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('..')
def main():
parser = argparse.ArgumentParser(
description=""
"Prepares the simulation system by performing the following actions:\n"
" - ligand parameterisation (with antechamber/prmchk2)\n"
" - pdb protonation (apart from ligands, they need to "
" be protonated already!)\n"
" - tleap to solvate and write starting parm7/rst7 (top/rst)\n\n",
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument("name", help="name of the job")
parser.add_argument("pdb",
help="protonated PDB file",
type=argparse.FileType())
parser.add_argument("ligand",
help="name of the residue to be used as the ligand")
parser.add_argument("charge", help="charge of the ligand", type=int)
parser.add_argument("params",
help="JSON file with advanced parameters",
type=argparse.FileType(),
nargs='?')
args = parser.parse_args()
job_name = args.name
ligand_name = args.ligand
ligand_charge = args.charge
params = {
'antechamber': {
'ligand': args.ligand,
'charge': args.charge,
'ligand_chainID': "L",
'ligand_index': 1,
},
'propka': {
'with_propka': True,
'ph': 7.0,
'ph_offset': 0.7,
},
'tleap': {
'template': 'sphere',
'solvent_radius': 20.0,
'solvent_closeness': 0.75,
'include': []
}
}
if args.params is not None:
params = utils.merge_dicts_of_dicts(params, json.load(args.params))
args.params.close()
params['tleap']['include'] = [
os.path.abspath(path) for path in params['tleap']['include']
]
if os.path.exists(job_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(job_name),
file=sys.stderr)
sys.exit(1)
print("Starting PREP protocol in {}/".format(job_name))
sys.stdout.flush()
utils.set_working_directory(job_name)
pdb = pdb_utils.Pdb(args.pdb)
ligand_index = params['antechamber']['ligand_index']
ligand_atoms = get_ligand_atoms(pdb, ligand_name, ligand_index)
# Only generate ligand frcmod if it is not found in include paths
ligand_frcmod = utils.file_in_paths(ligand_name + '.frcmod',
params['tleap']['include'])
antechamber = wrappers.AntechamberWrapper(
pdb_utils.Pdb(atoms=ligand_atoms),
ligand_name,
ligand_charge,
create_frcmod=ligand_frcmod is None)
sys.stdout.flush()
if ligand_frcmod is None:
params['tleap']['include'].append(antechamber.working_directory)
# Change ligand chain ID to ligand_chainID
ligand_chainID = params['antechamber']['ligand_chainID']
pdb_utils.modify_atoms(ligand_atoms, 'chainID', ligand_chainID)
# Run pdb4amber and reduce
reduceResults = wrappers.Pdb4AmberReduceWrapper(pdb)
sys.stdout.flush()
pdb = reduceResults.pdb
# Run propka31 if requested and found
if params['propka']['with_propka']:
pdb = run_propka(pdb=pdb,
ph=params['propka']['ph'],
ph_offset=params['propka']['ph_offset'])
sys.stdout.flush()
ligand = pdb.get_residues_by_name(ligand_name)[ligand_index - 1]
params['tleap']['name'] = os.path.basename(job_name)
params['tleap']['pdb'] = pdb
params['tleap']['ligand'] = ligand
tleap = wrappers.TleapWrapper(params['tleap']['template'],
params['tleap']['include'],
reduceResults.nonprot_residues,
params['tleap'])
sys.stdout.flush()
os.system("cp {} .".format(tleap.top))
os.system("cp {} .".format(tleap.rst))
print("Finished PREP protocol.")
def main():
parser = argparse.ArgumentParser(
description=""
"Performs a fast equilibration of a simulation system "
"prepared using prep.py. Does the following:"
" - initial brief minimization of hydrogens (100 steps)"
" - simulated annealing (10000 steps)"
" - final brief minimization (100 steps)",
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument("system",
help="name of the simulation system (as in prep.py)")
parser.add_argument('-relax', action='store_true')
parser.add_argument("params",
help="additional parameters",
type=argparse.FileType(),
nargs='?')
args = parser.parse_args()
if not os.path.isdir(args.system):
print("Directory {} is not found. Please run prep first.".format(
args.system),
file=sys.stderr)
print(
"If you HAVE run prep.sh, please run dynam.py "
"from the same directory as prep.sh.",
file=sys.stderr)
exit(1)
params = {"steps": 25000, "central_atom": None}
if args.params is not None:
params = {**params, **json.load(args.params)}
args.params.close()
prep_params_path = os.path.join(args.system, 'tleap', 'params')
if os.path.isfile(prep_params_path):
with open(prep_params_path, 'r') as f:
params = {**params, **json.load(f)}
mode = 'relax' if args.relax else 'dynam'
if mode == 'relax':
belly_radius = params["solvent_radius"] - 8
else:
belly_radius = params["solvent_radius"] - 4
bellymask = ":{} <@{}".format(params["central_atom"], belly_radius)
sander_params = {**params, "bellymask": bellymask}
relax_params = [{
"name": "minimize_h_all",
"template": "minh"
}, {
"name": "minimize_h_in_sphere",
"template": "minh_ibelly",
"params": sander_params
}, {
"name": "annealing_with_restraints",
"template": "sa_ca",
"params": sander_params
}, {
"name": "annealing_without_restraints",
"template": "sa",
"params": sander_params
}, {
"name": "minimize_all_in_sphere",
"template": "min_ibelly",
"params": sander_params
}]
dynam_params = [
{
"name": "heat",
"template": "heat",
"params": sander_params
},
{
"name": "md",
"template": "md",
"params": sander_params,
"monitor": True
},
{
"name": "minimize",
"template": "min",
"params": sander_params
},
]
tleap_dir = os.path.abspath(os.path.join(args.system, 'tleap'))
prmtop = "{}/{}.top".format(tleap_dir, args.system)
if mode == 'relax':
crd = "{}/{}.rst".format(tleap_dir, args.system)
sanderflow_params = relax_params
working_dir = '{}/{}'.format(args.system, 'relax')
else:
relax_dir = os.path.abspath(os.path.join(args.system, 'relax'))
crd = "{}/{}_relax.rst".format(relax_dir, args.system)
sanderflow_params = dynam_params
working_dir = '{}/{}'.format(args.system, get_dynam_dir(args.system))
utils.set_working_directory(working_dir)
status, result = sanderflow.run(prmtop, crd, sanderflow_params)
if not status:
sys.exit(1)
final_crd = "{system}_{mode}.rst".format(system=args.system, mode=mode)
os.system("cp {crd} {final_crd}".format(crd=result.crd,
final_crd=final_crd))