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# Revisions copyright 2020 Joao Rodrigues. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Unit tests for disordered atoms in the Bio.PDB module."""
import os
import tempfile
import unittest
from Bio.PDB import PDBParser, PDBIO
class TestDisordered(unittest.TestCase):
"""Tests for operations on DisorderedEntities."""
def unpack_all_atoms(self, structure):
"""Return a list of all atoms in the structure."""
return [a for r in structure.get_residues() for a in r.get_unpacked_list()]
def test_copy_disordered_atom(self):
"""Copies disordered atoms and all their children."""
parser = PDBParser(QUIET=1)
s = parser.get_structure("x", "PDB/disordered.pdb")
resi27 = s[0]["A"][27]
resi27_copy = resi27.copy()
self.assertNotEqual(id(resi27), id(resi27_copy)) # did we really copy
resi27_atoms = resi27.get_unpacked_list()
resi27_copy_atoms = resi27.get_unpacked_list()
self.assertEqual(len(resi27_atoms), len(resi27_copy_atoms))
for ai, aj in zip(resi27_atoms, resi27_copy_atoms):
self.assertEqual(ai.name, aj.name)
def test_copy_entire_chain(self):
"""Copy propagates throughout SMCRA object."""
parser = PDBParser(QUIET=1)
s = parser.get_structure("x", "PDB/disordered.pdb")
s_copy = s.copy()
self.assertNotEqual(id(s), id(s_copy)) # did we really copy
atoms = self.unpack_all_atoms(s)
copy_atoms = self.unpack_all_atoms(s_copy)
self.assertEqual(len(atoms), len(copy_atoms))
for ai, aj in zip(atoms, copy_atoms):
self.assertEqual(ai.name, aj.name)
def test_transform_disordered(self):
"""Transform propagates through disordered atoms."""
# This test relates to issue #455 where applying a transformation
# to a copied structure did not work for disordered atoms.
parser = PDBParser(QUIET=1)
s = parser.get_structure("x", "PDB/disordered.pdb")
s_copy = s.copy()
mtx = ((1, 0, 0), (0, 1, 0), (0, 0, 1))
tr_vec = (20.0, 0.0, 0.0)
s_copy.transform(mtx, tr_vec) # transform copy
atoms = self.unpack_all_atoms(s)
copy_atoms = self.unpack_all_atoms(s_copy)
self.assertEqual(len(atoms), len(copy_atoms))
for ai, aj in zip(atoms, copy_atoms):
self.assertEqual(ai - aj, 20.0) # check distance == 20.0
def test_copy_and_write_disordered(self):
"""Extract, save, and parse again disordered atoms."""
parser = PDBParser(QUIET=1)
writer = PDBIO()
s = parser.get_structure("x", "PDB/disordered.pdb")
# Extract the chain object
chain = s[0]["A"]
writer.set_structure(chain)
filenumber, filename = tempfile.mkstemp() # save to temp file
os.close(filenumber)
try:
writer.save(filename)
# Parse again
s2 = parser.get_structure("x_copy", filename)
# Do we have the same stuff?
atoms1 = self.unpack_all_atoms(s)
atoms2 = self.unpack_all_atoms(s2)
self.assertEqual(len(atoms1), len(atoms2))
for ai, aj in zip(atoms1, atoms2):
self.assertEqual(ai.name, aj.name)
finally:
os.remove(filename)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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