Hi Toby, I can reproduce this behavior and agree that it looks like a bug.
I'll take a look. -greg On Mon, Mar 31, 2014 at 12:49 PM, Toby Wright <[email protected]>wrote: > Further investigation shows that this issue is not related to the reaction > code at all, it's a general SMILES canonicalisation bug I'm afraid. > Consider the following: > > > mol = Chem.MolFromSmiles("C1C[C@@H](CC)CC[C@@H](CC)1") > > print Chem.MolToSmiles(mol, isomericSmiles=True) > CC[C@@H]1CC[C@@H](CC)CC1 > > The output should be the same as the input but plugging those strings into > the daylight website's depiction tool gives chirally different molecules. > This behaviour is observed in RDKit 2013.09 with no custom patches. > > Yours, > > Toby Wright > > -- > InhibOx Ltd > > > > On 28 March 2014 15:47, Toby Wright <[email protected]> wrote: > >> Oops, forgot to mention: This is with the solution to github issue >> #233<https://github.com/rdkit/rdkit/issues/233>patched into my RDKit build. >> >> Yours, >> >> Toby Wright >> >> -- >> InhibOx Ltd >> >> >> On 28 March 2014 15:43, Toby Wright <[email protected]> wrote: >> >>> Hi, >>> >>> I believe I've found a bug in the new code that deals with reactions >>> that have chirality specified for untagged product atoms. Consider the >>> following: >>> >>> > rxn = AllChem.ReactionFromSmarts("[C:1].[C:2]>>C1C[C@@H](C[C:1])CC[C@ >>> @H](C[C:2])1") >>> > m1 = Chem.MolFromSmiles('FC') >>> > m2 = Chem.MolFromSmiles('BrC') >>> > p = rxn.RunReactants((m1,m2))[0][0] >>> > Chem.SanitizeMol(p) >>> rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE >>> > Chem.MolToSmiles(p, isomericSmiles=True) >>> 'FCC[C@@H]1CC[C@@H](CCBr)CC1' >>> >>> The output looks about right, the [C@@H]s are both still [C@@H] but >>> whereas before they were both being approached from around the ring now the >>> canonicalisation has us approaching one from outside the ring. Both >>> extensions from the ring should be towards and if I convert the product >>> part of the above reaction to a png I get: >>> [image: Inline images 1] >>> but in the output one is towards and the other is away: >>> [image: Inline images 2] >>> >>> Note that I can work around this, if I specify my reaction as >>> [C:1].[C:2]>>[C:1]C[C@H]1CC[C@@H](C[C:2])CC1 thus apeing the atom >>> ordering of the product RDKit will give me I get the chirality I want, at >>> least in my test cases so far. >>> >>> Yours, >>> >>> Toby Wright >>> >>> -- >>> InhibOx Ltd >>> >> >> > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
<<inline: MadeProduct.png>>
<<inline: ReactionProduct.png>>
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