Trent scripts

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This is how to use Trent's scripts for preparing to dock.

/nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number.py
Usage: setup_db2_zinc15.py dir name filename number typr
dir: The full path of the directory where docking will be performed, subdirectorys will be created and contain databases.
name: The idenifying 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 subdiretorys to create, this devides the databases into ~ equal docking chunks to be submited.
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.

Here are examples of how to run it:

>> pwd
/mnt/nfs/work/tbalius/Water_Project_all_in_the_same_frame_ph4/vs_frags
>> python /nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number.py ./ vs_frag /nfs/work/tbalius/database_ph4/frags.txt 500  count

this will make 500 subdirectories with approximately the same number of databases. If "number" is grater than number of databases it will make have a directory for each database.

>> python /nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number.py ./ vs_frag /nfs/work/tbalius/database_ph4/frags.txt 500 size

this will give more or less the behavior now ($DOCKBASE/docking/setup/setup_db2_zinc15.py), It will limit the size of the database contain in each chunk to the maximum sized chunk. (however, biggest databases are submitted first, before they were submitted last.)


>> python /nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number.py ./ vs_frag /nfs/work/tbalius/database_ph4/frags.txt 500 both

this will make > 500 subdirectories. with approximately the same number of databases, and will also limit the size of the database contain in each chunk.

Please test it and let me know if it works for you.