def get_descriptors(mol, write=False): # Make a copy of the molecule dataframe desc = [ Lipinski.NumAromaticHeterocycles(mol), Lipinski.NumAromaticRings(mol), Lipinski.NumHDonors(mol), Lipinski.RingCount(mol), Lipinski.NHOHCount(mol), Lipinski.NumHeteroatoms(mol), Lipinski.NumAliphaticCarbocycles(mol), Lipinski.NumSaturatedCarbocycles(mol), Lipinski.NumAliphaticHeterocycles(mol), Lipinski.NumHAcceptors(mol), Lipinski.NumSaturatedHeterocycles(mol), Lipinski.NumAliphaticRings(mol), Descriptors.NumRadicalElectrons(mol), Descriptors.MaxPartialCharge(mol), Descriptors.NumValenceElectrons(mol), Lipinski.FractionCSP3(mol), Descriptors.MaxAbsPartialCharge(mol), Lipinski.NumAromaticCarbocycles(mol), Lipinski.NumSaturatedRings(mol), Lipinski.NumRotatableBonds(mol) ] desc = [0 if i != i else i for i in desc] return desc
def extract(x, from_smiles): if from_smiles: mol = Chem.MolFromSmiles(x) else: mol = x if (mol is None) or (len(mol.GetAtoms()) == 0): if include_3D: return [0] * 29 else: return [0] * 24 else: logP = Crippen.MolLogP(mol) refractivity = Crippen.MolMR(mol) weight = Descriptors.MolWt(mol) exact_weight = Descriptors.ExactMolWt(mol) heavy_weight = Descriptors.HeavyAtomMolWt(mol) heavy_count = Lipinski.HeavyAtomCount(mol) nhoh_count = Lipinski.NHOHCount(mol) no_count = Lipinski.NOCount(mol) hacceptor_count = Lipinski.NumHAcceptors(mol) hdonor_count = Lipinski.NumHDonors(mol) hetero_count = Lipinski.NumHeteroatoms(mol) rotatable_bond_count = Lipinski.NumRotatableBonds(mol) valance_electron_count = Descriptors.NumValenceElectrons(mol) amide_bond_count = rdMolDescriptors.CalcNumAmideBonds(mol) aliphatic_ring_count = Lipinski.NumAliphaticRings(mol) aromatic_ring_count = Lipinski.NumAromaticRings(mol) saturated_ring_count = Lipinski.NumSaturatedRings(mol) aliphatic_cycle_count = Lipinski.NumAliphaticCarbocycles(mol) aliphaticHetero_cycle_count = Lipinski.NumAliphaticHeterocycles( mol) aromatic_cycle_count = Lipinski.NumAromaticCarbocycles(mol) aromaticHetero_cycle_count = Lipinski.NumAromaticHeterocycles(mol) saturated_cycle_count = Lipinski.NumSaturatedCarbocycles(mol) saturatedHetero_cycle_count = Lipinski.NumSaturatedHeterocycles( mol) tpsa = rdMolDescriptors.CalcTPSA(mol) if include_3D: mol_3D = Chem.AddHs(mol) AllChem.EmbedMolecule(mol_3D) AllChem.MMFFOptimizeMolecule(mol_3D) eccentricity = rdMolDescriptors.CalcEccentricity(mol_3D) asphericity = rdMolDescriptors.CalcAsphericity(mol_3D) spherocity = rdMolDescriptors.CalcSpherocityIndex(mol_3D) inertial = rdMolDescriptors.CalcInertialShapeFactor(mol_3D) gyration = rdMolDescriptors.CalcRadiusOfGyration(mol_3D) return [ logP, refractivity, weight, exact_weight, heavy_weight, heavy_count, nhoh_count, no_count, hacceptor_count, hdonor_count, hetero_count, rotatable_bond_count, valance_electron_count, amide_bond_count, aliphatic_ring_count, aromatic_ring_count, saturated_ring_count, aliphatic_cycle_count, aliphaticHetero_cycle_count, aromatic_cycle_count, aromaticHetero_cycle_count, saturated_cycle_count, saturatedHetero_cycle_count, tpsa, eccentricity, asphericity, spherocity, inertial, gyration ] else: return [ logP, refractivity, weight, exact_weight, heavy_weight, heavy_count, nhoh_count, no_count, hacceptor_count, hdonor_count, hetero_count, rotatable_bond_count, valance_electron_count, amide_bond_count, aliphatic_ring_count, aromatic_ring_count, saturated_ring_count, aliphatic_cycle_count, aliphaticHetero_cycle_count, aromatic_cycle_count, aromaticHetero_cycle_count, saturated_cycle_count, saturatedHetero_cycle_count, tpsa ]
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