[modeller_usage] Parallel job

[Francesco Musiani <>]

Hi,
I would like to run a job on a QuadCore PC running linux,
but I do not have any experience of parallel programming.

Can you tell me how to parallelize a script like this?

---------- (script)

from modeller import *
from modeller.automodel import *
from modeller.scripts import complete_pdb

log.verbose()

class mymodel(allhmodel):
       def special_restraints(self, aln):
               s1 = selection(self.chains['A'])
               s2 = selection(self.chains['B'])
               self.restraints.symmetry.append(symmetry(s1, s2, 1.0))
       def user_after_single_model(self):
               self.restraints.symmetry.report(1.0)

env = environ()

env.io_atom_files_directory = './'

a = mymodel(env,
           alnfile = 'HpUreE.ali',
           knowns = 'dimerBp',
           sequence = 'HpUreE',
           assess_methods=(assess.DOPE, assess.GA341))

a.starting_model = 1
a.ending_model = 25

a.make()

# Output data
ok_models = filter(lambda x: x['failure'] is None, a.outputs)
key = 'DOPE score'
ok_models.sort(lambda a,b: cmp(a[key], b[key]))
m = ok_models[0]
print "Top model: %s (DOPE score %.3f)" % (m['name'], m[key])

env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')

# read model file
mdl = complete_pdb(env, m['name'])

# Assess with DOPE:
s = selection(mdl)
s.assess_dope(output='ENERGY_PROFILE NO_REPORT', file='HpUreE.best.profile',
             normalize_profile=True, smoothing_window=15)

---------- (end script)

Thanks

Francesco

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Francesco Musiani

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