# Copyright 2009-2011 by Eric Talevich. All rights reserved. # Revisions copyright 2009-2013 by Peter Cock. All rights reserved. # Revisions copyright 2013 Lenna X. Peterson. All rights reserved. # Revisions copyright 2020 Joao Rodrigues. All rights reserved. # # Converted by Eric Talevich from an older unit test copyright 2002 # by Thomas Hamelryck. # # 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 the Bio.PDB PDBParser module.""" from io import StringIO import os import tempfile import unittest import warnings try: import numpy except ImportError: from Bio import MissingPythonDependencyError raise MissingPythonDependencyError( "Install NumPy if you want to use Bio.PDB." ) from None from Bio import BiopythonWarning from Bio.PDB import PDBParser from Bio.PDB.PDBExceptions import PDBConstructionException, PDBConstructionWarning class FlawedPDB_tests(unittest.TestCase): """Errors and warnings while parsing flawed PDB files. These tests must be executed because of the way Python's warnings module works -- a warning is only logged the first time it is encountered. """ def setUp(self): self.permissive = PDBParser(PERMISSIVE=True) self.strict = PDBParser(PERMISSIVE=False) def test_1_flawedpdb_permissive(self): """Parse a flawed PDB file in permissive mode: check warnings.""" with warnings.catch_warnings(record=True) as w: warnings.simplefilter("always", PDBConstructionWarning) # Trigger warnings self.permissive.get_structure("example", "PDB/a_structure.pdb") self.assertEqual(len(w), 15) for wrn, msg in zip( w, [ # Expected warning messages: "Used element 'N' for Atom (name=N) with given element ''", "Used element 'C' for Atom (name=CA) with given element ''", "Atom names ' CA ' and 'CA ' differ only in spaces at line 18.", "Used element 'CA' for Atom (name=CA ) with given element ''", "Atom N defined twice in residue at line 22.", "disordered atom found with blank altloc before line 34.", "Residue (' ', 4, ' ') redefined at line 44.", "Blank altlocs in duplicate residue SER (' ', 4, ' ') at line 44.", "Residue (' ', 10, ' ') redefined at line 76.", "Residue (' ', 14, ' ') redefined at line 107.", "Residue (' ', 16, ' ') redefined at line 136.", "Residue (' ', 80, ' ') redefined at line 634.", "Residue (' ', 81, ' ') redefined at line 647.", "Ignoring unrecognized record 'ATOM 1' at line 777", "Atom O defined twice in residue at line 904.", ], ): self.assertIn(msg, str(wrn)) def test_2_flawedpdb_strict(self): """Parse a flawed PDB file in permissive mode: check errors.""" with warnings.catch_warnings(record=True) as w: warnings.simplefilter("always", PDBConstructionWarning) self.assertRaises( PDBConstructionException, self.strict.get_structure, "example", "PDB/a_structure.pdb", ) self.assertEqual(len(w), 4, w) def test_3_bad_xyz_permissive(self): """Parse an entry with bad x,y,z value with PERMISSIVE=True.""" data = "ATOM 9 N ASP A 152 21.554 34.953 27.691 1.00 19.26 N\n" _ = self.permissive.get_structure("example", StringIO(data)) def test_4_bad_xyz_strict(self): """Parse an entry with bad x,y,z value with PERMISSIVE=False.""" data = "ATOM 9 N ASP A 152 21.ish 34.953 27.691 1.00 19.26 N\n" with self.assertRaises(PDBConstructionException): self.strict.get_structure("example", StringIO(data)) def test_5_missing_occupancy_permissive(self): """Parse file with missing occupancy with PERMISSIVE=True.""" with warnings.catch_warnings(record=True) as w: warnings.simplefilter("always", PDBConstructionWarning) structure = self.permissive.get_structure("test", "PDB/occupancy.pdb") self.assertEqual(len(w), 3, w) atoms = structure[0]["A"][(" ", 152, " ")] # Blank occupancy behavior set in Bio/PDB/PDBParser self.assertEqual(atoms["N"].get_occupancy(), None) self.assertEqual(atoms["CA"].get_occupancy(), 1.0) self.assertEqual(atoms["C"].get_occupancy(), 0.0) def test_6_missing_occupancy_strict(self): """Parse file with missing occupancy with PERMISSIVE=False.""" with self.assertRaises(PDBConstructionException): _ = self.strict.get_structure("test", "PDB/occupancy.pdb") class ParseDummyPDB_test(unittest.TestCase): """Tests for artifical/dummy PDB files.""" @classmethod def setUpClass(cls): with warnings.catch_warnings(): warnings.simplefilter("ignore", PDBConstructionWarning) p = PDBParser(PERMISSIVE=1) cls.structure = p.get_structure("example", "PDB/a_structure.pdb") def test_structure_integrity(self): """Verify the structure of the parsed example PDB file.""" # Structure contains 2 models self.assertEqual(len(self.structure), 2) # --- Checking model 0 --- m0 = self.structure[0] # Model 0 contains 1 chain self.assertEqual(len(m0), 1) # Chain 'A' contains 1 residue self.assertEqual(len(m0["A"]), 1) # Residue ('H_PCA', 1, ' ') contains 9 atoms. residue = m0["A"].get_list()[0] self.assertEqual(residue.get_id(), ("H_PCA", 1, " ")) self.assertEqual(len(residue), 9) # --- Checking model 1 --- m1 = self.structure[1] # Model 1 contains 3 chains self.assertEqual(len(m1), 4) # Deconstruct this data structure to check each chain chain_data = [ # chain_id, chain_len, [(residue_id, residue_len), ...] ( "A", 86, [ ((" ", 0, " "), 1), ((" ", 2, " "), 11), ((" ", 3, " "), 6, 1), # disordered ((" ", 4, " "), 4), ((" ", 5, " "), 6), ((" ", 6, " "), 9), ((" ", 7, " "), 4), ((" ", 8, " "), 4), ((" ", 9, " "), 4), ((" ", 10, " "), 6, ["GLY", "SER"]), # point mut ((" ", 11, " "), 7), ((" ", 12, " "), 6), ((" ", 13, " "), 7), ((" ", 14, " "), 4, ["ALA", "GLY"]), # point mut ((" ", 15, " "), 8, 3), # disordered ((" ", 16, " "), 11, ["ARG", "TRP"]), # point mut ((" ", 17, " "), 6), ((" ", 18, " "), 6), ((" ", 19, " "), 6), ((" ", 20, " "), 8), ((" ", 21, " "), 14), ((" ", 22, " "), 4), ((" ", 23, " "), 14), ((" ", 24, " "), 6), ((" ", 25, " "), 4), ((" ", 26, " "), 8), ((" ", 27, " "), 6), ((" ", 28, " "), 9, 5), # disordered ((" ", 29, " "), 7), ((" ", 30, " "), 12), ((" ", 31, " "), 6), ((" ", 32, " "), 4), ((" ", 33, " "), 11), ((" ", 34, " "), 7), ((" ", 35, " "), 6), ((" ", 36, " "), 9), ((" ", 37, " "), 8), ((" ", 38, " "), 9), ((" ", 39, " "), 6), ((" ", 40, " "), 14), ((" ", 41, " "), 6), ((" ", 42, " "), 4), ((" ", 43, " "), 9), ((" ", 44, " "), 11), ((" ", 45, " "), 6, 1), # disordered ((" ", 46, " "), 8), ((" ", 47, " "), 10), ((" ", 48, " "), 11), ((" ", 49, " "), 6), ((" ", 50, " "), 4), ((" ", 51, " "), 5), ((" ", 52, " "), 5), ((" ", 53, " "), 7), ((" ", 54, " "), 4), ((" ", 55, " "), 8), ((" ", 56, " "), 7), ((" ", 57, " "), 7), ((" ", 58, " "), 6), ((" ", 59, " "), 4), ((" ", 60, " "), 9), ((" ", 61, " "), 8), ((" ", 62, " "), 11), ((" ", 63, " "), 6), ((" ", 64, " "), 6), ((" ", 65, " "), 6), ((" ", 66, " "), 7), ((" ", 67, " "), 10), ((" ", 68, " "), 4), ((" ", 69, " "), 14), ((" ", 70, " "), 6), ((" ", 71, " "), 4), ((" ", 72, " "), 4), ((" ", 73, " "), 4), ((" ", 74, " "), 8, 3), # disordered ((" ", 75, " "), 8), ((" ", 76, " "), 12), ((" ", 77, " "), 6), ((" ", 78, " "), 6), ((" ", 79, " "), 4, 4), # disordered ((" ", 80, " "), 4, ["GLY", "SER"]), # point mut ((" ", 81, " "), 8, ["ASN", "LYS"]), # point mut ((" ", 82, " "), 6), ((" ", 83, " "), 9), ((" ", 84, " "), 12), ((" ", 85, " "), 11), ((" ", 86, " "), 6), ], ), ( "B", 11, [ ((" ", 44, " "), 11), (("H_SEP", 45, " "), 10), # Phosphoserine ((" ", 46, " "), 8), ((" ", 47, " "), 10), ((" ", 48, " "), 11), ((" ", 49, " "), 6), ((" ", 50, " "), 4), ((" ", 51, " "), 5), ((" ", 51, "A"), 5), ((" ", 52, " "), 7), (("W", 0, " "), 1), ], ), ( "C", 5, [ (("W", 0, " "), 1), (("H_NAG", 1, " "), 14), (("H_NAG", 2, " "), 14), (("H_NAG", 4, " "), 14), (("H_NAG", 3, " "), 14), ], ), ( " ", 76, [ (("W", 1, " "), 1), (("W", 2, " "), 1), (("W", 3, " "), 1), (("W", 4, " "), 1), (("W", 5, " "), 1), (("W", 6, " "), 1), (("W", 7, " "), 1), (("W", 8, " "), 1), (("W", 9, " "), 1), (("W", 10, " "), 1), (("W", 11, " "), 1), (("W", 12, " "), 1), (("W", 13, " "), 1), (("W", 14, " "), 1), (("W", 15, " "), 1), (("W", 16, " "), 1), (("W", 17, " "), 1), (("W", 18, " "), 1), (("W", 19, " "), 1), (("W", 20, " "), 1), (("W", 21, " "), 1), (("W", 22, " "), 1), (("W", 23, " "), 1), (("W", 24, " "), 1), (("W", 25, " "), 1), (("W", 26, " "), 1), (("W", 27, " "), 1), (("W", 28, " "), 1), (("W", 29, " "), 1), (("W", 30, " "), 1), (("W", 31, " "), 1), (("W", 32, " "), 1), (("W", 33, " "), 1), (("W", 34, " "), 1), (("W", 35, " "), 1), (("W", 36, " "), 1), (("W", 37, " "), 1), (("W", 38, " "), 1), (("W", 39, " "), 1), (("W", 40, " "), 1), (("W", 41, " "), 1), (("W", 42, " "), 1), (("W", 43, " "), 1), (("W", 44, " "), 1), (("W", 45, " "), 1), (("W", 46, " "), 1), (("W", 47, " "), 1), (("W", 48, " "), 1), (("W", 49, " "), 1), (("W", 50, " "), 1), (("W", 51, " "), 1), (("W", 52, " "), 1), (("W", 53, " "), 1), (("W", 54, " "), 1), (("W", 55, " "), 1), (("W", 56, " "), 1), (("W", 57, " "), 1), (("W", 58, " "), 1), (("W", 59, " "), 1), (("W", 60, " "), 1), (("W", 61, " "), 1), (("W", 62, " "), 1), (("W", 63, " "), 1), (("W", 64, " "), 1), (("W", 65, " "), 1), (("W", 66, " "), 1), (("W", 67, " "), 1), (("W", 68, " "), 1), (("W", 69, " "), 1), (("W", 70, " "), 1), (("W", 71, " "), 1), (("W", 72, " "), 1), (("W", 73, " "), 1), (("W", 74, " "), 1), (("W", 75, " "), 1), (("W", 77, " "), 1), ], ), ] for c_idx, chn in enumerate(chain_data): # Check chain ID and length chain = m1.get_list()[c_idx] self.assertEqual(chain.get_id(), chn[0]) self.assertEqual(len(chain), chn[1]) for r_idx, res in enumerate(chn[2]): residue = chain.get_list()[r_idx] # Check residue ID and atom count self.assertEqual(residue.get_id(), res[0]) self.assertEqual(len(residue), res[1]) disorder_lvl = residue.is_disordered() if disorder_lvl == 1: # Check the number of disordered atoms disordered_count = sum( 1 for atom in residue if atom.is_disordered() ) if disordered_count: self.assertEqual(disordered_count, res[2]) elif disorder_lvl == 2: # Point mutation -- check residue names self.assertEqual(residue.disordered_get_id_list(), res[2]) def test_structure_details(self): """Verify details of the parsed example PDB file.""" structure = self.structure self.assertEqual(len(structure), 2) # First model model = structure[0] self.assertEqual(model.id, 0) self.assertEqual(model.level, "M") self.assertEqual(len(model), 1) chain = model["A"] self.assertEqual(chain.id, "A") self.assertEqual(chain.level, "C") self.assertEqual(len(chain), 1) self.assertEqual(" ".join(residue.resname for residue in chain), "PCA") self.assertEqual( " ".join(atom.name for atom in chain.get_atoms()), "N CA CB CG DA OE C O CA ", ) self.assertEqual( " ".join(atom.element for atom in chain.get_atoms()), "N C C C D O C O CA" ) # Second model model = structure[1] self.assertEqual(model.id, 1) self.assertEqual(model.level, "M") self.assertEqual(len(model), 4) chain = model["A"] self.assertEqual(chain.id, "A") self.assertEqual(chain.level, "C") self.assertEqual(len(chain), 86) self.assertEqual( " ".join(residue.resname for residue in chain), "CYS ARG CYS GLY SER GLN GLY GLY GLY SER THR CYS " "PRO GLY LEU ARG CYS CYS SER ILE TRP GLY TRP CYS " "GLY ASP SER GLU PRO TYR CYS GLY ARG THR CYS GLU " "ASN LYS CYS TRP SER GLY GLU ARG SER ASP HIS ARG " "CYS GLY ALA ALA VAL GLY ASN PRO PRO CYS GLY GLN " "ASP ARG CYS CYS SER VAL HIS GLY TRP CYS GLY GLY " "GLY ASN ASP TYR CYS SER GLY GLY ASN CYS GLN TYR " "ARG CYS", ) self.assertEqual( " ".join(atom.name for atom in chain.get_atoms()), "C N CA C O CB CG CD NE CZ NH1 NH2 N CA C O CB SG N " "CA C O N CA C O CB OG N CA C O CB CG CD OE1 NE2 N CA " "C O N CA C O N CA C O N CA C O CB OG N CA C O CB OG1 " "CG2 N CA C O CB SG N CA C O CB CG CD N CA C O N CA C " "O CB CG CD1 CD2 N CA C O CB CG CD NE CZ NH1 NH2 N CA " "C O CB SG N CA C O CB SG N CA C O CB OG N CA C O CB " "CG1 CG2 CD1 N CA C O CB CG CD1 CD2 NE1 CE2 CE3 CZ2 " "CZ3 CH2 N CA C O N CA C O CB CG CD1 CD2 NE1 CE2 CE3 " "CZ2 CZ3 CH2 N CA C O CB SG N CA C O N CA C O CB CG " "OD1 OD2 N CA C O CB OG N CA C O CB CG CD OE1 OE2 N " "CA C O CB CG CD N CA C O CB CG CD1 CD2 CE1 CE2 CZ OH " "N CA C O CB SG N CA C O N CA C O CB CG CD NE CZ NH1 " "NH2 N CA C O CB OG1 CG2 N CA C O CB SG N CA C O CB " "CG CD OE1 OE2 N CA C O CB CG OD1 ND2 N CA C O CB CG " "CD CE NZ N CA C O CB SG N CA C O CB CG CD1 CD2 NE1 " "CE2 CE3 CZ2 CZ3 CH2 N CA C O CB OG N CA C O N CA C " "O CB CG CD OE1 OE2 N CA C O CB CG CD NE CZ NH1 NH2 " "N CA C O CB OG N CA C O CB CG OD1 OD2 N CA C O CB " "CG ND1 CD2 CE1 NE2 N CA C O CB CG CD NE CZ NH1 NH2 " "N CA C O CB SG N CA C O N CA C O CB N CA C O CB N " "CA C O CB CG1 CG2 N CA C O N CA C O CB CG OD1 ND2 " "N CA C O CB CG CD N CA C O CB CG CD N CA C O CB SG " "N CA C O N CA C O CB CG CD OE1 NE2 N CA C O CB CG " "OD1 OD2 N CA C O CB CG CD NE CZ NH1 NH2 N CA C O CB " "SG N CA C O CB SG N CA C O CB OG N CA C O CB CG1 CG2 " "N CA C O CB CG ND1 CD2 CE1 NE2 N CA C O N CA C O CB " "CG CD1 CD2 NE1 CE2 CE3 CZ2 CZ3 CH2 N CA C O CB SG N " "CA C O N CA C O N CA C O CA N C O CB CG OD1 ND2 N CA " "C O CB CG OD1 OD2 N CA C O CB CG CD1 CD2 CE1 CE2 CZ " "OH N CA C O CB SG N CA C O CB OG N CA C O N CA C O N " "CA C O CB CG OD1 ND2 N CA C O CB SG N CA C O CB CG " "CD OE1 NE2 N CA C O CB CG CD1 CD2 CE1 CE2 CZ OH N CA " "C O CB CG CD NE CZ NH1 NH2 N CA C O CB SG", ) self.assertEqual( " ".join(atom.element for atom in chain.get_atoms()), "C N C C O C C C N C N N N C C O C S N C C O N C C O " "C O N C C O C C C O N N C C O N C C O N C C O N C C " "O C O N C C O C O C N C C O C S N C C O C C C N C C " "O N C C O C C C C N C C O C C C N C N N N C C O C S " "N C C O C S N C C O C O N C C O C C C C N C C O C C " "C C N C C C C C N C C O N C C O C C C C N C C C C C " "N C C O C S N C C O N C C O C C O O N C C O C O N C " "C O C C C O O N C C O C C C N C C O C C C C C C C O " "N C C O C S N C C O N C C O C C C N C N N N C C O C " "O C N C C O C S N C C O C C C O O N C C O C C O N N " "C C O C C C C N N C C O C S N C C O C C C C N C C C " "C C N C C O C O N C C O N C C O C C C O O N C C O C " "C C N C N N N C C O C O N C C O C C O O N C C O C C " "N C C N N C C O C C C N C N N N C C O C S N C C O N " "C C O C N C C O C N C C O C C C N C C O N C C O C C " "O N N C C O C C C N C C O C C C N C C O C S N C C O " "N C C O C C C O N N C C O C C O O N C C O C C C N C " "N N N C C O C S N C C O C S N C C O C O N C C O C C " "C N C C O C C N C C N N C C O N C C O C C C C N C C " "C C C N C C O C S N C C O N C C O N C C O C N C O C " "C O N N C C O C C O O N C C O C C C C C C C O N C C " "O C S N C C O C O N C C O N C C O N C C O C C O N N " "C C O C S N C C O C C C O N N C C O C C C C C C C O " "N C C O C C C N C N N N C C O C S", ) class ParseRealPDB_tests(unittest.TestCase): """Testing with real PDB files.""" @classmethod def setUpClass(cls): cls.permissive = PDBParser() cls.strict = PDBParser(PERMISSIVE=False) def test_empty(self): """Parse an empty file.""" handle = StringIO() with self.assertRaises(ValueError) as context_manager: _ = self.permissive.get_structure("MT", handle) self.assertEqual(str(context_manager.exception), "Empty file.") def test_SMCRA(self): """Walk down the structure hierarchy and test parser reliability.""" s = self.permissive.get_structure("scr", "PDB/1A8O.pdb") for m in s: p = m.get_parent() self.assertEqual(s, p) for c in m: p = c.get_parent() self.assertEqual(m, p) for r in c: p = r.get_parent() self.assertEqual(c, p) for a in r: p = a.get_parent() self.assertEqual(r.get_resname(), p.get_resname()) def test_1A8O_strict(self): """Parse 1A8O.pdb file in strict mode.""" structure = self.strict.get_structure("example", "PDB/1A8O.pdb") self.assertEqual(len(structure), 1) model = structure[0] self.assertEqual(model.id, 0) self.assertEqual(model.level, "M") self.assertEqual(len(model), 1) chain = model["A"] self.assertEqual(chain.id, "A") self.assertEqual(chain.level, "C") self.assertEqual(len(chain), 158) self.assertEqual( " ".join(residue.resname for residue in chain), "MSE ASP ILE ARG GLN GLY PRO LYS GLU PRO PHE ARG " "ASP TYR VAL ASP ARG PHE TYR LYS THR LEU ARG ALA " "GLU GLN ALA SER GLN GLU VAL LYS ASN TRP MSE THR " "GLU THR LEU LEU VAL GLN ASN ALA ASN PRO ASP CYS " "LYS THR ILE LEU LYS ALA LEU GLY PRO GLY ALA THR " "LEU GLU GLU MSE MSE THR ALA CYS GLN GLY HOH HOH " "HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH " "HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH " "HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH " "HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH " "HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH " "HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH " "HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH " "HOH HOH", ) self.assertEqual( " ".join(atom.name for atom in chain.get_atoms()), "N CA C O CB CG SE CE N CA C O CB CG OD1 OD2 N CA " "C O CB CG1 CG2 CD1 N CA C O CB CG CD NE CZ NH1 " "NH2 N CA C O CB CG CD OE1 NE2 N CA C O N CA C O " "CB CG CD N CA C O CB CG CD CE NZ N CA C O CB CG " "CD OE1 OE2 N CA C O CB CG CD N CA C O CB CG CD1 " "CD2 CE1 CE2 CZ N CA C O CB CG CD NE CZ NH1 NH2 N " "CA C O CB CG OD1 OD2 N CA C O CB CG CD1 CD2 CE1 " "CE2 CZ OH N CA C O CB CG1 CG2 N CA C O CB CG OD1 " "OD2 N CA C O CB CG CD NE CZ NH1 NH2 N CA C O CB " "CG CD1 CD2 CE1 CE2 CZ N CA C O CB CG CD1 CD2 CE1 " "CE2 CZ OH N CA C O CB CG CD CE NZ N CA C O CB " "OG1 CG2 N CA C O CB CG CD1 CD2 N CA C O CB CG CD " "NE CZ NH1 NH2 N CA C O CB N CA C O CB CG CD OE1 " "OE2 N CA C O CB CG CD OE1 NE2 N CA C O CB N CA C " "O CB OG N CA C O CB CG CD OE1 NE2 N CA C O CB CG " "CD OE1 OE2 N CA C O CB CG1 CG2 N CA C O CB CG CD " "CE NZ N CA C O CB CG OD1 ND2 N CA C O CB CG CD1 " "CD2 NE1 CE2 CE3 CZ2 CZ3 CH2 N CA C O CB CG SE CE " "N CA C O CB OG1 CG2 N CA C O CB CG CD OE1 OE2 N " "CA C O CB OG1 CG2 N CA C O CB CG CD1 CD2 N CA C " "O CB CG CD1 CD2 N CA C O CB CG1 CG2 N CA C O CB " "CG CD OE1 NE2 N CA C O CB CG OD1 ND2 N CA C O CB " "N CA C O CB CG OD1 ND2 N CA C O CB CG CD N CA C " "O CB CG OD1 OD2 N CA C O CB SG N CA C O CB CG CD " "CE NZ N CA C O CB OG1 CG2 N CA C O CB CG1 CG2 " "CD1 N CA C O CB CG CD1 CD2 N CA C O CB CG CD CE " "NZ N CA C O CB N CA C O CB CG CD1 CD2 N CA C O N " "CA C O CB CG CD N CA C O N CA C O CB N CA C O CB " "OG1 CG2 N CA C O CB CG CD1 CD2 N CA C O CB CG CD " "OE1 OE2 N CA C O CB CG CD OE1 OE2 N CA C O CB CG " "SE CE N CA C O CB CG SE CE N CA C O CB OG1 CG2 N " "CA C O CB N CA C O CB SG N CA C O CB CG CD OE1 " "NE2 N CA C O OXT O O O O O O O O O O O O O O O O " "O O O O O O O O O O O O O O O O O O O O O O O O " "O O O O O O O O O O O O O O O O O O O O O O O O " "O O O O O O O O O O O O O O O O O O O O O O O O", ) self.assertEqual( " ".join(atom.element for atom in chain.get_atoms()), "N C C O C C SE C N C C O C C O O N C C O C C C C " "N C C O C C C N C N N N C C O C C C O N N C C O " "N C C O C C C N C C O C C C C N N C C O C C C O " "O N C C O C C C N C C O C C C C C C C N C C O C " "C C N C N N N C C O C C O O N C C O C C C C C C " "C O N C C O C C C N C C O C C O O N C C O C C C " "N C N N N C C O C C C C C C C N C C O C C C C C " "C C O N C C O C C C C N N C C O C O C N C C O C " "C C C N C C O C C C N C N N N C C O C N C C O C " "C C O O N C C O C C C O N N C C O C N C C O C O " "N C C O C C C O N N C C O C C C O O N C C O C C " "C N C C O C C C C N N C C O C C O N N C C O C C " "C C N C C C C C N C C O C C SE C N C C O C O C N " "C C O C C C O O N C C O C O C N C C O C C C C N " "C C O C C C C N C C O C C C N C C O C C C O N N " "C C O C C O N N C C O C N C C O C C O N N C C O " "C C C N C C O C C O O N C C O C S N C C O C C C " "C N N C C O C O C N C C O C C C C N C C O C C C " "C N C C O C C C C N N C C O C N C C O C C C C N " "C C O N C C O C C C N C C O N C C O C N C C O C " "O C N C C O C C C C N C C O C C C O O N C C O C " "C C O O N C C O C C SE C N C C O C C SE C N C C " "O C O C N C C O C N C C O C S N C C O C C C O N " "N C C O O O O O O O O O O O O O O O O O O O O O " "O O O O O O O O O O O O O O O O O O O O O O O O " "O O O O O O O O O O O O O O O O O O O O O O O O " "O O O O O O O O O O O O O O O O O O O O O", ) def test_duplicated_residue_permissive(self): """Catch exception on duplicated residue.""" data = ( "HETATM 6289 O HOH 5 28.182 -5.239 31.370 1.00 22.99 O\n" "HETATM 6513 O HOH 6 21.829 3.361 14.003 1.00 14.25 O\n" "HETATM 6607 O HOH 5 33.861 40.044 18.022 1.00 18.73 O\n" "END \n" ) with warnings.catch_warnings(record=True) as w: s = self.permissive.get_structure("example", StringIO(data)) self.assertEqual(len(w), 1) reslist = list(s.get_residues()) n_res = len(reslist) resids = [r.id[1] for r in reslist] self.assertEqual(n_res, 2) self.assertEqual(resids, [5, 6]) def test_duplicated_residue_strict(self): """Throw exception on duplicated residue.""" data = ( "HETATM 6289 O HOH 5 28.182 -5.239 31.370 1.00 22.99 O\n" "HETATM 6513 O HOH 6 21.829 3.361 14.003 1.00 14.25 O\n" "HETATM 6607 O HOH 5 33.861 40.044 18.022 1.00 18.73 O\n" "END \n" ) with self.assertRaises(PDBConstructionException): _ = self.strict.get_structure("example", StringIO(data)) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)