March2019 protocol

Revision as of 23:28, 5 April 2019 by Dudenko (talk | contribs)
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Here is the tutorial for the setup script for DOCK3

python /mnt/nfs/home/tbalius/zzz.github/DOCK/docking/setup/ ./ leads ZINC-downloader-3D-db2.gz.wait-ok_new.database_index 30000 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: 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.