def test_1(self):
import StringIO
mol1 = read.readxyz(StringIO.StringIO(test_in_1))
mol2 = read.readxyz(StringIO.StringIO(test_in_2))
self.assertAlmostEqual(_rmsd.rmsd(mol1, mol2), 1.001, 3)
self.assertAlmostEqual(_rmsd.rmsd(mol1.coords.take([0], axis=0),
mol2.coords.take([0], axis=0)),
0.0)
def rmsd(mol1, mol2, atoms1=None, atoms2=None, mirror=False, loop_step=None):
coords1, coords2 = rmsd_common(mol1, mol2, atoms1, atoms2)
coords2s = [coords2]
if mirror:
coords2s.append(-coords2)
if loop_step is not None:
for t in coords2s[:]:
for i in range(loop_step, len(coords2), loop_step):
idx = tuple(range(i, len(coords2)) + range(i))
coords2s.append(t.take(idx, axis=0))
return min([_rmsd.rmsd(coords1, x) for x in coords2s])