DAOTHER-9317: Correct comments to avoid confusion when remapping chem…

…ical shift statistics of non-standard residues based on CCD since the error message is ignorable
wwPDB · Apr 19, 2024 · c3bab52 · c3bab52
1 parent 59108d6
commit c3bab52
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Showing 2 changed files with 9 additions and 7 deletions.
diff --git a/wwpdb/utils/nmr/BMRBChemShiftStat.py b/wwpdb/utils/nmr/BMRBChemShiftStat.py
@@ -16,7 +16,7 @@
 # 11-Nov-2022  M. Yokochi - add getProtonsInSameGroup() (NMR restraint remediation)
 # 20-Apr-2023  M. Yokochi - change backbone definition to be consistent with NMR restraint validation
 # 13-Dec-2023  M. Yokochi - support peptide-like residues containing symmetric aromatic ring (DAOTHER-8945)
-# 19-Apr-2024  M. Yokochi - add testAtomNomenclatureOfLibrary (DAOTHER-9317)
+# 19-Apr-2024  M. Yokochi - remap chemical shift statistics in reference to CCD (DAOTHER-9317)
 ##
 """ Wrapper class for retrieving BMRB chemical shift statistics.
     @author: Masashi Yokochi
@@ -1080,6 +1080,7 @@ def __appendExtraFromCcd(self, comp_id):
 
     def checkAtomNomenclature(self, atom_id, comp_id=None):
         """ Check atom nomenclature.
+            @return: status (bool), mapped comp_id, mapped atom_id
         """
 
         if comp_id is not None:
@@ -1114,7 +1115,7 @@ def checkAtomNomenclature(self, atom_id, comp_id=None):
 
         if len(ref_atom_ids) == 0 or cc_rel_status != 'REL':
             if self.__verbose:
-                self.__lfh.write(f"+BMRBChemShiftStat.checkAtomNomenclature() ++ Error  - {comp_id} is not valid CCD ID, status code: {cc_rel_status}\n")
+                self.__lfh.write(f"+BMRBChemShiftStat.checkAtomNomenclature() ++ Warning  - {comp_id} is not valid CCD ID, status code: {cc_rel_status}\n")
             return False, None, None
 
         ref_alt_atom_ids = [a[self.__ccU.ccaAltAtomId] for a in self.__ccU.lastAtomList]
@@ -1150,7 +1151,7 @@ def checkAtomNomenclature(self, atom_id, comp_id=None):
 
         if len(_ref_atom_ids) == 0:
             if self.__verbose:
-                self.__lfh.write(f"+BMRBChemShiftStat.checkAtomNomenclature() ++ Error  - {comp_id}:{atom_id} did not match with any atom in CCD. No candidates foud\n")
+                self.__lfh.write(f"+BMRBChemShiftStat.checkAtomNomenclature() ++ Warning  - {comp_id}:{atom_id} did not match with any atom in CCD. No candidates foud\n")
 
             return False, None, None
 
@@ -1168,7 +1169,7 @@ def checkAtomNomenclature(self, atom_id, comp_id=None):
             return True, comp_id, _atom_id
 
         if self.__verbose:
-            self.__lfh.write(f"+BMRBChemShiftStat.checkAtomNomenclature() ++ Error  - {comp_id}:{atom_id} did not match with any atom in CCD, {_ref_atom_ids}\n")
+            self.__lfh.write(f"+BMRBChemShiftStat.checkAtomNomenclature() ++ Warning  - {comp_id}:{atom_id} did not match with any atom in CCD, {_ref_atom_ids}\n")
 
         return False, None, None
 
@@ -1753,6 +1754,7 @@ def __updateCompIdSet(self):
 
     def testAtomNomenclatureOfLibrary(self):
         """ Report inconsistencies between BMRB chemical shift statistics and current CCD.
+            @return: status (bool)
         """
 
         def check_bmrb_cs_stat(atm_list):

diff --git a/wwpdb/utils/nmr/mr/ParserListenerUtil.py b/wwpdb/utils/nmr/mr/ParserListenerUtil.py
@@ -1826,15 +1826,15 @@ def translateToStdAtomName(atomId, refCompId=None, refAtomIdList=None, ccU=None,
                         return "H2'1"
                     if atomId == "H2''" and "H2'2" in refAtomIdList:  # DCZ, THM
                         return "H2'2"
-                    if atomId == "H2''" and "HO2'" in refAtomIdList:  # 5MC (DAOTHER-9313)
+                    if atomId == "H2''" and "HO2'" in refAtomIdList:  # 5MC (DAOTHER-9317)
                         return "HO2'"
                     if atomId == "H2''" and "H2'" in refAtomIdList:
                         return "H2'"
                     if atomId == "H2''''" and "H2''" in refAtomIdList:
                         return "H2''"
                     if atomId == "H2''''" and "H2'2" in refAtomIdList:  # DCZ, THM
                         return "H2'2"
-                    if atomId == "H2''''" and "HO2'" in refAtomIdList:  # 5MC (DAOTHER-9313)
+                    if atomId == "H2''''" and "HO2'" in refAtomIdList:  # 5MC (DAOTHER-9317)
                         return "HO2'"
                     if atomId == "H2''1" and "H2'1" in refAtomIdList:  # 4EN
                         return "H2'1"
@@ -1848,7 +1848,7 @@ def translateToStdAtomName(atomId, refCompId=None, refAtomIdList=None, ccU=None,
                     return "H2'1"
                 if atomId == "H2''" and "H2'2" in _refAtomIdList:  # DCZ, THM
                     return "H2'2"
-                if atomId == "H2''" and "HO2'" in _refAtomIdList:  # 5MC (DAOTHER-9313)
+                if atomId == "H2''" and "HO2'" in _refAtomIdList:  # 5MC (DAOTHER-9317)
                     return "HO2'"
                 if atomId == "H2''" and "H2'" in _refAtomIdList:
                     return "H2'"