diff --git a/CHANGELOG.md b/CHANGELOG.md
index 19205ba57d45d00b90e66f694bd1c4dee5f7e68e..dd6600dfda724293d007181cfd210cd9244d8e06 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,9 @@ Note that since we don't clearly distinguish between a public and private interf
## [Unreleased]
+- [Breaking] Rename the ``model-index`` color theme to ``trajectory-index``
+- Add a new ``model-index`` color theme that uniquely colors each loaded model
+- Add the new ``model-index`` color theme as an option for the carbon color in the ``element-symbol`` and ``ilustrative`` color themes
- Add nearest method to lookup3d
- Add mipmap-based blur for skybox backgrounds
diff --git a/src/mol-model-props/common/custom-model-property.ts b/src/mol-model-props/common/custom-model-property.ts
index 5d9b001ae9e6a15550e8177d057475656f0c6485..81004faf0939784f7e528319d2c3d17c4ac29889 100644
--- a/src/mol-model-props/common/custom-model-property.ts
+++ b/src/mol-model-props/common/custom-model-property.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -71,12 +71,12 @@ namespace CustomModelProperty {
},
ref: (data: Model, add: boolean) => data.customProperties.reference(builder.descriptor, add),
get: (data: Model) => get(data)?.data,
- set: (data: Model, props: Partial<PD.Values<Params>> = {}) => {
+ set: (data: Model, props: Partial<PD.Values<Params>> = {}, value?: Value) => {
const property = get(data);
const p = PD.merge(builder.defaultParams, property.props, props);
if (!PD.areEqual(builder.defaultParams, property.props, p)) {
// this invalidates property.value
- set(data, p, undefined);
+ set(data, p, value);
// dispose of assets
data.customProperties.assets(builder.descriptor);
}
@@ -96,7 +96,7 @@ namespace CustomModelProperty {
getParams: () => ({ value: PD.Value(defaultValue, { isHidden: true }) }),
isApplicable: () => true,
obtain: async (ctx: CustomProperty.Context, data: Model, props: Partial<PD.Values<typeof defaultParams>>) => {
- return { value: props.value ?? defaultValue };
+ return { ...PD.getDefaultValues(defaultParams), ...props };
}
});
}
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index 0301ef681b83f36adeb52f6d247c8ede6f6a27ba..76e9c4077a8134dda1e41cac9ee2facd5f601eb5 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -213,6 +213,9 @@ export namespace Model {
export type Index = number;
export const Index = CustomModelProperty.createSimple<Index>('index', 'static');
+ export type MaxIndex = number;
+ export const MaxIndex = CustomModelProperty.createSimple<MaxIndex>('max_index', 'static');
+
export function getRoot(model: Model) {
return model.parent || model;
}
diff --git a/src/mol-plugin-state/builder/structure/hierarchy-preset.ts b/src/mol-plugin-state/builder/structure/hierarchy-preset.ts
index b4b531e1585bb4057ae7a544c4949893f8beee8c..320df11dfe925d31383e342a7b6b1215001d508c 100644
--- a/src/mol-plugin-state/builder/structure/hierarchy-preset.ts
+++ b/src/mol-plugin-state/builder/structure/hierarchy-preset.ts
@@ -86,7 +86,7 @@ const allModels = TrajectoryHierarchyPresetProvider({
id: 'preset-trajectory-all-models',
display: {
name: 'All Models', group: 'Preset',
- description: 'Shows all models; colored by model-index.'
+ description: 'Shows all models; colored by trajectory-index.'
},
isApplicable: o => {
return o.data.frameCount > 1;
@@ -115,7 +115,7 @@ const allModels = TrajectoryHierarchyPresetProvider({
const quality = structure.obj ? getStructureQuality(structure.obj.data, { elementCountFactor: tr.frameCount }) : 'medium';
const representationPreset = params.representationPreset || plugin.config.get(PluginConfig.Structure.DefaultRepresentationPreset) || PresetStructureRepresentations.auto.id;
- await builder.representation.applyPreset(structureProperties, representationPreset, { theme: { globalName: 'model-index' }, quality });
+ await builder.representation.applyPreset(structureProperties, representationPreset, { theme: { globalName: 'trajectory-index' }, quality });
}
return { models, structures };
diff --git a/src/mol-plugin/behavior/dynamic/custom-props/structure-info.ts b/src/mol-plugin/behavior/dynamic/custom-props/structure-info.ts
index 469fca3463ec3e26164cb77ffec055deb2c0510e..f144a40cf4b83e608ba4e9c15ae18f5a4731e547 100644
--- a/src/mol-plugin/behavior/dynamic/custom-props/structure-info.ts
+++ b/src/mol-plugin/behavior/dynamic/custom-props/structure-info.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -52,17 +52,30 @@ export const StructureInfo = PluginBehavior.create({
return { auth, label };
}
+ private setModelMaxIndex() {
+ const value = this.maxModelIndex;
+ const cells = this.ctx.state.data.select(StateSelection.Generators.rootsOfType(PluginStateObject.Molecule.Model));
+ for (const c of cells) {
+ const m = c.obj?.data;
+ if (m) {
+ if (Model.MaxIndex.get(m).value !== value) {
+ Model.MaxIndex.set(m, { value }, value);
+ }
+ }
+ }
+ }
+
private handleModel(model: Model, oldModel?: Model) {
if (Model.Index.get(model).value === undefined) {
const oldIndex = oldModel && Model.Index.get(oldModel).value;
const value = oldIndex ?? (this.maxModelIndex + 1);
- Model.Index.set(model, { value });
+ Model.Index.set(model, { value }, value);
}
if (Model.AsymIdOffset.get(model).value === undefined) {
const oldOffset = oldModel && Model.AsymIdOffset.get(oldModel).value;
const value = oldOffset ?? { ...this.asymIdOffset };
- Model.AsymIdOffset.set(model, { value });
+ Model.AsymIdOffset.set(model, { value }, value);
}
}
@@ -72,7 +85,7 @@ export const StructureInfo = PluginBehavior.create({
const oldIndex = oldStructure && Structure.Index.get(oldStructure).value;
const value = oldIndex ?? (this.maxStructureIndex + 1);
- Structure.Index.set(structure, { value });
+ Structure.Index.set(structure, { value }, value);
}
private handle(ref: string, obj: StateObject<any, StateObject.Type<any>>, oldObj?: StateObject<any, StateObject.Type<any>>) {
@@ -92,10 +105,12 @@ export const StructureInfo = PluginBehavior.create({
register(): void {
this.ctx.customModelProperties.register(Model.AsymIdOffset, true);
this.ctx.customModelProperties.register(Model.Index, true);
+ this.ctx.customModelProperties.register(Model.MaxIndex, true);
this.ctx.customStructureProperties.register(Structure.Index, true);
this.subscribeObservable(this.ctx.state.data.events.object.created, o => {
this.handle(o.ref, o.obj);
+ this.setModelMaxIndex();
});
this.subscribeObservable(this.ctx.state.data.events.object.updated, o => {
@@ -106,6 +121,7 @@ export const StructureInfo = PluginBehavior.create({
unregister() {
this.ctx.customModelProperties.unregister(Model.AsymIdOffset.descriptor.name);
this.ctx.customModelProperties.unregister(Model.Index.descriptor.name);
+ this.ctx.customModelProperties.unregister(Model.MaxIndex.descriptor.name);
this.ctx.customStructureProperties.unregister(Structure.Index.descriptor.name);
}
}
diff --git a/src/mol-theme/color.ts b/src/mol-theme/color.ts
index 928137db106fe1c31ef1b577715e149a9e1c5857..2415d421bb860482d00cf6353efcd78e19a3c6bb 100644
--- a/src/mol-theme/color.ts
+++ b/src/mol-theme/color.ts
@@ -28,7 +28,7 @@ import { UncertaintyColorThemeProvider } from './color/uncertainty';
import { EntitySourceColorThemeProvider } from './color/entity-source';
import { IllustrativeColorThemeProvider } from './color/illustrative';
import { HydrophobicityColorThemeProvider } from './color/hydrophobicity';
-import { ModelIndexColorThemeProvider } from './color/model-index';
+import { TrajectoryIndexColorThemeProvider } from './color/trajectory-index';
import { OccupancyColorThemeProvider } from './color/occupancy';
import { OperatorNameColorThemeProvider } from './color/operator-name';
import { OperatorHklColorThemeProvider } from './color/operator-hkl';
@@ -38,6 +38,7 @@ import { EntityIdColorThemeProvider } from './color/entity-id';
import { Texture, TextureFilter } from '../mol-gl/webgl/texture';
import { VolumeValueColorThemeProvider } from './color/volume-value';
import { Vec3, Vec4 } from '../mol-math/linear-algebra';
+import { ModelIndexColorThemeProvider } from './color/model-index';
export type LocationColor = (location: Location, isSecondary: boolean) => Color
@@ -144,6 +145,7 @@ namespace ColorTheme {
'secondary-structure': SecondaryStructureColorThemeProvider,
'sequence-id': SequenceIdColorThemeProvider,
'shape-group': ShapeGroupColorThemeProvider,
+ 'trajectory-index': TrajectoryIndexColorThemeProvider,
'uncertainty': UncertaintyColorThemeProvider,
'unit-index': UnitIndexColorThemeProvider,
'uniform': UniformColorThemeProvider,
diff --git a/src/mol-theme/color/element-symbol.ts b/src/mol-theme/color/element-symbol.ts
index bb75aa34d3b42175020cb7dd2eb7a867ef1dc0a3..db1589b3559fed8c1d91584fd784075ad0de9580 100644
--- a/src/mol-theme/color/element-symbol.ts
+++ b/src/mol-theme/color/element-symbol.ts
@@ -19,6 +19,7 @@ import { OperatorNameColorThemeParams, OperatorNameColorTheme } from './operator
import { EntityIdColorTheme, EntityIdColorThemeParams } from './entity-id';
import { assertUnreachable } from '../../mol-util/type-helpers';
import { EntitySourceColorTheme, EntitySourceColorThemeParams } from './entity-source';
+import { ModelIndexColorTheme, ModelIndexColorThemeParams } from './model-index';
// from Jmol http://jmol.sourceforge.net/jscolors/ (or 0xFFFFFF)
export const ElementSymbolColors = ColorMap({
@@ -35,6 +36,7 @@ export const ElementSymbolColorThemeParams = {
'entity-id': PD.Group(EntityIdColorThemeParams),
'entity-source': PD.Group(EntitySourceColorThemeParams),
'operator-name': PD.Group(OperatorNameColorThemeParams),
+ 'model-index': PD.Group(ModelIndexColorThemeParams),
'element-symbol': PD.EmptyGroup()
}, { description: 'Use chain-id coloring for carbon atoms.' }),
saturation: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
@@ -46,7 +48,7 @@ export const ElementSymbolColorThemeParams = {
};
export type ElementSymbolColorThemeParams = typeof ElementSymbolColorThemeParams
export function getElementSymbolColorThemeParams(ctx: ThemeDataContext) {
- return ElementSymbolColorThemeParams; // TODO return copy
+ return PD.clone(ElementSymbolColorThemeParams);
}
export function elementSymbolColor(colorMap: ElementSymbolColors, element: ElementSymbol): Color {
@@ -63,8 +65,9 @@ export function ElementSymbolColorTheme(ctx: ThemeDataContext, props: PD.Values<
pcc.name === 'entity-id' ? EntityIdColorTheme(ctx, pcc.params).color :
pcc.name === 'entity-source' ? EntitySourceColorTheme(ctx, pcc.params).color :
pcc.name === 'operator-name' ? OperatorNameColorTheme(ctx, pcc.params).color :
- pcc.name === 'element-symbol' ? undefined :
- assertUnreachable(pcc);
+ pcc.name === 'model-index' ? ModelIndexColorTheme(ctx, pcc.params).color :
+ pcc.name === 'element-symbol' ? undefined :
+ assertUnreachable(pcc);
function elementColor(element: ElementSymbol, location: Location) {
return (carbonColor && element === 'C')
diff --git a/src/mol-theme/color/illustrative.ts b/src/mol-theme/color/illustrative.ts
index 7483f5d4b92d3426a59d879f8f0ccae142bb6360..89f21e2b5ace8749855ea68f37714bbbf809c3f7 100644
--- a/src/mol-theme/color/illustrative.ts
+++ b/src/mol-theme/color/illustrative.ts
@@ -17,9 +17,10 @@ import { assertUnreachable } from '../../mol-util/type-helpers';
import { EntityIdColorTheme, EntityIdColorThemeParams } from './entity-id';
import { MoleculeTypeColorTheme, MoleculeTypeColorThemeParams } from './molecule-type';
import { EntitySourceColorTheme, EntitySourceColorThemeParams } from './entity-source';
+import { ModelIndexColorTheme, ModelIndexColorThemeParams } from './model-index';
const DefaultIllustrativeColor = Color(0xEEEEEE);
-const Description = `Assigns an illustrative color that gives every chain a color based on the choosen style but with lighter carbons (inspired by David Goodsell's Molecule of the Month style).`;
+const Description = `Assigns an illustrative color that gives every chain a color based on the chosen style but with lighter carbons (inspired by David Goodsell's Molecule of the Month style).`;
export const IllustrativeColorThemeParams = {
style: PD.MappedStatic('entity-id', {
@@ -28,6 +29,7 @@ export const IllustrativeColorThemeParams = {
'entity-id': PD.Group(EntityIdColorThemeParams),
'entity-source': PD.Group(EntitySourceColorThemeParams),
'molecule-type': PD.Group(MoleculeTypeColorThemeParams),
+ 'model-index': PD.Group(ModelIndexColorThemeParams),
}),
carbonLightness: PD.Numeric(0.8, { min: -6, max: 6, step: 0.1 })
};
@@ -44,7 +46,8 @@ export function IllustrativeColorTheme(ctx: ThemeDataContext, props: PD.Values<I
props.style.name === 'entity-id' ? EntityIdColorTheme(ctx, props.style.params) :
props.style.name === 'entity-source' ? EntitySourceColorTheme(ctx, props.style.params) :
props.style.name === 'molecule-type' ? MoleculeTypeColorTheme(ctx, props.style.params) :
- assertUnreachable(props.style);
+ props.style.name === 'model-index' ? ModelIndexColorTheme(ctx, props.style.params) :
+ assertUnreachable(props.style);
function illustrativeColor(location: Location, typeSymbol: ElementSymbol) {
const baseColor = styleColor(location, false);
diff --git a/src/mol-theme/color/model-index.ts b/src/mol-theme/color/model-index.ts
index 51e2b4ea98ab4920a109dfad83e5f685394390dd..cbdfd683f10abebf07ceee1ba180b57331440ce0 100644
--- a/src/mol-theme/color/model-index.ts
+++ b/src/mol-theme/color/model-index.ts
@@ -1,6 +1,7 @@
/**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
+ * @author Jason Pattle <jpattle@exscientia.co.uk>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -14,14 +15,14 @@ import { getPaletteParams, getPalette } from '../../mol-util/color/palette';
import { TableLegend, ScaleLegend } from '../../mol-util/legend';
const DefaultColor = Color(0xCCCCCC);
-const Description = 'Gives every model a unique color based on the position (index) of the model in the list of models in the structure.';
+const Description = 'Gives every model a unique color based on its index.';
export const ModelIndexColorThemeParams = {
- ...getPaletteParams({ type: 'colors', colorList: 'purples' }),
+ ...getPaletteParams({ type: 'colors', colorList: 'many-distinct' }),
};
export type ModelIndexColorThemeParams = typeof ModelIndexColorThemeParams
export function getModelIndexColorThemeParams(ctx: ThemeDataContext) {
- return ModelIndexColorThemeParams; // TODO return copy
+ return PD.clone(ModelIndexColorThemeParams);
}
export function ModelIndexColorTheme(ctx: ThemeDataContext, props: PD.Values<ModelIndexColorThemeParams>): ColorTheme<ModelIndexColorThemeParams> {
@@ -29,24 +30,17 @@ export function ModelIndexColorTheme(ctx: ThemeDataContext, props: PD.Values<Mod
let legend: ScaleLegend | TableLegend | undefined;
if (ctx.structure) {
- const { models } = ctx.structure.root;
-
- let size = 0;
- for (const m of models) size = Math.max(size, Model.TrajectoryInfo.get(m)?.size || 0);
+ // max-index is the same for all models
+ const size = (Model.MaxIndex.get(ctx.structure.models[0]).value ?? -1) + 1;
const palette = getPalette(size, props);
legend = palette.legend;
- const modelColor = new Map<number, Color>();
- for (let i = 0, il = models.length; i < il; ++i) {
- const idx = Model.TrajectoryInfo.get(models[i])?.index || 0;
- modelColor.set(idx, palette.color(idx));
- }
color = (location: Location): Color => {
if (StructureElement.Location.is(location)) {
- return modelColor.get(Model.TrajectoryInfo.get(location.unit.model).index)!;
+ return palette.color(Model.Index.get(location.unit.model).value || 0)!;
} else if (Bond.isLocation(location)) {
- return modelColor.get(Model.TrajectoryInfo.get(location.aUnit.model).index)!;
+ return palette.color(Model.Index.get(location.aUnit.model).value || 0)!;
}
return DefaultColor;
};
@@ -71,5 +65,5 @@ export const ModelIndexColorThemeProvider: ColorTheme.Provider<ModelIndexColorTh
factory: ModelIndexColorTheme,
getParams: getModelIndexColorThemeParams,
defaultValues: PD.getDefaultValues(ModelIndexColorThemeParams),
- isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ctx.structure.elementCount > 0 && Model.TrajectoryInfo.get(ctx.structure.models[0]).size > 1
+ isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ctx.structure.elementCount > 0
};
\ No newline at end of file
diff --git a/src/mol-theme/color/trajectory-index.ts b/src/mol-theme/color/trajectory-index.ts
new file mode 100644
index 0000000000000000000000000000000000000000..87b1b995518805448bdffc7baab9d46447c3ef26
--- /dev/null
+++ b/src/mol-theme/color/trajectory-index.ts
@@ -0,0 +1,75 @@
+/**
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Color } from '../../mol-util/color';
+import { Location } from '../../mol-model/location';
+import { StructureElement, Bond, Model } from '../../mol-model/structure';
+import { ColorTheme, LocationColor } from '../color';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { ThemeDataContext } from '../theme';
+import { getPaletteParams, getPalette } from '../../mol-util/color/palette';
+import { TableLegend, ScaleLegend } from '../../mol-util/legend';
+
+const DefaultColor = Color(0xCCCCCC);
+const Description = 'Gives every model (frame) a unique color based on the index in its trajectory.';
+
+export const TrajectoryIndexColorThemeParams = {
+ ...getPaletteParams({ type: 'colors', colorList: 'purples' }),
+};
+export type TrajectoryIndexColorThemeParams = typeof TrajectoryIndexColorThemeParams
+export function getTrajectoryIndexColorThemeParams(ctx: ThemeDataContext) {
+ return PD.clone(TrajectoryIndexColorThemeParams);
+}
+
+export function TrajectoryIndexColorTheme(ctx: ThemeDataContext, props: PD.Values<TrajectoryIndexColorThemeParams>): ColorTheme<TrajectoryIndexColorThemeParams> {
+ let color: LocationColor;
+ let legend: ScaleLegend | TableLegend | undefined;
+
+ if (ctx.structure) {
+ const { models } = ctx.structure.root;
+
+ let size = 0;
+ for (const m of models) size = Math.max(size, Model.TrajectoryInfo.get(m)?.size || 0);
+
+ const palette = getPalette(size, props);
+ legend = palette.legend;
+ const modelColor = new Map<number, Color>();
+ for (let i = 0, il = models.length; i < il; ++i) {
+ const idx = Model.TrajectoryInfo.get(models[i])?.index || 0;
+ modelColor.set(idx, palette.color(idx));
+ }
+
+ color = (location: Location): Color => {
+ if (StructureElement.Location.is(location)) {
+ return modelColor.get(Model.TrajectoryInfo.get(location.unit.model).index)!;
+ } else if (Bond.isLocation(location)) {
+ return modelColor.get(Model.TrajectoryInfo.get(location.aUnit.model).index)!;
+ }
+ return DefaultColor;
+ };
+ } else {
+ color = () => DefaultColor;
+ }
+
+ return {
+ factory: TrajectoryIndexColorTheme,
+ granularity: 'instance',
+ color,
+ props,
+ description: Description,
+ legend
+ };
+}
+
+export const TrajectoryIndexColorThemeProvider: ColorTheme.Provider<TrajectoryIndexColorThemeParams, 'trajectory-index'> = {
+ name: 'trajectory-index',
+ label: 'Trajectory Index',
+ category: ColorTheme.Category.Chain,
+ factory: TrajectoryIndexColorTheme,
+ getParams: getTrajectoryIndexColorThemeParams,
+ defaultValues: PD.getDefaultValues(TrajectoryIndexColorThemeParams),
+ isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ctx.structure.elementCount > 0 && Model.TrajectoryInfo.get(ctx.structure.models[0]).size > 1
+};
\ No newline at end of file
diff --git a/src/mol-util/color/distinct.ts b/src/mol-util/color/distinct.ts
index c12a8c9e26b873171ba1c36b0e2c71c4eee62abd..e2e3c1507513798dab052a6e9d23a56828973d60 100644
--- a/src/mol-util/color/distinct.ts
+++ b/src/mol-util/color/distinct.ts
@@ -13,6 +13,7 @@ import { deepClone } from '../../mol-util/object';
import { deepEqual } from '../../mol-util';
import { arraySum } from '../../mol-util/array';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { ColorNames } from './names';
export const DistinctColorsParams = {
hue: PD.Interval([1, 360], { min: 0, max: 360, step: 1 }),
@@ -105,7 +106,8 @@ export function distinctColors(count: number, props: Partial<DistinctColorsProps
const samples = getSamples(Math.max(p.minSampleCount, count * 5), p);
if (samples.length < count) {
- throw new Error('Not enough samples to generate distinct colors, increase sample count.');
+ console.warn('Not enough samples to generate distinct colors, increase sample count.');
+ return (new Array(count)).fill(ColorNames.lightgrey);
}
const colors: Lab[] = [];