Re: [Rdkit-discuss] version.sdf.gz

[acanada <ac...@cn...>]

Hi Greg,

Thank you very much for your answer! I get what you mean, but still unclear to me. If for example, I want to draw molecules, in the documentation I need the sdf file as the input... But instead I have the SMILES.... How should I proceed? I thought to translate SMILES to sdf and then use the sdf as input. 

If it's as you say, I don't need the sdf file... So I think I can handle this by loading the sdf files of the molecules in my database (i.e using chebi web service to retrieve sdf and serializing to the database), then I can retrieve the sdf from the database and use 

		suppl = Chem.SDMolSupplier('data/cdk2.sdf')

to draw the molecule... But I should create a file with the data from the table and it seems to me not very efficient at all...


Am I messing too much? Is there an standard way to do this?


Bests regards,
Andrés


El Jun 25, 2014, a las 7:59 AM, Greg Landrum escribió:

> [Andres: sorry you're getting two copies of this; I forgot to include the mailing list on the first one]
> 
> Hi Andres,
> 
> On Tue, Jun 24, 2014 at 5:43 PM, acanada <ac...@cn...> wrote:
> 
> I'm very new to RDKit and the RDKit database cartridge. I'm not chemist so please my apologize for the simple question.
> After reading the documentation it's clear to me how to create the emolecules database with the raw_data table and populate with the version.smi.gz file (http://downloads.emolecules.com/free/2014-06-01/version.smi.gz). Then I create the mols table that will have only the smiles accepted by RDKit. Great!
> 
> My question, if it has any sense:  Is there a how-to to create a sdf table populating it with the version.sdf.gz file (http://downloads.emolecules.com/free/2014-06-01/version.sdf.gz)?? Can you please point me where the instructions are?
> 
> There is not currently an easy way to do this analogous to the way things are built from the smiles file. The SMILES file is easier for postgresql to manage on its own because it has one record per line. SDF files have multi-line records, so you would need to use something that understands the format (e.g. the RDKit python wrappers) to be able to load it.
>  
> Or what is the version.sdf.gz file used for?
> 
> It provides another format of more-or-less the same data. Unless you have a concrete reason for wanting that version of the data, there is probably no need to use the file at all.
> 
> Best,
> -greg
> 
> 
> On Tue, Jun 24, 2014 at 5:43 PM, acanada <ac...@cn...> wrote:
> Hello,
> 
> I'm very new to RDKit and the RDKit database cartridge. I'm not chemist so please my apologize for the simple question.
> After reading the documentation it's clear to me how to create the emolecules database with the raw_data table and populate with the version.smi.gz file (http://downloads.emolecules.com/free/2014-06-01/version.smi.gz). Then I create the mols table that will have only the smiles accepted by RDKit. Great!
> 
> My question, if it has any sense:  Is there a how-to to create a sdf table populating it with the version.sdf.gz file (http://downloads.emolecules.com/free/2014-06-01/version.sdf.gz)?? Can you please point me where the instructions are?
> Or what is the version.sdf.gz file used for?
> 
> Sorry for this basic questions and thank you for your time...
> 
> Andrés
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