interpretation of SMILES and mapping

Hi,





When I load this SMILES file into Marvin 4.0.3:

Code:

O1[C:2]=[C:2][C:3][C:3]1

and this structure is converted into MRV format, Marvin converts the mapped C atoms into monovalent or divalent radicals.





-- Bob

Hi Bob,





Thank you for the report we'll fix it.


Andras

Hi Bob!


I have just realised that you want it to be read as SMILES. That is exactly what Marvin does.


If it is SMILES, than all implicit hidrogens should be explicitly written inside the brackets. As in this case no implicit H is specified, this leads to radicals.





Andras

Well, then the problem is in converting the MarvinSketch picture into SMILES. I drew 2,3-dihydrofuran, mapped the atoms, and saved it as SMILES. I certainly didn't specify radicals before I saved the structure. The mapping must have required the brackets be included in the SMILES representation, but the brackets also implied a radical status that was not originally intended. The H atoms need to be specified explicitly for any atom that has mapping.

Hi Bob,





I could not reproduce this problem with Marvin 4.0.3. Are you sure the file was saved as smiles and not smarts? The smarts representation of your molecule would be correct, but in this case it should be read as smarts instead of smiles. For example from command line:

Code:

msketch 'O1[C:2]=[C:2][C:3][C:3]1{smarts}'

Or on the GUI use edit/source and set the format to SMARTS in the menu before importing. Pasting on the canvas is not enough in this case.





Best regards,


Szabolcs

Yes, I suppose this particular molecule must have been saved as SMARTS, although I did not have this problem with loading any other molecules directly into the Marvin window. Hmm.