Uniprotxml parse ligand tag (#5001)

* enable handling of <ligand> tags in UniProt XML files

* test parsing of <ligand> in UniProt XML

* add name to CONTRIB.rst

* format with black

* enable capture of multiple ligands from uniprot xml file. update tests accordingly

* add mock UniProt XML file with multiple ligand tags per feature

* test for correct len of all ligands list and multiple ligands per feature

Bio/SeqIO/UniprotIO.py

@@ -16,19 +16,15 @@ originally introduced by SwissProt ("swiss" format in Bio.SeqIO).
 
 """
 
+import warnings
 from xml.etree import ElementTree
 from xml.parsers.expat import errors
-import warnings
 
-from Bio import SeqFeature
+from Bio import BiopythonDeprecationWarning, SeqFeature
 from Bio.Seq import Seq
 from Bio.SeqRecord import SeqRecord
 
-from Bio import BiopythonDeprecationWarning
-
-from .Interfaces import _BytesIOSource
-from .Interfaces import SequenceIterator
-
+from .Interfaces import SequenceIterator, _BytesIOSource
 
 NS = "{http://uniprot.org/uniprot}"
 REFERENCE_JOURNAL = "%(name)s %(volume)s:%(first)s-%(last)s(%(pub_date)s)"
@@ -472,6 +468,19 @@ class UniprotIterator(SequenceIterator):
                 feature.location = SeqFeature.SimpleLocation(
                     start_position, end_position
                 )
+            elif feature_element.tag == NS + "ligand":
+                # Support multiple ligand entries per feature
+                name = None
+                db_ref = None
+                for child in feature_element:
+                    if child.tag == NS + "name":
+                        name = child.text.strip() if child.text else None
+                    elif child.tag == NS + "dbReference":
+                        db_ref = child.attrib.get("id")
+                # Append to a list of ligands in qualifiers
+                lig_list = feature.qualifiers.setdefault("ligands", [])
+                lig_list.append({"name": name, "db_ref": db_ref})
+                continue
             else:
                 try:
                     feature.qualifiers[feature_element.tag.replace(NS, "")] = (

CONTRIB.rst

@@ -155,6 +155,7 @@ please open an issue on GitHub or mention it on the mailing list.
 - Iddo Friedberg <https://github.com/idoerg>
 - Igor S. Gerasimov <https://github.com/foxtran>
 - Ilya Flyamer <https://github.com/Phlya>
+- Ira Horecka <https://github.com/irahorecka>
 - Isaac Ellmen <https://github.com/Ellmen>
 - Ivan Antonov <https://github.com/vanya-antonov>
 - Jacek Śmietański <https://github.com/dadoskawina>

Tests/SwissProt/multiligand.xml

@@ -0,0 +1,18 @@
+<uniprot xmlns="http://uniprot.org/uniprot">
+  <entry dataset="Swiss-Prot" created="2024-01-01" modified="2025-01-01" version="1">
+    <name>TEST_PROTEIN</name>
+    <accession>DUMMY123</accession>
+    <sequence length="1" mass="100" version="1">A</sequence>
+    <feature type="binding site">
+      <location><position position="1"/></location>
+      <ligand>
+        <name>ATP</name>
+        <dbReference type="ChEBI" id="CHEBI:15422"/>
+      </ligand>
+      <ligand>
+        <name>ADP</name>
+        <dbReference type="ChEBI" id="CHEBI:16761"/>
+      </ligand>
+    </feature>
+  </entry>
+</uniprot>

Tests/test_SeqIO_UniprotIO.py

@@ -498,6 +498,30 @@ class ParserTests(SeqRecordTestBaseClass):
         # test Entry version
         self.assertEqual(seq_record.annotations["entry_version"], 158)
 
+    def test_P62330_ligand(self):
+        """Test parsing of <ligand> in UniProt XML (P62330)."""
+        record = SeqIO.read("SwissProt/P62330.xml", "uniprot-xml")
+        all_ligands = []
+        for f in record.features:
+            all_ligands.extend(f.qualifiers.get("ligands", []))
+        self.assertEqual(len(all_ligands), 5)
+        self.assertEqual(all_ligands[0]["name"], "GTP")
+        self.assertEqual(all_ligands[0]["db_ref"], "CHEBI:37565")
+
+    def test_multiligand_binding_site(self):
+        """Test parsing of binding site with multiple ligands in UniProt XML."""
+        record = SeqIO.read("SwissProt/multiligand.xml", "uniprot-xml")
+        sites = [
+            f
+            for f in record.features
+            if f.type == "binding site" and "ligands" in f.qualifiers
+        ]
+        self.assertTrue(sites, "No binding site with ligands found")
+        self.assertEqual(len(sites[0].qualifiers["ligands"]), 2)
+        ligand_names = {lig["name"] for lig in sites[0].qualifiers["ligands"]}
+        self.assertIn("ATP", ligand_names)
+        self.assertIn("ADP", ligand_names)
+
     def compare_txt_xml(self, old, new):
         """Compare text and XML based parser output."""
         self.assertEqual(old.id, new.id)