DAOTHER-8905: V5.30 Release, Prevent infinite loop while parsing XEAS…

…Y PROT file
wwPDB · Feb 4, 2025 · 132a490 · 132a490
1 parent d25bc41
commit 132a490
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Showing 4 changed files with 28 additions and 0 deletions.
diff --git a/wwpdb/utils/nmr/mr/AmberPTParserListener.py b/wwpdb/utils/nmr/mr/AmberPTParserListener.py
@@ -910,6 +910,8 @@ def update_atom_num(seq_align, orphan):
                                 if atomNum['atom_id'] not in chemCompAtomIds or atomNum['atom_id'] in leavingAtomIds:
                                     delete_atom_nums.append(atom_num)
 
+            trial = 0
+
             while True:
 
                 orphanPolySeqPrmTop = []
@@ -961,6 +963,11 @@ def update_atom_num(seq_align, orphan):
                 if not resolved:
                     break
 
+                trial += 1
+
+                if trial > 10:
+                    break
+
             for ps in self.__polySeqPrmTop:
                 test_chain_id = ps['chain_id']
 

diff --git a/wwpdb/utils/nmr/mr/CharmmCRDParserListener.py b/wwpdb/utils/nmr/mr/CharmmCRDParserListener.py
@@ -630,6 +630,8 @@ def update_atom_num(seq_align, orphan):
                                 if atomNum['atom_id'] not in chemCompAtomIds or atomNum['atom_id'] in leavingAtomIds:
                                     delete_atom_nums.append(atom_num)
 
+            trial = 0
+
             while True:
 
                 orphanPolySeqPrmTop = []
@@ -681,6 +683,11 @@ def update_atom_num(seq_align, orphan):
                 if not resolved:
                     break
 
+                trial += 1
+
+                if trial > 10:
+                    break
+
             for ps in self.__polySeqPrmTop:
                 test_chain_id = ps['chain_id']
 

diff --git a/wwpdb/utils/nmr/mr/GromacsPTParserListener.py b/wwpdb/utils/nmr/mr/GromacsPTParserListener.py
@@ -846,6 +846,8 @@ def update_atom_num(seq_align, orphan):
                                 if atomNum['atom_id'] not in chemCompAtomIds or atomNum['atom_id'] in leavingAtomIds:
                                     delete_atom_nums.append(atom_num)
 
+            trial = 0
+
             while True:
 
                 orphanPolySeqPrmTop = []
@@ -897,6 +899,11 @@ def update_atom_num(seq_align, orphan):
                 if not resolved:
                     break
 
+                trial += 1
+
+                if trial > 10:
+                    break
+
             for ps in self.__polySeqPrmTop:
                 test_chain_id = ps['chain_id']
 

diff --git a/wwpdb/utils/nmr/pk/XeasyPROTParserListener.py b/wwpdb/utils/nmr/pk/XeasyPROTParserListener.py
@@ -649,6 +649,8 @@ def update_atom_num(seq_align, orphan):
                                 if atomNum['atom_id'] not in chemCompAtomIds or atomNum['atom_id'] in leavingAtomIds:
                                     delete_atom_nums.append(atom_num)
 
+            trial = 0
+
             while True:
 
                 orphanPolySeqPrmTop = []
@@ -700,6 +702,11 @@ def update_atom_num(seq_align, orphan):
                 if not resolved:
                     break
 
+                trial += 1
+
+                if trial > 10:
+                    break
+
             for ps in self.__polySeqPrmTop:
                 test_chain_id = ps['chain_id']