syntax-surgeon / id-prop-extractor

A simple database IDs and biochemical properties extractor for compounds in SMILES format using the pubchempy API.

id-prop-extractor

A simiple database IDs and biochemical properties extractor for compounds in SMILES format using the pubchempy API.

Author: Siddharth Yadav (syntax-surgeon)

Description of files:

main.py

• Contains the main program which prompts the user to provide a path to a smiles files and extracts PubChem, ZINC, CHEBI, CHEMBL & BDBM (BindingDB) ids
• REGEX is utilized to extract database ids from the synonyms column in the associated PubChem profile
• Several properties included in the PubChem profile of the compound can also be extracted
• The data is written to a file named 'molecular_properties.txt' in the directory from where the script was run
• Compounds not found are written as '***NO-COMPOUND-FOUND***' in the 'molecular_properties.txt' file
• Ctrl+C can be utilized to quit/pause the script

test.py

• Tests for the appropriate and intended functionality of the pubchempy API
• Uses three test cases based on the name, molecular formula and Inchi-Key of the drug 'Atorvastatin'