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# Copyright 2019-2020 by Konstantinos Zisis and Artemi Bendandi. All rights reserved.
#
# Converted by Konstantinos Zisis and Artemi Bendandi from an older unit test
# copyright 2009 by Eric Talevich.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Unit tests for the PQR parser in Bio.PDB module."""
from Bio.PDB.PDBParser import PDBParser
import unittest
import warnings
from io import StringIO
from Bio.PDB.PDBExceptions import PDBConstructionException, PDBConstructionWarning
from Bio.PDB.PDBIO import PDBIO
import tempfile
import os
class ParseSimplePQR(unittest.TestCase):
"""Parse a simple PQR entry and check behaviour for various problematic inputs."""
def test_single_input(self):
"""Test if a single ATOM entry correctly parsed."""
# Atom Entry
data = "ATOM 1 N PRO 1 000001 02.000 3.0000 -0.1000 1.0000 N\n"
# Get sole atom of this structure
parser = PDBParser(is_pqr=True) # default initialization
struct = parser.get_structure("test", StringIO(data))
atom = next(struct.get_atoms())
# Check that charge and radius are properly initallized
self.assertEqual(atom.get_charge(), -0.1)
self.assertEqual(atom.get_radius(), 1.0)
self.assertEqual(atom.get_occupancy(), None)
self.assertEqual(atom.get_bfactor(), None)
# Coordinates
for i in range(1, 3):
self.assertEqual(atom.get_coord()[i], i + 1)
def test_bad_xyz(self):
"""Test if bad coordinates exception is raised."""
# Atom Entry
data = "ATOM 1 N PRO 1 00abc1 02.000 3.0000 -0.1000 1.0000 N\n"
# Get sole atom of this structure
parser = PDBParser(is_pqr=True) # default initialization
self.assertRaises(
PDBConstructionException, parser.get_structure, "example", StringIO(data)
)
def test_bad_charge(self):
"""Test if missing or malformed charge case is handled correctly."""
# Test Entries
malformed = "ATOM 1 N PRO 1 000001 02.000 3.0000 -0.W000 1.0000 N\n"
missing = "ATOM 1 N PRO 1 000001 02.000 3.0000 1.0000 N\n"
# Malformed
parser = PDBParser(PERMISSIVE=True, is_pqr=True) # default initialization
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always", PDBConstructionWarning)
structure = parser.get_structure("test", StringIO(malformed))
atom = next(structure.get_atoms())
self.assertEqual(atom.get_charge(), None)
# Missing
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always", PDBConstructionWarning)
structure = parser.get_structure("test", StringIO(missing))
atom = next(structure.get_atoms())
self.assertEqual(atom.get_charge(), None)
# Test PERMISSIVE mode behaviour
parser = PDBParser(PERMISSIVE=False, is_pqr=True) # default initialization
self.assertRaises(
PDBConstructionException,
parser.get_structure,
"example",
StringIO(malformed),
)
def test_bad_radius(self):
"""Test if missing, malformed or negative radius case is handled correctly."""
# Test Entries
malformed = "ATOM 1 N PRO 1 000001 02.000 3.0000 -0.1000 1.a00f N\n"
missing = "ATOM 1 N PRO 1 000001 02.000 3.0000 -0.1000 N\n"
negative = "ATOM 1 N PRO 1 000001 02.000 3.0000 -0.1000 -1.0000 N\n"
# Malformed
parser = PDBParser(PERMISSIVE=True, is_pqr=True) # default initialization
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always", PDBConstructionWarning)
structure = parser.get_structure("test", StringIO(malformed))
atom = next(structure.get_atoms())
self.assertEqual(atom.get_radius(), None)
# Missing
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always", PDBConstructionWarning)
structure = parser.get_structure("test", StringIO(missing))
atom = next(structure.get_atoms())
self.assertEqual(atom.get_radius(), None)
# Negative
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always", PDBConstructionWarning)
structure = parser.get_structure("test", StringIO(negative))
atom = next(structure.get_atoms())
self.assertEqual(atom.get_radius(), None)
# Test PERMISSIVE mode behaviour
parser = PDBParser(PERMISSIVE=False, is_pqr=True) # default initialization
self.assertRaises(
PDBConstructionException,
parser.get_structure,
"example",
StringIO(malformed),
)
self.assertRaises(
PDBConstructionException,
parser.get_structure,
"example",
StringIO(negative),
)
self.assertRaises(
PDBConstructionException, parser.get_structure, "example", StringIO(missing)
)
class WriteTest(unittest.TestCase):
"""Test if the PDBIO module correctly exports .pqr files."""
def setUp(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore", PDBConstructionWarning)
# Open a parser in permissive mode and parse an example file
self.pqr_parser = PDBParser(PERMISSIVE=1, is_pqr=True)
self.example_structure = self.pqr_parser.get_structure(
"example", "PQR/1A80.pqr"
)
def test_pdbio_write_pqr_structure(self):
"""Write a full structure using PDBIO."""
# Create a PDBIO object in pqr mode with example_structure as an argument
io = PDBIO(is_pqr=True)
io.set_structure(self.example_structure)
# Write to a temporary file
filenumber, filename = tempfile.mkstemp()
os.close(filenumber)
try:
# Export example_structure to a temp file
io.save(filename)
# Parse exported structure
output_struct = self.pqr_parser.get_structure("1a8o", filename)
# Comparisons
self.assertEqual(
len(output_struct), len(self.example_structure)
) # Structure Length
original_residues = len(list(self.example_structure.get_residues()))
parsed_residues = len(list(output_struct.get_residues()))
self.assertEqual(parsed_residues, original_residues) # Number of Residues
# Atom-wise comparison
original_atoms = self.example_structure.get_atoms()
for atom in output_struct.get_atoms():
self.assertEqual(atom, next(original_atoms))
finally:
os.remove(filename)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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