def get_info_for(pdb_code):
pdb_suffix = pdb_code.lower().strip()
# print(f"start: {pdb_suffix}")
if pdb_suffix+".pkl" not in pdb_paths.PDB_PARSED_SET:
print(f"{pdb_suffix} not in pdb_paths.PDB_PARSED_SET")
if pdb_suffix+".pdb" in pdb_paths.PDB_FILES_SET:
print(f"{pdb_suffix} not in pdb_paths.PDB_FILES_SET")
logging.info(f"{pdb_suffix} not found in PDB_PARSED_SET, "
f"but is in PDB_FILES_SET.")
get_success = loaders.load_pdb_info(pdb_code)
else:
logging.info(f"{pdb_suffix} not found in PDB_PARSED_SET or "
f"PDB_FILES_SET.")
# todo: test this
get_success = download(pdb_code, silent=False)
if get_success:
get_success = loaders.load_pdb_info(pdb_code)
if not get_success:
print(f"get_info_for(pdb_code) failed for {pdb_code}")
logging.warning(f"Loading of pdb file {pdb_suffix} fails.")
return None
pdb_paths.PDB_PARSED_SET.add(pdb_suffix + ".pkl")
pdb_paths.PDB_FILES_SET.add(pdb_suffix + ".pdb")
filepath = os.path.join(pdb_paths.PDB_PARSED, pdb_suffix+'.pkl')
with open(filepath, 'rb') as file:
output = pickle.load(file)
return output
def get_info_for(pdb_code, reset=False):
pdb_suffix = pdb_code.lower().strip() + ".pkl"
if reset:
get_success = download(pdb_code, silent=False)
if not get_success:
print(f"download(pdb_code) failed for {pdb_code}")
return None
get_success = loaders.load_pdb_info(pdb_code)
if not get_success:
print(f"load_pdb_info(pdb_code) failed for {pdb_code}")
return None
else:
if pdb_suffix not in paths.PDB_PARSED_SET:
s3 = boto3.client('s3',
aws_access_key_id="AKIAY6UR252SQUQ3OSWZ",
aws_secret_access_key="08LQj"
"+ryk9SMojG18vERXKKzhNSYk5pLhAjrIAVX")
output_path = os.path.join(paths.PDB_PARSED, pdb_suffix)
print(f"S3: {pdb_suffix}")
with open(output_path, 'wb') as f:
try:
s3.download_fileobj('definedproteins', pdb_suffix, f)
paths.PDB_PARSED_SET = set(os.listdir(paths.PDB_PARSED))
get_success = True
print(f"S3 Success")
except:
print(f"S3 Fail")
if pdb_code.lower().strip(
) + ".pdb" in paths.PDB_FILES_SET:
get_success = loaders.load_pdb_info(pdb_code)
else:
get_success = download(pdb_code, silent=False)
if get_success:
paths.PDB_FILES_SET = set(
os.listdir(paths.PDB_FILES))
get_success = loaders.load_pdb_info(pdb_code)
else:
print(f"download(pdb_code) failed for {pdb_code}")
if not get_success:
print(f"get_info_for(pdb_code) failed for {pdb_code}")
return None
paths.PDB_PARSED_SET = set(os.listdir(paths.PDB_PARSED))
filepath = os.path.join(paths.PDB_PARSED, pdb_suffix)
with open(filepath, 'rb') as file:
output = pickle.load(file)
return output
def get_info_no_cache(pdb_code):
pdb_suffix = pdb_code.lower().strip()
get_success = download(pdb_code, silent=False)
if get_success:
get_success = loaders.load_pdb_info(pdb_code)
if not get_success:
logging.warning(f"Loading of pdb file {pdb_suffix} fails.")
return None
filepath = os.path.join(pdb_paths.PDB_PARSED, pdb_suffix + '.pkl')
with open(filepath, 'rb') as file:
output = pickle.load(file)
output_path = os.path.join(pdb_paths.PDB_FILES, pdb_code + ".pdb")
# os.remove(filepath)
# os.remove(output_path)
return output
def preload_all():
for filename in pdb_paths.PDB_FILES_SET:
print(filename)
pdb_code = filename.split(".")[0]
loaders.load_pdb_info(pdb_code)