PR feedback

- use arraySet since deps count is small
- cache default params

src/mol-plugin-state/actions/structure.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -436,12 +436,12 @@ export const LoadTrajectory = StateAction.build({
 
             //
 
-            const dependsOn = [model.ref, coordinates.ref];
+            // dependsOn is auto-derived from the `getDependencies` hook on TrajectoryFromModelAndCoordinates
             const traj = state.build().toRoot()
                 .apply(TrajectoryFromModelAndCoordinates, {
                     modelRef: model.ref,
                     coordinatesRef: coordinates.ref
-                }, { dependsOn })
+                })
                 .apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 });
 
             await state.updateTree(traj).runInContext(taskCtx);

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

@@ -22,7 +22,7 @@ import { PluginContext } from '../../mol-plugin/context';
 import { MolScriptBuilder } from '../../mol-script/language/builder';
 import { Expression } from '../../mol-script/language/expression';
 import { Script } from '../../mol-script/script';
-import { StateObject, StateTransformer } from '../../mol-state';
+import { StateObject, StateTransform, StateTransformer } from '../../mol-state';
 import { RuntimeContext, Task } from '../../mol-task';
 import { deepEqual } from '../../mol-util';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
@@ -247,6 +247,12 @@ const TrajectoryFromModelAndCoordinates = PluginStateTransform.BuiltIn({
         coordinatesRef: PD.Text('', { isHidden: true }),
     }
 })({
+    getDependencies: ({ modelRef, coordinatesRef }: { modelRef: string, coordinatesRef: string }) => {
+        const deps: StateTransform.Ref[] = [];
+        if (modelRef) deps.push(modelRef as StateTransform.Ref);
+        if (coordinatesRef) deps.push(coordinatesRef as StateTransform.Ref);
+        return deps;
+    },
     apply({ params, dependencies }) {
         return Task.create('Create trajectory from model/topology and coordinates', async ctx => {
             const coordinates = dependencies![params.coordinatesRef].data as Coordinates;

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

@@ -18,7 +18,7 @@ import { volumeFromCube } from '../../mol-model-formats/volume/cube';
 import { volumeFromDx } from '../../mol-model-formats/volume/dx';
 import { Grid, Volume } from '../../mol-model/volume';
 import { PluginContext } from '../../mol-plugin/context';
-import { StateSelection, StateTransformer } from '../../mol-state';
+import { StateSelection, StateTransform, StateTransformer } from '../../mol-state';
 import { volumeFromSegmentationData } from '../../mol-model-formats/volume/segmentation';
 import { getTransformFromParams, TransformParam, transformParamsNeedCentroid } from './helpers';
 
@@ -233,7 +233,8 @@ const AssignColorVolume = PluginStateTransform.BuiltIn({
             const props = { label: a.label, description: 'Volume + Colors' };
             return new SO.Volume.Data(volume, props);
         });
-    }
+    },
+    getDependencies: ({ ref }) => ref ? [ref as StateTransform.Ref] : []
 });
 
 type VolumeTransform = typeof VolumeTransform;

src/mol-state/_spec/dependencies.spec.ts

@@ -0,0 +1,324 @@
+/**
+ * Copyright (c) 2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { State, StateObject, StateObjectCell, StateTransform, StateTransformer, StateTreeCycleError } from '../../mol-state';
+import { Task } from '../../mol-task';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+
+interface TypeInfo { name: string; typeClass: 'Root' | 'Data' }
+const Create = StateObject.factory<TypeInfo>();
+
+class Root extends Create({ name: 'Root', typeClass: 'Root' }) { }
+class Leaf extends Create<{ value: number }>({ name: 'Leaf', typeClass: 'Data' }) { }
+
+const NS = 'state-deps-spec';
+let counter = 0;
+const uniq = (s: string) => `${s}-${counter++}`;
+
+function newState() {
+    return State.create(new Root({}), { runTask: <T>(t: Task<T>) => t.run() });
+}
+
+/** Plain leaf created from Root with a number param. */
+function constLeaf() {
+    return StateTransformer.create<Root, Leaf, { value: number }>(NS, {
+        name: uniq('const-leaf'),
+        from: [Root],
+        to: [Leaf],
+        display: { name: 'Const Leaf' },
+        params: () => ({ value: PD.Numeric(0) }) as any,
+        apply({ params }) { return new Leaf({ value: params.value }); },
+        update({ oldParams, newParams }) {
+            return oldParams.value === newParams.value
+                ? StateTransformer.UpdateResult.Unchanged
+                : StateTransformer.UpdateResult.Recreate;
+        }
+    });
+}
+
+/** Leaf whose value is read from a single explicit dependsOn ref. */
+function deriveFromDep(depRef: string) {
+    return StateTransformer.create<Root, Leaf, {}>(NS, {
+        name: uniq('derive-from-dep'),
+        from: [Root],
+        to: [Leaf],
+        display: { name: 'Derive From Dep' },
+        params: () => ({}) as any,
+        apply({ dependencies }) {
+            const dep = dependencies?.[depRef] as Leaf;
+            if (!dep) throw new Error('missing dep');
+            return new Leaf({ value: dep.data.value + 100 });
+        },
+        update({ b, dependencies }) {
+            const dep = dependencies?.[depRef] as Leaf;
+            if (!dep) throw new Error('missing dep');
+            (b.data as { value: number }).value = dep.data.value + 100;
+            return StateTransformer.UpdateResult.Updated;
+        }
+    });
+}
+
+describe('State dependencies - linking', () => {
+    it('explicit dependsOn establishes an edge and passes the dep object to apply', async () => {
+        const state = newState();
+        const A = constLeaf();
+        const B = deriveFromDep('leaf-a');
+
+        const builder = state.build();
+        builder.toRoot<Root>().apply(A as any, { value: 7 }, { ref: 'leaf-a' });
+        builder.toRoot<Root>().apply(B as any, {}, { ref: 'leaf-b', dependsOn: ['leaf-a'] });
+        await state.runTask(state.updateTree(builder));
+
+        const b = state.cells.get('leaf-b')!;
+        expect(b.dependencies.dependsOn.map(c => c.transform.ref)).toEqual(['leaf-a']);
+        expect((b.obj as Leaf).data.value).toBe(107);
+
+        const a = state.cells.get('leaf-a')!;
+        expect(a.dependencies.dependentBy.map(c => c.transform.ref)).toEqual(['leaf-b']);
+    });
+
+    it('re-evaluates dependents when the source updates', async () => {
+        const state = newState();
+        const A = constLeaf();
+        const B = deriveFromDep('leaf-a');
+
+        const builder1 = state.build();
+        builder1.toRoot<Root>().apply(A as any, { value: 1 }, { ref: 'leaf-a' });
+        builder1.toRoot<Root>().apply(B as any, {}, { ref: 'leaf-b', dependsOn: ['leaf-a'] });
+        await state.runTask(state.updateTree(builder1));
+        expect((state.cells.get('leaf-b')!.obj as Leaf).data.value).toBe(101);
+
+        const builder2 = state.build();
+        builder2.to('leaf-a').update({ value: 5 });
+        await state.runTask(state.updateTree(builder2));
+        expect((state.cells.get('leaf-b')!.obj as Leaf).data.value).toBe(105);
+    });
+
+    it('throws when an explicit dependsOn references a non-existent transform', async () => {
+        const state = newState();
+        const B = deriveFromDep('missing-ref');
+
+        const builder = state.build();
+        builder.toRoot<Root>().apply(B as any, {}, { ref: 'leaf-b', dependsOn: ['missing-ref'] });
+        await expect(state.runTask(state.updateTree(builder))).rejects.toThrow(/non-existent transform/);
+    });
+
+    it('honors getDependencies(params) and relinks when params change', async () => {
+        const state = newState();
+        const A = constLeaf();
+        const A2 = constLeaf();
+
+        const PickViaParams = StateTransformer.create<Root, Leaf, { which: string }>(NS, {
+            name: uniq('pick-via-params'),
+            from: [Root],
+            to: [Leaf],
+            display: { name: 'Pick' },
+            params: () => ({ which: PD.Text('leaf-a') }) as any,
+            getDependencies(params) { return params.which ? [params.which as StateTransform.Ref] : []; },
+            apply({ params, dependencies }) {
+                const dep = dependencies?.[params.which] as Leaf;
+                return new Leaf({ value: dep ? dep.data.value : -1 });
+            },
+            update({ b, newParams, dependencies }) {
+                const dep = dependencies?.[newParams.which] as Leaf;
+                (b.data as { value: number }).value = dep ? dep.data.value : -1;
+                return StateTransformer.UpdateResult.Updated;
+            }
+        });
+
+        const builder = state.build();
+        builder.toRoot<Root>().apply(A as any, { value: 11 }, { ref: 'leaf-a' });
+        builder.toRoot<Root>().apply(A2 as any, { value: 22 }, { ref: 'leaf-a2' });
+        builder.toRoot<Root>().apply(PickViaParams as any, { which: 'leaf-a' }, { ref: 'pick' });
+        await state.runTask(state.updateTree(builder));
+
+        const pick = state.cells.get('pick')!;
+        expect(pick.dependencies.dependsOn.map(c => c.transform.ref)).toEqual(['leaf-a']);
+        expect((pick.obj as Leaf).data.value).toBe(11);
+
+        const update = state.build();
+        update.to('pick').update({ which: 'leaf-a2' });
+        await state.runTask(state.updateTree(update));
+
+        const pick2 = state.cells.get('pick')!;
+        expect(pick2.dependencies.dependsOn.map(c => c.transform.ref)).toEqual(['leaf-a2']);
+        expect((pick2.obj as Leaf).data.value).toBe(22);
+        // Old source no longer reverse-linked.
+        expect(state.cells.get('leaf-a')!.dependencies.dependentBy.length).toBe(0);
+        expect(state.cells.get('leaf-a2')!.dependencies.dependentBy.map(c => c.transform.ref)).toEqual(['pick']);
+    });
+
+    it('auto-collects refs from PD.ValueRef parameter values', async () => {
+        const state = newState();
+        const A = constLeaf();
+
+        const ViaValueRef = StateTransformer.create<Root, Leaf, { target: { ref: string, getValue: () => Leaf } }>(NS, {
+            name: uniq('via-value-ref'),
+            from: [Root],
+            to: [Leaf],
+            display: { name: 'Via ValueRef' },
+            params: () => ({
+                target: PD.ValueRef<Leaf>(() => [], (ref, getData) => getData(ref))
+            }) as any,
+            apply({ params, dependencies }) {
+                const dep = dependencies?.[params.target.ref] as Leaf;
+                return new Leaf({ value: dep ? dep.data.value * 2 : -1 });
+            }
+        });
+
+        const builder = state.build();
+        builder.toRoot<Root>().apply(A as any, { value: 9 }, { ref: 'leaf-a' });
+        builder.toRoot<Root>().apply(ViaValueRef as any, {
+            target: { ref: 'leaf-a', getValue: () => null as any }
+        }, { ref: 'vr' });
+        await state.runTask(state.updateTree(builder));
+
+        const vr = state.cells.get('vr')!;
+        expect(vr.dependencies.dependsOn.map(c => c.transform.ref)).toEqual(['leaf-a']);
+        expect((vr.obj as Leaf).data.value).toBe(18);
+    });
+
+    it('falls back to a structural scan when the schema is unavailable', async () => {
+        const state = newState();
+        const A = constLeaf();
+
+        // No `def.params` - params normalization will drop unknown fields at
+        // evaluation time, but link-time collection (via the structural
+        // fallback) still happens against the original transform.params.
+        const Structural = StateTransformer.create<Root, Leaf, any>(NS, {
+            name: uniq('structural'),
+            from: [Root],
+            to: [Leaf],
+            display: { name: 'Structural' },
+            apply({ dependencies }) {
+                const ref = dependencies ? Object.keys(dependencies)[0] : undefined;
+                const dep = ref ? dependencies![ref] as Leaf : undefined;
+                return new Leaf({ value: dep ? dep.data.value + 1000 : -1 });
+            }
+        });
+
+        const builder = state.build();
+        builder.toRoot<Root>().apply(A as any, { value: 3 }, { ref: 'leaf-a' });
+        builder.toRoot<Root>().apply(Structural as any, {
+            link: { ref: 'leaf-a', getValue: () => null }
+        }, { ref: 'struct' });
+        await state.runTask(state.updateTree(builder));
+
+        const s = state.cells.get('struct')!;
+        expect(s.dependencies.dependsOn.map(c => c.transform.ref)).toEqual(['leaf-a']);
+        expect((s.obj as Leaf).data.value).toBe(1003);
+    });
+
+    it('filters out self and root refs from getDependencies', async () => {
+        const state = newState();
+
+        const SelfRef = StateTransformer.create<Root, Leaf, {}>(NS, {
+            name: uniq('self-ref'),
+            from: [Root],
+            to: [Leaf],
+            display: { name: 'Self Ref' },
+            params: () => ({}) as any,
+            getDependencies() { return ['self', StateTransform.RootRef as any]; },
+            apply() { return new Leaf({ value: 42 }); }
+        });
+
+        const builder = state.build();
+        builder.toRoot<Root>().apply(SelfRef as any, {}, { ref: 'self' });
+        await state.runTask(state.updateTree(builder));
+
+        const cell = state.cells.get('self')!;
+        expect(cell.dependencies.dependsOn.length).toBe(0);
+        expect((cell.obj as Leaf).data.value).toBe(42);
+    });
+});
+
+describe('State dependencies - cycle detection', () => {
+    it('throws StateTreeCycleError for a direct A → B → A cycle', async () => {
+        const state = newState();
+
+        // Two transformers, each declaring a getDependencies pointing at the other.
+        const A = StateTransformer.create<Root, Leaf, {}>(NS, {
+            name: uniq('cycle-a'),
+            from: [Root],
+            to: [Leaf],
+            display: { name: 'Cycle A' },
+            params: () => ({}) as any,
+            getDependencies() { return ['cyc-b' as any]; },
+            apply() { return new Leaf({ value: 0 }); }
+        });
+        const B = StateTransformer.create<Root, Leaf, {}>(NS, {
+            name: uniq('cycle-b'),
+            from: [Root],
+            to: [Leaf],
+            display: { name: 'Cycle B' },
+            params: () => ({}) as any,
+            getDependencies() { return ['cyc-a' as any]; },
+            apply() { return new Leaf({ value: 0 }); }
+        });
+
+        const builder = state.build();
+        builder.toRoot<Root>().apply(A as any, {}, { ref: 'cyc-a' });
+        builder.toRoot<Root>().apply(B as any, {}, { ref: 'cyc-b' });
+
+        let caught: unknown;
+        try {
+            await state.runTask(state.updateTree(builder));
+        } catch (e) { caught = e; }
+        expect(caught).toBeInstanceOf(StateTreeCycleError);
+        const cycle = (caught as StateTreeCycleError).cycle;
+        expect(cycle[0]).toBe(cycle[cycle.length - 1]);
+        expect(cycle).toEqual(expect.arrayContaining(['cyc-a', 'cyc-b']));
+    });
+});
+
+describe('State dependencies - deferred resolution', () => {
+    /** Force evaluation order: place dependent subtree first under root so
+     *  tree pre-order visits it before its dependency. */
+    it('resolves cross-subtree deps even when the dependent is scheduled first', async () => {
+        const state = newState();
+        const A = constLeaf();
+        const B = deriveFromDep('leaf-a');
+
+        const builder = state.build();
+        // B added FIRST - so its subtree comes before A's in tree pre-order.
+        builder.toRoot<Root>().apply(B as any, {}, { ref: 'leaf-b', dependsOn: ['leaf-a'] });
+        builder.toRoot<Root>().apply(A as any, { value: 4 }, { ref: 'leaf-a' });
+
+        await state.runTask(state.updateTree(builder));
+
+        expect((state.cells.get('leaf-a')!.obj as Leaf).data.value).toBe(4);
+        expect((state.cells.get('leaf-b')!.obj as Leaf).data.value).toBe(104);
+    });
+
+    it('propagates a clear error when a dep has errored and cannot resolve', async () => {
+        const state = newState();
+
+        const Boom = StateTransformer.create<Root, Leaf, {}>(NS, {
+            name: uniq('boom'),
+            from: [Root],
+            to: [Leaf],
+            display: { name: 'Boom' },
+            params: () => ({}) as any,
+            apply() { throw new Error('intentional'); }
+        });
+        const B = deriveFromDep('boom');
+
+        const builder = state.build();
+        builder.toRoot<Root>().apply(Boom as any, {}, { ref: 'boom' });
+        builder.toRoot<Root>().apply(B as any, {}, { ref: 'leaf-b', dependsOn: ['boom'] });
+        // The state surfaces transform errors via console.error; suppress the noise.
+        const err = jest.spyOn(console, 'error').mockImplementation(() => {});
+        try {
+            await state.runTask(state.updateTree(builder));
+        } finally {
+            err.mockRestore();
+        }
+
+        const b: StateObjectCell = state.cells.get('leaf-b')!;
+        expect(b.status).toBe('error');
+        expect(b.errorText).toMatch(/Unresolved dependency|missing dep|intentional/);
+    });
+});

src/mol-state/state.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { StateObject, StateObjectCell, StateObjectSelector } from './object';
@@ -24,7 +25,22 @@ import { arraySetAdd, arraySetRemove } from '../mol-util/array';
 import { UniqueArray } from '../mol-data/generic/unique-array';
 import { assignIfUndefined } from '../mol-util/object';
 
-export { State };
+export { State, StateTreeCycleError };
+
+/**
+ * Thrown when a cycle is detected in the state-tree dependency graph
+ * (the cross-edges defined by `transform.dependsOn` and effective
+ * dependencies derived from params). `cycle` holds the closed path,
+ * e.g. `['A', 'B', 'A']`.
+ */
+class StateTreeCycleError extends Error {
+    readonly cycle: StateTransform.Ref[];
+    constructor(cycle: StateTransform.Ref[]) {
+        super(`Cyclic state-tree dependency detected: ${cycle.join(' -> ')}`);
+        this.name = 'StateTreeCycleError';
+        this.cycle = cycle;
+    }
+}
 
 class State {
     private _tree: TransientTree;
@@ -494,6 +510,21 @@ interface UpdateContext {
     wasAborted: boolean,
     newCurrent?: Ref,
 
+    /**
+     * Refs that are scheduled to be (re-)evaluated in this update pass:
+     * the union of every `roots[i]` and its descendants. Used to distinguish
+     * "dep not yet produced this pass" (defer + retry) from "dep can never
+     * be produced this pass" (throw).
+     */
+    scheduled?: Set<Ref>,
+
+    /**
+     * Subtree roots that were skipped because at least one of their
+     * dependencies hadn't been evaluated yet. Drained after the main loop
+     * makes a fixpoint pass.
+     */
+    deferred?: Ref[],
+
     getCellData: (ref: string) => any
 }
 
@@ -573,11 +604,45 @@ async function update(ctx: UpdateContext) {
     // Set status of cells that will be updated to 'pending'.
     initCellStatus(ctx, roots);
 
+    // Build the set of refs that will be (re-)evaluated this pass so that
+    // `updateSubtree` can distinguish "dep not produced yet" (defer + retry)
+    // from "dep can never be produced" (throw via resolveDependencies).
+    ctx.scheduled = collectScheduled(ctx, roots);
+
     // Sequentially update all the subtrees.
     for (const root of roots) {
         await updateSubtree(ctx, root);
     }
 
+    // Drain the deferred queue: nodes whose `dependsOn` cells weren't yet
+    // evaluated when first visited get retried until either all succeed or
+    // a full pass makes no forward progress (true deadlock / unresolvable).
+    if (ctx.deferred && ctx.deferred.length > 0) {
+        while (ctx.deferred.length > 0) {
+            const pending = ctx.deferred;
+            ctx.deferred = [];
+            let progress = false;
+            for (const ref of pending) {
+                const before = ctx.deferred.length;
+                await updateSubtree(ctx, ref);
+                // Forward progress = this attempt did not re-defer the same ref.
+                const reDeferred = ctx.deferred.length > before
+                    && ctx.deferred[ctx.deferred.length - 1] === ref;
+                if (!reDeferred) progress = true;
+            }
+            if (!progress) {
+                const stuck = ctx.deferred.map(r => {
+                    const c = ctx.cells.get(r);
+                    if (!c) return r;
+                    const blockers = pendingBlockers(ctx, c);
+                    return `${r} (waiting on: ${blockers.length ? blockers.join(', ') : 'unknown'})`;
+                });
+                ctx.deferred = [];
+                throw new Error(`Unresolved dependency: ${stuck.join('; ')}`);
+            }
+        }
+    }
+
     // Sync cell states
     if (!ctx.editInfo) {
         syncNewStates(ctx);
@@ -663,7 +728,13 @@ function setCellStatus(ctx: UpdateContext, ref: Ref, status: StateObjectCell.Sta
 }
 
 function initCellStatusVisitor(t: StateTransform, _: any, ctx: UpdateContext) {
-    ctx.cells.get(t.ref)!.transform = t;
+    const cell = ctx.cells.get(t.ref)!;
+    cell.transform = t;
+    if (relinkCells(cell, ctx)) {
+        // Edges changed (e.g. param update added/removed dependencies) —
+        // re-verify there is no cycle.
+        checkDependenciesCycle(cell);
+    }
     setCellStatus(ctx, t.ref, 'pending');
 }
 
@@ -707,9 +778,10 @@ function addCellsVisitor(transform: StateTransform, _: any, { ctx, added, visite
 // type LinkCellsCtx = { ctx: UpdateContext, visited: Set<Ref>, dependent: UniqueArray<Ref, StateObjectCell> }
 
 function linkCells(target: StateObjectCell, ctx: UpdateContext) {
-    if (!target.transform.dependsOn) return;
+    const effective = StateTransform.getEffectiveDependsOn(target.transform);
+    if (effective.length === 0) return;
 
-    for (const ref of target.transform.dependsOn) {
+    for (const ref of effective) {
         const t = ctx.tree.transforms.get(ref);
         if (!t) {
             throw new Error(`Cannot depend on a non-existent transform.`);
@@ -721,6 +793,103 @@ function linkCells(target: StateObjectCell, ctx: UpdateContext) {
     }
 }
 
+/**
+ * Diff the current outgoing dependency edges of `target` against the effective
+ * set derived from its (possibly updated) transform. Unlinks stale edges and
+ * links new ones so the dependency graph reflects param changes. Idempotent
+ * when nothing has changed. Returns `true` if any edge was added or removed.
+ */
+function relinkCells(target: StateObjectCell, ctx: UpdateContext): boolean {
+    const effective = StateTransform.getEffectiveDependsOn(target.transform);
+    const current = target.dependencies.dependsOn;
+
+    // Fast path: same number and all current refs are still in effective.
+    if (current.length === effective.length) {
+        let same = true;
+        for (const c of current) {
+            if (effective.indexOf(c.transform.ref) < 0) { same = false; break; }
+        }
+        if (same) return false;
+    }
+
+    const desired = new Set(effective);
+    let changed = false;
+
+    // Remove stale outgoing edges.
+    for (let i = current.length - 1; i >= 0; i--) {
+        const dep = current[i];
+        if (!desired.has(dep.transform.ref)) {
+            current.splice(i, 1);
+            arraySetRemove(dep.dependencies.dependentBy, target);
+            changed = true;
+        }
+    }
+
+    // Add new outgoing edges.
+    const have = new Set(current.map(c => c.transform.ref));
+    for (const ref of effective) {
+        if (have.has(ref)) continue;
+        const t = ctx.tree.transforms.get(ref);
+        if (!t) {
+            throw new Error(`Cannot depend on a non-existent transform.`);
+        }
+        const cell = ctx.cells.get(ref)!;
+        arraySetAdd(target.dependencies.dependsOn, cell);
+        arraySetAdd(cell.dependencies.dependentBy, target);
+        changed = true;
+    }
+
+    return changed;
+}
+
+/**
+ * Detect a cycle in the `dependsOn` graph reachable from `start`.
+ *
+ * Iterative DFS, returning the closed cycle path (first occurrence of the
+ * repeated ref appended at the end) or `undefined` if none. Operates on the
+ * already-linked cell graph; safe to call after `linkCells` / `relinkCells`.
+ */
+function detectDependenciesCycle(start: StateObjectCell): StateTransform.Ref[] | undefined {
+    if (start.dependencies.dependsOn.length === 0) return void 0;
+    const stack: { cell: StateObjectCell, idx: number }[] = [{ cell: start, idx: 0 }];
+    const onPath = new Set<StateTransform.Ref>([start.transform.ref]);
+    const fully = new Set<StateTransform.Ref>();
+
+    while (stack.length > 0) {
+        const top = stack[stack.length - 1];
+        const deps = top.cell.dependencies.dependsOn;
+        if (top.idx >= deps.length) {
+            onPath.delete(top.cell.transform.ref);
+            fully.add(top.cell.transform.ref);
+            stack.pop();
+            continue;
+        }
+        const next = deps[top.idx++];
+        const ref = next.transform.ref;
+        if (fully.has(ref)) continue;
+        if (onPath.has(ref)) {
+            const path: StateTransform.Ref[] = [];
+            let started = false;
+            for (const s of stack) {
+                if (started || s.cell.transform.ref === ref) {
+                    started = true;
+                    path.push(s.cell.transform.ref);
+                }
+            }
+            path.push(ref);
+            return path;
+        }
+        onPath.add(ref);
+        stack.push({ cell: next, idx: 0 });
+    }
+    return void 0;
+}
+
+function checkDependenciesCycle(cell: StateObjectCell) {
+    const cycle = detectDependenciesCycle(cell);
+    if (cycle) throw new StateTreeCycleError(cycle);
+}
+
 function initCells(ctx: UpdateContext, roots: Ref[]) {
     const initCtx: InitCellsCtx = { ctx, visited: new Set(), added: [] };
 
@@ -734,6 +903,12 @@ function initCells(ctx: UpdateContext, roots: Ref[]) {
         linkCells(cell, ctx);
     }
 
+    // Cycle detection over the dependency cross-edges of newly added cells.
+    // Parent/child is already a tree, so cycles can only enter via dependsOn.
+    for (const cell of initCtx.added) {
+        checkDependenciesCycle(cell);
+    }
+
     let dependent: UniqueArray<Ref, StateObjectCell>;
 
     // Find dependent cells
@@ -834,7 +1009,54 @@ type UpdateNodeResult =
 
 const ParentNullErrorText = 'Parent is null';
 
+function collectScheduledVisitor(t: StateTransform, _: any, s: Set<Ref>) {
+    s.add(t.ref);
+}
+
+function collectScheduled(ctx: UpdateContext, roots: Ref[]): Set<Ref> {
+    const out = new Set<Ref>();
+    for (const root of roots) {
+        const node = ctx.tree.transforms.get(root);
+        if (!node) continue;
+        StateTree.doPreOrder(ctx.tree, node, out, collectScheduledVisitor);
+    }
+    return out;
+}
+
+/**
+ * Refs that `cell` depends on which are scheduled for evaluation in this
+ * pass but haven't produced an object yet (and aren't in an error state).
+ * An empty result means deps are either ready, in error, or out-of-scope —
+ * in any of those cases the cell should proceed (and may throw at
+ * `resolveDependencies` time if the dep is genuinely missing).
+ */
+function pendingBlockers(ctx: UpdateContext, cell: StateObjectCell): Ref[] {
+    const blockers: Ref[] = [];
+    const scheduled = ctx.scheduled;
+    if (!scheduled) return blockers;
+    for (const dep of cell.dependencies.dependsOn) {
+        if (dep.obj) continue;
+        if (dep.status === 'error') continue;
+        if (!scheduled.has(dep.transform.ref)) continue;
+        blockers.push(dep.transform.ref);
+    }
+    return blockers;
+}
+
 async function updateSubtree(ctx: UpdateContext, root: Ref) {
+    const cell = ctx.cells.get(root);
+    if (cell && cell.dependencies.dependsOn.length > 0) {
+        const blockers = pendingBlockers(ctx, cell);
+        if (blockers.length > 0) {
+            // A dependency hasn't been produced yet this pass — defer this
+            // subtree and retry after other roots have run. Children will be
+            // visited when the deferred re-attempt succeeds.
+            if (!ctx.deferred) ctx.deferred = [];
+            ctx.deferred.push(root);
+            return;
+        }
+    }
+
     setCellStatus(ctx, root, 'processing');
 
     let isNull = false;

src/mol-state/transform.ts

@@ -1,12 +1,15 @@
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { StateTransformer } from './transformer';
 import { UUID } from '../mol-util';
 import { hashMurmur128o } from '../mol-data/util/hash-functions';
+import { ParamDefinition as PD } from '../mol-util/param-definition';
+import { arraySetAdd, arraySetRemove } from '../mol-util/array';
 
 export { Transform as StateTransform };
 
@@ -170,6 +173,97 @@ namespace Transform {
         return true;
     }
 
+    /**
+     * Returns the default param schema for the transform's transformer, caching
+     * the result on the transform instance. Returns `undefined` if the transformer
+     * has no `params` definition or if calling it throws.
+     */
+    export function tryGetDefaultParamDefinition(t: Transform): PD.Params | undefined {
+        const any = t as any;
+        if (any._defaultSchemaSet) return any._defaultSchema;
+        any._defaultSchemaSet = true;
+        try {
+            const def = t.transformer.definition;
+            if (def.params) {
+                any._defaultSchema = def.params(undefined as any, undefined) as PD.Params;
+            }
+        } catch {
+            // Schema could not be obtained.
+        }
+        return any._defaultSchema;
+    }
+
+    /**
+     * Compute the effective set of sibling-like dependencies for a transform.
+     *
+     * Combines (in order, de-duplicated):
+     *   1. Explicit `t.dependsOn` (back-compat / non-param refs).
+     *   2. Refs from `transformer.definition.getDependencies(params)` if defined.
+     *   3. Refs collected from `PD.ValueRef` / `PD.DataRef` parameter values.
+     *
+     * Self-references and the root ref are filtered out. If the param schema
+     * can't be obtained, auto-derivation falls back to a structural scan of
+     * parameter values for `{ ref, getValue }` shaped objects.
+     */
+    export function getEffectiveDependsOn(t: Transform): Ref[] {
+        const out: string[] = [];
+
+        if (t.dependsOn) {
+            for (const r of t.dependsOn) {
+                arraySetAdd(out, r);
+            }
+        }
+
+        const def = t.transformer.definition;
+        const params = t.params as any;
+
+        if (def.getDependencies && params) {
+            try {
+                const extra = def.getDependencies(params);
+                if (extra) {
+                    for (const r of extra) {
+                        arraySetAdd(out, r);
+                    }
+                }
+            } catch {
+                // Keep reconciliation robust if a user hook misbehaves.
+            }
+        }
+
+        if (params) {
+            const schema = tryGetDefaultParamDefinition(t);
+            if (schema) {
+                PD.collectRefs(schema, params, out);
+            } else {
+                collectStructuralRefs(params, out);
+            }
+        }
+
+        // Filter out self-references and the root ref.
+        arraySetRemove(out, t.ref);
+        arraySetRemove(out, RootRef);
+        return out;
+    }
+
+    function collectStructuralRefs(value: any, out: string[], depth = 0): string[] {
+        if (!value || typeof value !== 'object' || depth > 6) return out;
+        if (Array.isArray(value)) {
+            for (const v of value) {
+                collectStructuralRefs(v, out, depth + 1);
+            }
+            return out;
+        }
+        const ref = (value as any).ref;
+        if (typeof ref === 'string' && typeof (value as any).getValue === 'function') {
+            arraySetAdd(out, ref);
+            return out;
+        }
+        for (const k of Object.keys(value)) {
+            collectStructuralRefs(value[k], out, depth + 1);
+        }
+        return out;
+    }
+
     const _emptyParams = {};
     /** Updates the version of the transform to be computed as hash of the parameters */
     export function setParamsHashVersion(t: Transform) {

src/mol-state/transformer.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { Task } from '../mol-task';
@@ -118,6 +119,16 @@ namespace Transformer {
 
         /** Custom conversion to and from JSON */
         readonly customSerialization?: { toJSON(params: P, obj?: B): any, fromJSON(data: any): P }
+
+        /**
+         * Derive sibling-like state-tree dependencies (other cells' refs) from the
+         * current parameter values. Returned refs are merged with explicit
+         * `dependsOn` and any refs auto-collected from `PD.ValueRef` / `PD.DataRef`
+         * parameters to form the effective dependency set used by reconciliation.
+         *
+         * Return an empty array or undefined to opt out.
+         */
+        getDependencies?(params: P): StateTransform.Ref[] | undefined
     }
 
     export interface Definition<A extends StateObject = StateObject, B extends StateObject = StateObject, P extends {} = {}> extends DefinitionBase<A, B, P> {

src/mol-util/param-definition.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -18,6 +18,7 @@ import { getColorListFromName, ColorListName } from './color/lists';
 import { Asset } from './assets';
 import { ColorListEntry } from './color/color';
 import { EPSILON } from '../mol-math/linear-algebra/3d/common';
+import { arraySetAdd } from './array';
 
 export namespace ParamDefinition {
     export interface Info {
@@ -445,6 +446,47 @@ export namespace ParamDefinition {
         }
     }
 
+    function collectRefValue(p: Any, value: any, out: string[]): string[] {
+        if (value === undefined || value === null) return out;
+
+        if (p.type === 'value-ref' || p.type === 'data-ref') {
+            const v = value as ValueRef['defaultValue'];
+            if (v && typeof v.ref === 'string' && v.ref) {
+                arraySetAdd(out, v.ref);
+            }
+        } else if (p.type === 'group') {
+            collectRefsImpl(p.params, value, out);
+        } else if (p.type === 'mapped') {
+            const v = value as NamedParams;
+            if (!v) return out;
+            const param = p.map(v.name);
+            collectRefValue(param, v.params, out);
+        } else if (p.type === 'object-list') {
+            if (!hasValueRef(p.element)) return out;
+            for (const e of value) {
+                collectRefsImpl(p.element, e, out);
+            }
+        }
+        return out;
+    }
+
+    function collectRefsImpl(params: Params, values: any, out: string[]): string[] {
+        for (const n of Object.keys(params)) {
+            collectRefValue(params[n], values?.[n], out);
+        }
+        return out;
+    }
+
+    /**
+     * Collect all non-empty `ref` strings of `value-ref` and `data-ref` parameter
+     * values into a set. Used by `mol-state` to derive transform dependencies from
+     * parameter values.
+     */
+    export function collectRefs(params: Params, values: any, out: string[]): string[] {
+        if (!params || !values) return out;
+        return collectRefsImpl(params, values, out);
+    }
+
     export function setDefaultValues<T extends Params>(params: T, defaultValues: Values<T>) {
         for (const k of Object.keys(params)) {
             if (params[k].isOptional) continue;