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import sys
from urllib.error import HTTPError
from urllib.request import urlopen
import lxml.etree as et
from plip.basic import logger
logger = logger.get_logger()
def check_pdb_status(pdbid):
"""Returns the status and up-to-date entry in the PDB for a given PDB ID"""
url = "http://www.rcsb.org/pdb/rest/idStatus?structureId=%s" % pdbid
xmlf = urlopen(url)
xml = et.parse(xmlf)
xmlf.close()
status = None
current_pdbid = pdbid
for df in xml.xpath("//record"):
status = df.attrib[
"status"
] # Status of an entry can be either 'UNKWOWN', 'OBSOLETE', or 'CURRENT'
if status == "OBSOLETE":
current_pdbid = df.attrib[
"replacedBy"
] # Contains the up-to-date PDB ID for obsolete entries
return [status, current_pdbid.lower()]
def fetch_pdb(pdbid):
"""Get the newest entry from the RCSB server for the given PDB ID. Exits with '1' if PDB ID is invalid."""
pdbid = pdbid.lower()
logger.info(f"checking status of PDB-ID {pdbid}")
state, current_entry = check_pdb_status(pdbid) # Get state and current PDB ID
if state == "OBSOLETE":
logger.info(f"entry is obsolete, getting {current_entry} instead")
elif state == "CURRENT":
logger.info("entry is up-to-date")
elif state == "UNKNOWN":
logger.error("invalid PDB-ID (entry does not exist on PDB server)")
sys.exit(1)
logger.info("downloading file from PDB")
# get URL for current entry
# @todo needs update to react properly on response codes of RCSB servers
pdburl = f"http://www.rcsb.org/pdb/files/{current_entry}.pdb"
try:
pdbfile = urlopen(pdburl).read().decode()
# If no PDB file is available, a text is now shown with "We're sorry, but ..."
# Could previously be distinguished by an HTTP error
if "sorry" in pdbfile:
logger.error(
"no file in PDB format available from wwPDB for the given PDB ID."
)
sys.exit(1)
except HTTPError:
logger.error("no file in PDB format available from wwPDB for the given PDB ID")
sys.exit(1)
return [pdbfile, current_entry]
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