Merge pull request #74 from rcsb/ro-3958

V1.21 Turn on GlyGen annotations loading
rcsb · Apr 2, 2024 · e7b7679 · e7b7679
2 parents bdc9959 + 68d11fb
commit e7b7679
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Showing 3 changed files with 43 additions and 41 deletions.
diff --git a/HISTORY.txt b/HISTORY.txt
@@ -127,4 +127,5 @@
                     Create separate providerType names 'pdbx_core' and 'pdbx_comp_model_core' to limit loading of unnecessary
                     resources for each dataset (via providerTypeExclude)
 26-Mar-2024 - V1.20 Add GlyGen annotation 'type' to polymer entity instances, but temporarily turn off loading
-                    Fix incremental update method for NeighborInteractionWorkflow
+                    Fix incremental update method for NeighborInteractionWorkflow
+ 1-Apr-2024 - V1.21 Turn on GlyGen annotations loading
diff --git a/rcsb/utils/dictionary/DictMethodEntityInstanceHelper.py b/rcsb/utils/dictionary/DictMethodEntityInstanceHelper.py
@@ -19,6 +19,7 @@
 #  19-Mar-2024 dwp Add GlyGen annotations to polymer entity instances with glycosylation sites;
 #                  Don't run 'buildInstanceLigandNeighbors' or 'buildInstanceTargetNeighbors' for CSMs (no neighbor data available)
 #  26-Mar-2024 dwp Add "type" to GlyGen annotations, but temporarily turn off loading
+#   1-Apr-2024 dwp Turn on GlyGen annotations loading
 ##
 """
 This helper class implements methods supporting entity-instance-level functions in the RCSB dictionary extension.
@@ -2117,45 +2118,45 @@ def buildEntityInstanceAnnotations(self, dataContainer, catName, **kwargs):
                     ii += 1
             #
             #  GlyGen
-            # ggP = rP.getResource("GlyGenProvider instance") if rP else None
-            # if ggP:
-            #     gS = set()
-            #     version = ggP.getVersion()
-            #     ggD = ggP.getGlycoproteins()
-            #     for asymId, authAsymId in asymAuthIdD.items():
-            #         if instTypeD[asymId] not in ["polymer"]:
-            #             continue
-            #         entityId = asymIdD[asymId]
-            #         logger.debug("entryId %r entityId %r, asymId %r", entryId, entityId, asymId)
-            #         instConnL = self.__commonU.getInstanceConnections(dataContainer)
-            #         for cD in instConnL:
-            #             if "role" in cD and cD["role"] in ["C-Mannosylation", "N-Glycosylation", "O-Glycosylation", "S-Glycosylation"]:
-            #                 if asymId == cD["connect_target_label_asym_id"] or asymId == cD["connect_partner_label_asym_id"]:
-            #                     # Get UniProt IDs from rcsb_polymer_entity_align
-            #                     # Note that this requires `addPolymerEntityReferenceAlignments` to be run before `buildEntityInstanceAnnotations` (in methods dictionary)
-            #                     unpIdL = self.__commonU.getPolymerEntityReferenceAlignments(dataContainer, entityId, "UniProt")
-            #                     unpIdL = [aD["reference_database_accession"] for aD in unpIdL]
-            #                     logger.debug("unpIdL %r", unpIdL)
-            #                     for unpId in unpIdL:
-            #                         if ggP.hasGlycoprotein(unpId):
-            #                             ggId = unpId + "-" + ggD[unpId]
-            #                             gTup = (entryId, entityId, asymId, authAsymId, ggId)
-            #                             logger.debug("gTup %r", gTup)
-            #                             gS.add(gTup)
-
-            #     for (entryId, entityId, asymId, authAsymId, ggId) in gS:
-            #         logger.debug("adding to cObj: %r %r %r %r %r", entryId, entityId, asymId, authAsymId, ggId)
-            #         cObj.setValue(ii + 1, "ordinal", ii)
-            #         cObj.setValue(entryId, "entry_id", ii)
-            #         cObj.setValue(entityId, "entity_id", ii)
-            #         cObj.setValue(asymId, "asym_id", ii)
-            #         cObj.setValue(authAsymId, "auth_asym_id", ii)
-            #         cObj.setValue("GlyGen", "type", ii)
-            #         cObj.setValue(ggId, "annotation_id", ii)
-            #         cObj.setValue("GlyGen", "provenance_source", ii)
-            #         cObj.setValue(version, "assignment_version", ii)
-            #         #
-            #         ii += 1
+            ggP = rP.getResource("GlyGenProvider instance") if rP else None
+            if ggP:
+                gS = set()
+                version = ggP.getVersion()
+                ggD = ggP.getGlycoproteins()
+                for asymId, authAsymId in asymAuthIdD.items():
+                    if instTypeD[asymId] not in ["polymer"]:
+                        continue
+                    entityId = asymIdD[asymId]
+                    logger.debug("entryId %r entityId %r, asymId %r", entryId, entityId, asymId)
+                    instConnL = self.__commonU.getInstanceConnections(dataContainer)
+                    for cD in instConnL:
+                        if "role" in cD and cD["role"] in ["C-Mannosylation", "N-Glycosylation", "O-Glycosylation", "S-Glycosylation"]:
+                            if asymId == cD["connect_target_label_asym_id"] or asymId == cD["connect_partner_label_asym_id"]:
+                                # Get UniProt IDs from rcsb_polymer_entity_align
+                                # Note that this requires `addPolymerEntityReferenceAlignments` to be run before `buildEntityInstanceAnnotations` (in methods dictionary)
+                                unpIdL = self.__commonU.getPolymerEntityReferenceAlignments(dataContainer, entityId, "UniProt")
+                                unpIdL = [aD["reference_database_accession"] for aD in unpIdL]
+                                logger.debug("unpIdL %r", unpIdL)
+                                for unpId in unpIdL:
+                                    if ggP.hasGlycoprotein(unpId):
+                                        ggId = unpId + "-" + ggD[unpId]
+                                        gTup = (entryId, entityId, asymId, authAsymId, ggId)
+                                        logger.debug("gTup %r", gTup)
+                                        gS.add(gTup)
+
+                for (entryId, entityId, asymId, authAsymId, ggId) in gS:
+                    logger.debug("adding to cObj: %r %r %r %r %r", entryId, entityId, asymId, authAsymId, ggId)
+                    cObj.setValue(ii + 1, "ordinal", ii)
+                    cObj.setValue(entryId, "entry_id", ii)
+                    cObj.setValue(entityId, "entity_id", ii)
+                    cObj.setValue(asymId, "asym_id", ii)
+                    cObj.setValue(authAsymId, "auth_asym_id", ii)
+                    cObj.setValue("GlyGen", "type", ii)
+                    cObj.setValue(ggId, "annotation_id", ii)
+                    cObj.setValue("GlyGen", "provenance_source", ii)
+                    cObj.setValue(version, "assignment_version", ii)
+                    #
+                    ii += 1
             #
             # Glycosylation annotations
             jj = 1

diff --git a/rcsb/utils/dictionary/__init__.py b/rcsb/utils/dictionary/__init__.py
@@ -2,4 +2,4 @@
 __author__ = "John Westbrook"
 __email__ = "[email protected]"
 __license__ = "Apache 2.0"
-__version__ = "1.20"
+__version__ = "1.21"