DAOTHER-8905, 9785, BMRB internal annotation: Enable to remove empty …

…spectral peak lists in NMR data remediation Phase 2 and BMRB internal annotation, except for OneDep
wwPDB · Feb 20, 2025 · d877cab · d877cab
1 parent 499250f
commit d877cab
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/wwpdb/utils/nmr/NmrDpUtility.py b/wwpdb/utils/nmr/NmrDpUtility.py
@@ -25295,7 +25295,7 @@ def __extractToNmrIf(self) -> bool:
 
         ann = BMRBAnnTasks(self.__verbose, self.__lfh,
                            self.__sf_category_list, self.__entry_id,
-                           self.__sail_flag, self.report,
+                           self.__internal_mode, self.__sail_flag, self.report,
                            ccU=self.__ccU, csStat=self.__csStat, c2S=self.__c2S)
 
         ann.perform(master_entry)
@@ -59804,7 +59804,7 @@ def __performBMRBAnnTasks(self) -> bool:
 
         ann = BMRBAnnTasks(self.__verbose, self.__lfh,
                            self.__sf_category_list, self.__entry_id,
-                           self.__sail_flag, self.report,
+                           self.__internal_mode, self.__sail_flag, self.report,
                            ccU=self.__ccU, csStat=self.__csStat, c2S=self.__c2S)
 
         is_done = ann.perform(master_entry)

diff --git a/wwpdb/utils/nmr/ann/BMRBAnnTasks.py b/wwpdb/utils/nmr/ann/BMRBAnnTasks.py
@@ -83,7 +83,7 @@ class BMRBAnnTasks:
 
     def __init__(self, verbose: bool, log: IO,
                  sfCategoryList: List[str], entryId: str,
-                 sailFlag: bool, report: NmrDpReport,
+                 internalMode: bool, sailFlag: bool, report: NmrDpReport,
                  ccU: Optional[ChemCompUtil] = None, csStat: Optional[BMRBChemShiftStat] = None,
                  c2S: Optional[CifToNmrStar] = None):
         self.__class_name__ = self.__class__.__name__
@@ -94,6 +94,8 @@ def __init__(self, verbose: bool, log: IO,
 
         self.__sfCategoryList = sfCategoryList
         self.__entryId = entryId
+
+        self.__internalMode = internalMode
         self.__sailFlag = sailFlag
         self.__report = report
 
@@ -1957,7 +1959,7 @@ def is_natural_abundance(isotopic_labeling: str):
 
         # resolve duplication of spectral peak lists
 
-        if sf_category in self.__sfCategoryList:
+        if sf_category in self.__sfCategoryList and self.__internalMode:
 
             tags_2d = ['Volume', 'Height', 'Position_1', 'Position_2', 'Auth_asym_ID_1']
             tags_3d = ['Volume', 'Height', 'Position_1', 'Position_2', 'Position_3', 'Auth_asym_ID_1']