Hi Andrew,
Since you don't have access to the database in-house you may want to check
the web services for simple queries:
https://www.ebi.ac.uk/chembldb/index.php/ws
Wrt to the names, you're right, there's no explicit name for the structures
in the sd and the chemblid is included just as a property. This is how it
has been historically but I'll pass on your request.
Regards,
George
EMBL-EBI
On 2 May 2012 12:34, Andrew Dalke <[email protected]> wrote:
> Hi George,
>
> > This is probably not going to solve the problem at hand but it may be
> useful to you or others in the future:
> > ChEMBLdb maintains a molecular hierarchy table where you can retrieve
> the parent (=desalted - using Pipeline Pilot) structures for each molecular
> entity.
> > You may try something like this:
> >
> > select distinct cs.molregno, cs.molfile, cs.canonical_smiles
> > from compound_structures cs, molecule_hierarchy mh
> > where cs.molregno = mh.parent_molregno
>
> I confess pure ignorance here. While I've worked with databases, it's far
> from the list of things I know well. Reading the ERD is not simple for me,
> I don't have MySQL or Oracle installed on my machines, and I don't know how
> to browse through the schema and tables like I've seen those who are more
> database proficient than I do. So while I have an idea of what you are
> talking about, it's not something I can easily put into place.
>
> But as you say, it's not the problem, because RDKit's failure exception
> comes even using the original, unprocessed/un-de-salted record.
>
>
> Since you're here -- how come ChEMBL doesn't put an identifier on the
> first line of the SD record? Nearly all of them are blank; the exceptions
> are a dozen with mostly useless titles like:
>
> Acetic acid 6-(1-phenyl-ethyl)-6-aza-bicyclo[3.2.1]oct-3-yl ester
> 4-(4-Fluoro-phenyl)-2-methylsulfanyl-thiophene-3-carbonitrile
>
> 6-amino-9-(5-{[(1,2,3,3-tetrahydroxy-1,2,3-trioxidotriphosphanyl)oxy]methyl}tetr
> 2-Methyl-2,3-dihydro-benzofuran-7-carboxylic acid
> 8-methyl-8-aza-bicyclo[3.2.1]o
>
> (S)-N-((S)-1,6-diamino-1-oxohexan-2-yl)-1-((S)-5-guanidino-2-((2S,3S)-2-((S)-5-g
> Acetic acid 6-(1-phenyl-ethyl)-6-aza-bicyclo[3.2.1]oct-3-yl ester
>
>
> I end up doing a mol.SetProp("_Name", mol.GetProp("chembl_id")) so that my
> output SMILES have an identifier tied to them, and that seems like a
> needless extra step.
>
>
> Andrew
> [email protected]
>
>
>
>
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