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import csv
import io
import logging
import os
import freewilson as fw
from rdkit import Chem, rdBase
PATH = os.path.join(os.path.dirname(fw.__file__), 'data')
assert os.path.exists(PATH), PATH
def test_chembl():
logging.getLogger().setLevel(logging.INFO)
smilesfile = os.path.join(PATH, "CHEMBL2321810.smi")
scaffoldfile = os.path.join(PATH, "CHEMBL2321810_scaffold.mol")
csvfile = os.path.join(PATH, "CHEMBL2321810_act.csv")
assert os.path.exists(smilesfile)
mols = []
for line in open(smilesfile):
smiles, name = line.strip().split()
m = Chem.MolFromSmiles(smiles)
m.SetProp("_Name", name)
mols.append(m)
scaffold = Chem.MolFromMolBlock(open(scaffoldfile).read())
data = {k: float(v) for k, v in list(csv.reader(open(csvfile)))[1:]}
scores = [data[m.GetProp("_Name")] for m in mols]
assert mols and len(mols) == len(scores)
with rdBase.BlockLogs():
free = fw.FWDecompose(scaffold, mols, scores)
# let's make sure the r squared is decent
assert free.r2 > 0.8
# assert we get something
preds = list(fw.FWBuild(free))
assert len(preds)
# check to see that the prediction filters work
preds2 = list(fw.FWBuild(free, pred_filter=lambda x: x > 8))
assert len(preds2)
assert len([p for p in preds if p.prediction > 8]) == len(list(preds2))
# check to see that the R groups are output in order, i.e. R10 after R3
s = io.StringIO()
fw.predictions_to_csv(s, free, preds2)
assert s.getvalue()
s2 = io.StringIO(s.getvalue())
for i, row in enumerate(csv.reader(s2)):
if i == 0:
assert row == ['smiles', 'prediction', 'Core_smiles', 'R1_smiles', 'R3_smiles', 'R10_smiles']
assert i > 0
def test_multicore():
# test that we can add rgroups for later cores and not throw an exception
scaffolds = [Chem.MolFromSmiles("c1ccccc1[*].NC=O"), Chem.MolFromSmiles("C1CCCCC1")]
mols = [
Chem.MolFromSmiles(x) for x in [
'c1ccccc1CC2CNC2C(=O)N', 'Cc1ccccc1CC2CNC2C(=O)N', 'Cc1ccccc1CC2CNCC(=O)NC2',
'C3c1ccccc1CC2CNC2C(=O)N3', 'C1CCCCC1F', 'ClC1CCCCC1F'
]
]
decomp = fw.FWDecompose(scaffolds, mols, [1, 2, 3, 4, 5, 6])
s = io.StringIO()
fw.predictions_to_csv(s, decomp, fw.FWBuild(decomp))
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