tweaked structure labeling

src/apps/viewer/extensions/cellpack/model.ts

@@ -8,7 +8,7 @@ import { StateAction } from '../../../../mol-state';
 import { PluginContext } from '../../../../mol-plugin/context';
 import { PluginStateObject as PSO } from '../../../../mol-plugin/state/objects';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
-import { Ingredient, Packing } from './data';
+import { Ingredient, CellPacking } from './data';
 import { getFromPdb, getFromCellPackDB } from './util';
 import { Model, Structure, StructureSymmetry, StructureSelection, Queries, QueryContext } from '../../../../mol-model/structure';
 import { trajectoryFromMmCIF } from '../../../../mol-model-formats/structure/mmcif';
@@ -106,8 +106,9 @@ async function getIngredientStructure(ingredient: Ingredient, baseUrl: string) {
     return assembly
 }
 
-export function createStructureFromCellPack(ingredients: Packing['ingredients'], baseUrl: string) {
+export function createStructureFromCellPack(packing: CellPacking, baseUrl: string) {
     return Task.create('Create Packing Structure', async ctx => {
+        const { ingredients, name } = packing
         const structures: Structure[] = []
         for (const iName in ingredients) {
             if (ctx.shouldUpdate) ctx.update(iName)
@@ -115,7 +116,7 @@ export function createStructureFromCellPack(ingredients: Packing['ingredients'],
             if (s) structures.push(s)
         }
 
-        const builder = Structure.Builder()
+        const builder = Structure.Builder({ label: name })
         let offsetInvariantId = 0
         for (const s of structures) {
             let maxInvariantId = 0

src/apps/viewer/extensions/cellpack/state.ts

@@ -64,9 +64,9 @@ const StructureFromCellpack = PluginStateTransform.BuiltIn({
 })({
     apply({ a, params }) {
         return Task.create('Structure from CellPack', async ctx => {
-            const { ingredients, name } = a.data.packings[params.packing]
-            const structure = await createStructureFromCellPack(ingredients, params.baseUrl).runInContext(ctx)
-            return new PSO.Molecule.Structure(structure, { label: name })
+            const packing = a.data.packings[params.packing]
+            const structure = await createStructureFromCellPack(packing, params.baseUrl).runInContext(ctx)
+            return new PSO.Molecule.Structure(structure, { label: packing.name })
         });
     }
 });

src/mol-model-formats/structure/mmcif/parser.ts

@@ -207,14 +207,18 @@ function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, sourceIn
     }
 
     const coarse = EmptyIHMCoarse;
-    const label = format.data.entry.id.valueKind(0) === Column.ValueKind.Present
+    const entry = format.data.entry.id.valueKind(0) === Column.ValueKind.Present
         ? format.data.entry.id.value(0)
         : format.data._name;
 
+    const label: string[] = []
+    if (entry) label.push(entry)
+    if (format.data.struct.title.valueKind(0) === Column.ValueKind.Present) label.push(format.data.struct.title.value(0))
+
     return {
         id: UUID.create22(),
-        label,
-        entry: label,
+        label: label.join(' | '),
+        entry,
         sourceData: format,
         modelNum,
         entities,
@@ -240,11 +244,16 @@ function createModelIHM(format: mmCIF_Format, data: IHMData, formatData: FormatD
     const entry = format.data.entry.id.valueKind(0) === Column.ValueKind.Present
         ? format.data.entry.id.value(0)
         : format.data._name;
-    const label = data.model_group_name ? `${data.model_name}: ${data.model_group_name}` : data.model_name
+
+    const label: string[] = []
+    if (entry) label.push(entry)
+    if (format.data.struct.title.valueKind(0) === Column.ValueKind.Present) label.push(format.data.struct.title.value(0))
+    if (data.model_group_name) label.push(data.model_name)
+    if (data.model_group_name) label.push(data.model_group_name)
 
     return {
         id: UUID.create22(),
-        label,
+        label: label.join(' | '),
         entry,
         sourceData: format,
         modelNum: data.model_id,

src/mol-model/structure/structure/structure.ts

@@ -55,6 +55,7 @@ class Structure {
         elementCount: number,
         polymerResidueCount: number,
         coordinateSystem: SymmetryOperator,
+        label: string,
         propertyData?: any,
         customProps?: CustomProperties
     } = {
@@ -62,7 +63,8 @@ class Structure {
         transformHash: -1,
         elementCount: 0,
         polymerResidueCount: 0,
-        coordinateSystem: SymmetryOperator.Default
+        coordinateSystem: SymmetryOperator.Default,
+        label: ''
     };
 
     subsetBuilder(isSorted: boolean) {
@@ -153,6 +155,10 @@ class Structure {
         return this._props.coordinateSystem;
     }
 
+    get label() {
+        return this._props.label;
+    }
+
     get boundary() {
         return this.lookup3d.boundary;
     }
@@ -268,6 +274,9 @@ class Structure {
         if (props.coordinateSystem) this._props.coordinateSystem = props.coordinateSystem;
         else if (props.parent) this._props.coordinateSystem = props.parent.coordinateSystem;
 
+        if (props.label) this._props.label = props.label;
+        else if (props.parent) this._props.label = props.parent.label;
+
         if (props.masterModel) this._props.masterModel = props.masterModel;
         else if (props.parent) this._props.masterModel = props.parent.masterModel;
 
@@ -368,6 +377,7 @@ namespace Structure {
     export interface Props {
         parent?: Structure
         coordinateSystem?: SymmetryOperator
+        label?: string
         /** Master model for structures of a protein model and multiple ligand models */
         masterModel?: Model
         /** Representative model for structures of a model trajectory */
@@ -420,7 +430,7 @@ namespace Structure {
             count = units.length
         }
 
-        return create(units, { representativeModel: trajectory[0] });
+        return create(units, { representativeModel: trajectory[0], label: trajectory[0].label });
     }
 
     /**
@@ -431,7 +441,7 @@ namespace Structure {
      */
     export function ofModel(model: Model): Structure {
         const chains = model.atomicHierarchy.chainAtomSegments;
-        const builder = new StructureBuilder();
+        const builder = new StructureBuilder({ label: model.label });
 
         for (let c = 0 as ChainIndex; c < chains.count; c++) {
             const start = chains.offsets[c];

src/mol-model/structure/structure/symmetry.ts

@@ -25,7 +25,7 @@ namespace StructureSymmetry {
             if (!assembly) throw new Error(`Assembly '${asmName}' is not defined.`);
 
             const coordinateSystem = SymmetryOperator.create(assembly.id, Mat4.identity(), { id: assembly.id, operList: [] })
-            const assembler = Structure.Builder({ coordinateSystem });
+            const assembler = Structure.Builder({ coordinateSystem, label: structure.label });
 
             const queryCtx = new QueryContext(structure);
 
@@ -138,7 +138,7 @@ function getOperatorsCached333(symmetry: ModelSymmetry) {
 }
 
 function assembleOperators(structure: Structure, operators: ReadonlyArray<SymmetryOperator>) {
-    const assembler = Structure.Builder();
+    const assembler = Structure.Builder({ label: structure.label });
     const { units } = structure;
     for (const oper of operators) {
         for (const unit of units) {

src/mol-plugin/state/transforms/model.ts

@@ -96,7 +96,7 @@ const TrajectoryFromMmCif = PluginStateTransform.BuiltIn({
             if (!block) throw new Error(`Data block '${[header]}' not found.`);
             const models = await trajectoryFromMmCIF(block).runInContext(ctx);
             if (models.length === 0) throw new Error('No models found.');
-            const props = { label: models[0].label, description: `${models.length} model${models.length === 1 ? '' : 's'}` };
+            const props = { label: `${models[0].entry}`, description: `${models.length} model${models.length === 1 ? '' : 's'}` };
             return new SO.Molecule.Trajectory(models, props);
         });
     }
@@ -114,7 +114,7 @@ const TrajectoryFromPDB = PluginStateTransform.BuiltIn({
             const parsed = await parsePDB(a.data, a.label).runInContext(ctx);
             if (parsed.isError) throw new Error(parsed.message);
             const models = await trajectoryFromPDB(parsed.result).runInContext(ctx);
-            const props = { label: models[0].label, description: `${models.length} model${models.length === 1 ? '' : 's'}` };
+            const props = { label: `${models[0].entry}`, description: `${models.length} model${models.length === 1 ? '' : 's'}` };
             return new SO.Molecule.Trajectory(models, props);
         });
     }
@@ -132,7 +132,7 @@ const TrajectoryFromGRO = PluginStateTransform.BuiltIn({
             const parsed = await parseGRO(a.data).runInContext(ctx);
             if (parsed.isError) throw new Error(parsed.message);
             const models = await trajectoryFromGRO(parsed.result).runInContext(ctx);
-            const props = { label: models[0].label, description: `${models.length} model${models.length === 1 ? '' : 's'}` };
+            const props = { label: `${models[0].entry}`, description: `${models.length} model${models.length === 1 ? '' : 's'}` };
             return new SO.Molecule.Trajectory(models, props);
         });
     }
@@ -156,7 +156,7 @@ const ModelFromTrajectory = PluginStateTransform.BuiltIn({
     apply({ a, params }) {
         if (params.modelIndex < 0 || params.modelIndex >= a.data.length) throw new Error(`Invalid modelIndex ${params.modelIndex}`);
         const model = a.data[params.modelIndex];
-        const label = a.data.length === 1 ? model.entry : `${model.entry}: ${model.modelNum}`
+        const label = `Model ${model.modelNum}`
         const description = a.data.length === 1 ? undefined : `Model ${params.modelIndex + 1} of ${a.data.length}`
         return new SO.Molecule.Model(model, { label, description });
     }
@@ -172,7 +172,7 @@ const StructureFromTrajectory = PluginStateTransform.BuiltIn({
     apply({ a }) {
         return Task.create('Build Structure', async ctx => {
             const s = Structure.ofTrajectory(a.data);
-            const props = { label: a.data[0].label, description: s.elementCount === 1 ? '1 element' : `${s.elementCount} elements` };
+            const props = { label: s.label, description: s.elementCount === 1 ? '1 element' : `${s.elementCount} elements` };
             return new SO.Molecule.Structure(s, props);
         })
     }