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.assertTrue( 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'])
class FailingTest(BT.BiskitTest):
"""Test class """
TAGS = [BT.NORMAL, BT.FAILS]
def test_capping_extra( self ):
"""PDBCleaner.capTerminals extra challenge"""
self.m2 = PDBModel( t.testRoot() + '/pdbclean/foldx_citche.pdb' )
self.c = PDBCleaner( self.m2, verbose=self.local, log=self.log)
self.assertRaises(CappingError, self.c.capTerminals, auto=True)
if self.local:
self.log.add('OK: CappingError has been raised indicating clash.' )
self.assertEqual( len(self.m2.takeChains([1]).chainBreaks()), 1 )
class FailingTest(BT.BiskitTest):
"""Test class """
TAGS = [BT.NORMAL, BT.FAILS]
def test_capping_extra(self):
"""PDBCleaner.capTerminals extra challenge"""
self.m2 = PDBModel(t.testRoot() + '/pdbclean/foldx_citche.pdb')
self.c = PDBCleaner(self.m2, verbose=self.local, log=self.log)
self.assertRaises(CappingError, self.c.capTerminals, auto=True)
if self.local:
self.log.add('OK: CappingError has been raised indicating clash.')
self.assertEqual(len(self.m2.takeChains([1]).chainBreaks()), 1)
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.assertTrue(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'])
class Test(BT.BiskitTest):
"""Test class """
def prepare(self):
from biskit import LogFile
import tempfile
def test_PDBCleaner( self ):
"""PDBCleaner general test"""
## Loading PDB...
self.c = PDBCleaner( t.testRoot() + '/rec/1A2P_rec_original.pdb',
log=self.log,
verbose=self.local)
self.m = self.c.process()
self.assertAlmostEqual( self.m.mass(), 34029.0115499993, 7 )
def test_DNACleaning( self ):
"""PDBCleaner DNA test"""
## Loading PDB...
self.c = PDBCleaner( t.testRoot() + 'amber/entropy/0_com.pdb',
log=self.log, verbose=self.local )
self.dna = self.c.process(amber=True)
self.assertAlmostEqual( self.dna.mass(), 26953.26, 1 )
def test_Capping( self ):
"""PDBCleaner.capTerminals test"""
## Loading PDB...
self.model = PDBModel(t.testRoot() + '/rec/1A2P_rec_original.pdb')
self.c = PDBCleaner( self.model, log=self.log, verbose=self.local )
self.m2 = self.c.capTerminals( breaks=True )
self.assertTrue( self.m2.atomNames() == self.model.atomNames() )
self.m3 = self.model.clone()
self.m3.removeRes( [10,11,12,13,14,15] )
self.m4 = self.m3.clone()
self.c = PDBCleaner( self.m3, log=self.log, verbose=self.local )
self.m3 = self.c.capTerminals( breaks=True, capC=[0], capN=[0,1])
self.assertEqual( self.m3.takeChains([0]).sequence()[:18],
'XVINTFDGVADXXKLPDN' )
if self.local:
self.log.add( '\nTesting automatic chain capping...\n' )
self.c = PDBCleaner( self.m4, log=self.log, verbose=self.local )
self.m4 = self.c.capTerminals( auto=True )
self.assertEqual( self.m4.takeChains([0]).sequence()[:18],
'XVINTFDGVADXXKLPDN' )
def test_capping_internal(self):
self.m3 = PDBModel(t.testRoot('pdbclean/foldx_citche.pdb'))
self.m3 = self.m3.takeChains([1]) # pick second chain; has chain break
self.c3 = PDBCleaner(self.m3, verbose=self.local, log=self.log)
m = self.c3.capACE(self.m3, 1, checkgap=False)
self.assertEqual(m.lenChains(breaks=True) -1,
self.m3.lenChains(breaks=True))
class Test(BT.BiskitTest):
"""Test class """
def prepare(self):
from biskit import LogFile
import tempfile
def test_PDBCleaner(self):
"""PDBCleaner general test"""
## Loading PDB...
self.c = PDBCleaner(t.testRoot() + '/rec/1A2P_rec_original.pdb',
log=self.log,
verbose=self.local)
self.m = self.c.process()
self.assertAlmostEqual(self.m.mass(), 34029.0115499993, 7)
def test_DNACleaning(self):
"""PDBCleaner DNA test"""
## Loading PDB...
self.c = PDBCleaner(t.testRoot() + 'amber/entropy/0_com.pdb',
log=self.log,
verbose=self.local)
self.dna = self.c.process(amber=True)
self.assertAlmostEqual(self.dna.mass(), 26953.26, 1)
def test_Capping(self):
"""PDBCleaner.capTerminals test"""
## Loading PDB...
self.model = PDBModel(t.testRoot() + '/rec/1A2P_rec_original.pdb')
self.c = PDBCleaner(self.model, log=self.log, verbose=self.local)
self.m2 = self.c.capTerminals(breaks=True)
self.assertTrue(self.m2.atomNames() == self.model.atomNames())
self.m3 = self.model.clone()
self.m3.removeRes([10, 11, 12, 13, 14, 15])
self.m4 = self.m3.clone()
self.c = PDBCleaner(self.m3, log=self.log, verbose=self.local)
self.m3 = self.c.capTerminals(breaks=True, capC=[0], capN=[0, 1])
self.assertEqual(
self.m3.takeChains([0]).sequence()[:18], 'XVINTFDGVADXXKLPDN')
if self.local:
self.log.add('\nTesting automatic chain capping...\n')
self.c = PDBCleaner(self.m4, log=self.log, verbose=self.local)
self.m4 = self.c.capTerminals(auto=True)
self.assertEqual(
self.m4.takeChains([0]).sequence()[:18], 'XVINTFDGVADXXKLPDN')
def test_capping_internal(self):
self.m3 = PDBModel(t.testRoot('pdbclean/foldx_citche.pdb'))
self.m3 = self.m3.takeChains([1]) # pick second chain; has chain break
self.c3 = PDBCleaner(self.m3, verbose=self.local, log=self.log)
m = self.c3.capACE(self.m3, 1, checkgap=False)
self.assertEqual(
m.lenChains(breaks=True) - 1, self.m3.lenChains(breaks=True))
