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 main():
infile = open("molecule_training.csv", 'r')
infile.readline()
with open('train_molecule_new_features.csv', 'w') as f:
writer = csv.writer(f)
# writer.writerow(['index', 'Maximum Degree', 'Minimum Degree', 'Molecular Weight', 'Number of H-Bond Donors',
# 'Number of Rings', 'Number of Rotatable Bonds', 'Polar Surface Area', 'Graph', 'smiles',
# 'target'])
writer.writerow([
'index', 'Maximum Degree', 'Minimum Degree', 'Molecular Weight',
'Number of H-Bond Donors', 'Number of Rings',
'Number of Rotatable Bonds', 'Polar Surface Area', 'fr_phos',
'aromatic_carbocycles', 'MolLogP', 'PEOE_VSA1', 'Fingerprint',
'smiles', 'target'
])
for line in infile:
line = line.strip('\n\r ')
line = line.split(",")
smiles = line[10].strip()
#edge_list = to_graph(smiles)
mol = Chem.MolFromSmiles(smiles)
# fingerprint_explicit_bitvector = RDKFingerprint(mol)
# fingerprint_bit_string = fingerprint_explicit_bitvector.ToBitString()
fingerprint_bit_string = GetMorganFingerprintAsBitVect(
mol, 2).ToBitString()
#writer.writerow(line[:8] + [fingerprint_bit_string, line[10], line[11]])
#writer.writerow(line[:8] + [edge_list] + [line[10], line[11]])
fr_phos = Fragments.fr_phos_acid(mol) + Fragments.fr_phos_ester(
mol)
aromatic_cc = Lipinski.NumAromaticCarbocycles(mol)
molLogP = Crippen.MolLogP(mol)
peoe_vsa1 = MolSurf.PEOE_VSA1(mol)
writer.writerow(line[:8] + [
fr_phos, aromatic_cc, molLogP, peoe_vsa1,
fingerprint_bit_string, line[10], line[11]
])
infile.close()
infile = open("molecule_TestFeatures.csv", 'r')
infile.readline()
with open('test_molecule_new_features.csv', 'w') as f:
writer = csv.writer(f)
# writer.writerow(['index', 'Maximum Degree', 'Minimum Degree', 'Molecular Weight', 'Number of H-Bond Donors',
# 'Number of Rings', 'Number of Rotatable Bonds', 'Polar Surface Area', 'Graph', 'smiles',
# 'target'])
writer.writerow([
'index', 'Maximum Degree', 'Minimum Degree', 'Molecular Weight',
'Number of H-Bond Donors', 'Number of Rings',
'Number of Rotatable Bonds', 'Polar Surface Area', 'fr_phos',
'aromatic_carbocycles', 'MolLogP', 'PEOE_VSA1', 'Fingerprint',
'smiles'
])
for line in infile:
line = line.strip('\n\r ')
line = line.split(",")
smiles = line[10].strip()
# edge_list = to_graph(smiles)
mol = Chem.MolFromSmiles(smiles)
# fingerprint_explicit_bitvector = RDKFingerprint(mol)
# fingerprint_bit_string = fingerprint_explicit_bitvector.ToBitString()
fingerprint_bit_string = GetMorganFingerprintAsBitVect(
mol, 2).ToBitString()
fr_phos = Fragments.fr_phos_acid(mol) + Fragments.fr_phos_ester(
mol)
aromatic_cc = Lipinski.NumAromaticCarbocycles(mol)
molLogP = Crippen.MolLogP(mol)
peoe_vsa1 = MolSurf.PEOE_VSA1(mol)
writer.writerow(line[:8] + [
fr_phos, aromatic_cc, molLogP, peoe_vsa1,
fingerprint_bit_string, line[10]
])
# writer.writerow(line[:8] + [edge_list] + [line[10], line[11]])
infile.close()
