settings['mem_free'] = '3.0G'
settings['scriptname'] = generated_scriptname
settings['appname'] = 'minimize_with_cst'
settings['rosetta_args_list'] = [
'-in:file:fullatom', '-ignore_unrecognized_res',
'-fa_max_dis', '9.0', '-ddg::harmonic_ca_tether', '0.5',
'-ddg::constraint_weight', '1.0',
'-ddg::out_pdb_prefix', 'min_cst_0.5',
'-ddg::sc_min_only', 'false'
]
if arguments['--talaris2014']:
settings['rosetta_args_list'].extend(['-talaris2014', 'true'])
elif arguments['--beta_july15']:
settings['rosetta_args_list'].extend(['-beta_july15'])
write_run_file(settings)
job_path = os.path.abspath(output_dir)
print('''Job files written to directory: %s.\n\nTo launch this job:
cd %s
python %s.py\n''' % (job_path, job_path, generated_scriptname))
except Exception, e:
print('\nAn exception occurred setting up the preminimization step: "%s".' % str(e))
sys.stdout.write('Removing the directory %s: ' % output_dir)
try:
shutil.rmtree(output_dir)
print('done.\n')
except Exception, e2:
print('failed.\n')
print(str(e2))
print(traceback.format_exc())
with open(os.path.join(output_data_dir, "job_dict.pickle"), "wb") as f:
pickle.dump(job_dict, f)
settings["scriptname"] = "alascan_run"
settings["appname"] = "rosetta_scripts"
settings["rosetta_args_list"] = [
"-parser:view",
"-inout:dbms:mode",
"sqlite3",
"-inout:dbms:database_name",
"rosetta_output.db3",
"-no_optH",
"true",
"-restore_talaris_behavior", #TODO: different restore_XXXXXXXX_behaviours are needed per score function
]
settings["tasks_per_process"] = 15
settings["numjobs"] = "%d" % len(job_dict)
settings["mem_free"] = "1.0G"
settings["output_dir"] = output_dir
write_run_file(settings)
import sys
#write a tasklist file
with open(os.path.abspath(output_dir) + "/task.list", 'w') as f:
for i in range(len(job_dict)):
print(
f'cd {os.path.abspath(output_dir)} && {sys.executable} alascan_run.py {i}',
file=f)
print("Job files written to directory:", os.path.abspath(output_dir))