diff --git a/src/mol-math/geometry/symmetry-operator.ts b/src/mol-math/geometry/symmetry-operator.ts
index 5064c7359c795f95573924b3f9c966e1c5859c0a..44ba2975516385dcf35260e7eddc971dd48c80b6 100644
--- a/src/mol-math/geometry/symmetry-operator.ts
+++ b/src/mol-math/geometry/symmetry-operator.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Vec3, Mat4, Mat3 } from '../linear-algebra/3d'
+import { Vec3, Mat4, Mat3, Quat } from '../linear-algebra/3d'
interface SymmetryOperator {
readonly name: string,
@@ -64,6 +64,26 @@ namespace SymmetryOperator {
return create(name, t, { id: '', operList: [] }, ncsId);
}
+ const _q1 = Quat.identity(), _q2 = Quat.zero(), _axis = Vec3.zero();
+ export function lerpFromIdentity(out: Mat4, op: SymmetryOperator, t: number): Mat4 {
+ const m = op.inverse;
+ if (op.isIdentity) return Mat4.copy(out, m);
+
+ const _t = 1 - t;
+ // interpolate rotation
+ Mat4.getRotation(_q2, m);
+ Quat.slerp(_q2, _q1, _q2, _t);
+ const angle = Quat.getAxisAngle(_axis, _q2);
+ Mat4.fromRotation(out, angle, _axis);
+
+ // interpolate translation
+ Mat4.setValue(out, 0, 3, _t * Mat4.getValue(m, 0, 3));
+ Mat4.setValue(out, 1, 3, _t * Mat4.getValue(m, 1, 3));
+ Mat4.setValue(out, 2, 3, _t * Mat4.getValue(m, 2, 3));
+
+ return out;
+ }
+
/**
* Apply the 1st and then 2nd operator. ( = second.matrix * first.matrix).
* Keep `name`, `assembly`, `ncsId` and `hkl` properties from second.
diff --git a/src/mol-math/linear-algebra/3d/mat4.ts b/src/mol-math/linear-algebra/3d/mat4.ts
index abf5cfb9660c20a43039510c799baa7e568f88f2..c8a307e8de9a57ab893dab678ce1bff9d1203076 100644
--- a/src/mol-math/linear-algebra/3d/mat4.ts
+++ b/src/mol-math/linear-algebra/3d/mat4.ts
@@ -22,6 +22,7 @@ import Vec3 from './vec3';
import Quat from './quat';
import { degToRad } from '../../misc';
import { NumberArray } from 'mol-util/type-helpers';
+import Mat3 from './mat3';
interface Mat4 extends Array<number> { [d: number]: number, '@type': 'mat4', length: 16 }
interface ReadonlyMat4 extends Array<number> { readonly [d: number]: number, '@type': 'mat4', length: 16 }
@@ -661,6 +662,22 @@ namespace Mat4 {
return out;
}
+ /**
+ * Copies the mat3 into upper-left 3x3 values.
+ */
+ export function fromMat3(out: Mat4, a: Mat3) {
+ out[0] = a[0];
+ out[1] = a[1];
+ out[2] = a[2];
+ out[4] = a[3];
+ out[5] = a[4];
+ out[6] = a[5];
+ out[8] = a[6];
+ out[9] = a[7];
+ out[10] = a[8];
+ return out;
+ }
+
export function makeTable(m: Mat4) {
let ret = '';
for (let i = 0; i < 4; i++) {
diff --git a/src/mol-plugin/behavior/dynamic/representation.ts b/src/mol-plugin/behavior/dynamic/representation.ts
index de55868e977da7566d2d48a95042ac64caa57235..99fb4cf56adc549b2a5a26bb5d788b905794b233 100644
--- a/src/mol-plugin/behavior/dynamic/representation.ts
+++ b/src/mol-plugin/behavior/dynamic/representation.ts
@@ -26,6 +26,7 @@ import { compile } from 'mol-script/runtime/query/compiler';
import { Overpaint } from 'mol-theme/overpaint';
import { parseMolScript } from 'mol-script/language/parser';
import { transpileMolScript } from 'mol-script/script/mol-script/symbols';
+import { SymmetryOperator } from 'mol-math/geometry';
export const HighlightLoci = PluginBehavior.create({
name: 'representation-highlight-loci',
@@ -290,4 +291,67 @@ export namespace ColorRepresentation3D {
}
export class Obj extends PluginStateObject.CreateBehavior<Behavior>({ name: 'Color Representation3D Behavior' }) { }
+}
+
+export namespace UnwindAssemblyRepresentation3D {
+ export const Params = {
+ t: PD.Numeric(0, { min: 0, max: 1, step: 0.01 })
+ }
+ export type Params = PD.Values<typeof Params>
+
+ export class Behavior implements PluginBehavior<Params> {
+ private currentT = 0;
+ private repr: StateObjectTracker<PluginStateObject.Molecule.Representation3D>;
+ private structure: StateObjectTracker<PluginStateObject.Molecule.Structure>;
+ private transforms: StructureUnitTransforms;
+
+ private updateData() {
+ const reprUpdated = this.repr.update();
+ const strUpdated = this.structure.update();
+ if (strUpdated && this.structure.data) {
+ this.transforms = new StructureUnitTransforms(this.structure.data);
+ }
+ return reprUpdated || strUpdated;
+ }
+
+ register(ref: string): void {
+ this.repr.setQuery(StateSelection.Generators.byRef(ref).ancestorOfType([PluginStateObject.Molecule.Representation3D]));
+ this.structure.setQuery(StateSelection.Generators.byRef(ref).rootOfType([PluginStateObject.Molecule.Structure]));
+ this.update(this.params);
+ }
+
+ private transMat = Mat4.zero();
+
+ update(params: Params): boolean | Promise<boolean> {
+ if (!this.updateData() && params.t === this.currentT) return false;
+ this.currentT = params.t;
+ if (!this.structure.data || !this.repr.data) return true;
+
+ const structure = this.structure.data;
+ for (let i = 0, _i = structure.units.length; i < _i; i++) {
+ const u = structure.units[i];
+ SymmetryOperator.lerpFromIdentity(this.transMat, u.conformation.operator, this.currentT);
+ this.transforms.setTransform(this.transMat, u);
+ }
+
+ this.repr.data.setState({ unitTransforms: this.transforms });
+ this.ctx.canvas3d.add(this.repr.data);
+ this.ctx.canvas3d.requestDraw(true);
+
+ return true;
+ }
+
+ unregister(): void {
+ this.update({ t: 0 })
+ this.repr.cell = void 0;
+ this.structure.cell = void 0;
+ }
+
+ constructor(private ctx: PluginContext, private params: Params) {
+ this.repr = new StateObjectTracker(ctx.state.dataState);
+ this.structure = new StateObjectTracker(ctx.state.dataState);
+ }
+ }
+
+ export class Obj extends PluginStateObject.CreateBehavior<Behavior>({ name: 'Explode Representation3D Behavior' }) { }
}
\ No newline at end of file
diff --git a/src/mol-plugin/index.ts b/src/mol-plugin/index.ts
index e1fdc8e433b63667617ca29118711fc0ca4e21a6..e9832b21aa9866dcbe07e9e2180444947846319c 100644
--- a/src/mol-plugin/index.ts
+++ b/src/mol-plugin/index.ts
@@ -12,7 +12,7 @@ import * as ReactDOM from 'react-dom';
import { PluginSpec } from './spec';
import { StateTransforms } from './state/transforms';
import { PluginBehaviors } from './behavior';
-import { AnimateModelIndex } from './state/animation/built-in';
+import { AnimateModelIndex, AnimateAssemblyUnwind } from './state/animation/built-in';
import { StateActions } from './state/actions';
import { InitVolumeStreaming, BoxifyVolumeStreaming, CreateVolumeStreamingBehavior } from './behavior/dynamic/volume-streaming/transformers';
import { StructureRepresentationInteraction } from './behavior/dynamic/selection/structure-representation-interaction';
@@ -47,6 +47,7 @@ export const DefaultPluginSpec: PluginSpec = {
PluginSpec.Action(StateTransforms.Representation.StructureRepresentation3D),
PluginSpec.Action(StateTransforms.Representation.StructureLabels3D),
PluginSpec.Action(StateTransforms.Representation.ExplodeStructureRepresentation3D),
+ PluginSpec.Action(StateTransforms.Representation.UnwindStructureAssemblyRepresentation3D),
PluginSpec.Action(StateTransforms.Representation.ColorStructureRepresentation3D),
PluginSpec.Action(StateTransforms.Representation.VolumeRepresentation3D),
@@ -64,7 +65,8 @@ export const DefaultPluginSpec: PluginSpec = {
PluginSpec.Behavior(StructureRepresentationInteraction)
],
animations: [
- AnimateModelIndex
+ AnimateModelIndex,
+ AnimateAssemblyUnwind
]
}
diff --git a/src/mol-plugin/state/animation/built-in.ts b/src/mol-plugin/state/animation/built-in.ts
index 91f581b1ad65433989e16a3906994cc85b8a93ec..91d78700e5aefb88a7529948993000d61a65b26d 100644
--- a/src/mol-plugin/state/animation/built-in.ts
+++ b/src/mol-plugin/state/animation/built-in.ts
@@ -10,6 +10,7 @@ import { StateTransforms } from '../transforms';
import { StateSelection } from 'mol-state';
import { PluginCommands } from 'mol-plugin/command';
import { ParamDefinition as PD } from 'mol-util/param-definition';
+import { UnwindAssemblyRepresentation3D } from 'mol-plugin/behavior/dynamic/representation';
export const AnimateModelIndex = PluginStateAnimation.create({
name: 'built-in.animate-model-index',
@@ -81,4 +82,35 @@ export const AnimateModelIndex = PluginStateAnimation.create({
if (params.mode.name === 'palindrome') return { kind: 'next', state: { palindromeDirections } };
return { kind: 'next', state: {} };
}
+})
+
+export const AnimateAssemblyUnwind = PluginStateAnimation.create({
+ name: 'built-in.animate-assembly-unwind',
+ display: { name: 'Unwind Assembly' },
+ params: () => ({
+ durationInMs: PD.Numeric(3000, { min: 100, max: 10000, step: 100})
+ }),
+ initialState: () => ({ t: 0 }),
+ async apply(animState, t, ctx) {
+ const state = ctx.plugin.state.dataState;
+ const anims = state.selectQ(q => q.ofType(UnwindAssemblyRepresentation3D.Obj));
+
+ if (anims.length === 0) {
+ // nothing more to do here
+ return { kind: 'finished' };
+ }
+
+ const update = state.build();
+
+ const d = (t.current - t.lastApplied) / ctx.params.durationInMs;
+ const newTime = (animState.t + d) % 1;
+
+ for (const m of anims) {
+ update.to(m.transform.ref).update(StateTransforms.Representation.UnwindStructureAssemblyRepresentation3D, _ => ({ t: newTime }));
+ }
+
+ await PluginCommands.State.Update.dispatch(ctx.plugin, { state, tree: update, options: { doNotLogTiming: true } });
+
+ return { kind: 'next', state: { t: newTime } };
+ }
})
\ No newline at end of file
diff --git a/src/mol-plugin/state/objects.ts b/src/mol-plugin/state/objects.ts
index c30240a4be52390a8bd85775db11b77a303b5463..3f2f1c21259f32c0d85f06a837bdb1df96150b5b 100644
--- a/src/mol-plugin/state/objects.ts
+++ b/src/mol-plugin/state/objects.ts
@@ -44,7 +44,6 @@ export namespace PluginStateObject {
}
export class Root extends Create({ name: 'Root', typeClass: 'Root' }) { }
-
export class Group extends Create({ name: 'Group', typeClass: 'Group' }) { }
export namespace Data {
@@ -82,6 +81,7 @@ export namespace PluginStateObject {
export class Model extends Create<_Model>({ name: 'Model', typeClass: 'Object' }) { }
export class Structure extends Create<_Structure>({ name: 'Structure', typeClass: 'Object' }) { }
export class Representation3D extends CreateRepresentation3D<StructureRepresentation<any> | ShapeRepresentation<any, any, any>>({ name: 'Structure 3D' }) { }
+ export class Representation3DState extends Create<{}>({ name: 'Structure 3D State', typeClass: 'Object' }) { }
}
export namespace Volume {
diff --git a/src/mol-plugin/state/transforms/representation.ts b/src/mol-plugin/state/transforms/representation.ts
index 1617502a8f9c81a6f5744df1cdca3fc94060c1c2..2badf987c4c2d814979d00709f9d4ea7e579240f 100644
--- a/src/mol-plugin/state/transforms/representation.ts
+++ b/src/mol-plugin/state/transforms/representation.ts
@@ -7,7 +7,7 @@
import { Structure } from 'mol-model/structure';
import { VolumeData, VolumeIsoValue } from 'mol-model/volume';
-import { ExplodeRepresentation3D, ColorRepresentation3D } from 'mol-plugin/behavior/dynamic/representation';
+import { ExplodeRepresentation3D, ColorRepresentation3D, UnwindAssemblyRepresentation3D } from 'mol-plugin/behavior/dynamic/representation';
import { PluginContext } from 'mol-plugin/context';
import { RepresentationProvider } from 'mol-repr/representation';
import { BuiltInStructureRepresentationsName } from 'mol-repr/structure/registry';
@@ -30,6 +30,7 @@ export { StructureRepresentation3D }
export { StructureRepresentation3DHelpers }
export { StructureLabels3D}
export { ExplodeStructureRepresentation3D }
+export { UnwindStructureAssemblyRepresentation3D }
export { ColorStructureRepresentation3D }
export { VolumeRepresentation3D }
@@ -229,6 +230,29 @@ const StructureLabels3D = PluginStateTransform.BuiltIn({
}
});
+type UnwindStructureAssemblyRepresentation3D = typeof UnwindStructureAssemblyRepresentation3D
+const UnwindStructureAssemblyRepresentation3D = PluginStateTransform.BuiltIn({
+ name: 'unwind-structure-assembly-representation-3d',
+ display: 'Unwind Assembly 3D Representation',
+ from: SO.Molecule.Representation3D,
+ to: UnwindAssemblyRepresentation3D.Obj,
+ params: UnwindAssemblyRepresentation3D.Params
+})({
+ canAutoUpdate() {
+ return true;
+ },
+ apply({ params }, plugin: PluginContext) {
+ return new UnwindAssemblyRepresentation3D.Obj(new UnwindAssemblyRepresentation3D.Behavior(plugin, params), { label: `Unwind T = ${params.t.toFixed(2)}` });
+ },
+ update({ b, newParams }) {
+ return Task.create('Update Unwind', async () => {
+ const updated = await b.data.update(newParams);
+ b.label = `Unwind T = ${newParams.t.toFixed(2)}`;
+ return updated ? StateTransformer.UpdateResult.Updated : StateTransformer.UpdateResult.Unchanged;
+ });
+ }
+});
+
type ExplodeStructureRepresentation3D = typeof ExplodeStructureRepresentation3D
const ExplodeStructureRepresentation3D = PluginStateTransform.BuiltIn({
name: 'explode-structure-representation-3d',