[Open Babel] OpenBabel Warnings

2010-01-24 Thread Björn Grüning 
Hi,

is there a way to suppress openbabel warnings, linke the inchi ones [1]?
A BABL_WARNINGS Flag maybe?

Thanks!
Bjoern

[1] *** Open Babel Warning  in InChI code
  44 :Proton(s) added/removed


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Re: [Open Babel] pybel install via synaptic

2010-09-20 Thread Björn Grüning 
Hi,

i thought ubuntu 8.4 installed both pybel and openbabel (python) in the
package python-openbabel.
Try to 'import openbabel'.

Cheers,
bjoern 

Am Montag, den 20.09.2010, 11:04 +0100 schrieb Noel O'Boyle:
> You should either install it all via synaptic, or you should install
> it all from the source code. Does Ubuntu 8.04 provide the python
> bindings?
> 
> - Noel
> 
> On 20 September 2010 10:41, macc_200  wrote:
> > Hi,
> > I have installed openbabel on an ubuntu 8.04 LTS machine using synaptic and
> > it is working fine but would like to install the python bindings too.  It
> > looks to be installing it in a variety of /usr/share /usr/bin and /usr/lib
> > directories but I cannot find anything relating to the setup.py script
> > described in the documentation.  Is is possible to install them this way or
> > do I have to do the installation from source code?
> > thanks,
> > Andy
> >
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Re: [Open Babel] Generating fs from sdf

2012-03-02 Thread Björn Grüning 
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 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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Re: [Open Babel] Generating fs from sdf

2012-03-02 Thread Björn Grüning 
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. You can split your SDF files in chucks so that the resulting
indices are <2GB ...

Ciao,
Bjoern

> 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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Institute of Pharmaceutical Sciences
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D-79104 Freiburg i. Br.

Tel.:  +49 761 203-4872
Fax.:  +49 761 203-97769
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Re: [Open Babel] Generating fs from sdf

2012-03-03 Thread Björn Grüning 
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 will 
> be over 2GB.
> 
> What can i do? If i split i need to call my search but i want one output for 
> the search and not several.
> 
> With best
> 
> Jochen Schreiber
> 
> Am 02.03.2012 um 18:52 schrieb Björn Grüning:
> 
> > 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. You can split your SDF files in chucks so that the resulting
> > indices are <2GB ...
> > 
> > Ciao,
> > Bjoern
> > 
> >> 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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> >> also focuses on allowing computing to be delivered as a service.
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> > -- 
> > Björn Grüning
> > Albert-Ludwigs-Universität Freiburg
> > Institute of Pharmaceutical Sciences
> > Pharmaceutical Bioinformatics
> > Hermann-Herder-Strasse 9
> > D-79104 Freiburg i. Br.
> > 
> > Tel.:  +49 761 203-4872
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> > E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
> > Web: http://www.pharmaceutical-bioinformatics.org/
> > 
> 



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Re: [Open Babel] Chembl fs file

2012-03-07 Thread Björn Grüning 
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
> ==
> *** Open Babel Warning  in Expand
>   Alias -N was not chemically interpreted
> 
> ==
> *** Open Babel Warning  in Expand
>   Alias -N was not chemically interpreted
> 
> 
> cat chembl_13.fps 
> #FPS1
> #num_bits=1021
> #software=OpenBabel/2.3.1
> #type=OpenBabel-FP2/1
> #source=/bioinf/MuDiSAR/db/chembl/chembl_13.sdf
> #date=2012-03-07T07:24:20
> 0026004008a00b000600100c0010004000800108180050838303300e25380001010208208002001008001c00188001201a90001600b003403008c2080800800a2c2000201000800e01040001107200010100
>  Record1
> 200600c2043806c04b04860a0e42430e515004906808812320c0022404001c0470830950883b588f2438280fd0c10102605000a0690604f28896710206100c210d0ae8101aa000a2610022c9009d00d885400490300df08808708009509e08101820004840c8ba5c0400100605d40a43100101ba80410a64
>  Record2
> 
> But i have one question: How can i start the sim search with babel. In my 
> case i do:
> 
> babel /bioinf/MuDiSAR/db/chembl/chembl_13.sdf search/babelchemblresult.sdf 
> -s"${smi}" -at0.85
> 
> where smi is the smiles string / query
> 
> with best
> 
> jochen schreiber
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Re: [Open Babel] fingerprints

2012-05-14 Thread Björn Grüning 
Am Sonntag, den 13.05.2012, 20:34 -0700 schrieb sandeep:
> hello evryone,
> 
>  How FP4 and MACCS fingerprints differ from each other ?

The underlying substructures are different.
Please see: http://openbabel.org/wiki/Tutorial:Fingerprints

Kind regards,
Bjoern

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Re: [Open Babel] Problems building OB 2.3.1 with static libs

2012-07-30 Thread Björn Grüning 
Am Montag, den 30.07.2012, 22:43 -0400 schrieb Geoff Hutchison:
> > I am having some problems to compile OpenBabel on Ubuntu with static
> > libs.  The compiler is GNU (GCC/G++), Eigen3, Zlib, Cairo and XML2
> > libraries were installed.
> > 
> > The error message appears during the linking step:
> > 
> > Linking CXX executable ../bin/babel
> > ../src/libopenbabel.a(plugin.o): In function 
> > `OpenBabel::EnableStaticPlugins()':
> > /home/asn/Downloads/openbabel/src/plugin.cpp:245: undefined reference
> > to `OpenBabel::theChemDrawBinaryFormat'
> 
> 
> My first suggestion would be to try SVN trunk.
> http://openbabel.org/wiki/Subversion
> 
> I know there have been multiple patches towards static compilation. Not all 
> of them can be incorporated into the v2.3 release branch.
> 

Current trunk has the same error. The ChemDrawBinaryFormat got a major
overhaul, the diff between 2.3.1 and trunk is not small.
As a temporary solution and if you do not need that format you can
comment line 245 in plugin.cpp. After that openbabel compiles fine.

Hope that helps,
Bjoern


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Re: [Open Babel] large-scale similarity search

2014-01-30 Thread Björn Grüning 
Hi Jörg,

as Noel already mentioned that is currently not possible with obabel,
but chemfp will help you. I also would take the opportunity and point
you to the ChemicalToolBox [1]. You can think of it as several
abstraction layers and a nice GUI (in a webbrowser) to run several
cheminformatic tools (including chemfp, Open Babel, RDKit) on your
workstation, but also on a cluster, grid or cloud. We were able to
cluster/search and filter >70 million of compounds.

Maybe it helps for your "large-scale" use case.
Cheers,
Bjoern

[1] https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox

> Hi all, a colleague is using OpenBabels similarity search and is
> struggling with the "-s" input option, which allows only one query
> molecule at a time.
> 
> Is there already any command line tool snippet to allow the input of a
> 
> 
> 1.  fingerprint file with a multi SDFile as query, or
> 
> 
> 2.  two fingerprint files, one as db, the other as query
> 
> 
> to get all similarities?
> 
> 
> With an option to write to more compressed binary objects or
> compressed text files?
> 
> Cheers
> 
> /.Joerg
> 
> 
> 
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