Polymer issue

Hi 

When drawing the structure the structure attached JChem (.. or mavin) does a some transformation on the structure.

How can I ensure that the structure will appear as intended after saving..?

Dann

Hi Dann,

Could you clarify which product is this, and exactly what version ?

Marvin is integrated into many tools - I guess it is not only the Marvin Sketch desktop GUI right ?

Best,

Szilard

 

Hi Szilard

Sorry for the missing information:

JChem version: 6.0.0.181

Marvin version: 6.0.4

Integrated into a ASP.NET application.

BR

Dann

Dann,

Since it is a custom application, there can be different places unknown to us where things can go "wrong".

To be sure, the developers of this application should be asked to investigate where exactly the structure changes, and correct their code or report it to us if they believe it is a problem with our API, with a code example to reproduce.

A quite frequent mistake developers make is to use the cd_smiles field of the JChem Base table for structure display. This is not advised ,as this field is for internal use only, and may also contain NULL values in certain cases.

Therefore always the cd_structure field should be used for display, or JChemSearch.getHitsAsMolecules:

http://www.chemaxon.com/jchem/doc/dev/java/api/chemaxon/jchem/db/JChemSearch.html#getHitsAsMolecules(int[], chemaxon.util.HitColoringAndAlignmentOptions, java.util.List, java.util.List)

I have noticed that by converting the structure to "cxsmiles" format (used in this column) and displaying in Marvin with the corresponding version provides exactly the same orientation. This is perfectly normal (this format by default does not preserve coordinates).

So that's why I suspect that either the cd_smiles column is used for displayed, or a conversion to cxsmiles happens some other place.

But as always in the case of a custom application, it is best to consult the developers first, this can spare a lot of guessing and speculation. Of course we can support them as needed.

Brest regards,

Szilard

Szilard

Thanks for the reply. I will investigate the points you have in your reply.

BR

Dann

Hi,

I experienced such structure change when saving the original structure in cxsmiles and reloading it to marvin.

Aren't you observing the contents of the cd_smiles column? This column contains the standardized structure and it's used for searching. It's not used for display. as data that are not used during searching may change, like rotation bracket size etc.

Regards,Robert

Hi

Thanks for all your valuable input on this issue.

I have made several adjustments to ensure that the data is retrived from the correct coloumn when displaying the structures.. And it worked!!

BR

Dann