def parse_propka_output(file):
while next(file) != "SUMMARY OF THIS PREDICTION\n":
pass
next(file)
return {
pdb_utils.residue_hash(entry): entry
for entry in map(line_to_pka_entry, file) if entry is not None
}
def get_renamed_histidines(pdb):
RENAME_DICT = {'no HE2': 'HID', 'no HD1': 'HIE', 'bothHN': 'HIP'}
renamed_histidines = {} # dict of residue_hash: new_name pairs
for line in pdb.other:
if line[:9] != 'USER MOD' or line[25:28] != 'HIS':
continue
his_name = RENAME_DICT.get(line[39:45])
if his_name is None:
continue
his_hash = pdb_utils.residue_hash({
'chainID': line[19],
'resSeq': int(line[20:24]),
'resName': "HIS"
})
renamed_histidines[his_hash] = his_name
return renamed_histidines
def test_residue_hash(self):
self.assertEqual(pdb_utils.residue_hash(self.parsed_atom), "A_36_ARG")