Issue #2: chain-selection to implement chain-level operations

src/apps/viewer/index.ts

@@ -22,7 +22,7 @@ require('mol-plugin-ui/skin/light.scss');
 
 export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
 export { setDebugMode, setProductionMode } from '../../mol-util/debug';
-export { loadWithUNITMPMembraneRepresentation } from '../../extensions/tmdet/behavior';
+export { loadWithUNITMPMembraneRepresentation, red } from '../../extensions/tmdet/behavior';
 
 const Extensions = {
     'tmdet-membrane-orientation': PluginSpec.Behavior(TMDETMembraneOrientation)

src/extensions/tmdet/behavior.ts

@@ -133,6 +133,36 @@ export async function loadWithUNITMPMembraneRepresentation(plugin: PluginUIConte
     requestAnimationFrame(() => plugin.canvas3d?.requestCameraReset());
 }
 
+/**
+ * Util/test function. Preparation for chain-level operations.
+ * Sets color of specified chain to red.
+ *
+ * @param plugin UI context
+ * @param chainId Id of chain to be selected for transformation
+ */
+export function red(plugin: PluginUIContext, chainId: string): void {
+    const color: Color = Color.fromArray([255, 0, 0], 0);
+    const query: Expression = getChainExpression(chainId);
+
+    const structure: StateObjectRef<PMS> = plugin.managers.structure.hierarchy.current.models[0].structures[0].cell;
+    const update: StateBuilder.To<any, any> = plugin.build().to(structure);
+    update
+        .apply(
+            StateTransforms.Model.StructureSelectionFromExpression,
+            { label: 'RED', expression: query }
+        )
+        .apply(
+            StateTransforms.Representation.StructureRepresentation3D,
+            createStructureRepresentationParams(plugin, update.selector.data, {
+                type: 'gaussian-surface',
+                color: 'uniform',
+                colorParams: { value: color }
+            })
+        );
+    update.commit();
+}
+
+
 type PDBTMChainLabel = string;
 type PDBTMChain = {
     chain_label: PDBTMChainLabel,
@@ -237,7 +267,7 @@ async function createStructureRepresentation(plugin: PluginUIContext, pdbtmDescr
         }
 
         //console.log(`REGIONS-${chain.chain_label}`, regionsBySite);
-        regionsBySite.map((region: PDBTMRegion) => {
+        regionsBySite.forEach((region: PDBTMRegion) => {
             const regionUpdates = plugin.build();
             createRegionRepresentation(plugin, chain.chain_label, region, regionUpdates.to(structure));
             regionUpdates.commit();
@@ -362,6 +392,16 @@ function getAtomGroupExpression(chainId: string, auth_array: number[]): Expressi
     return query;
 }
 
+export function getChainExpression(chainId: string): Expression {
+    // TODO console.log('auth_array:', auth_array);
+    const query: Expression =
+        MS.struct.generator.atomGroups({
+            'chain-test': MS.core.rel.eq([chainId, MS.ammp('label_asym_id')])
+        });
+    return query;
+}
+
+
 async function downloadRegionDescriptor(plugin: PluginUIContext, params: any): Promise<any> {
     // run a fetch task
     const downloadResult: string = await plugin.runTask(plugin.fetch({ url: params.regionDescriptorUrl })) as string;