def test_print_xyz():
"""Tests that xyz files are printed correctly."""
with open(local("test.pos_0.xyz"), "r") as f:
with open(local("test.pos_1.xyz"), "w") as out:
for num, ret in enumerate(iter_file("xyz", f)):
atoms = ret["atoms"]
assert len(atoms) == 3
assert_equal(pos_xyz * (num + 1), atoms.q)
print_file("xyz", atoms, ret["cell"], filedesc=out)
assert filecmp.cmp(local("test.pos_0.xyz"), local("test.pos_1.xyz"))
os.unlink(local("test.pos_1.xyz"))
def test_read_xyz2():
"""Tests that mode/xyz files are read correctly."""
with open(local("test.pos_0.xyz"), "r") as f:
ret = read_file("xyz", f)
atoms = ret["atoms"]
assert len(atoms) == 3
assert_equal(pos_xyz, atoms.q)
def test_read_pdb():
"""Tests that pdb files are read correctly."""
with open(local("test.pos_0.pdb"), "r") as f:
ret = read_file("pdb", f)
atoms = ret["atoms"]
assert len(atoms) == 3
assert_equal(pos_pdb, atoms.q)
def test_iter_pdb():
"""Tests that pdb files with multiple frames are read correctly."""
with open(local("test.pos_0.pdb"), "r") as f:
for num, ret in enumerate(iter_file("pdb", f)):
atoms = ret["atoms"]
assert len(atoms) == 3
assert_equal(pos_pdb * (num + 1), atoms.q)
def get_atoms(fin):
"""Reads atoms object from file @fin."""
with open(local(fin), "r") as f:
ret = read_file("xyz", f)
return ret["atoms"]