Atom selection numbers do not agree with SMILES location

I'm using MarvinSketch 3.5.1, via javascript1.1, to get user input of a structure. I want the user to select atoms and the result - both structure and list of selected atoms - to be sent to a CGI. I wanted to use SMILES as the format for compactness and convenience with what I do in the CGI, but although I can get the list of atoms selected as a comma-separated string using isAtomSelected(), the numbers do not necessarily coincide with the positions of the atoms in the SMILES string obtained with getMol(smiles). What I want is a SMILES with the atom order the same as the atom selections, so if 7,8 and 9 are selected, these are also the 7th, 8th and 9th atoms in the SMILES. Can that be done?

With the current Marvin, you can not solve this problem.


We will implement a JMSketch.getSelectedMol(String) method to be able to do this.


I can not guaranty that this method will be available in the next patch release (4.0.2) because its date is very close. But I can send you a pre-release when we implemented the above method.

The problem is that the smiles format contains atoms in different order from the original, and the selected atom indexes refer to the inner representation.





I suggest that you should use a format which preserves the original atom numbering. Any of mol, csmol or mrv is suitable for this. If size is a factor, I recommend csmol (compressed mol):





http://www.chemaxon.com/marvin/doc/user/mol-csmol-doc.html#csmol





Best regards,





Szabolcs