def extract_named_descriptors_of_seq(sequence):
'''
Returns a map ("descriptor" -> value) of descriptors when given a sequence of aminoacids (string)
:param sequence:
:return:
'''
#mol = Chem.MolFromSequence(str(sequence))
res = {}
sequence=str(sequence)
if len(sequence) > 3:
#print(Autocorrelation.CalculateGearyAutoTotal(sequence))
res = PseudoAAC.GetPseudoAAC(sequence, lamda=3, weight=0.05, AAP=[_Hydrophobicity, _hydrophilicity, _residuemass, _pK1, _pK2, _pI])
res.update(AAComposition_extra_PS.CalculateAAComposition(sequence))
res.update(CTD.CalculateCTD(sequence))
mol = Chem.MolFromSequence(str(sequence))
#res = geary.GetGearyAuto(mol)
res.update(kappa.GetKappa(mol))
res.update(charge.GetCharge(mol))
#res.update(moran.GetMoranAuto(mol))
res.update(moreaubroto.GetMoreauBrotoAuto(mol))
res.update(molproperty.GetMolecularProperty(mol))
#res.update(moe.GetMOE(mol))
res.update(basak.Getbasak(mol))
#print(res)
#input()
return res
def smiles_converter(self, smi, L):
res = []
try:
mol = Chem.MolFromSmiles(smi)
res.append(constitution.GetConstitutional(mol))
res.append(connectivity.GetConnectivity(mol))
res.append(fingerprint.CalculateMACCSFingerprint(mol)[1])
try:
res.append(kappa.GetKappa(mol))
except:
pass
try:
drug.ReadMolFromSmile(smi)
res.append(drug.GetMOE())
except:
pass
try:
res.append(charge.GetCharge(mol))
except:
pass
except:
pass
super_dict = {} # uses set to avoid duplicates
if len(res) >= 1:
for d in res:
for k, v in d.items(): # use d.iteritems() in python 2
super_dict[k] = v
super_dict["smiles"] = smi.strip()
L.append(super_dict)
def compute1D2DDesc(self, prDescbyChem):
self.prDesc = prDescbyChem
# check if descriptors already computed
pdes = prDescbyChem + self.name + ".txt"
if path.exists(pdes) and path.getsize(pdes) > 10:
filin = open(pdes, "r")
llines = filin.readlines()
filin.close()
ldesc = llines[0].strip().split("\t")[1:]
lval = llines[1].strip().split("\t")[1:]
ddes = {}
i = 0
while i < len(ldesc):
ddes[ldesc[i]] = lval[i]
i += 1
self.allDesc = ddes
self.log = self.log + "Desc already computed -> " + pdes + "\n"
return 0
if not "smiclean" in self.__dict__:
self.log = self.log + "No smiles prepared\n"
return 1
else:
self.mol = loader.ReadMolFromSmile(self.smiclean)
print self.smiclean
try:
self.consti = constitution.GetConstitutional(self.mol)
except:
self.consti = {}
self.compo = {}
try:
self.compo["nheavy"] = self.mol.GetNumHeavyAtoms()
except:
self.compo = {}
try:
self.molprop = molproperty.GetMolecularProperty(self.mol)
except:
self.molprop = {}
# 2D
try:
self.topo = topology.GetTopology(self.mol)
except:
self.topo = {}
try:
self.connect = connectivity.GetConnectivity(self.mol)
except:
self.connect = {}
try:
self.kap = kappa.GetKappa(self.mol)
except:
self.kap = {}
try:
self.burden = bcut.GetBurden(self.mol)
except:
self.burden = {}
try:
self.basakD = basak.Getbasak(self.mol)
except:
self.basakD = {}
try:
self.est = estate.GetEstate(self.mol)
except:
self.est = {}
try:
self.moreauBurto = moreaubroto.GetMoreauBrotoAuto(self.mol)
except:
self.moreauBurto = {}
try:
self.autcormoran = moran.GetMoranAuto(self.mol)
except:
self.autcormoran = {}
try:
self.gearycor = geary.GetGearyAuto(self.mol)
except:
self.gearycor = {}
try:
self.charges = charge.GetCharge(self.mol)
except:
self.charges = {}
try:
self.MOE = moe.GetMOE(self.mol)
except:
self.MOE = {}
# combine all 1D2D
if not "allDesc" in dir(self):
self.allDesc = dict()
self.allDesc.update(deepcopy(self.consti))
self.allDesc.update(deepcopy(self.compo))
self.allDesc.update(deepcopy(self.molprop))
self.allDesc.update(deepcopy(self.topo))
self.allDesc.update(deepcopy(self.connect))
self.allDesc.update(deepcopy(self.kap))
self.allDesc.update(deepcopy(self.burden))
self.allDesc.update(deepcopy(self.basakD))
self.allDesc.update(deepcopy(self.est))
self.allDesc.update(deepcopy(self.moreauBurto))
self.allDesc.update(deepcopy(self.autcormoran))
self.allDesc.update(deepcopy(self.gearycor))
self.allDesc.update(deepcopy(self.charges))
self.allDesc.update(deepcopy(self.MOE))
if self.allDesc == {}:
return 1
else:
return 0
def get_descriptor2D(self):
try:
self.topo = topology.GetTopology(self.mol)
except:
self.topo = {}
try:
self.connect = connectivity.GetConnectivity(self.mol)
except:
self.connect = {}
try:
self.kap = kappa.GetKappa(self.mol)
except:
self.kap = {}
try:
self.burden = bcut.GetBurden(self.mol)
except:
self.burden = {}
try:
self.basakD = basak.Getbasak(self.mol)
except:
self.basakD = {}
try:
self.est = estate.GetEstate(self.mol)
except:
self.est = {}
try:
self.moreauBurto = moreaubroto.GetMoreauBrotoAuto(self.mol)
except:
self.moreauBurto = {}
try:
self.autcormoran = moran.GetMoranAuto(self.mol)
except:
self.autcormoran = {}
try:
self.gearycor = geary.GetGearyAuto(self.mol)
except:
self.gearycor = {}
try:
self.charges = charge.GetCharge(self.mol)
except:
self.charges = {}
try:
self.MOE = moe.GetMOE(self.mol)
except:
self.MOE = {}
# list 2D -> modified in main library !!!!
self.l2D = topology._Topology.keys()
self.l2D = self.l2D + connectivity._connectivity.keys()
self.l2D = self.l2D + LKAPA
self.l2D = self.l2D + LBUCUT
self.l2D = self.l2D + basak._basak.keys()
self.l2D = self.l2D + LESTATE
self.l2D = self.l2D + LMOREAUBROTO
self.l2D = self.l2D + LMORAN
self.l2D = self.l2D + LGEARY
self.l2D = self.l2D + charge._Charge.keys()
self.l2D = self.l2D + LMOE
# combine all 2D
self.all2D = dict()
self.all2D.update(deepcopy(self.topo))
self.all2D.update(deepcopy(self.connect))
self.all2D.update(deepcopy(self.kap))
self.all2D.update(deepcopy(self.burden))
self.all2D.update(deepcopy(self.basakD))
self.all2D.update(deepcopy(self.est))
self.all2D.update(deepcopy(self.moreauBurto))
self.all2D.update(deepcopy(self.autcormoran))
self.all2D.update(deepcopy(self.gearycor))
self.all2D.update(deepcopy(self.charges))
self.all2D.update(deepcopy(self.MOE))
def get_descriptor1D2D(self):
try:
self.consti = constitution.GetConstitutional(self.mol)
except:
self.consti = {}
self.compo = {}
try:
self.compo["nheavy"] = self.mol.GetNumHeavyAtoms()
except:
self.compo = {}
try:
self.molprop = molproperty.GetMolecularProperty(self.mol)
except:
self.molprop = {}
try:
self.topo = topology.GetTopology(self.mol)
except:
self.topo = {}
try:
self.connect = connectivity.GetConnectivity(self.mol)
except:
self.connect = {}
try:
self.kap = kappa.GetKappa(self.mol)
except:
self.kap = {}
try:
self.burden = bcut.GetBurden(self.mol)
except:
self.burden = {}
try:
self.basakD = basak.Getbasak(self.mol)
except:
self.basakD = {}
try:
self.est = estate.GetEstate(self.mol)
except:
self.est = {}
try:
self.moreauBurto = moreaubroto.GetMoreauBrotoAuto(self.mol)
except:
self.moreauBurto = {}
try:
self.autcormoran = moran.GetMoranAuto(self.mol)
except:
self.autcormoran = {}
try:
self.gearycor = geary.GetGearyAuto(self.mol)
except:
self.gearycor = {}
try:
self.charges = charge.GetCharge(self.mol)
except:
self.charges = {}
try:
self.MOE = moe.GetMOE(self.mol)
except:
self.MOE = {}
# list 1D2D -> modified in main library !!!!
self.l1D2D = constitution._constitutional.keys()
self.l1D2D = self.l1D2D + ["nheavy"]
self.l1D2D = self.l1D2D + molproperty.MolecularProperty.keys()
self.l1D2D = self.l1D2D +topology._Topology.keys()
self.l1D2D = self.l1D2D + connectivity._connectivity.keys()
self.l1D2D = self.l1D2D + LKAPA
self.l1D2D = self.l1D2D + LBUCUT
self.l1D2D = self.l1D2D + basak._basak.keys()
self.l1D2D = self.l1D2D + LESTATE
self.l1D2D = self.l1D2D + LMOREAUBROTO
self.l1D2D = self.l1D2D + LMORAN
self.l1D2D = self.l1D2D + LGEARY
self.l1D2D = self.l1D2D + charge._Charge.keys()
self.l1D2D = self.l1D2D + LMOE
# combine all 1D-2D
self.all1D2D = dict()
self.all1D2D.update(self.consti)
self.all1D2D.update(self.compo)
self.all1D2D.update(self.molprop)
self.all1D2D.update(deepcopy(self.topo))
self.all1D2D.update(deepcopy(self.connect))
self.all1D2D.update(deepcopy(self.kap))
self.all1D2D.update(deepcopy(self.burden))
self.all1D2D.update(deepcopy(self.basakD))
self.all1D2D.update(deepcopy(self.est))
self.all1D2D.update(deepcopy(self.moreauBurto))
self.all1D2D.update(deepcopy(self.autcormoran))
self.all1D2D.update(deepcopy(self.gearycor))
self.all1D2D.update(deepcopy(self.charges))
self.all1D2D.update(deepcopy(self.MOE))