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

[Greg L. <gre...@gm...>]

[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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