molrender state rendering

src/viewer/helpers/chain/preset.ts

@@ -0,0 +1,60 @@
+
+
+import { StructureRepresentationPresetProvider } from 'molstar/lib/mol-plugin-state/builder/structure/representation-preset';
+import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
+import { StateObjectRef } from 'molstar/lib/mol-state';
+import reprBuilder = StructureRepresentationPresetProvider.reprBuilder;
+import updateFocusRepr = StructureRepresentationPresetProvider.updateFocusRepr;
+import { MolScriptBuilder as MS } from 'molstar/lib/mol-script/language/builder';
+import { StateTransform } from 'molstar/lib/mol-state/transform';
+
+export const RcsbChainRepresentationPreset = StructureRepresentationPresetProvider({
+    id: 'preset-superposition-representation-rcsb',
+    display: {
+        group: 'Chain',
+        name: 'Chain Representation',
+        description: 'Show representations based on the given chain asymId.'
+    },
+    params: () => ({
+        ...StructureRepresentationPresetProvider.CommonParams,
+        asymId: PD.Value<string>("A"),
+        colorTheme: PD.Value<string>('sequence-id'),
+    }),
+    async apply(ref, params, plugin) {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+        if (!structureCell) return {};
+        const structure = structureCell.obj!.data;
+        const cartoonProps = { sizeFactor: structure.isCoarseGrained ? 0.8 : 0.2 };
+        const components = Object.create(null);
+        const representations = Object.create(null);
+        const chain = await plugin.builders.structure.tryCreateComponentFromExpression(structureCell, chainSelection(params.asymId), `Chain ${params.asymId}`);
+        Object.assign(components, { [`Chain ${params.asymId}`]: chain });
+        const { update, builder, typeParams } = reprBuilder(plugin, params);
+        const typeProps = { typeParams,...cartoonProps };
+        const reprProps = {
+            typeParams: typeProps,
+            color: params.colorTheme as any
+        };
+        Object.assign(representations, {
+            [`Chain ${params.asymId}`]: builder.buildRepresentation(update, chain, reprProps, {
+                tag: `Chain ${params.asymId}`,
+                // this only hides the visuals but the state UI will still indicate them as visible
+                initialState: { isHidden: false }
+            })
+        });
+        // make sure UI state is consistent
+        if (chain?.cell?.state) {
+            StateTransform.assignState(chain?.cell?.state, { isHidden: false });
+        }
+        await update.commit({ revertOnError: false });
+        // needed to apply same coloring scheme to focus representation
+        await updateFocusRepr(plugin, structure, params.theme?.focus?.name, params.theme?.focus?.params);
+        return representations;
+    }
+});
+
+function chainSelection(auth_asym_id: string) {
+    return MS.struct.generator.atomGroups({
+        'chain-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.auth_asym_id(), auth_asym_id])
+    });
+}

src/viewer/helpers/preset.ts

@@ -47,11 +47,13 @@ import {
 } from 'molstar/lib/extensions/rcsb/assembly-symmetry/prop';
 import { Task } from 'molstar/lib/mol-task';
 import { PLDDTConfidenceColorThemeProvider } from 'molstar/lib/extensions/model-archive/quality-assessment/color/plddt';
+import { RcsbChainRepresentationPreset } from './chain/preset';
 
 type BaseProps = {
     assemblyId?: string
     modelIndex?: number
     plddt?: 'off' | 'single-chain' | 'on'
+    colorTheme?: string
 }
 
 export { Mat4 } from 'molstar/lib/mol-math/linear-algebra';
@@ -117,8 +119,15 @@ export type NakbProps = {
     kind: 'nakb'
 } & BaseProps
 
+type ChainProps = {
+    kind: 'chain',
+    asymId: string,
+} & BaseProps
+
 export type PresetProps = ValidationProps | StandardProps | SymmetryProps | FeatureProps | DensityProps | AlignmentProps |
-MembraneProps | FeatureDensityProps | MotifProps | NakbProps | EmptyProps;
+MembraneProps | FeatureDensityProps | MotifProps | NakbProps | ChainProps | EmptyProps;
+
+
 
 const RcsbParams = () => ({
     preset: PD.Value<PresetProps>({ kind: 'standard', assemblyId: '' }, { isHidden: true })
@@ -240,6 +249,8 @@ export const RcsbPreset = TrajectoryHierarchyPresetProvider({
             representation = await plugin.builders.structure.representation.applyPreset<any>(structureProperties!, RcsbSuperpositionRepresentationPreset, { ...presetParams, ...additions });
         } else if (p.kind === 'validation') {
             representation = await plugin.builders.structure.representation.applyPreset<any>(structureProperties!, ValidationReportGeometryQualityPreset, presetParams);
+        } else if (p.kind === 'chain'){
+            representation = await plugin.builders.structure.representation.applyPreset<any>(structureProperties!, RcsbChainRepresentationPreset, { asymId: p.asymId, colorTheme: p.colorTheme });
         } else if (p.kind === 'symmetry' && structure?.obj) {
             const data = structure!.obj.data;
             if (!AssemblySymmetryDataProvider.get(data).value) {
@@ -275,7 +286,7 @@ export const RcsbPreset = TrajectoryHierarchyPresetProvider({
         } else if (p.kind === 'nakb') {
             representation = await plugin.builders.structure.representation.applyPreset<any>(structureProperties!, 'auto', { ...presetParams, theme: { globalName: 'nakb', focus: { name: 'nakb' } } });
         } else {
-            representation = await plugin.builders.structure.representation.applyPreset(structureProperties!, 'auto', presetParams);
+            representation = await plugin.builders.structure.representation.applyPreset(structureProperties!, 'auto', {...presetParams, theme: { globalName: p.colorTheme, focus: { name: p.colorTheme } } });
         }
 
         // TODO align with 'motif'?

src/viewer/index.ts

@@ -53,6 +53,7 @@ import { AssemblySymmetry } from 'molstar/lib/extensions/rcsb/assembly-symmetry/
 import { wwPDBChemicalComponentDictionary } from 'molstar/lib/extensions/wwpdb/ccd/behavior';
 import { ChemicalCompontentTrajectoryHierarchyPreset } from 'molstar/lib/extensions/wwpdb/ccd/representation';
 import { StateTransforms } from 'molstar/lib/mol-plugin-state/transforms';
+import { Camera } from 'molstar/lib/mol-canvas3d/camera';
 
 /** package version, filled in at bundle build time */
 declare const __RCSB_MOLSTAR_VERSION__: string;
@@ -355,6 +356,22 @@ export class Viewer {
         this._plugin.layout.events.updated.next(void 0);
     }
 
+    async loadMolrenderStateFromUrl(url: string) {
+        try {
+            const response = await fetch(url);
+            if (!response.ok) {
+                throw new Error(`HTTP error! status: ${response.status}`);
+            }
+            const data = await response.json();
+            this.loadPdbId(data.id, { props: buildProps(data) }).then(_ => {
+                this._plugin.canvas3d?.camera.setState(data.cameraState);
+                this.resetCamera(0);
+            });
+        } catch (error) {
+            console.error('There was a problem fetching the JSON file:', error);
+        }
+    }
+
     exportLoadedStructures(options?: { format?: 'cif' | 'bcif' }) {
         return exportHierarchy(this.plugin, options);
     }
@@ -563,3 +580,43 @@ export class LigandViewer {
         }
     }
 }
+
+type MolRenderStateType = {
+    id: string;
+    colorTheme: 'plddt-confidence' | 'sequence-id' | 'polymer-index' | 'polymer-id';
+    cameraState: Camera.Snapshot;
+} & ({
+    case: 'chain';
+    asymId: string;
+} | {
+    case: 'model';
+    modelIndex: number;
+} | {
+    case: 'assembly';
+    assemblyId: string;
+});
+
+function buildProps(molrenderState: MolRenderStateType): PresetProps {
+    switch (molrenderState.case) {
+        case 'model':
+            return {
+                kind: 'standard',
+                modelIndex: molrenderState.modelIndex,
+                colorTheme: molrenderState.colorTheme,
+            };
+        case 'assembly':
+            return {
+                kind: 'standard' as const,
+                assemblyId: molrenderState.assemblyId,
+                colorTheme: molrenderState.colorTheme,
+            };
+        case 'chain':
+            return {
+                kind: 'chain' as const,
+                asymId: molrenderState.asymId,
+                colorTheme: molrenderState.colorTheme,
+            };
+        default:
+            throw new Error(`Unknown case '${molrenderState}'`);
+    }
+}