Dear All,
I am trying to process a SMILES file (.smi) and calculate InChIs, where there
are some SMILES that Open Babel will not be able to read, due to syntax or
other errors. In those cases, I would like to print a string such as
"Open_Babel_Error" on the line (or something even more descriptive).
However, everything I have tried results in Open Babel stopping once it reads a
SMILES string it cannot parse. Here is where I am at (code below), I did read
the Errors and Warnings documentation with OBMessageHandler class, but I could
not figure out how to incorporate that. Any direction/examples would be much
appreciated.
Thanks
Vin
--
import pybel
# Set up conversion to InChI
conv = pybel.ob.OBConversion()
conv.SetOutFormat("inchi")
conv.AddOption("X", conv.OUTOPTIONS, "DoNotAddH")
# Read a SMILES file
mols = pybel.readfile("smi","mySMILES.smi")
# loop through molecules and print InChI strings to a file
with open("InChI_ouput.inchi", 'w') as f:
for mol in mols:
if not mol:
f.write("Open_Babel_Error\n".format(inchi))
continue
# N.B. Adding H's to OB Molecular Object, and not through InChI
mol.OBMol.AddHydrogens()
inchi = conv.WriteString(mol.OBMol)
f.write("{}".format(inchi))
f.close()
--
Vincent F. Scalfani, Ph.D.
University Libraries
The University of Alabama
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