def testUnrecognizableWithoutRaising(self):
"""
An unrecognizable name must return the original name (not raise
a RuntimeError) if raiseOnError is passed as False.
"""
self.assertEqual('x' * 10,
pdbNameToPythonName('x' * 10, raiseOnError=False))
def testCanonicalPDBWithColonSequenceSuffix(self):
"""
A DXXX:X:sequence PDB name must be converted as expected.
"""
self.assertEqual('pdb_1mla_a', pdbNameToPythonName('1MLA:A:sequence'))
def testCanonicalPDBWithUnderscore(self):
"""
A canonical DXXX_X PDB name must be converted as expected.
"""
self.assertEqual('pdb_1mla_a', pdbNameToPythonName('1MLA_A'))
def testCanonicalPDBWithHyphen(self):
"""
A canonical DXXX-X PDB name must be converted as expected.
"""
self.assertEqual('pdb_1mla_a', pdbNameToPythonName('1MLA-A'))
def testCanonicalPDBLowerCase(self):
"""
A canonical DXXX:X PDB name in lower case must be converted as
expected.
"""
self.assertEqual('pdb_1mla_a', pdbNameToPythonName('1mla:a'))
def testCanonicalPDBUpperCase(self):
"""
A canonical DXXX:X PDB name must be converted as expected.
"""
self.assertEqual('pdb_1mla_a', pdbNameToPythonName('1MLA:A'))
resolution = pdbResolutions[pdbId]
except KeyError:
print('PDB id %r has unknown resolution!' % pdbId, file=sys.stderr)
else:
if resolution == NMR_RESOLUTION and discardNMR:
nmr.add(pdbId)
continue
if resolution > maxResolution:
poorResolution.add(pdbId)
continue
if minLength > 0 and len(sequence) < minLength:
tooShort.add(pdbId)
continue
sequence.id = pdbNameToPythonName(sequence.id)
print(sequence.toString(), end='')
if deleted:
if args.printIgnoredIds:
print('%d sequence ids ignored due to being marked as obsolete in '
'PDB: %s.' % (len(deleted), ', '.join(sorted(deleted))),
file=sys.stderr)
else:
print('%d sequence ids ignored due to being PDB marked as obsolete in '
'PDB.' % len(deleted),
file=sys.stderr)
if tooShort:
if args.printIgnoredIds: