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 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 get_descriptors(smiles):
"""
Get a dictionary of RDKit descriptors from a SMILES string.
Parameters
----------
smiles : str
The SMILES string of the chemical of interest
Returns
-------
descriptors : dict
A collection of molecular descriptors
Notes: Developed with RDKit 2019.03.4, although doc pages listed 2019.03.1
"""
mol = Chem.MolFromSmiles(smiles)
mol = Chem.AddHs(mol)
Chem.EmbedMolecule(mol, Chem.ETKDG())
descriptors = {}
# Starting with simple descriptors:
# https://www.rdkit.org/docs/source/rdkit.Chem.Descriptors.html
# Molecular weight
descriptors['molwt'] = Descriptors.ExactMolWt(mol)
# Partial charge metrics
descriptors['max_abs_partial_charge'] = Descriptors.MaxAbsPartialCharge(mol)
descriptors['max_partial_charge'] = Descriptors.MaxPartialCharge(mol)
descriptors['min_abs_partial_charge'] = Descriptors.MinAbsPartialCharge(mol)
descriptors['min_partial_charge'] = Descriptors.MinPartialCharge(mol)
# Basic electron counts
descriptors['num_radical_electrons'] = Descriptors.NumRadicalElectrons(mol)
descriptors['num_valence_electrons'] = Descriptors.NumValenceElectrons(mol)
# 3-D descriptors
# https://www.rdkit.org/docs/source/rdkit.Chem.Descriptors3D.html
# Calculating these should produce the same result, according to some basic tests
# descriptors['asphericity'] = rdMolDescriptors.CalcAsphericity(mol)
# descriptors['eccentricity'] = rdMolDescriptors.CalcEccentricity(mol)
descriptors['asphericity'] = Descriptors3D.Asphericity(mol)
descriptors['eccentricity'] = Descriptors3D.Eccentricity(mol)
descriptors['inertial_shape_factor'] = Descriptors3D.InertialShapeFactor(mol)
descriptors['radius_of_gyration'] = Descriptors3D.RadiusOfGyration(mol)
descriptors['spherocity_index'] = Descriptors3D.SpherocityIndex(mol)
# Graph descriptors
# https://www.rdkit.org/docs/source/rdkit.Chem.GraphDescriptors.html
descriptors['balaban_j'] = GraphDescriptors.BalabanJ(mol)
descriptors['bertz_ct'] = GraphDescriptors.BertzCT(mol)
descriptors['chi0'] = GraphDescriptors.Chi0(mol)
descriptors['chi0n'] = GraphDescriptors.Chi0n(mol)
descriptors['chi0v'] = GraphDescriptors.Chi0v(mol)
descriptors['chi1'] = GraphDescriptors.Chi1(mol)
descriptors['chi1n'] = GraphDescriptors.Chi1n(mol)
descriptors['chi1v'] = GraphDescriptors.Chi1v(mol)
descriptors['chi2n'] = GraphDescriptors.Chi2n(mol)
descriptors['chi2v'] = GraphDescriptors.Chi2v(mol)
descriptors['chi3n'] = GraphDescriptors.Chi3n(mol)
descriptors['chi3v'] = GraphDescriptors.Chi3v(mol)
descriptors['chi4n'] = GraphDescriptors.Chi4n(mol)
descriptors['chi4v'] = GraphDescriptors.Chi4v(mol)
descriptors['hall_kier_alpha'] = GraphDescriptors.HallKierAlpha(mol)
descriptors['kappa1'] = GraphDescriptors.Kappa1(mol)
descriptors['kappa2'] = GraphDescriptors.Kappa2(mol)
descriptors['kappa3'] = GraphDescriptors.Kappa3(mol)
# Predicted properties from Wildman and Crippen
descriptors['log_p'] = Descriptors.MolLogP(mol)
descriptors['refractivity'] = Descriptors.MolMR(mol)
return descriptors