self.r = self.dG.run()
## self.assertAlmostEqual( self.r['dG_kt'], 21., 0 )
self.assert_(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'])
if __name__ == '__main__':
BT.localTest(debug=False)
## 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
]
if __name__ == '__main__':
BT.localTest()
def cleanUp(self):
T.tryRemove( self.fout )
def test_AmberCrdParser(self):
"""AmberCrdParser test"""
self.p = AmberCrdParser( self.finp, self.fref, box=True, rnAmber=True,
log=self.log, verbose=self.local )
self.t = self.p.crd2traj()
self.t.removeAtoms(lambda a: a['residue_name'] in ['WAT','Na+','Cl-'] )
self.t.removeAtoms(lambda a: a['element'] == 'H' )
if self.local:
print "Dumping result to ", self.fout
T.dump( self.t, T.absfile(self.fout) )
if self.local:
print "Dumped Trajectory with %i frames and %i atoms." % \
(len(self.t), self.t.lenAtoms() )
self.assertEqual( len(self.t), 10 )
self.assertEqual( self.t.lenAtoms(), 440 )
if __name__ == '__main__':
BT.localTest()
self.outfolder + '/templates/nr' )
def cleanUp(self):
T.tryRemove( self.outfolder, tree=1 )
def test_TemplateCleaner(self):
"""Mod.TemplateCleaner test"""
import glob
self.c = TemplateCleaner( self.outfolder, log=self.l)
inp_dic = modUtils.parse_tabbed_file(
T.absfile( self.outfolder + '/templates/nr/chain_index.txt' ) )
self.c.process_all( inp_dic )
if self.local:
print 'TemplateCleaner log file written to: %s'% self.f_out
globals().update( locals() )
## check that cleaned pdbs have been written
f_cleaned = glob.glob(self.outfolder+ '/templates/nr_cleaned/*pdb')
self.assert_( len(f_cleaned) > 0 )
if __name__ == '__main__':
BT.localTest(debug=0)
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 )
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'])
if __name__ == '__main__':
BT.localTest(debug=False)
self.log.add( '' )
self.d.addDelphi( scale=1.2 )
self.assertAlmostEqual( self.M['delphi']['scharge'], 0.95, 1 )
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()
if __name__ == '__main__':
BT.localTest() ## pushes test PDBDope instance as 'd' into namespace
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 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()
if __name__ == '__main__':
BT.localTest() ## pushes test PDBDope instance as 'd' into namespace