Hello,
you could write a script to search the 94 x 2GB files. Either sequentially or
in parallel.
When doing it in parallel, you have to accumulate the search results either in
a place that allows concurrent access, e.g. a database table or write
independent search result files and concatenate
Hi Jochen,
On Mar 3, 2012, at 2:59 AM, Jochen Schreiber wrote:
> My problem now is that babel only one file expected and i have the complete
> pubchem compound sdf files with over 2000 sdf files.
>
> If i concat all sdf files to one file it has over 187 GB and the index will
> be over 2GB.
You
Hi Jochen,
one possibility is to convert all sdf-files to one SMILES file, that
will be 1.9 GB. From that you can try to build a fs-index. Maybe split
the SMILES file create different fs-indices and combine the results
later.
I would go with a database solution -> pgchem for the win!
Ciao,
Bjoern
Hello Bjoern,
My usechase is to do a similarity search on local sdf files with babel and cdk.
My problem now is that babel only one file expected and i have the complete
pubchem compound sdf files with over 2000 sdf files.
If i concat all sdf files to one file it has over 187 GB and the index w
On 02/03/2012 17:47, Björn Grüning wrote:
> Hi Jochen,
>
> maybe you can explain what you want to do with it. We are running such
> Setup in our lab using postgresql and pgchem and it works very well.
>
> The fs file from openbabel is smaller than the sdf file and as far as i
> know the fs file sho
Hi Jochen,
we are running such setup in our lab with postgresql and pgchem. Maybe
you can explain your usecase a little bit better. I don't think the
fs-index from openbabel is the way to go for such huge datasets.
As Chris mentioned the index should be smaller than 2GB. You will exceed
these. Yo
Hi Jochen,
maybe you can explain what you want to do with it. We are running such
Setup in our lab using postgresql and pgchem and it works very well.
The fs file from openbabel is smaller than the sdf file and as far as i
know the fs file should be smaller than 2GB.
Cioa,
Bjoern
> Must it be s
Must it be smaller then 2 GB?
If i do a concat on all i gain a file which is about 187 GB.
Any idea?
With best
Jochen Schreiber
--
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On 02/03/2012 15:23, Jochen Schreiber wrote:
> Hello everybody,
>
> i have the completed pubchem compound sdf file on my file system an want to
> to a smiliarity search on them.
>
> Can i execute babel with more then one input fs file or how is the way to do
> the search?
Put all the molecules i
Hello everybody,
i have the completed pubchem compound sdf file on my file system an want to to
a smiliarity search on them.
Can i execute babel with more then one input fs file or how is the way to do
the search?
With best
Jochen Schreiber
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