From a1288e83658dbb1a6434c9df6127cfe8dad0d801 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Tue, 5 Jun 2018 11:10:54 +0200
Subject: [PATCH] Removed Unit.label, fixed Model.label from mmCIF
---
src/mol-geo/representation/structure/index.ts | 2 +-
.../structure/model/formats/mmcif.ts | 6 +++-
.../structure/structure/structure.ts | 20 +++---------
src/mol-model/structure/structure/unit.ts | 31 +++++++------------
src/perf-tests/lookup3d.ts | 4 +--
src/servers/model/server/api.ts | 5 ++-
src/servers/model/server/query.ts | 2 +-
7 files changed, 28 insertions(+), 42 deletions(-)
diff --git a/src/mol-geo/representation/structure/index.ts b/src/mol-geo/representation/structure/index.ts
index b9716cef4..fdddec8de 100644
--- a/src/mol-geo/representation/structure/index.ts
+++ b/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)) {
diff --git a/src/mol-model/structure/model/formats/mmcif.ts b/src/mol-model/structure/model/formats/mmcif.ts
index 33c5897d3..a50d29311 100644
--- a/src/mol-model/structure/model/formats/mmcif.ts
+++ b/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,
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index 88abc9949..cac54e0b5 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -1,5 +1,5 @@
/**
- * 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;
}
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index 8c6e715ea..5c34fd555 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, 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> { }
diff --git a/src/perf-tests/lookup3d.ts b/src/perf-tests/lookup3d.ts
index 3b52eee9f..957ce7c01 100644
--- a/src/perf-tests/lookup3d.ts
+++ b/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);
}
diff --git a/src/servers/model/server/api.ts b/src/servers/model/server/api.ts
index a482fcf98..96820b82d 100644
--- a/src/servers/model/server/api.ts
+++ b/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 {
diff --git a/src/servers/model/server/query.ts b/src/servers/model/server/query.ts
index 01f3325d8..ed9ebedf8 100644
--- a/src/servers/model/server/query.ts
+++ b/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]);
--
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