def test_Benchmark(self):
"""Mod.Benchmark test"""
from Biskit import Pymoler
self.b = Benchmark(self.outfolder)
self.b.go()
pdb = T.load(self.outfolder + "/modeller/PDBModels.list")[0]
reference = PDBModel(self.outfolder + "/reference.pdb")
tmp_model = pdb.clone()
reference = reference.compress(reference.maskCA())
pdb = pdb.compress(pdb.maskCA())
tmp_model = tmp_model.compress(tmp_model.maskCA())
tm = tmp_model.transformation(reference,
n_it=0,
profname="rms_outliers")
pdb = pdb.transform(tm)
if self.local:
pm = Pymoler()
pm.addPdb(pdb, "m")
pm.addPdb(reference, "r")
pm.colorAtoms("m", tmp_model.profile("rms_outliers"))
pm.add('set ribbon_trace,1')
pm.add('show ribbon')
pm.show()
if self.DEBUG:
self.log.add(
'The result from the benchmarking is in %s/benchmark'%\
self.outfolder)
globals().update(locals())
def test_Benchmark(self):
"""Mod.Benchmark test"""
from Biskit import Pymoler
self.b = Benchmark( self.outfolder )
self.b.go()
pdb = T.load( self.outfolder + "/modeller/PDBModels.list" )[0]
reference = PDBModel(self.outfolder + "/reference.pdb" )
tmp_model = pdb.clone()
reference = reference.compress( reference.maskCA() )
pdb = pdb.compress( pdb.maskCA() )
tmp_model = tmp_model.compress(tmp_model.maskCA())
tm = tmp_model.transformation( reference, n_it=0,
profname="rms_outliers")
pdb = pdb.transform( tm )
if self.local:
pm = Pymoler()
pm.addPdb( pdb, "m" )
pm.addPdb( reference, "r" )
pm.colorAtoms( "m", tmp_model.profile("rms_outliers") )
pm.add('set ribbon_trace,1')
pm.add('show ribbon')
pm.show()
if self.DEBUG:
self.log.add(
'The result from the benchmarking is in %s/benchmark'%\
self.outfolder)
globals().update( locals() )
class Test(BT.BiskitTest):
"""Test case"""
def test_Complex(self):
"""Dock.Complex test"""
lig = PCRModel( t.testRoot() + "/com/1BGS.psf",
t.testRoot() + "/com/lig.model")
rec = PCRModel( t.testRoot() + "/com/1BGS.psf",
t.testRoot() + "/com/rec.model")
rec = rec.compress( rec.maskHeavy() )
lig = lig.compress( lig.maskHeavy() )
c = Complex(rec, lig)
c.info['soln'] = 1
cont = c.atomContacts( 6.0 )
contProfile_lig = N.sum( cont )
contProfile_rec = N.sum( cont, 1 )
try:
dope = PDBDope( c.rec_model )
dope.addSurfaceRacer( probe=1.4 )
rec_surf = c.rec_model.profile2mask( 'MS', 0.0000001, 1000 )
dope = PDBDope( c.lig_model )
dope.addSurfaceRacer( probe=1.4 )
lig_surf = c.lig_model.profile2mask( 'MS', 0.0000001, 1000 )
except:
pass
if self.local:
from Biskit import Pymoler
self.pm = Pymoler()
self.pm.addPdb( c.rec(), 'rec' )
self.pm.addPdb( c.lig(), 'lig' )
self.pm.colorAtoms( 'rec', contProfile_rec )
self.pm.colorAtoms( 'lig', contProfile_lig )
rec_sphere = c.rec().clone()
rec_sphere.xyz = mathUtils.projectOnSphere( rec_sphere.xyz )
lig_sphere = c.lig().clone()
lig_sphere.xyz = mathUtils.projectOnSphere( lig_sphere.xyz )
self.pm.addPdb( rec_sphere, 'rec_sphere' )
self.pm.addPdb( lig_sphere, 'lig_sphere' )
self.pm.colorAtoms( 'rec_sphere', contProfile_rec )
self.pm.colorAtoms( 'lig_sphere', contProfile_lig )
self.pm.add( 'hide all')
self.pm.add( 'color grey, (b=0)' )
self.pm.add( 'show stick, (rec or lig)' )
self.pm.add( 'show surf, rec_sphere')
self.pm.add( 'zoom all' )
self.pm.show()
globals().update( locals() )
self.assertEqual( N.sum(contProfile_lig) + N.sum(contProfile_rec),
2462 )
def visualize(self, profile='so_min', wat=None, xwat=None):
"""
Create a receptor / ligand / water view with a profile color-coded
on it.
@param profile: name of the profile to color-project ['so_min']
@type profile: str
@param wat: chain ids of water molecules (default: None)
These will end up as spheres in group 'water'
@type wat: [ int ]
@param xwat: chain ids of crystal water molecules (default: None)
These will end up as spheres in group 'xwater'
@type xwat: [ int ]
@return: Pymoler instance with receptor and ligand colored by shelling
order (use pm.run() to make it show up)
@rtype: Pymoler
"""
import Biskit.Pymoler as Pymoler
model = self.model.clone()
## replace all 0 values by -1 to distinguish them better by color
model[profile] += (model[profile] == 0) * -1
rec = model.takeChains(self.chains_rec, breaks=self.breaks)
lig = model.takeChains(self.chains_lig, breaks=self.breaks)
water = xwater = None
if wat:
water = model.takeChains(wat, breaks=self.breaks)
water = water.compress(N.greater(water['n_facets'], 0))
if xwat:
xwater = model.takeChains(
xwat, breaks=self.breaks) ## X-ray determined water
## kick out waters that do not belong to the interface
xwater = xwater.compress(N.greater(xwater['n_facets'], 0))
pm = Pymoler()
pm.addPdb(model, 'com')
pm.addPdb(rec, 'rec')
pm.addPdb(lig, 'lig')
pm.colorAtoms('rec', rec[profile])
pm.colorAtoms('lig', lig[profile])
if xwater:
pm.addPdb(xwater, 'x-water')
pm.colorAtoms('x-water', xwater[profile])
if water:
pm.addPdb(water, 'water')
pm.colorAtoms('water', water[profile])
pm.add('hide')
pm.add('show surface, rec')
pm.add('show mesh, lig')
pm.add('show spheres, x-water')
pm.add('show spheres, water')
pm.add('zoom')
return pm
def visualize( self, profile='so_min', wat=None, xwat=None ):
"""
Create a receptor / ligand / water view with a profile color-coded
on it.
@param profile: name of the profile to color-project ['so_min']
@type profile: str
@param wat: chain ids of water molecules (default: None)
These will end up as spheres in group 'water'
@type wat: [ int ]
@param xwat: chain ids of crystal water molecules (default: None)
These will end up as spheres in group 'xwater'
@type xwat: [ int ]
@return: Pymoler instance with receptor and ligand colored by shelling
order (use pm.run() to make it show up)
@rtype: Pymoler
"""
import Biskit.Pymoler as Pymoler
model = self.model.clone()
## replace all 0 values by -1 to distinguish them better by color
model[profile] += (model[profile] == 0) * -1
rec = model.takeChains( self.chains_rec, breaks=self.breaks )
lig = model.takeChains( self.chains_lig, breaks=self.breaks )
water = xwater = None
if wat:
water = model.takeChains(wat, breaks=self.breaks)
water = water.compress( N.greater( water['n_facets'], 0) )
if xwat:
xwater = model.takeChains( xwat, breaks=self.breaks ) ## X-ray determined water
## kick out waters that do not belong to the interface
xwater = xwater.compress( N.greater( xwater['n_facets'], 0) )
pm = Pymoler()
pm.addPdb( model, 'com' )
pm.addPdb( rec, 'rec' )
pm.addPdb( lig, 'lig' )
pm.colorAtoms( 'rec', rec[profile])
pm.colorAtoms( 'lig', lig[profile])
if xwater:
pm.addPdb( xwater, 'x-water' )
pm.colorAtoms( 'x-water', xwater[profile] )
if water:
pm.addPdb( water, 'water' )
pm.colorAtoms( 'water', water[profile] )
pm.add( 'hide' )
pm.add( 'show surface, rec' )
pm.add( 'show mesh, lig' )
pm.add( 'show spheres, x-water' )
pm.add( 'show spheres, water' )
pm.add( 'zoom' )
return pm
