diff --git a/src/apps/structure-info/model.ts b/src/apps/structure-info/model.ts
index c04627418a078014a7f89f061b8f0d5bbde55fef..fbc466845b97f16694d61f36f8afffd2462e7219 100644
--- a/src/apps/structure-info/model.ts
+++ b/src/apps/structure-info/model.ts
@@ -9,11 +9,10 @@ import * as argparse from 'argparse'
require('util.promisify').shim();
import { CifFrame } from 'mol-io/reader/cif'
-import { Model, Structure, StructureElement, Unit, Format, StructureProperties } from 'mol-model/structure'
+import { Model, Structure, StructureElement, Unit, Format, StructureProperties, UnitRing } from 'mol-model/structure'
// import { Run, Progress } from 'mol-task'
import { OrderedSet } from 'mol-data/int';
import { openCif, downloadCif } from './helpers';
-import { UnitRings } from 'mol-model/structure/structure/unit/rings';
import { Vec3 } from 'mol-math/linear-algebra';
@@ -136,7 +135,7 @@ export function printRings(structure: Structure) {
const { all, byFingerprint } = unit.rings;
const fps: string[] = [];
for (let i = 0, _i = Math.min(5, all.length); i < _i; i++) {
- fps[fps.length] = UnitRings.getRingFingerprint(unit, all[i]);
+ fps[fps.length] = UnitRing.fingerprint(unit, all[i]);
}
if (all.length > 5) fps.push('...')
console.log(`Unit ${unit.id}, ${all.length} ring(s), ${byFingerprint.size} different fingerprint(s).\n ${fps.join(', ')}`);
diff --git a/src/mol-model/structure/structure.ts b/src/mol-model/structure/structure.ts
index 3a924335ea86458fea0e1d2cb89d2be92310bdee..a6a25607900a4ac9912f878f6ac5ddc9abf9541b 100644
--- a/src/mol-model/structure/structure.ts
+++ b/src/mol-model/structure/structure.ts
@@ -11,4 +11,5 @@ import StructureSymmetry from './structure/symmetry'
import { Link } from './structure/unit/links'
import StructureProperties from './structure/properties'
-export { StructureElement, Link, Structure, Unit, StructureSymmetry, StructureProperties }
\ No newline at end of file
+export { StructureElement, Link, Structure, Unit, StructureSymmetry, StructureProperties }
+export * from './structure/unit/rings'
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/carbohydrates/compute.ts b/src/mol-model/structure/structure/carbohydrates/compute.ts
index 62ee0357f2ce9109f1897692b71e81b9c7e42cec..ab8c61fbafc358fb434ea785aa088fa2fc9b41fe 100644
--- a/src/mol-model/structure/structure/carbohydrates/compute.ts
+++ b/src/mol-model/structure/structure/carbohydrates/compute.ts
@@ -18,42 +18,11 @@ import Structure from '../structure';
import Unit from '../unit';
import { SaccharideNameMap, UnknownSaccharideComponent } from './constants';
import { CarbohydrateElement, CarbohydrateLink, Carbohydrates, CarbohydrateTerminalLink } from './data';
+import { UnitRings, UnitRing } from '../unit/rings';
-function getResidueIndex(elementIndex: number, unit: Unit.Atomic) {
- return unit.model.atomicHierarchy.residueAtomSegments.index[unit.elements[elementIndex]]
-}
-
-function sugarResidueIdx(unit: Unit.Atomic, ring: ArrayLike<StructureElement.UnitIndex>): ResidueIndex {
- const { elements } = unit;
- const residueIndex = unit.model.atomicHierarchy.residueAtomSegments.index;
- const idx = residueIndex[elements[ring[0]]];
- for (let rI = 1, _rI = ring.length; rI < _rI; rI++) {
- if (idx !== residueIndex[elements[ring[rI]]]) return -1 as ResidueIndex;
- }
- return idx;
-}
+const C = ElementSymbol('C'), O = ElementSymbol('O');
+const SugarRingFps = [UnitRing.elementFingerprint([C, C, C, C, C, O]), UnitRing.elementFingerprint([C, C, C, C, O])]
-function addSugarRings(unit: Unit.Atomic, fp: string, sugarResidues: Map<ResidueIndex, number[]>) {
- const rings = unit.rings;
- const byFp = rings.byFingerprint.get(fp);
- if (!byFp) return;
- for (const r of byFp) {
- const idx = sugarResidueIdx(unit, rings.all[r]);
- if (idx >= 0) {
- if (sugarResidues.has(idx)) sugarResidues.get(idx)!.push(r);
- else sugarResidues.set(idx, [r]);
- }
- }
-}
-
-function getSugarRingIndices(unit: Unit.Atomic) {
- const sugarResidues = new Map<ResidueIndex, number[]>();
- addSugarRings(unit, 'C-C-C-C-C-O', sugarResidues);
- addSugarRings(unit, 'C-C-C-C-O', sugarResidues);
- return sugarResidues;
-}
-
-const C = ElementSymbol('C')
function getDirection(direction: Vec3, unit: Unit.Atomic, indices: ArrayLike<StructureElement.UnitIndex>, center: Vec3) {
let indexC1 = -1, indexC1X = -1, indexC = -1
const { elements } = unit
@@ -85,6 +54,7 @@ function getAtomId(unit: Unit.Atomic, index: number) {
return label_atom_id.value(elements[index])
}
+
export function computeCarbohydrates(structure: Structure): Carbohydrates {
const links: CarbohydrateLink[] = []
const terminalLinks: CarbohydrateTerminalLink[] = []
@@ -120,7 +90,7 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
const chainIt = Segmentation.transientSegments(chainAtomSegments, unit.elements)
const residueIt = Segmentation.transientSegments(residueAtomSegments, unit.elements)
- let sugarResidueMap: Map<ResidueIndex, number[]> | undefined = void 0;
+ let sugarResidueMap: Map<ResidueIndex, UnitRings.Index[]> | undefined = void 0;
while (chainIt.hasNext) {
residueIt.setSegment(chainIt.move());
@@ -134,7 +104,7 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
}
if (!sugarResidueMap) {
- sugarResidueMap = getSugarRingIndices(unit);
+ sugarResidueMap = UnitRings.byFingerprintAndResidue(unit.rings, SugarRingFps);
}
const sugarRings = sugarResidueMap.get(residueIndex);
@@ -202,8 +172,8 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
pairBonds.getBonds(indexA).forEach(bondInfo => {
const { unitA, unitB } = pairBonds
const indexB = bondInfo.indexB
- const elementIndexA = elementsWithRingMap.get(elementKey(getResidueIndex(indexA, unitA), unitA.id))
- const elementIndexB = elementsWithRingMap.get(elementKey(getResidueIndex(indexB, unitB), unitB.id))
+ const elementIndexA = elementsWithRingMap.get(elementKey(unitA.getResidueIndex(indexA), unitA.id))
+ const elementIndexB = elementsWithRingMap.get(elementKey(unitB.getResidueIndex(indexB), unitB.id))
if (elementIndexA !== undefined && elementIndexB !== undefined) {
if (getAtomId(unitA, indexA).startsWith('C1')) {
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index 48f429a29dc65e7f1d883669d7ea6d112635a57a..8ec99349308a246bf74320c2b517233d85999e8b 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -117,6 +117,10 @@ namespace Unit {
return this.props.rings.ref;
}
+ getResidueIndex(elementIndex: StructureElement.UnitIndex) {
+ return this.model.atomicHierarchy.residueAtomSegments.index[this.elements[elementIndex]];
+ }
+
constructor(id: number, invariantId: number, model: Model, elements: StructureElement.Set, conformation: SymmetryOperator.ArrayMapping, props: AtomicProperties) {
this.id = id;
this.invariantId = invariantId;
diff --git a/src/mol-model/structure/structure/unit/links/data.ts b/src/mol-model/structure/structure/unit/links/data.ts
index ed046a026da9011b17f43602898b8c2f3e1fdf69..74ff5bd2d5aade0d8f93d0fed3bedf026ea75d63 100644
--- a/src/mol-model/structure/structure/unit/links/data.ts
+++ b/src/mol-model/structure/structure/unit/links/data.ts
@@ -8,6 +8,7 @@
import { LinkType } from '../../../model/types'
import { IntAdjacencyGraph } from 'mol-math/graph';
import Unit from '../../unit';
+import StructureElement from '../../element';
type IntraUnitLinks = IntAdjacencyGraph<{ readonly order: ArrayLike<number>, readonly flags: ArrayLike<LinkType.Flag> }>
@@ -76,14 +77,14 @@ namespace InterUnitBonds {
}
constructor(public unitA: Unit.Atomic, public unitB: Unit.Atomic,
- public bondCount: number, public linkedElementIndices: ReadonlyArray<number>,
+ public bondCount: number, public linkedElementIndices: ReadonlyArray<StructureElement.UnitIndex>,
private linkMap: Map<number, BondInfo[]>) {
}
}
export interface BondInfo {
/** indexInto */
- readonly indexB: number,
+ readonly indexB: StructureElement.UnitIndex,
readonly order: number,
readonly flag: LinkType.Flag
}
diff --git a/src/mol-model/structure/structure/unit/links/inter-compute.ts b/src/mol-model/structure/structure/unit/links/inter-compute.ts
index 03184c454ff8674d8471d65f76c442721c166f30..cd8e37397544128778502efe23fa2b664c1009a1 100644
--- a/src/mol-model/structure/structure/unit/links/inter-compute.ts
+++ b/src/mol-model/structure/structure/unit/links/inter-compute.ts
@@ -13,6 +13,7 @@ import { InterUnitBonds } from './data';
import { UniqueArray } from 'mol-data/generic';
import { SortedArray } from 'mol-data/int';
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
+import StructureElement from '../../element';
const MAX_RADIUS = 4;
@@ -24,8 +25,8 @@ function addMapEntry<A, B>(map: Map<A, B[]>, a: A, b: B) {
interface PairState {
mapAB: Map<number, InterUnitBonds.BondInfo[]>,
mapBA: Map<number, InterUnitBonds.BondInfo[]>,
- bondedA: UniqueArray<number, number>,
- bondedB: UniqueArray<number, number>
+ bondedA: UniqueArray<StructureElement.UnitIndex, StructureElement.UnitIndex>,
+ bondedB: UniqueArray<StructureElement.UnitIndex, StructureElement.UnitIndex>
}
function addLink(indexA: number, indexB: number, order: number, flag: LinkType.Flag, state: PairState) {
diff --git a/src/mol-model/structure/structure/unit/rings.ts b/src/mol-model/structure/structure/unit/rings.ts
index 83640e22689d6f688704c2bb4866439ba6c1a04c..64f9f857cb0f736216ea46ed887bbd84ba41cbc9 100644
--- a/src/mol-model/structure/structure/unit/rings.ts
+++ b/src/mol-model/structure/structure/unit/rings.ts
@@ -8,64 +8,123 @@ import { computeRings, getFingerprint, createIndex } from './rings/compute'
import Unit from '../unit';
import StructureElement from '../element';
import { SortedArray } from 'mol-data/int';
+import { ResidueIndex } from '../../model';
+import { ElementSymbol } from '../../model/types';
type UnitRing = SortedArray<StructureElement.UnitIndex>
-interface UnitRings {
+class UnitRings {
/** Each ring is specified as an array of indices in Unit.elements. */
- readonly all: ReadonlyArray<UnitRing>,
- readonly byFingerprint: ReadonlyMap<string, ReadonlyArray<UnitRings.Index>>,
+ readonly all: ReadonlyArray<UnitRing>;
- readonly index: {
- /** Maps atom index inside a Unit to the smallest ring index (an atom can be part of more than one ring) */
+ private _byFingerprint?: ReadonlyMap<UnitRing.Fingerprint, ReadonlyArray<UnitRings.Index>>;
+ private _index?: {
readonly elementRingIndices: ReadonlyMap<StructureElement.UnitIndex, UnitRings.Index[]>,
-
- /** Maps UnitRings.Index to index to ringComponents */
readonly ringComponentIndex: ReadonlyArray<UnitRings.ComponentIndex>,
readonly ringComponents: ReadonlyArray<ReadonlyArray<UnitRings.Index>>
+ };
+
+ private get index() {
+ if (this._index) return this._index;
+ this._index = createIndex(this.all);
+ return this._index;
+ }
+
+ get byFingerprint() {
+ if (this._byFingerprint) return this._byFingerprint;
+ this._byFingerprint = createByFingerprint(this.unit, this.all);
+ return this._byFingerprint;
+ }
+
+ /** Maps atom index inside a Unit to the smallest ring index (an atom can be part of more than one ring) */
+ get elementRingIndices() {
+ return this.index.elementRingIndices;
+ }
+
+ /** Maps UnitRings.Index to index to ringComponents */
+ get ringComponentIndex() {
+ return this.index.ringComponentIndex;
+ }
+
+ get ringComponents() {
+ return this.index.ringComponents;
+ }
+
+ constructor(all: ReadonlyArray<UnitRing>, public unit: Unit.Atomic) {
+ this.all = all;
}
}
-namespace UnitRings {
- /** Index into UnitRings.all */
- export type Index = { readonly '@type': 'unit-ring-index' } & number
- export type ComponentIndex = { readonly '@type': 'unit-ring-component-index' } & number
+namespace UnitRing {
+ export type Fingerprint = { readonly '@type': 'unit-ring-fingerprint' } & string
- export function getRingFingerprint(unit: Unit.Atomic, ring: UnitRing) {
+ export function fingerprint(unit: Unit.Atomic, ring: UnitRing): Fingerprint {
const { elements } = unit;
const { type_symbol } = unit.model.atomicHierarchy.atoms;
- const symbols: string[] = [];
- for (let i = 0, _i = ring.length; i < _i; i++) symbols[symbols.length] = type_symbol.value(elements[ring[i]]) as String as string;
- return getFingerprint(symbols);
+ const symbols: ElementSymbol[] = [];
+ for (let i = 0, _i = ring.length; i < _i; i++) symbols[symbols.length] = type_symbol.value(elements[ring[i]]);
+ return elementFingerprint(symbols);
}
+ export function elementFingerprint(elements: ArrayLike<ElementSymbol>) {
+ return getFingerprint(elements as ArrayLike<String> as string[]) as Fingerprint;
+ }
+}
+
+namespace UnitRings {
+ /** Index into UnitRings.all */
+ export type Index = { readonly '@type': 'unit-ring-index' } & number
+ export type ComponentIndex = { readonly '@type': 'unit-ring-component-index' } & number
+
export function create(unit: Unit.Atomic): UnitRings {
const rings = computeRings(unit);
+ return new UnitRings(rings, unit);
+ }
- let _byFingerprint: Map<string, Index[]> | undefined = void 0;
- let _index: UnitRings['index'] | undefined = void 0;
- return {
- all: rings,
- get byFingerprint() {
- if (_byFingerprint) return _byFingerprint;
- _byFingerprint = new Map();
- let idx = 0 as Index;
- for (const r of rings) {
- const fp = getRingFingerprint(unit, r);
- if (_byFingerprint.has(fp)) _byFingerprint.get(fp)!.push(idx);
- else _byFingerprint.set(fp, [idx]);
- idx++;
- }
- return _byFingerprint;
- },
- get index() {
- if (_index) return _index;
- _index = createIndex(rings);
- return _index;
- }
- };
+ /** Creates a mapping ResidueIndex -> list or rings that are on that residue and have one of the specified fingerprints. */
+ export function byFingerprintAndResidue(rings: UnitRings, fingerprints: ReadonlyArray<UnitRing.Fingerprint>) {
+ const map = new Map<ResidueIndex, Index[]>();
+ for (const fp of fingerprints) {
+ addSingleResidueRings(rings, fp, map);
+ }
+ return map;
}
}
+function createByFingerprint(unit: Unit.Atomic, rings: ReadonlyArray<UnitRing>) {
+ const byFingerprint = new Map<UnitRing.Fingerprint, UnitRings.Index[]>();
+ let idx = 0 as UnitRings.Index;
+ for (const r of rings) {
+ const fp = UnitRing.fingerprint(unit, r);
+ if (byFingerprint.has(fp)) byFingerprint.get(fp)!.push(idx);
+ else byFingerprint.set(fp, [idx]);
+ idx++;
+ }
+ return byFingerprint;
+}
+
+function ringResidueIdx(unit: Unit.Atomic, ring: ArrayLike<StructureElement.UnitIndex>): ResidueIndex {
+ const { elements } = unit;
+ const residueIndex = unit.model.atomicHierarchy.residueAtomSegments.index;
+ const idx = residueIndex[elements[ring[0]]];
+ for (let rI = 1, _rI = ring.length; rI < _rI; rI++) {
+ if (idx !== residueIndex[elements[ring[rI]]]) return -1 as ResidueIndex;
+ }
+ return idx;
+}
+
+function addSingleResidueRings(rings: UnitRings, fp: UnitRing.Fingerprint, map: Map<ResidueIndex, UnitRings.Index[]>) {
+ const byFp = rings.byFingerprint.get(fp);
+ if (!byFp) return;
+ for (const r of byFp) {
+ const idx = ringResidueIdx(rings.unit, rings.all[r]);
+ if (idx >= 0) {
+ if (map.has(idx)) map.get(idx)!.push(r);
+ else map.set(idx, [r]);
+ }
+ }
+}
+
+
export { UnitRing, UnitRings }
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/unit/rings/compute.ts b/src/mol-model/structure/structure/unit/rings/compute.ts
index 5485b49809e1c075944a70ecadd08c54ad85f57f..4517fb879f826cd4934682f6ab247d5075084f11 100644
--- a/src/mol-model/structure/structure/unit/rings/compute.ts
+++ b/src/mol-model/structure/structure/unit/rings/compute.ts
@@ -249,7 +249,7 @@ function buildFinderprint(elements: string[], offset: number) {
type RingIndex = import('../rings').UnitRings.Index
type RingComponentIndex = import('../rings').UnitRings.ComponentIndex
-export function createIndex(rings: SortedArray<StructureElement.UnitIndex>[]) {
+export function createIndex(rings: ArrayLike<SortedArray<StructureElement.UnitIndex>>) {
const elementRingIndices: Map<StructureElement.UnitIndex, RingIndex[]> = new Map();
// for each ring atom, assign all rings that it is present in