def recursive_dance(mols, check=set([]), thres=0.4): before_n = len(check) print before_n for mol in mols: danced_mols = dance_atom(mol) for mol_conv in danced_mols: aro_n = Fragments.fr_Ar_N(mol) aro_a = len(mol.GetAromaticAtoms()) ratio = float(aro_n) / float(aro_a) if ratio < thres: smi = Chem.MolToSmiles(mol_conv) check.add(smi) after_n = len(check) print before_n, after_n if before_n < after_n: mols = [Chem.MolFromSmiles(mol) for mol in check] recursive_dance(mols, check=check) return [Chem.MolFromSmiles(smi) for smi in check]
def recursive_dance(mols, check = set([]), thres = 0.4): before_n = len(check) print before_n for mol in mols: danced_mols = dance_atom( mol ) for mol_conv in danced_mols: aro_n = Fragments.fr_Ar_N( mol ) aro_a = len( mol.GetAromaticAtoms() ) ratio = float(aro_n) / float(aro_a) if ratio < thres: smi = Chem.MolToSmiles(mol_conv ) check.add( smi ) after_n = len(check) print before_n, after_n if before_n < after_n: mols = [ Chem.MolFromSmiles(mol) for mol in check ] recursive_dance( mols, check=check ) return [ Chem.MolFromSmiles(smi) for smi in check ]
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()