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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 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 = 30000 sub_number = 500 <- this is the number of subdirectories runtype = count 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:
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.