def test_fail_read(self):
"""
Test the bad formating of a gro file
"""
files = ["fail.gro", "fail_100000.gro", "missing_total_atoms.gro"]
files_desc = [os.path.join(REFDIR, filin) for filin in files]
print(files_desc)
for filin in files_desc:
with self.assertRaises(groIO.FormatError) as context:
groIO.parse_file(filin)
self.assertEqual("Something is wrong in the format", context.exception)
def test_raise_ref_objects(self):
"""
Test if the exception is raised when reference objects (atom or residue)
are missing in the file.
"""
path = os.path.join(REFDIR, "regular.gro")
title, atoms, box = groIO.parse_file(path)
# Lipid atom
with self.assertRaises(grw.RefObjectError) as context:
grw.perform_bilayer_removing(atoms, "P12", "OW", verbose=False)
# Water atom
with self.assertRaises(grw.RefObjectError) as context:
grw.perform_bilayer_removing(atoms, "P1", "IEW", verbose=False)
# Sphere residue
with self.assertRaises(grw.RefObjectError) as context:
grw.perform_sphere_removing(atoms,
"AZE",
0.4,
"SOL",
verbose=False)
# Water residue
with self.assertRaises(grw.RefObjectError) as context:
grw.perform_sphere_removing(atoms,
"POPC",
0.4,
"SO",
verbose=False)
def test_z_mean_values(self):
"""
Test the mean Z values returned for each leaflet by z_mean_values.
The result of the function is compared with the result obtained using
the g_traj gromacs tool with the following command::
echo 0 1 | g_traj -f regular.gro -s regular.gro -n leaflets.ndx \
-ox regular_com -com -ng 2
"""
reference = (2.14186, 5.71483)
# For the record, values for X are (2.23333, 2.5495), values for Y are
# (2.688, 2.50058)
path = os.path.join(REFDIR, "regular.gro")
title, atoms, box = groIO.parse_file(path)
z_low, z_top = grw.z_mean_values(atoms, "P1")
self.assertAlmostEqual(
reference[0], z_low, PRECISION,
("Z mean value for the lower leaflet do not "
"match with {0} places: {1} instead of {2}").format(
PRECISION, reference[0], z_low))
self.assertAlmostEqual(
reference[1], z_top, PRECISION,
("Z mean value for the upper leaflet do not "
"match with {0} places: {1} instead of {2}").format(
PRECISION, reference[1], z_top))
def test_z_mean_values(self):
"""
Test the mean Z values returned for each leaflet by z_mean_values.
The result of the function is compared with the result obtained using
the g_traj gromacs tool with the following command::
echo 0 1 | g_traj -f regular.gro -s regular.gro -n leaflets.ndx \
-ox regular_com -com -ng 2
"""
reference = (2.14186, 5.71483)
# For the record, values for X are (2.23333, 2.5495), values for Y are
# (2.688, 2.50058)
path = os.path.join(REFDIR, "regular.gro")
title, atoms, box = groIO.parse_file(path)
z_low, z_top = grw.z_mean_values(atoms, "P1")
self.assertAlmostEqual(reference[0], z_low, PRECISION,
("Z mean value for the lower leaflet do not "
"match with {0} places: {1} instead of {2}")
.format(PRECISION, reference[0], z_low))
self.assertAlmostEqual(reference[1], z_top, PRECISION,
("Z mean value for the upper leaflet do not "
"match with {0} places: {1} instead of {2}")
.format(PRECISION, reference[1], z_top))
def test_get_resids(self):
"""
Test the mapping of resids from resnames
"""
path = os.path.join(REFDIR, "regular.gro")
title, atoms, box = groIO.parse_file(path)
resname = ["POPC"]
resids = list(range(1, 73))
self.assertEqual(grw.get_resids(atoms, resname), resids)
def test_get_resids(self):
"""
Test the mapping of resids from resnames
"""
path = os.path.join(REFDIR, "regular.gro")
title, atoms, box = groIO.parse_file(path)
resname = ["POPC"]
resids = list(range(1,73))
self.assertEqual(grw.get_resids(atoms, resname), resids)
def test_renumber(self):
"""
Test the atom renumbering with the renumber function
"""
path = os.path.join(REFDIR, "regular.gro")
title, atoms, box = groIO.parse_file(path)
removed_res = (10, 50, 60)
# Remove some residues and renumber atoms and residues
renumbered = _create_runumbered(atoms, removed_res)
# Check numbering
# (number of atom per residue, number of residue)
topology = ((52, 72 - len(removed_res)), (3, 3739))
_test_renumber(renumbered, topology)
def main():
"""
Run everythin from the command line
"""
# Command line parsing
args = define_options(sys.argv[1:])
try:
title, atoms, box = groIO.parse_file(args.filin)
except groIO.FormatError as e:
print(e, file=sys.stderr)
return 1
if args.verbose:
print("The input coordinate file is {0}".format(args.filin))
print("The output file will be {0}".format(args.filout))
print("The reference atom for the lipid bilayer is {0}".format(
args.lipid_atom))
print("The reference atom for the water is {0}".format(
args.water_atom))
try:
if args.sphere is None:
output_atoms, nb_water = perform_bilayer_removing(
atoms, args.lipid_atom, args.water_atom, args.verbose)
else:
output_atoms, nb_water = perform_sphere_removing(
atoms, args.sphere, args.radius, args.water_residue,
args.verbose)
if args.verbose:
print()
print("The old system contained {0} atoms.".format(len(atoms)))
print("{0} water molecules have been removed.".format(nb_water))
print("The new system contains {0} atoms.".format(len(output_atoms)))
# Write in the output file
with open(args.filout, "w") as fout:
for line in groIO.write_gro(title, output_atoms, box):
print(line, end='', file=fout)
except RefObjectError as e:
print(e)
return 1
return 0
def test_find_ref_atom_regular(self):
"""
Test find_ref_atom function in the regular case where the reference
atom is present or absent from the file body.
"""
path = os.path.join(REFDIR, "regular.gro")
title, atoms, box = groIO.parse_file(path)
# P1 is present in the file
self.assertTrue(grw.find_ref_atom(atoms, "P1"),
"P1 should be find in {0} body.".format(path))
# ABS is absent from the file
self.assertFalse(grw.find_ref_atom(atoms, "ABS"),
"ABS should not be find in {0} body.".format(path))
# AA is present at the right place in the header but should be ignored
self.assertFalse(grw.find_ref_atom(atoms, "AA"),
"AA should be ignored in {0} head.".format(path))
def test_find_ref_atom_regular(self):
"""
Test find_ref_atom function in the regular case where the reference
atom is present or absent from the file body.
"""
path = os.path.join(REFDIR, "regular.gro")
title, atoms, box = groIO.parse_file(path)
# P1 is present in the file
self.assertTrue(grw.find_ref_atom(atoms, "P1"),
"P1 should be find in {0} body.".format(path))
# ABS is absent from the file
self.assertFalse(grw.find_ref_atom(atoms, "ABS"),
"ABS should not be find in {0} body.".format(path))
# AA is present at the right place in the header but should be ignored
self.assertFalse(grw.find_ref_atom(atoms, "AA"),
"AA should be ignored in {0} head.".format(path))
def main():
"""
Run everythin from the command line
"""
# Command line parsing
args = define_options(sys.argv[1:])
try:
title, atoms, box = groIO.parse_file(args.filin)
except groIO.FormatError as e:
print(e, file=sys.stderr)
return 1
if args.verbose:
print("The input coordinate file is {0}".format(args.filin))
print("The output file will be {0}".format(args.filout))
print("The reference atom for the lipid bilayer is {0}".format(args.lipid_atom))
print("The reference atom for the water is {0}".format(args.water_atom))
try:
if args.sphere is None:
output_atoms, nb_water = perform_bilayer_removing(atoms, args.lipid_atom,
args.water_atom, args.verbose)
else:
output_atoms, nb_water = perform_sphere_removing(atoms, args.sphere, args.radius,
args.water_residue, args.verbose)
if args.verbose:
print()
print("The old system contained {0} atoms.".format(len(atoms)))
print("{0} water molecules have been removed.".format(nb_water))
print("The new system contains {0} atoms.".format(len(output_atoms)))
# Write in the output file
with open(args.filout, "w") as fout:
for line in groIO.write_gro(title, output_atoms, box):
print(line, end='', file=fout)
except RefObjectError as e:
print(e)
return 1
return 0
def test_geometric_center(self):
"""
Test the geometric center calculation.
Reference coordinates were calculated with g_traj. The output of the
program is available in test_resources/center.xvg.
"""
reference = {"x": 0.000216667, "y": 0.00045, "z": 5.00003e-05}
resids = [1]
path = os.path.join(REFDIR, "center.gro")
title, atoms, box = groIO.parse_file(path)
center = grw.geometric_center(atoms, resids)
for ref, value in zip(reference.values(), center[resids[0]].values()):
self.assertAlmostEqual(ref, value, PRECISION,
("Geometric center is wrong: "
"{0} instead of {1}").format(
center, reference))
def test_geometric_center(self):
"""
Test the geometric center calculation.
Reference coordinates were calculated with g_traj. The output of the
program is available in test_resources/center.xvg.
"""
reference = {"x": 0.000216667, "y": 0.00045, "z": 5.00003e-05}
resids = [1]
path = os.path.join(REFDIR, "center.gro")
title, atoms, box = groIO.parse_file(path)
center = grw.geometric_center(atoms, resids)
for ref, value in zip(reference.values(), center[resids[0]].values()):
self.assertAlmostEqual(ref, value, PRECISION,
("Geometric center is wrong: "
"{0} instead of {1}")
.format(center, reference))
def test_read(self):
"""
Test the reading of a regular gro file
"""
path = os.path.join(REFDIR, "regular.gro")
title, atoms, box = groIO.parse_file(path)
nb_atoms = len(atoms)
self.assertEqual(title, "Regular AA\n")
self.assertEqual(box, " 5.15414 5.15414 7.93645\n")
self.assertEqual(nb_atoms, 14961)
# Pick a random atom
# 24POPC C220 1235 2.520 4.888 3.113
atom = atoms[1234]
keys_tested = ['resid', 'atomid', 'x', 'z']
values_tested = [24, 1235, 2.520, 3.113]
for key, value in zip(keys_tested, values_tested):
self.assertEqual(atom[key], value)
def test_raise_ref_objects(self):
"""
Test if the exception is raised when reference objects (atom or residue)
are missing in the file.
"""
path = os.path.join(REFDIR, "regular.gro")
title, atoms, box = groIO.parse_file(path)
# Lipid atom
with self.assertRaises(grw.RefObjectError) as context:
grw.perform_bilayer_removing(atoms, "P12", "OW", verbose=False)
# Water atom
with self.assertRaises(grw.RefObjectError) as context:
grw.perform_bilayer_removing(atoms, "P1", "IEW", verbose=False)
# Sphere residue
with self.assertRaises(grw.RefObjectError) as context:
grw.perform_sphere_removing(atoms, "AZE", 0.4, "SOL", verbose=False)
# Water residue
with self.assertRaises(grw.RefObjectError) as context:
grw.perform_sphere_removing(atoms, "POPC", 0.4, "SO", verbose=False)