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((range(1093, 1191), range(0,
1093), 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
