Component grouping not recognized in CDX and SKC imports

Assume we have an ISIS/Draw or ChemDraw file consisting of e.g. a reaction A + B -> C, where B is a group, e.g. the pyridine*HCl salt. After importing into Marvin Sketch, the grouping is lost and you get pyridine and HCl as *separate* reactants (A + B + C -> D), which is certainly not what we want. - For semantics: In ISIS or ChemDraw 'grouping' is used for defining e.g. salts, and is the same as 'Merge Reactants' in Marvin Sketch.

Can you confirm this issue? Again it exists for ISIS/Draw and ChemDraw imports.

Regards, Stefan

Dear Stefan,

I have moved your question to the structure representation and file formats topic, my colleagues who are dealing with file import related issues will answer for you soon.

Thank you for your patience.

Regards,
Istvan

Dear Stefan, 

 

Could you provide us an skc and a cdx file with an example reaction?

 

Regards,

Peter

 

Peter,

Here you go. In both files the reactant pyridinium hydrochloride salt is originally grouped into one component (B), i.e. you have A + B -> X both in ChemDraw and ISIS/Draw. After import into Marvin, this grouping is lost, and pyridine and chloride are treated as separate compounds, resulting in A + B1 + B2 -> X. So you end up with three instead of two reactants.

Regards, Stefan

Dear Stefan, 

Thanks for the files, we started to investigate the issue.

We will get back to you if we made any progress.

 

Regards, 

Peter

Peter,

Could you confirm the issue meanwhile, or do you need any additional information?

Stefan 

Hi Stefan,

 

we managed to fix it in case of CDX import, the fix will be available in Marvin 5.10. 

We are still working on the SKC import problem.

 

Regards,

Peter

Ok, thanks for the confirmation - looking forward to 5.10 then.
Stefan

Hi Stefan,

we have fixed the SKC import of component grouping as well, the fix will be available in Marvin 5.12. 

Regards,

Zsuzsa