Hi RDKitters, I am seeing some weird behaviour from the adding an atom and a bond to an EditableMol. It works fine in most cases however for this particular fragment I'm getting an extra hydrogen being added on for some reason.
>>> mol = Chem.MolFromSmiles('O=C1NC2=C(N1)C(=O)NC(=O)N2') >>> Chem.Kekulize(mol, clearAromaticFlags = True) >>> tempMol = Chem.EditableMol(mol) >>> firstIdx = tempMol.AddAtom(dumAtom) >>> tempMol.AddBond(8, firstIdx, Chem.BondType.SINGLE) 14 >>> print Chem.MolToSmiles(tempMol.GetMol()) [*][NH]1C(=O)NC2=C(NC(=O)N2)C1=O So this molecule is not RDKit friendly, I don't really know why this is happening. I guess some form of conversion of an implicit hydrogen to an explicit hydrogen... Is there any way of stopping the magic hydrogen from appearing? Or away of easily getting rid of it after it's appeared? Best, Nick Nicholas C. Firth | PhD Student | Cancer Therapeutics The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey | SM2 5NG T 020 8722 4033 | E nicholas.fi...@icr.ac.uk | W www.icr.ac.uk | Twitter @ICRnews The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. ------------------------------------------------------------------------------ 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=60135991&iu=/4140/ostg.clktrk _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss