Hi,
I'm using the KNIME implementation to write my own nodes, and I'm
running into an issue. For the process I'm trying to do I'm trying to
subtract the MCS between two molecules away from the larger molecule, to
leave a list of fragments. I'm aware of the substructure matching, but
I'm not sure how to subtract the matching atoms from a molecule graph
within RDKit. As I say, I'm working with the Java version, but any
pointers towards the fucntions needed would be useful. At the moment
I've got (in pseudo code)
RWMol mol1a = RWMol.MolFromSmiles(reactant_string, 0, true);
RWMol mol2a = RWMol.MolFromSmiles(product_string, 0, true);
frag_bonds = mol2a.GetSubstructMatches(mol1a);
But I'm unsure as to what to do with the array of matches to achieve
what I want. Can I strip out the dummy atoms automatically, or is this
something that is best achieved by processing the SMILES string?
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