class Test(BT.BiskitTest): """Test""" TAGS = [ BT.EXE ] def test_Prosa2003(self): """Prosa2003 test""" from Biskit import PDBModel ## Loading PDB... self.ml = PDBModel( T.testRoot()+'/lig/1A19.pdb' ) self.ml = self.ml.compress( self.ml.maskProtein() ) self.mr = PDBModel( T.testRoot()+'/rec/1A2P.pdb' ) self.mr = self.mr.compress( self.mr.maskProtein() ) ## Starting Prosa2003 self.prosa = Prosa2003( [self.ml, self.mr], debug=0, verbose=0 ) ## Running self.ene = self.prosa.run() self.result = self.prosa.prosaEnergy() if self.local: print "Result: ", self.result self.assert_( N.sum(self.result - [ -94.568, -64.903, -159.463 ] ) \ < 0.0000001 )
class Test(BT.BiskitTest): """Test""" TAGS = [BT.EXE] def test_Prosa2003(self): """Prosa2003 test""" from Biskit import PDBModel ## Loading PDB... self.ml = PDBModel(T.testRoot() + '/lig/1A19.pdb') self.ml = self.ml.compress(self.ml.maskProtein()) self.mr = PDBModel(T.testRoot() + '/rec/1A2P.pdb') self.mr = self.mr.compress(self.mr.maskProtein()) ## Starting Prosa2003 self.prosa = Prosa2003([self.ml, self.mr], debug=0, verbose=0) ## Running self.ene = self.prosa.run() self.result = self.prosa.prosaEnergy() if self.local: print "Result: ", self.result self.assert_( N0.sum(self.result - [ -94.568, -64.903, -159.463 ] ) \ < 0.0000001 )
def test_model(self): """PDBDope test final model""" from Biskit import PDBModel if self.local: print '\nData added to info record of model (key -- value):' for k in self.d.m.info.keys(): print '%s -- %s' % (k, self.d.m.info[k]) print '\nAdded atom profiles:' print self.M.atoms print '\nAdded residue profiles:' print self.M.residues ## check that nothing has changed print '\nChecking that models are unchanged by doping ...' m_ref = PDBModel(self.f) m_ref = m_ref.compress(m_ref.maskProtein()) for k in m_ref.atoms.keys(): #ref = [ m_ref.atoms[i][k] for i in m_ref.atomRange() ] #mod = [ self.M.atoms[i][k] for i in self.M.atomRange() ] self.assert_(N.all(m_ref[k] == self.M[k])) ## display in Pymol if self.local: print "Starting PyMol..." from Biskit.Pymoler import Pymoler pm = Pymoler() pm.addPdb(self.M, 'm') pm.colorAtoms('m', N0.clip(self.M.profile('relAS'), 0.0, 100.0)) pm.show()
class Test(BT.BiskitTest): """Test case""" def test_molTools(self): """molTools test""" from Biskit import PDBModel ## Loading PDB... self.m = PDBModel(T.testRoot() + '/lig/1A19.pdb') self.m = self.m.compress(self.m.maskProtein()) hb = hbonds(self.m) xyz = xyzOfNearestCovalentNeighbour(40, self.m) if self.local: print '\nThe nearest covalently attached atom to the' print ' atom with index 40 has the coordinates:' print xyz print 'Potential h-bonds in model:' print '(donor index, acceptor index, distance and angle)' for h in hb: print h globals().update(locals()) self.r = N0.sum(N0.ravel(hb[3:5])) + N0.sum(xyz) self.assertAlmostEqual(self.r, self.EXPECT, 3) EXPECT = 2025.8997840075292 + 152.687011719
class Test(BT.BiskitTest): """DSSP test""" TAGS = [BT.EXE] def prepare(self): self.f = T.testRoot() + "/com/1BGS.pdb" def test_DSSP(self): """DSSP test""" from Biskit import PDBModel if self.local: print 'Loading PDB...' self.m = PDBModel(self.f) self.m = self.m.compress(self.m.maskProtein()) if self.local: print 'Starting DSSP' self.dssp = Dssp(self.m, verbose=self.local, debug=self.DEBUG) if self.local: print 'Running DSSP' self.result = self.dssp.run() if self.local: print "Sequence :", self.m.sequence() print "Secondary:", self.result self.assertEquals(self.result, self.EXPECTED) EXPECTED = '.....SHHHHHHHHHHHSS..TTEE.HHHHHHHT..GGGT.HHHHSTT.EEEEEEE..TT..S...TT..EEEEE.S..SSS..S.EEEEETT..EEEESSSSSS.EE...EEEEETTT..SHHHHHHHHHHHHT..TT..SSHHHHHHHHHHT..SSEEEEEE.HHHHHHHTTTTHHHHHHHHHHHHHHT..EEEEE.'
class Test(BT.BiskitTest): """Test case""" def test_molTools(self): """molTools test""" from Biskit import PDBModel ## Loading PDB... self.m = PDBModel( T.testRoot() + '/lig/1A19.pdb' ) self.m = self.m.compress( self.m.maskProtein() ) hb = hbonds( self.m ) xyz = xyzOfNearestCovalentNeighbour( 40, self.m ) if self.local: print '\nThe nearest covalently attached atom to the' print ' atom with index 40 has the coordinates:' print xyz print 'Potential h-bonds in model:' print '(donor index, acceptor index, distance and angle)' for h in hb: print h globals().update( locals() ) self.r = N0.sum(N0.ravel(hb[3:5])) + N0.sum(xyz) self.assertAlmostEqual( self.r, self.EXPECT, 3 ) EXPECT = 2025.8997840075292 + 152.687011719
def test_SurfaceRacer(self): """SurfaceRacer test""" from Biskit import PDBModel import Biskit.mathUtils as MA if self.local: print 'Loading PDB...' f = T.testRoot() + '/lig/1A19.pdb' m = PDBModel(f) m = m.compress(m.maskProtein()) if self.local: print 'Starting SurfaceRacer' self.x = SurfaceRacer(m, 1.4, vdw_set=1, debug=self.DEBUG, verbose=0) if self.local: print 'Running ...' self.r = self.x.run() c = self.r['curvature'] ms = self.r['MS'] if self.local: print "Curvature: weighted mean %.6f and standard deviation %.3f"\ %(MA.wMean(c,ms), MA.wSD(c,ms)) print 'Relative MS of atoms 10 to 20:', self.r['relMS'][10:20] print 'Relative AS of atoms 10 to 20:', self.r['relAS'][10:20] self.e = (N.sum(self.r['relMS'][10:20]), N.sum(self.r['relAS'][10:20]), N.sum(self.r['curvature'][10:20])) self.assertAlmostEqual(self.e, self.EXPECT)
def test_SurfaceRacer(self): """SurfaceRacer test""" from Biskit import PDBModel import Biskit.mathUtils as MA if self.local: print 'Loading PDB...' f = T.testRoot()+'/lig/1A19.pdb' m = PDBModel(f) m = m.compress( m.maskProtein() ) if self.local: print 'Starting SurfaceRacer' self.x = SurfaceRacer( m, 1.4, vdw_set=1, debug=self.DEBUG, verbose=0 ) if self.local: print 'Running ...' self.r = self.x.run() c= self.r['curvature'] ms= self.r['MS'] if self.local: print "Curvature: weighted mean %.6f and standard deviation %.3f"\ %(MA.wMean(c,ms), MA.wSD(c,ms)) print 'Relative MS of atoms 10 to 20:',self.r['relMS'][10:20] print 'Relative AS of atoms 10 to 20:',self.r['relAS'][10:20] self.e = ( N.sum(self.r['relMS'][10:20]), N.sum(self.r['relAS'][10:20]), N.sum(self.r['curvature'][10:20]) ) self.assertAlmostEqual( self.e, self.EXPECT )
class Test(BT.BiskitTest): """Fold_X test""" TAGS = [ BT.EXE ] def test_Fold_X( self): """Fold_X test""" from Biskit import PDBModel ## Loading PDB... self.m = PDBModel( T.testRoot() + '/rec/1A2P.pdb' ) self.m = self.m.compress( self.m.maskProtein() ) ## Starting fold_X self.x = Fold_X( self.m, debug=self.DEBUG, verbose=(self.VERBOSITY>2) ) ## Running self.r = self.x.run() if self.local: print "Result: ", self.r for k, v in self.r.items(): self.assertAlmostEqual( v, self.EXPECTED[k], 6 ) EXPECTED = {'el': -13.766400000000001, 'wtbr': -4.8059700000000003, 'ene': -18.475000000000001, 'mc': 160.28800000000001, 'sloop': 0.0, 'dip': 0.00177626, 'sol_p': 167.71100000000001, 'disu': 0.0, 'tcl': 0.72696700000000003, 'cis': 0.0, 'p_cov': 0.0, 'sol_h': -134.613, 'bb_hb': -87.362499999999997, 'sc_hb': -48.350000000000001, 'vw': -116.67100000000001, 'sc': 58.089300000000001, 'el_kon': 0.0, 'mloop': 0.0, 'vwcl': 0.27728599999999998, 'bbcl': 0.37019200000000002}
class Test(BT.BiskitTest): """DSSP test""" TAGS = [BT.EXE] def prepare(self): self.f = T.testRoot()+"/com/1BGS.pdb" def test_DSSP( self ): """DSSP test""" from Biskit import PDBModel if self.local: print 'Loading PDB...' self.m = PDBModel(self.f) self.m = self.m.compress( self.m.maskProtein() ) if self.local: print 'Starting DSSP' self.dssp = Dssp( self.m ) if self.local: print 'Running DSSP' self.result = self.dssp.run() if self.local: print "Sequence :", self.m.sequence() print "Secondary:", self.result self.assertEquals( self.result, self.EXPECTED) EXPECTED = '.....SHHHHHHHHHHHSS..TTEE.HHHHHHHT..GGGT.HHHHSTT.EEEEEEE..TT..S...TT..EEEEE.S..SSS..S.EEEEETT..EEEESSSSSS.EE...EEEEETTT..SHHHHHHHHHHHHT..TT..SSHHHHHHHHHHT..SSEEEEEE.HHHHHHHTTTTHHHHHHHHHHHHHHT..EEEEE.'
class Test(BT.BiskitTest): """Test case""" TAGS = [ BT.OLD, BT.EXE ] ## msms is superseeded by SurfaceRacer def test_msms(self): """msms test""" from Biskit import PDBModel if self.local: print 'Loading PDB...' self.m = PDBModel( T.testRoot() + '/lig/1A19.pdb' ) self.m = self.m.compress( self.m.maskProtein() ) if self.local: print 'Getting surfaces via the MSMS executable' self.ms = MSMS( self.m, debug=self.DEBUG, verbose=self.local ) if self.local: print 'Running' out, sesList, sasList, atmList = self.ms.run() if self.local: print out print '\nResult from MSMS (first 5 lines): ' print 'SES \tSAS \tAtom name' for i in range(5): print '%.2f \t%.2f \t%s'%(sesList[i], sasList[i], atmList[i]) print 'MSMS done' globals().update( locals() ) self.assertAlmostEqual( out['sas'] + out['ses'], 5085.1580000000004 + 4208.7389999999996, 8 )
class Test(BT.BiskitTest): """Test case""" TAGS = [ BT.OLD, BT.EXE ] ## msms is superseeded by SurfaceRacer def test_msms(self): """msms test""" from Biskit import PDBModel if self.local: print 'Loading PDB...' self.m = PDBModel( T.testRoot() + '/lig/1A19.pdb' ) self.m = self.m.compress( self.m.maskProtein() ) if self.local: print 'Getting surfaces via the MSMS executable' self.ms = MSMS( self.m, debug=self.DEBUG, verbose=self.local ) if self.local: print 'Running' out, sesList, sasList, atmList = self.ms.run() if self.local: print out print '\nResult from MSMS (first 5 lines): ' print 'SES \tSAS \tAtom name' for i in range(5): print '%.2f \t%.2f \t%s'%(sesList[i], sasList[i], atmList[i]) print 'MSMS done' globals().update( locals() ) self.assertAlmostEqual( out['sas'] + out['ses'], 5085.1580000000004 + 4208.7389999999996, 8 )
def test_model(self): """PDBDope test final model""" from Biskit import PDBModel if self.local: print '\nData added to info record of model (key -- value):' for k in self.d.m.info.keys(): print '%s -- %s'%(k, self.d.m.info[k]) print '\nAdded atom profiles:' print self.M.atoms print '\nAdded residue profiles:' print self.M.residues ## check that nothing has changed print '\nChecking that models are unchanged by doping ...' m_ref = PDBModel( self.f ) m_ref = m_ref.compress( m_ref.maskProtein() ) for k in m_ref.atoms.keys(): #ref = [ m_ref.atoms[i][k] for i in m_ref.atomRange() ] #mod = [ self.M.atoms[i][k] for i in self.M.atomRange() ] self.assert_( N.all( m_ref[k] == self.M[k]) ) ## display in Pymol if self.local: print "Starting PyMol..." from Biskit.Pymoler import Pymoler pm = Pymoler() pm.addPdb( self.M, 'm' ) pm.colorAtoms( 'm', N.clip(self.M.profile('relAS'), 0.0, 100.0) ) pm.show()
def test_addSecondaryNonFiltered(self): from Biskit import PDBModel m = PDBModel('1R4Q') d = PDBDope(m) d.addSecondaryStructure() r = m.compress(m.maskProtein())['secondary'] self.assertEqual(''.join(r), self.EXPECT_1RQ4)
def test_Whatif(self): """Whatif test""" from Biskit import PDBModel ## Loading PDB... f = T.testRoot() + "/com/1BGS.pdb" m = PDBModel(f) m = m.compress(m.maskProtein()) m = m.compress(m.maskHeavy()) ## Starting WhatIf x = WhatIf(m, debug=0, verbose=0) ## Running atomAcc, resAcc, resMask = x.run() if self.local: ## check that model hasn't changed m_ref = PDBModel(f) m_ref = m.compress(m.maskProtein()) for k in m_ref.atoms.keys(): if not N0.all(m_ref[k] == m[k]): print 'Not equal ', k else: print 'Equal ', k ## display exposed residues in PyMol from Pymoler import Pymoler pm = Pymoler() model = pm.addPdb(m, '1') pm.colorRes('1', resAcc[:, 0]) pm.show() print "\nResult for first 10 atoms/residues: " print '\nAccessability (A^2):\n', atomAcc[:10] print '\nResidue accessability (A^2)' print '[total, backbone, sidechain]:\n', resAcc[:10] print '\nExposed residue mask:\n', resMask[:10] print '\nTotal atom accessability (A^2): %.2f' % sum(atomAcc) print ' residue accessability (A^2): %.2f' % sum(resAcc)[0] self.assertAlmostEqual(N0.sum(resAcc[:, 0]), 2814.6903, 7)
def test_Whatif(self): """Whatif test""" from Biskit import PDBModel ## Loading PDB... f = T.testRoot()+"/com/1BGS.pdb" m = PDBModel(f) m = m.compress( m.maskProtein() ) m = m.compress( m.maskHeavy() ) ## Starting WhatIf x = WhatIf( m, debug=0, verbose=0 ) ## Running atomAcc, resAcc, resMask = x.run() if self.local: ## check that model hasn't changed m_ref = PDBModel(f) m_ref = m.compress( m.maskProtein() ) for k in m_ref.atoms.keys(): if not N0.all(m_ref[k] == m[k]): print 'Not equal ', k else: print 'Equal ', k ## display exposed residues in PyMol from Pymoler import Pymoler pm = Pymoler() model = pm.addPdb( m, '1' ) pm.colorRes( '1', resAcc[:,0] ) pm.show() print "\nResult for first 10 atoms/residues: " print '\nAccessability (A^2):\n', atomAcc[:10] print '\nResidue accessability (A^2)' print '[total, backbone, sidechain]:\n', resAcc[:10] print '\nExposed residue mask:\n',resMask[:10] print '\nTotal atom accessability (A^2): %.2f'%sum(atomAcc) print ' residue accessability (A^2): %.2f'%sum(resAcc)[0] self.assertAlmostEqual( N0.sum(resAcc[:,0]), 2814.6903, 7 )
class Test(BT.BiskitTest): """DSSP test""" TAGS = [BT.EXE] def prepare(self): self.f = T.testRoot() + "/com/1BGS.pdb" def generic_test(self, pdb, expected=None, proteinonly=False): """generic DSSP test""" from Biskit import PDBModel if self.local: print 'Loading PDB...' self.m = PDBModel(pdb) if proteinonly: self.m = self.m.compress(self.m.maskProtein()) if self.local: print 'Starting DSSP' self.dssp = Dssp(self.m, verbose=self.local, debug=self.DEBUG) if self.local: print 'Running DSSP' self.result = self.dssp.run() if self.local: print "Sequence :", self.m.sequence() print "Secondary:", self.result if expected: self.assertEquals(self.result, expected) EXPECTED = '.....SHHHHHHHHHHHSS..TTEE.HHHHHHHT..GGGT.HHHHSTT.EEEEEEE..TT..S...TT..EEEEE.S..SSS..S.EEEEETT..EEEESSSSSS.EE...EEEEETTT..SHHHHHHHHHHHHT..TT..SSHHHHHHHHHHT..SSEEEEEE.HHHHHHHTTTTHHHHHHHHHHHHHHT..EEEEE.' def test_DSSP(self): """DSSP test""" self.generic_test(self.f, expected=self.EXPECTED, proteinonly=True) def test_DSSP_2W3A(self): """DSSP test 2W3A""" self.generic_test('2W3A', proteinonly=True) def test_DSSP_1R4Q(self): """DSSP test""" self.generic_test('1R4Q', proteinonly=True) def test_DSSP_1AM7(self): self.generic_test('1AM7') def test_DSSP_5FB8(self): self.generic_test('5fb8')
class LongTest(BT.BiskitTest): TAGS = [BT.EXE, BT.LONG] def prepare(self): from Biskit import PDBModel self.f = T.testRoot() + '/com/1BGS.pdb' self.M = PDBModel(self.f) self.M = self.M.compress(self.M.maskProtein()) self.d = PDBDope(self.M) def test_conservation(self): """PDBDope.addConservation (Hmmer) test""" if self.local: print "Adding conservation data...", self.d.addConservation() if self.local: print 'Done.' ## display in Pymol if self.local: print "Starting PyMol..." from Biskit.Pymoler import Pymoler pm = Pymoler() pm.addPdb(self.M, 'm') pm.colorAtoms('m', N0.clip(self.M.profile('cons_ent'), 0.0, 100.0)) pm.show() def test_delphi(self): """PDBDope.addDelphi test""" if self.local: self.log.add('Calculating Delphi electrostatic potential') self.log.add('') self.d.addDelphi(scale=1.2) self.assertAlmostEqual(self.M['delphi']['scharge'], 0.95, 1) ## EXPECT_1RQ4 = '.EEEEE.SSHHHHHHHHHHHHHHHEEEEEEEE.SS.EEEEE..SS...EEEEEEE.SSTTT.....EEEEEESSS..EEEEEETTTTEEEE.GGGTT...TT.EEEE.SS.SSHHHHHHHHTS.STT.EE.HHHHHHHHHHHHT..SS...HHHHHHHHHHHHHTHHHHH.HHHHHHHHGGGT.TT...EE..HHHHHHHTTHHHHHHHGGG.SS.SEEEETTEEESSHHHHHTT..EE.......SS.SSSS..EEEETTEEEEHHHHHHH.....EEEEE.SSHHHHHHHHHHHHHHHEEEEEEEEETTEEEEEE...S...EEEEEEE.SSSSS.....EEEEEETTT..EEEEEETTTTEEEE.GGGTT...TT.EEEE.SS..SHHHHHHHS...TTT.EE.TTHHHHHHHHHHT..SS...HHHHHHHHHHHHHHHHHHH.HHHHHHHGGGSS.TT...EE..HHHHHHHHTHHHHHHHGGG.SS.SEEEETTEEE.SHHHHHTT..EE........S.STTSS.EEESSSEEEEHHHHHHH.......EEEEE.EEEEEE.TTS.EEEEESS.EEEE..HHHHHHHHHHHHHT..EEEE.S..STT.B..EEEE...EEEEE...EEEE.TTS.EEEEETTEEEEE..TTHHHHHHHHHHTT..EEEE.S..STT.B..EEEE...EEEEEEEEEEEE.TTS.EEEEETTEEEEE..TTHHHHHHHHHHHT.EEEEE.S..STT.B..EEEE...EEEEEEEEEEEE.TTS.EEEEETTEEEEE..TTHHHHHHHHHHTT.EEEEE.S..STT.B..EEEE...EEEEE.EEEEEE.SSS.EEEEETTEEEEE..HHHHHHHHHHHHHT..EEEE.S..STT.B..EEEE...EEEEEEEEEEEE.TTS.EEEEETTEEEEE..HHHHHHHHHHHHTT.EEEEE.S..STT.B..EEEE...EEEEEEEEEEEE.TTS.EEEEETTEEEEE..TTHHHHHHHHHHTT.EEEEE.S..STT.B..EEEE...EEEEE.EEEEEE.TTS.EEEEETTB..EE..TTHHHHHHHHHHHT..EEEE.SS.STT.B..EEEE.....EEE.EEEEEE.TTS.EEEEETTEEEEE..THHHHHHHHHHHHT..EEEE.S..STT.B..EEEE...EEEEE.EEEEEE.SSS.EEEEETTEEEEE..TTHHHHHHHHHTTT..EEEE.S..STT.B..EEEE.' EXPECT_1RQ4 = '.EEEEE.SSHHHHHHHHHHHHHHHEEEEEEEE.SS.EEEEE..SS...EEEEEEE.SSTTT.....EEEEEESSS..EEEEEETTTTEEEE.GGGTT...TT.EEEE.SS.SSHHHHHHHHTS.STT.EE.HHHHHHHHHHHHT..SS...HHHHHHHHHHHIIIIIHHH.HHHHHHHHGGGT.TT...EE..HHHHHHHTTHHHHHHHGGG.SS.SEEEETTEEESSHHHHHTT..EE.......SS.SSSS..EEEETTEEEEHHHHHHH.....EEEEE.SSHHHHHHHHHHHHHHHEEEEEEEEETTEEEEEE...S...EEEEEEE.SSSSS.....EEEEEETTT..EEEEEETTTTEEEE.GGGTT...TT.EEEE.SS..SHHHHHHHS...TTT.EE.TTHHHHHHHHHHT..SS...HHHHHHHHHHHIIIIIHHH.HHHHHHHGGGSS.TT...EE..HHHHHHHHTHHHHHHHGGG.SS.SEEEETTEEE.SHHHHHTT..EE........S.STTSS.EEESSSEEEEHHHHHHH.......EEEEE.EEEEEE.TTS.EEEEESS.EEEE..HHHHHHHHHHHHHT..EEEE.S..STT.B..EEEE...EEEEE...EEEE.TTS.EEEEETTEEEEE..TTHHHHHHHHHHTT..EEEE.S..STT.B..EEEE...EEEEEEEEEEEE.TTS.EEEEETTEEEEE..TTHHHHHHHHHHHT.EEEEE.S..STT.B..EEEE...EEEEEEEEEEEE.TTS.EEEEETTEEEEE..TTHHHHHHHHHHTT.EEEEE.S..STT.B..EEEE...EEEEE.EEEEEE.SSS.EEEEETTEEEEE..HHHHHHHHHHHHHT..EEEE.S..STT.B..EEEE...EEEEEEEEEEEE.TTS.EEEEETTEEEEE..HHHHHHHHHHHHTT.EEEEE.S..STT.B..EEEE...EEEEEEEEEEEE.TTS.EEEEETTEEEEE..TTHHHHHHHHHHTT.EEEEE.S..STT.B..EEEE...EEEEE.EEEEEE.TTS.EEEEETTB..EE..TTHHHHHHHHHHHT..EEEE.SS.STT.B..EEEE.....EEE.EEEEEE.TTS.EEEEETTEEEEE..THHHHHHHHHHHHT..EEEE.S..STT.B..EEEE...EEEEE.EEEEEE.SSS.EEEEETTEEEEE..TTHHHHHHHHHTTT..EEEE.S..STT.B..EEEE.' def test_addSecondaryNonFiltered(self): from Biskit import PDBModel m = PDBModel('1R4Q') d = PDBDope(m) d.addSecondaryStructure() r = m.compress(m.maskProtein())['secondary'] self.assertEqual(''.join(r), self.EXPECT_1RQ4)
class OldTest( BT.BiskitTest ): TAGS = [ BT.EXE, BT.OLD ] def prepare(self): from Biskit import PDBModel self.f = T.testRoot() + '/com/1BGS.pdb' self.M = PDBModel( self.f ) self.M = self.M.compress( self.M.maskProtein() ) self.d = PDBDope( self.M ) def _test_addAsa(self): """PDBDope.addAsa (Whatif, obsolete) test""" self.d.addASA()
class OldTest(BT.BiskitTest): TAGS = [BT.EXE, BT.OLD] def prepare(self): from Biskit import PDBModel self.f = T.testRoot() + '/com/1BGS.pdb' self.M = PDBModel(self.f) self.M = self.M.compress(self.M.maskProtein()) self.d = PDBDope(self.M) def _test_addAsa(self): """PDBDope.addAsa (Whatif, obsolete) test""" self.d.addASA()
class Test(BT.BiskitTest): """Test case""" def test_surfaceRacerTools(self): """surfaceRacerTools test""" from Biskit import PDBModel import Biskit.tools as T ## load a structure self.m = PDBModel(T.testRoot() + '/lig/1A19.pdb') self.m = self.m.compress(self.m.maskProtein()) self.m = self.m.compress(self.m.maskHeavy()) ## some fake surface data surf = N0.ones(self.m.lenAtoms()) * 10.0 relExp = relExposure(self.m, surf) ## if self.local: ## globals().update( locals() ) self.assertAlmostEqual(N0.sum(relExp), 44276.86085222386, 8)
class Test(BT.BiskitTest): """Test case""" def test_surfaceRacerTools(self): """surfaceRacerTools test""" from Biskit import PDBModel import Biskit.tools as T ## load a structure self.m = PDBModel( T.testRoot()+'/lig/1A19.pdb' ) self.m = self.m.compress( self.m.maskProtein() ) self.m = self.m.compress( self.m.maskHeavy() ) ## some fake surface data surf = Numeric.ones( self.m.lenAtoms()) * 10.0 relExp = relExposure( self.m, surf ) ## if self.local: ## globals().update( locals() ) self.assertEqual( Numeric.sum(relExp), 44276.860852223857 )
class LongTest( BT.BiskitTest ): TAGS = [ BT.EXE, BT.LONG ] def prepare(self): from Biskit import PDBModel self.f = T.testRoot() + '/com/1BGS.pdb' self.M = PDBModel( self.f ) self.M = self.M.compress( self.M.maskProtein() ) self.d = PDBDope( self.M ) def test_conservation(self): """PDBDope.addConservation (Hmmer) test""" if self.local: print "Adding conservation data...", self.d.addConservation() if self.local: print 'Done.' ## display in Pymol if self.local: print "Starting PyMol..." from Biskit.Pymoler import Pymoler pm = Pymoler() pm.addPdb( self.M, 'm' ) pm.colorAtoms( 'm', N.clip(self.M.profile('cons_ent'), 0.0, 100.0) ) pm.show() def test_delphi(self): """PDBDope.addDelphi test""" if self.local: self.log.add( 'Calculating Delphi electrostatic potential' ) self.log.add( '' ) self.d.addDelphi( scale=1.2 ) self.assertAlmostEqual( self.M['delphi']['scharge'], 0.95, 1 )
class LongTest(BT.BiskitTest): TAGS = [BT.EXE, BT.LONG] def prepare(self): from Biskit import PDBModel self.f = T.testRoot() + '/com/1BGS.pdb' self.M = PDBModel(self.f) self.M = self.M.compress(self.M.maskProtein()) self.d = PDBDope(self.M) def test_conservation(self): """PDBDope.addConservation (Hmmer) test""" if self.local: print "Adding conservation data...", self.d.addConservation() if self.local: print 'Done.' ## display in Pymol if self.local: print "Starting PyMol..." from Biskit.Pymoler import Pymoler pm = Pymoler() pm.addPdb(self.M, 'm') pm.colorAtoms('m', N0.clip(self.M.profile('cons_ent'), 0.0, 100.0)) pm.show() def test_delphi(self): """PDBDope.addDelphi test""" if self.local: self.log.add('Calculating Delphi electrostatic potential') self.log.add('') self.d.addDelphi(scale=1.2) self.assertAlmostEqual(self.M['delphi']['scharge'], 0.95, 1)
class Test(BT.BiskitTest): """Test class""" TAGS = [BT.EXE] def test_IcmCad(self): """IcmCad test""" from Biskit import PDBModel if self.local: print 'Loading PDB...' self.f = T.testRoot() + '/lig/1A19.pdb' self.m1 = PDBModel(self.f) self.m1 = self.m1.compress(self.m1.maskProtein()) self.ms = [] self.lig_traj = T.load(T.testRoot() + '/lig_pcr_00/traj.dat') for m in self.lig_traj[:3]: m = m.compress(m.maskProtein()) self.ms.append(m) if self.local: print 'Starting ICM' self.x = IcmCad(self.m1, self.ms, debug=self.DEBUG, verbose=self.local) if self.local: print 'Running' self.r = self.x.run() if self.local: print "Result: ", self.r self.assertEqual( self.r, [8.8603529999999999, 9.0315890000000003, 8.5055429999999994])
class Test(BT.BiskitTest): """Test class""" TAGS = [ BT.EXE ] def test_IcmCad( self ): """IcmCad test""" from Biskit import PDBModel if self.local: print 'Loading PDB...' self.f = T.testRoot() + '/lig/1A19.pdb' self.m1 = PDBModel(self.f) self.m1 = self.m1.compress( self.m1.maskProtein() ) self.ms = [] self.lig_traj = T.load( T.testRoot() + '/lig_pcr_00/traj.dat' ) for m in self.lig_traj[:3]: m = m.compress( m.maskProtein() ) self.ms.append(m) if self.local: print 'Starting ICM' self.x = IcmCad( self.m1, self.ms, debug=self.DEBUG, verbose=self.local ) if self.local: print 'Running' self.r = self.x.run() if self.local: print "Result: ", self.r self.assertEqual( self.r, [8.8603529999999999, 9.0315890000000003, 8.5055429999999994] )
class Test(BT.BiskitTest): """DSSP test""" TAGS = [BT.EXE] def prepare(self): self.f = T.testRoot()+"/com/1BGS.pdb" def generic_test(self, pdb, expected=None, proteinonly=False): """generic DSSP test""" from Biskit import PDBModel if self.local: print 'Loading PDB...' self.m = PDBModel(pdb) if proteinonly: self.m = self.m.compress( self.m.maskProtein() ) if self.local: print 'Starting DSSP' self.dssp = Dssp( self.m, verbose=self.local, debug=self.DEBUG ) if self.local: print 'Running DSSP' self.result = self.dssp.run() ## returns modified PDBModel self.result = self.result.compress( self.result.maskProtein() ) self.result = ''.join(self.result['dssp']) if self.local: print "Sequence :", self.m.sequence() print "Secondary:", self.result if expected: self.assertEquals( self.result, expected) EXPECTED = '.....SHHHHHHHHHHHSS..TTEE.HHHHHHHT..GGGT.HHHHSTT.EEEEEEE..TT..S...TT..EEEEE.S..SSS..S.EEEEETT..EEEESSSSSS.EE...EEEEETTT..SHHHHHHHHHHHHT..TT..SSHHHHHHHHHHT..SSEEEEEE.HHHHHHHTTTTHHHHHHHHHHHHHHT..EEEEE.' def test_DSSP( self ): """DSSP test""" self.generic_test(self.f, expected=self.EXPECTED, proteinonly=False) def test_DSSP_2W3A( self ): """DSSP test 2W3A""" self.generic_test('2W3A', proteinonly=False) def test_DSSP_3TGI( self ): """DSSP test 3TGI""" ## handling of residues with insertion code (184A, 186A, 221A) self.generic_test('3TGI', proteinonly=False) def test_DSSP_1R4Q( self ): """DSSP test""" self.generic_test('1R4Q', proteinonly=False) def test_DSSP_1AM7(self): self.generic_test('1AM7') def test_DSSP_5FB8(self): self.generic_test('5fb8') def test_DSSP_3j4q(self): self.generic_test(T.testRoot('dssp') + '/3j4q.pdb')
class Test(BT.BiskitTest): """Hmmer test""" TAGS = [BT.EXE] M = None def prepare(self): from Biskit import PDBModel import Biskit.tools as T if not self.M: if self.local: print "Loading PDB...", self.M = PDBModel(T.testRoot() + '/lig/1A19.pdb') self.M = self.M.compress(self.M.maskProtein()) if self.local: print "Done" def test_HmmSearch(self): """HmmSearch test""" self.searcher = HmmerSearch(self.M, verbose=self.local, log=self.log) self.matches, self.hits = self.searcher.run() def test_HmmProfile(self): """HmmerProfile test""" profile = HmmerProfile('FH2', verbose=self.local, log=self.log) self.profileDic = profile.run() def test_HmmerFasta(self): """Hmmer test (search from fasta)""" h = Hmmer(hmmdb=settings.hmm_db) h.checkHmmdbIndex() self.searchMatches, self.searchHits = h.searchHmmdb( T.testRoot() + '/Mod/project/target.fasta') self.assertTrue(len(self.searchHits) > 3) def test_HmmerModel(self): """Hmmer test (search from model)""" ## initiate and check database status self.hmmer = Hmmer(hmmdb=settings.hmm_db, verbose=self.local, log=self.log) self.hmmer.checkHmmdbIndex() ## scoring methods to use method = ['emmScore', 'ent', 'maxAll', 'absSum', 'maxAllScale'] ## search searchMatches, searchHits = self.hmmer.searchHmmdb(self.M) hmmNames = self.hmmer.selectMatches(searchMatches, searchHits) ## hmmNames = {'Barstar': [[1, 89]]} self.cons = [] self.result = None for name in hmmNames.keys(): ## retrieve hmm model hmmDic = self.hmmer.getHmmProfile(name) ## align sequence with model fastaSeq, hmmSeq, repete, hmmGap = \ self.hmmer.align( self.M, hmmNames[ name ] ) ## cast hmm model hmmDic_cast = \ self.hmmer.castHmmDic( hmmDic, repete, hmmGap, method[0] ) ## Hmmer profile match scores for sequence self.cons = self.hmmer.matchScore(fastaSeq, hmmSeq, hmmDic_cast, method[0]) ## If there are more than one profile in the model, merge to one. ## Note: this can be problematic as scores depend on family size if self.result: self.result = self.hmmer.mergeProfiles(self.result, self.cons) else: self.result = self.cons self.hmmer.cleanup() self.assertEqual(self.result, self.EXPECTED) #: Hmmer emission scores EXPECTED = [ 2581.0, 3583.0, 1804.0, 2596.0, 3474.0, 2699.0, 3650.0, 2087.0, 2729.0, 2450.0, 2412.0, 2041.0, 3474.0, 1861.0, 2342.0, 2976.0, 5124.0, 2729.0, 2202.0, 2976.0, 3583.0, 2202.0, 2103.0, 2976.0, 1922.0, 2132.0, 4122.0, 2403.0, 4561.0, 4561.0, 3650.0, 2087.0, 4001.0, 2976.0, 3860.0, 3260.0, 2976.0, 6081.0, 3860.0, 5611.0, 2976.0, 3609.0, 3650.0, 6081.0, 3343.0, 2403.0, 3288.0, 4122.0, 2976.0, 2322.0, 2976.0, 1995.0, 4378.0, 2706.0, 2665.0, 4186.0, 3539.0, 2692.0, 3270.0, 2302.0, 2604.0, 2132.0, 2118.0, 2380.0, 2614.0, 2170.0, 3260.0, 2403.0, 1964.0, 3343.0, 2976.0, 2643.0, 3343.0, 2714.0, 2591.0, 3539.0, 3260.0, 2410.0, 1809.0, 3539.0, 2111.0, -774.0, 3860.0, 2450.0, 2063.0, 3474.0, 3474.0, 2057.0, 1861.0 ]
class Test(BT.BiskitTest): """Hmmer test""" TAGS = [ BT.EXE ] M = None def prepare( self ): from Biskit import PDBModel import Biskit.tools as T if not self.M: if self.local: print "Loading PDB...", self.M = PDBModel( T.testRoot()+'/lig/1A19.pdb') self.M = self.M.compress( self.M.maskProtein() ) if self.local: print "Done" def test_HmmSearch( self ): """HmmSearch test""" self.searcher = HmmerSearch( self.M, verbose=self.local, log=self.log ) self.matches, self.hits = self.searcher.run() def test_HmmProfile( self ): """HmmerProfile test""" profile = HmmerProfile( 'FH2', verbose=self.local, log=self.log) self.profileDic = profile.run() def test_HmmerFasta( self ): """Hmmer test (search from fasta)""" h = Hmmer(hmmdb=settings.hmm_db) h.checkHmmdbIndex() self.searchMatches, self.searchHits = h.searchHmmdb( T.testRoot()+'/Mod/project/target.fasta' ) self.assertTrue( len( self.searchHits ) > 3 ) def test_HmmerModel( self): """Hmmer test (search from model)""" ## initiate and check database status self.hmmer = Hmmer( hmmdb=settings.hmm_db, verbose=self.local, log=self.log ) self.hmmer.checkHmmdbIndex() ## scoring methods to use method = [ 'emmScore', 'ent', 'maxAll', 'absSum', 'maxAllScale' ] ## search searchMatches, searchHits = self.hmmer.searchHmmdb( self.M ) hmmNames = self.hmmer.selectMatches( searchMatches, searchHits ) ## hmmNames = {'Barstar': [[1, 89]]} self.cons = [] self.result = None for name in hmmNames.keys(): ## retrieve hmm model hmmDic = self.hmmer.getHmmProfile( name ) ## align sequence with model fastaSeq, hmmSeq, repete, hmmGap = \ self.hmmer.align( self.M, hmmNames[ name ] ) ## cast hmm model hmmDic_cast = \ self.hmmer.castHmmDic( hmmDic, repete, hmmGap, method[0] ) ## Hmmer profile match scores for sequence self.cons = self.hmmer.matchScore( fastaSeq, hmmSeq, hmmDic_cast, method[0] ) ## If there are more than one profile in the model, merge to one. ## Note: this can be problematic as scores depend on family size if self.result: self.result = self.hmmer.mergeProfiles( self.result, self.cons ) else: self.result = self.cons self.hmmer.cleanup() self.assertEqual( self.result, self.EXPECTED ) #: Hmmer emission scores EXPECTED = [2581.0, 3583.0, 1804.0, 2596.0, 3474.0, 2699.0, 3650.0, 2087.0, 2729.0, 2450.0, 2412.0, 2041.0, 3474.0, 1861.0, 2342.0, 2976.0, 5124.0, 2729.0, 2202.0, 2976.0, 3583.0, 2202.0, 2103.0, 2976.0, 1922.0, 2132.0, 4122.0, 2403.0, 4561.0, 4561.0, 3650.0, 2087.0, 4001.0, 2976.0, 3860.0, 3260.0, 2976.0, 6081.0, 3860.0, 5611.0, 2976.0, 3609.0, 3650.0, 6081.0, 3343.0, 2403.0, 3288.0, 4122.0, 2976.0, 2322.0, 2976.0, 1995.0, 4378.0, 2706.0, 2665.0, 4186.0, 3539.0, 2692.0, 3270.0, 2302.0, 2604.0, 2132.0, 2118.0, 2380.0, 2614.0, 2170.0, 3260.0, 2403.0, 1964.0, 3343.0, 2976.0, 2643.0, 3343.0, 2714.0, 2591.0, 3539.0, 3260.0, 2410.0, 1809.0, 3539.0, 2111.0, -774.0, 3860.0, 2450.0, 2063.0, 3474.0, 3474.0, 2057.0, 1861.0]