Greg, Thanks. I believe identifying anti-aromatic bonds even just with simple rings will be very helpful to my project. Could you please give me some links or sample codes about identifying all the conjugated simple rings and do an electron count? Would you also like to share me some relevant rules you think could be reasonable?
By the way, if there is a hard way to identify all anti-aromatic bonds, could you also please give me some hints? If fortunately I can implement it, I will share it by posting my code in this mailing list. Thanks. Yingfeng On Thu, Aug 27, 2015 at 10:08 AM, Greg Landrum <[email protected]> wrote: > Hi Yingfeng, > > Non-aromatic is not a problem, but there's no easy way I can think of off > the top of my head for identifying anti-aromatic systems without making C++ > code changes. > > If you were willing to limit yourself to simple rings, you could write > some python code to identify all the conjugated simple rings and do an > electron count according to whatever rules you think are relevant. > > -greg > > > On Thu, Aug 27, 2015 at 1:52 PM, Yingfeng Wang <[email protected]> wrote: > >> Could anyone please share your experience with identifying non-aromatic >> bonds using RDKit? I would greatly appreciate your help. >> >> Yingfeng >> >> >> On Mon, Aug 24, 2015 at 9:42 PM, Yingfeng Wang <[email protected]> >> wrote: >> >>> Sorry, my previous email has a typo. >>> >>> According to the following link, >>> >>> http://www.rdkit.org/docs/RDKit_Book.html >>> >>> I get sample code for identifying aromatic bonds like >>> >>> >>> from rdkit import Chem >>> >>> m=Chem.MolFromSmiles('O=C1C=CC(=O)C2=C1OC=CO2') >>> >>> m.GetBondBetweenAtoms(6,7).GetIsAromatic() >>> >>> Is there a way to identify anti-aromatic bonds using Rdkit? >>> >>> Thanks. >>> >>> Yingfeng >>> >>> On Mon, Aug 24, 2015 at 9:38 PM, Yingfeng Wang <[email protected]> >>> wrote: >>> >>>> According to the following link, >>>> >>>> http://www.rdkit.org/docs/RDKit_Book.html >>>> >>>> I get sample code for identifying identify anti-aromatic bonds like >>>> >>>> >>> from rdkit import Chem >>>> >>> m=Chem.MolFromSmiles('O=C1C=CC(=O)C2=C1OC=CO2') >>>> >>> m.GetBondBetweenAtoms(6,7).GetIsAromatic() >>>> >>>> Is there a way to identify anti-aromatic bonds using Rdkit? >>>> >>>> Thanks. >>>> >>>> Yingfeng >>>> >>> >>> >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> Rdkit-discuss mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> >
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