Issue #784: constant identity operation created to avoiding crash with 8gi9

src/apps/tm-viewer/index.html

@@ -108,6 +108,7 @@
             }
 
             let idList = [
+                '8gi9',
                 '1afo', // PASSED
                 '1a0s', // PASSED
                 '2atk', // PASSED

src/extensions/tmdet/symmetry.ts

@@ -61,11 +61,7 @@ function tmDetSymmetryFromMmCif(model: Model, excludedChains: string[]) {
     DebugUtil.log('Non-poly entities:', Table.formatToString(data.pdbx_entity_nonpoly));
     DebugUtil.log('Non-poly chains:', data.pdbx_nonpoly_scheme.asym_id.toArray());
 
-    DebugUtil.log('oper_list table: original:', Table.formatToString(data.pdbx_struct_oper_list));
-    const only_identity_operation = Table.ofRows(
-        data.pdbx_struct_oper_list._schema, [ Table.getRow(data.pdbx_struct_oper_list, 0) ]
-    );
-    DebugUtil.log('oper_list table: updated first row', Table.formatToString(only_identity_operation));
+    const only_identity_operation = createPdbxStructOperList(data.pdbx_struct_oper_list);
 
     return ModelSymmetry.fromData({
         symmetry: data.symmetry,
@@ -102,6 +98,36 @@ function createPdbxStructAssemblyGen(pdbx_struct_assembly_gen: Table<mmCIF_Schem
     return updated_pdbx_struct_assembly_gen;
 }
 
+function createPdbxStructOperList(pdbx_struct_oper_list: Table<mmCIF_Schema['pdbx_struct_oper_list']>):
+    Table<mmCIF_Schema['pdbx_struct_oper_list']> {
+
+    let updated_pdbx_struct_oper_list = Table.ofColumns(
+        pdbx_struct_oper_list._schema,
+        {
+            id: Column.ofStringArray([ '1' ]),
+            type: Column.ofArray({
+                array: [ 'identity operation' ],
+                schema: pdbx_struct_oper_list.type.schema
+            }),
+            name: Column.ofStringArray([ '1_555' ]),
+            symmetry_operation: Column.ofStringArray([ 'x,y,z' ]),
+            matrix:  Column.ofArray({
+                array: [[ 1, 0, 0, 0, 1, 0, 0, 0, 1 ]],
+                schema: pdbx_struct_oper_list.matrix.schema
+            }),
+            vector: Column.ofArray({
+                array: [ [ 0, 0, 0 ] ],
+                schema: pdbx_struct_oper_list.vector.schema
+            })
+        }
+    );
+
+    DebugUtil.log('Orig. pdbx_struct_oper_list', Table.formatToString(pdbx_struct_oper_list));
+    DebugUtil.log('Updated pdbx_struct_oper_list', Table.formatToString(updated_pdbx_struct_oper_list));
+
+    return updated_pdbx_struct_oper_list;
+}
+
 function createAsymIdColumn(pdbx_struct_assembly_gen: Table<mmCIF_Schema['pdbx_struct_assembly_gen']>,
     excludedChains: string[]) {