diff --git a/src/mol-math/geometry/symmetry-operator.ts b/src/mol-math/geometry/symmetry-operator.ts
index fe6cbc7aa04ca0deaa8869cb4afbe7998fc7669e..8f9cac24028275ce2a8882e3859e1bd8c8e63c87 100644
--- a/src/mol-math/geometry/symmetry-operator.ts
+++ b/src/mol-math/geometry/symmetry-operator.ts
@@ -18,13 +18,13 @@ interface SymmetryOperator {
}
namespace SymmetryOperator {
- export const DefaultName = '1_555'
+ export const DefaultName = 'identity'
export const Default: SymmetryOperator = create(DefaultName, Mat4.identity());
const RotationEpsilon = 0.0001;
export function create(name: string, matrix: Mat4, hkl?: Vec3): SymmetryOperator {
- const _hkl = hkl ? Vec3.copy(Vec3.zero(), hkl) : Vec3.zero();
+ const _hkl = hkl ? Vec3.clone(hkl) : Vec3.zero();
if (Mat4.isIdentity(matrix)) return { name, matrix, inverse: Mat4.identity(), isIdentity: true, hkl: _hkl };
if (!Mat4.isRotationAndTranslation(matrix, RotationEpsilon)) throw new Error(`Symmetry operator (${name}) must be a composition of rotation and translation.`);
return { name, matrix, inverse: Mat4.invert(Mat4.zero(), matrix), isIdentity: false, hkl: _hkl };
diff --git a/src/mol-model/structure/model/formats/mmcif.ts b/src/mol-model/structure/model/formats/mmcif.ts
index 6f135c7209df51cbb0721bc969a8510205f0711e..33c5897d3926237165403caff080e613b97daff5 100644
--- a/src/mol-model/structure/model/formats/mmcif.ts
+++ b/src/mol-model/structure/model/formats/mmcif.ts
@@ -144,6 +144,7 @@ function createModel(format: mmCIF_Format, bounds: Interval, previous?: Model):
return {
id: UUID.create(),
+ label: format.data.entry.id.value(0),
sourceData: format,
modelNum: format.data.atom_site.pdbx_PDB_model_num.value(Interval.start(bounds)),
entities,
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index 1053bde91c2382c05f3a64445ae12facec884b62..214dc8d8687ce1b59cfd871513163622b2162420 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -23,6 +23,7 @@ import from_mmCIF from './formats/mmcif'
*/
interface Model extends Readonly<{
id: UUID,
+ label: string,
modelNum: number,
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index bbc7b301d63319d52e34c354e27ef0d816fb44bd..88abc99496ed3bc540ea936dbc6c3764e49d2447 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -92,7 +92,8 @@ namespace Structure {
for (let c = 0; c < chains.count; c++) {
const elements = SortedArray.ofBounds(chains.segments[c], chains.segments[c + 1]);
- builder.addUnit(Unit.Kind.Atomic, model, SymmetryOperator.Default, elements);
+ const label = SymmetryOperator.Default.name
+ builder.addUnit(label, Unit.Kind.Atomic, model, SymmetryOperator.Default, elements);
}
const cs = model.coarseHierarchy;
@@ -112,15 +113,16 @@ namespace Structure {
const { chainSegments } = elements;
for (let cI = 0; cI < chainSegments.count; cI++) {
const elements = SortedArray.ofBounds(chainSegments.segments[cI], chainSegments.segments[cI + 1]);
- builder.addUnit(kind, model, SymmetryOperator.Default, elements);
+ const label = SymmetryOperator.Default.name
+ builder.addUnit(label, kind, model, SymmetryOperator.Default, elements);
}
}
export class StructureBuilder {
private units: Unit[] = [];
- addUnit(kind: Unit.Kind, model: Model, operator: SymmetryOperator, elements: SortedArray): Unit {
- const unit = Unit.create(this.units.length, kind, model, operator, elements);
+ 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);
this.units.push(unit);
return unit;
}
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index 5c34fd555248e6b3c2cf752446930b7d47116f6e..8c6e715eacfbca24beadfa8bab3d6fa7e35e7c62 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/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, kind: Kind, model: Model, operator: SymmetryOperator, elements: SortedArray): Unit {
+ export function create(id: number, label: string, kind: Kind, model: Model, operator: SymmetryOperator, elements: SortedArray): Unit {
switch (kind) {
- 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));
+ 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));
}
}
@@ -40,6 +40,7 @@ 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,
@@ -64,6 +65,7 @@ namespace Unit {
readonly id: number;
readonly invariantId: number;
+ readonly label: string;
readonly elements: SortedArray;
readonly model: Model;
readonly conformation: SymmetryOperator.ArrayMapping;
@@ -76,12 +78,13 @@ namespace Unit {
getChild(elements: SortedArray): Unit {
if (elements.length === this.elements.length) return this;
- return new Atomic(this.id, this.invariantId, this.model, elements, this.conformation, AtomicProperties());
+ return new Atomic(this.id, this.invariantId, this.label, this.model, elements, this.conformation, AtomicProperties());
}
applyOperator(id: number, operator: SymmetryOperator, dontCompose = false): Unit {
const op = dontCompose ? operator : SymmetryOperator.compose(this.conformation.operator, operator);
- return new Atomic(id, this.invariantId, this.model, this.elements, SymmetryOperator.createMapping(op, this.model.atomicConformation), this.props);
+ const label = operator.name
+ return new Atomic(id, this.invariantId, label, this.model, this.elements, SymmetryOperator.createMapping(op, this.model.atomicConformation), this.props);
}
get lookup3d() {
@@ -97,9 +100,10 @@ namespace Unit {
return this.props.bonds.ref;
}
- constructor(id: number, invariantId: number, model: Model, elements: SortedArray, conformation: SymmetryOperator.ArrayMapping, props: AtomicProperties) {
+ constructor(id: number, invariantId: number, label: string, 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;
@@ -124,6 +128,7 @@ namespace Unit {
readonly id: number;
readonly invariantId: number;
+ readonly label: string;
readonly elements: SortedArray;
readonly model: Model;
readonly conformation: SymmetryOperator.ArrayMapping;
@@ -133,12 +138,13 @@ 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.model, this.kind, elements, this.conformation);
+ return createCoarse(this.id, this.invariantId, this.label, 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 ret = createCoarse(id, this.invariantId, this.model, this.kind, this.elements, SymmetryOperator.createMapping(op, this.getCoarseElements()));
+ const label = operator.name
+ const ret = createCoarse(id, this.invariantId, label, this.model, this.kind, this.elements, SymmetryOperator.createMapping(op, this.getCoarseElements()));
(ret as Coarse<K, C>)._lookup3d = this._lookup3d;
return ret;
}
@@ -156,10 +162,11 @@ namespace Unit {
return this.kind === Kind.Spheres ? this.model.coarseConformation.spheres : this.model.coarseConformation.gaussians;
}
- constructor(id: number, invariantId: number, model: Model, kind: K, elements: SortedArray, conformation: SymmetryOperator.ArrayMapping) {
+ constructor(id: number, invariantId: number, label: string, 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;
@@ -168,8 +175,8 @@ namespace Unit {
}
}
- 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 */;
+ 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 */;
}
export class Spheres extends Coarse<Kind.Spheres, CoarseSphereConformation> { }