On Fri, Apr 4, 2008 at 12:45 PM, Adrian Schreyer <ams...@cam.ac.uk> wrote: > Thanks Greg, this is what I suspected. By the way, will you change > error handling in RDKit generally? Currently, > GetAtomPairFingerprintAsIntVect(mol) will throw a RuntimeError if the > molecule is invalid (an error occurs) - maybe this can be changed > analogous to the supplier functions.
I agree that it should do something more informative than a RuntimeError (a ValueError at the very least). Are you requesting that the fingerprinting code return None instead of generating an error if you pass it an empty molecule? That's not a solution I particularly like. > This would make the use of > generator expressions or list comprehensions easier. Something like this: fps = [GetAtomPairFingerprintAsIntVect(mol) for mol in suppl if mol] avoids the empty molecule problem. > In addition, > would it be possible to have a BulkDiceSimilarity function for > SparseIntVects as welll? I guess it would be considerably faster than > iterating through a Python list and calling > SparseIntVect.DiceSimilarity each time. Indeed it will be. I will come up with a solution for this. Thanks for the suggestions, -greg
