def test_format_residue_ids_and_ixs(self, residue_ids, residue_ixs,
residue_ids_formatted,
residue_ixs_formatted):
pocket = Pocket()
residue_ids, residue_ixs = pocket._format_residue_ids_and_ixs(
residue_ids, residue_ixs, "text")
assert residue_ids == residue_ids_formatted
assert residue_ixs == residue_ixs_formatted
def test_center_and_ca_atoms(
self, filepath, pocket_residue_ids, ca_atoms_residue_ids, pocket_center
):
"""
Test the pocket CA atoms and center calculation based on the pocket's residue PDB IDs.
"""
pocket = Pocket.from_file(filepath, pocket_residue_ids)
# Test property ca_atom
assert len(pocket.ca_atoms) == len(ca_atoms_residue_ids)
assert pocket.ca_atoms.columns.to_list() == [
"atom.id",
"atom.name",
"atom.x",
"atom.y",
"atom.z",
"residue.id",
"residue.name",
]
assert pocket.ca_atoms.dtypes.to_list() == [
"int32",
"string",
"float32",
"float32",
"float32",
"int32",
"string",
]
# Test attribute center
for i, j in zip(pocket.center, pocket_center):
assert pytest.approx(i, abs=1.0e-3) == j
def test_anchor_residue_by_residue_ix(
self,
filepath,
residue_ids,
residue_ixs,
anchor_residue_ix,
anchor_residue_id,
anchor_residue_id_alternative,
anchor_residue_color,
anchor_residue_center,
):
"""
Test anchor residue definitions generated based on residue indices.
"""
pocket = Pocket.from_file(filepath, residue_ids, residue_ixs)
anchor_residue = pocket._anchor_residue_by_residue_ix(
anchor_residue_ix, anchor_residue_color
)
assert isinstance(anchor_residue, AnchorResidue)
assert anchor_residue.residue_ix == anchor_residue_ix
if anchor_residue_id:
assert anchor_residue.residue_id == anchor_residue_id
assert anchor_residue.residue_id_alternative == anchor_residue_id_alternative
assert anchor_residue.color == anchor_residue_color
if anchor_residue_center:
assert pytest.approx(anchor_residue.center[0], abs=1.0e-3) == anchor_residue_center[0]
def test_add_subpocket(
self,
filepath,
pocket_residue_ids,
pocket_residue_ixs,
subpocket_name,
subpocket_color,
subpocket_center,
):
"""
Test adding subpocket and associated subpockets property and attribute.
"""
pocket = Pocket.from_file(filepath, pocket_residue_ids,
pocket_residue_ixs)
assert pocket.subpockets == None
assert pocket.anchor_residues == None
# Add subpocket
pocket.add_subpocket(subpocket_name,
anchor_residue_ids=pocket_residue_ids,
color=subpocket_color)
pocket.add_subpocket(subpocket_name,
anchor_residue_ixs=pocket_residue_ixs,
color=subpocket_color)
# Test the subpocket in the _subpockets attribute
assert all(
pocket._subpockets[0].center == pocket._subpockets[1].center)
subpocket = pocket._subpockets[0]
assert subpocket.name == subpocket_name
assert subpocket.color == subpocket_color
assert pytest.approx(subpocket.center, abs=1.0e-6) == subpocket_center
# Test subpockets property
assert isinstance(pocket.subpockets, pd.DataFrame)
assert pocket.subpockets.columns.to_list() == [
"subpocket.name",
"subpocket.color",
"subpocket.center",
]
# Test anchor_residues property
assert isinstance(pocket.anchor_residues, pd.DataFrame)
assert pocket.anchor_residues.columns.to_list() == [
"subpocket.name",
"anchor_residue.color",
"anchor_residue.id",
"anchor_residue.id_alternative",
"anchor_residue.ix",
"anchor_residue.center",
]
def test_from_file(self, filepath, residue_ids, residue_ixs, name, data_residue_ids):
"""
Initialize class from file and test class attributes and properties.
"""
pocket = Pocket.from_file(filepath, residue_ids, residue_ixs, name)
# Test attributes
assert pocket.name == name
assert isinstance(pocket._text, str)
assert pocket._extension == filepath.suffix[1:]
assert isinstance(pocket.data, pd.DataFrame)
assert list(pocket.data["residue.id"].unique()) == data_residue_ids
def test_ca_atoms_and_ca_atoms_center(self, filepath, pocket_residue_ids,
residue_ids, n_ca_atoms, center):
"""
Test CA atoms retrieval and center calculation based on a set of residue PDB IDs.
"""
pocket = Pocket.from_file(filepath, pocket_residue_ids)
# Test method _ca_atoms()
ca_atoms = pocket._ca_atoms(*residue_ids)
assert len(ca_atoms) == n_ca_atoms
# Test method _ca_atoms_center()
_, ca_atoms_center = pocket._ca_atoms_center(*residue_ids)
if center:
for i, j in zip(ca_atoms_center, center):
assert pytest.approx(i, abs=1.0e-3) == j
def test_add_regions(
self,
filepath,
pocket_residue_ids,
pocket_residue_ixs,
region_name,
region_color,
):
"""
Test adding regions and associated regions property and attribute.
"""
pocket = Pocket.from_file(filepath, pocket_residue_ids,
pocket_residue_ixs)
assert pocket.regions == None
# Add region
pocket.add_region(region_name,
residue_ids=pocket_residue_ids,
color=region_color)
pocket.add_region(region_name,
residue_ixs=pocket_residue_ixs,
color=region_color)
# Test the subpocket in the _subpockets attribute
assert pocket._regions[0].residue_ids == pocket._regions[1].residue_ids
assert pocket._regions[0].residue_ixs == pocket._regions[1].residue_ixs
# Test regions property
assert isinstance(pocket.regions, pd.DataFrame)
assert pocket.regions.columns.to_list() == [
"region.name",
"region.color",
"residue.id",
"residue.ix",
]
# Test an example region in the _regions attribute
region = pocket._regions[0]
assert region.name == region_name
assert region.color == region_color
def test_subpocket_by_residue_ids(
self,
filepath,
pocket_residue_ids,
subpocket_residue_ids,
subpocket_center,
subpocket_name,
subpocket_color,
):
"""
Test subpocket definitions generated based on residue PDB IDs.
"""
pocket = Pocket.from_file(filepath, pocket_residue_ids)
subpocket = pocket._subpocket_by_residue_ids(
subpocket_residue_ids, subpocket_name, subpocket_color
)
assert subpocket.name == subpocket_name
assert subpocket.color == subpocket_color
for i, j in zip(subpocket.center, subpocket_center):
assert pytest.approx(i, abs=1.0e-3) == j