T008: HTTPError: 403 Client Error: Forbidden for url: http://ligand-expo.rcsb.org/reports/8/8AM/

[khanmf]

Hi,

In T008, while running codes:

pdb_id = 5UG9

def get_ligands(pdb_id):
    info = pypdb.get_info(pdb_id)
    nonpolymers = info.get("rcsb_entry_info", {}).get("nonpolymer_bound_components", [])
    ligands = {}
    for ligand_expo_id in nonpolymers:
        r = requests.get(
            f"http://ligand-expo.rcsb.org/reports/{ligand_expo_id[0]}/{ligand_expo_id}/"
        )
        r.raise_for_status()
        html = BeautifulSoup(r.text)
        info = {}
        for table in html.find_all("table"):
            for row in table.find_all("tr"):
                cells = row.find_all("td")
                if len(cells) != 2:
                    continue
                key, value = cells
                if key.string and key.string.strip():
                    info[key.string.strip()] = "".join(value.find_all(text=True))
        # Postprocess some known values
        info["Molecular weight"] = float(info["Molecular weight"].split()[0])
        info["Formal charge"] = int(info["Formal charge"])
        info["Atom count"] = int(info["Atom count"])
        info["Chiral atom count"] = int(info["Chiral atom count"])
        info["Bond count"] = int(info["Bond count"])
        info["Aromatic bond count"] = int(info["Aromatic bond count"])
        ligands[ligand_expo_id] = info        
    return ligands

get_ligands(pdb_id)

I am getting following error:

Traceback (most recent call last):
  File "Script.py", line 405, in <module>
    ligands = get_ligands(pdb_id)
  File "Script.py", line 342, in get_ligands
    r.raise_for_status()
  File "/home/mfkhan91/anaconda3/lib/python3.8/site-packages/requests/models.py", line 1021, in raise_for_status
    raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 403 Client Error: Forbidden for url: http://ligand-expo.rcsb.org/reports/8/8AM/

Please help me in resolving the issue.

Thanks,
Faraz

[dominiquesydow]

Hi @khanmf,

Thanks a lot for raising this issue; I noticed problems yesterday as well (the website was still ok on Tuesday). I had hoped that the issue is resolved today (sometimes waiting a day helped in the past with other webservices) but that does not seem to be the case.

1. Search page: http://ligand-expo.rcsb.org/ld-search.html
   Entering e.g. STI in the first Search box returns now an “Oops - Search failed - “
2. Ligand page: In one of our Jupyter notebooks, we are accessing data directly from URLs like http://ligand-expo.rcsb.org/reports/S/STI/.
   This access to these URLs is now forbidden ("You don't have permission to access…”).

I contacted the RCSB team and will update you here, once I have an answer. Until then, there is, unfortunately, nothing we can do for T008 - except for fetching the ligand metadata that you need from another resource, e.g. directly from the CIF file, if available.

If you are in a hurry: I recently learned that you can access a PDB entry's ligand data from RCSB using GraphQL. Maybe this can help you while the Ligand Expo resolves the issue (though this will only fetch a subset of all the ligand metadata that the Ligand Expo website offers). #248 (comment)

[khanmf]

@dominiquesydow Thank you for your suggestions.

[dominiquesydow]

Good news, @khanmf, the RCSB team has resolved this issue 🎉

[khanmf]

@dominiquesydow Great! Thanks for letting me know.