Issue #646: fixed chain delete issue - excluding from transformations too

src/extensions/tmdet/symmetry.ts

@@ -85,9 +85,10 @@ function tmDetSymmetryFromMmCif(model: Model, excludedChains: string[]) {
     DebugUtil.log('Included chains:', result);
 
     DebugUtil.log('oper_list table: original:', Table.formatToString(data.pdbx_struct_oper_list));
-    DebugUtil.log('oper_list table: first row', Table.formatToString(
-        Table.ofRows(data.pdbx_struct_oper_list._schema, [ Table.getRow(data.pdbx_struct_oper_list, 0) ]))
+    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: first row', Table.formatToString(only_identity_operation));
 
     return ModelSymmetry.fromData({
         symmetry: data.symmetry,
@@ -96,7 +97,7 @@ function tmDetSymmetryFromMmCif(model: Model, excludedChains: string[]) {
         atom_sites: data.atom_sites,
         pdbx_struct_assembly: data.pdbx_struct_assembly,
         pdbx_struct_assembly_gen: updated_pdbx_struct_assembly_gen,
-        pdbx_struct_oper_list: data.pdbx_struct_oper_list
+        pdbx_struct_oper_list: only_identity_operation
     });
 }
 

src/extensions/tmdet/transformation.ts

@@ -29,6 +29,10 @@ export function applyTransformations(plugin: PluginUIContext, pdbtmDescriptor: P
             mx.apply_to_chain_list.forEach(function(chainPair) {
                 let id  = chainPair.chain_id;
                 let newId = chainPair.new_chain_id;
+                if (annotations.biomatrix.chain_deletes?.includes(newId)) {
+                    DebugUtil.log(`${id} -> ${newId} transformation skipped due to delete rule`);
+                    return;
+                }
                 const mtx = transformationForStateTransform(mx.transformation_matrix);
                 const composedTransformation = Mat4.mul(Mat4(), membraneTransformation, mtx);
                 chainTransformation(plugin, composedTransformation, id, newId);