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):
"""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))
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() )
