def test_loading_with_extra_args():
"""
Check if :func:`load_structure()` witt optional arguments does not
raise an exception and returns an object of appropriate type.
"""
template = join(data_dir("structure"), "1l2y.pdb")
trajectory = join(data_dir("structure"), "1l2y.xtc")
# test if arguments are passed to text files as get_structure arg
structure = strucio.load_structure(template, extra_fields=["b_factor"])
assert "b_factor" in structure.get_annotation_categories()
# test if arguments are passed to read for trajectories
stack = strucio.load_structure(trajectory,
template=structure[0],
start=5,
stop=6)
assert len(stack) == 1
# loading should fail with wrong arguments
with pytest.raises(TypeError):
strucio.load_structure(template, start=2)
# test if atom_i argument is passed to templates
stack = strucio.load_structure(trajectory, template, atom_i=[1, 2])
assert stack.shape[1] == 2
def test_saving(suffix):
"""
Check if loading a structure from a file written via
:func:`save_structure()` gives the same result as the input to
:func:`save_structure()`.
"""
path = join(data_dir("structure"), "1l2y.mmtf")
ref_array = strucio.load_structure(path)
if suffix in ("trr", "xtc", "tng", "dcd", "netcdf"):
# Reading a trajectory file requires a template
template = path
else:
template = None
temp = NamedTemporaryFile("w", suffix=f".{suffix}", delete=False)
strucio.save_structure(temp.name, ref_array)
temp.close()
test_array = strucio.load_structure(temp.name, template)
os.remove(temp.name)
for category in ref_array.get_annotation_categories():
if category == "chain_id" and suffix == "gro":
# The chain ID is not written to GRO files
continue
assert test_array.get_annotation(category).tolist() \
== ref_array.get_annotation(category).tolist()
assert test_array.coord.flatten().tolist() == pytest.approx(
ref_array.coord.flatten().tolist(), abs=1e-2)
def test_masked_superimposition(seed):
"""
Take two models of the same structure and superimpose based on a
single, randomly chosen atom.
Since two atoms can be superimposed perfectly, the distance between
the atom in both models should be 0.
"""
path = join(data_dir, "1l2y.mmtf")
fixed = strucio.load_structure(path, model=1)
mobile = strucio.load_structure(path, model=2)
# Create random mask for a single atom
np.random.seed(seed)
mask = np.full(fixed.array_length(), False)
mask[np.random.randint(fixed.array_length())] = True
# The distance between the atom in both models should not be
# already 0 prior to superimposition
assert struc.distance(fixed[mask], mobile[mask])[0] \
!= pytest.approx(0, abs=5e-4)
fitted, transformation = struc.superimpose(fixed, mobile, mask)
assert struc.distance(fixed[mask], fitted[mask])[0] \
== pytest.approx(0, abs=5e-4)
fitted = struc.superimpose_apply(mobile, transformation)
struc.distance(fixed[mask], fitted[mask])[0] \
== pytest.approx(0, abs=5e-4)
def test_loading(path):
if splitext(path)[1] in [".trr", ".xtc", ".tng", ".dcd", ".netcdf"]:
template = strucio.load_structure(
join(data_dir("structure"), "1l2y.mmtf"))
array = strucio.load_structure(path, template)
else:
array = strucio.load_structure(path)
def test_pdbx_consistency(path):
cif_path = splitext(path)[0] + ".cif"
array1 = strucio.load_structure(path)
array2 = strucio.load_structure(cif_path)
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_pdbx_consistency(path):
cif_path = splitext(path)[0] + ".cif"
array1 = strucio.load_structure(path)
array2 = strucio.load_structure(cif_path)
if array2.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_rdf():
""" General test to reproduce oxygen RDF for a box of water"""
test_file = TEST_FILE
stack = load_structure(test_file)
# calculate oxygen RDF for water
oxygen = stack[:, stack.atom_name == 'OW']
interval = np.array([0, 10])
n_bins = 100
bins, g_r = rdf(oxygen[:, 0].coord,
oxygen,
interval=interval,
bins=n_bins,
periodic=False)
# Compare with MDTraj
import mdtraj
traj = mdtraj.load(TEST_FILE)
ow = [a.index for a in traj.topology.atoms if a.name == 'O']
pairs = itertools.product([ow[0]], ow)
mdt_bins, mdt_g_r = mdtraj.compute_rdf(traj,
list(pairs),
r_range=interval / 10,
n_bins=n_bins,
periodic=False)
assert np.allclose(bins, mdt_bins * 10)
assert np.allclose(g_r, mdt_g_r, rtol=0.0001)
def test_rdf_multiple_center():
""" Test if the first argument allows to use multiple centers"""
stack = load_structure(TEST_FILE)
# calculate oxygen RDF for water with and without a selection
oxygen = stack[:, stack.atom_name == 'OW']
interval = np.array([0, 10])
n_bins = 100
# averaging individual calculations
bins1, g_r1 = rdf(oxygen[:, 1].coord,
oxygen[:, 2:],
interval=interval,
bins=n_bins,
periodic=False)
bins2, g_r2 = rdf(oxygen[:, 0].coord,
oxygen[:, 2:],
interval=interval,
bins=n_bins,
periodic=False)
mean = np.mean([g_r1, g_r2], axis=0)
# this should give the same result as averaging for oxygen 0 and 1
bins, g_r = rdf(oxygen[:, 0:2].coord,
oxygen[:, 2:],
interval=interval,
bins=n_bins,
periodic=False)
assert np.allclose(g_r, mean, rtol=0.0001)
def create(pdb_id, directory, include_gro):
# Create *.pdb", *.cif and *.mmtf
for file_format in ["pdb", "cif", "mmtf"]:
rcsb.fetch(pdb_id, file_format, directory, overwrite=True)
try:
array = strucio.load_structure(join(directory, pdb_id + ".pdb"))
except biotite.InvalidFileError:
# Structure probably contains multiple models with different
# number of atoms
# -> Cannot load AtomArrayStack
# -> Skip writing GRO and NPZ file
return
# Create *.gro file
strucio.save_structure(join(directory, pdb_id + ".npz"), array)
# Create *.gro files using GROMACS
# Clean PDB file -> remove inscodes and altlocs
if include_gro:
cleaned_file_name = biotite.temp_file("pdb")
strucio.save_structure(cleaned_file_name, array)
# Run GROMACS for file conversion
subprocess.run([
"editconf", "-f", cleaned_file_name, "-o",
join(directory, pdb_id + ".gro")
],
stdout=subprocess.DEVNULL,
stderr=subprocess.DEVNULL)
def test_hbond_with_selections():
"""
When selection1 and selection2 is defined, no hydrogen bonds outside
of this boundary should be found. Also, hbond should respect the
selection type.
"""
stack = load_structure(join(data_dir, "1l2y.mmtf"))
selection1 = (stack.res_id == 3) & (stack.atom_name == 'O') # 3TYR BB Ox
selection2 = stack.res_id == 7
# backbone hbond should be found if selection1/2 type is both
triplets, mask = struc.hbond(stack, selection1, selection2,
selection1_type="both")
assert len(triplets) == 1
assert triplets[0][0] == 116
assert triplets[0][2] == 38
# backbone hbond should be found if selection1 is acceptor and
# selection2 is donor
triplets, mask = struc.hbond(stack, selection1, selection2,
selection1_type="acceptor")
assert len(triplets) == 1
assert triplets[0][0] == 116
assert triplets[0][2] == 38
# no hbond should be found,
# because the backbone oxygen cannot be a donor
triplets, mask = struc.hbond(stack, selection1, selection2,
selection1_type="donor")
assert len(triplets) == 0
def test_small_molecule():
"""
Check if loading a small molecule file written via
:func:`save_structure()` gives the same result as the input to
:func:`save_structure()`.
"""
path = join(data_dir("structure"), "molecules", "TYR.sdf")
ref_array = strucio.load_structure(path)
temp = NamedTemporaryFile("w", suffix=".sdf", delete=False)
strucio.save_structure(temp.name, ref_array)
temp.close()
test_array = strucio.load_structure(temp.name)
os.remove(temp.name)
assert test_array == ref_array
def test_adjacency_matrix(cell_size, threshold, periodic):
"""
Compare the construction of an adjacency matrix using a cell list
and using a computationally expensive but simpler distance matrix.
"""
array = strucio.load_structure(join(data_dir, "3o5r.mmtf"))
if periodic:
# Create an orthorhombic box
# with the outer coordinates as bounds
array.box = np.diag(
np.max(array.coord, axis=-2) - np.min(array.coord, axis=-2))
cell_list = struc.CellList(array, cell_size=cell_size, periodic=periodic)
matrix = cell_list.create_adjacency_matrix(threshold)
# Create distance matrix
# Convert to float64 to avoid errorenous warning
# https://github.com/ContinuumIO/anaconda-issues/issues/9129
array.coord = array.coord.astype(np.float64)
length = array.array_length()
distance = struc.index_distance(
array,
np.stack([
np.repeat(np.arange(length), length),
np.tile(np.arange(length), length)
],
axis=-1), periodic)
distance = np.reshape(distance, (length, length))
# Create adjacency matrix from distance matrix
expected_matrix = (distance <= threshold)
# Both ways to create an adjacency matrix
# should give the same result
assert np.array_equal(matrix, expected_matrix)
def test_rdf_periodic():
""" Test if the periodic argument gives the correct results"""
test_file = TEST_FILE
stack = load_structure(test_file)
# calculate oxygen RDF for water
oxygen = stack[:, stack.atom_name == 'OW']
interval = np.array([0, 10])
n_bins = 100
bins, g_r = rdf(oxygen[:, 0].coord,
oxygen[:, 1:],
interval=interval,
bins=n_bins,
periodic=True)
# Compare with MDTraj
import mdtraj
traj = mdtraj.load(TEST_FILE)
ow = [a.index for a in traj.topology.atoms if a.name == 'O']
pairs = itertools.product([ow[0]], ow[1:])
mdt_bins, mdt_g_r = mdtraj.compute_rdf(traj,
list(pairs),
r_range=interval / 10,
n_bins=n_bins,
periodic=True)
assert np.allclose(bins, mdt_bins * 10)
assert np.allclose(g_r, mdt_g_r, rtol=0.0001)
def test_array_conversion(format):
template = strucio.load_structure(join(data_dir, "1l2y.mmtf"))[0]
# Add fake box
template.box = np.diag([1, 2, 3])
if format == "trr":
traj_file_cls = trr.TRRFile
if format == "xtc":
traj_file_cls = xtc.XTCFile
if format == "tng":
traj_file_cls = tng.TNGFile
if format == "dcd":
traj_file_cls = dcd.DCDFile
if format == "netcdf":
traj_file_cls = netcdf.NetCDFFile
traj_file = traj_file_cls()
traj_file.read(join(data_dir, f"1l2y.{format}"))
ref_array = traj_file.get_structure(template)
traj_file = traj_file_cls()
traj_file.set_structure(ref_array)
file_name = biotite.temp_file(format)
traj_file.write(file_name)
traj_file = traj_file_cls()
traj_file.read(file_name)
array = traj_file.get_structure(template)
assert ref_array.bonds == array.bonds
assert ref_array.equal_annotation_categories(array)
assert ref_array.box == pytest.approx(array.box)
assert ref_array.coord == pytest.approx(array.coord, abs=1e-2)
def write_atom_to_pdb(pdb_outname, atom_location, atom_ID, atomgroup):
"""
Write a new atom to a reference structure to visualise conserved non-protein atom sites.
Parameters
----------
pdb_outname : str
Filename of reference structure.
atom_location : array
(x,y,z) coordinates of the atom location with respect to the reference structure.
atom_ID : str
A unique ID for the atom.
atomgroup : str
MDAnalysis atomgroup to describe the atom.
"""
##PDB_VISUALISATION
##rescursively add waters to the pdb file one by one as they are processed
# # Read the file into Biotite's structure object (atom array)
atom_array = strucio.load_structure(pdb_outname)
res_id = atom_array.res_id[-1] + 1
# Add an HETATM
atom = struc.Atom(
coord=atom_location,
chain_id="X",
# The residue ID is the last ID in the file +1
res_id=res_id,
res_name=atom_ID,
hetero=True,
atom_name=atomgroup,
element="O")
atom_array += struc.array([atom])
# Save edited structure
strucio.save_structure(pdb_outname, atom_array)
def test_hbond_structure(pdb_id):
file_name = join(data_dir("structure"), pdb_id + ".mmtf")
array = load_structure(file_name)
# Only consider amino acids for consistency
# with bonded hydrogen detection in MDTraj
array = array[..., struc.filter_amino_acids(array)]
if isinstance(array, struc.AtomArrayStack):
# For consistency with MDTraj 'S' cannot be acceptor element
# https://github.com/mdtraj/mdtraj/blob/master/mdtraj/geometry/hbond.py#L365
triplets, mask = struc.hbond(array, acceptor_elements=("O", "N"))
else:
triplets = struc.hbond(array, acceptor_elements=("O", "N"))
# Save to new pdb file for consistent treatment of inscode/altloc
# im MDTraj
temp = NamedTemporaryFile("w+", suffix=".pdb")
save_structure(temp.name, array)
# Compare with MDTraj
import mdtraj
traj = mdtraj.load(temp.name)
temp.close()
triplets_ref = mdtraj.baker_hubbard(traj, freq=0, periodic=False)
# Both packages may use different order
# -> use set for comparison
triplets_set = set([tuple(tri) for tri in triplets])
triplets_ref_set = set([tuple(tri) for tri in triplets_ref])
assert triplets_set == triplets_ref_set
def test_index_functions():
"""
The `index_xxx()` functions should give the same result as the
corresponding `xxx` functions.
"""
stack = strucio.load_structure(join(data_dir, "1l2y.mmtf"))
array = stack[0]
# Test for atom array, stack and raw coordinates
samples = (array, stack, struc.coord(array), struc.coord(stack))
# Generate random indices
random.seed(42)
indices = random.randint(array.array_length(), size=(100, 4), dtype=int)
for sample in samples:
if isinstance(sample, np.ndarray):
atoms1 = sample[..., indices[:, 0], :]
atoms2 = sample[..., indices[:, 1], :]
atoms3 = sample[..., indices[:, 2], :]
atoms4 = sample[..., indices[:, 3], :]
else:
atoms1 = sample[..., indices[:, 0]]
atoms2 = sample[..., indices[:, 1]]
atoms3 = sample[..., indices[:, 2]]
atoms4 = sample[..., indices[:, 3]]
assert np.allclose(struc.displacement(atoms1, atoms2),
struc.index_displacement(sample, indices[:, :2]),
atol=1e-5)
assert np.allclose(struc.distance(atoms1, atoms2),
struc.index_distance(sample, indices[:, :2]),
atol=1e-5)
assert np.allclose(struc.angle(atoms1, atoms2, atoms3),
struc.index_angle(sample, indices[:, :3]),
atol=1e-5)
assert np.allclose(struc.dihedral(atoms1, atoms2, atoms3, atoms4),
struc.index_dihedral(sample, indices[:, :4]),
atol=1e-5)
def test_superimposition_stack(ca_only):
"""
Take a structure with multiple models where each model is not
(optimally) superimposed onto each other.
Then superimpose and expect an improved RMSD.
"""
path = join(data_dir, "1l2y.mmtf")
stack = strucio.load_structure(path)
fixed = stack[0]
mobile = stack[1:]
if ca_only:
mask = (mobile.atom_name == "CA")
else:
mask = None
fitted, transformation = struc.superimpose(fixed, mobile, mask)
if ca_only:
# The superimpositions are better for most cases than the
# superimpositions in the structure file
# -> Use average
assert np.mean(struc.rmsd(fixed, fitted)) \
< np.mean(struc.rmsd(fixed, mobile))
else:
# The superimpositions are better than the superimpositions
# in the structure file
assert (struc.rmsd(fixed, fitted) < struc.rmsd(fixed, mobile)).all()
def test_atom_array_consistency():
"""
Test whether the associated bonds of an `AtomArray` still point to
the same atoms after indexing with a boolean mask.
The boolean mask is constructed in a way that all bonded atoms are
masked.
"""
array = strucio.load_structure(join(data_dir("structure"), "1l2y.mmtf"))[0]
ca = array[array.atom_name == "CA"]
# Just for testing, does not reflect real bonds
bond_list = struc.BondList(
ca.array_length(),
np.array([(0, 1), (2, 8), (5, 15), (1, 5), (0, 9), (3, 18), (2, 9)]))
ca.bonds = bond_list
ref_ids = ca.res_id[bond_list.as_array()[:, :2].flatten()]
# Some random boolean mask as index,
# but all bonded atoms are included
mask = np.array(
[1, 1, 1, 1, 0, 1, 0, 0, 1, 1, 0, 1, 1, 0, 0, 1, 1, 0, 1, 1],
dtype=bool)
masked_ca = ca[mask]
test_ids = masked_ca.res_id[masked_ca.bonds.as_array()[:, :2].flatten()]
# The bonds, should always point to the same atoms (same res_id),
# irrespective of indexing
assert test_ids.tolist() == ref_ids.tolist()
def test_standardize_order(multi_model, seed):
original = load_structure(join(data_dir("structure"), "1l2y.mmtf"))
if not multi_model:
original = original[0]
# The box is not preserved when concatenating atom arrays later
# This would complicate the atom array equality later
original.box = None
# Randomly reorder the atoms in each residue
np.random.seed(seed)
if multi_model:
reordered = struc.AtomArrayStack(original.stack_depth(), 0)
else:
reordered = struc.AtomArray(0)
for residue in struc.residue_iter(original):
bound = residue.array_length()
indices = np.random.choice(np.arange(bound), bound, replace=False)
reordered += residue[..., indices]
# Restore the original PDB standard order
restored = reordered[..., strucinfo.standardize_order(reordered)]
assert restored.shape == original.shape
assert restored[..., restored.element != "H"] \
== original[..., original.element != "H"]
def test_sse():
array = strucio.load_structure(join(data_dir("structure"), "3o5r.mmtf"))
sse = struc.annotate_sse(array, "A")
sse_str = "".join(sse.tolist())
assert sse_str == ("caaaaaacccccccccccccbbbbbccccccbbbbccccccccccccccc"
"ccccccccccccbbbbbbcccccccaaaaaaaaaccccccbbbbbccccc"
"ccccccccccccbbbbbbbccccccccc")
def __getitem__(self, index):
print(os.path.join(self.fileDir, self.files[index]))
array = strucio.load_structure(
os.path.join(self.fileDir, self.files[index]))
if type(array) == biotite.structure.AtomArrayStack:
array = array[0]
# print(os.path.join(self.fileDir, self.files[index]))
# print(type(array))
ca = array[array.atom_name == "CA"]
cell_list = struc.CellList(ca, cell_size=self.threshold)
# cell_list = struc.CellList(array, cell_size=self.threshold)
adj_matrix = cell_list.create_adjacency_matrix(
self.threshold).astype(int)
shape = adj_matrix.shape
if shape[0] % 2 != 0:
print(shape)
adj_matrix = np.append(adj_matrix,
np.zeros((1, shape[0]), dtype=float),
axis=0)
adj_matrix = np.append(adj_matrix,
np.zeros((shape[0] + 1, 1), dtype=float),
axis=1)
print(adj_matrix.shape)
# return torch.tensor(adj_matrix.astype('float'))
return adj_matrix.astype('double')
def test_doctest(package_name, context_package_names):
"""
Run all doctest strings in all Biotite subpackages.
"""
# Collect all attributes of this package and its subpackages
# as globals for the doctests
globs = {}
mod_names = []
#The package itself is also used as context
for name in context_package_names + [package_name]:
context_package = import_module(name)
globs.update({
attr: getattr(context_package, attr)
for attr in dir(context_package)
})
# Add fixed names for certain paths
globs["path_to_directory"] = tempfile.gettempdir()
globs["path_to_structures"] = join(".", "tests", "structure", "data")
globs["path_to_sequences"] = join(".", "tests", "sequence", "data")
# Add frequently used modules
globs["np"] = np
# Add frequently used objects
globs["atom_array_stack"] = strucio.load_structure(
join(".", "tests", "structure", "data", "1l2y.mmtf"))
globs["atom_array"] = globs["atom_array_stack"][0]
# Adjust NumPy print formatting
np.set_printoptions(precision=3, floatmode="maxprec_equal")
# Run doctests
# This test does not use 'testfile()' or 'testmod()'
# due to problems with doctest identification for Cython modules
# More information below
package = import_module(package_name)
runner = doctest.DocTestRunner(verbose=False,
optionflags=doctest.ELLIPSIS
| doctest.REPORT_ONLY_FIRST_FAILURE)
for test in doctest.DocTestFinder(exclude_empty=False).find(
package,
package.__name__,
# It is necessary to set 'module' to 'False', as otherwise
# Cython functions and classes would be falsely identified
# as members of an external module by 'DocTestFinder._find()'
# and consequently would be ignored
#
# Setting 'module=False' omits this check
# This check is not necessary as the biotite subpackages
# ('__init__.py' modules) should only contain attributes, that
# are part of the package itself.
module=False,
extraglobs=globs):
runner.run(test)
results = doctest.TestResults(runner.failures, runner.tries)
try:
assert results.failed == 0
except AssertionError:
print(f"Failing doctest in module {package}")
raise
def nuc_sample_array():
"""
Sample structure.
"""
nuc_sample_array = strucio.load_structure(
join(data_dir("structure"), "4p5j.cif")
)
return nuc_sample_array[struc.filter_nucleotides(nuc_sample_array)]
def test_outside_location():
# Test result for location outside any cell
array = strucio.load_structure(join(data_dir, "3o5r.mmtf"))
array = array[struc.filter_amino_acids(array)]
cell_list = struc.CellList(array, cell_size=5)
outside_coord = np.min(array.coord, axis=0) - 100
# Expect empty array
assert len(cell_list.get_atoms(outside_coord, 5)) == 0
def get_reference_from_structure(
structure_path: str,
positions: t.Optional[t.Container[int]] = None) -> str:
aa_mapping = AminoAcidDict().aa_dict
residues = zip(*bst.get_residues(io.load_structure(structure_path)))
if positions is not None:
residues = (r for r in residues if r[0] in positions)
return "".join([aa_mapping[r[1]] for r in residues])
def test_loading_with_extra_args():
template = join(data_dir("structure"), "1l2y.pdb")
trajectory = join(data_dir("structure"), "1l2y.xtc")
# test if arguments are passed to text files as get_structure arg
structure = strucio.load_structure(template, extra_fields=["b_factor"])
assert "b_factor" in structure.get_annotation_categories()
# test if arguments are passed to read for trajectories
stack = strucio.load_structure(trajectory,
template=structure[0],
start=5,
stop=6)
assert len(stack) == 1
# loading should fail with wrong arguments
with pytest.raises(TypeError):
strucio.load_structure(template, start=2)
def test_loading(path):
"""
Just check if :func:`load_structure()` does not raise an exception
and returns an object of appropriate type.
"""
suffix = splitext(path)[1]
if suffix in [".trr", ".xtc", ".tng", ".dcd", ".netcdf"]:
template = strucio.load_structure(
join(data_dir("structure"), "1l2y.mmtf"))
array = strucio.load_structure(path, template)
else:
array = strucio.load_structure(path)
if suffix == ".gro":
# The test GRO file contains only a single model,
# since it is created by Gromacs
assert isinstance(array, struc.AtomArray)
else:
assert isinstance(array, struc.AtomArrayStack)
def test_saving_with_extra_args(suffix):
"""
Test if giving a wrong optional parameter to
:func:`save_structure()` raises a :class:`TypeError`
"""
array = strucio.load_structure(join(data_dir("structure"), "1l2y.mmtf"))
temp = NamedTemporaryFile("w+", suffix=f".{suffix}")
with pytest.raises(TypeError):
strucio.save_structure(temp.name, array, answer=42)
temp.close()
def test_rdf_bins():
""" Test if RDF produce correct bin ranges """
stack = load_structure(TEST_FILE)
center = stack[:, 0]
num_bins = 44
bin_range = (0, 11.7)
bins, g_r = rdf(center, stack, bins=num_bins, interval=bin_range)
assert (len(bins) == num_bins)
assert (bins[0] > bin_range[0])
assert (bins[1] < bin_range[1])