Updated script to query from URL for Chemical name and SMILES representation

from pysmiles import read_smiles

import networkx as nx

import random

import requests

import os

# returns the order number of the edge that appears using nx.edge_list

def getOrder(line):

     return int(line.split("{'order': ")[1].rstrip('}\n'))

    # only allow integer bond order values

    order = line.split("{'order': ")[1].rstrip('}\n')

    return int(line.split("{'order': ")[1].rstrip('}\n')) if order.isdigit() else -1

# multiplies the edge pair by the order number

def processContent(content):

    new_content = ""

    for line in content:

        # Check if the line contains bond order information

        # check if the line contains bond order information

        if "{'order':" in line:

            bond_order = getOrder(line)

            # if bond order is invalid, then return error

            if bond_order == -1:

                return -1

            # duplicate the edge for value of bond order

            vertex_pair = ' '.join(line.split()[:2])

            for i in range(bond_order):

             new_content += vertex_pair + '\n'

    random.shuffle(shuffled_nodes)

    new_map = dict(zip(nodes, shuffled_nodes))

    # Use the mapping to generate a new graph with shuffled labels

    # use the mapping to generate a new graph with shuffled labels

    scrambled_graph = nx.relabel_nodes(graph, new_map)

    return scrambled_graph

      mol_data += node[1] + '\n'

    # Read the existing contents of the file

    # read the generated edgelist

    with open(file_path_mol, 'r') as file:

        edgelist = file.read()

    # if theres an invalid edgelist, remove it from the file system

    modified_edgelist = processContent(edgelist.split('\n'))

    # Write the new content at the beginning and the original content

    if modified_edgelist == -1:

        os.remove(file_path_mol)

        return -1

    # write metadata at the beginning and the original content

    with open(file_path_mol, 'w') as file:

        file.write(mol_data + modified_edgelist)

    return 0

def writeIsomorphic(mol_name, smiles):

    iso_graph = scrambleLabels(read_smiles(smiles, explicit_hydrogen=True))

    file_path_iso = "./isomorphic_test/" + mol_name + "_iso.txt"

        isolist = file.read()

    modified_isolist = processContent(isolist.split('\n'))

    if modified_isolist == -1:

        os.remove(file_path_iso)

        return -1

    with open(file_path_iso, 'w') as file:

        file.write(iso_data + modified_isolist)

    return 0

if __name__ == "__main__":

    # replace with name of molecule

    mol_name = "adenine"

    # range(start, end, step) --> Change values for number of molecules required

    for indx in range(1,30,10):

        numbers = [str(i) for i in range(indx, indx + 10)]

        indexes = ",".join(numbers)

    # replace with smiles string of molecule

    smiles = 'c1[nH]c(c-2ncnc2n1)N'

        # query from pubchem URL

        url = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/' + indexes + '/property/Title,CanonicalSMILES/json'

        response = requests.get(url)

    writeMolecule(mol_name, smiles)

        # Check if the request was successful

        if response.status_code == 200:

            # Extract the json from the response

            page_text = response.json()

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

                # check if desired keys are in the json

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

                    mol_name = chemical['Title']

                    smiles = chemical['CanonicalSMILES']

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

                    if writeMolecule(mol_name, smiles) == 0:

                        writeIsomorphic(mol_name, smiles)

        else:

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

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