Hi,
I assume you have canonical SMILES strings in glass.sdf stored as titles or
properties. Correct me if this is incorrect. If so, it depends on what
program was used to create these canonical SMILES strings. If you used
openbabel for this, you can convert the molecules in result.smi to
openbabel canonical SMILES (or write canonical SMILES directly using the
.can extension).
In the case where another program was used to generate the canonical
SMILES, it would not be possible to use openbabel to generate the same
canonical SMILES starting from result.smi. If you have access to the other
program you could use this to convert results.smi to these canonical SMILES
and use these to search glass.sdf.
The reason for this is that there is no universal SMILES canonicalization
algorithm. Different toolkits will result in different canonical SMILES
(which are canonical only when using the same toolkit). InChI on the hand
has a single reference implementation.
Tim
On Wed, Jul 23, 2014 at 12:03 AM, Wallace Chan <walla...@umich.edu> wrote:
> 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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search up to 200,000 lines of code with a free copy of Black Duck
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search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
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