Rely on _pdbx_branched_scheme.pdb_asym_id due to carbohydrate remedia…

…tion (7yhh)
wwPDB · Jan 29, 2024 · 07bb358 · 07bb358
1 parent 6b4eff7
commit 07bb358
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Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/wwpdb/utils/nmr/mr/CnsMRReader.py b/wwpdb/utils/nmr/mr/CnsMRReader.py
@@ -208,6 +208,11 @@ def parse(self, mrFilePath, cifFilePath=None, isFilePath=True,
 
 
 if __name__ == "__main__":
+    reader = CnsMRReader(True)
+    reader.setDebugMode(True)
+    reader.parse('../../tests-nmr/mock-data-remediation/7yhh/all.tbl',
+                 '../../tests-nmr/mock-data-remediation/7yhh/7yhh.cif')
+
     reader = CnsMRReader(True)
     reader.setDebugMode(True)
     reader_listener, _, _ =\

diff --git a/wwpdb/utils/nmr/mr/ParserListenerUtil.py b/wwpdb/utils/nmr/mr/ParserListenerUtil.py
@@ -2980,7 +2980,7 @@ def coordAssemblyChecker(verbose=True, log=sys.stdout,
                      'branched': [{'name': 'asym_id', 'type': 'str', 'alt_name': 'chain_id'},
                                   {'name': 'pdb_seq_num', 'type': 'int', 'alt_name': 'seq_id'},
                                   {'name': 'mon_id', 'type': 'str', 'alt_name': 'comp_id'},
-                                  {'name': 'auth_asym_id', 'type': 'str', 'alt_name': 'auth_chain_id'},
+                                  {'name': 'pdb_asym_id', 'type': 'str', 'alt_name': 'auth_chain_id'},
                                   {'name': 'auth_seq_num', 'type': 'int', 'alt_name': 'auth_seq_id'},
                                   {'name': branchedPdbMonIdName, 'type': 'str', 'alt_name': 'auth_comp_id', 'default-from': 'mon_id'}
                                   ],
@@ -4047,7 +4047,7 @@ def to_np_array(a):
                         has_ins_code = cR.hasItem('pdbx_branch_scheme', 'pdb_ins_code')
 
                         dataItems = [{'name': 'asym_id', 'type': 'str', 'alt_name': 'label_asym_id'},
-                                     {'name': 'auth_asym_id', 'type': 'str'},
+                                     {'name': 'pdb_asym_id', 'type': 'str', 'alt_name': 'auth_asym_id'},
                                      {'name': 'auth_seq_num', 'type': 'int', 'alt_name': 'alt_seq_id'},
                                      {'name': 'pdb_seq_num', 'type': 'int', 'alt_name': 'auth_seq_id'},
                                      {'name': 'num', 'type': 'int', 'alt_name': 'seq_id'},