def do_run(self, line):
"""run
run PoC module"""
_fb = self._set_argument()
if not _fb:
print_info("wrong", "[-]", "red")
return
fb = prepare(_fb)
results = osprey.start(fb)
self._print_result(results)
def main(args):
# Record relevant parameters
data = dict.fromkeys(design.HEADERS)
print args
data["status"] = design.STATUS.ESTIMATING.value
data["slurm out"] = args.slurm_out
data["slurm err"] = args.slurm_err
data["design name"] = design.get_emat_name(args.cfsfile)
data["host"] = socket.gethostname()
data["memory (GB)"] = design.HEAP_GB
data["epsilon"] = args.epsilon
data["algorithm"] = design.ALGO_LIST[args.algo]
# Print out misc information
print("Output_file: %s" % args.output)
print("Emat id for this design: %s" % data["design name"])
print("Running on host: %s" % socket.gethostname())
sys.stdout.flush()
osprey.start(
heapSizeMiB=floor(design.HEAP_GB * 953.674), # Convert to MiB
allowRemoteManagement=False)
conf_spaces = design.make_confspace(args.cfsfile, data)
shark = design.setup_design(args.num_cores, conf_spaces, args.epsilon,
args.numseqs, args.algo, data)
# Write out JSON file before beginning computation
with open(os.path.abspath(args.output), 'w') as f:
f.write(json.dumps(data, indent=4, sort_keys=True) + '\n')
design.run(shark, data)
# Print out JSON output
with open(os.path.abspath(args.output), 'w') as f:
f.write(json.dumps(data, indent=4, sort_keys=True) + '\n')
print("Finished writing")
import osprey osprey.start() osprey.printGpuInfo()
def main(args):
# Record relevant parameters
data = dict.fromkeys(design.HEADERS)
print args
data["status"] = design.STATUS.ESTIMATING.value
data["slurm out"] = args.slurm_out
data["slurm err"] = args.slurm_err
data["design name"] = design.get_emat_name(args.cfsfile)
data["host"] = socket.gethostname()
data["memory (GB)"] = design.HEAP_GB
data["epsilon"] = args.epsilon
data["algorithm"] = design.ALGO_LIST[args.algo]
# Print out misc information
print("Output_file: %s" % args.output)
print("Emat id for this design: %s" % data["design name"])
print("Running on host: %s" % socket.gethostname())
sys.stdout.flush()
osprey.start(heapSizeMiB=floor(design.HEAP_GB * 953.674),
allowRemoteManagement=False) # Convert to MiB
conf_spaces = design.make_confspace(args.cfsfile, data)
# Write out JSON file before beginning computation
with open(os.path.abspath(args.output), 'w') as f:
f.write(json.dumps(data, indent=4, sort_keys=True) + '\n')
print("\nRunning Algorithm")
design_start = datetime.now()
data['start_time'] = design_start.strftime(design.DATETIME_FORMAT)
try:
pfunc = design.make_complex_pfunc(args.num_cores, conf_spaces,
args.epsilon, args.numseqs,
args.algo, data)
if args.algo == 2:
pfunc.setReportProgress(True)
pfunc.compute(2147483647)
elif args.algo == 1:
pfunc.compute()
data["status"] = design.STATUS.FINISHED.value
except (jpype.JavaException, AttributeError) as e:
data["status"] = design.STATUS.ERROR.value
print str(e)
print e.stacktrace()
data['errmsg'] = str(e)
design_end = datetime.now()
data['end_time'] = design_end.strftime(design.DATETIME_FORMAT)
data['runtime (s)'] = (design_end - design_start).total_seconds()
print("Algorithm Runtime (s): %d" % data['runtime (s)'])
# Print out JSON output
with open(os.path.abspath(args.output), 'w') as f:
f.write(json.dumps(data, indent=4, sort_keys=True) + '\n')
print("Finished writing")
import osprey
osprey.start(heapSizeMiB=200000)
# choose a forcefield
ffparams = osprey.ForcefieldParams()
# INSERT SCRIPT OUTPUT HERE
mol = osprey.readPdb('../../pdb/1GWC.shell.pdb')
pos = [0, 1, 2, 3, 4, 5, 6, 7, 8]
posP = [0, 1, 2, 3, 4]
posL = [5, 6, 7, 8]
resNumsPL = ['C53', 'C64', 'C67', 'C71', 'C78', 'B93', 'B100', 'B101', 'B104']
resNumsP = ['C53', 'C64', 'C67', 'C71', 'C78']
resNumsL = ['B93', 'B100', 'B101', 'B104']
startResP = 'C7'
endResP = 'C80'
startResL = 'B89'
endResL = 'B161'
AATypeOptions = [['HID', 'ASP', 'GLU', 'SER', 'THR', 'ASN', 'GLN', 'ALA', 'VAL', 'ILE', 'LEU', 'CYS', 'GLY'], ['ALA', 'LEU', 'ILE', 'VAL', 'PHE', 'TYR', 'MET', 'GLU', 'ASP','HID', 'ASN', 'GLN', 'GLY'], ['CYS', 'SER', 'THR', 'ASN', 'GLN', 'HIE', 'ALA', 'VAL', 'ILE', 'LEU', 'PHE', 'TYR', 'GLY'], ['ILE', 'ALA', 'LEU', 'VAL', 'PHE', 'TYR', 'MET','GLU', 'ASP', 'HID', 'ASN', 'GLN', 'GLY'], ['GLU', 'ASP', 'PHE', 'TYR', 'ALA', 'VAL', 'ILE', 'LEU', 'HIE', 'HID', 'ASN', 'GLN', 'GLY'], ['TYR', 'PHE', 'ALA', 'VAL', 'ILE','LEU', 'GLU', 'ASP', 'HID', 'HIE', 'ASN', 'GLN', 'GLY'], ['PHE', 'TYR', 'ALA', 'VAL', 'ILE', 'LEU', 'GLU', 'ASP', 'HID', 'HIE', 'ASN', 'GLN', 'GLY'], ['TRP', 'ALA', 'VAL','ILE', 'LEU', 'PHE', 'TYR', 'MET', 'SER', 'THR', 'ASN', 'GLN', 'GLY'], ['TYR', 'PHE', 'ALA', 'VAL', 'ILE', 'LEU', 'GLU', 'ASP', 'HID', 'HIE', 'ASN', 'GLN', 'GLY']]
# make sure all strands share the same template library (including wild-type rotamers)
templateLib = osprey.TemplateLibrary(ffparams.forcefld, moleculesForWildTypeRotamers=[mol])
# define the protein strand
ligand = osprey.Strand(mol, templateLib=templateLib, residues=[startResL, endResL])
for i in range(0,len(resNumsL)):
ligand.flexibility[resNumsL[i]].setLibraryRotamers(*AATypeOptions[posL[i]]).addWildTypeRotamers().setContinuous()
# define the ligand strand
protein = osprey.Strand(mol, templateLib=templateLib, residues=[startResP, endResP])
for i in range(0,len(resNumsP)):
def main(args):
# Record relevant parameters
data = dict.fromkeys(design.HEADERS)
print args
data["status"] = design.STATUS.ESTIMATING.value
data["slurm out"] = args.slurm_out
data["slurm err"] = args.slurm_err
data["design name"] = design.get_emat_name(args.cfsfile)
data["host"] = socket.gethostname()
data["memory (GB)"] = design.HEAP_GB
data["epsilon"] = args.epsilon
data["algorithm"] = design.ALGO_LIST[args.algo]
# Print out misc information
print("Output_file: %s" % args.output)
print("Emat id for this design: %s" % data["design name"])
print("Running on host: %s" % socket.gethostname())
sys.stdout.flush()
osprey.start(heapSizeMiB=floor(design.HEAP_GB * 953.674),
allowRemoteManagement=False) # Convert to MiB
conf_spaces = design.make_confspace(args.cfsfile, data,
cfs_dir =
"/usr/project/dlab/Users/gth/projects/osprey_test_suite/augmented_MARK_known"
)
# make structure to store compute time per sequence
compute_time_list = []
# Write out JSON file before beginning computation
with open(os.path.abspath(args.output), 'w') as f:
f.write(json.dumps(data, indent = 4, sort_keys=True)+
'\n')
print("\nRunning Algorithm")
design_start = datetime.now()
data['start_time'] = design_start.strftime(design.DATETIME_FORMAT)
try:
print("\nMaking pfunc factory")
pfunc_factory = design.make_pfunc_factory(
conf_spaces['complex'],
conf_spaces['ffparams'],
args.num_cores,
args.epsilon,
args.algo,
"manual_seq_alg%d" % args.algo,
data)
for sequence in data["sequences"]:
precalc_start = datetime.now()# Handle timing for precalculation
print("\nMaking pfunc for %s" % sequence)
pfunc = design.make_pfunc_for_sequence(
conf_spaces['complex'],
pfunc_factory,
args.epsilon,
data,
sequence
)
precalc_end = datetime.now()
data['precalc_time'] = (precalc_end - precalc_start).total_seconds()
print("\nComputing pfunc")
compute_start = datetime.now()
if args.algo == 2:
pfunc.setReportProgress(True)
pfunc.compute(2147483647)
else:
pfunc.compute()
compute_end = datetime.now()
compute_time_list.append((compute_end - compute_start)
.total_seconds())
result_dict = {"lowerbound" : pfunc.getValues().calcLowerBound()
.toString(),
"upperbound" : pfunc.getValues().calcUpperBound()
.toString(),
"kscore" : None}
if data["results"] is None:
data["results"] = {', '.join(sequence): result_dict}
else:
data["results"][', '.join(sequence)] = result_dict
data["status"] = design.STATUS.FINISHED.value
# can't use lists as keys, so turn into strings
seq_keys = [', '.join(e) for e in data["sequences"]]
data["time_per_seq"] = dict(zip(seq_keys, compute_time_list))
except (jpype.JavaException, AttributeError) as e:
data["status"] = design.STATUS.ERROR.value
print str(e)
print e.stacktrace()
data['errmsg'] = str(e)
design_end = datetime.now()
data['end_time'] = design_end.strftime(design.DATETIME_FORMAT)
data['runtime (s)'] = (design_end - design_start).total_seconds()
print("Algorithm Runtime (s): %d" % data['runtime (s)'])
# Print out JSON output
with open(os.path.abspath(args.output) , 'w') as f:
f.write(json.dumps(data ,indent = 4, sort_keys=True)+'\n')
print("Finished writing")