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@@ -1,10 +1,10 @@
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/**
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- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
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+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
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*
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* @author Alexander Rose <alexander.rose@weirdbyte.de>
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*/
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-import { Unit, StructureProperties, StructureElement, Bond, Structure } from '../../mol-model/structure';
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+import { Unit, StructureProperties, StructureElement, Bond, Structure, Model } from '../../mol-model/structure';
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import { Color } from '../../mol-util/color';
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import { Location } from '../../mol-model/location';
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import { ColorTheme, LocationColor } from '../color';
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@@ -12,66 +12,58 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
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import { ThemeDataContext } from '../../mol-theme/theme';
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import { getPaletteParams, getPalette } from '../../mol-util/color/palette';
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import { TableLegend, ScaleLegend } from '../../mol-util/legend';
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-import { Segmentation } from '../../mol-data/int';
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-import { ColorLists, getColorListFromName } from '../../mol-util/color/lists';
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-const DefaultList = 'dark-2';
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+const DefaultList = 'many-distinct';
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const DefaultColor = Color(0xFAFAFA);
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const Description = 'Gives every chain a color based on its `asym_id` value.';
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export const ChainIdColorThemeParams = {
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+ asymId: PD.Select('auth', PD.arrayToOptions<AsymIdType>(['auth', 'label'])),
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...getPaletteParams({ type: 'colors', colorList: DefaultList }),
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};
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export type ChainIdColorThemeParams = typeof ChainIdColorThemeParams
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export function getChainIdColorThemeParams(ctx: ThemeDataContext) {
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const params = PD.clone(ChainIdColorThemeParams);
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- if (ctx.structure) {
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- if (getAsymIdSerialMap(ctx.structure.root).size > ColorLists[DefaultList].list.length) {
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- params.palette.defaultValue.name = 'colors';
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- params.palette.defaultValue.params = {
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- ...params.palette.defaultValue.params,
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- list: { kind: 'interpolate', colors: getColorListFromName(DefaultList).list }
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- };
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- }
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- }
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return params;
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}
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-function getAsymId(unit: Unit): StructureElement.Property<string> {
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+type AsymIdType = 'auth' | 'label';
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+
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+function getAsymId(unit: Unit, type: AsymIdType): StructureElement.Property<string> {
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switch (unit.kind) {
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case Unit.Kind.Atomic:
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- return StructureProperties.chain.label_asym_id;
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+ return type === 'auth'
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+ ? StructureProperties.chain.auth_asym_id
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+ : StructureProperties.chain.label_asym_id;
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case Unit.Kind.Spheres:
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case Unit.Kind.Gaussians:
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return StructureProperties.coarse.asym_id;
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}
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}
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-function getAsymIdSerialMap(structure: Structure) {
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+function getAsymIdKey(location: StructureElement.Location, type: AsymIdType) {
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+ const asymId = getAsymId(location.unit, type)(location);
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+ return location.structure.models.length > 1
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+ ? getKey(location.unit.model, asymId)
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+ : asymId;
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+}
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+
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+function getKey(model: Model, asymId: string) {
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+ return `${asymId} | ${(Model.Index.get(model).value || 0) + 1}`;
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+}
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+
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+function getAsymIdSerialMap(structure: Structure, type: AsymIdType) {
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const map = new Map<string, number>();
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- for (let i = 0, il = structure.unitSymmetryGroups.length; i < il; ++i) {
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- const unit = structure.unitSymmetryGroups[i].units[0];
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- const { model } = unit;
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- if (Unit.isAtomic(unit)) {
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- const { chainAtomSegments, chains } = model.atomicHierarchy;
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- const chainIt = Segmentation.transientSegments(chainAtomSegments, unit.elements);
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- while (chainIt.hasNext) {
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- const { index: chainIndex } = chainIt.move();
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- const asymId = chains.label_asym_id.value(chainIndex);
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- if (!map.has(asymId)) map.set(asymId, map.size);
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- }
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- } else if (Unit.isCoarse(unit)) {
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- const { chainElementSegments, asym_id } = Unit.isSpheres(unit)
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- ? model.coarseHierarchy.spheres
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- : model.coarseHierarchy.gaussians;
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- const chainIt = Segmentation.transientSegments(chainElementSegments, unit.elements);
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- while (chainIt.hasNext) {
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- const { index: chainIndex } = chainIt.move();
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- const elementIndex = chainElementSegments.offsets[chainIndex];
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- const asymId = asym_id.value(elementIndex);
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- if (!map.has(asymId)) map.set(asymId, map.size);
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- }
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- }
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+ for (const m of structure.models) {
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+ const asymIdOffset = Model.AsymIdOffset.get(m).value;
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+ const offset = (type === 'auth' ? asymIdOffset?.auth : asymIdOffset?.label) || 0;
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+ m.properties.structAsymMap.forEach(({ auth_id }, label_id) => {
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+ const asymId = type === 'auth' ? auth_id : label_id;
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+ const k = structure.models.length > 1
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+ ? getKey(m, asymId)
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+ : asymId;
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+ if (!map.has(k)) map.set(k, map.size + offset);
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+ });
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}
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return map;
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}
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@@ -82,7 +74,7 @@ export function ChainIdColorTheme(ctx: ThemeDataContext, props: PD.Values<ChainI
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if (ctx.structure) {
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const l = StructureElement.Location.create(ctx.structure);
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- const asymIdSerialMap = getAsymIdSerialMap(ctx.structure.root);
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+ const asymIdSerialMap = getAsymIdSerialMap(ctx.structure.root, props.asymId);
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const labelTable = Array.from(asymIdSerialMap.keys());
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props.palette.params.valueLabel = (i: number) => labelTable[i];
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@@ -93,13 +85,13 @@ export function ChainIdColorTheme(ctx: ThemeDataContext, props: PD.Values<ChainI
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color = (location: Location): Color => {
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let serial: number | undefined = undefined;
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if (StructureElement.Location.is(location)) {
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- const asym_id = getAsymId(location.unit);
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- serial = asymIdSerialMap.get(asym_id(location));
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+ const k = getAsymIdKey(location, props.asymId);
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+ serial = asymIdSerialMap.get(k);
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} else if (Bond.isLocation(location)) {
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- const asym_id = getAsymId(location.aUnit);
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l.unit = location.aUnit;
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l.element = location.aUnit.elements[location.aIndex];
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- serial = asymIdSerialMap.get(asym_id(l));
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+ const k = getAsymIdKey(l, props.asymId);
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+ serial = asymIdSerialMap.get(k);
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}
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return serial === undefined ? DefaultColor : palette.color(serial);
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};
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Alexander Rose