From 2a3f2e99697e38baeff93a6c8569a8a51eac9070 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Thu, 7 Jun 2018 11:53:03 +0200
Subject: [PATCH] Added UnitRings
---
src/apps/structure-info/model.ts | 17 ++
src/mol-model/structure/structure/unit.ts | 10 +-
.../structure/structure/unit/rings.ts | 107 +++++++++++
.../structure/structure/unit/rings/compute.ts | 177 ++++++++++++++++++
4 files changed, 310 insertions(+), 1 deletion(-)
create mode 100644 src/mol-model/structure/structure/unit/rings.ts
create mode 100644 src/mol-model/structure/structure/unit/rings/compute.ts
diff --git a/src/apps/structure-info/model.ts b/src/apps/structure-info/model.ts
index 0728dde5d..9c7f0d9a9 100644
--- a/src/apps/structure-info/model.ts
+++ b/src/apps/structure-info/model.ts
@@ -18,6 +18,7 @@ import { mmCIF_Database } from 'mol-io/reader/cif/schema/mmcif';
import { openCif, downloadCif } from './helpers';
import { BitFlags } from 'mol-util';
import { SecondaryStructureType } from 'mol-model/structure/model/types';
+import { UnitRings } from 'mol-model/structure/structure/unit/rings';
async function downloadFromPdb(pdb: string) {
@@ -100,6 +101,21 @@ export function printSequence(model: Model) {
console.log();
}
+export function printRings(structure: Structure) {
+ console.log('\nRings\n=============');
+ for (const unit of structure.units) {
+ if (!Unit.isAtomic(unit)) continue;
+ 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]);
+ }
+ if (all.length > 5) fps.push('...')
+ console.log(`Unit ${unit.id}, ${all.length} ring(s), ${byFingerprint.size} different fingerprint(s).\n ${fps.join(', ')}`);
+ }
+ console.log();
+}
+
export function printUnits(structure: Structure) {
console.log('\nUnits\n=============');
const l = Element.Location();
@@ -143,6 +159,7 @@ async function run(mmcif: mmCIF_Database) {
printSequence(models[0]);
//printIHMModels(models[0]);
printUnits(structure);
+ printRings(structure);
//printBonds(structure);
//printSecStructure(models[0]);
}
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index 5c34fd555..f90d51272 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -12,6 +12,7 @@ import { idFactory } from 'mol-util/id-factory';
import { IntraUnitBonds, computeIntraUnitBonds } from './unit/bonds'
import { CoarseElements, CoarseSphereConformation, CoarseGaussianConformation } from '../model/properties/coarse';
import { ValueRef } from 'mol-util';
+import { UnitRings } from './unit/rings';
// A building block of a structure that corresponds to an atomic or a coarse grained representation
// 'conveniently grouped together'.
@@ -97,6 +98,12 @@ namespace Unit {
return this.props.bonds.ref;
}
+ get rings() {
+ if (this.props.rings.ref) return this.props.rings.ref;
+ this.props.rings.ref = UnitRings.create(this);
+ return this.props.rings.ref;
+ }
+
constructor(id: number, invariantId: number, model: Model, elements: SortedArray, conformation: SymmetryOperator.ArrayMapping, props: AtomicProperties) {
this.id = id;
this.invariantId = invariantId;
@@ -113,10 +120,11 @@ namespace Unit {
interface AtomicProperties {
lookup3d: ValueRef<Lookup3D | undefined>,
bonds: ValueRef<IntraUnitBonds | undefined>,
+ rings: ValueRef<UnitRings | undefined>
}
function AtomicProperties() {
- return { lookup3d: ValueRef.create(void 0), bonds: ValueRef.create(void 0) };
+ return { lookup3d: ValueRef.create(void 0), bonds: ValueRef.create(void 0), rings: ValueRef.create(void 0) };
}
class Coarse<K extends Kind.Gaussians | Kind.Spheres, C extends CoarseSphereConformation | CoarseGaussianConformation> implements Base {
diff --git a/src/mol-model/structure/structure/unit/rings.ts b/src/mol-model/structure/structure/unit/rings.ts
new file mode 100644
index 000000000..ed22f5418
--- /dev/null
+++ b/src/mol-model/structure/structure/unit/rings.ts
@@ -0,0 +1,107 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import computeRings from './rings/compute'
+import Unit from '../unit';
+
+interface UnitRings {
+ /** Each ring is specified as an array of indices in Unit.elements. */
+ readonly all: ReadonlyArray<ReadonlyArray<number>>,
+ readonly byFingerprint: Map<string, ReadonlyArray<number>>
+}
+
+namespace UnitRings {
+ export function getRingFingerprint(unit: Unit.Atomic, ring: ArrayLike<number>) {
+ 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);
+ }
+
+ export function create(unit: Unit.Atomic): UnitRings {
+ const rings = computeRings(unit);
+ const byFingerprint = new Map<string, number[]>();
+
+ let idx = 0;
+ 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 { all: rings, byFingerprint };
+ }
+}
+
+export { UnitRings }
+
+function getFingerprint(elements: string[]) {
+ const len = elements.length;
+ const reversed: string[] = new Array(len);
+
+ for (let i = 0; i < len; i++) reversed[i] = elements[len - i - 1];
+
+ const rotNormal = getMinimalRotation(elements);
+ const rotReversed = getMinimalRotation(reversed);
+
+ let isNormalSmaller = false;
+
+ for (let i = 0; i < len; i++) {
+ const u = elements[(i + rotNormal) % len], v = reversed[(i + rotReversed) % len];
+ if (u !== v) {
+ isNormalSmaller = u < v;
+ break;
+ }
+ }
+
+ if (isNormalSmaller) return buildFinderprint(elements, rotNormal);
+ return buildFinderprint(reversed, rotReversed);
+}
+
+function getMinimalRotation(elements: string[]) {
+ // adapted from http://en.wikipedia.org/wiki/Lexicographically_minimal_string_rotation
+
+ const len = elements.length;
+ const f = new Int32Array(len * 2);
+ for (let i = 0; i < f.length; i++) f[i] = -1;
+
+ let u = '', v = '', k = 0;
+
+ for (let j = 1; j < f.length; j++) {
+ let i = f[j - k - 1];
+ while (i !== -1) {
+ u = elements[j % len]; v = elements[(k + i + 1) % len];
+ if (u === v) break;
+ if (u < v) k = j - i - 1;
+ i = f[i];
+ }
+
+ if (i === -1) {
+ u = elements[j % len]; v = elements[(k + i + 1) % len];
+ if (u !== v) {
+ if (u < v) k = j;
+ f[j - k] = -1;
+ } else f[j - k] = i + 1;
+ } else f[j - k] = i + 1;
+ }
+
+ return k;
+}
+
+function buildFinderprint(elements: string[], offset: number) {
+ const len = elements.length;
+ const ret: string[] = [];
+ let i;
+ for (i = 0; i < len - 1; i++) {
+ ret.push(elements[(i + offset) % len]);
+ ret.push('-');
+ }
+ ret.push(elements[(i + offset) % len]);
+ return ret.join('');
+}
\ 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
new file mode 100644
index 000000000..a76cd6e47
--- /dev/null
+++ b/src/mol-model/structure/structure/unit/rings/compute.ts
@@ -0,0 +1,177 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import Unit from '../../unit';
+import { IntraUnitBonds } from '../bonds/intra-data';
+import { Segmentation } from 'mol-data/int';
+
+export default function computeRings(unit: Unit.Atomic) {
+ const size = largestResidue(unit);
+ const state = State(unit, size);
+
+ const residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueSegments, unit.elements);
+ while (residuesIt.hasNext) {
+ const seg = residuesIt.move();
+ processResidue(state, seg.start, seg.end);
+ }
+
+ return state.rings;
+}
+
+const enum Constants {
+ MaxDepth = 4
+}
+
+interface State {
+ startVertex: number,
+ endVertex: number,
+ count: number,
+ visited: Int32Array,
+ queue: Int32Array,
+ color: Int32Array,
+ pred: Int32Array,
+
+ left: Int32Array,
+ right: Int32Array,
+
+ currentColor: number,
+
+ rings: number[][],
+ bonds: IntraUnitBonds,
+ unit: Unit.Atomic
+}
+
+function State(unit: Unit.Atomic, capacity: number): State {
+ return {
+ startVertex: 0,
+ endVertex: 0,
+ count: 0,
+ visited: new Int32Array(capacity),
+ queue: new Int32Array(capacity),
+ pred: new Int32Array(capacity),
+ left: new Int32Array(Constants.MaxDepth),
+ right: new Int32Array(Constants.MaxDepth),
+ color: new Int32Array(capacity),
+ currentColor: 0,
+ rings: [],
+ unit,
+ bonds: unit.bonds
+ };
+}
+
+function resetState(state: State) {
+ state.count = state.endVertex - state.startVertex;
+ const { visited, pred, color } = state;
+ for (let i = 0; i < state.count; i++) {
+ visited[i] = -1;
+ pred[i] = -1;
+ color[i] = 0;
+ }
+ state.currentColor = 0;
+}
+
+function largestResidue(unit: Unit.Atomic) {
+ const residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueSegments, unit.elements);
+ let size = 0;
+ while (residuesIt.hasNext) {
+ const seg = residuesIt.move();
+ size = Math.max(size, seg.end - seg.start);
+ }
+ return size;
+}
+
+function processResidue(state: State, start: number, end: number) {
+ const { visited } = state;
+ state.startVertex = start;
+ state.endVertex = end;
+
+ // no two atom rings
+ if (state.endVertex - state.startVertex < 3) return;
+
+ resetState(state);
+
+ for (let i = 0; i < state.count; i++) {
+ if (visited[i] >= 0) continue;
+ findRings(state, i);
+ }
+}
+
+function addRing(state: State, a: number, b: number) {
+ // only "monotonous" rings
+ if (b < a) return;
+
+ const { pred, color, left, right } = state;
+ const nc = ++state.currentColor;
+
+ let current = a;
+
+ for (let t = 0; t < Constants.MaxDepth; t++) {
+ color[current] = nc;
+ current = pred[current];
+ if (current < 0) break;
+ }
+
+ let leftOffset = 0, rightOffset = 0;
+
+ let found = false, target = 0;
+ current = b;
+ for (let t = 0; t < Constants.MaxDepth; t++) {
+ if (color[current] === nc) {
+ target = current;
+ found = true;
+ break;
+ }
+ right[rightOffset++] = current;
+ current = pred[current];
+ if (current < 0) break;
+ }
+ if (!found) return;
+
+ current = a;
+ for (let t = 0; t < Constants.MaxDepth; t++) {
+ left[leftOffset++] = current;
+ if (target === current) break;
+ current = pred[current];
+ if (current < 0) break;
+ }
+
+ const ring = new Int32Array(leftOffset + rightOffset);
+ let ringOffset = 0;
+ for (let t = 0; t < leftOffset; t++) ring[ringOffset++] = state.startVertex + left[t];
+ for (let t = rightOffset - 1; t >= 0; t--) ring[ringOffset++] = state.startVertex + right[t];
+
+ state.rings.push(ring as any as number[]);
+}
+
+function findRings(state: State, from: number) {
+ const { bonds, startVertex, endVertex, visited, queue, pred } = state;
+ const { b: neighbor, flags: bondFlags, offset } = bonds;
+ visited[from] = 1;
+ queue[0] = from;
+ let head = 0, size = 1;
+
+ while (head < size) {
+ const top = queue[head++];
+ const a = startVertex + top;
+ const start = offset[a], end = offset[a + 1];
+
+ for (let i = start; i < end; i++) {
+ const b = neighbor[i];
+ if (b < startVertex || b >= endVertex || !IntraUnitBonds.isCovalent(bondFlags[i])) continue;
+
+ const other = b - startVertex;
+
+ if (visited[other] > 0) {
+ if (pred[other] !== top && pred[top] !== other) addRing(state, top, other);
+ continue;
+ }
+
+ visited[other] = 1;
+ queue[size++] = other;
+ pred[other] = top;
+ }
+ }
+}
\ No newline at end of file
--
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