def test( model ):
from Biskit import Pymoler
g = PatchGenerator( model )
r = g.randomPatches( 85, 50, max_overlap=25 )
profile = N.sum( N.array(r) )
pm = Pymoler()
pm.addPdb( model, 'o' )
ms = [ model.take( N.flatnonzero(mask) ) for mask in r ]
pm.addMovie( ms )
return pm
def test(model, center2center, nAtoms=10, exclude=None):
from Biskit import Pymoler, PDBModel
g = PatchGeneratorFromOrbit(model, center2center)
overlap = int(round(nAtoms / 4.0))
r = g.randomPatches(nAtoms, 500, max_overlap=overlap, exclude=exclude)
profile = N0.sum(N0.array(r))
pm = Pymoler()
pm.addPdb(model, 'all')
ms = [model.take(N0.nonzero(mask)) for mask in r]
pm.addMovie(ms)
return pm
def test( model, center2center, nAtoms=10, exclude=None ):
from Biskit import Pymoler, PDBModel
g = PatchGeneratorFromOrbit( model, center2center )
overlap = int( round( nAtoms / 4.0 ) )
r = g.randomPatches( nAtoms, 500, max_overlap=overlap, exclude=exclude )
profile = N0.sum( N0.array(r) )
pm = Pymoler()
pm.addPdb( model, 'all' )
ms = [ model.take( N0.nonzero(mask) ) for mask in r ]
pm.addMovie( ms )
return pm
class Test(BT.BiskitTest):
"""Test case
The test generates 3 random complexes. In interactive mode,
the 3 complexes are displayed as movie in Pymol. They are
written out as Amber trajectory if debug=True.
"""
TAGS = [ BT.EXE, BT.LONG ]
def prepare(self):
import tempfile
self.f_pfb = tempfile.mktemp('_test.pdb')
self.f_crd = tempfile.mktemp('_test.crd')
def cleanUp(self):
t.tryRemove( self.f_pfb )
t.tryRemove( self.f_crd )
def test_ComplexRandomizer(self):
"""Dock.ComplexRandomizer test"""
from Biskit import Trajectory
if self.local:
print "\nLoading Rec and Lig files ...",
rec_pdb = t.testRoot() + '/rec/1A2P.pdb'
lig_pdb = t.testRoot() + '/lig/1A19.pdb'
rec_psf = t.testRoot() + '/rec/1A2P.psf'
lig_psf = t.testRoot() + '/lig/1A19.psf'
rec = PCRModel( rec_psf, rec_pdb )
lig = PCRModel( lig_psf, lig_pdb )
if self.local:
print "Initializing Randomizer..."
self.cr = ComplexRandomizer( rec, lig, debug=self.DEBUG )
if self.local:
print "Creating 3 random complexes..."
cs = [ self.cr.random_complex() for i in range(3) ]
self.traj = Trajectory( [ c.model() for c in cs ] )
if self.local:
self.display( self.traj )
globals().update( locals() )
self.assertEqual( len(self.traj), 3 )
def display(self, traj ):
"""Display random complexes as trajectory in Pymol.
Only run in local interactive mode.
"""
from Biskit import Pymoler
print "activate debug switch to get random complexes written to disc!"
if self.DEBUG:
print "writing random complex as trajectory to file..."
traj.ref.writePdb( self.f_pfb )
traj.writeCrd( self.f_crd )
print 'Wrote reference pdb file to: %s' % self.f_pfb
print 'Wrote crd file to: %s' % self.f_crd
self.pm = Pymoler( full=0 )
mname = self.pm.addMovie( [ traj[i] for i in range(len(traj)) ] )
self.pm.add('hide all')
self.pm.add('show cartoon')
self.pm.add('spectrum')
self.pm.add('mplay')
self.pm.run()
class Test(BT.BiskitTest):
"""Test case
The test generates 3 random complexes. In interactive mode,
the 3 complexes are displayed as movie in Pymol. They are
written out as Amber trajectory if debug=True.
"""
TAGS = [BT.EXE, BT.LONG]
def prepare(self):
import tempfile
self.f_pfb = tempfile.mktemp('_test.pdb')
self.f_crd = tempfile.mktemp('_test.crd')
def cleanUp(self):
t.tryRemove(self.f_pfb)
t.tryRemove(self.f_crd)
def test_ComplexRandomizer(self):
"""Dock.ComplexRandomizer test"""
from Biskit import Trajectory
if self.local:
print "\nLoading Rec and Lig files ...",
rec_pdb = t.testRoot() + '/rec/1A2P.pdb'
lig_pdb = t.testRoot() + '/lig/1A19.pdb'
rec_psf = t.testRoot() + '/rec/1A2P.psf'
lig_psf = t.testRoot() + '/lig/1A19.psf'
rec = PCRModel(rec_psf, rec_pdb)
lig = PCRModel(lig_psf, lig_pdb)
if self.local:
print "Initializing Randomizer..."
self.cr = ComplexRandomizer(rec, lig, debug=self.DEBUG)
if self.local:
print "Creating 3 random complexes..."
cs = [self.cr.random_complex() for i in range(3)]
self.traj = Trajectory([c.model() for c in cs])
if self.local:
self.display(self.traj)
globals().update(locals())
self.assertEqual(len(self.traj), 3)
def display(self, traj):
"""Display random complexes as trajectory in Pymol.
Only run in local interactive mode.
"""
from Biskit import Pymoler
print "activate debug switch to get random complexes written to disc!"
if self.DEBUG:
print "writing random complex as trajectory to file..."
traj.ref.writePdb(self.f_pfb)
traj.writeCrd(self.f_crd)
print 'Wrote reference pdb file to: %s' % self.f_pfb
print 'Wrote crd file to: %s' % self.f_crd
self.pm = Pymoler(full=0)
mname = self.pm.addMovie([traj[i] for i in range(len(traj))])
self.pm.add('hide all')
self.pm.add('show cartoon')
self.pm.add('spectrum')
self.pm.add('mplay')
self.pm.run()
