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from rdkit import Chem
from rdkit.Chem import rdPartialCharges
from rdkit import RDConfig
import unittest
import os
import cPickle as pickle
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
infil = file(os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','PartialCharges','Wrap','test_data','halgren_out.txt'),
'r')
lines = infil.readlines()
infil.close()
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.failUnless(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')
cchFile = open(infile, 'rb')
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.failIf(failed)
def test2Params(self):
""" tests handling of Issue187 """
m1 = Chem.MolFromSmiles('C(=O)[O-]')
rdPartialCharges.ComputeGasteigerCharges(m1)
m2 = Chem.MolFromSmiles('C(=O)[O-].[Na+]')
try:
rdPartialCharges.ComputeGasteigerCharges(m2)
except:
self.fail('should not have hit an exception')
for i in range(m1.GetNumAtoms()):
c1 = float(m1.GetAtomWithIdx(i).GetProp('_GasteigerCharge'))
c2 = float(m2.GetAtomWithIdx(i).GetProp('_GasteigerCharge'))
self.failUnless(feq(c1,c2,1e-4))
def test3Params(self):
""" tests handling of Issue187 """
m2 = Chem.MolFromSmiles('C(=O)[O-].[Na+]')
try:
rdPartialCharges.ComputeGasteigerCharges(m2,12,1)
except:
pass
else:
self.fail('should have hit an exception')
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.failUnlessAlmostEqual(c1,chgs[i],3)
if __name__== '__main__':
unittest.main()
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