achiral (meso) molecules marked as chiral

[m.k.bo...@gmail.com]

For example C[C@H]1CCCC[C@H]1C

See here: http://www.chemicalforums.com/index.php?topic=64128.msg237479#msg237479

[m.k.bo...@gmail.com]

This one is even more obvious: C[C@H]1CCCCC1

As a friend of mine guessed, perhaps depict assumes every molecule that has specified configuration (with @ or @@) is chiral?

[Mikhail Rybalkin]

Hello Marcin,

I was focus on your second example and added a method  IndigoObject.resetSymmetricStereocenters in the version Indigo 1.1.9. There was another similar question here: https://groups.google.com/d/msg/indigo-bugs/FGkPE3Funkc/cDkN4rJAo6IJ

But now I checked your first example and I understand that it is a different thing. We should check if a molecule matches a mirrored one and clear a chirality flag is such case. I will add a method validateChirality in the next version.

And yes, each molecule with @ and @@ is marked as chiral when loading from SMILES. The the extended Molfile format there are three types of sterecenters: abs, or, and. And we assume that all stereocenters in the SMILES have "abs" type by default.

Best regards,

Mikhail

[Mikhail Rybalkin]

Hello Marcin,

We've just release a new version with a new documentation that has examples to the function you requested. Look either to the announcement on the indigo-general, or directly to the documentation preview. 

Best regards,

Mikhail