def test_read_gro(self):
"""
Test gro file reading on a very simple case.
"""
path = os.path.join(REFDIR, "simple.gro")
reference = [
{"resid":1, "resname":"FOO", "atom_name":"BAR", "atomid":1,
"x":0.0, "y":1.0, "z":2.0},
{"resid":1, "resname":"FOO", "atom_name":"BAR2", "atomid":2,
"x":3.0, "y":4.0, "z":5.0},
{"resid":2, "resname":"OOF", "atom_name":"BAR3", "atomid":3,
"x":6.0, "y":7.0, "z":-8.0},
]
with open(path) as infile:
atoms = list(splitleafs.read_gro(infile))
for ref, atom in zip(reference, atoms):
for key, value in ref.items():
if not key in "xyz":
self.assertEqual(value, atom[key],
("Different value for key {0}: {1} "
"instead of {2}")
.format(key, atom[key], value))
else:
self.assertAlmostEqual(value, atom[key], PRECISION,
("Different value for key {0}: {1} "
"instead of {2}")
.format(key, atom[key], value))
def test_multiple_references(self):
"""
Test if it works with several reference atoms in the same residue.
"""
# Split the bilayer using POPC:P1 and POPC:C12 as reference atoms
path = os.path.join(REFDIR, "membrane.gro")
axis = "z"
select_code = [("POPC", "P1"), ("POPC", "C12")]
with open(path) as infile:
atoms = list(splitleafs.read_gro(infile))
print(len(atoms))
selection = list(splitleafs.select_atoms(atoms, select_code))
print(len(selection))
coordinates = splitleafs.axis_coordinates(selection, axis)
average = splitleafs.mean(coordinates)
groups = splitleafs.split_get_res(atoms, average, axis, select_code)
# The resulting groups should be the exact same as the one from the
# reference output built with just POPC:P1 as reference atom
ndx_reference = os.path.join(REFDIR, "leafs.ndx")
with open(ndx_reference) as infile:
reference = read_ndx(infile)
for key, value in reference.items():
self.assertEqual(value, groups[key],
("The {0} group is different between the "
"function output and the reference.")
.format(key))
def test_split_get_res(self):
"""
Test if the group formed by the split_get_res function are consistent.
"""
# Split the bilayer
path = os.path.join(REFDIR, "membrane.gro")
axis = "z"
with open(path) as infile:
atoms = list(splitleafs.read_gro(infile))
selection = list(splitleafs.select_atoms(atoms, [("P1",)]))
coordinates = splitleafs.axis_coordinates(selection, axis)
average = splitleafs.mean(coordinates)
groups = splitleafs.split_get_res(atoms, average, axis, [("P1",)])
# Do the group have the right size?
natoms_popc = sum((1 for atom in atoms if atom["resname"] == "POPC"))
print("natom_popc: {0}".format(natoms_popc))
for key, value in groups.items():
self.assertEqual(len(value) * 2, natoms_popc,
("The {0} group contains {1} atoms it should "
"contain {2} ones.")
.format(key, len(value), natoms_popc // 2))
# Is there doubles in the groups?
for key, value in groups.items():
self.assertEqual(len(value), len(set(value)),
"There is double values in the {0} group."
.format(key))
# Is the group sorted? A group can not be sorted if the input file
# is not but the test input file is correctly sorted.
for key, value in groups.items():
ordered = value[:]
ordered.sort()
self.assertEqual(value, ordered,
"The {0} group is nor correctly ordered."
.format(key))
# Are the groups the same as the reference?
ndx_reference = os.path.join(REFDIR, "leafs.ndx")
with open(ndx_reference) as infile:
reference = read_ndx(infile)
for key, value in reference.items():
self.assertEqual(value, groups[key],
("The {0} group is different between the "
"function output and the reference.")
.format(key))