Re: [Rdkit-discuss] RuntimeError creating MolBlock
Open-Source Cheminformatics and Machine Learning
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From: Noel O'B. <bao...@gm...> - 2008-04-22 17:23:16
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On 22/04/2008, Greg Landrum <gre...@gm...> wrote: > Hi Noel, > > > On Tue, Apr 22, 2008 at 2:48 PM, Noel O'Boyle <bao...@gm...> wrote: > > Yes, I should have said - I'm using the latest release on Windows. > > > > > > > By latest release do you mean the Jan2008 release or did you do a > build of the svn version yourself? "The most recent officially-blessed version". Jan2008. :-) > I just tried this with the svn version on windows: > [4] >>> print Chem.MolToMolBlock(Chem.MolFromSmiles("CCCC")) > > > RDKit > > 4 3 0 0 0 0 0 0 0 0999 V2000 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 1 0 > 2 3 1 0 > 3 4 1 0 > M END > > > so that looks ok > > I can reproduce the error using the Jan2008 release though. The way to > solve the problem with the Jan release is to add 2D coords to the > molecule: > [5] >>> from Chem import AllChem > [6] >>> m = Chem.MolFromSmiles('CCCC') > [7] >>> AllChem.Compute2DCoords(m) > Out[7]: 0 > [8] >>> print Chem.MolToMolBlock(m) > > > > > 4 3 0 0 0 0 0 0 0 0999 V2000 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > > 1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.5981 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 3.8971 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > > 1 2 1 0 > 2 3 1 0 > 3 4 1 0 > M END > Thanks, Noel |