Re: [IMP-dev] examples not working in IMP version 1.0

[Friedrich Foerster <>]

thanks. it seems like my browser cached an older version of the
example or something. the example i now have on my browser seems to be
ok.

cheers

frido

On Fri, Apr 16, 2010 at 9:40 AM, Keren Lasker <> wrote:
> hey Frido -
> not sure if it is going to solve all of the problem but
> ListSingletonContainer is now part of IMP.container
> On Apr 16, 2010, at 12:36 AM, Friedrich Foerster wrote:
>
>> dear all,
>>
>> i have been trying to run the example for the non-bonded list in IMP
>> (the official release 1.0) and sadly, it did not work:
>>
>> sendling 1026% /fs/pool/pool-foerster/apps/src/imp/branches/1.0/
>> tools/imppy.sh
>> python test_imp.py
>> Traceback (most recent call last):
>>  File "test_imp.py", line 10, in <module>
>>    ps =
>> IMP.core.ListSingletonContainer(IMP.core.create_xyzr_particles(m,
>> 20, 1.0))
>> AttributeError: 'module' object has no attribute
>> 'ListSingletonContainer'
>>
>>
>>
>> test_imp.py is the IMP example:
>>
>> import IMP
>> import IMP.core
>> import IMP.atom
>>
>> # This example addes a restraint on nonbonded interactions
>> # after excluding a set of bonded interactions.
>>
>> m= IMP.Model()
>> # The set of particles
>> ps =
>> IMP.core.ListSingletonContainer(IMP.core.create_xyzr_particles(m,
>> 20, 1.0))
>>
>> # create a bond between two particles
>> bd0= IMP.atom.Bonded.setup_particle(ps.get_particle(0))
>> bd1= IMP.atom.Bonded.setup_particle(ps.get_particle(1))
>> IMP.atom.custom_bond(bd0, bd1, 2.0)
>>
>> # Set up the nonbonded list for all pairs at are touching
>> # and let things move 3 before updating the list
>> nbl= IMP.core.ClosePairContainer(ps, 0.0, 3.0)
>> nbl.add_pair_filter(IMP.atom.BondedPairFilter())
>>
>> # Set up excluded volume
>> sdps=
>> IMP.core.SphereDistancePairScore(IMP.core.HarmonicLowerBound(0,1))
>> evr= IMP.core.PairsRestraint(sdps, nbl)
>> m.add_restraint(evr)
>>
>> # Set up optimizer
>> o= IMP.core.ConjugateGradients()
>> o.set_model(m)
>>
>> o.optimize(1000)
>>
>>
>>
>> any suggestions?
>>
>> thanks
>>
>>
>> p.s.: IMP is compiled with build='fast'.
>> all 'required' packages (specified in the installation doc) are
>> installed:
>>    * scons (0.98 or later)
>>    * Boost (1.33 or later)
>>    * A Subversion (svn) client to access the repository
>>
>> If you wish to build the Python interfaces, you will also need:
>>
>>    * Python (2.3 or later)
>>    * SWIG (1.3.40 or later)
>>
>>
>>
>> --
>> Dr. Friedrich Foerster
>> Max-Planck Institut fuer Biochemie
>> Am Klopferspitz 18
>> D-82152 Martinsried
>>
>> Tel: +49 89 8578 2632
>> Fax: +49 89 8578 2641
>>
>> www.biochem.mpg.de/foerster
>> _______________________________________________
>> IMP-dev mailing list
>> 
>> https://salilab.org/mailman/listinfo/imp-dev
>
> _______________________________________________
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> 
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>
>



-- 
Dr. Friedrich Foerster
Max-Planck Institut fuer Biochemie
Am Klopferspitz 18
D-82152 Martinsried

Tel: +49 89 8578 2632
Fax: +49 89 8578 2641

www.biochem.mpg.de/foerster