extended smiles with multiple labels

Hi,





I am trying to understand the cx-smiles format with respect to atom labels.


The following string, pasted into Marvin, labels one atom correctly as R1, leaving the other one as "A"

C1=CC2=C(C=C1)C(

)=CC=C2 |$R1$|





I thought that, according to documentation the string

C1=CC2=C(C=C1)C(

)=CC=C2 |$R1;R2$|





would label both of them, but the result is not expected. Perhaps I am missing something?

Hi Julian,





The labels specified between the dollar signs are in atom index order and all atoms should be considered, not only any atoms. So, R2 is attached to atom numbered 2. It will help if you turn on atom indexes in Marvin (View/Misc/Atom Numbers), see the picture below.





You can also leave out labels by not writing anything between the separator semicolons. So this string will generate your expected molecule:

C1=CC2=C(C=C1)C(

)=CC=C2 |$R1;;;;;;;;R2$|





Maybe you will also find experimenting with Marvin helpful. You can quickly see the source of a sketched molecule using menu Edit/Source and changing the format in the format menu of the source window. You can also edit the source and import it back into Marvin.





Furthermore, the Extended smiles specification can be reached on the following link:


http://www.chemaxon.com/marvin/doc/user/cxsmiles-doc.html





Best regards,


Szabolcs