Aromatized structure vs dearomatized

Hi,





Although there are options in Marvin Sketch or View to aromatize structures on the applet, the underlining sdfile or smiles seems not change accordingly. When sdfile from the applet is used as file format to insert into database, it is found that the structure will be automatically aromatized even if the molecule was shown as a dearomatized structure in applet.





Another issue is that when we use a dearomatized structure to do the structure perfect search, the relevant aromatized structure will become a hit.





So my question is how does the Sketch or View actually deal with aromatized issue besides the image appears to be changed correspondingly? And how about the sd file of the structure? Thanks.





Ben

benli wrote:

Although there are options in Marvin Sketch or View to aromatize structures on the applet, the underlining sdfile or smiles seems not change accordingly. When sdfile from the applet is used as file format to insert into database, it is found that the structure will be automatically aromatized even if the molecule was shown as a dearomatized structure in applet.

I guess you are talking about JChem Base tables. There are two columns for storing the stuctures:


- cd_structure that stores the original structure file


- cd_smiles that stores the structure in standardized (aromatized) format.

benli wrote:

Another issue is that when we use a dearomatized structure to do the structure perfect search, the relevant aromatized structure will become a hit.

Because cd_smiles is used for structure searching

benli wrote:

So my question is: how does the Sketch or View actually deal with aromatized issue besides the image appears to be changed correspondingly? And how about the sd file of the structure? Thanks.

If you want to display the original structure, use cd_structure.


I am not sure that I understand the problem. Please give me more details if you need a better answer.





Ben