On Mar 7, 2012, at 2:31 AM, Jochen Schreiber wrote:
> and this is not what i want.
> I must do an evaluation. This is my task. And i need to use open babel and
> other tools for the similarity search.
How is the simsearch program from chemfp not part of 'other tools'? What is the
underlying reas
a) The parameter of the -s option has to be a SMILES string (or a
filename) The ${...} syntax is not recognised.
b) It is better to use obabel rather than babel because it is safer and
more versatile. The syntax difference is very small ( -O before output
filename).
So this works for me:
obab
Hi,
and this is not what i want.
I must do an evaluation. This is my task. And i need to use open babel and
other tools for the similarity search.
So now the question again:
How could i perform the similarity search with babel on chembl?
babel /bioinf/MuDiSAR/db/chembl/chembl_13.sdf search/bab
Hi,
you can't. FPS is a new format from the chemfp project. You have to use
chemfp. There is a nice script called simsearch, that assist you with
the searching.
Kind regards,
Bjoern
> Hello,
>
> ok i think this works:
>
> ob2fps /bioinf/MuDiSAR/db/chembl/chembl_13.sdf -o chembl_13.fps
> ==
Hello,
ok i think this works:
ob2fps /bioinf/MuDiSAR/db/chembl/chembl_13.sdf -o chembl_13.fps
==
*** Open Babel Warning in Expand
Alias -N was not chemically interpreted
==
*** Open Babel Warning in Expand
Alias -N was not chemically
Hi Jochen,
On Mar 6, 2012, at 10:45 AM, Jochen Schreiber wrote:
> this sounds great. But i NEED Open Babel. This is not my decision.
What does it mean to "NEED Open Babel"?
Chemfp's 'ob2fps' command-line tool uses the Open Babel Python API
for the fingerprint generation.
Hello,
this sounds great. But i NEED Open Babel. This is not my decision.
Any other ideas why this not work?
With best
Jochen Schreiber
On Mar 5, 2012, at 3:22 AM, Jochen Schreiber wrote:
> i have download the chembl_sdf archive and unpack it.
>
> The resulting sd file from that archive has
On Mar 5, 2012, at 3:22 AM, Jochen Schreiber wrote:
> i have download the chembl_sdf archive and unpack it.
>
> The resulting sd file from that archive has 2.5 GB.
>
> Now i want to create the fs index datei from that sd file with:
>
> babel -isdf chemble_13.sdf -ofs chembl_13.fs
>
> This comma
Hey guys,
i have download the chembl_sdf archive and unpack it.
The resulting sd file from that archive has 2.5 GB.
Now i want to create the fs index datei from that sd file with:
babel -isdf chemble_13.sdf -ofs chembl_13.fs
This command works but if i want to search with an sd file against th
