# 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), "") # 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), "") disatm = s[1]["A"][(" ", 3, " ")]["N"] if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)