FastROCS - Revision history

Khtang: /* 2. Run search */

2022-10-07T20:23:09Z

2. Run search

← Older revision		Revision as of 20:23, 7 October 2022
Line 25:		Line 25:
	$ source /nfs/home/khtang/ex9/openeye/FastROCS/source_Shape		$ source /nfs/home/khtang/ex9/openeye/FastROCS/source_Shape

	Convert smiles into sdf molecules. I wrote a script that converts each smiles into sdf ~~file~~		Convert smiles into sdf molecules. I wrote a script that converts each smiles into individual sdf files
	$ python /nfs/ex9/work/khtang/openeye/FastROCS/scripts/smi2sdf.py [smiles]		$ python /nfs/ex9/work/khtang/openeye/FastROCS/scripts/smi2sdf.py [smiles]

2022-10-07T20:22:50Z

2. Run search

← Older revision		Revision as of 20:22, 7 October 2022
Line 23:		Line 23:

	====2. Run search====		====2. Run search====
			$ source /nfs/home/khtang/ex9/openeye/FastROCS/source_Shape

			Convert smiles into sdf molecules. I wrote a script that converts each smiles into sdf file
			$ python /nfs/ex9/work/khtang/openeye/FastROCS/scripts/smi2sdf.py [smiles]

	$ ShapeDatabaseClient.py [-h] [--tversky] [--shapeOnly]		$ ShapeDatabaseClient.py [-h] [--tversky] [--shapeOnly]
	[--alternativeStarts {random,subrocs,inertialAtHeavyAtoms,inertialAtColorAtoms}]		[--alternativeStarts {random,subrocs,inertialAtHeavyAtoms,inertialAtColorAtoms}]

2022-10-07T19:58:27Z

2. Run search

← Older revision		Revision as of 19:58, 7 October 2022
Line 26:		Line 26:
	[--alternativeStarts {random,subrocs,inertialAtHeavyAtoms,inertialAtColorAtoms}]		[--alternativeStarts {random,subrocs,inertialAtHeavyAtoms,inertialAtColorAtoms}]
	server:port query results [nHits]		server:port query results [nHits]
	example: ShapeDatabaseClient.py n-~~1-141~~.cluster.ucsf.bkslab.org:8080 ZINC000000002837.sdf result.sdf 3000		example: ShapeDatabaseClient.py epyc-a40.cluster.ucsf.bkslab.org:8080 ZINC000000002837.sdf result.sdf 3000

	Send a query to a specified ShapeDatabaseServer and print the histogram of scores for the entire database of molecules		Send a query to a specified ShapeDatabaseServer and print the histogram of scores for the entire database of molecules

2020-04-16T18:47:38Z

1. Set up virtual environment

← Older revision		Revision as of 18:47, 16 April 2020
Line 17:		Line 17:
	====1. Set up virtual environment====		====1. Set up virtual environment====
	On bash shell		On bash shell
	$ source /nfs/~~home~~/khtang~~/ex9~~/openeye/FastROCS/source_venv		$ source /nfs/ex9/work/khtang/openeye/FastROCS/source_venv

	To deactivate conda environment		To deactivate conda environment

2020-04-16T18:46:16Z

2. Run search

← Older revision		Revision as of 18:46, 16 April 2020
Line 26:		Line 26:
	[--alternativeStarts {random,subrocs,inertialAtHeavyAtoms,inertialAtColorAtoms}]		[--alternativeStarts {random,subrocs,inertialAtHeavyAtoms,inertialAtColorAtoms}]
	server:port query results [nHits]		server:port query results [nHits]
	example: ShapeDatabaseClient.py n-9-34.cluster.ucsf.bkslab.org:8080 ZINC000000002837.sdf result.sdf 3000		example: ShapeDatabaseClient.py n-1-141.cluster.ucsf.bkslab.org:8080 ZINC000000002837.sdf result.sdf 3000

	Send a query to a specified ShapeDatabaseServer and print the histogram of scores for the entire database of molecules		Send a query to a specified ShapeDatabaseServer and print the histogram of scores for the entire database of molecules

2019-10-10T20:44:53Z

← Older revision		Revision as of 20:44, 10 October 2019
Line 35:		Line 35:


	[[Category:Tutorials]]		[[Category:Tutorials]][[Category:Khanh]]

2019-04-20T00:25:40Z

← Older revision		Revision as of 00:25, 20 April 2019
Line 32:		Line 32:
	$ ShapeDatabaseClientHistogram.py <server:port> <query> <results> [num_hits = 100]		$ ShapeDatabaseClientHistogram.py <server:port> <query> <results> [num_hits = 100]

			===Running FastROCS on command line on a small database===


	[[Category:Tutorials]]		[[Category:Tutorials]]

2019-03-23T00:20:09Z

2. Run search

← Older revision		Revision as of 00:20, 23 March 2019
Line 26:		Line 26:
	[--alternativeStarts {random,subrocs,inertialAtHeavyAtoms,inertialAtColorAtoms}]		[--alternativeStarts {random,subrocs,inertialAtHeavyAtoms,inertialAtColorAtoms}]
	server:port query results [nHits]		server:port query results [nHits]
	example: ShapeDatabaseClient.py n-9-34.cluster.ucsf.bkslab.org:8080 ZINC000000002837.sdf result.sdf		example: ShapeDatabaseClient.py n-9-34.cluster.ucsf.bkslab.org:8080 ZINC000000002837.sdf result.sdf 3000

	Send a query to a specified ShapeDatabaseServer and print the histogram of scores for the entire database of molecules		Send a query to a specified ShapeDatabaseServer and print the histogram of scores for the entire database of molecules

2019-03-22T23:53:35Z

1. Set up virtual environment

← Older revision		Revision as of 23:53, 22 March 2019
Line 18:		Line 18:
	On bash shell		On bash shell
	$ source /nfs/home/khtang/ex9/openeye/FastROCS/source_venv		$ source /nfs/home/khtang/ex9/openeye/FastROCS/source_venv

			To deactivate conda environment
			$ conda deactivate

	====2. Run search====		====2. Run search====

2019-03-20T21:30:22Z

1. Set up virtual environment

← Older revision		Revision as of 21:30, 20 March 2019
Line 17:		Line 17:
	====1. Set up virtual environment====		====1. Set up virtual environment====
	On bash shell		On bash shell
	source /nfs/home/khtang/ex9/openeye/FastROCS/source_venv		$ source /nfs/home/khtang/ex9/openeye/FastROCS/source_venv

	====2. Run search====		====2. Run search====