class Test(BT.BiskitTest):
"""Test class"""
TAGS = [ BT.EXE, BT.LONG ]
def test_bindingE( self ):
"""bindingEnergyDelphi test (Barnase:Barstar)"""
self.com = T.load( T.testRoot() + '/com/ref.complex' )
self.dG = DelphiBindingEnergy( self.com, log=self.log, scale=1.2,
verbose=self.local )
self.r = self.dG.run()
self.assertAlmostEqual( self.r['dG_kt'], 21., 0 )
if self.local:
self.log.add(
'\nFinal result: dG = %3.2f kcal/mol'%self.r['dG_kcal'])
def test_errorcase1( self ):
"""bindinEnergyDelphi test (error case 01)"""
self.m = PDBModel( T.testRoot() + '/delphi/case01.pdb' )
rec = self.m.takeChains( [0,1] )
lig = self.m.takeChains( [2] )
self.com = Complex( rec, lig )
self.dG = DelphiBindingEnergy( self.com, log = self.log, scale=0.5,
verbose=self.local )
self.r = self.dG.run()
if self.local:
self.log.add(
'\nFinal result: dG = %3.2f kcal/mol'%self.r['dG_kcal'])
class Test(BT.BiskitTest):
"""Test class"""
TAGS = [BT.EXE, BT.LONG]
def test_bindingE(self):
"""bindingEnergyDelphi test (Barnase:Barstar)"""
self.com = T.load(T.testRoot() + '/com/ref.complex')
self.dG = DelphiBindingEnergy(self.com,
log=self.log,
scale=1.2,
verbose=self.local)
self.r = self.dG.run()
## self.assertAlmostEqual( self.r['dG_kt'], 21., 0 )
self.assert_(abs(self.r['dG_kt'] - 24.6) < 4)
if self.local:
self.log.add('\nFinal result: dG = %3.2f kcal/mol' %
self.r['dG_kcal'])
def test_errorcase1(self):
"""bindinEnergyDelphi test (error case 01)"""
self.m = PDBModel(T.testRoot() + '/delphi/case01.pdb')
rec = self.m.takeChains([0, 1])
lig = self.m.takeChains([2])
self.com = Complex(rec, lig)
self.dG = DelphiBindingEnergy(self.com,
log=self.log,
scale=0.5,
verbose=self.local)
self.r = self.dG.run()
if self.local:
self.log.add('\nFinal result: dG = %3.2f kcal/mol' %
self.r['dG_kcal'])
def inputComplex(options):
if 'c' in options:
return T.load(T.absfile(options['c']))
m = PDBModel(T.absfile(options['i']))
## extract rec and lig chains
rec_chains = T.toIntList(options['r'])
lig_chains = T.toIntList(options['l'])
rec = m.takeChains(rec_chains)
lig = m.takeChains(lig_chains)
## create Protein complex
com = Complex(rec, lig)
return com
def inputComplex( options ):
if 'c' in options:
return T.load( T.absfile( options['c'] ) )
m = PDBModel( T.absfile( options['i'] ) )
## extract rec and lig chains
rec_chains = T.toIntList( options['r'] )
lig_chains = T.toIntList( options['l'] )
rec = m.takeChains( rec_chains )
lig = m.takeChains( lig_chains )
## create Protein complex
com = Complex( rec, lig )
return com
_use()
options = cmdDict({})
f1 = absfile(options['i1'])
f2 = absfile(options['i2'])
o1 = absfile(options['o1'])
o2 = absfile(options['o2'])
errWriteln("loading pdbs...")
m1 = PDBModel(f1)
m2 = PDBModel(f2)
if options.has_key('c1'):
m1 = m1.takeChains(toIntList(options['c1']))
if options.has_key('c2'):
m2 = m2.takeChains(toIntList(options['c2']))
m1.removeRes('TIP3')
m2.removeRes('TIP3')
m1.sort()
m2.sort()
errWriteln("compare atoms of pdbs...")
mask1, mask2 = m1.equalAtoms(m2)
errWriteln("removing %i atoms from %s" % (sum(logical_not(mask1)), f1))
m1.remove(logical_not(mask1))
############
options = T.cmdDict( {'o':'ref.complex', 'lo':'lig.model', 'ro':'rec.model' } )
if len (sys.argv) < 3:
_use( options )
## create a reference complex
print "Loading..."
ref_com = PDBModel( options['c'] )
print "Removing water..."
ref_com.remove( lambda a: a['residue_name'] in ['TIP3','HOH','WAT'] )
## extract rec and lig chains
rec_chains = T.toIntList( options['r'] )
lig_chains = T.toIntList( options['l'] )
print "Extracting rec and lig..."
ref_rec = ref_com.takeChains( rec_chains )
ref_lig = ref_com.takeChains( lig_chains )
## create Protein complex
com = ProteinComplex( ref_rec, ref_lig )
print "Saving..."
ref_lig.saveAs( T.absfile( options['lo'] ) )
ref_rec.saveAs( T.absfile( options['ro'] ) )
T.dump( com, T.absfile( options['o']) )
_use()
options = cmdDict( {} )
f1 = absfile( options['i1'] )
f2 = absfile( options['i2'] )
o1 = absfile( options['o1'] )
o2 = absfile( options['o2'] )
errWriteln("loading pdbs...")
m1 = PDBModel( f1 )
m2 = PDBModel( f2 )
if options.has_key('c1'):
m1 = m1.takeChains( toIntList( options['c1'] ) )
if options.has_key('c2'):
m2 = m2.takeChains( toIntList( options['c2'] ) )
m1.removeRes( 'TIP3' )
m2.removeRes( 'TIP3' )
m1.sort()
m2.sort()
errWriteln("compare atoms of pdbs...")
mask1, mask2 = m1.equalAtoms( m2 )
errWriteln("removing %i atoms from %s" % (sum( logical_not( mask1 ) ), f1))
m1.remove( logical_not( mask1 ) )
