fix TransformData issues, see #133

- handle structure vs structure.root in ExplodeStructureRepresentation3D and SpinStructureRepresentation3D

CHANGELOG.md

@@ -6,6 +6,7 @@ Note that since we don't clearly distinguish between a public and private interf
 
 ## [Unreleased]
 
+- Fix ``TransformData`` issues [#133](https://github.com/molstar/molstar/issues/133)
 
 ## [v2.2.1] - 2021-08-02
 

src/mol-geo/geometry/transform-data.ts

 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -43,12 +43,13 @@ export function createTransform(transformArray: Float32Array, instanceCount: num
 
     if (transformData) {
         ValueCell.update(transformData.matrix, transformData.matrix.ref.value);
-        ValueCell.update(transformData.transform, transformArray);
+        const transform = transformData.transform.ref.value.length >= instanceCount * 16 ? transformData.transform.ref.value : new Float32Array(instanceCount * 16);
+        transform.set(transformArray);
+        ValueCell.update(transformData.transform, transform);
         ValueCell.updateIfChanged(transformData.uInstanceCount, instanceCount);
         ValueCell.updateIfChanged(transformData.instanceCount, instanceCount);
 
         const aTransform = transformData.aTransform.ref.value.length >= instanceCount * 16 ? transformData.aTransform.ref.value : new Float32Array(instanceCount * 16);
-        aTransform.set(transformArray);
         ValueCell.update(transformData.aTransform, aTransform);
 
         // Note that this sets `extraTransform` to identity transforms
@@ -64,9 +65,9 @@ export function createTransform(transformArray: Float32Array, instanceCount: num
         return transformData;
     } else {
         return {
-            aTransform: ValueCell.create(new Float32Array(transformArray)),
+            aTransform: ValueCell.create(new Float32Array(instanceCount * 16)),
             matrix: ValueCell.create(Mat4.identity()),
-            transform: ValueCell.create(transformArray),
+            transform: ValueCell.create(new Float32Array(transformArray)),
             extraTransform: ValueCell.create(fillIdentityTransform(new Float32Array(instanceCount * 16), instanceCount)),
             uInstanceCount: ValueCell.create(instanceCount),
             instanceCount: ValueCell.create(instanceCount),

src/mol-plugin-state/animation/helpers.ts

@@ -6,12 +6,12 @@
  */
 
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { SymmetryOperator } from '../../mol-math/geometry';
+import { Sphere3D, SymmetryOperator } from '../../mol-math/geometry';
 import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
 import { Structure } from '../../mol-model/structure';
 import { StructureUnitTransforms } from '../../mol-model/structure/structure/util/unit-transforms';
 
-const _unwindMatrix = Mat4.zero();
+const _unwindMatrix = Mat4();
 export function unwindStructureAssembly(structure: Structure, unitTransforms: StructureUnitTransforms, t: number) {
     for (let i = 0, _i = structure.units.length; i < _i; i++) {
         const u = structure.units[i];
@@ -20,15 +20,14 @@ export function unwindStructureAssembly(structure: Structure, unitTransforms: St
     }
 }
 
-const _centerVec = Vec3.zero(), _transVec = Vec3.zero(), _transMat = Mat4.zero();
-export function explodeStructure(structure: Structure, unitTransforms: StructureUnitTransforms, t: number) {
-    const boundary = structure.boundary.sphere;
-    const d = boundary.radius * t;
+const _centerVec = Vec3(), _transVec = Vec3(), _transMat = Mat4();
+export function explodeStructure(structure: Structure, unitTransforms: StructureUnitTransforms, t: number, sphere: Sphere3D) {
+    const d = sphere.radius * t;
 
     for (let i = 0, _i = structure.units.length; i < _i; i++) {
         const u = structure.units[i];
         Vec3.transformMat4(_centerVec, u.lookup3d.boundary.sphere.center, u.conformation.operator.matrix);
-        Vec3.sub(_transVec, _centerVec, boundary.center);
+        Vec3.sub(_transVec, _centerVec, sphere.center);
         Vec3.setMagnitude(_transVec, _transVec, d);
         Mat4.fromTranslation(_transMat, _transVec);
 

src/mol-plugin-state/transforms/representation.ts

@@ -236,23 +236,23 @@ const ExplodeStructureRepresentation3D = PluginStateTransform.BuiltIn({
     },
     apply({ a, params }) {
         const structure = a.data.sourceData;
-        const unitTransforms = new StructureUnitTransforms(structure.root);
-        explodeStructure(structure, unitTransforms, params.t);
+        const unitTransforms = new StructureUnitTransforms(structure);
+        explodeStructure(structure, unitTransforms, params.t, structure.root.boundary.sphere);
         return new SO.Molecule.Structure.Representation3DState({
             state: { unitTransforms },
-            initialState: { unitTransforms: new StructureUnitTransforms(structure.root) },
-            info: structure.root,
+            initialState: { unitTransforms: new StructureUnitTransforms(structure) },
+            info: structure,
             repr: a.data.repr
         }, { label: `Explode T = ${params.t.toFixed(2)}` });
     },
     update({ a, b, newParams, oldParams }) {
         const structure = a.data.sourceData;
-        if (b.data.info !== structure.root) return StateTransformer.UpdateResult.Recreate;
+        if (b.data.info !== structure) return StateTransformer.UpdateResult.Recreate;
         if (a.data.repr !== b.data.repr) return StateTransformer.UpdateResult.Recreate;
 
         if (oldParams.t === newParams.t) return StateTransformer.UpdateResult.Unchanged;
         const unitTransforms = b.data.state.unitTransforms!;
-        explodeStructure(structure.root, unitTransforms, newParams.t);
+        explodeStructure(structure, unitTransforms, newParams.t, structure.root.boundary.sphere);
         b.label = `Explode T = ${newParams.t.toFixed(2)}`;
         b.data.repr = a.data.repr;
         return StateTransformer.UpdateResult.Updated;
@@ -275,27 +275,27 @@ const SpinStructureRepresentation3D = PluginStateTransform.BuiltIn({
     },
     apply({ a, params }) {
         const structure = a.data.sourceData;
-        const unitTransforms = new StructureUnitTransforms(structure.root);
+        const unitTransforms = new StructureUnitTransforms(structure);
 
         const { axis, origin } = getSpinStructureAxisAndOrigin(structure.root, params);
         spinStructure(structure, unitTransforms, params.t, axis, origin);
         return new SO.Molecule.Structure.Representation3DState({
             state: { unitTransforms },
-            initialState: { unitTransforms: new StructureUnitTransforms(structure.root) },
-            info: structure.root,
+            initialState: { unitTransforms: new StructureUnitTransforms(structure) },
+            info: structure,
             repr: a.data.repr
         }, { label: `Spin T = ${params.t.toFixed(2)}` });
     },
     update({ a, b, newParams, oldParams }) {
         const structure = a.data.sourceData;
-        if (b.data.info !== structure.root) return StateTransformer.UpdateResult.Recreate;
+        if (b.data.info !== structure) return StateTransformer.UpdateResult.Recreate;
         if (a.data.repr !== b.data.repr) return StateTransformer.UpdateResult.Recreate;
 
         if (oldParams.t === newParams.t && oldParams.axis === newParams.axis && oldParams.origin === newParams.origin) return StateTransformer.UpdateResult.Unchanged;
 
         const unitTransforms = b.data.state.unitTransforms!;
         const { axis, origin } = getSpinStructureAxisAndOrigin(structure.root, newParams);
-        spinStructure(structure.root, unitTransforms, newParams.t, axis, origin);
+        spinStructure(structure, unitTransforms, newParams.t, axis, origin);
         b.label = `Spin T = ${newParams.t.toFixed(2)}`;
         b.data.repr = a.data.repr;
         return StateTransformer.UpdateResult.Updated;