args = parser.parse_args()
do = os.system
cd = os.chdir
with open('commandline_args.txt', 'a') as f:
f.write(' '.join(sys.argv))
f.write('\n')
# simulation_platform = "CPU" # OpenCL, CUDA, CPU, or Reference
# simulation_platform = "OpenCL"
simulation_platform = args.platform
platform = Platform.getPlatformByName(simulation_platform)
if simulation_platform == "CPU":
if args.thread != -1:
platform.setPropertyDefaultValue("Threads", str(args.thread))
print(
f"{simulation_platform}: {platform.getPropertyDefaultValue('Threads')} threads"
)
proteinName = pdb_id = args.protein
chain = args.chain.upper()
pdb = f"{pdb_id}.pdb"
if chain == "-1":
chain = getAllChains("crystal_structure.pdb")
print("Chains to simulate: ", chain)
if args.to != "./":
os.system(f"mkdir -p {args.to}")
# os.system(f"cp {pdb} {args.to}/{pdb}")
args = parser.parse_args()
do = os.system
cd = os.chdir
with open('commandline_args.txt', 'a') as f:
f.write(' '.join(sys.argv))
f.write('\n')
simulation_platform = "CPU" # OpenCL, CUDA, CPU, or Reference
simulation_platform = "OpenCL"
platform = Platform.getPlatformByName(simulation_platform)
if simulation_platform == "CPU":
platform.setPropertyDefaultValue("Threads", "1")
print(f"{simulation_platform}: {platform.getPropertyDefaultValue('Threads')} threads")
proteinName = pdb_id = args.protein
chain=args.chain.upper()
pdb = f"{pdb_id}.pdb"
if chain == "-1":
chain = getAllChains("crystal_structure.pdb")
print("Chains to simulate: ", chain)
input_pdb_filename, cleaned_pdb_filename = prepare_pdb(pdb, chain)
ensure_atom_order(input_pdb_filename)
getSeqFromCleanPdb(input_pdb_filename, chains=chain)
