name2smiles_list.py

import subprocess

file = open("names", "r+")

for line in file:
    name = line.split()
    subprocess.call(['./name2smiles', name[0]])
    subprocess.call(['echo'])

name2smiles_list.sh

#!/bin/bash
while IFS='' read -r line || [[ -n "$line" ]]; do
    ./name2smiles "$line"
    echo " "
done < "$1"

smiles2coord_list.py

import subprocess, sys

filename = sys.argv[1]
file = open(filename, "r+")

for line in file:
    name = line.split()
    subprocess.call(['./smiles2coord', name[0]])