def OH(mol):
total = Fragments.fr_Ar_OH(mol)
total += Fragments.fr_Al_OH(mol)
return total
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 makeFeatures(fileName):
from rdkit import Chem
from rdkit.Chem import Fragments
from rdkit.Chem import AllChem
from rdkit.Chem import MolSurf
global featuresFile, numFeatures
featuresFile = open(fileName, 'w') # Molecule features output file
# run gaussian jobs
# gaussian.setNumMols()
# gaussian.makeAllGinps()
# gaussian.runGaussianOnAllGinps()
# open database file
drugDB = Chem.SDMolSupplier("FKBP12_binders.sdf")
if debug:
print "\n\tNo features data file found. Writing new features data file.\n"
text = "" # Placeholder for feature data
molCount = 0
convergedCount = 0
converged_and_different = 0
drug_name = []
# load fragment descriptor
Fragments._LoadPatterns(fileName='/usr/local/anaconda/pkgs/rdkit-2015.03.1-np19py27_0/share/RDKit/Data/FragmentDescriptors.csv')
# Select features of interest
for mol in drugDB:
if molCount > -1:
# print mol.GetProp("BindingDB Target Chain Sequence")
gaussian_log_file = "gaussian_files/drug_"+str(molCount)+".log"
converged, dipole, quadrupole, octapole, hexadecapole, dg_solv = gaussian.parseGaussianLog(gaussian_log_file)
if converged == "True" and mol.GetProp("BindingDB Target Chain Sequence") == "MGVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE":
if convergedCount ==0:
diff = "True"
else:
diff = "True"
for i in range(converged_and_different):
if mol.GetProp("BindingDB Ligand Name") == drug_name[i]:
diff = "False"
break
if diff == "True":
drug_name.append(mol.GetProp("BindingDB Ligand Name"))
text += "{}\n".format(AllChem.ComputeMolVolume(mol))
text += "{}\n".format(MolSurf.pyLabuteASA(mol))
text += "{}\n".format(mol.GetNumAtoms())
text += "{}\n".format(mol.GetNumBonds())
text += "{}\n".format(mol.GetNumHeavyAtoms())
text += "{}\n".format(dipole)
text += "{}\n".format(quadrupole)
text += "{}\n".format(octapole)
text += "{}\n".format(hexadecapole)
text += "{}\n".format(dg_solv)
text += "{}\n".format(Fragments.fr_Al_OH(mol)) # aliphatic alcohols
text += "{}\n".format(Fragments.fr_Ar_OH(mol)) # aromatic alcohols
text += "{}\n".format(Fragments.fr_ketone(mol)) # number of ketones
text += "{}\n".format(Fragments.fr_ether(mol)) # number of ether oxygens
text += "{}\n".format(Fragments.fr_ester(mol)) # number of esters
text += "{}\n".format(Fragments.fr_aldehyde(mol)) # number of aldehydes
text += "{}\n".format(Fragments.fr_COO(mol)) # number of carboxylic acids
text += "{}\n".format(Fragments.fr_benzene(mol)) # number of benzenes
text += "{}\n".format(Fragments.fr_Ar_N(mol)) # number of aromatic nitrogens
text += "{}\n".format(Fragments.fr_NH0(mol)) # number of tertiary amines
text += "{}\n".format(Fragments.fr_NH1(mol)) # number of secondary amines
text += "{}\n".format(Fragments.fr_NH2(mol)) # number of primary amines
text += "{}\n".format(Fragments.fr_amide(mol)) # number of amides
text += "{}\n".format(Fragments.fr_SH(mol)) # number of thiol groups
text += "{}\n".format(Fragments.fr_nitro(mol)) # number of nitro groups
text += "{}\n".format(Fragments.fr_furan(mol)) # number of furan rings
text += "{}\n".format(Fragments.fr_imidazole(mol)) # number of imidazole rings
text += "{}\n".format(Fragments.fr_oxazole(mol)) # number of oxazole rings
text += "{}\n".format(Fragments.fr_morpholine(mol)) # number of morpholine rings
text += "{}\n".format(Fragments.fr_halogen(mol)) # number of halogens
text += "\nKI: {}\n".format(mol.GetProp("Ki (nM)"))
text += "\n" # Use a blank line to divide molecule data
featuresFile.write(text)
text = ""
converged_and_different += 1
convergedCount += 1
else:
break
molCount += 1
print "Number of molecules with converged gaussian log files and correct sequence:", convergedCount, "\n"
print "Number of overlap drugs:", convergedCount - converged_and_different
featuresFile.close()