Dr. Hutchison,
Yes, this helps. I do have another question about substructure searching.
We are building a database with roughly 270,000 molecules and want users to
be able to do a substructure and similarity search. I've read the following
documentation, http://openbabel.org/docs/dev/Fingerprints/fingerprints.html,
and it helps in understand how this process works. However, I want to ask
whether or not the output file from the query can contain the exact same
SMILES strings that were generated from the fast search index. Currently,
the SMILES strings generated from the query in the result.smi file are not
the canonical SMILES that I used to create the fast search index. For
example, if I were to look for a benzene substructure with the following
command,
*babel glass.fs -ifs -sc1ccccc1 result.smi*
would I be able to retrieve the SMILES string from glass.sdf, which was
used to create glass.fs? Many thanks for your patience.
Wallace
On Tue, Jul 22, 2014 at 2:52 PM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:
> A valid SMILES string is generally a SMARTS. It might not be the best
> possible SMARTS, but we do have a set of tests for SMILES to match
> themselves as SMARTS.
>
> Hope that helps,
> -Geoff
--
Wallace Chan
PhD Candidate
Zhang Lab
Department of Biological Chemistry
University of Michigan
walla...@umich.edu
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