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):
"""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):
"""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 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', 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 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]