def test_load(self):
sut = PQRReader()
pqr_imput = (
pathlib.Path(__file__).parent.parent.parent.parent.absolute()
/ "examples/actin-dimer/mol1.pqr"
)
atomlist: AtomList = sut.load(pqr_imput)
assert len(atomlist.atoms) == 5861
def test_load_all(self):
"""Test to load all the data from all the example files"""
sut = PQRReader()
# NOTE: There are 77 files under the examples directory
matches = pathlib.Path(search_dir("")).glob("**/*.pqr")
for match in matches:
print(f"FILE: {match}")
atomlist: AtomList = sut.load(match)
assert len(atomlist) > 0
def test_bad(self):
"""This test will fail because there is a typo in the sample data"""
sut = PQRReader()
sample = r"""
ATOM 5226 HD1 TYR 337 -24.642 -2.718 30.187 0.115 1.358
REMARK The next line is incorrect on purpose (e.g. ATAM instead of ATOM)
ATAM 39 O3PB ADP 1 D -16.362 -6.763 26.980 -0.900 1.700
"""
atomlist: AtomList = sut.loads(sample)
def get_atom_list(tmp_path) -> AtomList:
"""Return the AtomList from the file generated."""
fqpn = tmp_path / "atom.pdb"
with open(fqpn, "w") as f:
f.write("HETATM 1 C ALK 1 "
"1.000 4.000 7.000 0.000 1.000\n")
f.write("HETATM 1 C ALK 1 "
"2.000 5.000 8.000 0.000 2.000\n")
f.write("HETATM 1 C ALK 1 "
"3.000 6.000 9.000 0.000 3.000\n")
reader = PQRReader()
return reader.load(fqpn)
def test_ctor(self):
sut = PQRReader()
sample = r"""
ATOM 5226 HD1 TYR 337 -24.642 -2.718 30.187 0.115 1.358
ATOM 7 CD LYS D 1 44.946 37.289 9.712 -0.0608 1.9080
REMARK This is just a comment hiding in the data
HETATM 39 O3PB ADP 1 -16.362 -6.763 26.980 -0.900 1.700
ATOM 39 O3PB ADP 1 D -16.362 -6.763 26.980 -0.900 1.700
REMARK The next line is incorrect on purpose (e.g. ATAM instead of ATOM)
ATAM 39 O3PB ADP 1 D -16.362 -6.763 26.980 -0.900 1.700
"""
atomlist: AtomList = sut.loads(sample)
for idx in range(1):
assert abs(atomlist.atoms[idx].x - -24.642) < 0.001
assert int(atomlist.atoms[idx].x) == -24
print(atomlist.atoms)
def test_basic(self):
"""This test values in the records in the sample data"""
sut = PQRReader()
sample = r"""
ATOM 5226 HD1 TYR 337 -24.642 -2.718 30.187 0.115 1.358
HETATM 39 O3PB ADP 1 -16.362 -6.763 26.980 -0.900 1.700
ATOM 7 CD LYS D 1 44.946 37.289 9.712 -0.0608 1.9080
REMARK This is just a comment hid ing in the data
ATOM 39 O3PB ADP 1 D -16.362 -6.763 26.980 -0.900 1.700
"""
atomlist: AtomList = sut.loads(sample)
assert len(atomlist) == 4
assert atomlist[1].field_name in "HETATM"
for idx in range(1):
assert abs(atomlist[idx].x - -24.642) < 0.001
assert int(atomlist[idx].x) == -24
def test_load(self):
"""Test to load all the data from an example file"""
sut = PQRReader()
pqr_imput = search_dir("actin-dimer/mol1.pqr")
atomlist: AtomList = sut.load(pqr_imput)
assert len(atomlist) == 5877