Merge pull request #75 from rcsb/dev-dwp

V1.22 Adjust BIRD citation method in DictMethodChemRefHelper

HISTORY.txt

@@ -128,4 +128,5 @@
                     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
- 1-Apr-2024 - V1.21 Turn on GlyGen annotations loading
+ 1-Apr-2024 - V1.21 Turn on GlyGen annotations loading
+ 3-May-2024 - V1.22 Adjust BIRD citation method in DictMethodChemRefHelper

rcsb/utils/dictionary/DictMethodChemRefHelper.py

@@ -8,6 +8,7 @@
 #   29-Mar-2023 dwp Correct attribute name '_rcsb_chem_comp_target.provenance_code' to '_rcsb_chem_comp_target.provenance_source'
 #    5-Apr-2023 dwp Stop loading rcsb_chem_comp_synonyms for rcsb_chem_comp_synonyms.type 'Brand Name' (to be loaded to new separate data item later)
 #   18-Sep-2023 dwp Load COD references separately from CCDC/CSD references
+#    3-May-2024 dwp Change BIRD citation method to copy categories instead of just renaming, and only apply to BIRD entries
 ##
 """
 Helper class implements external method references supporting chemical
@@ -809,12 +810,15 @@ def renameCitationCategory(self, dataContainer, catName, **kwargs):
             logger.debug("Starting with  %r %r", dataContainer.getName(), catName)
             if not (dataContainer.exists("chem_comp") and dataContainer.exists("pdbx_chem_comp_identifier")):
                 return False
+            containerName = dataContainer.getName()
+            if not containerName.upper().startswith("PRD_"):
+                return False
             #
-            # Rename target categories
+            # Copy target categories to new name
             if dataContainer.exists("citation"):
-                dataContainer.rename("citation", "rcsb_bird_citation")
+                dataContainer.copy("citation", "rcsb_bird_citation")
             if dataContainer.exists("citation_author"):
-                dataContainer.rename("citation_author", "rcsb_bird_citation_author")
+                dataContainer.copy("citation_author", "rcsb_bird_citation_author")
             return True
         except Exception as e:
             logger.exception("For %s failing with %s", catName, str(e))

rcsb/utils/dictionary/__init__.py

@@ -2,4 +2,4 @@
 __author__ = "John Westbrook"
 __email__ = "[email protected]"
 __license__ = "Apache 2.0"
-__version__ = "1.21"
+__version__ = "1.22"

requirements.txt

@@ -1,6 +1,6 @@
 scipy
 numpy
-mmcif >= 0.75
+mmcif >= 0.88.0
 rcsb.utils.chemref >= 0.79
 rcsb.utils.citation >= 0.16
 rcsb.utils.config >= 0.35