def test_ComplexTraj(self):
"""Dock.ComplexTraj test"""
import biskit.tools as T
## there is no complex trajectory in the test folder so will have
## to create a fake trajectory with a complex
f = [ T.testRoot()+ '/com/1BGS.pdb' ] * 5
t = Trajectory( f, verbose=self.local )
t = ComplexTraj( t, recChains=[0] )
#if self.local:
#print 'plotting contact density...'
#t.plotContactDensity( step=2 )
## create a fake second chain in the ligand
for i in range( 1093+98, 1968 ):
t.ref.atoms['chain_id'][i] = 'B'
t.ref.chainIndex( force=1, cache=1 )
t.cl = [1,2]
r = N0.concatenate((list(range(1093,1191)), list(range(0,1093)), list(range(1191,1968))))
tt = t.takeAtoms( r )
contactMat = tt.atomContacts( 1 )
if self.local:
print('Receptor chains: %s Ligand chains: %s'%(t.cr, t.cl))
self.assertEqual( N0.sum(N0.ravel(contactMat)), 308 )
def test_ComplexTraj(self):
"""Dock.ComplexTraj test"""
import biskit.tools as T
## there is no complex trajectory in the test folder so will have
## to create a fake trajectory with a complex
f = [T.testRoot() + '/com/1BGS.pdb'] * 5
t = Trajectory(f, verbose=self.local)
t = ComplexTraj(t, recChains=[0])
#if self.local:
#print 'plotting contact density...'
#t.plotContactDensity( step=2 )
## create a fake second chain in the ligand
for i in range(1093 + 98, 1968):
t.ref.atoms['chain_id'][i] = 'B'
t.ref.chainIndex(force=1, cache=1)
t.cl = [1, 2]
r = N0.concatenate(
(list(range(1093,
1191)), list(range(0, 1093)), list(range(1191, 1968))))
tt = t.takeAtoms(r)
contactMat = tt.atomContacts(1)
if self.local:
print('Receptor chains: %s Ligand chains: %s' % (t.cr, t.cl))
self.assertEqual(N0.sum(N0.ravel(contactMat)), 308)
def takeAtoms( self, indices, returnClass=None ):
"""
takeAtoms( indices, [returnClass] ) -> ComplexTraj
@param indices: atoms to extract
@type indices: [int]
@param returnClass: return type (default: current class)
@type returnClass: class
@return: ComplexTraj
@rtype: ComplexTraj
@raise ComplexTrajError: if (parts of) chains are inserted into
each other
"""
r = Trajectory.takeAtoms( self, indices, returnClass )
oldToNew = self.__translateChainIndices( indices, r.ref.chainMap() )
r.cr = [ oldToNew[ c ] for c in self.cr if c in oldToNew ]
r.cl = [ oldToNew[ c ] for c in self.cl if c in oldToNew ]
return r
def takeAtoms(self, indices, returnClass=None):
"""
takeAtoms( indices, [returnClass] ) -> ComplexTraj
@param indices: atoms to extract
@type indices: [int]
@param returnClass: return type (default: current class)
@type returnClass: class
@return: ComplexTraj
@rtype: ComplexTraj
@raise ComplexTrajError: if (parts of) chains are inserted into
each other
"""
r = Trajectory.takeAtoms(self, indices, returnClass)
oldToNew = self.__translateChainIndices(indices, r.ref.chainMap())
r.cr = [oldToNew[c] for c in self.cr if c in oldToNew]
r.cl = [oldToNew[c] for c in self.cl if c in oldToNew]
return r