Issue #2: debug log util and tslib update

package.json

@@ -153,7 +153,7 @@
     "rxjs": "^6.6.6",
     "source-map-loader": "^3.0.1",
     "swagger-ui-dist": "^3.37.2",
-    "tslib": "^2.1.0",
+    "tslib": "^2.4.0",
     "util.promisify": "^1.0.1",
     "xhr2": "^0.2.0"
   }

src/apps/tm-viewer/index.html

@@ -108,7 +108,8 @@
             // Debug section
             var dbg = tm_molstar.DebugUtil;
             dbg.init(viewer.plugin);
-            console.log("'dbg' object has been initialized. Functions can be accessed via it.");
+            dbg.enableLog();
+            dbg.log("'dbg' object has been initialized. Functions can be accessed via it.");
 
         </script>
     </body>

src/extensions/tmdet/debug-utils.ts

@@ -14,11 +14,34 @@ import { PDBTMTransformationMatrix } from "./types";
 
 export namespace DebugUtil {
     let plugin: PluginUIContext;
+    let logEnabled = false;
 
     export function init(ctx: PluginUIContext) {
         plugin = ctx;
     }
 
+    //
+    // logging
+    //
+    export function enableLog() {
+        logEnabled = true;
+    }
+
+    export function disableLog() {
+        logEnabled = false;
+    }
+
+    export function log(...args: any[]) {
+        if (logEnabled) {
+            console.log(...args);
+        }
+    }
+
+    //
+    //
+    // lin.alg.
+    //
+
     export function transformVector(v: Vec3, matrix: Mat4): Vec3 {
         const result = Vec3.transformMat4(Vec3(), v, matrix);
         console.log("transformVector: Input v & matrix:", v, Mat4.makeTable(matrix));

src/extensions/tmdet/transformation.ts

@@ -8,6 +8,7 @@ import { StateObjectRef, StateBuilder } from '../../mol-state';
 import { Expression } from '../../mol-script/language/expression';
 import { MembraneOrientation } from './prop';
 import { TmDetColorThemeProvider } from './tmdet-color-theme';
+import { DebugUtil } from '../../apps/tm-viewer';
 
 export async function applyTransformations(plugin: PluginUIContext, pdbtmDescriptor: PDBTMDescriptor) {
     const annotations = pdbtmDescriptor.additional_entry_annotations;
@@ -29,6 +30,11 @@ export async function applyTransformations(plugin: PluginUIContext, pdbtmDescrip
         });
     }
 
+    // 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);
     // await plugin.runTask(Task.create(`TMDET: Apply membrane transformation`, async () => {
     //     transformWholeModel(plugin, pdbtmDescriptor.additional_entry_annotations.membrane.transformation_matrix);
@@ -43,15 +49,15 @@ export function transformWholeModel(plugin: PluginUIContext, membraneMatrix: PDB
     const membraneTransformation = transformationForStateTransform(membraneMatrix);
 
     // transform each component
-    console.log("STRUCTURES", getCurrentHierarchy(plugin).structures);
+    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();
-        console.log("memb.transform of ", label, component.cell.obj?.id);
-        // console.log(`${label} component.cell.obj:`, component.cell.obj);
-        // console.log(`${label} component:`, component);
+        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, {