Given a set of structures such as
I would like to be able to say ‘this molecule has 5 molecules of water.’ (There is a list of known salt counterions and solvents to use for matching fragments.)
I’ve gotten part of the way using the RDKit Molecule Extractor, which creates a new record for each fragment.
The next step is to put a name (or identifier) on each fragment.
The RDKit Molecule Substructure almost works.
It tells me that the the extracted water molecules match ‘[OH2]’ but [OH2] also matches the parent fragment, which is not what my team is looking for.
How can I perform an exact match of a set of generated fragments against a set of known molecules?