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"""
Run Bio.PDB.Selection tests.
Currently only tests unfold_entities.
"""
import unittest
from Bio.PDB import PDBParser
from Bio.PDB.PDBExceptions import PDBException
from Bio.PDB.Residue import Residue
from Bio.PDB.Selection import unfold_entities
def res_full_id(res: Residue):
"""Return full residue identifier for thoroughly comparing residues."""
return (res.get_resname(), *res.get_id())
class UnfoldEntitiesTests(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.parser = PDBParser(PERMISSIVE=True)
cls.structure = cls.parser.get_structure("scr", "PDB/1A8O.pdb")
def test_from_structure_level(self):
"""Unfold from highest level to all levels."""
struct_unfold = unfold_entities(self.structure, "S")[0]
for res1, res2 in zip(
self.structure.get_residues(), struct_unfold.get_residues()
):
assert res_full_id(res1) == res_full_id(res2)
model_unfold = unfold_entities(self.structure, "M")[0]
for res1, res2 in zip(
self.structure.get_residues(), model_unfold.get_residues()
):
assert res_full_id(res1) == res_full_id(res2)
residue_unfold = unfold_entities(self.structure, "R")
for res1, res2 in zip(self.structure.get_residues(), residue_unfold):
assert res_full_id(res1) == res_full_id(res2)
atom_unfold = unfold_entities(self.structure, "A")
for at1, at2 in zip(self.structure.get_atoms(), atom_unfold):
assert at1 is at2
def test_from_model_level(self):
"""Unfold from model to all levels."""
structure_models = list(self.structure.get_models())
struct_unfold = unfold_entities(structure_models, "S")[0]
for res1, res2 in zip(
self.structure.get_residues(), struct_unfold.get_residues()
):
assert res_full_id(res1) == res_full_id(res2)
model_unfold = unfold_entities(structure_models, "M")[0]
for res1, res2 in zip(
self.structure.get_residues(), model_unfold.get_residues()
):
assert res_full_id(res1) == res_full_id(res2)
residue_unfold = unfold_entities(structure_models, "R")
for res1, res2 in zip(self.structure.get_residues(), residue_unfold):
assert res_full_id(res1) == res_full_id(res2)
atom_unfold = unfold_entities(structure_models, "A")
for at1, at2 in zip(self.structure.get_atoms(), atom_unfold):
assert at1 is at2
def test_from_chain_level(self):
"""Unfold from chain level to all levels."""
structure_chains = list(self.structure.get_chains())
struct_unfold = unfold_entities(structure_chains, "S")[0]
for res1, res2 in zip(
self.structure.get_residues(), struct_unfold.get_residues()
):
assert res_full_id(res1) == res_full_id(res2)
model_unfold = unfold_entities(structure_chains, "M")[0]
for res1, res2 in zip(
self.structure.get_residues(), model_unfold.get_residues()
):
assert res_full_id(res1) == res_full_id(res2)
residue_unfold = unfold_entities(structure_chains, "R")
for res1, res2 in zip(self.structure.get_residues(), residue_unfold):
assert res_full_id(res1) == res_full_id(res2)
atom_unfold = unfold_entities(structure_chains, "A")
for at1, at2 in zip(self.structure.get_atoms(), atom_unfold):
assert at1 is at2
def test_from_residue_level(self):
"""Unfold from chain level to all levels."""
structure_residues = list(self.structure.get_residues())
struct_unfold = unfold_entities(structure_residues, "S")[0]
for res1, res2 in zip(structure_residues, struct_unfold.get_residues()):
assert res_full_id(res1) == res_full_id(res2)
model_unfold = unfold_entities(structure_residues, "M")[0]
for res1, res2 in zip(structure_residues, model_unfold.get_residues()):
assert res_full_id(res1) == res_full_id(res2)
residue_unfold = unfold_entities(structure_residues, "R")
for res1, res2 in zip(structure_residues, residue_unfold):
assert res_full_id(res1) == res_full_id(res2)
atom_unfold = unfold_entities(structure_residues, "A")
for at1, at2 in zip(self.structure.get_atoms(), atom_unfold):
assert at1 is at2
def test_from_atom_level(self):
"""Unfold from lowest level to all levels."""
structure_atoms = list(self.structure.get_atoms())
struct_unfold = unfold_entities(structure_atoms, "S")[0]
for res1, res2 in zip(
self.structure.get_residues(), struct_unfold.get_residues()
):
assert res_full_id(res1) == res_full_id(res2)
model_unfold = unfold_entities(structure_atoms, "M")[0]
for res1, res2 in zip(
self.structure.get_residues(), model_unfold.get_residues()
):
assert res_full_id(res1) == res_full_id(res2)
residue_unfold = unfold_entities(structure_atoms, "R")
for res1, res2 in zip(self.structure.get_residues(), residue_unfold):
assert res_full_id(res1) == res_full_id(res2)
atom_unfold = unfold_entities(structure_atoms, "A")
for at1, at2 in zip(structure_atoms, atom_unfold):
assert at1 is at2
def test_invalid_level(self):
with self.assertRaises(PDBException):
unfold_entities(self.structure, "Z")
def test_entities_not_homogenous(self):
structure_atom = next(self.structure.get_atoms())
structure_chain = next(self.structure.get_chains())
with self.assertRaises(PDBException):
unfold_entities([structure_atom, structure_chain], "A")
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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