def get(obj, p, gotten_stuff, used_ps, check = True):
global past
used_ps.add(p.get_copy())
print >> sys.stderr, 'starting: ', p.get_param('uniprot_id'), obj, which_job, total_jobs
to_get = True
gotten_stuff.append([obj, p.get_copy()])
global whether_to_get_anything
if whether_to_get_anything and not wc.get_wrapper_instance(obj).has(p, False, whether_to_check_remote):
ans = wc.get_stuff(obj, p, False, False, False)
print >> sys.stderr, 'took: ', datetime.datetime.now() - past
past = datetime.datetime.now()
return ans
print >> sys.stderr, 'already have: ', p.get_param('uniprot_id'), obj
import wc
i = 0
for line in f:
name = line.strip()
if i % 50 == 0:
print i
i += 1
p.set_param('uniprot_id',name)
ok = True
for obj in to_check_for:
for filter_co in [0.35]:
p.set_param('filter_co', filter_co)
inst = wc.get_wrapper_instance(obj)
if not inst.has(p, False):
ok = False
if ok:
completed.append(name)
g = open(out_list, 'w')
for name in completed:
g.write(name + '\n')
f.close
g.close()
if whether_to_temp:
global_stuff.home = global_stuff.temp_home
assert global_stuff.base_folder == global_stuff.real_base_folder
try:
os.makedirs(global_stuff.temp_base_folder)
except:
pass
try:
os.makedirs(global_stuff.get_holding_folder())
except:
pass
real_uniprot_folder = wc.get_wrapper_instance(objects.dW).get_folder(p)
#real_pdb_folder = wc.get_wrapper_instance(objects.pdb_chain_seq).get_folder(p)
global_stuff.base_folder = global_stuff.temp_base_folder
temp_uniprot_folder = wc.get_wrapper_instance(objects.dW).get_folder(p)
if os.path.isdir(temp_uniprot_folder):
shutil.rmtree(temp_uniprot_folder)
mv_cmd = 'cp -r ' + real_uniprot_folder + ' ' + temp_uniprot_folder
subprocess.call(mv_cmd, shell=True, executable='/bin/bash')
print >> sys.stderr, 'hhhhhhhhhhhhhh', past
g.write('started: ' + protein_name + ' ' + str(i) + ' out of ' + str(num_proteins) + ' by ' + str(total_jobs) + ' ' + str(datetime.datetime.now()) + ' ' + str(datetime.datetime.now()-past2) + '\n')
past2 = datetime.datetime.now()
