def __init__(self,
pdb,
name,
charge=0,
working_directory="antechamber",
create_frcmod=True):
amberhome = get_amberhome()
utils.set_working_directory(working_directory)
pdb.to_filename('ligand.pdb')
antechamber_command = (amberhome + "/bin/antechamber " +
"-i ligand.pdb -fi pdb -o {name}.prepc "
"-fo prepc -rn {name} -c bcc -nc {charge} "
"-at gaff2".format(name=name, charge=charge))
utils.run_in_shell(antechamber_command, 'antechamber.out')
utils.check_file(
name + '.prepc',
"Antechamber failed to generate {name}.prepc file".format(
name=name))
self.working_directory = os.getcwd()
if create_frcmod:
parmchk_command = (
amberhome + "/bin/parmchk2 " +
"-i {name}.prepc -f prepc -o {name}.frcmod".format(name=name))
utils.run_in_shell(parmchk_command, 'parmchk2.out')
# TODO: check for ATTN warnings
os.chdir('..')
def __init__(self, pychemsh, working_directory='chemshell'):
# get path information as needed
utils.set_working_directory(working_directory)
# get input files
chemsh_input = ('../' + pychemsh + '.py')
# run Py-ChemShell command
chemshell_command = ('chemsh ' + chemsh_input)
utils.run_in_shell(chemshell_command, "chemshell.out")
def __init__(self,
pdb,
working_directory="pdb4amber_reduce",
pdb4amber_extra_args="",
reduce_extra_args=""):
amberhome = get_amberhome()
utils.set_working_directory(working_directory)
pdb.to_filename('input.pdb')
pdb4amber_command = (amberhome + "/bin/pdb4amber " +
pdb4amber_extra_args +
" -i input.pdb -o pdb4amber.pdb --nohyd")
utils.run_in_shell(pdb4amber_command, 'pdb4amber.out')
reduce_command = (amberhome + "/bin/reduce " + reduce_extra_args +
" -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'])
]
os.chdir('..')
def __init__(self,
template_name,
include=[],
nonprot_residues=[],
params={},
working_directory='tleap'):
utils.set_working_directory(working_directory)
enlighten_path = os.path.dirname(__import__(__name__).__file__)
tleap_module_path = os.path.join(enlighten_path, 'tleap')
template_path = os.path.join(tleap_module_path, template_name + '.in')
template_contents = None
if os.path.isfile(template_path):
with open(template_path) as f:
template_contents = f.read()
params['include'] = get_tleap_includes(include, nonprot_residues)
template_module = getattr(
__import__('enlighten2.tleap', fromlist=[template_name]),
template_name)
params['pdb'].to_filename('input.pdb')
with open('tleap.in', 'w') as f:
f.write(template_module.run(params, template_contents))
utils.run_in_shell('tleap -f tleap.in', 'tleap.log')
try:
check_result = template_module.check(params, self)
if check_result:
sys.exit(check_result)
except AttributeError:
pass
if 'export' in params:
with open('params', 'w') as f:
json.dump(params['export'], f)
os.chdir('..')
def __init__(self, pdb, ph=7.0, ph_offset=0.7, working_directory="propka"):
utils.set_working_directory(working_directory)
pdb.to_filename('input.pdb')
utils.run_in_shell("propka31 input.pdb", "propka31.out")
with open('input.pka') as f:
propka_results = parse_propka_output(f)
self.pdb = pdb.copy()
residues = self.pdb.residues()
self.prot_pka = ph + ph_offset
self.deprot_pka = ph - ph_offset
self.prot_list = []
self.deprot_list = []
for hash, pka_entry in propka_results.items():
if hash not in residues:
continue
if prot_residue(pka_entry, self.prot_pka):
pdb_utils.modify_atoms(residues[hash], 'resName',
PROT_DICT[pka_entry['resName']])
self.prot_list.append(pka_entry)
if deprot_residue(pka_entry, self.deprot_pka):
pdb_utils.modify_atoms(residues[hash], 'resName',
DEPROT_DICT[pka_entry['resName']])
self.deprot_list.append(pka_entry)
# Need to remove hydrogens added by reduce on deprotonated
# residues - else top-file creation will fail.
self.pdb.remove_atom(
pdb_utils.find_atom(residues[hash],
lambda atom: 'new' in atom['extras']))
# Also remove HZ1 atoms from deprotonated LYS and CYS
if pka_entry['resName'] == 'LYS':
self.pdb.remove_atom(
pdb_utils.find_atom(
residues[hash],
lambda atom: atom['name'] == 'HZ1'))
if pka_entry['resName'] == 'CYS':
self.pdb.remove_atom(
pdb_utils.find_atom(residues[hash],
lambda atom: atom['name'] == 'HG'))
PRINT_PKA_FORMAT = "{resName:>6}{resSeq:>4}{chainID:>2}{pKa:>9.2f}"
if len(self.prot_list) > 0:
print("The following ASP/GLU residues have predicted pKa's above "
"{:4.2f} and will be protonated (on OD2/OE2):".format(
self.prot_pka))
print(" pKa")
for pka_entry in self.prot_list:
print(PRINT_PKA_FORMAT.format(**pka_entry))
if len(self.deprot_list) > 0:
print("The following CYS/LYS residues have predicted pKa's below "
"{:4.2f} and will be deprotonated:".format(self.deprot_pka))
print(" pKa")
for pka_entry in self.deprot_list:
print(PRINT_PKA_FORMAT.format(**pka_entry))
os.chdir('..')