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))