def test_right_type_impropers(self):
assert_equal(self.igroup.torsions(),
calc_torsions(self.igroup.atom1.positions,
self.igroup.atom2.positions,
self.igroup.atom3.positions,
self.igroup.atom4.positions))
assert_equal(self.igroup.torsions(pbc=True),
calc_torsions(self.igroup.atom1.positions,
self.igroup.atom2.positions,
self.igroup.atom3.positions,
self.igroup.atom4.positions,
box=self.u.dimensions))
def test_right_type_impropers(self):
assert_equal(
self.igroup.torsions(),
calc_torsions(self.igroup.atom1.positions,
self.igroup.atom2.positions,
self.igroup.atom3.positions,
self.igroup.atom4.positions))
assert_equal(
self.igroup.torsions(pbc=True),
calc_torsions(self.igroup.atom1.positions,
self.igroup.atom2.positions,
self.igroup.atom3.positions,
self.igroup.atom4.positions,
box=self.u.dimensions))
def test_torsions(self):
from MDAnalysis.core.distances import calc_torsions
a2 = (self.a + self.box * (-1, 0, 0)).astype(np.float32)
b2 = (self.b + self.box * (1, 0, 1)).astype(np.float32)
c2 = (self.c + self.box * (-2, 5, -7)).astype(np.float32)
d2 = (self.d + self.box * (0, -5, 0)).astype(np.float32)
ref = calc_torsions(self.a, self.b, self.c, self.d)
test1 = calc_torsions(a2, self.b, self.c, self.d, box=self.box)
test2 = calc_torsions(self.a, b2, self.c, self.d, box=self.box)
test3 = calc_torsions(self.a, self.b, c2, self.d, box=self.box)
test4 = calc_torsions(self.a, self.b, self.c, d2, box=self.box)
test5 = calc_torsions(a2, b2, c2, d2, box=self.box)
for val in [test1, test2, test3, test4, test5]:
assert_almost_equal(ref, val, self.prec, err_msg="Min image in torsion calculation failed")