def test_pdb_to_gro(path, single_model):
# Converting stacks between formats should not change data
model = 1 if single_model else None
# Read in data
pdb_file = pdb.PDBFile()
pdb_file.read(path)
a1 = pdb_file.get_structure(model=model)
# Save stack as gro
tmp_file_name = biotite.temp_file("gro")
gro_file = gro.GROFile()
gro_file.set_structure(a1)
gro_file.write(tmp_file_name)
# Reload stack from gro
gro_file = gro.GROFile()
gro_file.read(tmp_file_name)
a2 = gro_file.get_structure(model=model)
assert a1.array_length() == a2.array_length()
for category in ["res_id", "res_name", "atom_name"]:
assert a1.get_annotation(category).tolist() == \
a2.get_annotation(category).tolist()
# Mind rounding errors when converting pdb to gro (A -> nm)
assert a1.coord.flatten().tolist() \
== approx(a2.coord.flatten().tolist(), abs=1e-2)
def test_array_conversion(path, single_model):
model = 1 if single_model else None
gro_file = gro.GROFile()
gro_file.read(path)
array1 = gro_file.get_structure(model=model)
gro_file = gro.GROFile()
gro_file.set_structure(array1)
array2 = gro_file.get_structure(model=model)
assert array1 == array2
def test_array_conversion(path, single_model):
model = 1 if single_model else None
gro_file = gro.GROFile()
gro_file.read(path)
array1 = gro_file.get_structure(model=model)
gro_file = gro.GROFile()
gro_file.set_structure(array1)
array2 = gro_file.get_structure(model=model)
if array1.box is not None:
assert np.allclose(array1.box, array2.box)
assert array1.bonds == array2.bonds
for category in array1.get_annotation_categories():
assert array1.get_annotation(category).tolist() == \
array2.get_annotation(category).tolist()
assert array1.coord.tolist() == array2.coord.tolist()
def test_gro_no_box():
"""
.gro file format requires valid box parameters at the end of each
model. However, if we read such a file in, the resulting object should not
need to have an assigned box.
"""
# Create an AtomArray
atom = Atom([1, 2, 3], atom_name="CA", element="C", res_name="X", res_id=1)
atoms = array([atom])
# Write .gro file
temp = TemporaryFile("w+")
gro_file = gro.GROFile()
gro_file.set_structure(atoms)
gro_file.write(temp)
# Read in file
temp.seek(0)
gro_file = gro.GROFile.read(temp)
temp.close()
s = gro_file.get_structure()
# Assert no box with 0 dimension
assert s.box is None
def test_gro_id_overflow():
# Create an oversized AtomArray where atom_id > 100000 and res_id > 10000
num_atoms = 100005
atoms = array([
Atom([1, 2, 3],
atom_name="CA",
element="C",
res_name="X",
res_id=i + 1) for i in range(num_atoms)
])
atoms.box = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
# Write .gro file
temp = TemporaryFile("w+")
gro_file = gro.GROFile()
gro_file.set_structure(atoms)
gro_file.write(temp)
# Read .gro file
temp.seek(0)
gro_file = gro.GROFile.read(temp)
temp.close()
s = gro_file.get_structure()
assert s.array_length() == num_atoms
def test_pdb_consistency(path):
pdb_path = splitext(path)[0] + ".pdb"
pdb_file = pdb.PDBFile()
pdb_file.read(pdb_path)
a1 = pdb_file.get_structure(model=1)
gro_file = gro.GROFile()
gro_file.read(path)
a2 = gro_file.get_structure(model=1)
assert a1.array_length() == a2.array_length()
for category in ["res_id", "res_name", "atom_name"]:
assert a1.get_annotation(category).tolist() == \
a2.get_annotation(category).tolist()
# Mind rounding errors when converting pdb to gro (A -> nm)
assert a1.coord.flatten().tolist() \
== approx(a2.coord.flatten().tolist(), abs=1e-2)
def test_gro_id_overflow():
# Create an oversized AtomArray where atom_id > 100000 and res_id > 10000
num_atoms = 100005
atoms = array([
Atom([1, 2, 3],
atom_name="CA",
element="C",
res_name="X",
res_id=i + 1) for i in range(num_atoms)
])
atoms.box = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
# Write .gro file
tmp_file_name = biotite.temp_file(".gro")
io.save_structure(tmp_file_name, atoms)
# Read .gro file
gro_file = gro.GROFile()
gro_file.read(tmp_file_name)
s = gro_file.get_structure()
assert s.array_length() == num_atoms
def test_gro_no_box():
"""
.gro file format requires valid box parameters at the end of each
model. However, if we read such a file in, the resulting object should not
have an assigned box.
"""
# Create an AtomArray
atom = Atom([1, 2, 3], atom_name="CA", element="C", res_name="X", res_id=1)
atoms = array([atom])
# Write .gro file
tmp_file_name = biotite.temp_file(".gro")
io.save_structure(tmp_file_name, atoms)
# Read in file
gro_file = gro.GROFile()
gro_file.read(tmp_file_name)
s = gro_file.get_structure()
# Assert no box with 0 dimension
assert s.box is None
def test_pdb_to_gro(path, model):
"""
Converting stacks between formats should not change data
"""
# Read in data
pdb_file = pdb.PDBFile.read(path)
try:
a1 = pdb_file.get_structure(model=model)
except biotite.InvalidFileError:
if model is None:
# The file cannot be parsed into an AtomArrayStack,
# as the models contain different numbers of atoms
# -> skip this test case
return
else:
raise
# Save stack as gro
temp = TemporaryFile("w+")
gro_file = gro.GROFile()
gro_file.set_structure(a1)
gro_file.write(temp)
# Reload stack from gro
temp.seek(0)
gro_file = gro.GROFile.read(temp)
temp.close()
a2 = gro_file.get_structure(model=model)
assert a1.array_length() == a2.array_length()
for category in ["res_id", "res_name", "atom_name"]:
assert a1.get_annotation(category).tolist() == \
a2.get_annotation(category).tolist()
# Mind rounding errors when converting pdb to gro (A -> nm)
assert a1.coord.flatten().tolist() \
== approx(a2.coord.flatten().tolist(), abs=1e-2)