fragment stereochemistries in SMILES format

I don't know whether it's possible to do this, but I'm going to ask anyway. Consider the SMILES code for a drawing that has more than one molecule, such as that for benzene and toluene:

C1=CC=CC=C1.CC1=CC=CC=C1 |c:0,2,4,9,11,t:7|

If I want to fragment this code into the code for the separate molecules, I can't just split the code at the . marks, because that makes the stereochemistry indicators inconsistent. Instead, I have to import, fragment, and then export back to SMILES format. It would be nice if each individual fragment had its own stereochemistry indicators, something like this:

C1=CC=CC=C1 |c:0,2,4|.CC1=CC=CC=C1 |c:3,5,t:1|

Hi,

At the moment the cxsmiles I/O is not capable of either create or import such strings. So I would suggest to use the aforementioned workaround as the seemingly easiest solution. I would mention for the sake of completeness that Marvin provides possibility to integrate custom formats into it but that solution requires much more work in my opinion. (Though if you are still interested the details can be found here: IntegratingCustomFormat).

Regards, Domi

I'm suggesting making it an option for output of CXSMILES from the applet or from the API.

Hi,

I regret it but we will not implement this option as we expect it to be rarely used and because of many other important issues (including the parity calculation) that precedes this one.

Best regards,
Domi