How to obtain SMARTS-matching atoms

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

How to obtain SMARTS-matching atoms

cristallino
Hi all,
I'm new with OpenBabel. I'm using it to check if a molecule contains a specific sub-structure SMARTS. I can convert a molecule from a format to another if it matches the specified SMARTS. Is it possible to obtain only the list of atoms that make the molecule match the SMARTS?

For example... i want to convert the PDB file of an ATP molecule into the corresponding SMILES only if it matches the SMARTS of a 5-atoms carbohydrate ring. The output is the SMILES of the whole ATP molecule, while i'm wanting the SMILES of the only ribose carbohydrate (that made the ATP molecule match the specified SMARTS).

Can someone help me? (thanks a lot)
Luca