molstar 3.0.0 → 3.0.1

package/lib/commonjs/mol-theme/color/shape-group.js

@@ -1,43 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.ShapeGroupColorThemeProvider = exports.ShapeGroupColorTheme = exports.getShapeGroupColorThemeParams = exports.ShapeGroupColorThemeParams = void 0;
-var color_1 = require("../../mol-util/color");
-var shape_1 = require("../../mol-model/shape");
-var param_definition_1 = require("../../mol-util/param-definition");
-var DefaultColor = (0, color_1.Color)(0xCCCCCC);
-var Description = 'Assigns colors as defined by the shape object.';
-exports.ShapeGroupColorThemeParams = {};
-function getShapeGroupColorThemeParams(ctx) {
-    return exports.ShapeGroupColorThemeParams; // TODO return copy
-}
-exports.getShapeGroupColorThemeParams = getShapeGroupColorThemeParams;
-function ShapeGroupColorTheme(ctx, props) {
-    return {
-        factory: ShapeGroupColorTheme,
-        granularity: 'groupInstance',
-        color: function (location) {
-            if (shape_1.ShapeGroup.isLocation(location)) {
-                return location.shape.getColor(location.group, location.instance);
-            }
-            return DefaultColor;
-        },
-        props: props,
-        description: Description
-    };
-}
-exports.ShapeGroupColorTheme = ShapeGroupColorTheme;
-exports.ShapeGroupColorThemeProvider = {
-    name: 'shape-group',
-    label: 'Shape Group',
-    category: "Miscellaneous" /* Misc */,
-    factory: ShapeGroupColorTheme,
-    getParams: getShapeGroupColorThemeParams,
-    defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.ShapeGroupColorThemeParams),
-    isApplicable: function (ctx) { return !!ctx.shape; }
-};
-//# sourceMappingURL=shape-group.js.map

package/lib/commonjs/mol-theme/color/uncertainty.js

@@ -1,70 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.UncertaintyColorThemeProvider = exports.UncertaintyColorTheme = exports.getUncertainty = exports.getUncertaintyColorThemeParams = exports.UncertaintyColorThemeParams = void 0;
-var color_1 = require("../../mol-util/color");
-var structure_1 = require("../../mol-model/structure");
-var param_definition_1 = require("../../mol-util/param-definition");
-var DefaultUncertaintyColor = (0, color_1.Color)(0xffff99);
-var Description = "Assigns a color based on the uncertainty or disorder of an element's position, e.g. B-factor or RMSF, depending on the data availability and experimental technique.";
-exports.UncertaintyColorThemeParams = {
-    domain: param_definition_1.ParamDefinition.Interval([0, 100]),
-    list: param_definition_1.ParamDefinition.ColorList('red-white-blue', { presetKind: 'scale' }),
-};
-function getUncertaintyColorThemeParams(ctx) {
-    return exports.UncertaintyColorThemeParams; // TODO return copy
-}
-exports.getUncertaintyColorThemeParams = getUncertaintyColorThemeParams;
-function getUncertainty(unit, element) {
-    if (structure_1.Unit.isAtomic(unit)) {
-        return unit.model.atomicConformation.B_iso_or_equiv.value(element);
-    }
-    else if (structure_1.Unit.isSpheres(unit)) {
-        return unit.model.coarseConformation.spheres.rmsf[element];
-    }
-    else {
-        return 0;
-    }
-}
-exports.getUncertainty = getUncertainty;
-function UncertaintyColorTheme(ctx, props) {
-    var scale = color_1.ColorScale.create({
-        reverse: true,
-        domain: props.domain,
-        listOrName: props.list.colors,
-    });
-    // TODO calc domain based on data, set min/max as 10/90 percentile to be robust against outliers
-    function color(location) {
-        if (structure_1.StructureElement.Location.is(location)) {
-            return scale.color(getUncertainty(location.unit, location.element));
-        }
-        else if (structure_1.Bond.isLocation(location)) {
-            return scale.color(getUncertainty(location.aUnit, location.aUnit.elements[location.aIndex]));
-        }
-        return DefaultUncertaintyColor;
-    }
-    return {
-        factory: UncertaintyColorTheme,
-        granularity: 'group',
-        preferSmoothing: true,
-        color: color,
-        props: props,
-        description: Description,
-        legend: scale ? scale.legend : undefined
-    };
-}
-exports.UncertaintyColorTheme = UncertaintyColorTheme;
-exports.UncertaintyColorThemeProvider = {
-    name: 'uncertainty',
-    label: 'Uncertainty/Disorder',
-    category: "Atom Property" /* Atom */,
-    factory: UncertaintyColorTheme,
-    getParams: getUncertaintyColorThemeParams,
-    defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.UncertaintyColorThemeParams),
-    isApplicable: function (ctx) { return !!ctx.structure && ctx.structure.models.some(function (m) { return m.atomicConformation.B_iso_or_equiv.isDefined || m.coarseHierarchy.isDefined; }); }
-};
-//# sourceMappingURL=uncertainty.js.map

package/lib/commonjs/mol-theme/color/uniform.js

@@ -1,43 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.UniformColorThemeProvider = exports.UniformColorTheme = exports.getUniformColorThemeParams = exports.UniformColorThemeParams = void 0;
-var color_1 = require("../../mol-util/color");
-var param_definition_1 = require("../../mol-util/param-definition");
-var legend_1 = require("../../mol-util/legend");
-var mol_util_1 = require("../../mol-util");
-var DefaultColor = (0, color_1.Color)(0xCCCCCC);
-var Description = 'Gives everything the same, uniform color.';
-exports.UniformColorThemeParams = {
-    value: param_definition_1.ParamDefinition.Color(DefaultColor),
-};
-function getUniformColorThemeParams(ctx) {
-    return exports.UniformColorThemeParams; // TODO return copy
-}
-exports.getUniformColorThemeParams = getUniformColorThemeParams;
-function UniformColorTheme(ctx, props) {
-    var color = (0, mol_util_1.defaults)(props.value, DefaultColor);
-    return {
-        factory: UniformColorTheme,
-        granularity: 'uniform',
-        color: function () { return color; },
-        props: props,
-        description: Description,
-        legend: (0, legend_1.TableLegend)([['uniform', color]])
-    };
-}
-exports.UniformColorTheme = UniformColorTheme;
-exports.UniformColorThemeProvider = {
-    name: 'uniform',
-    label: 'Uniform',
-    category: "Miscellaneous" /* Misc */,
-    factory: UniformColorTheme,
-    getParams: getUniformColorThemeParams,
-    defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.UniformColorThemeParams),
-    isApplicable: function (ctx) { return true; }
-};
-//# sourceMappingURL=uniform.js.map

package/lib/commonjs/mol-theme/color/unit-index.js

@@ -1,73 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.UnitIndexColorThemeProvider = exports.UnitIndexColorTheme = exports.getUnitIndexColorThemeParams = exports.UnitIndexColorThemeParams = void 0;
-var tslib_1 = require("tslib");
-var color_1 = require("../../mol-util/color");
-var structure_1 = require("../../mol-model/structure");
-var param_definition_1 = require("../../mol-util/param-definition");
-var palette_1 = require("../../mol-util/color/palette");
-var lists_1 = require("../../mol-util/color/lists");
-var DefaultList = 'dark-2';
-var DefaultColor = (0, color_1.Color)(0xCCCCCC);
-var Description = 'Gives every chain instance (single chain or collection of single elements) a unique color based on the position (index) of the chain in the list of chains in the structure.';
-exports.UnitIndexColorThemeParams = (0, tslib_1.__assign)({}, (0, palette_1.getPaletteParams)({ type: 'colors', colorList: DefaultList }));
-function getUnitIndexColorThemeParams(ctx) {
-    var params = param_definition_1.ParamDefinition.clone(exports.UnitIndexColorThemeParams);
-    if (ctx.structure) {
-        if (ctx.structure.root.units.length > lists_1.ColorLists[DefaultList].list.length) {
-            params.palette.defaultValue.name = 'colors';
-            params.palette.defaultValue.params = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params.palette.defaultValue.params), { list: { kind: 'interpolate', colors: (0, lists_1.getColorListFromName)(DefaultList).list } });
-        }
-    }
-    return params;
-}
-exports.getUnitIndexColorThemeParams = getUnitIndexColorThemeParams;
-function UnitIndexColorTheme(ctx, props) {
-    var color;
-    var legend;
-    if (ctx.structure) {
-        var units = ctx.structure.root.units;
-        var palette = (0, palette_1.getPalette)(units.length, props);
-        legend = palette.legend;
-        var unitIdColor_1 = new Map();
-        for (var i = 0, il = units.length; i < il; ++i) {
-            unitIdColor_1.set(units[i].id, palette.color(i));
-        }
-        color = function (location) {
-            if (structure_1.StructureElement.Location.is(location)) {
-                return unitIdColor_1.get(location.unit.id);
-            }
-            else if (structure_1.Bond.isLocation(location)) {
-                return unitIdColor_1.get(location.aUnit.id);
-            }
-            return DefaultColor;
-        };
-    }
-    else {
-        color = function () { return DefaultColor; };
-    }
-    return {
-        factory: UnitIndexColorTheme,
-        granularity: 'instance',
-        color: color,
-        props: props,
-        description: Description,
-        legend: legend
-    };
-}
-exports.UnitIndexColorTheme = UnitIndexColorTheme;
-exports.UnitIndexColorThemeProvider = {
-    name: 'unit-index',
-    label: 'Chain Instance',
-    category: "Chain Property" /* Chain */,
-    factory: UnitIndexColorTheme,
-    getParams: getUnitIndexColorThemeParams,
-    defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.UnitIndexColorThemeParams),
-    isApplicable: function (ctx) { return !!ctx.structure; }
-};
-//# sourceMappingURL=unit-index.js.map

package/lib/commonjs/mol-theme/color/volume-value.js

@@ -1,57 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.VolumeValueColorThemeProvider = exports.VolumeValueColorTheme = exports.getVolumeValueColorThemeParams = exports.VolumeValueColorThemeParams = void 0;
-var color_1 = require("../../mol-util/color");
-var param_definition_1 = require("../../mol-util/param-definition");
-var names_1 = require("../../mol-util/color/names");
-var DefaultColor = (0, color_1.Color)(0xCCCCCC);
-var Description = 'Assign color based on the given value of a volume cell.';
-exports.VolumeValueColorThemeParams = {
-    colorList: param_definition_1.ParamDefinition.ColorList({
-        kind: 'interpolate',
-        colors: [
-            [names_1.ColorNames.white, 0],
-            [names_1.ColorNames.red, 0.25],
-            [names_1.ColorNames.white, 0.5],
-            [names_1.ColorNames.blue, 0.75],
-            [names_1.ColorNames.white, 1]
-        ]
-    }, { offsets: true, isEssential: true }),
-};
-function getVolumeValueColorThemeParams(ctx) {
-    return exports.VolumeValueColorThemeParams; // TODO return copy
-}
-exports.getVolumeValueColorThemeParams = getVolumeValueColorThemeParams;
-function VolumeValueColorTheme(ctx, props) {
-    var scale = color_1.ColorScale.create({ domain: [0, 1], listOrName: props.colorList.colors });
-    var colors = [];
-    for (var i = 0; i < 256; ++i) {
-        colors[i] = scale.color(i / 255);
-    }
-    var palette = { colors: colors, filter: 'linear' };
-    return {
-        factory: VolumeValueColorTheme,
-        granularity: 'direct',
-        color: function () { return DefaultColor; },
-        props: props,
-        description: Description,
-        legend: scale.legend,
-        palette: palette,
-    };
-}
-exports.VolumeValueColorTheme = VolumeValueColorTheme;
-exports.VolumeValueColorThemeProvider = {
-    name: 'volume-value',
-    label: 'Volume Value',
-    category: "Miscellaneous" /* Misc */,
-    factory: VolumeValueColorTheme,
-    getParams: getVolumeValueColorThemeParams,
-    defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.VolumeValueColorThemeParams),
-    isApplicable: function (ctx) { return !!ctx.volume; },
-};
-//# sourceMappingURL=volume-value.js.map

package/lib/commonjs/mol-theme/label.js

@@ -1,362 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018-2020 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>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.dihedralLabel = exports.angleLabel = exports.distanceLabel = exports.elementLabel = exports._bundleLabel = exports.bundleLabel = exports.bondLabel = exports.structureElementLociLabelMany = exports.structureElementStatsLabel = exports.lociLabel = exports.DefaultLabelOptions = void 0;
-var tslib_1 = require("tslib");
-var structure_1 = require("../mol-model/structure");
-var loci_1 = require("../mol-model/loci");
-var int_1 = require("../mol-data/int");
-var string_1 = require("../mol-util/string");
-var linear_algebra_1 = require("../mol-math/linear-algebra");
-var misc_1 = require("../mol-math/misc");
-var volume_1 = require("../mol-model/volume");
-exports.DefaultLabelOptions = {
-    granularity: 'element',
-    condensed: false,
-    reverse: false,
-    countsOnly: false,
-    hidePrefix: false,
-    htmlStyling: true,
-};
-function lociLabel(loci, options) {
-    if (options === void 0) { options = {}; }
-    switch (loci.kind) {
-        case 'structure-loci':
-            return loci.structure.models.map(function (m) { return m.entry; }).filter(function (l) { return !!l; }).join(', ');
-        case 'element-loci':
-            return structureElementStatsLabel(structure_1.StructureElement.Stats.ofLoci(loci), options);
-        case 'bond-loci':
-            var bond = loci.bonds[0];
-            return bond ? bondLabel(bond) : '';
-        case 'shape-loci':
-            return loci.shape.name;
-        case 'group-loci':
-            var g = loci.groups[0];
-            return g ? loci.shape.getLabel(int_1.OrderedSet.start(g.ids), g.instance) : '';
-        case 'every-loci':
-            return 'Everything';
-        case 'empty-loci':
-            return 'Nothing';
-        case 'data-loci':
-            return loci.getLabel();
-        case 'volume-loci':
-            return loci.volume.label || 'Volume';
-        case 'isosurface-loci':
-            return [
-                "".concat(loci.volume.label || 'Volume'),
-                "Isosurface at ".concat(volume_1.Volume.IsoValue.toString(loci.isoValue))
-            ].join(' | ');
-        case 'cell-loci':
-            var size = int_1.OrderedSet.size(loci.indices);
-            var start = int_1.OrderedSet.start(loci.indices);
-            var absVal = volume_1.Volume.IsoValue.absolute(loci.volume.grid.cells.data[start]);
-            var relVal = volume_1.Volume.IsoValue.toRelative(absVal, loci.volume.grid.stats);
-            var label = [
-                "".concat(loci.volume.label || 'Volume'),
-                "".concat(size === 1 ? "Cell #".concat(start) : "".concat(size, " Cells"))
-            ];
-            if (size === 1) {
-                label.push("".concat(volume_1.Volume.IsoValue.toString(absVal), " (").concat(volume_1.Volume.IsoValue.toString(relVal), ")"));
-            }
-            return label.join(' | ');
-    }
-}
-exports.lociLabel = lociLabel;
-function countLabel(count, label) {
-    return count === 1 ? "1 ".concat(label) : "".concat(count, " ").concat(label, "s");
-}
-function otherLabel(count, location, granularity, hidePrefix, reverse, condensed) {
-    return "".concat(elementLabel(location, { granularity: granularity, hidePrefix: hidePrefix, reverse: reverse, condensed: condensed }), " <small>[+ ").concat(countLabel(count - 1, "other ".concat((0, string_1.capitalize)(granularity))), "]</small>");
-}
-/** Gets residue count of the model chain segments the unit is a subset of */
-function getResidueCount(unit) {
-    var elements = unit.elements, model = unit.model;
-    var _a = model.atomicHierarchy, chainAtomSegments = _a.chainAtomSegments, residueAtomSegments = _a.residueAtomSegments;
-    var elementStart = chainAtomSegments.offsets[chainAtomSegments.index[elements[0]]];
-    var elementEnd = chainAtomSegments.offsets[chainAtomSegments.index[elements[elements.length - 1]] + 1] - 1;
-    return residueAtomSegments.index[elementEnd] - residueAtomSegments.index[elementStart] + 1;
-}
-function structureElementStatsLabel(stats, options) {
-    if (options === void 0) { options = {}; }
-    var o = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, exports.DefaultLabelOptions), options);
-    var label = _structureElementStatsLabel(stats, o.countsOnly, o.hidePrefix, o.condensed, o.reverse);
-    return o.htmlStyling ? label : (0, string_1.stripTags)(label);
-}
-exports.structureElementStatsLabel = structureElementStatsLabel;
-function structureElementLociLabelMany(locis, options) {
-    if (options === void 0) { options = {}; }
-    var stats = structure_1.StructureElement.Stats.create();
-    for (var _i = 0, locis_1 = locis; _i < locis_1.length; _i++) {
-        var l = locis_1[_i];
-        structure_1.StructureElement.Stats.add(stats, stats, structure_1.StructureElement.Stats.ofLoci(l));
-    }
-    return structureElementStatsLabel(stats, options);
-}
-exports.structureElementLociLabelMany = structureElementLociLabelMany;
-function _structureElementStatsLabel(stats, countsOnly, hidePrefix, condensed, reverse) {
-    if (countsOnly === void 0) { countsOnly = false; }
-    if (hidePrefix === void 0) { hidePrefix = false; }
-    if (condensed === void 0) { condensed = false; }
-    if (reverse === void 0) { reverse = false; }
-    var structureCount = stats.structureCount, chainCount = stats.chainCount, residueCount = stats.residueCount, conformationCount = stats.conformationCount, elementCount = stats.elementCount;
-    if (!countsOnly && elementCount === 1 && residueCount === 0 && chainCount === 0) {
-        return elementLabel(stats.firstElementLoc, { hidePrefix: hidePrefix, condensed: condensed, granularity: 'element', reverse: reverse });
-    }
-    else if (!countsOnly && elementCount === 0 && residueCount === 1 && chainCount === 0) {
-        return elementLabel(stats.firstResidueLoc, { hidePrefix: hidePrefix, condensed: condensed, granularity: 'residue', reverse: reverse });
-    }
-    else if (!countsOnly && elementCount === 0 && residueCount === 0 && chainCount === 1) {
-        var unit = stats.firstChainLoc.unit;
-        var granularity = (structure_1.Unit.isAtomic(unit) && getResidueCount(unit) === 1)
-            ? 'residue' : structure_1.Unit.Traits.is(unit.traits, 1 /* MultiChain */)
-            ? 'residue' : 'chain';
-        return elementLabel(stats.firstChainLoc, { hidePrefix: hidePrefix, condensed: condensed, granularity: granularity, reverse: reverse });
-    }
-    else if (!countsOnly) {
-        var label = [];
-        if (structureCount > 0) {
-            label.push(structureCount === 1 ? elementLabel(stats.firstStructureLoc, { hidePrefix: hidePrefix, condensed: condensed, granularity: 'structure', reverse: reverse }) : otherLabel(structureCount, stats.firstStructureLoc, 'structure', hidePrefix, reverse, condensed));
-        }
-        if (chainCount > 0) {
-            label.push(chainCount === 1 ? elementLabel(stats.firstChainLoc, { condensed: condensed, granularity: 'chain', hidePrefix: hidePrefix, reverse: reverse }) : otherLabel(chainCount, stats.firstChainLoc, 'chain', hidePrefix, reverse, condensed));
-            hidePrefix = true;
-        }
-        if (residueCount > 0) {
-            label.push(residueCount === 1 ? elementLabel(stats.firstResidueLoc, { condensed: condensed, granularity: 'residue', hidePrefix: hidePrefix, reverse: reverse }) : otherLabel(residueCount, stats.firstResidueLoc, 'residue', hidePrefix, reverse, condensed));
-            hidePrefix = true;
-        }
-        if (conformationCount > 0) {
-            label.push(conformationCount === 1 ? elementLabel(stats.firstConformationLoc, { condensed: condensed, granularity: 'conformation', hidePrefix: hidePrefix, reverse: reverse }) : otherLabel(conformationCount, stats.firstConformationLoc, 'conformation', hidePrefix, reverse, condensed));
-            hidePrefix = true;
-        }
-        if (elementCount > 0) {
-            label.push(elementCount === 1 ? elementLabel(stats.firstElementLoc, { condensed: condensed, granularity: 'element', hidePrefix: hidePrefix, reverse: reverse }) : otherLabel(elementCount, stats.firstElementLoc, 'element', hidePrefix, reverse, condensed));
-        }
-        return label.join('<small> + </small>');
-    }
-    else {
-        var label = [];
-        if (structureCount > 0)
-            label.push(countLabel(structureCount, 'Structure'));
-        if (chainCount > 0)
-            label.push(countLabel(chainCount, 'Chain'));
-        if (residueCount > 0)
-            label.push(countLabel(residueCount, 'Residue'));
-        if (conformationCount > 0)
-            label.push(countLabel(conformationCount, 'Conformation'));
-        if (elementCount > 0)
-            label.push(countLabel(elementCount, 'Element'));
-        return label.join('<small> + </small>');
-    }
-}
-function bondLabel(bond, options) {
-    if (options === void 0) { options = {}; }
-    return bundleLabel({ loci: [
-            structure_1.StructureElement.Loci(bond.aStructure, [{ unit: bond.aUnit, indices: int_1.OrderedSet.ofSingleton(bond.aIndex) }]),
-            structure_1.StructureElement.Loci(bond.bStructure, [{ unit: bond.bUnit, indices: int_1.OrderedSet.ofSingleton(bond.bIndex) }])
-        ] }, options);
-}
-exports.bondLabel = bondLabel;
-function bundleLabel(bundle, options) {
-    if (options === void 0) { options = {}; }
-    var o = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, exports.DefaultLabelOptions), options);
-    var label = _bundleLabel(bundle, o);
-    return o.htmlStyling ? label : (0, string_1.stripTags)(label);
-}
-exports.bundleLabel = bundleLabel;
-function _bundleLabel(bundle, options) {
-    var granularity = options.granularity, hidePrefix = options.hidePrefix, reverse = options.reverse, condensed = options.condensed;
-    var isSingleElements = true;
-    for (var _i = 0, _a = bundle.loci; _i < _a.length; _i++) {
-        var l = _a[_i];
-        if (!structure_1.StructureElement.Loci.is(l) || structure_1.StructureElement.Loci.size(l) !== 1) {
-            isSingleElements = false;
-            break;
-        }
-    }
-    if (isSingleElements) {
-        var locations = bundle.loci.map(function (l) {
-            var _a = l.elements[0], unit = _a.unit, indices = _a.indices;
-            return structure_1.StructureElement.Location.create(l.structure, unit, unit.elements[int_1.OrderedSet.start(indices)]);
-        });
-        var labels = locations.map(function (l) { return _elementLabel(l, granularity, hidePrefix, reverse || condensed); });
-        if (condensed) {
-            return labels.map(function (l) { return l[0].replace(/\[.*\]/g, '').trim(); }).filter(function (l) { return !!l; }).join(' \u2014 ');
-        }
-        var offset = 0;
-        for (var i = 0, il = Math.min.apply(Math, labels.map(function (l) { return l.length; })) - 1; i < il; ++i) {
-            var areIdentical = true;
-            for (var j = 1, jl = labels.length; j < jl; ++j) {
-                if (labels[0][i] !== labels[j][i]) {
-                    areIdentical = false;
-                    break;
-                }
-            }
-            if (areIdentical)
-                offset += 1;
-            else
-                break;
-        }
-        if (offset > 0) {
-            var offsetLabels = [labels[0].join(' | ')];
-            for (var j = 1, jl = labels.length; j < jl; ++j) {
-                offsetLabels.push(labels[j].slice(offset).filter(function (l) { return !!l; }).join(' | '));
-            }
-            return offsetLabels.join(' \u2014 ');
-        }
-        else {
-            return labels.map(function (l) { return l.filter(function (l) { return !!l; }).join(' | '); }).filter(function (l) { return !!l; }).join('</br>');
-        }
-    }
-    else {
-        var labels = bundle.loci.map(function (l) { return lociLabel(l, options); });
-        return labels.filter(function (l) { return !!l; }).join(condensed ? ' \u2014 ' : '</br>');
-    }
-}
-exports._bundleLabel = _bundleLabel;
-function elementLabel(location, options) {
-    var _a, _b;
-    if (options === void 0) { options = {}; }
-    var o = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, exports.DefaultLabelOptions), options);
-    var _label = _elementLabel(location, o.granularity, o.hidePrefix, o.reverse || o.condensed);
-    // TODO: condensed label for single atom structure returns empty label.. handle this case here?
-    var label = o.condensed ? (_b = (_a = _label[0]) === null || _a === void 0 ? void 0 : _a.replace(/\[.*\]/g, '').trim()) !== null && _b !== void 0 ? _b : '' : _label.filter(function (l) { return !!l; }).join(' | ');
-    return o.htmlStyling ? label : (0, string_1.stripTags)(label);
-}
-exports.elementLabel = elementLabel;
-function _elementLabel(location, granularity, hidePrefix, reverse) {
-    if (granularity === void 0) { granularity = 'element'; }
-    if (hidePrefix === void 0) { hidePrefix = false; }
-    if (reverse === void 0) { reverse = false; }
-    var label = [];
-    if (!hidePrefix) {
-        var entry = location.unit.model.entry;
-        if (entry.length > 30)
-            entry = entry.substr(0, 27) + '\u2026'; // ellipsis
-        label.push("<small>".concat(entry, "</small>")); // entry
-        if (granularity !== 'structure') {
-            label.push("<small>Model ".concat(location.unit.model.modelNum, "</small>")); // model
-            label.push("<small>Instance ".concat(location.unit.conformation.operator.name, "</small>")); // instance
-        }
-    }
-    if (structure_1.Unit.isAtomic(location.unit)) {
-        label.push.apply(label, _atomicElementLabel(location, granularity, reverse));
-    }
-    else if (structure_1.Unit.isCoarse(location.unit)) {
-        label.push.apply(label, _coarseElementLabel(location, granularity));
-    }
-    else {
-        label.push('Unknown');
-    }
-    return reverse ? label.reverse() : label;
-}
-function _atomicElementLabel(location, granularity, hideOccupancy) {
-    if (hideOccupancy === void 0) { hideOccupancy = false; }
-    var rI = structure_1.StructureElement.Location.residueIndex(location);
-    var label_asym_id = structure_1.StructureProperties.chain.label_asym_id(location);
-    var auth_asym_id = structure_1.StructureProperties.chain.auth_asym_id(location);
-    var has_label_seq_id = location.unit.model.atomicHierarchy.residues.label_seq_id.valueKind(rI) === 0 /* Present */;
-    var label_seq_id = structure_1.StructureProperties.residue.label_seq_id(location);
-    var auth_seq_id = structure_1.StructureProperties.residue.auth_seq_id(location);
-    var ins_code = structure_1.StructureProperties.residue.pdbx_PDB_ins_code(location);
-    var comp_id = structure_1.StructureProperties.atom.label_comp_id(location);
-    var atom_id = structure_1.StructureProperties.atom.label_atom_id(location);
-    var alt_id = structure_1.StructureProperties.atom.label_alt_id(location);
-    var occupancy = structure_1.StructureProperties.atom.occupancy(location);
-    var microHetCompIds = structure_1.StructureProperties.residue.microheterogeneityCompIds(location);
-    var compId = granularity === 'residue' && microHetCompIds.length > 1 ?
-        "(".concat(microHetCompIds.join('|'), ")") : comp_id;
-    var label = [];
-    switch (granularity) {
-        case 'element':
-            label.push("<b>".concat(atom_id, "</b>").concat(alt_id ? "%".concat(alt_id) : ''));
-        case 'conformation':
-            if (granularity === 'conformation' && alt_id) {
-                label.push("<small>Conformation</small> <b>".concat(alt_id, "</b>"));
-            }
-        case 'residue':
-            var seq_id = label_seq_id === auth_seq_id || !has_label_seq_id ? auth_seq_id : label_seq_id;
-            label.push("<b>".concat(compId, " ").concat(seq_id, "</b>").concat(seq_id !== auth_seq_id ? " <small>[auth</small> <b>".concat(auth_seq_id, "</b><small>]</small>") : '', "<b>").concat(ins_code ? ins_code : '', "</b>"));
-        case 'chain':
-            if (label_asym_id === auth_asym_id) {
-                label.push("<b>".concat(label_asym_id, "</b>"));
-            }
-            else {
-                if (granularity === 'chain' && structure_1.Unit.Traits.is(location.unit.traits, 1 /* MultiChain */)) {
-                    label.push("<small>[auth</small> <b>".concat(auth_asym_id, "</b><small>]</small>"));
-                }
-                else {
-                    label.push("<b>".concat(label_asym_id, "</b> <small>[auth</small> <b>").concat(auth_asym_id, "</b><small>]</small>"));
-                }
-            }
-    }
-    if (label.length > 0 && occupancy !== 1 && !hideOccupancy) {
-        label[0] = "".concat(label[0], " <small>[occupancy</small> <b>").concat(Math.round(100 * occupancy) / 100, "</b><small>]</small>");
-    }
-    return label.reverse();
-}
-function _coarseElementLabel(location, granularity) {
-    var asym_id = structure_1.StructureProperties.coarse.asym_id(location);
-    var seq_id_begin = structure_1.StructureProperties.coarse.seq_id_begin(location);
-    var seq_id_end = structure_1.StructureProperties.coarse.seq_id_end(location);
-    var label = [];
-    switch (granularity) {
-        case 'element':
-        case 'conformation':
-        case 'residue':
-            if (seq_id_begin === seq_id_end) {
-                var entityIndex = structure_1.StructureProperties.coarse.entityKey(location);
-                var seq = location.unit.model.sequence.byEntityKey[entityIndex];
-                var comp_id = seq.sequence.compId.value(seq_id_begin - 1); // 1-indexed
-                label.push("<b>".concat(comp_id, " ").concat(seq_id_begin, "</b>"));
-            }
-            else {
-                label.push("<b>".concat(seq_id_begin, "-").concat(seq_id_end, "</b>"));
-            }
-        case 'chain':
-            label.push("<b>".concat(asym_id, "</b>"));
-    }
-    return label.reverse();
-}
-//
-function distanceLabel(pair, options) {
-    if (options === void 0) { options = {}; }
-    var o = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, exports.DefaultLabelOptions), { measureOnly: false, unitLabel: '\u212B' }), options);
-    var _a = pair.loci.map(function (l) { return loci_1.Loci.getCenter(l); }), cA = _a[0], cB = _a[1];
-    var distance = "".concat(linear_algebra_1.Vec3.distance(cA, cB).toFixed(2), " ").concat(o.unitLabel);
-    if (o.measureOnly)
-        return distance;
-    var label = bundleLabel(pair, o);
-    return o.condensed ? "".concat(distance, " | ").concat(label) : "Distance ".concat(distance, "</br>").concat(label);
-}
-exports.distanceLabel = distanceLabel;
-function angleLabel(triple, options) {
-    if (options === void 0) { options = {}; }
-    var o = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, exports.DefaultLabelOptions), { measureOnly: false }), options);
-    var _a = triple.loci.map(function (l) { return loci_1.Loci.getCenter(l); }), cA = _a[0], cB = _a[1], cC = _a[2];
-    var vAB = linear_algebra_1.Vec3.sub((0, linear_algebra_1.Vec3)(), cA, cB);
-    var vCB = linear_algebra_1.Vec3.sub((0, linear_algebra_1.Vec3)(), cC, cB);
-    var angle = "".concat((0, misc_1.radToDeg)(linear_algebra_1.Vec3.angle(vAB, vCB)).toFixed(2), "\u00B0");
-    if (o.measureOnly)
-        return angle;
-    var label = bundleLabel(triple, o);
-    return o.condensed ? "".concat(angle, " | ").concat(label) : "Angle ".concat(angle, "</br>").concat(label);
-}
-exports.angleLabel = angleLabel;
-function dihedralLabel(quad, options) {
-    if (options === void 0) { options = {}; }
-    var o = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, exports.DefaultLabelOptions), { measureOnly: false }), options);
-    var _a = quad.loci.map(function (l) { return loci_1.Loci.getCenter(l); }), cA = _a[0], cB = _a[1], cC = _a[2], cD = _a[3];
-    var dihedral = "".concat((0, misc_1.radToDeg)(linear_algebra_1.Vec3.dihedralAngle(cA, cB, cC, cD)).toFixed(2), "\u00B0");
-    if (o.measureOnly)
-        return dihedral;
-    var label = bundleLabel(quad, o);
-    return o.condensed ? "".concat(dihedral, " | ").concat(label) : "Dihedral ".concat(dihedral, "</br>").concat(label);
-}
-exports.dihedralLabel = dihedralLabel;
-//# sourceMappingURL=label.js.map