def test_pdbstructure_2():
atom = pdbstructure.Atom(
"ATOM 2209 CB TYR A 299 6.167 22.607 20.046 1.00 8.12 C"
)
expected = np.array([6.167, 22.607, 20.046])
for i, c in enumerate(atom.iter_coordinates()):
eq(expected[i], c)
def test_pdbstructure_0():
pdb_lines = [
"ATOM 188 N CYS A 42 40.714 -5.292 12.123 1.00 11.29 N ",
"ATOM 189 CA CYS A 42 39.736 -5.883 12.911 1.00 10.01 C ",
"ATOM 190 C CYS A 42 40.339 -6.654 14.087 1.00 22.28 C ",
"ATOM 191 O CYS A 42 41.181 -7.530 13.859 1.00 13.70 O ",
"ATOM 192 CB CYS A 42 38.949 -6.825 12.002 1.00 9.67 C ",
"ATOM 193 SG CYS A 42 37.557 -7.514 12.922 1.00 20.12 S "
]
res = pdbstructure.Residue("CYS", 42)
for l in pdb_lines:
res._add_atom(pdbstructure.Atom(l))
for i, atom in enumerate(res):
eq(pdb_lines[i], str(atom))
def test_pdbstructure_1():
pdb_lines = [
"ATOM 188 N CYS A 42 40.714 -5.292 12.123 1.00 11.29 N",
"ATOM 189 CA CYS A 42 39.736 -5.883 12.911 1.00 10.01 C",
"ATOM 190 C CYS A 42 40.339 -6.654 14.087 1.00 22.28 C",
"ATOM 191 O CYS A 42 41.181 -7.530 13.859 1.00 13.70 O",
"ATOM 192 CB CYS A 42 38.949 -6.825 12.002 1.00 9.67 C",
"ATOM 193 SG CYS A 42 37.557 -7.514 12.922 1.00 20.12 S"
]
positions = np.array([[40.714, -5.292, 12.123], [39.736, -5.883, 12.911],
[40.339, -6.654, 14.087], [41.181, -7.53, 13.859],
[38.949, -6.825, 12.002], [37.557, -7.514, 12.922]])
res = pdbstructure.Residue("CYS", 42)
for l in pdb_lines:
res._add_atom(pdbstructure.Atom(l))
for i, c in enumerate(res.iter_positions()):
eq(c, positions[i])
