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):
"""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 )
