Issue #805: fixed whole-model transformation

src/examples/assembly-tm/tmdet-extension/transformation.ts

@@ -12,7 +12,7 @@ import { Mat4, Quat, Vec3 } from 'molstar/lib/mol-math/linear-algebra';
 import { PDBTMDescriptor, PDBTMTransformationMatrix, PMS } from './types';
 import { createStructureRepresentationParams } from 'molstar/lib/mol-plugin-state/helpers/structure-representation-params';
 import { StateTransforms } from 'molstar/lib/mol-plugin-state/transforms';
-import { StateObjectRef, StateBuilder } from 'molstar/lib/mol-state';
+import { StateObjectRef, StateBuilder, StateObjectSelector } from 'molstar/lib/mol-state';
 import { Expression } from 'molstar/lib/mol-script/language/expression';
 import { MembraneOrientation } from './prop';
 import { TmDetColorThemeProvider } from './tmdet-color-theme';
@@ -40,11 +40,6 @@ export function applyTransformations(plugin: PluginContext, pdbtmDescriptor: PDB
         });
     }
 
-    // WARNING: the components cannot be accessed here (created by chainTransformations in the above loop)
-    //          Maybe due to some kind of synchronization behavior.
-    //          plugin.runTask with "await" also cannot synchronize here.
-    //
-    // So this function call transforms only already existing components due to a side effect of another issue.
     transformWholeModel(plugin, pdbtmDescriptor.additional_entry_annotations.membrane.transformation_matrix);
 }
 
@@ -54,23 +49,12 @@ export function transformWholeModel(plugin: PluginContext, membraneMatrix: PDBTM
     //
     const membraneTransformation = transformationForStateTransform(membraneMatrix);
 
-    // transform each component
-    DebugUtil.log("STRUCTURES", getCurrentHierarchy(plugin).structures);
-    getCurrentHierarchy(plugin).structures[0].components.forEach(component => {
-        const structure: StateObjectRef<PMS> = component.cell;
-        const update: StateBuilder.To<any, any> = plugin.build().to(structure);
-
-        const label = component.cell.obj!.label.toUpperCase();
-        DebugUtil.log("memb.transform of", label, component.cell.obj?.id);
-        DebugUtil.log(`${label} component.cell.obj:`, component.cell.obj);
-        // DebugUtil.log(`${label} component:`, component);
-
-        update
-            .apply(StateTransforms.Model.TransformStructureConformation, {
-                "transform": { name: "matrix", params: { data: membraneTransformation, transpose: false } }
-            });
-        update.commit();
-    });
+    const update: StateBuilder.To<any, any> = plugin.state.data.build().to('assembly');
+    update
+        .apply(StateTransforms.Model.TransformStructureConformation, {
+            "transform": { name: "matrix", params: { data: membraneTransformation, transpose: false } }
+        });
+    update.commit();
 }
 
 /**