class Test(BT.BiskitTest):
"""Test"""
TAGS = [ BT.EXE, BT.OLD ]
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.assertTrue( 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 list(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 list(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.assertTrue( N.all( m_ref[k] == self.M[k]) )
## display in Pymol
if self.local:
print("Starting PyMol...")
from biskit.exe.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()
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 list(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 list(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.assertTrue(N.all(m_ref[k] == self.M[k]))
## display in Pymol
if self.local:
print("Starting PyMol...")
from biskit.exe.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()
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_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 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 )
## test de-activated as we don't have a running Hmmer module any longer
def __test_conservation(self):
"""PDBDope.addConservation (Hmmer) test"""
if self.local: print("Adding conservation data...", end=' ')
self.d.addConservation()
if self.local: print('Done.')
## display in Pymol
if self.local:
print("Starting PyMol...")
from biskit.exe.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 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)
## test de-activated as we don't have a running Hmmer module any longer
def __test_conservation(self):
"""PDBDope.addConservation (Hmmer) test"""
if self.local: print("Adding conservation data...", end=' ')
self.d.addConservation()
if self.local: print('Done.')
## display in Pymol
if self.local:
print("Starting PyMol...")
from biskit.exe.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 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 = 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 )
def test_SurfaceRacer(self):
"""SurfaceRacer test"""
from biskit import PDBModel
import biskit.mathUtils as MA
import numpy as N
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 = (N0.sum(self.r['relMS'][10:20]),
N0.sum(self.r['relAS'][10:20]),
N0.sum(self.r['curvature'][10:20]))
delta = N.sum(N.abs(N.array(self.e) - N.array(self.EXPECT)))
self.assertAlmostEqual(delta, 0.0, 5)
def test_SurfaceRacer(self):
"""SurfaceRacer test"""
from biskit import PDBModel
import biskit.mathUtils as MA
import numpy as N
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 = ( N0.sum(self.r['relMS'][10:20]), N0.sum(self.r['relAS'][10:20]),
N0.sum(self.r['curvature'][10:20]) )
delta = N.sum(N.abs(N.array(self.e) - N.array(self.EXPECT)))
self.assertAlmostEqual( delta, 0.0, 5 )
class Test( BT.BiskitTest ):
"""Test AmberParmBuilder"""
TAGS = [ BT.EXE ]
def prepare(self):
root = T.testRoot('amber/leap/')
self.ref = PDBModel( T.testRoot('amber/leap/1HPT_solvated.pdb'))
self.refdry = root + '1HPT_dry.pdb'
self.dryparm = tempfile.mktemp('.parm', 'dry_')
self.drycrd = tempfile.mktemp('.crd', 'dry_')
self.drypdb = tempfile.mktemp('.pdb', 'dry_')
self.wetparm = tempfile.mktemp('.parm', 'wet_')
self.wetcrd = tempfile.mktemp('.crd', 'wet_')
self.wetpdb = tempfile.mktemp('.pdb', 'wet_')
self.leapout = tempfile.mktemp('.out', 'leap_')
def cleanUp(self):
if not self.DEBUG:
T.tryRemove( self.dryparm )
T.tryRemove( self.drycrd )
T.tryRemove( self.drypdb )
T.tryRemove( self.wetparm )
T.tryRemove( self.wetcrd )
T.tryRemove( self.wetpdb )
T.tryRemove( self.leapout )
def test_AmberParmMirror(self):
"""AmberParmBuilder.parmMirror test"""
ref = self.ref
mask = N0.logical_not( ref.maskH2O() ) ## keep protein and Na+ ion
self.mdry = ref.compress( mask )
self.a = AmberParmBuilder( self.mdry, verbose=self.local,
leap_out=self.leapout,
debug=self.DEBUG )
self.a.parmMirror(f_out=self.dryparm,
f_out_crd=self.drycrd )
self.a.parm2pdb( self.dryparm, self.drycrd, self.drypdb )
self.m1 = PDBModel(self.drypdb)
self.m2 = PDBModel(self.refdry)
eq = N0.array( self.m1.xyz == self.m2.xyz )
self.assertTrue( eq.all() )
def test_AmberParmSolvated( self ):
"""AmberParmBuilder.parmSolvated test"""
## remove waters and hydrogens
self.mdry = self.ref.compress( self.ref.maskProtein() )
self.mdry = self.mdry.compress( self.mdry.maskHeavy() )
self.a = AmberParmBuilder( self.mdry,
leap_out=self.leapout,
verbose=self.local, debug=self.DEBUG)
self.a.parmSolvated( self.wetparm, f_out_crd=self.wetcrd,
f_out_pdb=self.wetpdb,
box=2.5 )
self.m3 = PDBModel( self.wetpdb )
m3prot = self.m3.compress( self.m3.maskProtein() )
refprot= self.ref.compress( self.ref.maskProtein() )
refprot.xplor2amber()
self.assertEqual( self.ref.lenChains(), self.m3.lenChains() )
self.assertEqual( refprot.atomNames(), m3prot.atomNames() )
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.assertEqual( 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 ):
"""Test AmberParmBuilder"""
TAGS = [ BT.EXE ]
def prepare(self):
root = T.testRoot('amber/leap/')
self.ref = PDBModel( T.testRoot('amber/leap/1HPT_solvated.pdb'))
self.refdry = root + '1HPT_dry.pdb'
self.dryparm = tempfile.mktemp('.parm', 'dry_')
self.drycrd = tempfile.mktemp('.crd', 'dry_')
self.drypdb = tempfile.mktemp('.pdb', 'dry_')
self.wetparm = tempfile.mktemp('.parm', 'wet_')
self.wetcrd = tempfile.mktemp('.crd', 'wet_')
self.wetpdb = tempfile.mktemp('.pdb', 'wet_')
self.leapout = tempfile.mktemp('.out', 'leap_')
def cleanUp(self):
if not self.DEBUG:
T.tryRemove( self.dryparm )
T.tryRemove( self.drycrd )
T.tryRemove( self.drypdb )
T.tryRemove( self.wetparm )
T.tryRemove( self.wetcrd )
T.tryRemove( self.wetpdb )
T.tryRemove( self.leapout )
def test_AmberParmMirror(self):
"""AmberParmBuilder.parmMirror test"""
ref = self.ref
mask = N0.logical_not( ref.maskH2O() ) ## keep protein and Na+ ion
self.mdry = ref.compress( mask )
self.a = AmberParmBuilder( self.mdry, verbose=self.local,
leap_out=self.leapout,
debug=self.DEBUG )
self.a.parmMirror(f_out=self.dryparm,
f_out_crd=self.drycrd )
self.a.parm2pdb( self.dryparm, self.drycrd, self.drypdb )
self.m1 = PDBModel(self.drypdb)
self.m2 = PDBModel(self.refdry)
eq = N0.array( self.m1.xyz == self.m2.xyz )
self.assertTrue( eq.all() )
def test_AmberParmSolvated( self ):
"""AmberParmBuilder.parmSolvated test"""
## remove waters and hydrogens
self.mdry = self.ref.compress( self.ref.maskProtein() )
self.mdry = self.mdry.compress( self.mdry.maskHeavy() )
self.a = AmberParmBuilder( self.mdry,
leap_out=self.leapout,
verbose=self.local, debug=self.DEBUG)
self.a.parmSolvated( self.wetparm, f_out_crd=self.wetcrd,
f_out_pdb=self.wetpdb,
box=2.5 )
self.m3 = PDBModel( self.wetpdb )
m3prot = self.m3.compress( self.m3.maskProtein() )
refprot= self.ref.compress( self.ref.maskProtein() )
refprot.xplor2amber()
self.assertEqual( self.ref.lenChains(), self.m3.lenChains() )
self.assertEqual( refprot.atomNames(), m3prot.atomNames() )
