def test_dihedral_special_cases(self):
a = Position(random(), random(), random())
# not sure what it should be in such undefined cases
#self.assertTrue(isnan(gemmi.calculate_dihedral(a, a, a, a)))
self.assertEqual(gemmi.calculate_dihedral(a, a, a, a), 0.0)
# Special cases from scitbx tst_math.py
# atan2 is guaranteed to give exact values (I think)
p000 = Position(0, 0, 0)
p100 = Position(1, 0, 0)
p010 = Position(0, 1, 0)
def xy_dihedral(last_point):
return gemmi.calculate_dihedral(p100, p000, p010, last_point)
self.assertEqual(xy_dihedral(Position(1, 1, 0)), 0.0)
self.assertEqual(xy_dihedral(Position(-1, 1, 0)), pi)
p01_ = Position(0, 1, -1)
self.assertEqual(xy_dihedral(p01_), pi/2)
p01_.z = 1
self.assertEqual(xy_dihedral(p01_), -pi/2)
def calculate_dihedral_angles(seq1: SequenceVariant, seq2: SequenceVariant, atom_names_seq1: [str],
atom_names_seq2: [str]):
"""
calculates a dihedral angles of given points from two following sequences.
The arrays may be empty, but it should be 4 points all together
:param seq1: dict structure of the first sequence
:param seq2: dict structure of the first sequence
:param atom_names_seq1: the atoms that are needed from the first sequence
:param atom_names_seq2: the atoms that are needed from the second sequence
:return: an dihedral angle
"""
points = [make_gemmi_position_format_from_coords(seq1.atoms[atom_name].coords) for atom_name in atom_names_seq1] + \
[make_gemmi_position_format_from_coords(seq2.atoms[atom_name].coords) for atom_name in atom_names_seq2]
if len(points) == 4:
result = degrees(gemmi.calculate_dihedral(points[0], points[1], points[2], points[3]))
return round(result, 1) if result >= 0 else round(360 + result, 1) # angles should be > 0
else:
raise WrongNumberOfArgumentsException(len(points))
def check_dihedral(a, b, c, d, angle):
deg = gemmi.calculate_dihedral(a, b, c, d) * 180 / pi
self.assertAlmostEqual(deg, angle, places=4)
def xy_dihedral(last_point):
return gemmi.calculate_dihedral(p100, p000, p010, last_point)
