def rmsd2(mol1, mol2, atoms1=None, atoms2=None, mirror=False):
coords1, coords2 = rmsd_common(mol1, mol2, atoms1, atoms2)
if mirror:
return min(_rmsd.rmsd2(coords1, coords2),
_rmsd.rmsd2(coords1, -coords2))
else:
return _rmsd.rmsd2(coords1, coords2)
def test_2(self):
import StringIO
mol1 = read.readxyz(StringIO.StringIO(test_in_1))
mol2 = read.readxyz(StringIO.StringIO(test_in_2))
res = _rmsd.rmsd2(mol1, mol2)
self.assertAlmostEqual(res[0], 1.001, 3)
for i in range(3):
self.assertAlmostEqual(res[1][3][i], 0.0)
self.assertAlmostEqual(res[1][3][3], 1.0)
mat = numpy.array([x[:3] for x in res[1][:3]])
self.assertAlmostEqual(abs((numpy.dot(mat, mat.transpose()) - numpy.eye(3))).max(), 0.0)
self.assertAlmostEqual(numpy.linalg.det(mat), 1.0)
newcoords2 = numpy.dot(mat, mol2.coords.transpose()).transpose() \
+ numpy.array([res[1][i][3] for i in range(3)])
diff = newcoords2 - mol1.coords
self.assertAlmostEqual(((diff**2).sum()/(len(mol1)-1)) ** 0.5, res[0])
res2 = _rmsd.rmsd2(mol1, mol1)
self.assertAlmostEqual(res2[0], 0.0)
self.assertAlmostEqual(abs(res2[1] - numpy.eye(4)).max(), 0.0)
def rotate_to(idx_ifile, mol_ifile, ofile):
mol = read.readxyz(mol_ifile)
idxs = []
coords = []
for line in idx_ifile:
if not line.strip() or line.strip()[0] == '#':
continue
words = line.split()
assert len(words) == 4
idx = int(words[0]) - 1
assert 0 <= idx < len(mol)
idxs.append(idx)
coords.append([float(x) for x in words[1:]])
coords = numpy.array(coords)
res = _rmsd.rmsd2(coords, mol.coords.take(idxs, axis=0))
mat = numpy.array(res[1])
mol.coords = numpy.dot(mat[:3,:3], mol.coords.transpose()).transpose() + mat[:3,3]
write.writexyz(mol, ofile)
