Commit 7124b511 authored by Phuong Khanh Tran's avatar Phuong Khanh Tran
Browse files

Update downloadPubChem.py

parent f0ee6d4f

testcases/downloadPubChem.py

+6 −5
Original line number Diff line number Diff line
@@ -31,9 +31,9 @@ def processContent(content): 
            new_content += line

    return new_content



def writeMolecule(mol_name, smiles):

def writeMolecule(chemID, mol_name, smiles):

    mol_with_H = read_smiles(smiles, explicit_hydrogen=True)

    file_path_mol = "./testcases/molecules/" + mol_name + ".txt"

    file_path_mol = "./testcases/molecules/molecule" + chemID + ".txt"

    

    nx.write_edgelist(mol_with_H, file_path_mol)
@@ -85,8 +85,9 @@ def writePubChem(start, end): 
            

            for chemical in page_text['PropertyTable']['Properties']:

                # check if desired keys are in the json

                if 'CanonicalSMILES' in chemical:

                    mol_name = "molecule" + str(chemical['CID'])

                if 'CanonicalSMILES' in chemical and 'Title' in chemical:

                    chemID = str(chemical["CID"])

                    mol_name = str(chemical['Title'])

                    smiles = chemical['CanonicalSMILES']

                    # ignore Hydrogen Molecules

                    if smiles == "[HH]":
@@ -94,7 +95,7 @@ def writePubChem(start, end): 
                    

                    # print("molecule "+ str(chemical['CID']) + ": " +  mol_name + "\t" + "smiles: " + smiles)

                

                    writeMolecule(mol_name, smiles)

                    writeMolecule(chemID, mol_name, smiles)

        else:

            print("Failed to retrieve the page. Status code:", response.status_code)