Explicit hydrogens on Si atoms in Marvin sketch

When you draw a nitrogen atom in Marvin sketch, it puts on implicit hydrogens but when you retrieve the SMILES it returns N without the explicit hydrogens - this is the expected behaviour and works well for us when you feed it into a chemical search.





However, when you draw Si it adds explicit hydrogens to the SMILES string by default - this causes problems when you use the SMILES to do a substructure search as it will not find any molecules where substitutions exist





Can this be changed ?





Many thanks


Alistair

If you draw Si it adds implicit hydrogens to the SMILES: [SiH4]


For queries you should rather use SMARTS format instead of SMILES.


The SMARTS of Si is: [#14]


Please note that SMILES is used for molecules and SMARTS for queries.


Andras