cas to property

cas2property.py

import pandas as pd
import pubchempy as pcp
import argparse
 
def search_molecule_from_cas(CAS):
    """ search molecules from CAS number
    @parma molecule_name
    @return molecule
    """
    searched_results = pcp.get_compounds(CAS,"name")  # ｇget a compounds list

    if len(searched_results) <= 0:
        return None
    elif len(searched_results) >= 1:
        return searched_results[0]

def main():
    parser = argparse.ArgumentParser(description='filename')
    parser.add_argument('filename')
    args = parser.parse_args()
    data = pd.read_csv(args.filename)

    cas_lst=data["CAS"]
    out_dict = {"CAS":[],'cid':[], 'exact_mass':[], 'isomeric_smiles':[],'iupac_name':[],'molecular_formula':[],'molecular_weight':[]}

    for i in range(len(cas_lst)):
        cas = cas_lst[i]
        current_molecule = search_molecule_from_cas(cas)
        out_dict['CAS'].append(cas)
        out_dict['cid'].append(current_molecule.cid) if current_molecule else out_dict['cid'].append(None)
        out_dict['exact_mass'].append(current_molecule.exact_mass) if current_molecule else out_dict['exact_mass'].append(None)
        out_dict['isomeric_smiles'].append(current_molecule.isomeric_smiles)if current_molecule else out_dict['isomeric_smiles'].append(None)
        out_dict['iupac_name'].append(current_molecule.iupac_name)if current_molecule else out_dict['iupac_name'].append(None)
        out_dict['molecular_formula'].append(current_molecule.molecular_formula)if current_molecule else out_dict['molecular_formula'].append(None)
        out_dict['molecular_weight'].append(current_molecule.molecular_weight)if current_molecule else out_dict['molecular_weight'].append(None)

        print(i, cas, current_molecule.isomeric_smiles if current_molecule else "not found")
    
    pd.DataFrame(out_dict).to_csv("CAS2property.csv")


if __name__ == "__main__":
    main()

What is it?

This is a script that uses pubchempy library to get some simple properties of molecules from the PubChem website. And get a list in "CSV" format.

What are its requirements?

python3
pubchempy
pandas

The input file must be in "CSV" format.

How to use it in the command line?

python cas2property.py yourfilename