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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 sys
import tempfile
import unittest
import warnings
import numpy as np
from Bio.PDB import PDBIO
from Bio.PDB import PDBParser
from Bio.PDB.Atom import DisorderedAtom
class TestDisordered(unittest.TestCase):
"""Tests for operations on DisorderedEntities."""
@classmethod
def setUpClass(cls):
cls.parser = parser = PDBParser(QUIET=1)
cls.structure = parser.get_structure("x", "PDB/disordered.pdb")
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()]
# Copying
def test_copy_disordered_atom(self):
"""Copies disordered atoms and all their children."""
resi27 = self.structure[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."""
s = self.structure
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)
# Transforming
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.
s = self.structure
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
# Extract and write
def test_copy_and_write_disordered(self):
"""Extract, save, and parse again disordered atoms."""
writer = PDBIO()
s = self.structure
# 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 = self.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)
# DisorderedAtom.center_of_mass
def test_structure_w_disordered_com(self):
"""Calculate center of mass of structure including DisorderedAtoms."""
with warnings.catch_warnings():
warnings.simplefilter("ignore")
s = self.parser.get_structure("b", "PDB/disordered.pdb")
com = s.center_of_mass()
self.assertTrue(np.allclose(com, [54.545, 19.868, 31.212], atol=1e-3))
def test_disordered_cog(self):
"""Calculate DisorderedAtom center of geometry."""
with warnings.catch_warnings():
warnings.simplefilter("ignore")
s = self.parser.get_structure("b", "PDB/disordered.pdb")
arg27 = s[0]["A"][27]
# Detach all children but NH1
for atom in list(arg27):
if atom.name != "NH1":
arg27.detach_child(atom.name)
res_cog = arg27.center_of_mass()
self.assertTrue(np.allclose(res_cog, [59.555, 21.033, 25.954], atol=1e-3))
# Now compare to DisorderedAtom.center_of_mass
da_cog = arg27["NH1"].center_of_mass()
self.assertTrue(np.allclose(res_cog, da_cog, atol=1e-3))
def test_empty_disordered(self):
"""Raise ValueError on center of mass calculation of empty DisorderedAtom."""
da = DisorderedAtom("dummy")
with self.assertRaises(ValueError):
da.center_of_mass()
# disordered_remove
def test_remove_disordered_residue(self):
"""Remove residues from DisorderedResidue entities."""
with warnings.catch_warnings():
warnings.simplefilter("ignore")
s = self.parser.get_structure("a", "PDB/a_structure.pdb")
# Residue 10 of chain A is disordered
disres = s[1]["A"][(" ", 10, " ")]
self.assertEqual(disres.is_disordered(), 2)
self.assertEqual(len(disres.child_dict), 2) # GLY and SER
disres.disordered_remove("GLY")
self.assertEqual(len(disres.child_dict), 1)
self.assertEqual(disres.resname, "SER") # selects new child?
disres.disordered_remove("SER")
self.assertEqual(len(disres.child_dict), 0)
self.assertIsNone(disres.selected_child)
with self.assertRaises(AttributeError):
_ = disres.resname
self.assertEqual(str(disres), "<Empty DisorderedResidue>")
# Should still be in chain with the same id though
# Up to the user to detach the DisorderedResidue from its parent.
disres = s[1]["A"][(" ", 10, " ")]
def test_remove_disordered_atom(self):
"""Remove altlocs from DisorderedAtom entities."""
with warnings.catch_warnings():
warnings.simplefilter("ignore")
s = self.parser.get_structure("a", "PDB/a_structure.pdb")
# Residue 3 of chain A is disordered
disres = s[1]["A"][(" ", 3, " ")]
self.assertEqual(disres.is_disordered(), 1)
disatom = disres["N"]
self.assertEqual(len(disatom.child_dict), 2) # "A" and " "
# Add new atom with bogus occupancy to test selection on removal
atom = disatom.child_dict["A"].copy()
atom.altloc = "B"
atom.occupancy = 2.0
disatom.disordered_add(atom)
disatom.disordered_remove(" ")
self.assertEqual(len(disatom.child_dict), 2)
self.assertEqual(disatom.altloc, "B")
# Remove all children
disatom.disordered_remove("A")
disatom.disordered_remove("B")
self.assertEqual(len(disatom.child_dict), 0)
self.assertIsNone(disatom.selected_child)
self.assertEqual(disatom.last_occupancy, -sys.maxsize)
with self.assertRaises(AttributeError):
_ = disatom.altloc
self.assertEqual(str(disatom), "<Empty DisorderedAtom N>")
disatm = s[1]["A"][(" ", 3, " ")]["N"]
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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