DAOTHER-9520: Do not remediate a cs line without mandatory atom_id an…

…d ignore it
wwPDB · Jul 1, 2024 · d3c7de7 · d3c7de7
1 parent 26812c8
commit d3c7de7
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Showing 5 changed files with 15 additions and 3 deletions.
diff --git a/wwpdb/utils/nmr/BMRBChemShiftStat.py b/wwpdb/utils/nmr/BMRBChemShiftStat.py
@@ -817,6 +817,9 @@ def loadStatFromCsvFile(self, file_name, primary_th, secondary_th=None, comp_id_
                 elif comp_id == 'THR' and _atom_id == 'MG':
                     _atom_id = 'MG2'
 
+                elif _atom_id.endswith('"'):
+                    _atom_id = _atom_id[:-1] + "'"
+
                 # methyl proton group
                 if _atom_id.startswith('M'):
                     _atom_id = re.sub(r'^M', 'H', _atom_id)
@@ -1706,6 +1709,9 @@ def checkAtomNomenclature(self, atom_id, comp_id=None, verbose=False):
             # print(f'case 4. {_comp_id}:{atom_id} -> {comp_id}:{_atom_id}')
             return True, comp_id, _atom_id
 
+        if comp_id == 'DC' and atom_id == 'H3':  # DAOTHER-9198
+            return True, 'DNR', 'HN3'
+
         if verbose:
             self.__lfh.write(f"+BMRBChemShiftStat.checkAtomNomenclature() ++ Warning  - {comp_id}:{atom_id} did not match with any atom in CCD, {_ref_atom_ids}\n")
 

diff --git a/wwpdb/utils/nmr/NmrDpUtility.py b/wwpdb/utils/nmr/NmrDpUtility.py
@@ -20792,7 +20792,10 @@ def __testDataConsistencyInLoop__(self, file_list_id, file_name, file_type, cont
                             item = 'insufficient_data'
                         has_bad_pattern = True
                     elif clea:
-                        if content_subtype.startswith('spectral_peak'):
+                        if content_subtype == 'chem_shift':
+                            warn += ' Partially assiged chemical shifts should be resolved or removed.'
+                            item = 'incompletely_assigned_chemical_shift'
+                        elif content_subtype.startswith('spectral_peak'):
                             warn += ' Unassigned spectral peaks can be included in your peak list(s).'
                             item = 'incompletely_assigned_spectral_peak'
                         else:
@@ -26982,9 +26985,10 @@ def test_seq_id_offset_as_is(lp, index, _row, _idx, chain_id, seq_id, comp_id, o
                         elif ambig_code in (4, 5, 6, 9):
                             has_genuine_ambig_code = True
 
-                    lp.add_data(_row)
+                    if _row[8] not in emptyValue:  # DAOTHER-9520: Atom_isotppe_number is mandatory
+                        lp.add_data(_row)
 
-                    index += 1
+                        index += 1
 
                 if trial == 0 and len(incomplete_comp_id_annotation) > 0:  # DAOTHER-9286
                     regenerate_request = True

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/tests-nmr/test_BMRBChemShiftStat.py b/wwpdb/utils/tests-nmr/test_BMRBChemShiftStat.py
@@ -188,6 +188,8 @@ def test_dc_h3_stat(self):
         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)
+        hn3_stat = next(cs_stat for cs_stat in self.bmrb_cs_stat.get('DNR') if cs_stat['atom_id'] == "HN3")
+        self.assertTrue(hn3_stat['avg'] > 5.0)
 
 
 if __name__ == '__main__':