Search zinc22.py

usage: search_zinc22.py [-h] [--get-vendors]
                        [--configuration-server-url CONFIGURATION_SERVER_URL]
                        zinc_id_in results_out

search for smiles by zinc22 id

positional arguments:
  zinc_id_in            file containing list of zinc ids to look up
  results_out           destination file for output

optional arguments:
  -h, --help            show this help message and exit
  --get-vendors         get vendor supplier codes associated with zinc id
  --configuration-server-url CONFIGURATION_SERVER_URL
                        database containing configuration for zinc22 system

search_zinc22.py is a script for looking up zinc ids on the zinc22 system. The operation is simple- provide a file containing a list of zincids and a destination file to write to. The script will give you a progress bar as it searches the system. If a database is down, the script will let you know and continue gathering the results it can.

The output format is as follows:

SMILES ZINC_ID TRANCHE_NAME

With --get-vendors the output format looks like this:

SMILES ZINC_ID VENDOR_ID TRANCHE_NAME CATALOG

Meaning the script will find all vendor codes and smiles associated with the provided zinc ids.

Usage w/ Bash on BKS cluster

source /nfs/soft/zinc22/search_zinc/env/bin/activate
python /nfs/soft/zinc22/search_zinc/search_zinc.py input_zinc_ids.txt output_zinc_ids.txt
python /nfs/soft/zinc22/search_zinc/search_zinc.py --get-vendors input_zinc_ids.txt output_vendor_ids.txt

Usage w/ Csh on BKS cluster

source /nfs/soft/zinc22/search_zinc/env/bin/activate.csh
python /nfs/soft/zinc22/search_zinc/search_zinc.py input_zinc_ids.txt output_zinc_ids.txt
python /nfs/soft/zinc22/search_zinc/search_zinc.py --get-vendors input_zinc_ids.txt output_vendor_ids.txt