diff --git a/src/apps/viewer/extensions/cellpack/model.ts b/src/apps/viewer/extensions/cellpack/model.ts
index 179e3c8fec205ba19a2047ec0e0bc35cbc636396..4383c786faf2ed9ad9dc8e877454527643f9386d 100644
--- a/src/apps/viewer/extensions/cellpack/model.ts
+++ b/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
diff --git a/src/apps/viewer/extensions/cellpack/state.ts b/src/apps/viewer/extensions/cellpack/state.ts
index b8b6ce3470d93741ecdaae2bbeb308e43f10d2d6..79a992a960ca4e4967e65034aec2de419801c241 100644
--- a/src/apps/viewer/extensions/cellpack/state.ts
+++ b/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 })
});
}
});
diff --git a/src/mol-model-formats/structure/mmcif/parser.ts b/src/mol-model-formats/structure/mmcif/parser.ts
index 4ac7d77b791e3489d15071892928b3486e3767b4..b9446b4bc3a648d950deecabbcec6dab7103a251 100644
--- a/src/mol-model-formats/structure/mmcif/parser.ts
+++ b/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,
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index 708eee3f3c2486c91dca749130c4438b5cb1aa48..08bc5c107c58568d9053260b751fce0817ec47c9 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/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];
diff --git a/src/mol-model/structure/structure/symmetry.ts b/src/mol-model/structure/structure/symmetry.ts
index 4ae63f47d445fde4356a68d8e4b5f7c395d51097..b472051b1e9cd5473d486353441768dfa06cc34e 100644
--- a/src/mol-model/structure/structure/symmetry.ts
+++ b/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) {
diff --git a/src/mol-plugin/state/transforms/model.ts b/src/mol-plugin/state/transforms/model.ts
index f78a0e94a39c5dd89ca824c87e2a170769168b79..5b3192e61aba717b8a0858b0df4a01d90096d009 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/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);
})
}