The problem is in the data file -- I added an example, benzene, from wikipedia, and fixed the first one of your molecules for you (attached).
Amongst other things - the first three lines are header lines ( http://en.wikipedia.org/wiki/Chemical_table_file), you only have two of those. I find the specification very useful when I hit these kind of problems. Here it is: http://c4.cabrillo.edu/404/ctfile.pdf On 23 July 2014 22:26, Abhik Seal <[email protected]> wrote: > Hi RDkiters, > > I have a sdf file attached(2 molecules only) and when i want to do simple > printing of the mol using code below i am getting an error not sure what is > wrong with the file > > >>> from rdkit import Chem > > >>> suppl = Chem.SDMolSupplier('data.sdf') > > >>> for mol in suppl: > > ... print mol > > ... > > [21:15:14] ERROR: Cannot convert to int on line 4 > > [21:15:14] ERROR: moving to the begining of the next molecule > > None > > [21:15:14] ERROR: Cannot convert to int on line 106 > > [21:15:14] ERROR: moving to the begining of the next molecule > Any help on this problem ? > > Abhik Seal > Indiana University Bloomington > School of Informatics and Computing > Cheminformatics and Chemgenomics group <http://registratio54.wix.com/ccrg> > [email protected] > http://mypage.iu.edu/~abseal/index.htm > > > ------------------------------------------------------------------------------ > Want fast and easy access to all the code in your enterprise? Index and > search up to 200,000 lines of code with a free copy of Black Duck > Code Sight - the same software that powers the world's largest code > search on Ohloh, the Black Duck Open Hub! Try it now. > http://p.sf.net/sfu/bds > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
data2.sdf
Description: Binary data
------------------------------------------------------------------------------ Want fast and easy access to all the code in your enterprise? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds
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