Re: [Rdkit-discuss] Error in reading sdf format

Thanks for pointing me to that missing blank like Andrew and JP Abhik Seal Indiana University Bloomington School of Informatics and Computing Cheminformatics and Chemgenomics group abs...@indiana.edu http://mypage.iu.edu/~abseal/index.htm On Wed, Jul 23, 201

Re: [Rdkit-discuss] Error in reading sdf format

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 s

Re: [Rdkit-discuss] Error in reading sdf format

On Jul 23, 2014, at 10:26 PM, Abhik Seal wrote: > I have a sdf file attached(2 molecules only) What you have isn't an SD file. It's missing a line in the header block. The header block is supposed to contain three lines. I quote from the specification: > Line 1: Molecule name. This line is unfo

[Rdkit-discuss] Error in reading sdf format

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