def __init__(self, pdb, working_directory="pdb4amber_reduce"):
amberhome = get_amberhome()
utils.set_working_directory(working_directory)
pdb.to_filename('input.pdb')
pdb4amber_command = (amberhome + "/bin/pdb4amber "
"-i input.pdb -o pdb4amber.pdb --nohyd --dry")
utils.run_in_shell(pdb4amber_command, 'pdb4amber.out')
reduce_command = (amberhome + "/bin/reduce "
"-build -nuclear pdb4amber.pdb")
utils.run_in_shell(reduce_command, 'reduce.pdb')
with open('reduce.pdb') as f:
self.pdb = pdb_utils.Pdb(f)
renamed_histidines = get_renamed_histidines(self.pdb)
residues = self.pdb.residues()
for res_hash, res_name in renamed_histidines.items():
pdb_utils.modify_atoms(residues.get(res_hash, []), 'resName',
res_name)
# Remove hydrogens on HETATMs
self.pdb.atoms = [
atom for atom in self.pdb.atoms
if (atom['record'] != 'HETATM' or 'new' not in atom['extras'])
]
# Remove hydrogens added by reduce to non-protein residues
with open('pdb4amber_nonprot.pdb') as f:
self.nonprotPdb = pdb_utils.Pdb(f)
self.nonprot_residues = set(atom['resName']
for atom in self.nonprotPdb.atoms)
self.pdb.atoms = [
atom for atom in self.pdb.atoms
if (atom['resName'] not in self.nonprot_residues
or 'new' not in atom['extras'])
]
# store crystalline waters
with open('pdb4amber_water.pdb') as f:
self.waterPdb = pdb_utils.Pdb(f)
os.chdir('..')
def test_get_renamed_histidines(self):
renamed_histidines = {
'A_262_HIS': 'HIE',
'A_1_HIS': 'HIE',
'A_71_HIS': 'HIE',
'A_87_HIS': 'HID',
'A_128_HIS': 'HIE',
'A_133_HIS': 'HIE'
}
with open('tests/test_files/reduce.pdb') as f:
reducePdb = pdb_utils.Pdb(f)
self.assertEqual(wrappers.get_renamed_histidines(reducePdb),
renamed_histidines)
def test_propka_call(self, mock_os, mock_os_path, mock_print, mock_utils):
setup_mock(mock_os, mock_os_path)
with open('tests/test_files/reduce.pdb') as f:
pdb = pdb_utils.Pdb(f)
pdb.to_filename = mock.MagicMock()
with open('tests/test_files/propka.pka') as f:
mock_open = iterable_mock_open(read_data=f.read())
with mock.patch('wrappers.open', mock_open):
result = wrappers.PropkaWrapper(pdb)
residues = result.pdb.residues()
self.assertEqual(len(result.prot_list), 1)
self.assertEqual(len(result.deprot_list), 0)
self.assertNotIn('A_189_ASP', residues)
self.assertIn('A_189_ASH', residues)
self.assertEqual(len(residues['A_189_ASH']), 12)
def setUpClass(cls):
cls.atom_string = ("ATOM 278 HG2 ARG A 36 "
"17.074 -2.417 17.463 1.00 11.39"
" H new")
cls.parsed_atom = {
'record': "ATOM",
'serial': 278,
'name': "HG2",
'altLoc': "",
'resName': "ARG",
'chainID': "A",
'resSeq': 36,
'iCode': "",
'x': 17.074,
'y': -2.417,
'z': 17.463,
'occupancy': 1.0,
'tempFactor': 11.39,
'element': "H",
'charge': "",
'extras': " new"
}
with open('tests/test_files/full.pdb') as f:
cls.pdb = pdb_utils.Pdb(f)
if args.params is not None:
params = utils.merge_dicts_of_dicts(params, json.load(args.params))
args.params.close()
print("Starting PREP protocol in {}/".format(pdb_name))
if os.path.exists(pdb_name):
print(
"It appears you've already (attempted to) run prep.py with {0}. "
"Delete folder {0} or rename pdb if you want to run it again.".format(
pdb_name))
sys.exit()
utils.set_working_directory(pdb_name)
pdb = pdb_utils.Pdb(args.pdb)
ligands = pdb.get_residues_by_name(ligand_name)
if len(ligands) == 0:
raise ValueError("No ligands found")
ligand_index = params['antechamber']['ligand_index']
if ligand_index > len(ligands):
raise ValueError("ligand_index is larger than the number of ligands")
ligand_atoms = ligands[ligand_index - 1]
if len(ligands) > 1:
print("More than one ligand detected. Using coordinates from the ligand"
" with chainID={} and resSeq={}".format(ligand_atoms[0]['chainID'],
ligand_atoms[0]['resSeq']))