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import io
import os
import pickle
import unittest
from rdkit import Chem, RDConfig
from rdkit.Chem import rdPartialCharges
def feq(v1, v2, tol2=1e-4):
return abs(v1 - v2) <= tol2
class TestCase(unittest.TestCase):
def setUp(self):
pass
def test0HalgrenSet(self):
smiSup = Chem.SmilesMolSupplier(
os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'PartialCharges', 'Wrap', 'test_data',
'halgren.smi'), delimiter='\t')
# parse the original file
with open(
os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'PartialCharges', 'Wrap', 'test_data',
'halgren_out.txt'), 'r') as infil:
lines = infil.readlines()
tab = Chem.GetPeriodicTable()
olst = []
for mol in smiSup:
rdPartialCharges.ComputeGasteigerCharges(mol)
tstr = "Molecule: "
tstr += mol.GetProp("_Name")
olst.append(tstr)
for i in range(mol.GetNumAtoms()):
at = mol.GetAtomWithIdx(i)
en = tab.GetElementSymbol(at.GetAtomicNum())
chg = float(at.GetProp("_GasteigerCharge"))
tstr = "%i %s %6.4f" % (i, en, chg)
olst.append(tstr)
i = 0
for line in lines:
self.assertTrue(line.strip() == olst[i])
i += 1
def test1PPDataset(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'PartialCharges', 'Wrap',
'test_data', 'PP_descrs_regress.2.csv')
infil = open(fileN, 'r')
lines = infil.readlines()
infil.close()
infile = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'PartialCharges', 'Wrap',
'test_data', 'PP_combi_charges.pkl')
with open(infile, 'r') as cchtFile:
buf = cchtFile.read().replace('\r\n', '\n').encode('utf-8')
cchtFile.close()
with io.BytesIO(buf) as cchFile:
combiCharges = pickle.load(cchFile)
for lin in lines:
if (lin[0] == '#'):
continue
tlst = lin.strip().split(',')
smi = tlst[0]
rdmol = Chem.MolFromSmiles(smi)
rdPartialCharges.ComputeGasteigerCharges(rdmol)
nat = rdmol.GetNumAtoms()
failed = False
for ai in range(nat):
rdch = float(rdmol.GetAtomWithIdx(ai).GetProp('_GasteigerCharge'))
if not feq(rdch, combiCharges[smi][ai], 1.e-2):
failed = True
print(smi, ai, rdch, combiCharges[smi][ai])
if failed:
rdmol.Debug()
self.assertFalse(failed)
def test2Params(self):
""" tests handling of Issue187 """
m1 = Chem.MolFromSmiles('C(=O)[O-]')
rdPartialCharges.ComputeGasteigerCharges(m1)
m2 = Chem.MolFromSmiles('C(=O)[O-].[Na+]')
rdPartialCharges.ComputeGasteigerCharges(m2)
for i in range(m1.GetNumAtoms()):
c1 = float(m1.GetAtomWithIdx(i).GetProp('_GasteigerCharge'))
c2 = float(m2.GetAtomWithIdx(i).GetProp('_GasteigerCharge'))
self.assertTrue(feq(c1, c2, 1e-4))
def test3Params(self):
""" tests handling of Issue187 """
m2 = Chem.MolFromSmiles('C(=O)[O-].[Na+]')
with self.assertRaisesRegex(Exception, ""):
rdPartialCharges.ComputeGasteigerCharges(m2, 12, 1)
def testGithubIssue20(self):
""" tests handling of Github issue 20 """
m1 = Chem.MolFromSmiles('CB(O)O')
rdPartialCharges.ComputeGasteigerCharges(m1)
chgs = [-0.030, 0.448, -0.427, -0.427]
for i in range(m1.GetNumAtoms()):
c1 = float(m1.GetAtomWithIdx(i).GetProp('_GasteigerCharge'))
self.assertAlmostEqual(c1, chgs[i], 3)
def testGithubIssue577(self):
""" tests handling of Github issue 577 """
m1 = Chem.MolFromSmiles('CCO')
from locale import LC_NUMERIC, setlocale
try:
setlocale(LC_NUMERIC, "de_DE")
except Exception:
# can't set the required locale, might as well just return
return
try:
rdPartialCharges.ComputeGasteigerCharges(m1)
for at in m1.GetAtoms():
float(at.GetProp('_GasteigerCharge'))
finally:
setlocale(LC_NUMERIC, "C")
rdPartialCharges.ComputeGasteigerCharges(m1)
for at in m1.GetAtoms():
float(at.GetProp('_GasteigerCharge'))
def testGithub2480(self):
with self.assertRaisesRegex(Exception, "^Python argument types"):
rdPartialCharges.ComputeGasteigerCharges(None)
if __name__ == '__main__':
unittest.main()
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