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 loadModels( psfName, pdbNames ):
"""
psfName - str, psf file name, same for all pdbs
filenames - [ str, str, ..], set of pdb filenames
filenames with ~, ~user, ../ are expanded to absolute names
-> {1:PCRModel, 2:PCRModel, 3:..}, model dictionary
"""
modelDic = {}
## if only one pdb file, instead of list
if type(pdbNames) is StringType:
pdbNames = [pdbNames]
counter = 0
for f in pdbNames:
counter += 1
model = PCRModel( absfile(psfName), absfile(f) )
# chain id removed by xplor, must be identical to ref complex
model.addChainFromSegid()
model.removeRes( 'TIP3' )
modelDic[ counter ] = model
return modelDic
def go( fin, fout, fpsf=None, skipRes=None, amber=0, pdb=None ):
if fpsf:
m = PCRModel( absfile(fpsf), absfile(fin), skipRes=skipRes )
else:
m = PDBModel( absfile(fin), skipRes=skipRes )
if amber:
renameAmberRes( m )
m.pdbCode = pdb or m.pdbCode
m.saveAs( absfile(fout) )
def dumpModel( m, options, fout ):
if options.has_key('psf'):
m = PCRModel( options['psf'], m )
m.addChainFromSegid( verbose=0 ) # chain id removed by xplor
m.removeRes( 'TIP3' )
m.saveAs( fout )
return m
def loadModels(psfName, pdbNames):
"""
psfName - str, psf file name, same for all pdbs
filenames - [ str, str, ..], set of pdb filenames
filenames with ~, ~user, ../ are expanded to absolute names
-> {1:PCRModel, 2:PCRModel, 3:..}, model dictionary
"""
modelDic = {}
## if only one pdb file, instead of list
if type(pdbNames) is StringType:
pdbNames = [pdbNames]
counter = 0
for f in pdbNames:
counter += 1
model = PCRModel(absfile(psfName), absfile(f))
# chain id removed by xplor, must be identical to ref complex
model.addChainFromSegid()
model.removeRes('TIP3')
modelDic[counter] = model
return modelDic
def dumpModel( m, options, fout ):
if options.has_key('psf'):
m = PCRModel( options['psf'], m )
m.addChainFromSegid( verbose=0 ) # chain id removed by xplor
m.removeRes( 'TIP3' )
m.saveAs( fout )
return m
def go(fin, fout, fpsf=None, skipRes=None, amber=0, pdb=None):
if fpsf:
m = PCRModel(absfile(fpsf), absfile(fin), skipRes=skipRes)
else:
m = PDBModel(absfile(fin), skipRes=skipRes)
if amber:
renameAmberRes(m)
m.pdbCode = pdb or m.pdbCode
m.saveAs(absfile(fout))
def finish(self):
"""
When done, write result to disc.
"""
self.rec = PCRModel(self.com.rec_model.getPsfFile(), self.rec_out)
self.lig = PCRModel(self.com.lig_model.getPsfFile(), self.lig_out)
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 )