def left_to_renumber_mmCIF(
default_input_path_to_mmCIF=current_directory + "/mmCIF",
default_output_path_to_mmCIF=current_directory + "/output_mmCIF"):
without_already_renumbered_mmCIF = list()
# output_mmCIF_files_were_found_4Char = set()
# input_mmCIF_files_were_found_4Char = set()
output_mmCIF_files_were_found_set = set()
input_mmCIF_files_were_found_set = set()
mmCIF_files_were_found = look_what_is_inside(
"mmCIF", default_input_path_to_mmCIF=default_input_path_to_mmCIF)
output_mmCIF_files_were_found = look_what_is_inside(
"output_mmCIF",
default_output_path_to_mmCIF=default_output_path_to_mmCIF)
for output_mmCIF_file in output_mmCIF_files_were_found:
output_mmCIF_files_were_found_set.add(output_mmCIF_file)
for input_mmCIF_file in mmCIF_files_were_found:
input_mmCIF_files_were_found_set.add(input_mmCIF_file)
set_difference = input_mmCIF_files_were_found_set - output_mmCIF_files_were_found_set
for mmCIF_file in mmCIF_files_were_found:
if mmCIF_file in set_difference:
without_already_renumbered_mmCIF.append(mmCIF_file)
return without_already_renumbered_mmCIF
def left_to_renumber_PDB(default_input_path_to_PDB=current_directory + "/PDB",
default_output_path_to_PDB=current_directory +
"/output_PDB"):
without_already_renumbered_PDB = list()
output_PDB_files_were_found_4Char = set()
input_PDB_files_were_found_4Char = set()
input_PDB_files_were_found = look_what_is_inside(
"PDB", default_input_path_to_PDB=default_input_path_to_PDB)
output_PDB_files_were_found = look_what_is_inside(
"output_PDB", default_output_path_to_PDB=default_output_path_to_PDB)
for output_PDB_file in output_PDB_files_were_found:
output_PDB_files_were_found_4Char.add(output_PDB_file[:4])
for input_PDB_file in input_PDB_files_were_found:
input_PDB_files_were_found_4Char.add(input_PDB_file[3:7])
set_difference = input_PDB_files_were_found_4Char - output_PDB_files_were_found_4Char
list_difference = list(set_difference)
for PDB_id in list_difference:
without_already_renumbered_PDB.append("pdb" + PDB_id + ".ent.gz")
return without_already_renumbered_PDB
def ProcessPool_run_renum_mmCIF(format_mmCIF, mmCIF_to_renumber,
default_input_path_to_mmCIF,
default_input_path_to_SIFTS,
default_output_path_to_mmCIF,
default_mmCIF_num, gzip_mode,
exception_AccessionIDs, nproc):
first_res = 0
for i in range(3):
if not os.path.exists(default_output_path_to_mmCIF):
os.makedirs(default_output_path_to_mmCIF)
# renumber loop
resulting = list()
executor = ProcessPoolExecutor(max_workers=nproc)
partial_master_mmCIF_renumber_function = partial(
master_mmCIF_renumber_function,
default_input_path_to_mmCIF=default_input_path_to_mmCIF,
default_input_path_to_SIFTS=default_input_path_to_SIFTS,
default_output_path_to_mmCIF=default_output_path_to_mmCIF,
default_mmCIF_num=default_mmCIF_num,
gzip_mode=gzip_mode,
exception_AccessionIDs=exception_AccessionIDs)
jobs = [
executor.submit(partial_master_mmCIF_renumber_function,
mmCIF_files) for mmCIF_files in mmCIF_to_renumber
]
for job in tqdm.tqdm(as_completed(jobs),
total=len(jobs),
miniters=1,
position=0,
leave=True,
desc="Renumbering " + format_mmCIF + " files"):
result = job.result()
if result is None:
continue
resulting.append(result)
if i == 0:
first_res = resulting
if format_mmCIF == "mmCIF_assembly":
output_mmCIF = look_what_is_inside(
'output_mmCIF_assembly',
default_output_path_to_mmCIF_assembly=
default_output_path_to_mmCIF)
else:
output_mmCIF = look_what_is_inside(
'output_mmCIF',
default_output_path_to_mmCIF=default_output_path_to_mmCIF)
# checker loop
check_list = list()
executor = ProcessPoolExecutor(max_workers=nproc)
partial_reform_assembly = partial(
check_assemblies,
default_output_path_to_mmCIF_assembly=default_output_path_to_mmCIF)
jobs = [
executor.submit(partial_reform_assembly, assembly_files)
for assembly_files in output_mmCIF
]
for job in tqdm.tqdm(as_completed(jobs),
total=len(jobs),
miniters=1,
position=0,
leave=True,
desc="Checking " + format_mmCIF + " files"):
resultus = job.result()
check_list.append(resultus)
if format_mmCIF == "mmCIF_assembly":
output_mmCIF = look_what_is_inside(
'output_mmCIF_assembly',
default_output_path_to_mmCIF_assembly=
default_output_path_to_mmCIF)
else:
output_mmCIF = look_what_is_inside(
'output_mmCIF',
default_output_path_to_mmCIF=default_output_path_to_mmCIF)
output_mmCIF_4char = set()
for n in output_mmCIF:
output_mmCIF_4char.add(n[:4])
if len(check_list) <= len(output_mmCIF):
break
else:
new_round_mmCIF_to_renumber = set()
for n in mmCIF_to_renumber:
if n[:4] in output_mmCIF_4char:
continue
else:
new_round_mmCIF_to_renumber.add(n)
mmCIF_to_renumber = new_round_mmCIF_to_renumber
return first_res
def run_downloads_with_ThreadPool(
format_to_download="mmCIF",
urls_to_target=(),
default_input_path_to_mmCIF=current_directory + "/mmCIF",
default_input_path_to_PDB=current_directory + "/PDB",
default_input_path_to_SIFTS=current_directory + "/SIFTS",
default_input_path_to_mmCIF_assembly=current_directory +
"/mmCIF_assembly",
default_input_path_to_PDB_assembly=current_directory +
"/PDB_assembly"):
for i in range(3):
executor = ThreadPoolExecutor()
partial_download_with_pool = partial(
download_with_pool,
default_input_path_to_mmCIF=default_input_path_to_mmCIF,
default_input_path_to_PDB=default_input_path_to_PDB,
default_input_path_to_SIFTS=default_input_path_to_SIFTS,
default_input_path_to_mmCIF_assembly=
default_input_path_to_mmCIF_assembly,
default_input_path_to_PDB_assembly=
default_input_path_to_PDB_assembly)
jobs = [
executor.submit(partial_download_with_pool, url)
for url in urls_to_target
]
for _ in tqdm.tqdm(as_completed(jobs),
total=len(jobs),
miniters=1,
position=0,
leave=True,
desc="Downloading " + format_to_download +
" files"):
pass
files_targeted = list()
format_of_db = 0
for url in urls_to_target:
file_name_start_pos = url.rfind("/") + 1
file_name = url[file_name_start_pos:]
files_targeted.append(file_name)
format_start_pos = file_name_start_pos - 4
format_of_db = url[format_start_pos:format_start_pos + 3]
if format_of_db == "CIF":
input_files = look_what_is_inside(
"mmCIF",
default_input_path_to_mmCIF=default_input_path_to_mmCIF)
elif format_of_db == "pdb":
input_files = look_what_is_inside(
'PDB', default_input_path_to_PDB=default_input_path_to_PDB)
elif format_of_db == "xml":
input_files = look_what_is_inside(
'SIFTS',
default_input_path_to_SIFTS=default_input_path_to_SIFTS)
elif format_of_db == "all":
input_files = look_what_is_inside(
'PDB_assembly',
default_input_path_to_PDB_assembly=
default_input_path_to_PDB_assembly)
elif format_of_db == "try":
input_files = look_what_is_inside(
'mmCIF_assembly',
default_input_path_to_mmCIF_assembly=
default_input_path_to_mmCIF_assembly)
else:
input_files = set()
# check_if_all_files_in = False
#
# for files_in in files_targeted:
# if files_in in input_files:
# pass
# else:
# check_if_all_files_in = True
#
# if check_if_all_files_in:
# urls_to_target = list(set(files_targeted) - set(input_files))c
# else:
# break
output_4char = set()
for n in input_files:
output_4char.add(n[:4])
new_round_files_targeted = set()
for n in files_targeted:
if n[:4] in output_4char:
continue
else:
new_round_files_targeted.add(n)
files_targeted = new_round_files_targeted
if len(files_targeted) == 0:
break
urls_to_target_mmCIF_assembly_files = url_formation_for_pool("mmCIF_assembly", parsed_input_text,
default_input_path_to_mmCIF_assembly=default_input_path_to_mmCIF_assembly)
urls_to_target_PDB_files = url_formation_for_pool("PDB", parsed_input_text, default_input_path_to_PDB=default_input_path_to_PDB)
urls_to_target_SIFTS_files = url_formation_for_pool("SIFTS", parsed_input_text, default_input_path_to_SIFTS=default_input_path_to_SIFTS)
run_downloads_with_ThreadPool("mmCIF", urls_to_target_mmCIF_files, default_input_path_to_mmCIF=default_input_path_to_mmCIF)
run_downloads_with_ThreadPool("mmCIF_assembly", urls_to_target_mmCIF_assembly_files,
default_input_path_to_mmCIF_assembly=default_input_path_to_mmCIF_assembly)
run_downloads_with_ThreadPool("PDB", urls_to_target_PDB_files, default_input_path_to_PDB=default_input_path_to_PDB)
run_downloads_with_ThreadPool("SIFTS", urls_to_target_SIFTS_files, default_input_path_to_SIFTS=default_input_path_to_SIFTS)
# renum PDB
passed_as_arg_file_4Char_PDB = list()
for file_name in parsed_input_text:
passed_as_arg_file_4Char_PDB.append(file_name[:4])
input_PDB_files_were_found = look_what_is_inside("PDB", default_input_path_to_PDB=default_input_path_to_PDB)
target_files_list_PDB = list()
for file_name in input_PDB_files_were_found:
if file_name[3:7] in passed_as_arg_file_4Char_PDB:
target_files_list_PDB.append(file_name)
ProcessPool_run_renum_PDB("PDB", target_files_list_PDB, default_input_path_to_PDB, default_input_path_to_SIFTS,
default_output_path_to_PDB, default_PDB_num, gzip_mode, exception_AccessionIDs, nproc)
# renum mmCIF_assembly
input_mmCIF_files_were_found = look_what_is_inside("mmCIF_assembly",
default_input_path_to_mmCIF_assembly=default_input_path_to_mmCIF_assembly)
passed_as_arg_file_4Char_mmCIF = list()
for file_name in parsed_input_text:
passed_as_arg_file_4Char_mmCIF.append(file_name[:4])
target_files_list_mmCIF = list()
for file_name in input_mmCIF_files_were_found:
def supreme_download_master(format_of_db, job_type=None,
default_input_path_to_mmCIF=current_directory + "/mmCIF",
default_input_path_to_PDB=current_directory + "/PDB",
default_input_path_to_SIFTS=current_directory + "/SIFTS",
default_input_path_to_mmCIF_assembly=current_directory + "/mmCIF_assembly",
default_input_path_to_PDB_assembly=current_directory + "/PDB_assembly",
default_output_path_to_mmCIF=current_directory + "/output_mmCIF",
default_output_path_to_PDB=current_directory + "/output_PDB",
default_output_path_to_mmCIF_assemblies=current_directory + "/output_mmCIF_assembly",
default_output_path_to_PDB_assemblies=current_directory + "/output_PDB_assembly"):
catalogdownloader.catalog_downloader()
if job_type == "refresh":
if os.path.exists(default_input_path_to_SIFTS):
shutil.rmtree(default_input_path_to_SIFTS)
if format_of_db == "mmCIF":
if os.path.exists(default_input_path_to_mmCIF):
shutil.rmtree(default_input_path_to_mmCIF)
if os.path.exists(default_output_path_to_mmCIF):
shutil.rmtree(default_output_path_to_mmCIF)
if format_of_db == "mmCIF_assembly":
if os.path.exists(default_input_path_to_mmCIF_assembly):
shutil.rmtree(default_input_path_to_mmCIF_assembly)
if os.path.exists(default_output_path_to_mmCIF_assemblies):
shutil.rmtree(default_output_path_to_mmCIF_assemblies)
if format_of_db == "PDB":
if os.path.exists(default_input_path_to_PDB):
shutil.rmtree(default_input_path_to_PDB)
if os.path.exists(default_output_path_to_PDB):
shutil.rmtree(default_output_path_to_PDB)
if format_of_db == "PDB_assembly":
if os.path.exists(default_input_path_to_PDB_assembly):
shutil.rmtree(default_input_path_to_PDB_assembly)
if os.path.exists(default_output_path_to_PDB_assemblies):
shutil.rmtree(default_output_path_to_PDB_assemblies)
if format_of_db == "all":
if os.path.exists(default_input_path_to_PDB):
shutil.rmtree(default_input_path_to_PDB)
if os.path.exists(default_input_path_to_mmCIF):
shutil.rmtree(default_input_path_to_mmCIF)
if os.path.exists(default_input_path_to_PDB_assembly):
shutil.rmtree(default_input_path_to_PDB_assembly)
if os.path.exists(default_input_path_to_mmCIF_assembly):
shutil.rmtree(default_input_path_to_mmCIF_assembly)
if os.path.exists(default_output_path_to_mmCIF):
shutil.rmtree(default_output_path_to_mmCIF)
if os.path.exists(default_output_path_to_mmCIF_assemblies):
shutil.rmtree(default_output_path_to_mmCIF_assemblies)
if os.path.exists(default_output_path_to_PDB):
shutil.rmtree(default_output_path_to_PDB)
if os.path.exists(default_output_path_to_PDB_assemblies):
shutil.rmtree(default_output_path_to_PDB_assemblies)
if format_of_db == "mmCIF":
all_data_from_catreader = latestcatreader.latest_catalog_reader()
all_mmCIF_files_from_latest_catalog = all_data_from_catreader[0]
all_SIFTS_files_from_latest_catalog = all_data_from_catreader[2]
input_mmCIF_files_were_found = lookfilesinside.look_what_is_inside("mmCIF", default_input_path_to_mmCIF=default_input_path_to_mmCIF)
left_to_download_mmCIF = lefttodownload.what_is_left_to_download(input_mmCIF_files_were_found, all_mmCIF_files_from_latest_catalog)
urls_to_target_mmCIF_files = url_formation_for_pool("mmCIF", left_to_download_mmCIF, default_input_path_to_mmCIF=default_input_path_to_mmCIF)
run_downloads_with_ThreadPool("mmCIF", urls_to_target_mmCIF_files, default_input_path_to_mmCIF=default_input_path_to_mmCIF)
input_SIFTS_files_were_found = lookfilesinside.look_what_is_inside("SIFTS", default_input_path_to_SIFTS=default_input_path_to_SIFTS)
left_to_download_SIFTS = lefttodownload.what_is_left_to_download(input_SIFTS_files_were_found, all_SIFTS_files_from_latest_catalog)
urls_to_target_SIFTS_files = url_formation_for_pool("SIFTS", left_to_download_SIFTS, default_input_path_to_SIFTS=default_input_path_to_SIFTS)
run_downloads_with_ThreadPool("SIFTS", urls_to_target_SIFTS_files, default_input_path_to_SIFTS=default_input_path_to_SIFTS)
return left_to_download_mmCIF
if format_of_db == "mmCIF_assembly":
all_data_from_catreader = latestcatreader.latest_catalog_reader()
all_mmCIF_files = all_data_from_catreader[0]
all_SIFTS_files_from_latest_catalog = all_data_from_catreader[2]
lefttodownload_mmCIF_assemblies = list()
input_mmCIF_assembly_files_were_found = lookfilesinside.look_what_is_inside(
"mmCIF_assembly", default_input_path_to_mmCIF_assembly=default_input_path_to_mmCIF_assembly)
all_mmCIF_files_4char = set()
for mmCIF_file in all_mmCIF_files:
all_mmCIF_files_4char.add(mmCIF_file[:4])
input_mmCIF_assembly_files_were_found_4char = set()
for mmCIF_assembly_file in input_mmCIF_assembly_files_were_found:
input_mmCIF_assembly_files_were_found_4char.add(mmCIF_assembly_file[:4])
set_difference = all_mmCIF_files_4char - input_mmCIF_assembly_files_were_found_4char
list_difference = list(set_difference)
for mmCIF_id in list_difference:
lefttodownload_mmCIF_assemblies.append(mmCIF_id + ".cif.gz")
urls_to_target_mmCIF_assembly_files = url_formation_for_pool("mmCIF_assembly", lefttodownload_mmCIF_assemblies)
run_downloads_with_ThreadPool("mmCIF_assembly", urls_to_target_mmCIF_assembly_files,
default_input_path_to_mmCIF_assembly=default_input_path_to_mmCIF_assembly)
input_SIFTS_files_were_found = lookfilesinside.look_what_is_inside("SIFTS", default_input_path_to_SIFTS=default_input_path_to_SIFTS)
left_to_download_SIFTS = lefttodownload.what_is_left_to_download(input_SIFTS_files_were_found, all_SIFTS_files_from_latest_catalog)
urls_to_target_SIFTS_files = url_formation_for_pool("SIFTS", left_to_download_SIFTS, default_input_path_to_SIFTS=default_input_path_to_SIFTS)
run_downloads_with_ThreadPool("SIFTS", urls_to_target_SIFTS_files, default_input_path_to_SIFTS=default_input_path_to_SIFTS)
return lefttodownload_mmCIF_assemblies
if format_of_db == "PDB":
all_data_from_catreader = latestcatreader.latest_catalog_reader()
all_PDB_files_from_latest_catalog = all_data_from_catreader[1]
all_SIFTS_files_from_latest_catalog = all_data_from_catreader[2]
input_PDB_files_were_found = lookfilesinside.look_what_is_inside("PDB", default_input_path_to_PDB=default_input_path_to_PDB)
left_to_download_PDB = lefttodownload.what_is_left_to_download(input_PDB_files_were_found, all_PDB_files_from_latest_catalog)
urls_to_target_PDB_files = url_formation_for_pool("PDB", left_to_download_PDB, default_input_path_to_PDB=default_input_path_to_PDB)
run_downloads_with_ThreadPool("PDB", urls_to_target_PDB_files, default_input_path_to_PDB=default_input_path_to_PDB)
input_SIFTS_files_were_found = lookfilesinside.look_what_is_inside("SIFTS", default_input_path_to_SIFTS=default_input_path_to_SIFTS)
left_to_download_SIFTS = lefttodownload.what_is_left_to_download(input_SIFTS_files_were_found, all_SIFTS_files_from_latest_catalog)
urls_to_target_SIFTS_files = url_formation_for_pool("SIFTS", left_to_download_SIFTS, default_input_path_to_SIFTS=default_input_path_to_SIFTS)
run_downloads_with_ThreadPool("SIFTS", urls_to_target_SIFTS_files, default_input_path_to_SIFTS=default_input_path_to_SIFTS)
return left_to_download_PDB
if format_of_db == "PDB_assembly":
all_data_from_catreader = latestcatreader.latest_catalog_reader()
all_SIFTS_files_from_latest_catalog = all_data_from_catreader[2]
download_all_PDB_assemblies = download_pdb_assemblies_list_with_lxml()
input_PDB_assembly_files_were_found = lookfilesinside.look_what_is_inside(
"PDB_assembly", default_input_path_to_PDB_assembly=default_input_path_to_PDB_assembly)
try:
len(download_all_PDB_assemblies)
except TypeError:
return print("Cannot reach https://ftp.wwpdb.org/pub/pdb/data/biounit/PDB/all/ maybe try again later")
lefttodownload_PDB_assemblies = [assembly for assembly in download_all_PDB_assemblies
if assembly.rsplit('/', 1)[-1] not in input_PDB_assembly_files_were_found]
run_downloads_with_ThreadPool("PDB_assembly", lefttodownload_PDB_assemblies,
default_input_path_to_PDB_assembly=default_input_path_to_PDB_assembly)
input_SIFTS_files_were_found = lookfilesinside.look_what_is_inside("SIFTS", default_input_path_to_SIFTS=default_input_path_to_SIFTS)
left_to_download_SIFTS = lefttodownload.what_is_left_to_download(input_SIFTS_files_were_found, all_SIFTS_files_from_latest_catalog)
urls_to_target_SIFTS_files = url_formation_for_pool("SIFTS", left_to_download_SIFTS, default_input_path_to_SIFTS=default_input_path_to_SIFTS)
run_downloads_with_ThreadPool("SIFTS", urls_to_target_SIFTS_files, default_input_path_to_SIFTS=default_input_path_to_SIFTS)
return lefttodownload_PDB_assemblies
if format_of_db == "all":
all_data_from_catreader = latestcatreader.latest_catalog_reader()
all_mmCIF_files_from_latest_catalog = all_data_from_catreader[0]
all_PDB_files_from_latest_catalog = all_data_from_catreader[1]
all_SIFTS_files_from_latest_catalog = all_data_from_catreader[2]
input_mmCIF_files_were_found = lookfilesinside.look_what_is_inside("mmCIF", default_input_path_to_mmCIF=default_input_path_to_mmCIF)
input_PDB_files_were_found = lookfilesinside.look_what_is_inside("PDB", default_input_path_to_PDB=default_input_path_to_PDB)
input_SIFTS_files_were_found = lookfilesinside.look_what_is_inside("SIFTS", default_input_path_to_SIFTS=default_input_path_to_SIFTS)
left_to_download_mmCIF = lefttodownload.what_is_left_to_download(input_mmCIF_files_were_found, all_mmCIF_files_from_latest_catalog)
left_to_download_PDB = lefttodownload.what_is_left_to_download(input_PDB_files_were_found, all_PDB_files_from_latest_catalog)
left_to_download_SIFTS = lefttodownload.what_is_left_to_download(input_SIFTS_files_were_found, all_SIFTS_files_from_latest_catalog)
urls_to_target_mmCIF_files = url_formation_for_pool("mmCIF", left_to_download_mmCIF, default_input_path_to_mmCIF=default_input_path_to_mmCIF)
urls_to_target_PDB_files = url_formation_for_pool("PDB", left_to_download_PDB, default_input_path_to_PDB=default_input_path_to_PDB)
urls_to_target_SIFTS_files = url_formation_for_pool("SIFTS", left_to_download_SIFTS, default_input_path_to_SIFTS=default_input_path_to_SIFTS)
run_downloads_with_ThreadPool("mmCIF", urls_to_target_mmCIF_files, default_input_path_to_mmCIF=default_input_path_to_mmCIF)
run_downloads_with_ThreadPool("PDB", urls_to_target_PDB_files, default_input_path_to_PDB=default_input_path_to_PDB)
run_downloads_with_ThreadPool("SIFTS", urls_to_target_SIFTS_files, default_input_path_to_SIFTS=default_input_path_to_SIFTS)
# PDB_assembly
download_all_PDB_assemblies = download_pdb_assemblies_list_with_lxml()
input_PDB_assembly_files_were_found = lookfilesinside.look_what_is_inside("PDB_assembly")
try:
len(download_all_PDB_assemblies)
except TypeError:
return print("Cannot reach https://ftp.wwpdb.org/pub/pdb/data/biounit/PDB/all/ maybe try again later")
lefttodownload_PDB_assemblies = [assembly for assembly in download_all_PDB_assemblies
if assembly.rsplit('/', 1)[-1] not in input_PDB_assembly_files_were_found]
run_downloads_with_ThreadPool("PDB_assembly", lefttodownload_PDB_assemblies,
default_input_path_to_PDB_assembly=default_input_path_to_PDB_assembly)
# mmCIF_assembly
lefttodownload_mmCIF_assemblies = list()
input_mmCIF_assembly_files_were_found = lookfilesinside.look_what_is_inside(
"mmCIF_assembly", default_input_path_to_mmCIF_assembly=default_input_path_to_mmCIF_assembly)
all_mmCIF_files_4char = set()
for mmCIF_file in all_mmCIF_files_from_latest_catalog:
all_mmCIF_files_4char.add(mmCIF_file[:4])
input_mmCIF_assembly_files_were_found_4char = set()
for mmCIF_assembly_file in input_mmCIF_assembly_files_were_found:
input_mmCIF_assembly_files_were_found_4char.add(mmCIF_assembly_file[:4])
set_difference = all_mmCIF_files_4char - input_mmCIF_assembly_files_were_found_4char
list_difference = list(set_difference)
for mmCIF_id in list_difference:
lefttodownload_mmCIF_assemblies.append(mmCIF_id + ".cif.gz")
urls_to_target_mmCIF_assembly_files = url_formation_for_pool("mmCIF_assembly", lefttodownload_mmCIF_assemblies,
default_input_path_to_mmCIF_assembly=default_input_path_to_mmCIF_assembly)
run_downloads_with_ThreadPool("mmCIF_assembly", urls_to_target_mmCIF_assembly_files,
default_input_path_to_mmCIF_assembly=default_input_path_to_mmCIF_assembly)
return [left_to_download_mmCIF, left_to_download_PDB, lefttodownload_mmCIF_assemblies, lefttodownload_PDB_assemblies]