Yes, C++ code examples for preprocessed molecules and fingerprints would be
extremely helpful too.
By the way, if the query is a SMARTS like e.g. "c1aaccc1" (representing several
substructures), what fingerprint is exposed to AllProbeBitsMatch, the union of
all the possible fingerprints, all the possible fingerprints sequentially, etc?
Thanks a lot for your help,
Gonzalo
From: Greg Landrum [mailto:[email protected]]
Sent: 09 June 2013 06:33
To: Gonzalo Colmenarejo-Sanchez
Cc: [email protected]
Subject: Re: [Rdkit-discuss] substructure search with fingerprints in C++
Hi Gonzalo,
On Sat, Jun 8, 2013 at 10:31 AM, Gonzalo Colmenarejo-Sanchez
<[email protected]<mailto:[email protected]>> wrote:
Could anyone provide some advice about how to run (fast but approximate)
substructure searches with fingerprints using C++? I have a large set of SMILES
for molecules and a relatively large set of SMILES/SMARTS for substructures.
Sorry, I meant to do this last weekend but it ended up slipping my mind.
The attached file demonstrates how to use fingerprints for substructure
screening.
The usual required caveat: the substructure fingerprints are quite efficient
for molecules that don't contain query features, but their efficacy drops as
query features are introduced.
If you're going to be processing the same molecules/queries repeatedly (i.e.
multiple runs on the same sets), it probably makes sense to use the RDKit's
serialization code to save the pre-processed molecules and fingerprints. If
applicable, let me know and I can generate some sample code for that too.
Hope this helps,
-greg
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