Merge pull request #13 from molstar/strucmotif

Add APIs to support interactive 3D visualization required by the Advanced Search UI

Author: valasatava

CHANGELOG.md

@@ -2,6 +2,23 @@
 
 [Semantic Versioning](https://semver.org/)
 
+## [2.14.0] - Unreleased
+### General
+- Default assembly preset
+- More configuration options for controls in the layout and viewport
+
+### API
+- Subscribe to a structural selection-related event in the plugin
+- Update the interactivity settings in the plugin's interactivity manager
+- Retrieve the list of assembly IDs for a default structure model
+- Retrieve asym and author chain IDs for a default structure model
+- Set the current structure view based on the provided assembly ID
+- Add custom labels to specified targets within the current structure
+- Focus on a specific residue within the current structure
+- Set ball and stick representation for a specific target
+- Determine the unknown assemblyId for a set of targets
+- Toggle visibility of structure component groups
+
 ## [2.13.0] - 2025-09-29
 ### General
 - Dependency update: Mol* to v5.0.0

package-lock.json

@@ -1,6 +1,6 @@
 {
     "name": "@rcsb/rcsb-molstar",
-    "version": "2.13.0",
+    "version": "2.14.0-dev.6",
     "description": "RCSB PDB apps and props based on Mol*.",
     "homepage": "https://github.com/molstar/rcsb-molstar#readme",
     "repository": {

package.json

@@ -41,6 +41,9 @@ export class ModelLoader {
         params?: P
     ): Promise<S | ReturnType<typeof RcsbPreset.apply> | undefined> {
         const trajectory = await this.plugin.builders.structure.parseTrajectory(data, format);
+        if (!trajectory) {
+            throw new Error('Trajectory data is unavailable or invalid');
+        }
         if (reprProvider) {
             return this.plugin.builders.structure.hierarchy.applyPreset(trajectory, reprProvider, params);
         } else {

src/viewer/helpers/model.ts

@@ -35,7 +35,7 @@ import {
 import {
     createGlyGenSelectionExpressions,
     createSelectionExpressions,
-    normalizeTargets,
+    normalizeTarget,
     SelectionExpression,
     Target,
     targetToLoci,
@@ -48,6 +48,7 @@ import {
 } from 'molstar/lib/extensions/assembly-symmetry/prop';
 import { Task } from 'molstar/lib/mol-task';
 import { QualityAssessment } from 'molstar/lib/extensions/model-archive/quality-assessment/prop';
+import { getAssemblyIdsFromModel, firstMatchingAssemblyId } from './viewer';
 
 type BaseProps = {
     assemblyId?: string
@@ -126,8 +127,12 @@ export type GlyGenProps = {
     glycosylation: Target[],
 } & BaseProps
 
+export type DefaultAssembly = {
+    kind: 'default-assembly'
+} & BaseProps;
+
 export type PresetProps = ValidationProps | StandardProps | SymmetryProps | FeatureProps | DensityProps | AlignmentProps |
-MembraneProps | FeatureDensityProps | MotifProps | NakbProps | GlyGenProps | EmptyProps;
+MembraneProps | FeatureDensityProps | MotifProps | NakbProps | GlyGenProps | EmptyProps | DefaultAssembly;
 
 const RcsbParams = () => ({
     preset: PD.Value<PresetProps>({ kind: 'standard', assemblyId: '' }, { isHidden: true })
@@ -150,17 +155,27 @@ export const RcsbPreset = TrajectoryHierarchyPresetProvider({
         // jump through some hoops to determine the unknown assemblyId of query selections
         if (p.kind === 'motif') determineAssemblyId(trajectory, p);
 
-        const structureParams: RootStructureDefinition.Params = { name: 'model', params: {} };
-        if (p.assemblyId && p.assemblyId !== '' && p.assemblyId !== '0') {
-            Object.assign(structureParams, {
-                name: 'assembly',
-                params: { id: p.assemblyId }
-            } as RootStructureDefinition.Params);
-        }
-
         const model = await builder.createModel(trajectory, modelParams);
         const modelProperties = await builder.insertModelProperties(model);
 
+        const structureParams: RootStructureDefinition.Params = { name: 'model', params: {} };
+        if (p.kind === 'default-assembly') {
+            const assemblyIds = getAssemblyIdsFromModel(model.cell?.obj?.data);
+            if (assemblyIds.length > 0) {
+                Object.assign(structureParams, {
+                    name: 'assembly',
+                    params: { id: assemblyIds[0] }
+                } as RootStructureDefinition.Params);
+            }
+        } else {
+            if (p.assemblyId && p.assemblyId !== '' && p.assemblyId !== '0') {
+                Object.assign(structureParams, {
+                    name: 'assembly',
+                    params: { id: p.assemblyId }
+                } as RootStructureDefinition.Params);
+            }
+        }
+
         let structure: StructureObject | undefined = undefined;
         let structureProperties: StructureObject | undefined = undefined;
         let unitcell: StateObjectSelector | undefined = undefined;
@@ -232,7 +247,7 @@ export const RcsbPreset = TrajectoryHierarchyPresetProvider({
         } else if (p.kind === 'motif' && structure?.obj) {
             // let's force ASM_1 for motifs (as we use this contract in the rest of the stack)
             // TODO should ASM_1 be the default, seems like we'd run into problems when selecting ligands that are e.g. ambiguous with asym_id & seq_id alone?
-            const targets = normalizeTargets(p.targets, structure!.obj.data);
+            const targets = p.targets.map(t => normalizeTarget(t, structure!.obj!.data));
             let selectionExpressions = createSelectionExpressions(p.label || model.data!.entryId, targets);
             const globalExpressions = createSelectionExpressions(p.label || model.data!.entryId);
             selectionExpressions = selectionExpressions.concat(globalExpressions.map(e => { return { ...e, alpha: 0.21 }; }));
@@ -359,62 +374,15 @@ function determineAssemblyId(traj: any, p: MotifProps) {
     // nothing to do if assembly is known
     if (p.assemblyId && p.assemblyId !== '' && p.assemblyId !== '0') return;
 
-    function equals(expr: string, val: string): boolean {
-        const list = parseOperatorList(expr);
-        const split = val.split('x');
-        let matches = 0;
-        for (let i = 0, il = Math.min(list.length, split.length); i < il; i++) {
-            if (list[i].indexOf(split[i]) !== -1) matches++;
-        }
-        return matches === split.length;
-    }
-
-    function parseOperatorList(value: string): string[][] {
-        // '(X0)(1-5)' becomes [['X0'], ['1', '2', '3', '4', '5']]
-        // kudos to Glen van Ginkel.
-
-        const oeRegex = /\(?([^()]+)\)?]*/g, groups: string[] = [], ret: string[][] = [];
-
-        let g: any;
-        while (g = oeRegex.exec(value)) groups[groups.length] = g[1];
-
-        groups.forEach(g => {
-            const group: string[] = [];
-            g.split(',').forEach(e => {
-                const dashIndex = e.indexOf('-');
-                if (dashIndex > 0) {
-                    const from = parseInt(e.substring(0, dashIndex)), to = parseInt(e.substring(dashIndex + 1));
-                    for (let i = from; i <= to; i++) group[group.length] = i.toString();
-                } else {
-                    group[group.length] = e.trim();
-                }
-            });
-            ret[ret.length] = group;
-        });
-
-        return ret;
-    }
-
     // set of provided [structOperId, labelAsymId] combinations
     const ids = p.targets.map(t => [t.structOperId || '1', t.labelAsymId!]).filter((x, i, a) => a.indexOf(x) === i);
-
     try {
-        // find first assembly that contains all requested structOperIds - if multiple, the first will be returned
         const pdbx_struct_assembly_gen = traj.obj.data.representative.sourceData.data.frame.categories.pdbx_struct_assembly_gen;
-        if (pdbx_struct_assembly_gen) {
-            const assembly_id = pdbx_struct_assembly_gen.getField('assembly_id');
-            const oper_expression = pdbx_struct_assembly_gen.getField('oper_expression');
-            const asym_id_list = pdbx_struct_assembly_gen.getField('asym_id_list');
-
-            for (let i = 0, il = pdbx_struct_assembly_gen.rowCount; i < il; i++) {
-                if (ids.some(val => !equals(oper_expression.str(i), val[0]) || asym_id_list.str(i).indexOf(val[1]) === -1)) continue;
-
-                Object.assign(p, { assemblyId: assembly_id.str(i) });
-                return;
-            }
-        } else {
-            // this happens e.g. for AlphaFold structures
-            console.warn(`Source file is missing 'pdbx_struct_assembly_gen' category`);
+        // find first assembly that contains all requested structOperIds - if multiple, the first will be returned
+        const assemblyId = firstMatchingAssemblyId(pdbx_struct_assembly_gen, ids);
+        if (assemblyId) {
+            Object.assign(p, { assemblyId: assemblyId });
+            return;
         }
     } catch (error) {
         console.warn(error);
@@ -466,3 +434,4 @@ async function initVolumeStreaming(plugin: PluginContext, structure: StructureOb
         volume: false
     });
 }
+