Issue #805: clean ups

src/examples/assembly-tm/FeatureViewConfig.ts

@@ -128,9 +128,7 @@ export async function createFeatureViewerConfing(params: { pdbEntry: string, pdb
         loadConfig: {
             loadMethod: LoadMethod.loadStructureFromUrl,
             loadParams: {
-                //url: `https://pdbtm.unitmp.org/api/v1/entry/${params.pdbEntry}.trpdb`,
                 url: `https://www.ebi.ac.uk/pdbe/entry-files/download/${params.pdbEntry}_updated.cif`,
-                //url: `/${params.pdbEntry}.cif`,
                 format: 'mmcif',
                 isBinary: false,
                 id: `${params.pdbEntry}_model`,

src/examples/assembly-tm/preset2.ts

@@ -119,12 +119,6 @@ export const TmDetRcsbPreset = TrajectoryHierarchyPresetProvider({
         await plugin.state.data.build().to(trajectory)
             .apply(StateTransforms.Model.ModelFromTrajectory, modelParams, { ref: 'model' })
             .apply(StateTransforms.Model.StructureFromModel, props, { ref: 'assembly' })
-            // .apply(StateTransforms.Model.TransformStructureConformation, {
-            //         transform: {
-            //             name: 'components',
-            //             params: { axis: Vec3.unitY, angle: 90, translation: Vec3.zero() }
-            //         }
-            //     })
             .commit();
 
         const builder = plugin.builders.structure;

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

@@ -36,9 +36,6 @@ export function applyTransformations(plugin: PluginContext, pdbtmDescriptor: PDB
                 const mtx = transformationForStateTransform(mx.transformation_matrix);
                 const composedTransformation = Mat4.mul(Mat4(), membraneTransformation, mtx);
                 chainTransformation(plugin, composedTransformation, id, newId);
-                // await plugin.runTask(Task.create(`TMDET: Transform '${id}' into '${newId}'`, async () => {
-                //     chainTransformation(plugin, mx.transformation_matrix, id, newId);
-                // }));
             });
         });
     }
@@ -49,10 +46,6 @@ export function applyTransformations(plugin: PluginContext, pdbtmDescriptor: PDB
     //
     // 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);
-    // }));
-
 }
 
 export function transformWholeModel(plugin: PluginContext, membraneMatrix: PDBTMTransformationMatrix) {

src/examples/assembly-tm/tmdet-viewer/TmViewer.ts

@@ -9,15 +9,8 @@
 
 import { Viewer, ViewerProps } from '@rcsb/rcsb-molstar/build/src/viewer';
 import { TmDetColorThemeProvider } from '../tmdet-extension/tmdet-color-theme';
-import { PluginBehavior } from 'molstar/lib/mol-plugin/behavior';
-import { PluginSpec } from 'molstar/lib/mol-plugin/spec';
-import { MembraneOrientationPreset, TMDETMembraneOrientation } from '../tmdet-extension/behavior';
-import { SyncBehaviors } from 'molstar/lib/mol-plugin/behavior/static/state';
-import { PluginStateObject } from 'molstar/lib/mol-plugin-state/objects';
-import { MembraneOrientationProvider, TmDetDescriptorCache } from '../tmdet-extension/prop';
-import { MembraneOrientationRepresentationProvider } from '../tmdet-extension/representation';
+import { MembraneOrientationPreset } from '../tmdet-extension/behavior';
 import { TmDetLabelProvider } from '../tmdet-extension/labeling';
-import { registerTmDetSymmetry } from '../tmdet-extension/symmetry';
 
 
 /** package version, filled in at bundle build time */
@@ -34,7 +27,7 @@ export class TmViewer extends Viewer {
     constructor(elementOrId: string | HTMLElement, props: Partial<ViewerProps> = {}) {
         console.log("TmViewer constructor");
         super(elementOrId, props);
-        //this.plugin.representation.structure.themes.colorThemeRegistry.add(TmDetColorThemeProvider);
+
         this.initBehavior();
     }
 
@@ -46,35 +39,6 @@ export class TmViewer extends Viewer {
         this.plugin.representation.structure.themes.colorThemeRegistry.add(TmDetColorThemeProvider);
         this.plugin.managers.lociLabels.addProvider(TmDetLabelProvider);
 
-        // const behavior = PluginSpec.Behavior(TMDETMembraneOrientation);
-        // this.plugin.customStructureProperties.register(MembraneOrientationProvider, false);
-        // this.plugin.representation.structure.registry.add(MembraneOrientationRepresentationProvider);
-
-
-        // // // Init custom properties 1st
-        // let cat = PluginBehavior.getCategoryId(behavior.transformer);
-        // console.log('Behavior', behavior);
-        // console.log('Transformer', behavior.transformer);
-        // if (cat === 'custom-props') {
-        //     tree.to(PluginBehavior.getCategoryId(behavior.transformer)).apply(behavior.transformer, behavior.defaultParams, { ref: behavior.transformer.id });
-        // }
-        // // this.plugin.state.events.object.created.subscribe(o => {
-        // //     if (!PluginStateObject.isBehavior(o.obj)) return;
-        // //     console.log({ o });
-        // // });
-        // //o.obj.data.register(o.ref);
-        // //behavior.re
-        // console.log('behavior', behavior);
-        // console.log(PluginBehavior.Categories);
-    
-        // // await this.plugin.runTask(this.plugin.state.behaviors.updateTree(tree, { doNotUpdateCurrent: true, doNotLogTiming: true }));
-
-        // tree = this.plugin.state.behaviors.build();
-        // //const cat = PluginBehavior.getCategoryId(behavior.transformer);
-        // if (cat !== 'custom-props') {
-        //     tree.to(PluginBehavior.getCategoryId(behavior.transformer)).apply(behavior.transformer, behavior.defaultParams, { ref: behavior.transformer.id });
-        // }
-
         await this.plugin.runTask(this.plugin.state.behaviors.updateTree(tree, { doNotUpdateCurrent: true, doNotLogTiming: true }));
     }