The problem was that I caught exceptions and parsed molecules without sanitization, which eventually led to RuntimeErrors. Using only sanitized mols, the list comprehension works fine - request withdrawn! :)
On Fri, Apr 4, 2008 at 3:27 PM, Greg Landrum <greg.land...@gmail.com> wrote: > 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 >
