If "base_name" is meant to just be a fast access for the substring up to the first variant (ie. res.base_name == res.name.partition(":")[0]), then the base-name for CYD ought to be "CYD" and not "CYS." Making that change currently triggers an error because cart-bonded uses the base_name to perform lookup. I suggest that what cart bonded should do is what the Dunbrack term does: it keeps a mapping from base_name to what set of parameters should be used:
If "base_name" is meant to just be a fast access for the substring up to the first variant (ie.
res.base_name == res.name.partition(":")[0]), then the base-name for CYD ought to be "CYD" and not "CYS." Making that change currently triggers an error because cart-bonded uses the base_name to perform lookup. I suggest that what cart bonded should do is what the Dunbrack term does: it keeps a mapping from base_name to what set of parameters should be used:https://github.com/uw-ipd/tmol/blob/master/tmol/database/default/scoring/dunbrack.yaml
Then both "CYS" and "CYD" can use the same set of parameters