Re: [Open Babel] Error in Pybel.readstring() - smi format not recognized

[Andrew D. <da...@da...>]

On Oct 24, 2014, at 1:13 AM, ftorazyne wrote:
> I modified code in accordance with your recommendation and obtained in
> general same output:

I cannot explain it. Looking at the code, there are two different OBConversion instances. There's no way that's supposed to cause a problem, but try this anyway - I call the lower-level functions directly:


import openbabel as ob
obconversion = ob.OBConversion()
print "SetInFormat", obconversion.SetInFormat("smi")
for description in obconversion.GetSupportedInputFormat():
    if "smi" in description:
        print repr(description)


On my system the last few lines produce:

>>> print "SetInFormat", obconversion.SetInFormat("smi")
SetInFormat True
>>> for description in obconversion.GetSupportedInputFormat():
...     if "smi" in description:
...         print repr(description)
... 
'rsmi -- Reaction SMILES format'
'smi -- SMILES format'
'smiles -- SMILES format'


				Andrew
				da...@da...