_qsub_generate_decoys.py {NEW_DIR_NAME}		python /mnt/nfs/ex9/work/stefan/Covid-19/20210804_Mpro_CUBS/decoys_larger_SMILES/test-code/0001_qsub_generate_decoys.py {NEW_DIR_NAME}

	Jobs will run for 15 minutes to 1-2 hours depending on how many ligands you input.		Jobs will run for 15 minutes to 1-2 hours depending on how many ligands you input.

Fliu at 03:48, 18 September 2020

2020-09-18T03:48:08Z

← Older revision		Revision as of 03:48, 18 September 2020
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	source /nfs/soft/jchem/current/env.csh		source /nfs/soft/jchem/current/env.csh

			If the below script still not run:
			source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh
	== Querying ZINC for Protomers ==		== Querying ZINC for Protomers ==

Rstein at 01:23, 19 May 2020

2020-05-19T01:23:34Z

← Older revision		Revision as of 01:23, 19 May 2020
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	updated 3/6/2020		updated 3/6/2020

			updated 5/18/2020

	This pipeline will generate property-matched decoys for a set of ligand SMILES. To build ligands yourself, see "ligand prep" in:		This pipeline will generate property-matched decoys for a set of ligand SMILES. To build ligands yourself, see "ligand prep" in:
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	=== Step 1) Setting up directories for Protomers ===		=== Step 1) Setting up directories for Protomers ===

	Before starting, you need a SMILES file with the format (SMILES first, ID second):		Before starting, you need a SMILES file with the format (SMILES first, <B>unique</B> ID second):
	S(Nc1c(O)cc(C(=O)O)cc1)(c2c(scc2)C(=O)O)(=O)=O 116		S(Nc1c(O)cc(C(=O)O)cc1)(c2c(scc2)C(=O)O)(=O)=O 116

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	If your input ligand SMILES file is already protonated as you want it, set "PROTONATE NO".		If your input ligand SMILES file is already protonated as you want it, set "PROTONATE NO".

			If you want your input ligand SMILES protonated, only protomer SMILES with unique properties will be kept for generating decoys. Therefore, if you have one ligand that exists in 4 tautomers, all of which have identical molecular weight, cLogP, # rotatable bonds, # H-bond acceptors and donors, and net charge, only <B>one</B> will be maintained for decoy matching. This doesn't apply if you set "PROTONATE NO".

	This file specifies that for each ligand protomer, at least 20 decoys will be retrieved with the following properties:		This file specifies that for each ligand protomer, at least 20 decoys will be retrieved with the following properties:

Rstein: /* Querying ZINC for SMILES */

2020-03-24T21:15:14Z

Querying ZINC for SMILES

← Older revision		Revision as of 21:15, 24 March 2020
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	== Querying ZINC for SMILES ==		== Querying ZINC for SMILES ==

	If you would like to query ZINC for decoy SMILES so that you can build decoys yourself or if your ligands are >400 Da, start here. If not, go to "Querying ZINC for Protomers"		This procedure generates decoys for your input ligand SMILES by finding decoy SMILES in ZINC that are property-matched. This procedure will provide decoy SMILES that you can build yourself into 3D models for docking. If you would like to query ZINC for decoy SMILES so that you can build decoys yourself or if your ligands are >400 Da, start here. If not, go to "Querying ZINC for Protomers" to generate decoys that already have 3D models.

	=== Step 1) Setting up SMILES directory ===		=== Step 1) Setting up SMILES directory ===

Rstein: /* Querying ZINC for Protomers */

2020-03-24T21:12:51Z

Querying ZINC for Protomers

← Older revision		Revision as of 21:12, 24 March 2020
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	== Querying ZINC for Protomers ==		== Querying ZINC for Protomers ==

	This procedure is advised if you want decoys to be charge-matched to ligands.		This procedure generates decoys for your input ligands by searching through 3D conformers that are already built in ZINC. This procedure is advised if you want decoys to be charge-matched to ligands.

	=== Step 1) Setting up directories for Protomers ===		=== Step 1) Setting up directories for Protomers ===

Rstein at 02:03, 11 March 2020

2020-03-11T02:03:29Z

← Older revision		Revision as of 02:03, 11 March 2020
Line 4:		Line 4:

	updated 8/15/2019		updated 8/15/2019

			updated 3/6/2020

	This pipeline will generate property-matched decoys for a set of ligand SMILES. To build ligands yourself, see "ligand prep" in:		This pipeline will generate property-matched decoys for a set of ligand SMILES. To build ligands yourself, see "ligand prep" in:

Rstein: /* Querying ZINC for SMILES */

2020-03-11T01:59:53Z

Querying ZINC for SMILES

← Older revision		Revision as of 01:59, 11 March 2020
Line 119:		Line 119:
	== Querying ZINC for SMILES ==		== Querying ZINC for SMILES ==

	If you would like to query ZINC for decoy SMILES so that you can build decoys yourself or if your ligands are >400 Da, ~~continue~~ here. If not, go to "Querying ZINC for Protomers"		If you would like to query ZINC for decoy SMILES so that you can build decoys yourself or if your ligands are >400 Da, start here. If not, go to "Querying ZINC for Protomers"

	=== Step 1) Setting up SMILES directory ===		=== Step 1) Setting up SMILES directory ===