def add_mols(data):
namec = ""
altnamec = ""
suppc = ""
suppidc = ""
storc = ""
storidc = ""
amountc = ""
unitc = ""
casc = ""
altsupplierc = ""
altsupplierIDc = ""
commc = ""
classc = ""
counter = 0
head = data.next()
for c in head:
#Get the indexes of columns
cl = c.lower()
if cl == "name":
namec = counter
elif cl == "altname":
altnamec = counter
elif cl == "supplier":
suppc = counter
elif cl == "supplierid":
suppidc = counter
elif cl == "storage":
storc = counter
elif cl == "storageid":
storidc = counter
elif cl == "amount":
amountc = counter
elif cl == "unit":
unitc = counter
elif cl == "cas":
casc = counter
elif cl == "smiles":
smilesc = counter
elif cl == "supplier2":
altsupplierc = counter
elif cl == "supplierid2":
altsupplierIDc = counter
elif cl == "comment":
commc = counter
elif cl == "molclass":
classc = counter
counter += 1
if type(smilesc) == int or type(namec) == int:
# has to have either smiles or name column
print "Following columns were found and will be imported:"
if type(namec) == int:
print head[namec] + " ",
if type(altnamec) == int:
print head[altnamec] + " ",
if type(suppc) == int:
print head[suppc] + " ",
if type(suppidc) == int:
print head[suppidc] + " ",
if type(storc) == int:
print head[storc] + " ",
if type(storidc) == int:
print head[storidc] + " ",
if type(amountc) == int:
print head[amountc] + " ",
if type(unitc) == int:
print head[unitc] + " ",
if type(casc) == int:
print head[casc] + " ",
if type(smilesc) == int:
print head[smilesc] + " ",
if type(altsupplierc) == int:
print head[altsupplierc] + " ",
if type(altsupplierIDc) == int:
print head[altsupplierIDc] + " ",
if type(commc) == int:
print head[commc] + " ",
if type(classc) == int:
print head[classc] + " ",
print ""
userinput = raw_input("Is this ok? yes/no: ")
#Check with user if everything looks OK
if userinput == "yes":
for line in data:
#do some datachecks and encode in ACSII since some databases have problems with UTF-8
if type(namec) == int:
name = line[namec].decode("windows-1252").encode('utf-8','ignore')
else:
name = ""
if type(altnamec) == int:
altname = line[altnamec].decode("windows-1252").encode('utf-8','ignore')
else:
altname = ""
if type(suppc) == int:
supp = line[suppc].decode("windows-1252").encode('utf-8','ignore')
else:
supp = ""
if type(suppidc) == int:
suppid = line[suppidc].decode("windows-1252").encode('utf-8','ignore')
else:
suppid = ""
if type(storc) == int:
storage = line[storc].decode("windows-1252").encode('utf-8','ignore')
else:
storage = ""
if type(storidc) == int:
storageid = line[storidc].decode("windows-1252").encode('utf-8','ignore')
else:
storageid = ""
if type(amountc) == int:
amount = line[amountc]
else:
amount = ""
if type(unitc) == int:
unit = line[unitc].decode("windows-1252").encode('utf-8','ignore')
else:
unit = ""
if type(casc) == int:
cas = line[casc].decode("windows-1252").encode('utf-8','ignore')
else:
cas = ""
if type(smilesc) == int:
smiles = line[smilesc].decode("windows-1252").encode('utf-8','ignore')
else:
smiles = ""
if type(altsupplierc) == int:
altsupplier = line[altsupplierc].decode("windows-1252").encode('utf-8','ignore')
else:
altsupplier = ""
if type(altsupplierIDc) == int:
altsupplierID = line[altsupplierIDc].decode("windows-1252").encode('utf-8','ignore')
else:
altsupplierID = ""
if type(commc) == int:
comm = line[commc].decode("windows-1252").encode('utf-8','ignore')
else:
comm = ""
if type(classc) == int:
molclass = line[classc].decode("windows-1252").encode('utf-8','ignore')
else:
molclass = ""
try:
amount = float(line[amountc])
unit = line[unitc]
except:
amount = 0
unit = "X"
try:
mol = pybel.readstring("smi",smiles)
descs = mol.calcdesc()
#generate 2D coordinates, needs openbabel
obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats("smi", "mdl")
obmol = openbabel.OBMol()
obConversion.ReadString(obmol, smiles)
gen2d = openbabel.OBOp.FindType("gen2d")
gen2d.Do(obmol)
MDL = obConversion.WriteString(obmol)
outMDL = MDL.replace("\n", r"\n")
CMW=descs["MW"]
CHN=mol.formula
HBA=descs["HBA1"]
HBD=descs["HBD"]
logP=descs["logP"]
tpsa=descs["TPSA"]
#Get number of rotatable bonds
smarts = pybel.Smarts("[!$([NH]!@C(=O))&!D1&!$(*#*)]\&!@[!$([NH]!@C(=O))&!D1&!$(*#*)]")
rb = smarts.findall(mol)
nrb = len(rb)
#Calculate Fsp3
sp3c = pybel.Smarts("[CX4]")
nsp3c = sp3c.findall(mol)
nsp3c = float(len(nsp3c))
allc = pybel.Smarts("[#6]")
nallc = allc.findall(mol)
nallc = float(len(nallc))
if nallc > 0:
fsp3 = nsp3c/nallc
print fsp3
else:
fsp3 = ""
#Get fingerprint and molecular complexity
fprint = mol.calcfp()
bitson = fprint.bits
nbitson = len(bitson)
print name
m = Molecule(name=name,SMILES=smiles, altname=altname, supplier=supp, supplierID=suppid, CMW=descs["MW"], CHN=CHN, HBA=HBA, HBD=HBD, logP=logP, tpsa=tpsa, amount=amount, unit=unit, CAS=cas, storage=storage, storageID=storageid, molfile=outMDL, nrb=nrb, fingerprint=bitson, complexity=nbitson, altsupplier=altsupplier, altsupplierID=altsupplierID , comment=comm, molclass=molclass, fsp3=fsp3)
m.save()
except:
m = Molecule(name=name,SMILES=smiles, altname=altname, supplier=supp, supplierID=suppid, amount=amount, unit=unit, CAS=cas, storage=storage, storageID=storageid, altsupplier=altsupplier, altsupplierID=altsupplierID , comment=comm, molclass=molclass)
m.save()
#Save data to database
else:
print "Exiting, no changes were made..."
return False
else:
print "No valid columns were found in the table"
def addsingle(name, altname, supplier, supplierID, storage, storageID, unit, amount, cas, smiles, comment, molclass, platebarcode, samplebarcode, randomstring):
#do some datachecks and encode in ACSII since some databases have problems with UTF-8
name = name.decode("windows-1252").encode('utf-8','ignore')
altname = altname.decode("windows-1252").encode('utf-8','ignore')
supplier = supplier.decode("windows-1252").encode('utf-8','ignore')
supplierID = supplierID.decode("windows-1252").encode('utf-8','ignore')
storage = storage.decode("windows-1252").encode('utf-8','ignore')
storageID = storageID.decode("windows-1252").encode('utf-8','ignore')
unit = unit.decode("windows-1252").encode('utf-8','ignore')
cas = cas.decode("windows-1252").encode('utf-8','ignore')
smiles = smiles.decode("windows-1252").encode('utf-8','ignore')
comment = comment.decode("windows-1252").encode('utf-8','ignore')
molclass = molclass.decode("windows-1252").encode('utf-8','ignore')
platebarcode = platebarcode.decode("windows-1252").encode('utf-8','ignore')
samplebarcode = samplebarcode.decode("windows-1252").encode('utf-8','ignore')
# Make sure amount is a number
try:
amount = float(line[amountc])
unit = line[unitc]
except:
amount = 0
unit = "X"
try:
mol = pybel.readstring("smi",smiles)
descs = mol.calcdesc()
#generate 2D coordinates, needs openbabel
obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats("smi", "mdl")
obmol = openbabel.OBMol()
obConversion.ReadString(obmol, smiles)
gen2d = openbabel.OBOp.FindType("gen2d")
gen2d.Do(obmol)
MDL = obConversion.WriteString(obmol)
outMDL = MDL.replace("\n", r"\n")
CMW=descs["MW"]
CHN=mol.formula
HBA=descs["HBA1"]
HBD=descs["HBD"]
logP=descs["logP"]
tpsa=descs["TPSA"]
#Get number of rotatable bonds
smarts = pybel.Smarts(r"[!$([NH]!@C(=O))&!D1&!$(*#*)]\&!@[!$([NH]!@C(=O))&!D1&!$(*#*)]")
rb = smarts.findall(mol)
nrb = len(rb)
#Calculate Fsp3
sp3c = pybel.Smarts("[CX4]")
nsp3c = sp3c.findall(mol)
nsp3c = float(len(nsp3c))
allc = pybel.Smarts("[#6]")
nallc = allc.findall(mol)
nallc = float(len(nallc))
if nallc > 0:
fsp3 = nsp3c/nallc
else:
fsp3 = ""
#Get fingerprint and molecular complexity
fprint = mol.calcfp()
bitson = fprint.bits
nbitson = len(bitson)
if 'hts' in molclass.lower() or 'compound' in molclass.lower():
#print "hts"
pains = detect_pains(mol)
else:
pains = 'Not checked'
m = Molecule(name=name,SMILES=smiles, altname=altname, supplier=supplier, supplierID=supplierID,
CMW=descs["MW"], CHN=CHN, HBA=HBA, HBD=HBD, logP=logP, tpsa=tpsa, amount=amount, unit=unit,
CAS=cas, storage=storage, storageID=storageID, molfile=outMDL, nrb=nrb, fingerprint=bitson, complexity=nbitson,
comment=comment, molclass=molclass, fsp3=fsp3, pains=pains, platebarcode=platebarcode,
samplebarcode=samplebarcode, randomstring=randomstring)
m.save()
except:
# OpenBabel failed, no properties, etc..
m = Molecule(name=name,SMILES=smiles, altname=altname, supplier=supplier, supplierID=supplierID,
amount=amount, unit=unit, CAS=cas, storage=storage, storageID=storageID, comment=comment, molclass=molclass,
platebarcode=platebarcode, samplebarcode=samplebarcode, randomstring=randomstring)
m.save()
def addsingle(name, altname, supplier, supplierID, storage, storageID, unit,
amount, cas, smiles, comment, molclass, platebarcode,
samplebarcode, randomstring):
#do some datachecks and encode in ACSII since some databases have problems with UTF-8
name = name.decode("windows-1252").encode('utf-8', 'ignore')
altname = altname.decode("windows-1252").encode('utf-8', 'ignore')
supplier = supplier.decode("windows-1252").encode('utf-8', 'ignore')
supplierID = supplierID.decode("windows-1252").encode('utf-8', 'ignore')
storage = storage.decode("windows-1252").encode('utf-8', 'ignore')
storageID = storageID.decode("windows-1252").encode('utf-8', 'ignore')
unit = unit.decode("windows-1252").encode('utf-8', 'ignore')
cas = cas.decode("windows-1252").encode('utf-8', 'ignore')
smiles = smiles.decode("windows-1252").encode('utf-8', 'ignore')
comment = comment.decode("windows-1252").encode('utf-8', 'ignore')
molclass = molclass.decode("windows-1252").encode('utf-8', 'ignore')
platebarcode = platebarcode.decode("windows-1252").encode(
'utf-8', 'ignore')
samplebarcode = samplebarcode.decode("windows-1252").encode(
'utf-8', 'ignore')
# Make sure amount is a number
try:
amount = float(line[amountc])
unit = line[unitc]
except:
amount = 0
unit = "X"
try:
mol = pybel.readstring("smi", smiles)
descs = mol.calcdesc()
#generate 2D coordinates, needs openbabel
obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats("smi", "mdl")
obmol = openbabel.OBMol()
obConversion.ReadString(obmol, smiles)
gen2d = openbabel.OBOp.FindType("gen2d")
gen2d.Do(obmol)
MDL = obConversion.WriteString(obmol)
outMDL = MDL.replace("\n", r"\n")
CMW = descs["MW"]
CHN = mol.formula
HBA = descs["HBA1"]
HBD = descs["HBD"]
logP = descs["logP"]
tpsa = descs["TPSA"]
#Get number of rotatable bonds
smarts = pybel.Smarts(
r"[!$([NH]!@C(=O))&!D1&!$(*#*)]\&!@[!$([NH]!@C(=O))&!D1&!$(*#*)]")
rb = smarts.findall(mol)
nrb = len(rb)
#Calculate Fsp3
sp3c = pybel.Smarts("[CX4]")
nsp3c = sp3c.findall(mol)
nsp3c = float(len(nsp3c))
allc = pybel.Smarts("[#6]")
nallc = allc.findall(mol)
nallc = float(len(nallc))
if nallc > 0:
fsp3 = nsp3c / nallc
else:
fsp3 = ""
#Get fingerprint and molecular complexity
fprint = mol.calcfp()
bitson = fprint.bits
nbitson = len(bitson)
if 'hts' in molclass.lower() or 'compound' in molclass.lower():
#print "hts"
pains = detect_pains(mol)
else:
pains = 'Not checked'
m = Molecule(name=name,
SMILES=smiles,
altname=altname,
supplier=supplier,
supplierID=supplierID,
CMW=descs["MW"],
CHN=CHN,
HBA=HBA,
HBD=HBD,
logP=logP,
tpsa=tpsa,
amount=amount,
unit=unit,
CAS=cas,
storage=storage,
storageID=storageID,
molfile=outMDL,
nrb=nrb,
fingerprint=bitson,
complexity=nbitson,
comment=comment,
molclass=molclass,
fsp3=fsp3,
pains=pains,
platebarcode=platebarcode,
samplebarcode=samplebarcode,
randomstring=randomstring)
m.save()
except:
# OpenBabel failed, no properties, etc..
m = Molecule(name=name,
SMILES=smiles,
altname=altname,
supplier=supplier,
supplierID=supplierID,
amount=amount,
unit=unit,
CAS=cas,
storage=storage,
storageID=storageID,
comment=comment,
molclass=molclass,
platebarcode=platebarcode,
samplebarcode=samplebarcode,
randomstring=randomstring)
m.save()
def add_mols(data):
namec = ""
altnamec = ""
suppc = ""
suppidc = ""
storc = ""
storidc = ""
amountc = ""
unitc = ""
casc = ""
altsupplierc = ""
altsupplierIDc = ""
commc = ""
classc = ""
counter = 0
head = data.next()
for c in head:
#Get the indexes of columns
cl = c.lower()
if cl == "name":
namec = counter
elif cl == "altname":
altnamec = counter
elif cl == "supplier":
suppc = counter
elif cl == "supplierid":
suppidc = counter
elif cl == "storage":
storc = counter
elif cl == "storageid":
storidc = counter
elif cl == "amount":
amountc = counter
elif cl == "unit":
unitc = counter
elif cl == "cas":
casc = counter
elif cl == "smiles":
smilesc = counter
elif cl == "supplier2":
altsupplierc = counter
elif cl == "supplierid2":
altsupplierIDc = counter
elif cl == "comment":
commc = counter
elif cl == "molclass":
classc = counter
counter += 1
if type(smilesc) == int or type(namec) == int:
# has to have either smiles or name column
print "Following columns were found and will be imported:"
if type(namec) == int:
print head[namec] + " ",
if type(altnamec) == int:
print head[altnamec] + " ",
if type(suppc) == int:
print head[suppc] + " ",
if type(suppidc) == int:
print head[suppidc] + " ",
if type(storc) == int:
print head[storc] + " ",
if type(storidc) == int:
print head[storidc] + " ",
if type(amountc) == int:
print head[amountc] + " ",
if type(unitc) == int:
print head[unitc] + " ",
if type(casc) == int:
print head[casc] + " ",
if type(smilesc) == int:
print head[smilesc] + " ",
if type(altsupplierc) == int:
print head[altsupplierc] + " ",
if type(altsupplierIDc) == int:
print head[altsupplierIDc] + " ",
if type(commc) == int:
print head[commc] + " ",
if type(classc) == int:
print head[classc] + " ",
print ""
userinput = raw_input("Is this ok? yes/no: ")
#Check with user if everything looks OK
if userinput == "yes":
for line in data:
#do some datachecks and encode in ACSII since some databases have problems with UTF-8
if type(namec) == int:
name = line[namec].decode("windows-1252").encode(
'utf-8', 'ignore')
else:
name = ""
if type(altnamec) == int:
altname = line[altnamec].decode("windows-1252").encode(
'utf-8', 'ignore')
else:
altname = ""
if type(suppc) == int:
supp = line[suppc].decode("windows-1252").encode(
'utf-8', 'ignore')
else:
supp = ""
if type(suppidc) == int:
suppid = line[suppidc].decode("windows-1252").encode(
'utf-8', 'ignore')
else:
suppid = ""
if type(storc) == int:
storage = line[storc].decode("windows-1252").encode(
'utf-8', 'ignore')
else:
storage = ""
if type(storidc) == int:
storageid = line[storidc].decode("windows-1252").encode(
'utf-8', 'ignore')
else:
storageid = ""
if type(amountc) == int:
amount = line[amountc]
else:
amount = ""
if type(unitc) == int:
unit = line[unitc].decode("windows-1252").encode(
'utf-8', 'ignore')
else:
unit = ""
if type(casc) == int:
cas = line[casc].decode("windows-1252").encode(
'utf-8', 'ignore')
else:
cas = ""
if type(smilesc) == int:
smiles = line[smilesc].decode("windows-1252").encode(
'utf-8', 'ignore')
else:
smiles = ""
if type(altsupplierc) == int:
altsupplier = line[altsupplierc].decode(
"windows-1252").encode('utf-8', 'ignore')
else:
altsupplier = ""
if type(altsupplierIDc) == int:
altsupplierID = line[altsupplierIDc].decode(
"windows-1252").encode('utf-8', 'ignore')
else:
altsupplierID = ""
if type(commc) == int:
comm = line[commc].decode("windows-1252").encode(
'utf-8', 'ignore')
else:
comm = ""
if type(classc) == int:
molclass = line[classc].decode("windows-1252").encode(
'utf-8', 'ignore')
else:
molclass = ""
try:
amount = float(line[amountc])
unit = line[unitc]
except:
amount = 0
unit = "X"
try:
mol = pybel.readstring("smi", smiles)
descs = mol.calcdesc()
#generate 2D coordinates, needs openbabel
obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats("smi", "mdl")
obmol = openbabel.OBMol()
obConversion.ReadString(obmol, smiles)
gen2d = openbabel.OBOp.FindType("gen2d")
gen2d.Do(obmol)
MDL = obConversion.WriteString(obmol)
outMDL = MDL.replace("\n", r"\n")
CMW = descs["MW"]
CHN = mol.formula
HBA = descs["HBA1"]
HBD = descs["HBD"]
logP = descs["logP"]
tpsa = descs["TPSA"]
#Get number of rotatable bonds
smarts = pybel.Smarts(
"[!$([NH]!@C(=O))&!D1&!$(*#*)]\&!@[!$([NH]!@C(=O))&!D1&!$(*#*)]"
)
rb = smarts.findall(mol)
nrb = len(rb)
#Calculate Fsp3
sp3c = pybel.Smarts("[CX4]")
nsp3c = sp3c.findall(mol)
nsp3c = float(len(nsp3c))
allc = pybel.Smarts("[#6]")
nallc = allc.findall(mol)
nallc = float(len(nallc))
if nallc > 0:
fsp3 = nsp3c / nallc
print fsp3
else:
fsp3 = ""
#Get fingerprint and molecular complexity
fprint = mol.calcfp()
bitson = fprint.bits
nbitson = len(bitson)
print name
m = Molecule(name=name,
SMILES=smiles,
altname=altname,
supplier=supp,
supplierID=suppid,
CMW=descs["MW"],
CHN=CHN,
HBA=HBA,
HBD=HBD,
logP=logP,
tpsa=tpsa,
amount=amount,
unit=unit,
CAS=cas,
storage=storage,
storageID=storageid,
molfile=outMDL,
nrb=nrb,
fingerprint=bitson,
complexity=nbitson,
altsupplier=altsupplier,
altsupplierID=altsupplierID,
comment=comm,
molclass=molclass,
fsp3=fsp3)
m.save()
except:
m = Molecule(name=name,
SMILES=smiles,
altname=altname,
supplier=supp,
supplierID=suppid,
amount=amount,
unit=unit,
CAS=cas,
storage=storage,
storageID=storageid,
altsupplier=altsupplier,
altsupplierID=altsupplierID,
comment=comm,
molclass=molclass)
m.save()
#Save data to database
else:
print "Exiting, no changes were made..."
return False
else:
print "No valid columns were found in the table"
