mol2img.sh

#!/bin/bash

# This script will read a CSV file containing a list of compunds 
# indentified by their chembl ids. For each compound it will download 
# its image and save it to the output folder.

# Some constants first: we need to know the root URL of the ChEMBL API.
# We will also use a tool called "resty" and we first need to download it
# from the Internet so we need to know its adress.
DEFAULT_INPUT=${1-"./compounds_list.csv"}
DEFAULT_OUTPUT=${1-"./images"}
URL_ROOT="https://www.ebi.ac.uk/chembl/api/data"

# OK, let's create the output directory
mkdir -p $DEFAULT_OUTPUT

# Now we can loop through the CSV file line by line
cat $DEFAULT_INPUT|while read line
  do
  	# For each line we extract the first column and store it in the "chembl_id" variable
    read -d, chembl_id < <(echo $line)

    # Just prinint the id here to see if reading from CSV works...
    echo "Getting image for: $chembl_id"

    # For each chembl_id extracted from the file we make a single API call to retrive 
    # information about this compound in JSON format
    curl -s ${URL_ROOT}/molecule/$chembl_id.png > $DEFAULT_OUTPUT/$chembl_id.png
  done

# Finally do a cleanup: remove empty files, ones corresponding to compounds 
# without a structure
find $DEFAULT_OUTPUT -size 0 -delete