March2019 protocol - Revision history

Dudenko at 02:11, 6 April 2019

2019-04-06T02:11:35Z

← Older revision		Revision as of 02:11, 6 April 2019
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	sub_number = 500 <- this is the number of subdirectories		sub_number = 500 <- this is the number of subdirectories
	runtype = count		runtype = count
	out_number = ~~100~~ <- this is the number of outer directories ( calculated from tot_number/sub_number)		out_number = 60 <- this is the number of outer directories ( calculated from tot_number/sub_number)

	Here is a description of the inputs to the script:		Here is a description of the inputs to the script:

Dudenko at 23:28, 5 April 2019

2019-04-05T23:28:28Z

← Older revision		Revision as of 23:28, 5 April 2019
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	name = leads		name = leads
	infile = ZINC-downloader-3D-db2.gz.wait-ok_new.database_index		infile = ZINC-downloader-3D-db2.gz.wait-ok_new.database_index
	tot_number = ~~50000~~		tot_number = 30000
	sub_number = 500 <- this is the number of subdirectories		sub_number = 500 <- this is the number of subdirectories
	runtype = count		runtype = count

Dudenko at 23:28, 5 April 2019

2019-04-05T23:28:07Z

← Older revision		Revision as of 23:28, 5 April 2019
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	Here is the tutorial for the setup script for DOCK3		Here is the tutorial for the setup script for DOCK3

	python /mnt/nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number_newstruc.py '.' leads ZINC-downloader-3D-db2.gz.wait-ok_new.database_index ~~50000~~ 500 count		python /mnt/nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number_newstruc.py ./ leads ZINC-downloader-3D-db2.gz.wait-ok_new.database_index 30000 500 count

	In this example, the parameter values are as follows:		In this example, the parameter values are as follows:

Jklyu at 23:20, 15 March 2019

2019-03-15T23:20:10Z

← Older revision		Revision as of 23:20, 15 March 2019
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	~~ere~~ is the tutorial for the setup script for DOCK3		Here is the tutorial for the setup script for DOCK3

	python /mnt/nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number_newstruc.py '.' leads ZINC-downloader-3D-db2.gz.wait-ok_new.database_index 50000 500 count		python /mnt/nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number_newstruc.py '.' leads ZINC-downloader-3D-db2.gz.wait-ok_new.database_index 50000 500 count

Frodo: asdf

2019-03-15T23:18:45Z

asdf

New page

ere is the tutorial for the setup script for DOCK3

python /mnt/nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number_newstruc.py '.' leads ZINC-downloader-3D-db2.gz.wait-ok_new.database_index 50000 500 count

In this example, the parameter values are as follows:
workdir = .
name = leads
infile = ZINC-downloader-3D-db2.gz.wait-ok_new.database_index
tot_number = 50000
sub_number = 500 <- this is the number of subdirectories
runtype = count
out_number = 100 <- this is the number of outer directories ( calculated from tot_number/sub_number)

Here is a description of the inputs to the script:

Usage:
setup_db2_zinc15_file_number_newstruc.py dir name filename number subnumber type
dir: The full path of the directory where docking will be performed, subdirectoriss will be created and contain databases.
name: The identifying name of subdirectorys (these are created in the "dir" directory).
filename: the file that contains the full paths where dbs are located,
this you can download from zinc15.
number: number of total diretories to create, this devides the databases into ~ equal docking chunks to be submited.
subnumber: number of subdiretories to create, this will make listing files much easer.
type: size, count, or both
* size will make dirs equal chunks in terms of size,
* "count" option will put equal numbers of database files in the number directory spesified,
* the option "both" will try and satisfy both size and count options.