def process_test_32():
"""
# SMILES,
Interlab.SD,
Num.Lit.Sources,
Experimental.MP.(*C),
log.Poct-water.calc.in.RDKit,
log.S0.calc.by.GSE
"""
fname = f"{TEST_PATH}/set_32.csv"
fout = f"{TEST_PATH}/test_32.smi"
fout_gse = f"{TEST_PATH}/test_32.with.gse.smi"
logging.info(f"Processing {fname}")
cmpd_list = []
with open(fname, 'r') as fin:
for line in fin:
if not line.startswith("#"):
pairs = line.rstrip('\n').split(',')
canon_smiles = canonicalize_smiles(pairs[0])
logS = float(pairs[5])
cmpd_list.append((canon_smiles, logS))
with open(fout, 'w', encoding="ascii") as fo:
for el in cmpd_list:
smiles = el[0]
fo.write(f"{smiles}\n")
with open(fout_gse, 'w', encoding="ascii") as fo:
for el in cmpd_list:
smiles = el[0]
logS = el[1]
fo.write(f"{smiles},{logS}\n")
logging.info(f"Saved {fout}")
def process_POG_2007_JCIM_train():
fname = f"{DATA_PATH}/POG.2007.JCIM.train.txt"
fout = f"{PROCESSED_PATH}/POG.2007.JCIM.train.smi"
logging.info(f"Processing {fname}")
cmpd_list = []
with open(fname, 'r') as fin:
for line in fin:
if not line.startswith("#"):
try:
pairs = line.rstrip('\n').split(";")
canon_smiles = canonicalize_smiles(pairs[1].strip("\""))
logS = float(pairs[4])
cmpd_list.append((canon_smiles, logS))
except:
smiles = pairs[1]
logging.info(f"Failed to process {smiles}")
with open(fout, 'w', encoding="ascii") as fo:
for el in cmpd_list:
smiles = el[0]
logS = el[1]
fo.write(f"{smiles},{logS}\n")
logging.info(f"Saved {fout}")
def process_LGG_2008_JCIM_32():
fname = f"{DATA_PATH}/LGG.2008.JCIM.32.txt"
fout = f"{PROCESSED_PATH}/LGG.2008.JCIM.32.smi"
logging.info(f"Processing {fname}")
cmpd_list = []
with open(fname, 'r') as fin:
cnt = 0
for line in fin:
if not line.startswith("#"):
pairs = line.rstrip('\n').split(',')
canon_smiles = canonicalize_smiles(pairs[0])
mg = float(pairs[1]) / 1000
try:
mw = mol_wt(canon_smiles)
except TypeError as e:
logging.error(f"TypeError for {canon_smiles}: {e}")
continue
logS = np.log10(mg / mw)
cmpd_list.append((canon_smiles, logS))
cnt += 1
with open(fout, 'w', encoding="ascii") as fo:
for el in cmpd_list:
smiles = el[0]
logS = el[1]
fo.write(f"{smiles},{logS}\n")
logging.info(f"Saved {fout}")
def process_HXZ_2004_JCIC_data():
fname = f"{DATA_PATH}/HXZ.2004.JCIC.data_set.txt"
fout = f"{PROCESSED_PATH}/HXZ.2004.JCIC.data_set.smi"
logging.info(f"Processing {fname}")
cmpd_list = []
with open(fname, 'r') as fin:
for line in fin:
if not line.startswith("#"):
try:
pairs = line.rstrip('\n').split()
canon_smiles = canonicalize_smiles(pairs[0])
logS = float(pairs[2])
cmpd_list.append((canon_smiles, logS))
except:
smiles = pairs[0]
logging.info(f"Failed to process {smiles}")
with open(fout, 'w', encoding="ascii") as fo:
for el in cmpd_list:
smiles = el[0]
logS = el[1]
fo.write(f"{smiles},{logS}\n")
logging.info(f"Saved {fout}")
def process_H_2000_JCIC_test2():
fname = f"{DATA_PATH}/H.2000.JCIC.test2.txt"
fout = f"{PROCESSED_PATH}/H.2000.JCIC.test2.smi"
logging.info(f"Processing {fname}")
cmpd_list = []
with open(fname, 'r', encoding="ISO-8859-1") as fin:
for line in fin:
if not line.startswith("#"):
try:
pairs = line.rstrip('\n').split()
canon_smiles = canonicalize_smiles(pairs[6], SLN=True)
logS = float(pairs[3])
cmpd_list.append((canon_smiles, logS))
except:
smiles = pairs[6]
logging.info(f"Failed to process {smiles}")
with open(fout, 'w', encoding='ascii') as fo:
for el in cmpd_list:
smiles = el[0]
logS = el[1]
fo.write(f"{smiles},{logS}\n")
logging.info(f"Saved {fout}")
def process_WKH_2007_JCIM():
fname = f"{DATA_PATH}/WKH.2007.JCIM.solubility.sdf"
fout = f"{PROCESSED_PATH}/WKH.2007.JCIM.smi"
logging.info(f"Processing {fname}")
suppl = Chem.SDMolSupplier(fname)
with open(fout, 'w', encoding='ascii') as fo:
for mol in suppl:
smiles = canonicalize_smiles(Chem.MolToSmiles(mol))
logS = str(mol.GetProp('EXPT'))
fo.write(f'{smiles},{logS}\n')
logging.info(f"Saved to {fout}")
def process_HXZ_2004_JCIC_test():
fname = f"{DATA_PATH}/HXZ.2004.JCIC.test_set1.sdf"
fout = f"{PROCESSED_PATH}/HXZ.2004.JCIC.test.smi"
logging.info(f"Processing {fname}")
suppl = Chem.SDMolSupplier(fname)
with open(fout, 'w', encoding='ascii') as fo:
for mol in suppl:
smiles = canonicalize_smiles(Chem.MolToSmiles(mol))
logS = str(mol.GetProp('logS'))
fo.write(f'{smiles},{logS}\n')
logging.info(f"Saved to {fout}")
def process_BOM_2017_JC():
fname = f"{DATA_PATH}/BOM.2017.JC.txt"
fout = f"{PROCESSED_PATH}/BOM.2017.JC.smi"
logging.info(f"Processing {fname}")
cmpd_list = []
with open(fname, 'r') as fin:
for line in fin:
pairs = line.rstrip('\n').split(",")
canon_smiles = canonicalize_smiles(pairs[0])
logS = float(pairs[1])
cmpd_list.append((canon_smiles, logS))
with open(fout, 'w', encoding='ascii') as fo:
for el in cmpd_list:
smiles = el[0]
logS = el[1]
fo.write(f"{smiles},{logS}\n")
logging.info(f"Saved {fout}")
def process_D_2008_JCIC():
fname = f"{DATA_PATH}/D.2008.JCIC.solubility.v1.txt"
fout = f"{PROCESSED_PATH}/D.2008.JCIC.smi"
logging.info(f"Processing {fname}")
cmpd_list = []
with open(fname, 'r') as fin:
for line in fin:
if not line.startswith("#"):
pairs = line.rstrip('\n').split(",")
canon_smiles = canonicalize_smiles(pairs[-1])
logS = float(pairs[-3])
cmpd_list.append((canon_smiles, logS))
with open(fout, 'w', encoding='ascii') as fo:
for el in cmpd_list:
smiles = el[0]
logS = el[1]
fo.write(f"{smiles},{logS}\n")
logging.info(f"Saved {fout}")
def process_ABB_2000_PR():
fname = f"{DATA_PATH}/ABB.2000.PR.txt"
fout = f"{PROCESSED_PATH}/ABB.2000.PR.smi"
logging.info(f"Processing {fname}")
cmpd_list = []
with open(fname, 'r') as fin:
for line in fin:
if not line.startswith("#"):
pairs = line.rstrip('\n').split(",")
canon_smiles = canonicalize_smiles(pairs[1])
logS = float(pairs[2])
cmpd_list.append((canon_smiles, logS))
with open(fout, 'w') as fo:
for el in cmpd_list:
smiles = el[0]
logS = el[1]
fo.write(f"{smiles},{logS}\n")
logging.info(f"Saved {fout}")
def process_A_2019_ADMET_DMPK():
""" Process A.2019_ADMET_DMPK data.
Two values are gien in the raw file, so two output files are saved.
"""
fname = f"{DATA_PATH}/A.2019.ADMET_DMPK.csv"
fout_1 = f"{PROCESSED_PATH}/A.2019.ADMET_DMPK.SSF.smi"
fout_2 = f"{PROCESSED_PATH}/A.2019.ADMET_DMPK.CS.smi"
logging.info(f"Processing {fname}")
try:
import pubchempy as pcp
except ModuleNotFoundError as e:
print(e)
return
with open(fname, 'r') as fin, open(fout_1,
'w') as fout1, open(fout_2,
'w') as fout2:
fin.readline()
for line in fin:
if line.startswith("\""):
pairs = line.rstrip().split("\"")
name = pairs[1]
pairs = pairs[2].split(',')
logS0_SFF = pairs[0]
logS0_CS = pairs[2]
else:
pairs = line.rstrip().split(',')
name = pairs[0]
logS0_SFF = pairs[1]
logS0_CS = pairs[3]
name = name.replace('\"', '')
results = pcp.get_compounds(name, 'name')
if len(results) > 0:
isomeric_smiles = results[0].isomeric_smiles
canon_smiles = canonicalize_smiles(isomeric_smiles)
fout1.write("{},{}\n".format(canon_smiles, logS0_SFF))
fout2.write("{},{}\n".format(canon_smiles, logS0_CS))
def process_WHX_2009_JCIM():
files_in = [
"WHX.2009.JCIM.Set-001.csv", "WHX.2009.JCIM.Set-002.csv",
"WHX.2009.JCIM.Set-003.csv", "WHX.2009.JCIM.Set-004.csv",
"WHX.2009.JCIM.Set-005.csv"
]
files_out = [
"WHX.2009.JCIM.Set-001.smi", "WHX.2009.JCIM.Set-002.smi",
"WHX.2009.JCIM.Set-003.smi", "WHX.2009.JCIM.Set-004.smi",
"WHX.2009.JCIM.Set-005.smi"
]
for i, file_in in enumerate(files_in):
fname = f"{DATA_PATH}/{file_in}"
file_out = files_out[i]
fout = f"{PROCESSED_PATH}/{file_out}"
logging.info(f"Processing {fname}")
cmpd_list = []
with open(fname, 'r') as fin:
for line in fin:
if not line.startswith("#"):
try:
pairs = line.rstrip('\n').split(",")
canon_smiles = canonicalize_smiles(pairs[1], SLN=True)
logS = float(pairs[0])
cmpd_list.append((canon_smiles, logS))
except:
smiles = pairs[1]
logging.info(f"Failed to process {smiles}")
with open(fout, 'w', encoding="ascii") as fo:
for el in cmpd_list:
smiles = el[0]
logS = el[1]
fo.write(f"{smiles},{logS}\n")
logging.info(f"Saved {fout}")
def process_LGG_2008_JCIM_100():
fname = f"{DATA_PATH}/LGG.2008.JCIM.100.txt"
fout = f"{PROCESSED_PATH}/LGG.2008.JCIM.100.smi"
logging.info(f"Processing {fname}")
cmpd_list = []
with open(fname, 'r') as fin:
cnt = 0
for line in fin:
if not line.startswith("#"):
pairs = line.rstrip('\n').split(',')
canon_smiles = canonicalize_smiles(pairs[0])
logS = float(pairs[2])
cmpd_list.append((canon_smiles, logS))
cnt += 1
with open(fout, 'w', encoding="ascii") as fo:
for el in cmpd_list:
smiles = el[0]
logS = el[1]
fo.write(f"{smiles},{logS}\n")
logging.info(f"Saved {fout}")
def process_OCHEM():
fname = f"{DATA_PATH}/OCHEM.Water.Solublity.05.27.2019.txt"
fout = f"{PROCESSED_PATH}/OCHEM.Water.Solublity.05.27.2019.smi"
logging.info(f"Processing {fname}")
cmpd_list = []
with open(fname, 'r') as fin:
for line in fin:
try:
pairs = line.rstrip('\n').split(",")
canon_smiles = canonicalize_smiles(pairs[0])
logS = float(pairs[1])
cmpd_list.append((canon_smiles, logS))
except:
smiles = pairs[0]
logging.info(f"Failed to process {smiles}")
with open(fout, 'w', encoding='ascii') as fo:
for el in cmpd_list:
smiles = el[0]
logS = el[1]
fo.write(f"{smiles},{logS}\n")
logging.info(f"Saved {fout}")
