def test_dihedral_rotation(self):
"""Checks all angles in 0.2 degree intervals."""
# constructs vectors using sin/cos and then calculates dihedrals
precision = 5.0 # the higher the better
v1 = array([1,0,1])
v2 = array([0,0,1])
v3 = array([0,0,2])
for i in range(int(360*precision)):
degrees = i/precision
radians = pi*degrees/180.0
opp_degrees = 360-degrees
if opp_degrees == 360.0: opp_degrees = 0.0
# construct circular motion of vector
v4 = array([cos(radians), sin(radians),2])
self.assertAlmostEqualAngle(dihedral(v4,v3,v2,v1), degrees, 5)
# check rotation in the opposite direction
self.assertAlmostEqualAngle(dihedral(v1,v2,v3,v4), degrees, 5)
def test_dihedral_rotation(self):
"""Checks all angles in 0.2 degree intervals."""
# constructs vectors using sin/cos and then calculates dihedrals
precision = 5.0 # the higher the better
v1 = array([1, 0, 1])
v2 = array([0, 0, 1])
v3 = array([0, 0, 2])
for i in range(int(360 * precision)):
degrees = i / precision
radians = pi * degrees / 180.0
opp_degrees = 360 - degrees
if opp_degrees == 360.0: opp_degrees = 0.0
# construct circular motion of vector
v4 = array([cos(radians), sin(radians), 2])
self.assertAlmostEqualAngle(dihedral(v4, v3, v2, v1), degrees, 5)
# check rotation in the opposite direction
self.assertAlmostEqualAngle(dihedral(v1, v2, v3, v4), degrees, 5)
def test_dihedral_eight_basic_directions(self):
"""Checks dihedrals in all 45 degree intervals."""
# using vectors with integer positions.
self.assertAlmostEqualAngle(\
dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2,-1, 0]), 0.0)
self.assertAlmostEqualAngle(\
dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2,-1,-1]), 45.0)
self.assertAlmostEqualAngle(\
dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2, 0,-1]), 90.0)
self.assertAlmostEqualAngle(\
dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2, 1,-1]),135.0)
self.assertAlmostEqualAngle(\
dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2, 1, 0]),180.0)
self.assertAlmostEqualAngle(\
dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2, 1, 1]),225.0)
self.assertAlmostEqualAngle(\
dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2, 0, 1]),270.0)
self.assertAlmostEqualAngle(\
dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2,-1, 1]),315.0)
def test_dihedral_eight_basic_directions(self):
"""Checks dihedrals in all 45 degree intervals."""
# using vectors with integer positions.
self.assertAlmostEqualAngle(\
dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2,-1, 0]), 0.0)
self.assertAlmostEqualAngle(\
dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2,-1,-1]), 45.0)
self.assertAlmostEqualAngle(\
dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2, 0,-1]), 90.0)
self.assertAlmostEqualAngle(\
dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2, 1,-1]),135.0)
self.assertAlmostEqualAngle(\
dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2, 1, 0]),180.0)
self.assertAlmostEqualAngle(\
dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2, 1, 1]),225.0)
self.assertAlmostEqualAngle(\
dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2, 0, 1]),270.0)
self.assertAlmostEqualAngle(\
dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2,-1, 1]),315.0)
def test_dihedral_identical(self):
"""The dihedral function should fail if two vectors are the same."""
# except for the first and last (the vectors form a triangle),
# in which case the dihedral angle should be 0.0
for i in range(100):
v1 = self.get_random_array()
v2 = self.get_random_array()
v3 = self.get_random_array()
self.assertRaises(DihedralGeometryError,dihedral,v1,v1,v2,v3)
self.assertRaises(DihedralGeometryError,dihedral,v1,v2,v1,v3)
self.assertRaises(DihedralGeometryError,dihedral,v1,v2,v2,v3)
self.assertRaises(DihedralGeometryError,dihedral,v1,v2,v3,v3)
self.assertRaises(DihedralGeometryError,dihedral,v1,v3,v2,v3)
# now the triangular case
# make sure that 359.999998 is equal to 0.0
torsion = dihedral(v1,v2,v3,v1) + 0.000001
if torsion > 360.0: torsion -= 360.0
self.assertAlmostEqualAngle(torsion,0.0,5)
def test_dihedral_identical(self):
"""The dihedral function should fail if two vectors are the same."""
# except for the first and last (the vectors form a triangle),
# in which case the dihedral angle should be 0.0
for i in range(100):
v1 = self.get_random_array()
v2 = self.get_random_array()
v3 = self.get_random_array()
self.assertRaises(DihedralGeometryError, dihedral, v1, v1, v2, v3)
self.assertRaises(DihedralGeometryError, dihedral, v1, v2, v1, v3)
self.assertRaises(DihedralGeometryError, dihedral, v1, v2, v2, v3)
self.assertRaises(DihedralGeometryError, dihedral, v1, v2, v3, v3)
self.assertRaises(DihedralGeometryError, dihedral, v1, v3, v2, v3)
# now the triangular case
# make sure that 359.999998 is equal to 0.0
torsion = dihedral(v1, v2, v3, v1) + 0.000001
if torsion > 360.0: torsion -= 360.0
self.assertAlmostEqualAngle(torsion, 0.0, 5)
def test_dihedral_samples(self):
"""Checks values measured manually from atoms in PyMOL."""
coordinates = [
[(-1.225,4.621,42.070),(-1.407,4.455,43.516),\
(-2.495,4.892,44.221),(-3.587,5.523,43.715)],
[(-2.495,4.892,44.221),(1.513,0.381,40.711),\
(-3.091,4.715,47.723),(-0.567,3.892,44.433)],
[(-0.349,5.577,39.446),(-1.559,3.400,41.427),\
(-4.304,5.563,45.998),(-2.495,4.892,44.221)],
[(-45.819,84.315,19.372),(-31.124,72.286,14.035),\
(-27.975,58.688,7.025),(-16.238,78.659,23.731)],
[(-29.346,66.973,24.152),(-29.977,69.635,24.580),\
(-30.875,68.788,24.663),(-30.668,67.495,24.449)],
[(-34.586,84.884,14.064),(-23.351,69.756,11.028),\
(-40.924,69.442,24.630),(-30.875,68.788,24.663)]
]
angles = [1.201, 304.621, 295.672, 195.184, 358.699, 246.603]
for i in range(len(coordinates)):
v1,v2,v3,v4 = coordinates[i]
self.assertAlmostEqualAngle(dihedral(v1,v2,v3,v4), angles[i],3)
def test_dihedral_samples(self):
"""Checks values measured manually from atoms in PyMOL."""
coordinates = [
[(-1.225,4.621,42.070),(-1.407,4.455,43.516),\
(-2.495,4.892,44.221),(-3.587,5.523,43.715)],
[(-2.495,4.892,44.221),(1.513,0.381,40.711),\
(-3.091,4.715,47.723),(-0.567,3.892,44.433)],
[(-0.349,5.577,39.446),(-1.559,3.400,41.427),\
(-4.304,5.563,45.998),(-2.495,4.892,44.221)],
[(-45.819,84.315,19.372),(-31.124,72.286,14.035),\
(-27.975,58.688,7.025),(-16.238,78.659,23.731)],
[(-29.346,66.973,24.152),(-29.977,69.635,24.580),\
(-30.875,68.788,24.663),(-30.668,67.495,24.449)],
[(-34.586,84.884,14.064),(-23.351,69.756,11.028),\
(-40.924,69.442,24.630),(-30.875,68.788,24.663)]
]
angles = [1.201, 304.621, 295.672, 195.184, 358.699, 246.603]
for i in range(len(coordinates)):
v1, v2, v3, v4 = coordinates[i]
self.assertAlmostEqualAngle(dihedral(v1, v2, v3, v4), angles[i], 3)