On Mar 21, 2012, at 6:48 PM, Greg Landrum wrote:
> I don't think it's actually reading the molecule from SDF that's slow.
> The slow part is sanitizing it. More carefully: the slowest part is
> cleaning up the stereochemistry.
Without looking at the code, I can agree with that. RDKit's SD reader
used to be slower than Open Babel's. OB supported stereochemistry starting
with 2.3. Now its SD file reader is slower than RDKit's. They believe
the slowdown comes from handling stereo.
Andrew
da...@dalkescientific.com
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