[ENH] pdb to String loader using UniProt id

pyaptamer/utils/__init__.py

@@ -8,11 +8,13 @@
     "rna2vec",
     "pdb_to_struct",
     "struct_to_aaseq",
+    "pdb_to_seq_uniprot",
     "pdb_to_aaseq",
 ]
 
 from pyaptamer.utils._aa_str_to_letter import aa_str_to_letter
 from pyaptamer.utils._pdb_to_aaseq import pdb_to_aaseq
+from pyaptamer.utils._pdb_to_seq_uniprot import pdb_to_seq_uniprot
 from pyaptamer.utils._pdb_to_struct import pdb_to_struct
 from pyaptamer.utils._rna import (
     dna2rna,

pyaptamer/utils/_pdb_to_seq_uniprot.py

@@ -0,0 +1,53 @@
+import io
+
+import pandas as pd
+import requests
+from Bio import SeqIO
+
+
+def pdb_to_seq_uniprot(pdb_id, return_type="list"):
+    """
+    Retrieve the canonical UniProt amino-acid sequence for a given PDB ID.
+
+    Parameters
+    ----------
+    pdb_id : str
+        PDB ID (e.g., '1a3n').
+    return_type : {'list', 'pd.df'}, optional, default='list'
+        Format of returned value:
+
+          - ``'list'`` : list with one amino-acid sequence
+          - ``'pd.df'`` : pandas.DataFrame with a single column ['sequence']
+
+    Returns
+    -------
+    list of str or pandas.DataFrame
+        Depending on ``return_type``.
+    """
+    pdb_id = pdb_id.lower()
+
+    mapping_url = f"https://www.ebi.ac.uk/pdbe/api/mappings/uniprot/{pdb_id}"
+    mapping_resp = requests.get(mapping_url)
+    mapping_data = mapping_resp.json()
+
+    uniprot_ids = list(mapping_data.get(pdb_id, {}).get("UniProt", {}).keys())
+    if not uniprot_ids:
+        raise ValueError(f"No UniProt mapping found for PDB ID '{pdb_id}'")
+
+    uniprot_id = uniprot_ids[0]
+
+    fasta_url = f"https://rest.uniprot.org/uniprotkb/{uniprot_id}.fasta"
+    fasta_resp = requests.get(fasta_url)
+    fasta_data = fasta_resp.text
+
+    record = next(SeqIO.parse(io.StringIO(fasta_data), "fasta"))
+    sequence = str(record.seq)
+
+    df = pd.DataFrame({"sequence": [sequence]})
+
+    if return_type == "list":
+        return df["sequence"].tolist()
+    elif return_type == "pd.df":
+        return df.reset_index(drop=True)
+    else:
+        raise ValueError("`return_type` must be either 'list' or 'pd.df'")

pyaptamer/utils/tests/test_pdb_to_seq_uniprot.py

@@ -0,0 +1,18 @@
+import pandas as pd
+
+from pyaptamer.utils import pdb_to_seq_uniprot
+
+
+def test_pdb_to_seq_uniprot():
+    """Test the `pdb_to_seq_uniprot` function."""
+    pdb_id = "1a3n"
+
+    df = pdb_to_seq_uniprot(pdb_id, return_type="pd.df")
+    assert isinstance(df, pd.DataFrame)
+    assert "sequence" in df.columns
+    assert len(df.iloc[0]["sequence"]) > 0
+
+    lst = pdb_to_seq_uniprot(pdb_id, return_type="list")
+    assert isinstance(lst, list)
+    assert len(lst) == 1
+    assert len(lst[0]) > 0