Hello RDKitters, I'm using a function to convert a molecular graph to RDKit's mol object. Input molecules have a maximum size of N atoms. Molecules with less than N atoms have dummy atoms on the corresponding node. Currently, I use hydrogen as the dummy atom when building the editable RWmol object. This results in hydrogen atoms without neighbours. An example of such a molecule has SMILES representation 'C#CC(O)C1CCN1.[HH]'. I was wondering
1. How can I remove the hydrogen's without neighbours? These hydrogen are currently affecting the molecular properties. 2. Is there a better option to use as the dummy atom? Something that potentially would not affect the molecular properties. PS: I can't skip the dummy atoms while building the mol object b/c some graphs mistakenly have bonds connected to these atoms and I need the statistics on the defective molecules. Thanks, Navid
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