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Commit b2d2546e authored by David Sehnal's avatar David Sehnal
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mol-model: added chainGroupId

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src/mol-model/structure/structure/structure.ts
+ 18
− 2
View file @ b2d2546e
......@@ -540,7 +540,8 @@ namespace Structure {
for (let j = 0, jl = structure.units.length; j < jl; ++j) {
const u = structure.units[j]
const invariantId = u.invariantId + count
const newUnit = Unit.create(units.length, invariantId, u.kind, u.model, u.conformation.operator, u.elements)
const chainGroupId = u.chainGroupId + count
const newUnit = Unit.create(units.length, invariantId, chainGroupId, u.kind, u.model, u.conformation.operator, u.elements)
units.push(newUnit)
}
count = units.length
......@@ -644,6 +645,7 @@ namespace Structure {
const lookup = GridLookup3D({ x, y, z, indices: SortedArray.ofSortedArray(startIndices) }, gridCellCount);
const { offset, count, array } = lookup.buckets;
builder.beginChainGroup();
for (let i = 0, _i = offset.length; i < _i; i++) {
const start = offset[i];
const set: number[] = [];
......@@ -655,6 +657,7 @@ namespace Structure {
}
builder.addUnit(Unit.Kind.Atomic, model, SymmetryOperator.Default, SortedArray.ofSortedArray(new Int32Array(set)));
}
builder.endChainGroup();
}
function addCoarseUnits(builder: StructureBuilder, model: Model, elements: CoarseElements, kind: Unit.Kind) {
......@@ -685,9 +688,22 @@ namespace Structure {
private units: Unit[] = [];
private invariantId = idFactory()
private chainGroupId = -1;
private inChainGroup = false;
beginChainGroup() {
this.chainGroupId++;
this.inChainGroup = true;
}
endChainGroup() {
this.inChainGroup = false;
}
addUnit(kind: Unit.Kind, model: Model, operator: SymmetryOperator, elements: StructureElement.Set, invariantId?: number): Unit {
if (invariantId === undefined) invariantId = this.invariantId()
const unit = Unit.create(this.units.length, invariantId, kind, model, operator, elements);
const chainGroupId = this.inChainGroup ? this.chainGroupId : ++this.chainGroupId;
const unit = Unit.create(this.units.length, invariantId, chainGroupId, kind, model, operator, elements);
this.units.push(unit);
return unit;
}
......
src/mol-model/structure/structure/unit.ts
+ 18
− 12
View file @ b2d2546e
......@@ -33,11 +33,11 @@ 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, invariantId: number, kind: Kind, model: Model, operator: SymmetryOperator, elements: StructureElement.Set): Unit {
export function create(id: number, invariantId: number, chainGroupId: number, kind: Kind, model: Model, operator: SymmetryOperator, elements: StructureElement.Set): Unit {
switch (kind) {
case Kind.Atomic: return new Atomic(id, invariantId, model, elements, SymmetryOperator.createMapping(operator, model.atomicConformation, void 0), AtomicProperties());
case Kind.Spheres: return createCoarse(id, invariantId, model, Kind.Spheres, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.spheres, getSphereRadiusFunc(model)), CoarseProperties());
case Kind.Gaussians: return createCoarse(id, invariantId, model, Kind.Gaussians, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.gaussians, getGaussianRadiusFunc(model)), CoarseProperties());
case Kind.Atomic: return new Atomic(id, invariantId, chainGroupId, model, elements, SymmetryOperator.createMapping(operator, model.atomicConformation, void 0), AtomicProperties());
case Kind.Spheres: return createCoarse(id, invariantId, chainGroupId, model, Kind.Spheres, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.spheres, getSphereRadiusFunc(model)), CoarseProperties());
case Kind.Gaussians: return createCoarse(id, invariantId, chainGroupId, model, Kind.Gaussians, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.gaussians, getGaussianRadiusFunc(model)), CoarseProperties());
}
}
......@@ -98,6 +98,7 @@ namespace Unit {
readonly id: number,
/** invariant ID stays the same even if the Operator/conformation changes. */
readonly invariantId: number,
readonly chainGroupId: number,
readonly elements: StructureElement.Set,
readonly model: Model,
readonly conformation: SymmetryOperator.ArrayMapping<ElementIndex>,
......@@ -139,6 +140,8 @@ namespace Unit {
readonly id: number;
readonly invariantId: number;
/** Used to identify a single chain split into multiple units. */
readonly chainGroupId: number;
readonly elements: StructureElement.Set;
readonly model: Model;
readonly conformation: SymmetryOperator.ArrayMapping<ElementIndex>;
......@@ -152,12 +155,12 @@ namespace Unit {
getChild(elements: StructureElement.Set): 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.chainGroupId, 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.conformation.r), this.props);
return new Atomic(id, this.invariantId, this.chainGroupId, this.model, this.elements, SymmetryOperator.createMapping(op, this.model.atomicConformation, this.conformation.r), this.props);
}
get lookup3d() {
......@@ -221,9 +224,10 @@ namespace Unit {
return this.model.atomicHierarchy.residueAtomSegments.index[this.elements[elementIndex]];
}
constructor(id: number, invariantId: number, model: Model, elements: StructureElement.Set, conformation: SymmetryOperator.ArrayMapping<ElementIndex>, props: AtomicProperties) {
constructor(id: number, invariantId: number, chainGroupId: number, model: Model, elements: StructureElement.Set, conformation: SymmetryOperator.ArrayMapping<ElementIndex>, props: AtomicProperties) {
this.id = id;
this.invariantId = invariantId;
this.chainGroupId = chainGroupId;
this.model = model;
this.elements = elements;
this.conformation = conformation;
......@@ -264,6 +268,7 @@ namespace Unit {
readonly id: number;
readonly invariantId: number;
readonly chainGroupId: number;
readonly elements: StructureElement.Set;
readonly model: Model;
readonly conformation: SymmetryOperator.ArrayMapping<ElementIndex>;
......@@ -275,12 +280,12 @@ namespace Unit {
getChild(elements: StructureElement.Set): 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, CoarseProperties());
return createCoarse(this.id, this.invariantId, this.chainGroupId, this.model, this.kind, elements, this.conformation, CoarseProperties());
}
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.getCoarseConformation(), this.conformation.r), this.props);
const ret = createCoarse(id, this.invariantId, this.chainGroupId, this.model, this.kind, this.elements, SymmetryOperator.createMapping(op, this.getCoarseConformation(), this.conformation.r), this.props);
// (ret as Coarse<K, C>)._lookup3d = this._lookup3d;
return ret;
}
......@@ -309,11 +314,12 @@ 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: StructureElement.Set, conformation: SymmetryOperator.ArrayMapping<ElementIndex>, props: CoarseProperties) {
constructor(id: number, invariantId: number, chainGroupId: number, model: Model, kind: K, elements: StructureElement.Set, conformation: SymmetryOperator.ArrayMapping<ElementIndex>, props: CoarseProperties) {
this.kind = kind;
this.objectPrimitive = kind === Kind.Spheres ? 'sphere' : 'gaussian'
this.id = id;
this.invariantId = invariantId;
this.chainGroupId = chainGroupId;
this.model = model;
this.elements = elements;
this.conformation = conformation;
......@@ -337,8 +343,8 @@ namespace Unit {
};
}
function createCoarse<K extends Kind.Gaussians | Kind.Spheres>(id: number, invariantId: number, model: Model, kind: K, elements: StructureElement.Set, conformation: SymmetryOperator.ArrayMapping<ElementIndex>, props: CoarseProperties): Unit {
return new Coarse(id, invariantId, model, kind, elements, conformation, props) as any as Unit /** lets call this an ugly temporary hack */;
function createCoarse<K extends Kind.Gaussians | Kind.Spheres>(id: number, invariantId: number, chainGroupId: number, model: Model, kind: K, elements: StructureElement.Set, conformation: SymmetryOperator.ArrayMapping<ElementIndex>, props: CoarseProperties): Unit {
return new Coarse(id, invariantId, chainGroupId, model, kind, elements, conformation, props) as any as Unit /** lets call this an ugly temporary hack */;
}
export class Spheres extends Coarse<Kind.Spheres, CoarseSphereConformation> { }
......
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