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 CalculateIpc(mol):
"""
#################################################################
This returns the information content of the coefficients of the
characteristic polynomial of the adjacency matrix of a
hydrogen-suppressed graph of a molecule.
'avg = 1' returns the information content divided by the total
population.
From D. Bonchev & N. Trinajstic, J. Chem. Phys. vol 67,
4517-4533 (1977)
---->Ipc(log value)
Usage:
result=CalculateIpc(mol)
Input: mol is a molecule object
Output: result is a numeric value
#################################################################
"""
co = GD.Ipc(mol)
if co == 0:
return 0
else:
return numpy.log10(GD.Ipc(mol))
def testIpc(self):
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)
self.assertAlmostEqual(Ipc_avg, res1, delta=1e-3,
msg='mol %s (Ipc_avg=%f) should have Ipc_avg=%f' % (smi, Ipc_avg,
res1))
self.assertAlmostEqual(Ipc, res2, delta=1e-3,
msg='mol %s (Ipc=%f) should have Ipc=%f' % (smi, Ipc, res2))
Ipc = GraphDescriptors.Ipc(m)
Ipc_avg = GraphDescriptors.Ipc(m, avg=1)
self.assertAlmostEqual(Ipc_avg, res1, delta=1e-3,
msg='2nd pass: mol %s (Ipc_avg=%f) should have Ipc_avg=%f' % (
smi, Ipc_avg, res1))
self.assertAlmostEqual(Ipc, res2, delta=1e-3,
msg='2nd pass: mol %s (Ipc=%f) should have Ipc=%f' % (smi, Ipc, res2))
if doLong:
self.__testDesc('PP_descrs_regress.csv', 4, GraphDescriptors.Ipc)
self.__testDesc('PP_descrs_regress.2.csv', 4, GraphDescriptors.Ipc)
def CalculateIpc(mol: Chem.Mol) -> float:
"""Get Bonchev-Trinajstic complexity index.
Or Ipc.
From Bonchev D. & Trinajstic N., J. Chem. Phys. (1977) 67,4517-4533.
"""
return numpy.log10(GD.Ipc(mol))
def CalculateIpc(mol):
"""
Ipc index is the information for polynomial coefficients
based information theory.
Parameters:
mol: RDKit molecule object
Returns:
Ipc: Ipc index
"""
temp = GD.Ipc(mol)
if temp > 0:
return numpy.log10(temp)
else:
return "NaN"
def CalculateIpc(mol):
"""
This returns the information content of the coefficients
of the characteristic polynomial of the adjacency matrix
of a hydrogen-suppressed graph of a molecule.
'avg = 1' returns the information content divided by the total population.
From D. Bonchev & N. Trinajstic, J. Chem. Phys. vol 67, 4517-4533 (1977)
log of log values for index
"""
temp = GD.Ipc(mol)
if temp <= 0:
temp = MINVALUE
res = np.log10(temp) + 8 + MINVALUE
return np.log(res)
def calc_rdkit(mol):
descriptors = pd.Series(
np.array([
Crippen.MolLogP(mol),
Crippen.MolMR(mol),
Descriptors.FpDensityMorgan1(mol),
Descriptors.FpDensityMorgan2(mol),
Descriptors.FpDensityMorgan3(mol),
Descriptors.FractionCSP3(mol),
Descriptors.HeavyAtomMolWt(mol),
Descriptors.MaxAbsPartialCharge(mol),
Descriptors.MaxPartialCharge(mol),
Descriptors.MinAbsPartialCharge(mol),
Descriptors.MinPartialCharge(mol),
Descriptors.MolWt(mol),
Descriptors.NumRadicalElectrons(mol),
Descriptors.NumValenceElectrons(mol),
EState.EState.MaxAbsEStateIndex(mol),
EState.EState.MaxEStateIndex(mol),
EState.EState.MinAbsEStateIndex(mol),
EState.EState.MinEStateIndex(mol),
EState.EState_VSA.EState_VSA1(mol),
EState.EState_VSA.EState_VSA10(mol),
EState.EState_VSA.EState_VSA11(mol),
EState.EState_VSA.EState_VSA2(mol),
EState.EState_VSA.EState_VSA3(mol),
EState.EState_VSA.EState_VSA4(mol),
EState.EState_VSA.EState_VSA5(mol),
EState.EState_VSA.EState_VSA6(mol),
EState.EState_VSA.EState_VSA7(mol),
EState.EState_VSA.EState_VSA8(mol),
EState.EState_VSA.EState_VSA9(mol),
Fragments.fr_Al_COO(mol),
Fragments.fr_Al_OH(mol),
Fragments.fr_Al_OH_noTert(mol),
Fragments.fr_aldehyde(mol),
Fragments.fr_alkyl_carbamate(mol),
Fragments.fr_alkyl_halide(mol),
Fragments.fr_allylic_oxid(mol),
Fragments.fr_amide(mol),
Fragments.fr_amidine(mol),
Fragments.fr_aniline(mol),
Fragments.fr_Ar_COO(mol),
Fragments.fr_Ar_N(mol),
Fragments.fr_Ar_NH(mol),
Fragments.fr_Ar_OH(mol),
Fragments.fr_ArN(mol),
Fragments.fr_aryl_methyl(mol),
Fragments.fr_azide(mol),
Fragments.fr_azo(mol),
Fragments.fr_barbitur(mol),
Fragments.fr_benzene(mol),
Fragments.fr_benzodiazepine(mol),
Fragments.fr_bicyclic(mol),
Fragments.fr_C_O(mol),
Fragments.fr_C_O_noCOO(mol),
Fragments.fr_C_S(mol),
Fragments.fr_COO(mol),
Fragments.fr_COO2(mol),
Fragments.fr_diazo(mol),
Fragments.fr_dihydropyridine(mol),
Fragments.fr_epoxide(mol),
Fragments.fr_ester(mol),
Fragments.fr_ether(mol),
Fragments.fr_furan(mol),
Fragments.fr_guanido(mol),
Fragments.fr_halogen(mol),
Fragments.fr_hdrzine(mol),
Fragments.fr_hdrzone(mol),
Fragments.fr_HOCCN(mol),
Fragments.fr_imidazole(mol),
Fragments.fr_imide(mol),
Fragments.fr_Imine(mol),
Fragments.fr_isocyan(mol),
Fragments.fr_isothiocyan(mol),
Fragments.fr_ketone(mol),
Fragments.fr_ketone_Topliss(mol),
Fragments.fr_lactam(mol),
Fragments.fr_lactone(mol),
Fragments.fr_methoxy(mol),
Fragments.fr_morpholine(mol),
Fragments.fr_N_O(mol),
Fragments.fr_Ndealkylation1(mol),
Fragments.fr_Ndealkylation2(mol),
Fragments.fr_NH0(mol),
Fragments.fr_NH1(mol),
Fragments.fr_NH2(mol),
Fragments.fr_Nhpyrrole(mol),
Fragments.fr_nitrile(mol),
Fragments.fr_nitro(mol),
Fragments.fr_nitro_arom(mol),
Fragments.fr_nitro_arom_nonortho(mol),
Fragments.fr_nitroso(mol),
Fragments.fr_oxazole(mol),
Fragments.fr_oxime(mol),
Fragments.fr_para_hydroxylation(mol),
Fragments.fr_phenol(mol),
Fragments.fr_phenol_noOrthoHbond(mol),
Fragments.fr_phos_acid(mol),
Fragments.fr_phos_ester(mol),
Fragments.fr_piperdine(mol),
Fragments.fr_piperzine(mol),
Fragments.fr_priamide(mol),
Fragments.fr_prisulfonamd(mol),
Fragments.fr_pyridine(mol),
Fragments.fr_quatN(mol),
Fragments.fr_SH(mol),
Fragments.fr_sulfide(mol),
Fragments.fr_sulfonamd(mol),
Fragments.fr_sulfone(mol),
Fragments.fr_term_acetylene(mol),
Fragments.fr_tetrazole(mol),
Fragments.fr_thiazole(mol),
Fragments.fr_thiocyan(mol),
Fragments.fr_thiophene(mol),
Fragments.fr_unbrch_alkane(mol),
Fragments.fr_urea(mol),
GraphDescriptors.BalabanJ(mol),
GraphDescriptors.BertzCT(mol),
GraphDescriptors.Chi0(mol),
GraphDescriptors.Chi0n(mol),
GraphDescriptors.Chi0v(mol),
GraphDescriptors.Chi1(mol),
GraphDescriptors.Chi1n(mol),
GraphDescriptors.Chi1v(mol),
GraphDescriptors.Chi2n(mol),
GraphDescriptors.Chi2v(mol),
GraphDescriptors.Chi3n(mol),
GraphDescriptors.Chi3v(mol),
GraphDescriptors.Chi4n(mol),
GraphDescriptors.Chi4v(mol),
GraphDescriptors.HallKierAlpha(mol),
GraphDescriptors.Ipc(mol),
GraphDescriptors.Kappa1(mol),
GraphDescriptors.Kappa2(mol),
GraphDescriptors.Kappa3(mol),
Lipinski.HeavyAtomCount(mol),
Lipinski.NHOHCount(mol),
Lipinski.NOCount(mol),
Lipinski.NumAliphaticCarbocycles(mol),
Lipinski.NumAliphaticHeterocycles(mol),
Lipinski.NumAliphaticRings(mol),
Lipinski.NumAromaticCarbocycles(mol),
Lipinski.NumAromaticHeterocycles(mol),
Lipinski.NumAromaticRings(mol),
Lipinski.NumHAcceptors(mol),
Lipinski.NumHDonors(mol),
Lipinski.NumHeteroatoms(mol),
Lipinski.NumRotatableBonds(mol),
Lipinski.NumSaturatedCarbocycles(mol),
Lipinski.NumSaturatedHeterocycles(mol),
Lipinski.NumSaturatedRings(mol),
Lipinski.RingCount(mol),
MolSurf.LabuteASA(mol),
MolSurf.PEOE_VSA1(mol),
MolSurf.PEOE_VSA10(mol),
MolSurf.PEOE_VSA11(mol),
MolSurf.PEOE_VSA12(mol),
MolSurf.PEOE_VSA13(mol),
MolSurf.PEOE_VSA14(mol),
MolSurf.PEOE_VSA2(mol),
MolSurf.PEOE_VSA3(mol),
MolSurf.PEOE_VSA4(mol),
MolSurf.PEOE_VSA5(mol),
MolSurf.PEOE_VSA6(mol),
MolSurf.PEOE_VSA7(mol),
MolSurf.PEOE_VSA8(mol),
MolSurf.PEOE_VSA9(mol),
MolSurf.SlogP_VSA1(mol),
MolSurf.SlogP_VSA10(mol),
MolSurf.SlogP_VSA11(mol),
MolSurf.SlogP_VSA12(mol),
MolSurf.SlogP_VSA2(mol),
MolSurf.SlogP_VSA3(mol),
MolSurf.SlogP_VSA4(mol),
MolSurf.SlogP_VSA5(mol),
MolSurf.SlogP_VSA6(mol),
MolSurf.SlogP_VSA7(mol),
MolSurf.SlogP_VSA8(mol),
MolSurf.SlogP_VSA9(mol),
MolSurf.SMR_VSA1(mol),
MolSurf.SMR_VSA10(mol),
MolSurf.SMR_VSA2(mol),
MolSurf.SMR_VSA3(mol),
MolSurf.SMR_VSA4(mol),
MolSurf.SMR_VSA5(mol),
MolSurf.SMR_VSA6(mol),
MolSurf.SMR_VSA7(mol),
MolSurf.SMR_VSA8(mol),
MolSurf.SMR_VSA9(mol),
MolSurf.TPSA(mol)
]))
return descriptors
def CalculateIpc(mol):
return numpy.log10(GD.Ipc(mol))