diff --git a/src/mol-model/structure/export/mmcif.ts b/src/mol-model/structure/export/mmcif.ts
index a5924f652740c6d08ccf44c2802d0008a6be4cc8..d955721395a2fbb3fd5788dee2f8c1c616831ce4 100644
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -42,9 +42,9 @@ function copy_mmCif_category(name: keyof mmCIF_Schema): CifCategory<CifExportCon
const _entity: CifCategory<CifExportContext> = {
name: 'entity',
- instance({ structures}) {
- const keys = Structure.getEntityKeys(structures[0]);
- return CifCategory.ofTable(structures[0].model.entities.data, keys);
+ instance({ structures }) {
+ const indices = structures[0].entityIndices;
+ return CifCategory.ofTable(structures[0].model.entities.data, indices);
}
}
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index 7f41cc5fc2752df73c23c6c2eae557b8c0af5003..c40256f4584fad43821c2368baf110d87d22010d 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -18,12 +18,13 @@ import { InterUnitBonds, computeInterUnitBonds } from './unit/links';
import { PairRestraints, CrossLinkRestraint, extractCrossLinkRestraints } from './unit/pair-restraints';
import StructureSymmetry from './symmetry';
import StructureProperties from './properties';
-import { ResidueIndex, ChainIndex } from '../model/indexing';
+import { ResidueIndex, ChainIndex, EntityIndex } from '../model/indexing';
import { Carbohydrates } from './carbohydrates/data';
import { computeCarbohydrates } from './carbohydrates/compute';
import { Vec3 } from 'mol-math/linear-algebra';
import { idFactory } from 'mol-util/id-factory';
import { GridLookup3D } from 'mol-math/geometry';
+import { UUID } from 'mol-util';
class Structure {
/** Maps unit.id to unit */
@@ -39,6 +40,9 @@ class Structure {
carbohydrates?: Carbohydrates,
models?: ReadonlyArray<Model>,
model?: Model,
+ uniqueResidueNames?: Set<string>,
+ entityIndices?: ReadonlyArray<EntityIndex>,
+ uniqueAtomicResidueIndices?: ReadonlyMap<UUID, ReadonlyArray<ResidueIndex>>,
hashCode: number,
elementCount: number,
polymerResidueCount: number,
@@ -129,6 +133,20 @@ class Structure {
return this._props.models;
}
+ get uniqueResidueName() {
+ return this._props.uniqueResidueNames
+ || (this._props.uniqueResidueNames = getUniqueResidueNames(this));
+ }
+
+ get entityIndices() {
+ return this._props.entityIndices || (this._props.entityIndices = getEntityIndices(this));
+ }
+
+ get uniqueAtomicResidueIndices() {
+ return this._props.uniqueAtomicResidueIndices
+ || (this._props.uniqueAtomicResidueIndices = getUniqueAtomicResidueIndices(this));
+ }
+
/** If the structure is based on a single model, return it. Otherwise throw an exception. */
get model(): Model {
if (this._props.model) return this._props.model;
@@ -176,6 +194,81 @@ function getModels(s: Structure) {
return arr.array;
}
+function getUniqueResidueNames(s: Structure) {
+ const prop = StructureProperties.residue.label_comp_id;
+ const names = new Set<string>();
+ const loc = StructureElement.create();
+ for (const unit of s.units) {
+ // TODO: support coarse unit?
+ if (!Unit.isAtomic(unit)) continue;
+ const residues = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
+ loc.unit = unit;
+ while (residues.hasNext) {
+ const seg = residues.move();
+ loc.element = unit.elements[seg.start];
+ names.add(prop(loc));
+ }
+ }
+ return names;
+}
+
+function getEntityIndices(structure: Structure): ReadonlyArray<EntityIndex> {
+ const { units } = structure;
+ const l = StructureElement.create();
+ const keys = UniqueArray.create<number, EntityIndex>();
+
+ for (const unit of units) {
+ const prop = unit.kind === Unit.Kind.Atomic ? StructureProperties.entity.key : StructureProperties.coarse.entityKey;
+
+ l.unit = unit;
+ const elements = unit.elements;
+
+ const chainsIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
+ while (chainsIt.hasNext) {
+ const chainSegment = chainsIt.move();
+ l.element = elements[chainSegment.start];
+ const key = prop(l);
+ UniqueArray.add(keys, key, key);
+ }
+ }
+
+ sortArray(keys.array);
+ return keys.array;
+}
+
+function getUniqueAtomicResidueIndices(structure: Structure): ReadonlyMap<UUID, ReadonlyArray<ResidueIndex>> {
+ const map = new Map<UUID, UniqueArray<ResidueIndex, ResidueIndex>>();
+ const modelIds: UUID[] = [];
+
+ const unitGroups = structure.unitSymmetryGroups;
+ for (const unitGroup of unitGroups) {
+ const unit = unitGroup.units[0];
+ if (!Unit.isAtomic(unit)) continue;
+
+ let uniqueResidues: UniqueArray<ResidueIndex, ResidueIndex>;
+ if (map.has(unit.model.id)) uniqueResidues = map.get(unit.model.id)!;
+ else {
+ uniqueResidues = UniqueArray.create<ResidueIndex, ResidueIndex>();
+ modelIds.push(unit.model.id);
+ map.set(unit.model.id, uniqueResidues);
+ }
+
+ const residues = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
+ while (residues.hasNext) {
+ const seg = residues.move();
+ UniqueArray.add(uniqueResidues, seg.index, seg.index);
+ }
+ }
+
+ const ret = new Map<UUID, ReadonlyArray<ResidueIndex>>();
+ for (const id of modelIds) {
+ const array = map.get(id)!.array;
+ sortArray(array);
+ ret.set(id, array)
+ }
+ return ret;
+}
+
namespace Structure {
export const Empty = new Structure([]);
@@ -346,49 +439,6 @@ namespace Structure {
}
}
- export function getEntityKeys(structure: Structure) {
- const { units } = structure;
- const l = StructureElement.create();
- const keys = UniqueArray.create<number, number>();
-
- for (const unit of units) {
- const prop = unit.kind === Unit.Kind.Atomic ? StructureProperties.entity.key : StructureProperties.coarse.entityKey;
-
- l.unit = unit;
- const elements = unit.elements;
-
- const chainsIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
- while (chainsIt.hasNext) {
- const chainSegment = chainsIt.move();
- l.element = elements[chainSegment.start];
- const key = prop(l);
- UniqueArray.add(keys, key, key);
- }
- }
-
- sortArray(keys.array);
- return keys.array;
- }
-
- export function getUniqueAtomicResidueIndices(structure: Structure, model: Model): ReadonlyArray<ResidueIndex> {
- const uniqueResidues = UniqueArray.create<ResidueIndex, ResidueIndex>();
- const unitGroups = structure.unitSymmetryGroups;
- for (const unitGroup of unitGroups) {
- const unit = unitGroup.units[0];
- if (unit.model !== model || !Unit.isAtomic(unit)) {
- continue;
- }
-
- const residues = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
- while (residues.hasNext) {
- const seg = residues.move();
- UniqueArray.add(uniqueResidues, seg.index, seg.index);
- }
- }
- sortArray(uniqueResidues.array);
- return uniqueResidues.array;
- }
-
const distVec = Vec3.zero();
function unitElementMinDistance(unit: Unit, p: Vec3, eRadius: number) {
const { elements, conformation: { position, r } } = unit, dV = distVec;
diff --git a/src/servers/model/config.ts b/src/servers/model/config.ts
index a18919c842ebc67959c4ef6b86fc09a031b2969c..1bf830d00639fd568c5adebbe8d9bbda7da03cbd 100644
--- a/src/servers/model/config.ts
+++ b/src/servers/model/config.ts
@@ -51,8 +51,8 @@ const config = {
* Paths (relative to the root directory of the model server) to JavaScript files that specify custom properties
*/
customPropertyProviders: [
- './properties/pdbe',
- './properties/rcsb'
+ // './properties/pdbe',
+ // './properties/rcsb'
],
/**
@@ -66,9 +66,9 @@ const config = {
mapFile(source: string, id: string) {
switch (source.toLowerCase()) {
// case 'pdb': return `e:/test/quick/${id}_updated.cif`;
- case 'pdb': return `e:/test/mol-star/model/out/${id}_updated.bcif`;
- case 'pdb-bcif': return `e:/test/mol-star/model/out/${id}_updated.bcif`;
- case 'pdb-cif': return `e:/test/mol-star/model/out/${id}_updated.cif`;
+ case 'pdb': return `c:/test/mol-star/model/out/${id}_updated.bcif`;
+ case 'pdb-bcif': return `c:/test/mol-star/model/out/${id}_updated.bcif`;
+ case 'pdb-cif': return `c:/test/mol-star/model/out/${id}_updated.cif`;
default: return void 0;
}
}