Merge pull request #24 from rcsb/ro-4209

RO-4209: Adjust LigandNeighborMappingExtractor in response to changes to rcsb_ligand_neighbors
rcsb · Jul 25, 2024 · f79d637 · f79d637
2 parents 0375129 + a6c9ec1
commit f79d637
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Showing 5 changed files with 8 additions and 5 deletions.
diff --git a/HISTORY.txt b/HISTORY.txt
@@ -101,3 +101,4 @@
                   Update unit tests and setuptools config
  9-May-2024 V1.2  Adjust provider type exclusion input to accept a list of types
 13-May-2024 V1.21 Update requirements; fix linting
+17-Jul-2024 V1.22 Adjust LigandNeighborMappingExtractor
diff --git a/rcsb/exdb/cli/__init__.py b/rcsb/exdb/cli/__init__.py
@@ -2,4 +2,4 @@
 __author__ = "John Westbrook"
 __email__ = "[email protected]"
 __license__ = "Apache 2.0"
-__version__ = "1.21"
+__version__ = "1.22"
diff --git a/rcsb/exdb/seq/LigandNeighborMappingExtractor.py b/rcsb/exdb/seq/LigandNeighborMappingExtractor.py
@@ -5,6 +5,7 @@
 # Utilities to extract ligand neighbor mapping details from the exchange collections.
 #
 # Updates:
+#  17-Jul-2024 dwp Stop fetching and including rcsb_ligand_neighbors.ligand_is_bound, since no longer populating that field
 #
 ##
 __docformat__ = "google en"
@@ -58,7 +59,6 @@ def __extractLigandNeighbors(self):
                     "rcsb_polymer_entity_instance_container_identifiers.entity_id",
                     "rcsb_polymer_entity_instance_container_identifiers.asym_id",
                     "rcsb_ligand_neighbors.ligand_comp_id",
-                    "rcsb_ligand_neighbors.ligand_is_bound",
                 ],
             )
             eCount = obEx.getCount()
@@ -71,8 +71,8 @@ def __extractLigandNeighbors(self):
                     entityId = peiD["rcsb_polymer_entity_instance_container_identifiers"]["entity_id"]
                     ky = entryId + "_" + entityId
                     for lnD in peiD["rcsb_ligand_neighbors"] if "rcsb_ligand_neighbors" in peiD else []:
-                        if "ligand_comp_id" in lnD and "ligand_is_bound" in lnD:
-                            rD.setdefault(ky, set()).add((lnD["ligand_comp_id"], lnD["ligand_is_bound"]))
+                        if "ligand_comp_id" in lnD:
+                            rD.setdefault(ky, set()).add(lnD["ligand_comp_id"])
                         else:
                             logger.warning("%s %s missing details lnD %r", entryId, entityId, lnD)
                 except Exception as e:

diff --git a/rcsb/exdb/seq/LigandNeighborMappingProvider.py b/rcsb/exdb/seq/LigandNeighborMappingProvider.py
@@ -56,7 +56,7 @@ def getLigandNeighbors(self, rcsbEntityId):
             list: [chem_comp_id, ... ]
         """
         try:
-            return list(set([t[0] for t in self.__mapD["mapping"][rcsbEntityId.upper()]]))
+            return list(set([t for t in self.__mapD["mapping"][rcsbEntityId.upper()]]))
         except Exception:
             return []
 

diff --git a/rcsb/exdb/tests/testLigandNeighborMappingProvider.py b/rcsb/exdb/tests/testLigandNeighborMappingProvider.py
@@ -69,7 +69,9 @@ def testLigandNeighborMapping(self):
             ok = crmP.testCache(minCount=2)
             self.assertTrue(ok)
             nL = crmP.getLigandNeighbors("3VFJ_2")
+            logger.info("ligand neighbor list nL %r", nL)
             self.assertGreaterEqual(len(nL), 4)
+            self.assertGreater(len(nL[0]), 1)
             #
         except Exception as e:
             logger.exception("Failing with %s", str(e))