def test_sequence_alignment():
u = mda.Universe(PSF)
reference = u.atoms
mobile = u.select_atoms("resid 122-159")
aln = align.sequence_alignment(mobile, reference)
assert len(aln) == 5, "return value has wrong tuple size"
seqA, seqB, score, begin, end = aln
assert_equal(seqA, reference.residues.sequence(format="string"),
err_msg="reference sequence mismatch")
assert mobile.residues.sequence(
format="string") in seqB, "mobile sequence mismatch"
assert_almost_equal(score, 54.6)
assert_array_equal([begin, end], [0, reference.n_residues])
def test_sequence_alignment():
u = mda.Universe(PSF)
reference = u.atoms
mobile = u.select_atoms("resid 122-159")
aln = align.sequence_alignment(mobile, reference)
assert_equal(len(aln), 5, err_msg="return value has wrong tuple size")
seqA, seqB, score, begin, end = aln
assert_equal(seqA, reference.residues.sequence(format="string"),
err_msg="reference sequence mismatch")
assert_(mobile.residues.sequence(format="string") in seqB,
"mobile sequence mismatch")
assert_almost_equal(score, 54.6)
assert_array_equal([begin, end], [0, reference.n_residues])