Hi Andrea,Hmm, maybe not very helpful, but it's at least not a general bug. I'm not able to reproduce it on my system (CentOS, rdkit version 2013.03.1beta1).
Something that caught my eye: The smiles looks a little strange to me because of the mix of aromatic and aliphatic carbons in one ring, but it is parsed without an error by the rdkit. However, the Avalon smiles parser interprets it differently (see 2nd screenshot). Maybe it's safer switching to a representation like C1C=CC=C1CCN?
Best, Markus On 09/26/2013 04:59 PM, Andrea Volkamer wrote:
Hi there,I am relatively new to rdkit, and just started using IPython notebook under Windows.I installed WinPython-64bit-2.7.5.3 and RDKit_2013_06_1 as well as Pillow-2.1.0.win-amd64-py2.7 to do so.Anyhow, I have some trouble drawing molecules:For some reason, drawing this molecule Chem.MolFromSmiles('C1cccc1CC') works, adding, e.g., a nitrogen (Chem.MolFromSmiles('C1cccc1CCN')) doesn't work (<rdkit.Chem.rdchem.Mol at 0x7a6e8d0>)?This happens for many other examples as well. Any suggestions? Thanks Andrea ------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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