grow_mol error when used on fragments with dummy atoms

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grow_mol error when used on fragments with dummy atoms

[DrrDom]

You are welcome!

If you would like to make replacements at a particular position there are two options.

Option 1. Remove a dummy atom, store the id of the attached atom (idx) and pass it as an argument replace_ids=[idx] to grow_mol. Before calling grow_mol you need to sanitize a molecule Chem.SanitizeMol(fragment) (that is why you have an error in the second case, after manipulation with a molecule you need to update internal states).

Option 2 (tricky). Replace a dummy atom with a hydrogen, sanitize a molecule and then call mutate_mol with min_size=0 and max_size=0. This will replace all explicit hydrogens in a molecule. While you maintain explicit hydrogens at attachment points only you will get what you want. This is less explicit and a more dangerous way.
In the example I decreased the radius to 2, because it cannot find such a context at radius 3 in a database.

idx = None
for atom in fragment.GetAtoms():
    if atom.GetAtomicNum() == 0:
        idx = atom.GetIdx()
        break

frag = Chem.EditableMol(fragment)
frag.ReplaceAtom(idx, Chem.Atom(1))
frag = frag.GetMol()
Chem.SanitizeMol(frag)

res = list(mutate_mol(frag, db_name='replacements.db', max_replacements=9, return_mol=True, min_size=0, max_size=0, radius=2))

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It seems like removing the dummy atom and running SanitizeMol solved my problems. Thank you for the timely help!