Removed Unit.label, fixed Model.label from mmCIF

src/mol-geo/representation/structure/index.ts

@@ -34,7 +34,7 @@ interface GroupRepresentation<T> {
 
 function label(loc: Element.Location) {
     const model = loc.unit.model.label
-    const instance = loc.unit.label
+    const instance = loc.unit.conformation.operator.name
     let element = ''
 
     if (Unit.isAtomic(loc.unit)) {

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

@@ -142,9 +142,13 @@ function createModel(format: mmCIF_Format, bounds: Interval, previous?: Model):
 
     const coarse = getIHMCoarse(format.data, entities);
 
+    const label = format.data.entry.id.valueKind(0) === Column.ValueKind.Present
+        ? format.data.entry.id.value(0)
+        : format.data._name;
+
     return {
         id: UUID.create(),
-        label: format.data.entry.id.value(0),
+        label,
         sourceData: format,
         modelNum: format.data.atom_site.pdbx_PDB_model_num.value(Interval.start(bounds)),
         entities,

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

 /**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
@@ -92,8 +92,7 @@ namespace Structure {
 
         for (let c = 0; c < chains.count; c++) {
             const elements = SortedArray.ofBounds(chains.segments[c], chains.segments[c + 1]);
-            const label = SymmetryOperator.Default.name
-            builder.addUnit(label, Unit.Kind.Atomic, model, SymmetryOperator.Default, elements);
+            builder.addUnit(Unit.Kind.Atomic, model, SymmetryOperator.Default, elements);
         }
 
         const cs = model.coarseHierarchy;
@@ -113,16 +112,15 @@ namespace Structure {
         const { chainSegments } = elements;
         for (let cI = 0; cI < chainSegments.count; cI++) {
             const elements = SortedArray.ofBounds(chainSegments.segments[cI], chainSegments.segments[cI + 1]);
-            const label = SymmetryOperator.Default.name
-            builder.addUnit(label, kind, model, SymmetryOperator.Default, elements);
+            builder.addUnit(kind, model, SymmetryOperator.Default, elements);
         }
     }
 
     export class StructureBuilder {
         private units: Unit[] = [];
 
-        addUnit(label: string, kind: Unit.Kind, model: Model, operator: SymmetryOperator, elements: SortedArray): Unit {
-            const unit = Unit.create(this.units.length, label, kind, model, operator, elements);
+        addUnit(kind: Unit.Kind, model: Model, operator: SymmetryOperator, elements: SortedArray): Unit {
+            const unit = Unit.create(this.units.length, kind, model, operator, elements);
             this.units.push(unit);
             return unit;
         }
@@ -153,14 +151,6 @@ namespace Structure {
         return arr.array;
     }
 
-    export function getLookup3d(s: Structure): StructureLookup3D {
-        return 0 as any;
-    }
-
-    export function getBoundary(s: Structure) {
-        return getLookup3d(s).boundary;
-    }
-
     export function hashCode(s: Structure) {
         return s.hashCode;
     }

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

@@ -25,11 +25,11 @@ namespace Unit {
     export function isSpheres(u: Unit): u is Spheres { return u.kind === Kind.Spheres; }
     export function isGaussians(u: Unit): u is Gaussians { return u.kind === Kind.Gaussians; }
 
-    export function create(id: number, label: string, kind: Kind, model: Model, operator: SymmetryOperator, elements: SortedArray): Unit {
+    export function create(id: number, kind: Kind, model: Model, operator: SymmetryOperator, elements: SortedArray): Unit {
         switch (kind) {
-            case Kind.Atomic: return new Atomic(id, unitIdFactory(), label, model, elements, SymmetryOperator.createMapping(operator, model.atomicConformation), AtomicProperties());
-            case Kind.Spheres: return createCoarse(id, unitIdFactory(), label, model, Kind.Spheres, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.spheres));
-            case Kind.Gaussians: return createCoarse(id, unitIdFactory(), label, model, Kind.Gaussians, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.gaussians));
+            case Kind.Atomic: return new Atomic(id, unitIdFactory(), model, elements, SymmetryOperator.createMapping(operator, model.atomicConformation), AtomicProperties());
+            case Kind.Spheres: return createCoarse(id, unitIdFactory(), model, Kind.Spheres, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.spheres));
+            case Kind.Gaussians: return createCoarse(id, unitIdFactory(), model, Kind.Gaussians, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.gaussians));
         }
     }
 
@@ -40,7 +40,6 @@ namespace Unit {
         readonly id: number,
         // invariant ID stays the same even if the Operator/conformation changes.
         readonly invariantId: number,
-        readonly label: string,
         readonly elements: SortedArray,
         readonly model: Model,
         readonly conformation: SymmetryOperator.ArrayMapping,
@@ -65,7 +64,6 @@ namespace Unit {
 
         readonly id: number;
         readonly invariantId: number;
-        readonly label: string;
         readonly elements: SortedArray;
         readonly model: Model;
         readonly conformation: SymmetryOperator.ArrayMapping;
@@ -78,13 +76,12 @@ namespace Unit {
 
         getChild(elements: SortedArray): Unit {
             if (elements.length === this.elements.length) return this;
-            return new Atomic(this.id, this.invariantId, this.label, this.model, elements, this.conformation, AtomicProperties());
+            return new Atomic(this.id, this.invariantId, this.model, elements, this.conformation, AtomicProperties());
         }
 
         applyOperator(id: number, operator: SymmetryOperator, dontCompose = false): Unit {
             const op = dontCompose ? operator : SymmetryOperator.compose(this.conformation.operator, operator);
-            const label = operator.name
-            return new Atomic(id, this.invariantId, label, this.model, this.elements, SymmetryOperator.createMapping(op, this.model.atomicConformation), this.props);
+            return new Atomic(id, this.invariantId, this.model, this.elements, SymmetryOperator.createMapping(op, this.model.atomicConformation), this.props);
         }
 
         get lookup3d() {
@@ -100,10 +97,9 @@ namespace Unit {
             return this.props.bonds.ref;
         }
 
-        constructor(id: number, invariantId: number, label: string, model: Model, elements: SortedArray, conformation: SymmetryOperator.ArrayMapping, props: AtomicProperties) {
+        constructor(id: number, invariantId: number, model: Model, elements: SortedArray, conformation: SymmetryOperator.ArrayMapping, props: AtomicProperties) {
             this.id = id;
             this.invariantId = invariantId;
-            this.label = label;
             this.model = model;
             this.elements = elements;
             this.conformation = conformation;
@@ -128,7 +124,6 @@ namespace Unit {
 
         readonly id: number;
         readonly invariantId: number;
-        readonly label: string;
         readonly elements: SortedArray;
         readonly model: Model;
         readonly conformation: SymmetryOperator.ArrayMapping;
@@ -138,13 +133,12 @@ namespace Unit {
 
         getChild(elements: SortedArray): Unit {
             if (elements.length === this.elements.length) return this as any as Unit /** lets call this an ugly temporary hack */;
-            return createCoarse(this.id, this.invariantId, this.label, this.model, this.kind, elements, this.conformation);
+            return createCoarse(this.id, this.invariantId, this.model, this.kind, elements, this.conformation);
         }
 
         applyOperator(id: number, operator: SymmetryOperator, dontCompose = false): Unit {
             const op = dontCompose ? operator : SymmetryOperator.compose(this.conformation.operator, operator);
-            const label = operator.name
-            const ret = createCoarse(id, this.invariantId, label, this.model, this.kind, this.elements, SymmetryOperator.createMapping(op, this.getCoarseElements()));
+            const ret = createCoarse(id, this.invariantId, this.model, this.kind, this.elements, SymmetryOperator.createMapping(op, this.getCoarseElements()));
             (ret as Coarse<K, C>)._lookup3d = this._lookup3d;
             return ret;
         }
@@ -162,11 +156,10 @@ namespace Unit {
             return this.kind === Kind.Spheres ? this.model.coarseConformation.spheres : this.model.coarseConformation.gaussians;
         }
 
-        constructor(id: number, invariantId: number, label: string, model: Model, kind: K, elements: SortedArray, conformation: SymmetryOperator.ArrayMapping) {
+        constructor(id: number, invariantId: number, model: Model, kind: K, elements: SortedArray, conformation: SymmetryOperator.ArrayMapping) {
             this.kind = kind;
             this.id = id;
             this.invariantId = invariantId;
-            this.label = label;
             this.model = model;
             this.elements = elements;
             this.conformation = conformation;
@@ -175,8 +168,8 @@ namespace Unit {
         }
     }
 
-    function createCoarse<K extends Kind.Gaussians | Kind.Spheres>(id: number, invariantId: number, label: string, model: Model, kind: K, elements: SortedArray, conformation: SymmetryOperator.ArrayMapping): Unit {
-        return new Coarse(id, invariantId, label, model, kind, elements, conformation) as any as Unit /** lets call this an ugly temporary hack */;
+    function createCoarse<K extends Kind.Gaussians | Kind.Spheres>(id: number, invariantId: number, model: Model, kind: K, elements: SortedArray, conformation: SymmetryOperator.ArrayMapping): Unit {
+        return new Coarse(id, invariantId, model, kind, elements, conformation) as any as Unit /** lets call this an ugly temporary hack */;
     }
 
     export class Spheres extends Coarse<Kind.Spheres, CoarseSphereConformation> { }

src/perf-tests/lookup3d.ts

@@ -52,11 +52,11 @@ export async function test() {
     const result = lookup.find(-30.07, 8.178, -13.897, 10);
     console.log(result.count)//, sortArray(result.indices));
 
-    const sl = Structure.getLookup3d(structures[0]);
+    const sl = structures[0].lookup3d;
     const result1 = sl.find(-30.07, 8.178, -13.897, 10);
     console.log(result1.count);//, result1.indices);
 
-    console.log(Structure.getBoundary(structures[0]));
+    console.log(structures[0].boundary);
     console.log(lookup.boundary);
 }
 

src/servers/model/server/api.ts

@@ -52,10 +52,9 @@ const AtomSiteParameters = {
 // }
 
 function entityTest1_555(params: any): Element.Predicate | undefined {
-    const oper = Queries.props.unit.operator_name;
-    if (typeof params.entity_id === 'undefined') return Element.property(l => oper(l) === '1_555');
+    if (typeof params.entity_id === 'undefined') return Element.property(l => l.unit.conformation.operator.isIdentity);
     const p = Queries.props.entity.id, id = '' + params.entityId;
-    return Element.property(l => p(l) === id && oper(l) === '1_555');
+    return Element.property(l => l.unit.conformation.operator.isIdentity && p(l) === id);
 }
 
 function chainTest(params: any): Element.Predicate | undefined {

src/servers/model/server/query.ts

@@ -77,7 +77,7 @@ export async function resolveRequest(req: Request, writer: Writer) {
     const encoder = CifWriter.createEncoder({ binary: req.responseFormat.isBinary, encoderName: `ModelServer ${Version}` });
 
     perf.start('encode');
-    encoder.startDataBlock('result');
+    encoder.startDataBlock(structure.units[0].model.label.toUpperCase());
     encoder.writeCategory(_model_server_result, [req]);
     encoder.writeCategory(_model_server_params, [req]);