wip structure superposition

src/mol-math/linear-algebra/3d/minimize-rmsd.ts

@@ -19,6 +19,11 @@ namespace MinimizeRmsd {
     }
 
     export interface Positions { x: ArrayLike<number>, y: ArrayLike<number>, z: ArrayLike<number> }
+    export namespace Positions {
+        export function empty(n: number) {
+            return { x: new Float64Array(n), y: new Float64Array(n), z: new Float64Array(n) };
+        }
+    }
 
     export interface Input {
         a: Positions,
@@ -54,10 +59,10 @@ class RmsdTransformState {
         this.b = data.b;
 
         if (data.centerA) this.centerA = data.centerA;
-        else this.centerA = CentroidHelper.compute(data.a, Vec3.zero());
+        else this.centerA = data.centerA = CentroidHelper.compute(data.a, Vec3.zero());
 
         if (data.centerB) this.centerB = data.centerB;
-        else this.centerB = CentroidHelper.compute(data.b, Vec3.zero());
+        else this.centerB = data.centerB = CentroidHelper.compute(data.b, Vec3.zero());
 
         this.result = into;
     }

src/mol-model/structure/structure/element.ts

@@ -118,6 +118,12 @@ namespace StructureElement {
     }
 
     export namespace Loci {
+        export function size(loci: Loci) {
+            let s = 0;
+            for (const u of loci.elements) s += OrderedSet.size(u.indices);
+            return s;
+        }
+
         export function all(structure: Structure): Loci {
             return Loci(structure, structure.units.map(unit => ({
                 unit,

src/mol-model/structure/structure/util/superposition.ts

+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { MinimizeRmsd } from 'mol-math/linear-algebra';
+import StructureElement from '../element';
+import { OrderedSet } from 'mol-data/int';
+
+export function superposeStructures(xs: StructureElement.Loci[]): MinimizeRmsd.Result[] {
+    const ret: MinimizeRmsd.Result[] = [];
+    if (xs.length <= 0) return ret;
+
+    const n = getMinSize(xs);
+    const input: MinimizeRmsd.Input = { a: getPositionTable(xs[0], n), b: getPositionTable(xs[1], n) };
+    ret[0] = MinimizeRmsd.compute(input);
+    for (let i = 2; i < xs.length; i++) {
+        input.b = getPositionTable(xs[i], n);
+        input.centerB = void 0;
+        ret.push(MinimizeRmsd.compute(input));
+    }
+
+    return ret;
+}
+
+function getPositionTable(xs: StructureElement.Loci, n: number): MinimizeRmsd.Positions {
+    const ret = MinimizeRmsd.Positions.empty(n);
+    let o = 0;
+    for (const u of xs.elements) {
+        const { unit, indices } = u;
+        const { elements } = unit;
+        const { x, y, z } = unit.conformation;
+        for (let i = 0, _i = OrderedSet.size(indices); i < _i; i++) {
+            const e = elements[OrderedSet.getAt(indices, i)];
+            ret.x[o] = x(e);
+            ret.y[o] = y(e);
+            ret.z[o] = z(e);
+            o++;
+            if (o >= n) break;
+        }
+        if (o >= n) break;
+    }
+    return ret;
+}
+
+function getMinSize(xs: StructureElement.Loci[]) {
+    if (xs.length === 0) return 0;
+    let s = StructureElement.Loci.size(xs[0]);
+    for (let i = 1; i < xs.length; i++) {
+        const t = StructureElement.Loci.size(xs[i]);
+        if (t < s) s = t;
+    }
+    return s;
+}
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