def test_superposition():
n = 4
crds1 = [v3.random_vector() for i in range(n)]
random_m = v3.random_rotation()
crds2 = [v3.transform(random_m, c) for c in crds1]
rms, m = rmsd.calc_rmsd_rot(crds1, crds2)
for crd1, crd2 in zip(crds1, crds2):
assert v3.is_similar_vector(v3.transform(m, crd1), crd2)
def test_superposition():
n = 4
crds1 = [v3.random_vector() for i in range(n)]
random_m = v3.random_rotation()
crds2 = [v3.transform(random_m, c) for c in crds1]
rms, m = rmsd.calc_rmsd_rot(crds1, crds2)
for crd1, crd2 in zip(crds1, crds2):
assert v3.is_similar_vector(v3.transform(m, crd1), crd2)
def center_vlist(vlist):
"""
Center a list of v3 vectors and return (center, centered_vlist_copy)
"""
center = v3.get_center(vlist)
center_matrix = v3.translation(-center)
return (center, [v3.transform(center_matrix, v) for v in vlist])
def test_rmsd():
n = 4
crds1 = [v3.random_vector() for i in range(n)]
random_m = v3.random_rotation()
crds2 = [v3.transform(random_m, c) for c in crds1]
rms, m = rmsd.calc_rmsd_rot(crds1, crds2)
assert v3.is_similar_mag(0, rms)
# test the two algorithms separately
rms, m = rmsd.pyqcprot_rmsd_rot(crds1, crds2)
assert v3.is_similar_mag(0, rms)
if rmsd.is_numpy:
rms, m = rmsd.numpy_svd_rmsd_rot(crds1, crds2)
assert v3.is_similar_mag(0, rms)
def test_rmsd():
n = 4
crds1 = [v3.random_vector() for i in range(n)]
random_m = v3.random_rotation()
crds2 = [v3.transform(random_m, c) for c in crds1]
rms, m = rmsd.calc_rmsd_rot(crds1, crds2)
assert v3.is_similar_mag(0, rms)
# test the two algorithms separately
rms, m = rmsd.pyqcprot_rmsd_rot(crds1, crds2)
assert v3.is_similar_mag(0, rms)
if rmsd.is_numpy:
rms, m = rmsd.numpy_svd_rmsd_rot(crds1, crds2)
assert v3.is_similar_mag(0, rms)
def get_position(self, matrix):
"""
Get position of residue transformed by matrix, as a new v3 vector.
Does not modify instance variable.
"""
return v3.transform(matrix, self.position)
