DAOTHER-9317, 9511: Prevent wrong atom_id mapping DC:H3 (extended imi…

…no proton) -> DC:H3' of BMRB chemical shift statistics
wwPDB · Jun 27, 2024 · 93cce50 · 93cce50
1 parent 2a00b69
commit 93cce50
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Showing 6 changed files with 8 additions and 1 deletion.
diff --git a/wwpdb/utils/nmr/BMRBChemShiftStat.py b/wwpdb/utils/nmr/BMRBChemShiftStat.py
@@ -1701,7 +1701,8 @@ def checkAtomNomenclature(self, atom_id, comp_id=None, verbose=False):
             return True, comp_id, atom_id[:-1]
 
         _atom_id = translateToStdAtomName(atom_id, comp_id, refAtomIdList=_ref_atom_ids, ccU=self.__ccU, unambig=False)
-        if _atom_id in _ref_atom_ids:
+        # prevent wrong atom_id mapping DC:H3 (extended imino proton) -> DC:H3' (DAOTHER-9317, 9511)
+        if _atom_id in _ref_atom_ids and (("'" not in atom_id and "'" not in _atom_id) or ("'" in atom_id and "'" in _atom_id)):
             # print(f'case 4. {_comp_id}:{atom_id} -> {comp_id}:{_atom_id}')
             return True, comp_id, _atom_id
 

diff --git a/wwpdb/utils/nmr/bmrb_cs_stat/dna_filt.pkl b/wwpdb/utils/nmr/bmrb_cs_stat/dna_filt.pkl
diff --git a/wwpdb/utils/nmr/bmrb_cs_stat/dna_full.pkl b/wwpdb/utils/nmr/bmrb_cs_stat/dna_full.pkl
diff --git a/wwpdb/utils/nmr/bmrb_cs_stat/others.pkl b/wwpdb/utils/nmr/bmrb_cs_stat/others.pkl
diff --git a/wwpdb/utils/nmr/bmrb_cs_stat/rna_full.pkl b/wwpdb/utils/nmr/bmrb_cs_stat/rna_full.pkl
diff --git a/wwpdb/utils/tests-nmr/test_BMRBChemShiftStat.py b/wwpdb/utils/tests-nmr/test_BMRBChemShiftStat.py
@@ -183,6 +183,12 @@ def test_get_ile_cs_stat(self):
         self.assertEqual([stat['atom_id'] for stat in self.bmrb_cs_stat.get('ILE') if 'avg' in stat and stat['desc'] == 'methyl' and stat['atom_id'][0] == 'H'],
                          ['HD11', 'HD12', 'HD13', 'HG21', 'HG22', 'HG23'])
 
+    def test_dc_h3_stat(self):
+        h3c_stat = next(cs_stat for cs_stat in self.bmrb_cs_stat.get('DC') if cs_stat['atom_id'] == "H3'")
+        self.assertTrue(h3c_stat['avg'] < 5.0)
+        h3_stat = next((cs_stat for cs_stat in self.bmrb_cs_stat.get('DC') if cs_stat['atom_id'] == "H3"), None)
+        self.assertIsNone(h3_stat)
+
 
 if __name__ == '__main__':
     unittest.main()