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rdkit/Python/Chem/UnitTestGraphDescriptors.2.py

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# $Id$
#
# Copyright (C) 2003-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
#
"""unit testing code for graph-theoretical descriptors
"""
import RDConfig
import unittest,os.path
import Chem
from Chem import GraphDescriptors,MolSurf,Lipinski,Crippen
from Numeric import *
def feq(n1,n2,tol=1e-4):
return abs(n1-n2)<=tol
class TestCase(unittest.TestCase):
def setUp(self):
if doLong:
print '\n%s: '%self.shortDescription(),
def testBertzCTShort(self):
""" test calculation of Bertz 'C(T)' index
"""
data = [('C=CC=C',21.01955),
('O=CC=O',25.01955),
('FCC(=O)CF',46.7548875),
('O=C1C=CC(=O)C=C1',148.705216),
('C12C(F)=C(O)C(F)C1C(F)=C(O)C(F)2',315.250442),
('C12CC=CCC1C(=O)C3CC=CCC3C(=O)2',321.539522)]
for smi,CT in data:
m = Chem.MolFromSmiles(smi)
newCT = GraphDescriptors.BertzCT(m, forceDMat = 1)
assert feq(newCT,CT,1e-3),'mol %s (CT calc = %f) should have CT = %f'%(smi,newCT,CT)
def _testBertzCTLong(self):
""" test calculation of Bertz 'C(T)' index
NOTE: this is a backwards compatibility test, because of the changes
w.r.t. the treatment of aromatic atoms in the new version, we need
to ignore molecules with aromatic rings...
"""
col = 1
inF = open(os.path.join(RDConfig.RDCodeDir,'Chem','tests','PP_descrs_regress.2.csv'),'r')
lineNum=0
for line in inF.xreadlines():
lineNum+=1
if line[0] != '#':
splitL = line.split(',')
smi = splitL[0]
try:
m = Chem.MolFromSmiles(smi)
except:
m = None
assert m,'line %d, smiles: %s'%(lineNum,smi)
useIt=1
for atom in m.GetAtoms():
if atom.GetIsAromatic():
useIt=0
break
if useIt:
tgtVal = float(splitL[col])
try:
val = GraphDescriptors.BertzCT(m)
except:
val = 666
assert feq(val,tgtVal,1e-4),'line %d, mol %s (CT calc = %f) should have CT = %f'%(lineNum,smi,val,tgtVal)
def __testDesc(self,fileN,col,func):
inF = open(os.path.join(RDConfig.RDCodeDir,'Chem','tests',fileN),'r')
lineNum=0
for line in inF.xreadlines():
lineNum+=1
if line[0] != '#':
splitL = line.split(',')
smi = splitL[0]
try:
m = Chem.MolFromSmiles(smi)
except:
m = None
assert m,'line %d, smiles: %s'%(lineNum,smi)
useIt=1
if useIt:
tgtVal = float(splitL[col])
if not feq(tgtVal,666.0):
try:
val = func(m)
except:
val = 666
assert feq(val,tgtVal,1e-4),'line %d, mol %s (calc = %f) should have val = %f'%(lineNum,smi,val,tgtVal)
def testChi0Long(self):
""" test calculation of Chi0
"""
col = 2
self.__testDesc('PP_descrs_regress.csv',col,GraphDescriptors.Chi0)
def _testChi0Long2(self):
""" test calculation of Chi0
"""
col = 2
self.__testDesc('PP_descrs_regress.2.csv',col,GraphDescriptors.Chi0)
def testHallKierAlphaLong(self):
""" test calculation of the Hall-Kier Alpha value
"""
col = 3
self.__testDesc('PP_descrs_regress.csv',col,GraphDescriptors.HallKierAlpha)
def _testHallKierAlphaLong2(self):
""" test calculation of the Hall-Kier Alpha value
"""
col = 3
self.__testDesc('PP_descrs_regress.2.csv',col,GraphDescriptors.HallKierAlpha)
def testIpc(self):
""" test calculation of Ipc.
"""
data = [('CCCCC',1.40564,11.24511),('CCC(C)C',1.37878, 9.65148),('CC(C)(C)C',0.72193,3.60964),('CN(CC)CCC',1.67982,31.91664),('C1CCCCC1',1.71997,34.39946),('CC1CCCCC1',1.68562,47.19725),('Cc1ccccc1',1.68562,47.19725),('CC(C)=C(C)C',1.36096,13.60964),('C#N',1.00000,2.00000),('OC#N',0.91830,2.75489)]
for smi,res1,res2 in data:
m = Chem.MolFromSmiles(smi)
Ipc = GraphDescriptors.Ipc(m, forceDMat=1)
Ipc_avg = GraphDescriptors.Ipc(m,avg = 1, forceDMat=1)
assert feq(Ipc_avg,res1,1e-3),'mol %s (Ipc_avg=%f) should have Ipc_avg=%f'%(smi,Ipc_avg,res1)
assert feq(Ipc,res2,1e-3),'mol %s (Ipc=%f) should have Ipc=%f'%(smi,Ipc,res2)
Ipc = GraphDescriptors.Ipc(m)
Ipc_avg = GraphDescriptors.Ipc(m,avg = 1)
assert feq(Ipc_avg,res1,1e-3),'2nd pass: mol %s (Ipc_avg=%f) should have Ipc_avg=%f'%(smi,Ipc_avg,res1)
assert feq(Ipc,res2,1e-3),'2nd pass: mol %s (Ipc=%f) should have Ipc=%f'%(smi,Ipc,res2)
def _testIpcLong(self):
""" test calculation of Ipc
"""
col = 4
self.__testDesc('PP_descrs_regress.csv',col,GraphDescriptors.Ipc)
def _testIpcLong2(self):
""" test calculation of Ipc
"""
col = 4
self.__testDesc('PP_descrs_regress.2.csv',col,GraphDescriptors.Ipc)
def testKappa1(self):
""" test calculation of the Hall-Kier kappa1 value
corrected data from Tables 3 and 6 of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
data = [('C12CC2C3CC13',2.344),
('C1CCC12CC2',3.061),
('C1CCCCC1',4.167),
('CCCCCC',6.000),
('CCC(C)C1CCC(C)CC1',9.091),
('CC(C)CC1CCC(C)CC1',9.091),
('CC(C)C1CCC(C)CCC1',9.091)
]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
kappa = GraphDescriptors.Kappa1(m)
assert feq(kappa,res,1e-3),'mol %s (kappa1=%f) should have kappa1=%f'%(smi,kappa,res)
def testKappa2(self):
""" test calculation of the Hall-Kier kappa2 value
corrected data from Tables 5 and 6 of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
data = [
('[C+2](C)(C)(C)(C)(C)C',0.667),
('[C+](C)(C)(C)(C)(CC)',1.240),
('C(C)(C)(C)(CCC)',2.3444),
('CC(C)CCCC',4.167),
('CCCCCCC',6.000),
('CCCCCC',5.000),
('CCCCCCC',6.000),
('C1CCCC1',1.440),
('C1CCCC1C',1.633),
('C1CCCCC1',2.222),
('C1CCCCCC1',3.061),
('CCCCC',4.00),
('CC=CCCC',4.740),
('C1=CN=CN1',0.884),
('c1ccccc1',1.606),
('c1cnccc1',1.552),
('n1ccncc1',1.500),
('CCCCF',3.930),
('CCCCCl',4.290),
('CCCCBr',4.480),
('CCC(C)C1CCC(C)CC1',4.133),
('CC(C)CC1CCC(C)CC1',4.133),
('CC(C)C1CCC(C)CCC1',4.133)
]
for smi,res in data:
#print smi
m = Chem.MolFromSmiles(smi)
kappa = GraphDescriptors.Kappa2(m)
assert feq(kappa,res,1e-3),'mol %s (kappa2=%f) should have kappa2=%f'%(smi,kappa,res)
def testKappa3(self):
""" test calculation of the Hall-Kier kappa3 value
corrected data from Tables 3 and 6 of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
data = [
('C[C+](C)(C)(C)C(C)(C)C',2.000),
('CCC(C)C(C)(C)(CC)',2.380),
('CCC(C)CC(C)CC',4.500),
('CC(C)CCC(C)CC',5.878),
('CC(C)CCCC(C)C',8.000),
('CCC(C)C1CCC(C)CC1',2.500),
('CC(C)CC1CCC(C)CC1',3.265),
('CC(C)C1CCC(C)CCC1',2.844)
]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
kappa = GraphDescriptors.Kappa3(m)
assert feq(kappa,res,1e-3),'mol %s (kappa3=%f) should have kappa3=%f'%(smi,kappa,res)
def testKappa3Long(self):
""" test calculation of kappa3
"""
col = 5
self.__testDesc('PP_descrs_regress.csv',col,GraphDescriptors.Kappa3)
def _testKappa3Long2(self):
""" test calculation of kappa3
"""
col = 5
self.__testDesc('PP_descrs_regress.2.csv',col,GraphDescriptors.Kappa3)
def _testLabuteASALong(self):
""" test calculation of Labute's ASA value
"""
col = 6
self.__testDesc('PP_descrs_regress.csv',col,lambda x:MolSurf.LabuteASA(x,includeHs=1))
def _testLabuteASALong2(self):
""" test calculation of Labute's ASA value
"""
col = 6
self.__testDesc('PP_descrs_regress.2.csv',col,lambda x:MolSurf.LabuteASA(x,includeHs=1))
def _testTPSAShortNCI(self):
" Short TPSA test "
inName = RDConfig.RDDataDir+'/NCI/first_200.tpsa.csv'
inF = open(inName,'r')
lines = inF.readlines()
for line in lines:
if line[0] != '#':
line.strip()
smi,ans = line.split(',')
ans = float(ans)
mol = Chem.MolFromSmiles(smi)
calc = MolSurf.TPSA(mol)
assert feq(calc,ans),'bad TPSA for SMILES %s (%.2f != %.2f)'%(smi,calc,ans)
def _testTPSALongNCI(self):
" Long TPSA test "
fileN = 'tpsa_regr.csv'
inF = open(os.path.join(RDConfig.RDCodeDir,'Chem','tests',fileN),'r')
lines = inF.readlines()
lineNo = 0
for line in lines:
lineNo+=1
if line[0] != '#':
line.strip()
smi,ans = line.split(',')
ans = float(ans)
try:
mol = Chem.MolFromSmiles(smi)
except:
import traceback
traceback.print_exc()
mol = None
assert mol,"line %d, failed for smiles: %s"%(lineNo,smi)
calc = MolSurf.TPSA(mol)
assert feq(calc,ans),'line %d: bad TPSA for SMILES %s (%.2f != %.2f)'%(lineNo,smi,calc,ans)
def testTPSALong(self):
""" test calculation of TPSA
"""
col = 28
self.__testDesc('PP_descrs_regress.csv',col,MolSurf.TPSA)
def _testTPSALong2(self):
""" test calculation of TPSA
"""
col = 28
self.__testDesc('PP_descrs_regress.2.csv',col,MolSurf.TPSA)
def _testLipinskiLong(self):
""" test calculation of Lipinski params
"""
fName = 'PP_descrs_regress.csv'
# we can't do H Acceptors for these pyridine-containing molecules
# because the values will be wrong for EVERY one.
#col = 29
#self.__testDesc(fName,col,Lipinski.NumHAcceptors)
col = 30
self.__testDesc(fName,col,Lipinski.NumHDonors)
col = 31
self.__testDesc(fName,col,Lipinski.NumHeteroatoms)
col = 32
self.__testDesc(fName,col,Lipinski.NumRotatableBonds)
def _testHAcceptorsLong(self):
""" test calculation of Lipinski params
"""
fName = 'Block_regress.Lip.csv'
col = 1
self.__testDesc(fName,col,Lipinski.NumHAcceptors)
def _testHDonorsLong(self):
""" test calculation of Lipinski params
"""
fName = 'Block_regress.Lip.csv'
col = 2
self.__testDesc(fName,col,Lipinski.NumHDonors)
def _testHeterosLong(self):
""" test calculation of Lipinski params
"""
fName = 'Block_regress.Lip.csv'
col = 3
self.__testDesc(fName,col,Lipinski.NumHeteroatoms)
def _testRotBondsLong(self):
""" test calculation of Lipinski params
"""
fName = 'Block_regress.Lip.csv'
col = 4
self.__testDesc(fName,col,Lipinski.NumRotatableBonds)
def _testLogPLong(self):
""" test calculation of Lipinski params
"""
fName = 'PP_descrs_regress.csv'
col = 33
self.__testDesc(fName,col,lambda x:Crippen.MolLogP(x,addHs=1))
def _testLogPLong2(self):
""" test calculation of Lipinski params
"""
fName = 'PP_descrs_regress.2.csv'
col = 33
self.__testDesc(fName,col,lambda x:Crippen.MolLogP(x,addHs=1))
def _testMOELong(self):
""" test calculation of MOE-type descriptors
"""
fName = 'PP_descrs_regress.VSA.csv'
col = 1
self.__testDesc(fName,col,MolSurf.SMR_VSA1)
col = 2
self.__testDesc(fName,col,MolSurf.SMR_VSA10)
col = 3
self.__testDesc(fName,col,MolSurf.SMR_VSA2)
col = 4
self.__testDesc(fName,col,MolSurf.SMR_VSA3)
col = 5
self.__testDesc(fName,col,MolSurf.SMR_VSA4)
col = 6
self.__testDesc(fName,col,MolSurf.SMR_VSA5)
col = 7
self.__testDesc(fName,col,MolSurf.SMR_VSA6)
col = 8
self.__testDesc(fName,col,MolSurf.SMR_VSA7)
col = 9
self.__testDesc(fName,col,MolSurf.SMR_VSA8)
col = 10
self.__testDesc(fName,col,MolSurf.SMR_VSA9)
col = 11
self.__testDesc(fName,col,MolSurf.SlogP_VSA1)
col = 12
self.__testDesc(fName,col,MolSurf.SlogP_VSA10)
col = 13
self.__testDesc(fName,col,MolSurf.SlogP_VSA11)
col = 14
self.__testDesc(fName,col,MolSurf.SlogP_VSA12)
def _testMOELong2(self):
""" test calculation of MOE-type descriptors
"""
fName = 'PP_descrs_regress.VSA.2.csv'
col = 1
self.__testDesc(fName,col,MolSurf.SMR_VSA1)
col = 2
self.__testDesc(fName,col,MolSurf.SMR_VSA10)
col = 11
self.__testDesc(fName,col,MolSurf.SlogP_VSA1)
col = 12
self.__testDesc(fName,col,MolSurf.SlogP_VSA10)
col = 13
self.__testDesc(fName,col,MolSurf.SlogP_VSA11)
col = 14
self.__testDesc(fName,col,MolSurf.SlogP_VSA12)
def testBalabanJ(self):
""" test calculation of the Balaban J value
J values are from Balaban's paper and have had roundoff
errors and typos corrected.
"""
data = [# alkanes
('CC',1.0),('CCC',1.6330),
('CCCC',1.9747),('CC(C)C',2.3238),
('CCCCC',2.1906),('CC(C)CC',2.5396),('CC(C)(C)C',3.0237),
('CCCCCC',2.3391),('CC(C)CCC',2.6272),('CCC(C)CC',2.7542),('CC(C)(C)CC',3.1685),
('CC(C)C(C)C',2.9935),
# cycloalkanes
('C1CCCCC1',2.0000),
('C1C(C)CCCC1',2.1229),
('C1C(CC)CCCC1',2.1250),
('C1C(C)C(C)CCC1',2.2794),
('C1C(C)CC(C)CC1',2.2307),
('C1C(C)CCC(C)C1',2.1924),
('C1C(CCC)CCCC1',2.0779),
('C1C(C(C)C)CCCC1',2.2284),
('C1C(CC)C(C)CCC1',2.2973),
('C1C(CC)CC(C)CC1',2.2317),
('C1C(CC)CCC(C)C1',2.1804),
('C1C(C)C(C)C(C)CC1',2.4133),
('C1C(C)C(C)CC(C)C1',2.3462),
('C1C(C)CC(C)CC1(C)',2.3409),
# aromatics
('c1ccccc1',3.0000),
('c1c(C)cccc1',3.0215),
('c1c(CC)cccc1',2.8321),
('c1c(C)c(C)ccc1',3.1349),
('c1c(C)cc(C)cc1',3.0777),
('c1c(C)ccc(C)c1',3.0325),
('c1c(CCC)cccc1',2.6149),
('c1c(C(C)C)cccc1',2.8483),
('c1c(CC)c(C)ccc1',3.0065),
('c1c(CC)cc(C)cc1',2.9369),
('c1c(CC)ccc(C)c1',2.8816),
('c1c(C)c(C)c(C)cc1',3.2478),
('c1c(C)c(C)cc(C)c1',3.1717),
('c1c(C)cc(C)cc1(C)',3.1657)
]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
j = GraphDescriptors.BalabanJ(m,forceDMat=1)
assert feq(j,res),'mol %s (J=%f) should have J=%f'%(smi,j,res)
j = GraphDescriptors.BalabanJ(m)
assert feq(j,res),'second pass: mol %s (J=%f) should have J=%f'%(smi,j,res)
def _testBalabanJLong(self):
""" test calculation of the balaban j value
"""
fName = 'PP_descrs_regress.rest.2.csv'
col = 1
self.__testDesc(fName,col,GraphDescriptors.BalabanJ)
def _testKappa1Long(self):
""" test calculation of kappa1
"""
fName = 'PP_descrs_regress.rest.2.csv'
col = 31
self.__testDesc(fName,col,GraphDescriptors.Kappa1)
def _testKappa2Long(self):
""" test calculation of kappa2
"""
fName = 'PP_descrs_regress.rest.2.csv'
col = 32
self.__testDesc(fName,col,GraphDescriptors.Kappa2)
def _testChi0Long(self):
fName = 'PP_descrs_regress.rest.2.csv'
col = 5
self.__testDesc(fName,col,GraphDescriptors.Chi0)
def _testChi1Long(self):
fName = 'PP_descrs_regress.rest.2.csv'
col = 8
self.__testDesc(fName,col,GraphDescriptors.Chi1)
def _testChi0v(self):
""" test calculation of Chi0v
"""
data = [('CCCCCC',4.828),('CCC(C)CC',4.992),('CC(C)CCC',4.992),
('CC(C)C(C)C',5.155),('CC(C)(C)CC',5.207),
('CCCCCO',4.276),('CCC(O)CC',4.439),('CC(O)(C)CC',4.654),('c1ccccc1O',3.834),
('CCCl',2.841),('CCBr',3.671),('CCI',4.242)]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
chi = GraphDescriptors.Chi0v(m)
assert feq(chi,res,1e-3),'mol %s (Chi0v=%f) should have Chi0V=%f'%(smi,chi,res)
def _testChi0vLong(self):
fName = 'PP_descrs_regress.rest.2.csv'
col = 7
self.__testDesc(fName,col,GraphDescriptors.Chi0v)
def testChi1v(self):
""" test calculation of Chi1v
"""
data = [('CCCCCC',2.914),('CCC(C)CC',2.808),('CC(C)CCC',2.770),
('CC(C)C(C)C',2.643),('CC(C)(C)CC',2.561),
('CCCCCO',2.523),('CCC(O)CC',2.489),('CC(O)(C)CC',2.284),('c1ccccc1O',2.134)]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
chi = GraphDescriptors.Chi1v(m)
assert feq(chi,res,1e-3),'mol %s (Chi1v=%f) should have Chi1V=%f'%(smi,chi,res)
def _testChi1vLong(self):
fName = 'PP_descrs_regress.rest.2.csv'
col = 10
self.__testDesc(fName,col,GraphDescriptors.Chi1v)
def testPathCounts(self):
""" FIX: this should be in some other file
"""
data = [('CCCCCC',(6,5,4,3,2,1)),
('CCC(C)CC',(6,5,5,4,1,0)),
('CC(C)CCC',(6,5,5,3,2,0)),
('CC(C)C(C)C',(6,5,6,4,0,0)),
('CC(C)(C)CC',(6,5,7,3,0,0)),
('CCCCCO',(6,5,4,3,2,1)),
('CCC(O)CC',(6,5,5,4,1,0)),
('CC(O)(C)CC',(6,5,7,3,0,0)),
('c1ccccc1O',(7,7,8,8,8,8)),
]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
for i in range(1,6):
cnt = len(Chem.FindAllPathsOfLengthN(m,i,useBonds=1))
assert cnt==res[i],(smi,i,cnt,res[i],Chem.FindAllPathsOfLengthN(m,i,useBonds=1))
cnt = len(Chem.FindAllPathsOfLengthN(m,i+1,useBonds=0))
assert cnt==res[i],(smi,i,cnt,res[i],Chem.FindAllPathsOfLengthN(m,i+1,useBonds=1))
def testChi2v(self):
""" test calculation of Chi2v
"""
data = [('CCCCCC',1.707),('CCC(C)CC',1.922),('CC(C)CCC',2.183),
('CC(C)C(C)C',2.488),('CC(C)(C)CC',2.914),
('CCCCCO',1.431),('CCC(O)CC',1.470),('CC(O)(C)CC',2.166),('c1ccccc1O',1.336),
]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
chi = GraphDescriptors.Chi2v(m)
assert feq(chi,res,1e-3),'mol %s (Chi2v=%f) should have Chi2V=%f'%(smi,chi,res)
def _testChi2vLong(self):
fName = 'PP_descrs_regress.rest.2.csv'
col = 12
self.__testDesc(fName,col,GraphDescriptors.Chi2v)
def testChi3v(self):
""" test calculation of Chi3v
"""
data = [('CCCCCC',0.957),('CCC(C)CC',1.394),('CC(C)CCC',0.866),('CC(C)C(C)C',1.333),('CC(C)(C)CC',1.061),
('CCCCCO',0.762),('CCC(O)CC',0.943),('CC(O)(C)CC',0.865),('c1ccccc1O',0.756)]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
chi = GraphDescriptors.Chi3v(m)
assert feq(chi,res,1e-3),'mol %s (Chi3v=%f) should have Chi3V=%f'%(smi,chi,res)
def _testChi3vLong(self):
fName = 'PP_descrs_regress.rest.2.csv'
col = 14
self.__testDesc(fName,col,GraphDescriptors.Chi3v)
def testChi4v(self):
""" test calculation of Chi4v
"""
data = [('CCCCCC',0.500),('CCC(C)CC',0.289),('CC(C)CCC',0.577),
('CC(C)C(C)C',0.000),('CC(C)(C)CC',0.000),
('CCCCCO',0.362),('CCC(O)CC',0.289),('CC(O)(C)CC',0.000),('c1ccccc1O',0.428)]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
chi = GraphDescriptors.Chi4v(m)
assert feq(chi,res,1e-3),'mol %s (Chi4v=%f) should have Chi4V=%f'%(smi,chi,res)
def testChi5v(self):
""" test calculation of Chi5v
"""
data = [('CCCCCC',0.250),('CCC(C)CC',0.000),('CC(C)CCC',0.000),
('CC(C)C(C)C',0.000),('CC(C)(C)CC',0.000),
('CCCCCO',0.112),('CCC(O)CC',0.000),('CC(O)(C)CC',0.000),('c1ccccc1O',0.242)]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
chi = GraphDescriptors.ChiNv_(m,5)
assert feq(chi,res,1e-3),'mol %s (Chi5v=%f) should have Chi5V=%f'%(smi,chi,res)
def testChi0n(self):
""" test calculation of Chi0n
"""
data = [('CCCCCC',4.828),('CCC(C)CC',4.992),('CC(C)CCC',4.992),
('CC(C)C(C)C',5.155),('CC(C)(C)CC',5.207),
('CCCCCO',4.276),('CCC(O)CC',4.439),('CC(O)(C)CC',4.654),('c1ccccc1O',3.834),
('CCCl',2.085),('CCBr',2.085),('CCI',2.085),]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
chi = GraphDescriptors.Chi0n(m)
assert feq(chi,res,1e-3),'mol %s (Chi0n=%f) should have Chi0n=%f'%(smi,chi,res)
def _testChi0nLong(self):
fName = 'PP_descrs_regress.rest.2.csv'
col = 6
self.__testDesc(fName,col,GraphDescriptors.Chi0n)
def testChi1n(self):
""" test calculation of Chi1n
"""
data = [('CCCCCC',2.914),('CCC(C)CC',2.808),('CC(C)CCC',2.770),
('CC(C)C(C)C',2.643),('CC(C)(C)CC',2.561),
('CCCCCO',2.523),('CCC(O)CC',2.489),('CC(O)(C)CC',2.284),('c1ccccc1O',2.134)]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
chi = GraphDescriptors.Chi1n(m)
assert feq(chi,res,1e-3),'mol %s (Chi1n=%f) should have Chi1N=%f'%(smi,chi,res)
def _testChi1nLong(self):
fName = 'PP_descrs_regress.rest.2.csv'
col = 9
self.__testDesc(fName,col,GraphDescriptors.Chi1n)
def testChi2n(self):
""" test calculation of Chi2n
"""
data = [('CCCCCC',1.707),('CCC(C)CC',1.922),('CC(C)CCC',2.183),
('CC(C)C(C)C',2.488),('CC(C)(C)CC',2.914),
('CCCCCO',1.431),('CCC(O)CC',1.470),('CC(O)(C)CC',2.166),('c1ccccc1O',1.336)]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
chi = GraphDescriptors.Chi2n(m)
assert feq(chi,res,1e-3),'mol %s (Chi2n=%f) should have Chi2N=%f'%(smi,chi,res)
def _testChi2nLong(self):
fName = 'PP_descrs_regress.rest.2.csv'
col = 11
self.__testDesc(fName,col,GraphDescriptors.Chi2n)
def testChi3n(self):
""" test calculation of Chi3n
"""
data = [('CCCCCC',0.957),('CCC(C)CC',1.394),('CC(C)CCC',0.866),('CC(C)C(C)C',1.333),('CC(C)(C)CC',1.061),
('CCCCCO',0.762),('CCC(O)CC',0.943),('CC(O)(C)CC',0.865),('c1ccccc1O',0.756)]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
chi = GraphDescriptors.Chi3n(m)
assert feq(chi,res,1e-3),'mol %s (Chi3n=%f) should have Chi3N=%f'%(smi,chi,res)
def _testChi3nLong(self):
fName = 'PP_descrs_regress.rest.2.csv'
col = 13
self.__testDesc(fName,col,GraphDescriptors.Chi3n)
def testChi4n(self):
""" test calculation of Chi4n
"""
data = [('CCCCCC',0.500),('CCC(C)CC',0.289),('CC(C)CCC',0.577),
('CC(C)C(C)C',0.000),('CC(C)(C)CC',0.000),
('CCCCCO',0.362),('CCC(O)CC',0.289),('CC(O)(C)CC',0.000),('c1ccccc1O',0.428)]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
chi = GraphDescriptors.Chi4n(m)
assert feq(chi,res,1e-3),'mol %s (Chi4n=%f) should have Chi4N=%f'%(smi,chi,res)
def testIssue125(self):
""" test an issue with calculating BalabanJ
"""
smi = 'O=C(OC)C1=C(C)NC(C)=C(C(OC)=O)C1C2=CC=CC=C2[N+]([O-])=O'
m1 = Chem.MolFromSmiles(smi)
m2 = Chem.MolFromSmiles(smi)
Chem.MolToSmiles(m1)
j1=GraphDescriptors.BalabanJ(m1)
j2=GraphDescriptors.BalabanJ(m2)
assert feq(j1,j2)
def testOrderDepend(self):
""" test order dependence of some descriptors:
"""
data = [('C=CC=C',21.01955,2.73205),
('O=CC=O',25.01955,2.73205),
('FCC(=O)CF',46.7548875,2.98816),
('O=C1C=CC(=O)C=C1',148.705216,2.8265),
('C12C(F)=C(O)C(F)C1C(F)=C(O)C(F)2',315.250442,2.4509),
('C12CC=CCC1C(=O)C3CC=CCC3C(=O)2',321.539522,1.95986)]
for smi,CT,bal in data:
m = Chem.MolFromSmiles(smi)
newBal = GraphDescriptors.BalabanJ(m, forceDMat = 1)
assert feq(newBal,bal,1e-4),'mol %s %f!=%f'%(smi,newBal,bal)
m = Chem.MolFromSmiles(smi)
newCT = GraphDescriptors.BertzCT(m, forceDMat = 1)
assert feq(newCT,CT,1e-4),'mol %s (CT calc = %f) should have CT = %f'%(smi,newCT,CT)
m = Chem.MolFromSmiles(smi)
newCT = GraphDescriptors.BertzCT(m, forceDMat = 1)
assert feq(newCT,CT,1e-4),'mol %s (CT calc = %f) should have CT = %f'%(smi,newCT,CT)
newBal = GraphDescriptors.BalabanJ(m, forceDMat = 1)
assert feq(newBal,bal,1e-4),'mol %s %f!=%f'%(smi,newBal,bal)
m = Chem.MolFromSmiles(smi)
newBal = GraphDescriptors.BalabanJ(m, forceDMat = 1)
assert feq(newBal,bal,1e-4),'mol %s %f!=%f'%(smi,newBal,bal)
newCT = GraphDescriptors.BertzCT(m, forceDMat = 1)
assert feq(newCT,CT,1e-4),'mol %s (CT calc = %f) should have CT = %f'%(smi,newCT,CT)
if __name__ == '__main__':
import sys,getopt,re
doLong=0
if len(sys.argv) >1:
args,extras=getopt.getopt(sys.argv[1:],'l')
for arg,val in args:
if arg=='-l':
doLong=1
sys.argv.remove('-l')
if doLong:
for methName in dir(TestCase):
if re.match('_test',methName):
newName = re.sub('_test','test',methName)
exec('TestCase.%s = TestCase.%s'%(newName,methName))
unittest.main()
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