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|
# 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 <Residue ARG het= resseq=2 icode= > 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 <Residue HOH het=W resseq=67 icode= > 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)
|
