def test_broken(self):
lattice=CubicLattice()
coords=[[0,0,0],
[0,0,1],
[0,5,1],
[0,5,0]]
structure=LatticeStructure(lattice,coords)
self.assertTrue(structure.broken_chain())
def test_overlap(self):
lattice=CubicLattice()
coords=[[0,0,0],
[0,0,1],
[0,0,0]]
structure=LatticeStructure(lattice,coords)
structure.make_contact_map()
self.assertEqual(0,len(structure.overlap_map))
self.assertEqual(1,structure.num_chains)
def test_free_moves(self):
lattice=CubicLattice()
coords=[[0,0,0],
[0,0,1],
[0,1,1],
[0,1,0]]
structure=LatticeStructure(lattice,coords)
structure.make_contact_map()
self.assertEqual(4,len(structure.free_moves(0)))
def test_multidomain(self):
lattice=CubicLattice()
coords=[[0,0,0],
[0,0,1],
[0,0,2],
[0,0,3],
[0,1,3],
[0,1,2],
[0,1,1],
[0,1,0]]
structure=LatticeStructure(lattice,coords, chain_list=[4,4])
structure.make_contact_map()
self.assertEqual(4,len(structure.contact_map))
self.assertEqual(0,len(structure.overlap_map))
self.assertFalse(structure.broken_chain())
self.assertEqual(2,structure.num_chains)
self.assertEqual(1,structure.coordination_no[0])
self.assertEqual(1,structure.coordination_no[1])
def to_lattice(structure, lattice):
'''Fit an OffLatticeStrucure to a lattice.
This only performs a quick fit and is intended to generate the
starting point for the pdb2lattice optimiser.'''
unit_coords = structure.coords / lattice.angstrom
unit_coords -= unit_coords[0]
lattice_structure = LatticeStructure(lattice,
np.zeros((structure.natoms,3),dtype=int),
chainID = structure.chainID)
for i in range(1,structure.natoms):
next_move = lattice_structure.free_moves(i-1)
my_move = closest_move(next_move,unit_coords[i])
lattice_structure.coords[i] = my_move
lattice_structure.make_contact_map()
lattice_structure.off_latt_coords = unit_coords
return lattice_structure
