diff --git a/src/mol-plugin/behavior/dynamic/representation.ts b/src/mol-plugin/behavior/dynamic/representation.ts
index 84d811e25e5120b2a54b70b68db7890c4dfd18b4..32afe8027de6dc5f73fc03987a0fe2fea4ddb53a 100644
--- a/src/mol-plugin/behavior/dynamic/representation.ts
+++ b/src/mol-plugin/behavior/dynamic/representation.ts
@@ -7,21 +7,11 @@
import { MarkerAction } from 'mol-geo/geometry/marker-data';
import { EmptyLoci } from 'mol-model/loci';
-import { QueryContext, StructureElement, StructureSelection } from 'mol-model/structure';
+import { StructureElement } from 'mol-model/structure';
import { PluginContext } from 'mol-plugin/context';
-import { PluginStateObject } from 'mol-plugin/state/objects';
import { Representation } from 'mol-repr/representation';
-import Expression from 'mol-script/language/expression';
-import { parseMolScript } from 'mol-script/language/parser';
-import { compile } from 'mol-script/runtime/query/compiler';
-import { transpileMolScript } from 'mol-script/script/mol-script/symbols';
-import { StateObjectTracker, StateSelection } from 'mol-state';
import { labelFirst } from 'mol-theme/label';
-import { Overpaint } from 'mol-theme/overpaint';
-import { Color } from 'mol-util/color';
-import { ColorNames } from 'mol-util/color/tables';
import { ButtonsType } from 'mol-util/input/input-observer';
-import { ParamDefinition as PD } from 'mol-util/param-definition';
import { PluginBehavior } from '../behavior';
export const HighlightLoci = PluginBehavior.create({
@@ -124,105 +114,3 @@ export const DefaultLociLabelProvider = PluginBehavior.create({
},
display: { name: 'Provide Default Loci Label' }
});
-
-type ColorMappings = { query: Expression, color: Color }[]
-namespace ColorMappings {
- export function areEqual(colorMappingsA: ColorMappings, colorMappingsB: ColorMappings) {
- return false
- }
-}
-
-export namespace ColorRepresentation3D {
- export const Params = {
- layers: PD.ObjectList({
- query: PD.ScriptExpression({ language: 'mol-script', expression: '(sel.atom.atom-groups :residue-test (= atom.resname LYS))' }),
- color: PD.Color(ColorNames.blueviolet)
- }, e => `${Color.toRgbString(e.color)}`, {
- defaultValue: [
- {
- query: {
- language: 'mol-script',
- expression: '(sel.atom.atom-groups :residue-test (= atom.resname LYS))'
- },
- color: ColorNames.blueviolet
- },
- {
- query: {
- language: 'mol-script',
- expression: '(sel.atom.atom-groups :residue-test (= atom.resname ALA))'
- },
- color: ColorNames.chartreuse
- }
- ]
- }),
- alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }, { label: 'Opacity' }),
- }
- export type Params = PD.Values<typeof Params>
-
- export class Behavior implements PluginBehavior<Params> {
- private currentColorMappings: ColorMappings = [];
- private repr: StateObjectTracker<PluginStateObject.Molecule.Structure.Representation3D>;
- private structure: StateObjectTracker<PluginStateObject.Molecule.Structure>;
-
- private updateData() {
- const reprUpdated = this.repr.update();
- const strucUpdated = this.structure.update();
- return reprUpdated || strucUpdated;
- }
-
- register(ref: string): void {
- this.repr.setQuery(StateSelection.Generators.byRef(ref).ancestorOfType([PluginStateObject.Molecule.Structure.Representation3D]));
- this.structure.setQuery(StateSelection.Generators.byRef(ref).ancestorOfType([PluginStateObject.Molecule.Structure]));
- this.update(this.params);
- }
-
- update(params: Params): boolean {
- const { layers, alpha } = params
- const colorMappings: ColorMappings = []
- for (let i = 0, il = params.layers.length; i < il; ++i) {
- const { query, color } = layers[i]
- const parsed = parseMolScript(query.expression);
- if (parsed.length === 0) throw new Error('No query');
- colorMappings.push({ query: transpileMolScript(parsed[0]), color })
- }
- return this.applyMappings(colorMappings, alpha)
- }
-
- private applyMappings(colorMappings: ColorMappings, alpha: number): boolean {
- if (!this.updateData() && ColorMappings.areEqual(colorMappings, this.currentColorMappings)) return false;
- this.currentColorMappings = colorMappings;
- if (!this.repr.data || !this.structure.data) return true;
-
- const layers: Overpaint.Layer[] = []
- for (let i = 0, il = this.currentColorMappings.length; i < il; ++i) {
- const { query, color } = this.currentColorMappings[i]
- const compiled = compile<StructureSelection>(query);
- const result = compiled(new QueryContext(this.structure.data));
- const loci = StructureSelection.toLoci2(result)
- layers.push({ loci, color })
- }
- return this.applyLayers({ alpha, layers })
- }
-
- private applyLayers(overpaint: Overpaint): boolean {
- if (!this.repr.data) return true;
- this.repr.data.repr.setState({ overpaint })
- this.ctx.canvas3d.add(this.repr.data.repr);
- this.ctx.canvas3d.requestDraw(true);
- return true;
- }
-
- unregister(): void {
- this.applyLayers(Overpaint.Empty) // clear
- 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: 'Color Representation3D Behavior' }) { }
-}
\ No newline at end of file
diff --git a/src/mol-plugin/state/animation/helpers.ts b/src/mol-plugin/state/animation/helpers.ts
index cf83143f16707f7effb6819f17a81887d1f91181..df6bfb962bbc35bfe78088aed47fc39df1d854f2 100644
--- a/src/mol-plugin/state/animation/helpers.ts
+++ b/src/mol-plugin/state/animation/helpers.ts
@@ -7,8 +7,13 @@
import { SymmetryOperator } from 'mol-math/geometry';
import { Mat4, Vec3 } from 'mol-math/linear-algebra';
-import { Structure } from 'mol-model/structure';
+import { Structure, StructureSelection, QueryContext } from 'mol-model/structure';
import { StructureUnitTransforms } from 'mol-model/structure/structure/util/unit-transforms';
+import { Color } from 'mol-util/color';
+import { Overpaint } from 'mol-theme/overpaint';
+import { parseMolScript } from 'mol-script/language/parser';
+import { transpileMolScript } from 'mol-script/script/mol-script/symbols';
+import { compile } from 'mol-script/runtime/query/compiler';
const _unwindMatrix = Mat4.zero();
export function unwindStructureAssembly(structure: Structure, unitTransforms: StructureUnitTransforms, t: number) {
@@ -33,4 +38,22 @@ export function explodeStructure(structure: Structure, unitTransforms: Structure
unitTransforms.setTransform(_transMat, u);
}
+}
+
+type ScriptLayers = { script: { language: string, expression: string }, color: Color }[]
+export function getStructureOverpaint(structure: Structure, scriptLayers: ScriptLayers, alpha: number): Overpaint {
+ const layers: Overpaint.Layer[] = []
+ for (let i = 0, il = scriptLayers.length; i < il; ++i) {
+ const { script, color } = scriptLayers[i]
+ const parsed = parseMolScript(script.expression)
+ if (parsed.length === 0) throw new Error('No query')
+ const query = transpileMolScript(parsed[0])
+
+ const compiled = compile<StructureSelection>(query)
+ const result = compiled(new QueryContext(structure))
+ const loci = StructureSelection.toLoci2(result)
+
+ layers.push({ loci, color })
+ }
+ return { layers, alpha }
}
\ No newline at end of file
diff --git a/src/mol-plugin/state/transforms/representation.ts b/src/mol-plugin/state/transforms/representation.ts
index c1e9e8bef41b344141e87001ba50bf5bab96b6b0..e59d77c6af86eb15312df14eadbd1e7af3746b9f 100644
--- a/src/mol-plugin/state/transforms/representation.ts
+++ b/src/mol-plugin/state/transforms/representation.ts
@@ -7,7 +7,6 @@
import { Structure } from 'mol-model/structure';
import { VolumeData, VolumeIsoValue } from 'mol-model/volume';
-import { ColorRepresentation3D } 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';
@@ -26,14 +25,16 @@ import { ColorNames } from 'mol-util/color/tables';
import { getLabelRepresentation } from 'mol-plugin/util/structure-labels';
import { ShapeRepresentation } from 'mol-repr/shape/representation';
import { StructureUnitTransforms } from 'mol-model/structure/structure/util/unit-transforms';
-import { unwindStructureAssembly, explodeStructure } from '../animation/helpers';
+import { unwindStructureAssembly, explodeStructure, getStructureOverpaint } from '../animation/helpers';
+import { Color } from 'mol-util/color';
+import { Overpaint } from 'mol-theme/overpaint';
export { StructureRepresentation3D }
export { StructureRepresentation3DHelpers }
export { StructureLabels3D}
export { ExplodeStructureRepresentation3D }
export { UnwindStructureAssemblyRepresentation3D }
-export { ColorStructureRepresentation3D }
+export { OverpaintStructureRepresentation3D as ColorStructureRepresentation3D }
export { VolumeRepresentation3D }
namespace StructureRepresentation3DHelpers {
@@ -278,21 +279,20 @@ const ExplodeStructureRepresentation3D = PluginStateTransform.BuiltIn({
canAutoUpdate() {
return true;
},
- apply({ a, params, spine }) {
- const rootStructure = spine.getRootOfType(SO.Molecule.Structure)!.data;
- const unitTransforms = new StructureUnitTransforms(rootStructure);
- explodeStructure(rootStructure, unitTransforms, params.t);
+ apply({ a, params }) {
+ const structure = a.data.source.data;
+ const unitTransforms = new StructureUnitTransforms(structure);
+ explodeStructure(structure, unitTransforms, params.t);
return new SO.Molecule.Structure.Representation3DState({
state: { unitTransforms },
- initialState: { unitTransforms: new StructureUnitTransforms(rootStructure) },
- info: rootStructure,
+ initialState: { unitTransforms: new StructureUnitTransforms(structure) },
+ info: structure,
source: a
}, { label: `Explode T = ${params.t.toFixed(2)}` });
},
- update({ a, b, newParams, oldParams, spine }) {
- const rootStructure = spine.getRootOfType(SO.Molecule.Structure)!.data;
+ update({ a, b, newParams, oldParams }) {
const structure = b.data.info as Structure;
- if (rootStructure !== structure) return StateTransformer.UpdateResult.Recreate;
+ if (a.data.source.data !== structure) return StateTransformer.UpdateResult.Recreate;
if (oldParams.t === newParams.t) return StateTransformer.UpdateResult.Unchanged;
const unitTransforms = b.data.state.unitTransforms!;
explodeStructure(structure, unitTransforms, newParams.t);
@@ -302,26 +302,62 @@ const ExplodeStructureRepresentation3D = PluginStateTransform.BuiltIn({
}
});
-type ColorStructureRepresentation3D = typeof ColorStructureRepresentation3D
-const ColorStructureRepresentation3D = PluginStateTransform.BuiltIn({
- name: 'color-structure-representation-3d',
- display: 'Color 3D Representation',
+type OverpaintStructureRepresentation3D = typeof OverpaintStructureRepresentation3D
+const OverpaintStructureRepresentation3D = PluginStateTransform.BuiltIn({
+ name: 'overpaint-structure-representation-3d',
+ display: 'Overpaint 3D Representation',
from: SO.Molecule.Structure.Representation3D,
- to: ColorRepresentation3D.Obj,
- params: ColorRepresentation3D.Params
+ to: SO.Molecule.Structure.Representation3DState,
+ params: {
+ layers: PD.ObjectList({
+ script: PD.ScriptExpression({ language: 'mol-script', expression: '(sel.atom.atom-groups :residue-test (= atom.resname LYS))' }),
+ color: PD.Color(ColorNames.blueviolet)
+ }, e => `${Color.toRgbString(e.color)}`, {
+ defaultValue: [
+ {
+ script: {
+ language: 'mol-script',
+ expression: '(sel.atom.atom-groups :residue-test (= atom.resname LYS))'
+ },
+ color: ColorNames.blueviolet
+ },
+ {
+ script: {
+ language: 'mol-script',
+ expression: '(sel.atom.atom-groups :residue-test (= atom.resname ALA))'
+ },
+ color: ColorNames.chartreuse
+ }
+ ]
+ }),
+ alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }, { label: 'Opacity' }),
+ }
})({
canAutoUpdate() {
return true;
},
- apply({ params }, plugin: PluginContext) {
- return new ColorRepresentation3D.Obj(new ColorRepresentation3D.Behavior(plugin, params), { label: `Coloring` });
+ apply({ a, params }) {
+ const structure = a.data.source.data
+ const overpaint = getStructureOverpaint(structure, params.layers, params.alpha)
+
+ return new SO.Molecule.Structure.Representation3DState({
+ state: { overpaint },
+ initialState: { overpaint: Overpaint.Empty },
+ info: structure,
+ source: a
+ }, { label: `Overpaint (${overpaint.layers.length} Layers)` })
},
- update({ b, newParams }) {
- return Task.create('Update Coloring', async () => {
- const updated = await b.data.update(newParams);
- b.label = `Coloring`;
- return updated ? StateTransformer.UpdateResult.Updated : StateTransformer.UpdateResult.Unchanged;
- });
+ update({ a, b, newParams, oldParams }) {
+ const structure = b.data.info as Structure
+ if (a.data.source.data !== structure) return StateTransformer.UpdateResult.Recreate
+ const oldOverpaint = b.data.state.overpaint!
+ const newOverpaint = getStructureOverpaint(structure, newParams.layers, newParams.alpha)
+ if (oldParams.alpha === newParams.alpha && Overpaint.areEqual(oldOverpaint, newOverpaint)) return StateTransformer.UpdateResult.Unchanged
+
+ b.data.state.overpaint = newOverpaint
+ b.data.source = a
+ b.label = `Overpaint (${newOverpaint.layers.length} Layers)`
+ return StateTransformer.UpdateResult.Updated
}
});