Hi Greg, One additional question about this subject: If we have molecules in both tautomeric forms:'C[N+](=O)([O-])' and CN(=O)(=O)' than what we will have after SmilesToMol() and MolToSmiles() (which will sanitise molecule)?
Regards, Evgueni 2009/5/25 Greg Landrum <[email protected]> > Dear Tao-wei, > > On Fri, May 22, 2009 at 2:59 AM, Tao-wei Huang <[email protected]> wrote: > > Dear All, > > I encountered problems while reading compounds containing Nitro group > (-NO2) > > or building molecules containing smarts like [N+][O-]. It seems that > rdkit > > only allows the maximum valence of N to be 3 in these processes. One > example > > is as followings (the sdf file is attached): > >>>> spl=cm.SDMolSupplier('pyrazoloacridine.sdf') > >>>> print spl[0] > > None > >>>> mm=cm.MolFromMolFile('pyrazoloacridine.sdf') > > Traceback (most recent call last): > > File "<pyshell#20>", line 1, in <module> > > mm=cm.MolFromMolFile('pyrazoloacridine.sdf') > > ValueError: Sanitization error: Explicit valence for atom # 13 N greater > > than permitted > > Could anyone provide some solution for this problem? I did't notice this > > problem when I started building model. But now I cannot run through the > > whole dataset probably because of this problem. Thanks in advance. > > The RDKit is, by design, very picky about valence and only tries to > repair bad valences in very limited situations. Nitro groups are, in > fact, one case where the system will clean things up. For example, > both of these work: > > [2] >>> m = Chem.MolFromSmiles('C[N+](=O)([O-])') > [3] >>> m = Chem.MolFromSmiles('CN(=O)(=O)') > > But here an error is raised: > [4] >>> m = Chem.MolFromSmiles('CN(=O)(O)') > [06:11:51] Explicit valence for atom # 1 N greater than permitted > > Your input file contains an N like the one in [4] above: neutral and > four coordinate. The fix is to either change the single N-O bond (the > bond between atoms 14 and 19) to a double or to set the appropriate > charges on atoms 14 and 19 in your SD file. [Note: just in case it > causes confusion, the RDKit numbers the atoms starting at zero, but in > the SD file they are numbered starting at 1, so when the RDKit > complains about atom #13, it's numbered 14 in the SD file.] > > Best Regards, > -greg > > > ------------------------------------------------------------------------------ > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT > is a gathering of tech-side developers & brand creativity professionals. > Meet > the minds behind Google Creative Lab, Visual Complexity, Processing, & > iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian > Group, R/GA, & Big Spaceship. http://www.creativitycat.com > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
