def remove_pdbs_only(pwd, name, time):
pdb_files = [a for a in os.listdir(pwd) if a[-7:] == '.pdb.gz']
run_filters = DCRP.generate_run_filters(
args={
'ddg': 24.0,
'sasa': 1400,
'shape': 0.6,
'packstat': 0.6,
'buried_2': 3,
'hbonds': -10.
})
score_dict = RF.score2dict('%sall_%s_%s.score' % (pwd, name, time))
passed, failed = DCRP.all_who_pass_run_filters({}, score_dict, run_filters)
if len(passed) != 0:
print('there are %i passed scores, so choosing from there' %
len(list(passed.keys())))
best_structs = DCRP.best_n_structures(
{
'filter': 'ddg',
'n': min([10, len(list(passed.keys()))])
}, passed)
else:
print('there are no passed, so choosing from the failed')
best_structs = DCRP.best_n_structures(
{
'filter': 'ddg',
'n': min([5, len(list(failed.keys()))])
}, failed)
best_names = [a['description'] for a in best_structs]
[os.remove(pdb) for pdb in pdb_files if pdb[:-7] not in best_names]
def process_folder(args):
import time
pwd = os.getcwd()+'/'
os.chdir(args['folder'])
name = pwd.split('/')[-2]
time = time.strftime("%d.%0-m")
if not args['force_process']:
if os.path.isfile('%sall_%s_%s.err' % (pwd, name, time)):
print('found %sall_%s_%s.err, STOPPING' % (pwd, name, time))
if args['remove_pdbs']:
remove_pdbs_only(pwd, name, time)
sys.exit()
return 'not finished'
if not is_folder_finished(pwd):
return 'not finished'
sc_files = [a for a in os.listdir(pwd) if a[-3:] == '.sc']
pdb_files = [a for a in os.listdir(pwd) if a[-7:] == '.pdb.gz']
err_files = [a for a in os.listdir(pwd) if a[:4] == 'err.']
job_files = [a for a in os.listdir(pwd) if a[:4] == 'job.']
print('found a total of %i job files, %i err files, %i pdbs and %i scores' % (len(job_files), len(err_files),
len(pdb_files), len(sc_files)))
if len(sc_files) == 0:
return 'no scores'
combine_scores('%sall_%s_%s.score' % (pwd, name, time), sc_files)
non_triv_errs = process_errors('%sall_%s_%s.err' % (pwd, name, time), err_files)
if non_triv_errs == 0:
print('removing out.* and job.*')
[os.remove(out) for out in os.listdir(pwd) if out[:4] == 'out.']
[os.remove(job) for job in job_files]
try:
os.remove('./command')
except:
pass
run_filters = DCRP.generate_run_filters(args={'ddg': 24.0, 'sasa': 1400, 'shape': 0.6, 'packstat': 0.6,
'buried_2': 3, 'hbonds': -10.})
score_dict = RF.score2dict('%sall_%s_%s.score' % (pwd, name, time))
passed, failed = DCRP.all_who_pass_run_filters({}, score_dict, run_filters)
if len(passed) != 0:
print('there are %i passed scores, so choosing from there' % len(list(passed.keys())))
best_structs = DCRP.best_n_structures({'filter': 'ddg', 'n': min([10, len(list(passed.keys()))])}, passed)
else:
print('there are no passed, so choosing from the failed')
best_structs = DCRP.best_n_structures({'filter': 'ddg', 'n': min([10, len(list(failed.keys()))])}, failed)
best_names = [a['description'] for a in best_structs]
print('the best:', best_names)
print('removing all other pdbs')
[os.remove(pdb) for pdb in pdb_files if pdb[:-7] not in best_names]
os.chdir(pwd)
def remove_pdbs_only(pwd, name, time):
pdb_files = [a for a in os.listdir(pwd) if a[-7:] == '.pdb.gz']
run_filters = DCRP.generate_run_filters(args={'ddg': 24.0, 'sasa': 1400, 'shape': 0.6, 'packstat': 0.6,
'buried_2': 3, 'hbonds': -10.})
score_dict = RF.score2dict('%sall_%s_%s.score' % (pwd, name, time))
passed, failed = DCRP.all_who_pass_run_filters({}, score_dict, run_filters)
if len(passed) != 0:
print('there are %i passed scores, so choosing from there' % len(list(passed.keys())))
best_structs = DCRP.best_n_structures({'filter': 'ddg', 'n': min([10, len(list(passed.keys()))])}, passed)
else:
print('there are no passed, so choosing from the failed')
best_structs = DCRP.best_n_structures({'filter': 'ddg', 'n': min([5, len(list(failed.keys()))])}, failed)
best_names = [a['description'] for a in best_structs]
[os.remove(pdb) for pdb in pdb_files if pdb[:-7] not in best_names]
def process_folder(args):
import time
pwd = os.getcwd() + '/'
os.chdir(args['folder'])
name = pwd.split('/')[-2]
time = time.strftime("%d.%0-m")
if not args['force_process']:
if os.path.isfile('%sall_%s_%s.err' % (pwd, name, time)):
print('found %sall_%s_%s.err, STOPPING' % (pwd, name, time))
if args['remove_pdbs']:
remove_pdbs_only(pwd, name, time)
sys.exit()
return 'not finished'
if not is_folder_finished(pwd):
return 'not finished'
sc_files = [a for a in os.listdir(pwd) if a[-3:] == '.sc']
pdb_files = [a for a in os.listdir(pwd) if a[-7:] == '.pdb.gz']
err_files = [a for a in os.listdir(pwd) if a[:4] == 'err.']
job_files = [a for a in os.listdir(pwd) if a[:4] == 'job.']
print(
'found a total of %i job files, %i err files, %i pdbs and %i scores' %
(len(job_files), len(err_files), len(pdb_files), len(sc_files)))
if len(sc_files) == 0:
return 'no scores'
combine_scores('%sall_%s_%s.score' % (pwd, name, time), sc_files)
non_triv_errs = process_errors('%sall_%s_%s.err' % (pwd, name, time),
err_files)
if non_triv_errs == 0:
print('removing out.* and job.*')
[os.remove(out) for out in os.listdir(pwd) if out[:4] == 'out.']
[os.remove(job) for job in job_files]
try:
os.remove('./command')
except:
pass
run_filters = DCRP.generate_run_filters(
args={
'ddg': 24.0,
'sasa': 1400,
'shape': 0.6,
'packstat': 0.6,
'buried_2': 3,
'hbonds': -10.
})
score_dict = RF.score2dict('%sall_%s_%s.score' % (pwd, name, time))
passed, failed = DCRP.all_who_pass_run_filters({}, score_dict, run_filters)
if len(passed) != 0:
print('there are %i passed scores, so choosing from there' %
len(list(passed.keys())))
best_structs = DCRP.best_n_structures(
{
'filter': 'ddg',
'n': min([10, len(list(passed.keys()))])
}, passed)
else:
print('there are no passed, so choosing from the failed')
best_structs = DCRP.best_n_structures(
{
'filter': 'ddg',
'n': min([10, len(list(failed.keys()))])
}, failed)
best_names = [a['description'] for a in best_structs]
print('the best:', best_names)
print('removing all other pdbs')
[os.remove(pdb) for pdb in pdb_files if pdb[:-7] not in best_names]
os.chdir(pwd)
