stereo disappearing after transformation

[Ken]

A curious case of missing stereo on an adjacent atom that was not involved in transformation...

Indigo indigo = new Indigo();

IndigoObject reaction = indigo.loadReactionSmarts("[H:1][O,S,Se,Te:2][C:3]([H,*:7])=[C:4]([H,*:6])[H,*:5]>>[H:1][C:4]([H,*:6])([H,*:5])[C:3]([H,*:7])=[O,S,Se,Te:2]");

IndigoObject mol = indigo.loadMolecule("C[C@]1(O)[C@H]2C[C@H]3[C@@H](C(O)=C(C(N)=O)C(=O)[C@@]3(O)C(=O)C2C(=O)C2=C1C=CC=C2O)N(C)C");

indigo.transform(reaction, mol);

mol.layout();

System.Console.WriteLine("After:");

System.Console.WriteLine(mol.smiles());

smiles after transformation: "[H]C1(C(=O)C([C@H]2[C@@](C(C3C(C4C(O)=CC=CC=4[C@]([C@H]3C2)(O)C)=O)=O)(O)C1=O)N(C)C)C(N)=O";

Though transformation should not affect stereo on the carbon with amine, the stereo is missing on it after transformation.

Thanks,

Ken

[Mikhail Rybalkin]

Hello Ken,

Thank you for this bug report. We will try to fix it and make a new release soon.

Best regards,

Mikhail

[Andrey Churinov]

Hello Ken

 

This bug was fixed. New version will be released soon.

 

Thanks,

Andrey

[Mikhail Rybalkin]

Hello Ken,

Sorry for such a long delay in preparing the next release of Indigo. If you still have such issues with the transformations you can try the latest Indigo 1.1.3: http://ggasoftware.com/download/indigo

With best regards,

Mikhail