[Rdkit-discuss] Catching errors in SMILES files

[David Cosgrove]

Hi,

I'm trying to catch the line numbers of lines in a SMILES file that aren't
parsed by the SmilesMolSupplier.  Example code is attached, along with 2
SMILES files.  When there is a bad SMILES string on the last line, the
error is not reported, as in test2.smi.  I've tried iterating through the
file in a loop using next(suppl1) and catching the StopIteration exception,
but I have the same issue.  Is there a way to spot a last bad record in a
file?

Thanks,
Dave

-- 
David Cosgrove
Freelance computational chemistry and chemoinformatics developer
http://cozchemix.co.uk

test1.smi
Description: application/diskcopy

test2.smi
Description: application/diskcopy

#!/usr/bin/env python

from rdkit import Chem

suppl1 = Chem.SmilesMolSupplier('test1.smi', titleLine=False, nameColumn=1)
rec_num = 0
for mol in suppl1:
    rec_num += 1
    if not mol:
        print('Record {} not read.'.format(rec_num))
    else:
        print('Record {} read ok.'.format(rec_num))


suppl2 = Chem.SmilesMolSupplier('test2.smi', titleLine=False, nameColumn=1)
rec_num = 0
for mol in suppl2:
    rec_num += 1
    if not mol:
        print('Record {} not read.'.format(rec_num))
    else:
        print('Record {} read ok.'.format(rec_num))

    


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