Commit 7b9ce902 authored by Hyun Soo Kim's avatar Hyun Soo Kim
Browse files

restructure loop, reformat code

parent e5704dfd

testcases/simple_database.py

+34 −24
Original line number Diff line number Diff line
@@ -3,13 +3,13 @@ import random 
import requests

import time



MIN_ISOMER_COUNT = 500

MIN_ISOMER_COUNT = 100



MAX_CID_SEGMENT_LEN = 4000  # maybe 3997

MAX_MOLECULE_COUNT = 10_000_000

MAX_MOLECULE_COUNT = 1



C_count_max = 56

C_count_min = 16

C_count_max = 10000

C_count_min = C_count_max // 2



H_C_ratio_max = 48 / 25

H_C_ratio_min = 17 / 15
@@ -18,7 +18,7 @@ N_C_ratio_max = 4 / 13 
N_C_ratio_min = 0



O_C_ratio_max = 2 / 5

O_C_ratio_min = 1 / 4

O_C_ratio_min = 0





def add_atom(atom: str, C_count: int, ratio_max: float, ratio_min: float):
@@ -32,7 +32,7 @@ def add_atom(atom: str, C_count: int, ratio_max: float, ratio_min: float): 
    return ret





def wait_for_api(previous_time):

def wait_for_api_ready(previous_time):

    if previous_time != None:

        while time.time() - previous_time < 0.2:

            pass
@@ -61,9 +61,10 @@ if __name__ == "__main__": 
            + chemical_formula

            + "/cids/JSON"

        )

        previous_time = wait_for_api(previous_time)

        previous_time = wait_for_api_ready(previous_time)

        response = requests.get(url)

        if response.status_code != 200:

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

            continue



        data = response.json()
@@ -75,17 +76,13 @@ if __name__ == "__main__": 
        cids = data["IdentifierList"]["CID"]

        isomer_count = len(cids)

        if isomer_count < MIN_ISOMER_COUNT:

            print(chemical_formula + ": Has only " + str(isomer_count) + " isomers")

            # print(chemical_formula + ": Has only " + str(isomer_count) + " isomers")

            previous_formulae.append(chemical_formula)

            continue



        cid_segment = None

        cid_idx = 0

        while True:

            cid_segment = str(cids[cid_idx])

            cid_idx += 1

            if cid_idx == isomer_count:

                break

        cid_segment = str(cids[0])

        cid_idx = 1

        while cid_idx < isomer_count:

            cid = cids[cid_idx]

            while len(cid_segment + "," + str(cid)) < MAX_CID_SEGMENT_LEN:

                cid_segment += "," + str(cid)
@@ -96,16 +93,29 @@ if __name__ == "__main__": 
                + cid_segment

                + "/property/Title,CanonicalSMILES/json"

            )

            previous_time = wait_for_api(previous_time)

            previous_time = wait_for_api_ready(previous_time)

            response = requests.get(url)



            if response.status_code == 200:

                data = response.json()

                for molecule_struct in data["PropertyTable"]["Properties"]:

                    if "CanonicalSMILES" in molecule_struct:

                    molecule_name = chemical_formula + "_" + str(molecule_struct["CID"])

                        molecule_name = (

                            chemical_formula + "_" + str(molecule_struct["CID"])

                        )

                        smiles = molecule_struct["CanonicalSMILES"]

                    if mi.writeMolecule(molecule_name, smiles, "simple_molecules") == 0:

                        if (

                            mi.writeMolecule(molecule_name, smiles, "simple_molecules")

                            == 0

                        ):

                            molecule_count += 1

                        mi.writeIsomorphic(molecule_name, smiles, "simple_isomorphic")

                            mi.writeIsomorphic(

                                molecule_name, smiles, "simple_isomorphic"

                            )

            else:

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



            cid_segment = str(cids[cid_idx])

            cid_idx += 1



    print("goodbye")