def CalculateLabuteASA(mol):
"""
#################################################################
Calculation of Labute's Approximate Surface Area (ASA from MOE)
Usage:
result=CalculateLabuteASA(mol)
Input: mol is a molecule object
Output: result is a dict form
#################################################################
"""
res={}
temp=MOE.pyLabuteASA(mol,includeHs=1)
res['LabuteASA']=round(temp,3)
return res
def CalculateLabuteASA(mol):
"""
#################################################################
Calculation of Labute's Approximate Surface Area (ASA from MOE)
Usage:
result=CalculateLabuteASA(mol)
Input: mol is a molecule object
Output: result is a dict form
#################################################################
"""
res={}
temp=MOE.pyLabuteASA(mol,includeHs=1)
res['LabuteASA']=round(temp,3)
return res
def testTPSAShort(self):
" Short TPSA test "
inName = RDConfig.RDDataDir + '/NCI/first_200.tpsa.csv'
inF = open(inName, 'r')
lines = inF.readlines()
for line in lines:
if line[0] != '#':
line.strip()
smi, ans = line.split(',')
ans = float(ans)
mol = Chem.MolFromSmiles(smi)
calc = MolSurf.TPSA(mol)
assert feq(
calc,
ans), 'bad TPSA for SMILES %s (%.2f != %.2f)' % (smi, calc,
ans)
def PhyChem(smiles):
""" Calculating the 19D physicochemical descriptors for each molecules,
the value has been normalized with Gaussian distribution.
Arguments:
smiles (list): list of SMILES strings.
Returns:
props (ndarray): m X 19 matrix as normalized PhysChem descriptors.
m is the No. of samples
"""
props = []
for smile in smiles:
mol = Chem.MolFromSmiles(smile)
try:
MW = desc.MolWt(mol)
LOGP = Crippen.MolLogP(mol)
HBA = Lipinski.NumHAcceptors(mol)
HBD = Lipinski.NumHDonors(mol)
rotable = Lipinski.NumRotatableBonds(mol)
amide = AllChem.CalcNumAmideBonds(mol)
bridge = AllChem.CalcNumBridgeheadAtoms(mol)
heteroA = Lipinski.NumHeteroatoms(mol)
heavy = Lipinski.HeavyAtomCount(mol)
spiro = AllChem.CalcNumSpiroAtoms(mol)
FCSP3 = AllChem.CalcFractionCSP3(mol)
ring = Lipinski.RingCount(mol)
Aliphatic = AllChem.CalcNumAliphaticRings(mol)
aromatic = AllChem.CalcNumAromaticRings(mol)
saturated = AllChem.CalcNumSaturatedRings(mol)
heteroR = AllChem.CalcNumHeterocycles(mol)
TPSA = MolSurf.TPSA(mol)
valence = desc.NumValenceElectrons(mol)
mr = Crippen.MolMR(mol)
# charge = AllChem.ComputeGasteigerCharges(mol)
prop = [MW, LOGP, HBA, HBD, rotable, amide, bridge, heteroA, heavy, spiro,
FCSP3, ring, Aliphatic, aromatic, saturated, heteroR, TPSA, valence, mr]
except Exception:
print(smile)
prop = [0] * 19
props.append(prop)
props = np.array(props)
props = Scaler().fit_transform(props)
return props
def _testTPSALongNCI(self):
" Long TPSA test "
fileN = 'tpsa_regr.csv'
with open(os.path.join(RDConfig.RDCodeDir,'Chem','test_data',fileN),'r') as inF:
lines = inF.readlines()
lineNo = 0
for line in lines:
lineNo+=1
if line[0] != '#':
line.strip()
smi,ans = line.split(',')
ans = float(ans)
mol = Chem.MolFromSmiles(smi)
assert mol,"line %d, failed for smiles: %s"%(lineNo,smi)
calc = MolSurf.TPSA(mol)
assert feq(calc,ans),'line %d: bad TPSA for SMILES %s (%.2f != %.2f)'%(lineNo,smi,calc,ans)
def CalculateTPSA(mol):
"""
#################################################################
Calculation of topological polar surface area based on fragments.
Implementation based on the Daylight contrib program tpsa.
Usage:
result=CalculateTPSA(mol)
Input: mol is a molecule object
Output: result is a dict form
#################################################################
"""
res = {}
temp = MOE.TPSA(mol)
res['TPSA'] = round(temp, 3)
return res
def describe_atom(atom_object, use_formal_charge=False, use_Gasteiger=False):
mol = atom_object.GetOwningMol()
contribs = MolSurf._LabuteHelper(mol)
idx = atom_object.GetIdx()
code = {
'SP': 1,
'SP2': 2,
'SP3': 3,
'UNSPECIFIED': -1,
'UNKNOWN': -1,
'S': 0,
'SP3D': 4,
'SP3D2': 5
}
result = []
symbol = atom_object.GetSymbol()
result.append(atom_object.GetAtomicNum())
try:
one_hot = [0.0 for _ in range(7)]
hib = code[atom_object.GetHybridization().name]
one_hot[hib + 1] = 1.0
#result+=one_hot
result.append(hib)
result.append(atom_object.GetTotalValence())
except:
print(Chem.MolToSmiles(mol, canonical=0), idx)
raise
result.append(
max(atom_object.GetNumImplicitHs(), atom_object.GetNumExplicitHs()))
result.append(p_table.GetNOuterElecs(symbol))
result.append(electronegativity.get(symbol, 0))
result.append(float(atom_object.GetIsAromatic()))
if use_formal_charge:
result.append(atom_object.GetFormalCharge())
if use_Gasteiger:
q_in_neu = atom_object.GetDoubleProp(
'_GasteigerHCharge') + atom_object.GetDoubleProp(
'_GasteigerCharge')
result.append(q_in_neu)
result.append(contribs[idx + 1])
return result
def filter_druglikeness_5_rules(self, smiles):
count = 0
for i in smiles:
mol = Chem.MolFromSmiles(i)
mol = Chem.RemoveHs(mol)
MW = rdmd._CalcMolWt(mol)
ALOGP = Crippen.MolLogP(mol)
HBA = rdmd.CalcNumHBA(mol)
HBD = rdmd.CalcNumHBD(mol)
PSA = MolSurf.TPSA(mol)
ROTB = rdmd.CalcNumRotatableBonds(
mol, rdmd.NumRotatableBondsOptions.Strict)
if MW > 600 or ALOGP > 6 or ALOGP < 0 or HBA > 11 or HBD > 7 or PSA > 180 or ROTB > 11:
smiles.remove(i)
count = count + 1
print("unavaliable rule_5_drug:%i" % count)
return smiles
def testBug12a(self):
from rdkit.Chem import MolSurf
inD = [
('OC(=O)[CH](CC1=CC=CC=C1)C2=CC=CC=C2', 37.3),
('OC(=O)C(C1=CC=CC=C1)(C2=CC=CC=C2)C3=CC=CC=C3', 37.3),
('CCC(CC)(CC)[CH](OC(=O)C1=C(C=CC=C1)C(O)=O)C2=CC=CC=C2', 63.6),
('C[C](O)([CH](C(O)=O)C1=CC=CC=C1)C2=CC=CC=C2', 57.53),
('C[CH]([CH](C(O)=O)C1=CC=CC=C1)C2=CC=CC=C2', 37.3),
('OC(=O)CBr', 37.3),
('OC(=O)CCl', 37.3),
('OC(=O)C=CC(=O)C1=CC=CC=C1', 54.37),
('NC1=C(C=CC=C1)C(O)=O', 63.32),
('OC(=O)C1=CC=CC=C1', 37.3),
('CN(C)C(=N)NC1=NC(=C2C=C(Cl)C=CC2=N1)C.O[N+]([O-])=O', 128.27),
('CCN(CC)C(=N)NC1=NC(=C2C=C(Cl)C=CC2=N1)C.O[N+]([O-])=O', 128.27),
('ON(O)NC(=N)NN=C1C(=O)NC2=C1C=CC=C2', 133.07),
('NC1=CC=C(C=C1)C=NNC(=N)NN(O)O', 129.99),
('CC(=O)NC1=CC=C(C=C1)C=NNC(=N)NN(O)O', 133.07),
('COC1=CC=C(C=C1)C=NNC(=N)NN(O)O', 113.2),
('ON(O)NC(=N)NN=CC1=CC=CC=C1', 103.97),
('ON(O)NC(=N)NN=CC=CC1=CC=CC=C1', 103.97),
('ON(O)NC(=N)NN=CC1=C(Cl)C=C(Cl)C=C1', 103.97),
('CC(C)=CCCC(C)=CC=NNC(=N)NN(O)O', 103.97),
('CN(C)C1=CC=C(C=C1)C=NNC(=N)NN(O)O', 107.21),
('ON(O)NC(=N)NN=CC1=CC=CO1', 117.11),
('ON(O)NC(=N)NN=CC1=CC=C(O)C=C1', 124.2),
('CC(C)C1=CC=C(C=C1)C=NNC(=N)NN(O)O', 103.97),
('COC1=C(C=CC=C1)C=NNC(=N)NN(O)O', 113.2),
('ON(O)NC(=N)NN=CC1=C(C=CC=C1)[N+]([O-])=O', 147.11),
('ON(O)NC(=N)NN=CC1=CC=C(C=C1)[N+]([O-])=O', 147.11),
('ON(O)NC(=N)NN=CC1=C(O)C=CC(=C1)[N+]([O-])=O', 167.34),
('ON(O)NC(=N)NN=CC1=CC=NC=C1', 116.86),
('ON(O)NC(=N)NN=CC1=CC=CC=N1', 116.86),
('ON(O)NC(=N)NN=CC1=CC=CN=C1', 116.86),
]
for smi, val in inD:
mol = Chem.MolFromSmiles(smi)
v = MolSurf.TPSA(mol)
assert feq(
v, val), 'bad TPSA (%f != %f) for smiles: %s' % (v, val, smi)
def properties(mol):
"""
Calculates the properties that are required to calculate the QED descriptor.
"""
matches = []
if (mol is None):
raise TypeError('You need to provide a mol argument.')
x = [0] * 8
x[0] = rdmd._CalcMolWt(mol) # MW
x[1] = Crippen.MolLogP(mol) # ALOGP
for hbaPattern in Acceptors: # HBA
if (mol.HasSubstructMatch(hbaPattern)):
matches = mol.GetSubstructMatches(hbaPattern)
x[2] += len(matches)
x[3] = Lipinski.NumHDonors(mol) # HBD
x[4] = MolSurf.TPSA(mol) # PSA
x[5] = Lipinski.NumRotatableBonds(mol) # ROTB
x[6] = Chem.GetSSSR(Chem.DeleteSubstructs(deepcopy(mol),
AliphaticRings)) # AROM
for alert in StructuralAlerts: # ALERTS
if (mol.HasSubstructMatch(alert)): x[7] += 1
return x
def makeFeatures(fileName):
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import MolSurf
global featuresFile, numFeatures
featuresFile = open(fileName, 'w') # Molecule features output 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
# Select features of interest
for mol in drugDB:
#text += "{}\n".format(molCount)
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 += "\nKI: {}\n".format(mol.GetProp("Ki (nM)"))
text += "\n" # Use a blank line to divide molecule data
featuresFile.write(text)
text = ""
molCount += 1
featuresFile.close()
def test_pySMR_VSA_(self):
for data in TestCase.readNCI_200():
molPy = Chem.MolFromSmiles(data.smiles)
for calcC, calcPy in zip(MolSurf.SMR_VSA_(data.mol), MolSurf.pySMR_VSA_(molPy, force=False)):
self.assertAlmostEqual(calcC, calcPy)
def test_pyLabuteASA(self):
for data in TestCase.readNCI_200():
molPy = Chem.MolFromSmiles(data.smiles)
self.assertAlmostEqual(MolSurf.LabuteASA(data.mol), MolSurf.pyLabuteASA(molPy))
def test_pyLabuteHelper(self):
for data in TestCase.readNCI_200():
molPy = Chem.MolFromSmiles(data.smiles)
for calcC, calcPy in zip(MolSurf._LabuteHelper(data.mol),
MolSurf._pyLabuteHelper(molPy)):
self.assertAlmostEqual(calcC, calcPy)
def test_pySMR_VSA_(self):
for data in TestCase.readNCI_200():
molPy = Chem.MolFromSmiles(data.smiles)
for calcC, calcPy in zip(MolSurf.SMR_VSA_(data.mol),
MolSurf.pySMR_VSA_(molPy, force=False)):
self.assertAlmostEqual(calcC, calcPy)
def test_pyLabuteASA(self):
for data in TestCase.readNCI_200():
molPy = Chem.MolFromSmiles(data.smiles)
self.assertAlmostEqual(MolSurf.LabuteASA(data.mol),
MolSurf.pyLabuteASA(molPy))
def CalculateTPSA(mol):
return round(MS.TPSA(mol), 3)
def _testLabuteASALong2(self):
""" test calculation of Labute's ASA value
"""
col = 6
self.__testDesc('PP_descrs_regress.2.csv',col,lambda x:MolSurf.LabuteASA(x,includeHs=1))
def calculate(self):
return MolSurf.LabuteASA(self.mol)
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()
def test_pyLabuteHelper(self):
for data in TestCase.readNCI_200():
molPy = Chem.MolFromSmiles(data.smiles)
for calcC, calcPy in zip(MolSurf._LabuteHelper(data.mol), MolSurf._pyLabuteHelper(molPy)):
self.assertAlmostEqual(calcC, calcPy)
def CalculateTPSA(mol: Chem.Mol) -> float:
"""Calculate the topological polar surface area.
From Ertl P. et al., J.Med.Chem. (2000), 43,3714-3717.
"""
return round(MS.TPSA(mol), 3)
def CalculatePEOEVSA(mol, bins=None):
temp = MOE.PEOE_VSA_(mol, bins, force=1)
res = {}
for i, j in enumerate(temp):
res['PEOEVSA' + str(i)] = round(j, 3)
return 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 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()
def CalculateTPSA(mol):
res = {}
temp = MOE.TPSA(mol)
res['TPSA'] = round(temp, 3)
return res
def CalculateSLOGPVSA(mol, bins=None):
temp = MOE.SlogP_VSA_(mol, bins, force=1)
res = {}
for i, j in enumerate(temp):
res['slogPVSA' + str(i)] = round(j, 3)
return res
def CalculateLabuteASA(mol: Chem.Mol) -> dict:
"""Calculate Labute's Approximate Surface Area (ASA from MOE)."""
res = {}
temp = MOE.pyLabuteASA(mol, includeHs=1)
res['LabuteASA'] = round(temp, 3)
return res
def CalculateLabuteASA(mol):
res = {}
temp = MOE.pyLabuteASA(mol, includeHs=1)
res['LabuteASA'] = round(temp, 3)
return res