def test_pdb_fixer(self):
"""
It checks the PDB fixer prior parsing a PDB input file for
a peleffy Molecule.
"""
from .utils import compare_blocks
# Check default
molecule = Molecule()
assert molecule.fix_pdb is True, \
'Unexpected default settings for the PDB fixer'
# Activate fixer
molecule = Molecule(fix_pdb=True)
ref_path = get_data_file_path('tests/ligSUV_fixed.pdb')
path1 = get_data_file_path('tests/ligSUV_no_elements1.pdb')
path2 = get_data_file_path('tests/ligSUV_no_elements2.pdb')
ref_pdb_block = molecule._read_and_fix_pdb(ref_path)
pdb_block1 = molecule._read_and_fix_pdb(path1)
pdb_block2 = molecule._read_and_fix_pdb(path2)
compare_blocks(ref_pdb_block, pdb_block1, (76, 78))
compare_blocks(ref_pdb_block, pdb_block2, (76, 78))
# Deactivate fixer
molecule = Molecule(fix_pdb=False)
ref_path = get_data_file_path('tests/ligSUV_fixed.pdb')
path1 = get_data_file_path('tests/ligSUV_no_elements1.pdb')
path2 = get_data_file_path('tests/ligSUV_no_elements2.pdb')
ref_pdb_block = molecule._read_and_fix_pdb(ref_path)
pdb_block1 = molecule._read_and_fix_pdb(path1)
pdb_block2 = molecule._read_and_fix_pdb(path2)
with pytest.raises(AssertionError):
compare_blocks(ref_pdb_block, pdb_block1, (76, 78))
with pytest.raises(AssertionError):
compare_blocks(ref_pdb_block, pdb_block2, (76, 78))
def test_pdb_fixer_logger_messages(self):
"""It checks the logger messages of the PDB fixer."""
from peleffy.utils import Logger
import io
molecule = Molecule(fix_pdb=True)
# Check logger messages
path3 = get_data_file_path('tests/ligSUV_no_elements3.pdb')
import logging
# Force a hard reset of logging library and the logger it manages
from importlib import reload
logging.shutdown()
reload(logging)
# Initiate logger
log = Logger()
# Try the default level (INFO)
# Catch logger messages to string buffer
with io.StringIO() as buf:
# Add custom handler to logger
log_handler = logging.StreamHandler(buf)
log._logger.handlers = list()
log._logger.addHandler(log_handler)
_ = molecule._read_and_fix_pdb(path3)
# Get string from buffer
output = buf.getvalue()
assert output == "Warning: input PDB has no information " \
+ "about atom elements and they were inferred from " \
+ "atom names. " \
+ "Please, verify that the resulting elements are " \
+ "correct\n" \
+ "Error: PDB could not be fixed\n"
