[modeller_usage] Parallel job

17 Jun 2008


      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
---
Francesco Musiani
francesco.musiani@unibo.it
---