molstar 3.3.0 → 3.5.0

package/lib/commonjs/extensions/dnatco/confal-pyramids/color.js

@@ -10,141 +10,239 @@ exports.ConfalPyramidsColorThemeProvider = exports.ConfalPyramidsColorTheme = ex
 var property_1 = require("./property");
 var types_1 = require("./types");
 var color_1 = require("../../../mol-util/color");
+var params_1 = require("../../../mol-util/color/params");
 var param_definition_1 = require("../../../mol-util/param-definition");
 var legend_1 = require("../../../mol-util/legend");
-var util_1 = require("../../../mol-data/util");
-var DefaultColor = (0, color_1.Color)(0xCCCCCC);
+var type_helpers_1 = require("../../../mol-util/type-helpers");
 var Description = 'Assigns colors to confal pyramids';
+var DefaultClassColors = {
+    A: 0xFFC1C1,
+    B: 0xC8CFFF,
+    BII: 0x0059DA,
+    miB: 0x3BE8FB,
+    Z: 0x01F60E,
+    IC: 0xFA5CFB,
+    OPN: 0xE90000,
+    SYN: 0xFFFF01,
+    N: 0xF2F2F2,
+};
 var ErrorColor = (0, color_1.Color)(0xFFA10A);
-var ColorMapping = new Map([
-    ['A', (0, color_1.Color)(0xFFC1C1)],
-    ['B', (0, color_1.Color)(0xC8CFFF)],
-    ['BII', (0, color_1.Color)(0x0059DA)],
-    ['miB', (0, color_1.Color)(0x3BE8FB)],
-    ['Z', (0, color_1.Color)(0x01F60E)],
-    ['IC', (0, color_1.Color)(0xFA5CFB)],
-    ['OPN', (0, color_1.Color)(0xE90000)],
-    ['SYN', (0, color_1.Color)(0xFFFF01)],
-    ['N', (0, color_1.Color)(0xF2F2F2)],
-]);
-var NtCToClasses = new Map([
-    ['NANT', ['N', 'N']],
-    ['AA00', ['A', 'A']],
-    ['AA02', ['A', 'A']],
-    ['AA03', ['A', 'A']],
-    ['AA04', ['A', 'A']],
-    ['AA08', ['A', 'A']],
-    ['AA09', ['A', 'A']],
-    ['AA01', ['A', 'A']],
-    ['AA05', ['A', 'A']],
-    ['AA06', ['A', 'A']],
-    ['AA10', ['A', 'A']],
-    ['AA11', ['A', 'A']],
-    ['AA07', ['A', 'A']],
-    ['AA12', ['A', 'A']],
-    ['AA13', ['A', 'A']],
-    ['AB01', ['A', 'B']],
-    ['AB02', ['A', 'B']],
-    ['AB03', ['A', 'B']],
-    ['AB04', ['A', 'B']],
-    ['AB05', ['A', 'B']],
-    ['BA01', ['B', 'A']],
-    ['BA05', ['B', 'A']],
-    ['BA09', ['B', 'A']],
-    ['BA08', ['BII', 'A']],
-    ['BA10', ['B', 'A']],
-    ['BA13', ['BII', 'A']],
-    ['BA16', ['BII', 'A']],
-    ['BA17', ['BII', 'A']],
-    ['BB00', ['B', 'B']],
-    ['BB01', ['B', 'B']],
-    ['BB17', ['B', 'B']],
-    ['BB02', ['B', 'B']],
-    ['BB03', ['B', 'B']],
-    ['BB11', ['B', 'B']],
-    ['BB16', ['B', 'B']],
-    ['BB04', ['B', 'BII']],
-    ['BB05', ['B', 'BII']],
-    ['BB07', ['BII', 'BII']],
-    ['BB08', ['BII', 'BII']],
-    ['BB10', ['miB', 'miB']],
-    ['BB12', ['miB', 'miB']],
-    ['BB13', ['miB', 'miB']],
-    ['BB14', ['miB', 'miB']],
-    ['BB15', ['miB', 'miB']],
-    ['BB20', ['miB', 'miB']],
-    ['IC01', ['IC', 'IC']],
-    ['IC02', ['IC', 'IC']],
-    ['IC03', ['IC', 'IC']],
-    ['IC04', ['IC', 'IC']],
-    ['IC05', ['IC', 'IC']],
-    ['IC06', ['IC', 'IC']],
-    ['IC07', ['IC', 'IC']],
-    ['OP01', ['OPN', 'OPN']],
-    ['OP02', ['OPN', 'OPN']],
-    ['OP03', ['OPN', 'OPN']],
-    ['OP04', ['OPN', 'OPN']],
-    ['OP05', ['OPN', 'OPN']],
-    ['OP06', ['OPN', 'OPN']],
-    ['OP07', ['OPN', 'OPN']],
-    ['OP08', ['OPN', 'OPN']],
-    ['OP09', ['OPN', 'OPN']],
-    ['OP10', ['OPN', 'OPN']],
-    ['OP11', ['OPN', 'OPN']],
-    ['OP12', ['OPN', 'OPN']],
-    ['OP13', ['OPN', 'OPN']],
-    ['OP14', ['OPN', 'OPN']],
-    ['OP15', ['OPN', 'OPN']],
-    ['OP16', ['OPN', 'OPN']],
-    ['OP17', ['OPN', 'OPN']],
-    ['OP18', ['OPN', 'OPN']],
-    ['OP19', ['OPN', 'OPN']],
-    ['OP20', ['OPN', 'OPN']],
-    ['OP21', ['OPN', 'OPN']],
-    ['OP22', ['OPN', 'OPN']],
-    ['OP23', ['OPN', 'OPN']],
-    ['OP24', ['OPN', 'OPN']],
-    ['OP25', ['OPN', 'OPN']],
-    ['OP26', ['OPN', 'OPN']],
-    ['OP27', ['OPN', 'OPN']],
-    ['OP28', ['OPN', 'OPN']],
-    ['OP29', ['OPN', 'OPN']],
-    ['OP30', ['OPN', 'OPN']],
-    ['OP31', ['OPN', 'OPN']],
-    ['OPS1', ['OPN', 'OPN']],
-    ['OP1S', ['OPN', 'SYN']],
-    ['AAS1', ['SYN', 'A']],
-    ['AB1S', ['A', 'SYN']],
-    ['AB2S', ['A', 'SYN']],
-    ['BB1S', ['B', 'SYN']],
-    ['BB2S', ['B', 'SYN']],
-    ['BBS1', ['SYN', 'B']],
-    ['ZZ01', ['Z', 'Z']],
-    ['ZZ02', ['Z', 'Z']],
-    ['ZZ1S', ['Z', 'SYN']],
-    ['ZZ2S', ['Z', 'SYN']],
-    ['ZZS1', ['SYN', 'Z']],
-    ['ZZS2', ['SYN', 'Z']],
-]);
-function getConformerColor(ntc, useLower) {
-    var _a;
-    var item = NtCToClasses.get(ntc);
-    if (!item)
-        return ErrorColor;
-    return (_a = ColorMapping.get(useLower ? item[1] : item[0])) !== null && _a !== void 0 ? _a : ErrorColor;
-}
-exports.ConfalPyramidsColorThemeParams = {};
+var PyramidsColors = (0, color_1.ColorMap)({
+    NANT_Upr: DefaultClassColors.N,
+    NANT_Lwr: DefaultClassColors.N,
+    AA00_Upr: DefaultClassColors.A,
+    AA00_Lwr: DefaultClassColors.A,
+    AA02_Upr: DefaultClassColors.A,
+    AA02_Lwr: DefaultClassColors.A,
+    AA03_Upr: DefaultClassColors.A,
+    AA03_Lwr: DefaultClassColors.A,
+    AA04_Upr: DefaultClassColors.A,
+    AA04_Lwr: DefaultClassColors.A,
+    AA08_Upr: DefaultClassColors.A,
+    AA08_Lwr: DefaultClassColors.A,
+    AA09_Upr: DefaultClassColors.A,
+    AA09_Lwr: DefaultClassColors.A,
+    AA01_Upr: DefaultClassColors.A,
+    AA01_Lwr: DefaultClassColors.A,
+    AA05_Upr: DefaultClassColors.A,
+    AA05_Lwr: DefaultClassColors.A,
+    AA06_Upr: DefaultClassColors.A,
+    AA06_Lwr: DefaultClassColors.A,
+    AA10_Upr: DefaultClassColors.A,
+    AA10_Lwr: DefaultClassColors.A,
+    AA11_Upr: DefaultClassColors.A,
+    AA11_Lwr: DefaultClassColors.A,
+    AA07_Upr: DefaultClassColors.A,
+    AA07_Lwr: DefaultClassColors.A,
+    AA12_Upr: DefaultClassColors.A,
+    AA12_Lwr: DefaultClassColors.A,
+    AA13_Upr: DefaultClassColors.A,
+    AA13_Lwr: DefaultClassColors.A,
+    AB01_Upr: DefaultClassColors.A,
+    AB01_Lwr: DefaultClassColors.B,
+    AB02_Upr: DefaultClassColors.A,
+    AB02_Lwr: DefaultClassColors.B,
+    AB03_Upr: DefaultClassColors.A,
+    AB03_Lwr: DefaultClassColors.B,
+    AB04_Upr: DefaultClassColors.A,
+    AB04_Lwr: DefaultClassColors.B,
+    AB05_Upr: DefaultClassColors.A,
+    AB05_Lwr: DefaultClassColors.B,
+    BA01_Upr: DefaultClassColors.B,
+    BA01_Lwr: DefaultClassColors.A,
+    BA05_Upr: DefaultClassColors.B,
+    BA05_Lwr: DefaultClassColors.A,
+    BA09_Upr: DefaultClassColors.B,
+    BA09_Lwr: DefaultClassColors.A,
+    BA08_Upr: DefaultClassColors.BII,
+    BA08_Lwr: DefaultClassColors.A,
+    BA10_Upr: DefaultClassColors.B,
+    BA10_Lwr: DefaultClassColors.A,
+    BA13_Upr: DefaultClassColors.BII,
+    BA13_Lwr: DefaultClassColors.A,
+    BA16_Upr: DefaultClassColors.BII,
+    BA16_Lwr: DefaultClassColors.A,
+    BA17_Upr: DefaultClassColors.BII,
+    BA17_Lwr: DefaultClassColors.A,
+    BB00_Upr: DefaultClassColors.B,
+    BB00_Lwr: DefaultClassColors.B,
+    BB01_Upr: DefaultClassColors.B,
+    BB01_Lwr: DefaultClassColors.B,
+    BB17_Upr: DefaultClassColors.B,
+    BB17_Lwr: DefaultClassColors.B,
+    BB02_Upr: DefaultClassColors.B,
+    BB02_Lwr: DefaultClassColors.B,
+    BB03_Upr: DefaultClassColors.B,
+    BB03_Lwr: DefaultClassColors.B,
+    BB11_Upr: DefaultClassColors.B,
+    BB11_Lwr: DefaultClassColors.B,
+    BB16_Upr: DefaultClassColors.B,
+    BB16_Lwr: DefaultClassColors.B,
+    BB04_Upr: DefaultClassColors.B,
+    BB04_Lwr: DefaultClassColors.BII,
+    BB05_Upr: DefaultClassColors.B,
+    BB05_Lwr: DefaultClassColors.BII,
+    BB07_Upr: DefaultClassColors.BII,
+    BB07_Lwr: DefaultClassColors.BII,
+    BB08_Upr: DefaultClassColors.BII,
+    BB08_Lwr: DefaultClassColors.BII,
+    BB10_Upr: DefaultClassColors.miB,
+    BB10_Lwr: DefaultClassColors.miB,
+    BB12_Upr: DefaultClassColors.miB,
+    BB12_Lwr: DefaultClassColors.miB,
+    BB13_Upr: DefaultClassColors.miB,
+    BB13_Lwr: DefaultClassColors.miB,
+    BB14_Upr: DefaultClassColors.miB,
+    BB14_Lwr: DefaultClassColors.miB,
+    BB15_Upr: DefaultClassColors.miB,
+    BB15_Lwr: DefaultClassColors.miB,
+    BB20_Upr: DefaultClassColors.miB,
+    BB20_Lwr: DefaultClassColors.miB,
+    IC01_Upr: DefaultClassColors.IC,
+    IC01_Lwr: DefaultClassColors.IC,
+    IC02_Upr: DefaultClassColors.IC,
+    IC02_Lwr: DefaultClassColors.IC,
+    IC03_Upr: DefaultClassColors.IC,
+    IC03_Lwr: DefaultClassColors.IC,
+    IC04_Upr: DefaultClassColors.IC,
+    IC04_Lwr: DefaultClassColors.IC,
+    IC05_Upr: DefaultClassColors.IC,
+    IC05_Lwr: DefaultClassColors.IC,
+    IC06_Upr: DefaultClassColors.IC,
+    IC06_Lwr: DefaultClassColors.IC,
+    IC07_Upr: DefaultClassColors.IC,
+    IC07_Lwr: DefaultClassColors.IC,
+    OP01_Upr: DefaultClassColors.OPN,
+    OP01_Lwr: DefaultClassColors.OPN,
+    OP02_Upr: DefaultClassColors.OPN,
+    OP02_Lwr: DefaultClassColors.OPN,
+    OP03_Upr: DefaultClassColors.OPN,
+    OP03_Lwr: DefaultClassColors.OPN,
+    OP04_Upr: DefaultClassColors.OPN,
+    OP04_Lwr: DefaultClassColors.OPN,
+    OP05_Upr: DefaultClassColors.OPN,
+    OP05_Lwr: DefaultClassColors.OPN,
+    OP06_Upr: DefaultClassColors.OPN,
+    OP06_Lwr: DefaultClassColors.OPN,
+    OP07_Upr: DefaultClassColors.OPN,
+    OP07_Lwr: DefaultClassColors.OPN,
+    OP08_Upr: DefaultClassColors.OPN,
+    OP08_Lwr: DefaultClassColors.OPN,
+    OP09_Upr: DefaultClassColors.OPN,
+    OP09_Lwr: DefaultClassColors.OPN,
+    OP10_Upr: DefaultClassColors.OPN,
+    OP10_Lwr: DefaultClassColors.OPN,
+    OP11_Upr: DefaultClassColors.OPN,
+    OP11_Lwr: DefaultClassColors.OPN,
+    OP12_Upr: DefaultClassColors.OPN,
+    OP12_Lwr: DefaultClassColors.OPN,
+    OP13_Upr: DefaultClassColors.OPN,
+    OP13_Lwr: DefaultClassColors.OPN,
+    OP14_Upr: DefaultClassColors.OPN,
+    OP14_Lwr: DefaultClassColors.OPN,
+    OP15_Upr: DefaultClassColors.OPN,
+    OP15_Lwr: DefaultClassColors.OPN,
+    OP16_Upr: DefaultClassColors.OPN,
+    OP16_Lwr: DefaultClassColors.OPN,
+    OP17_Upr: DefaultClassColors.OPN,
+    OP17_Lwr: DefaultClassColors.OPN,
+    OP18_Upr: DefaultClassColors.OPN,
+    OP18_Lwr: DefaultClassColors.OPN,
+    OP19_Upr: DefaultClassColors.OPN,
+    OP19_Lwr: DefaultClassColors.OPN,
+    OP20_Upr: DefaultClassColors.OPN,
+    OP20_Lwr: DefaultClassColors.OPN,
+    OP21_Upr: DefaultClassColors.OPN,
+    OP21_Lwr: DefaultClassColors.OPN,
+    OP22_Upr: DefaultClassColors.OPN,
+    OP22_Lwr: DefaultClassColors.OPN,
+    OP23_Upr: DefaultClassColors.OPN,
+    OP23_Lwr: DefaultClassColors.OPN,
+    OP24_Upr: DefaultClassColors.OPN,
+    OP24_Lwr: DefaultClassColors.OPN,
+    OP25_Upr: DefaultClassColors.OPN,
+    OP25_Lwr: DefaultClassColors.OPN,
+    OP26_Upr: DefaultClassColors.OPN,
+    OP26_Lwr: DefaultClassColors.OPN,
+    OP27_Upr: DefaultClassColors.OPN,
+    OP27_Lwr: DefaultClassColors.OPN,
+    OP28_Upr: DefaultClassColors.OPN,
+    OP28_Lwr: DefaultClassColors.OPN,
+    OP29_Upr: DefaultClassColors.OPN,
+    OP29_Lwr: DefaultClassColors.OPN,
+    OP30_Upr: DefaultClassColors.OPN,
+    OP30_Lwr: DefaultClassColors.OPN,
+    OP31_Upr: DefaultClassColors.OPN,
+    OP31_Lwr: DefaultClassColors.OPN,
+    OPS1_Upr: DefaultClassColors.OPN,
+    OPS1_Lwr: DefaultClassColors.OPN,
+    OP1S_Upr: DefaultClassColors.OPN,
+    OP1S_Lwr: DefaultClassColors.SYN,
+    AAS1_Upr: DefaultClassColors.SYN,
+    AAS1_Lwr: DefaultClassColors.A,
+    AB1S_Upr: DefaultClassColors.A,
+    AB1S_Lwr: DefaultClassColors.SYN,
+    AB2S_Upr: DefaultClassColors.A,
+    AB2S_Lwr: DefaultClassColors.SYN,
+    BB1S_Upr: DefaultClassColors.B,
+    BB1S_Lwr: DefaultClassColors.SYN,
+    BB2S_Upr: DefaultClassColors.B,
+    BB2S_Lwr: DefaultClassColors.SYN,
+    BBS1_Upr: DefaultClassColors.SYN,
+    BBS1_Lwr: DefaultClassColors.B,
+    ZZ01_Upr: DefaultClassColors.Z,
+    ZZ01_Lwr: DefaultClassColors.Z,
+    ZZ02_Upr: DefaultClassColors.Z,
+    ZZ02_Lwr: DefaultClassColors.Z,
+    ZZ1S_Upr: DefaultClassColors.Z,
+    ZZ1S_Lwr: DefaultClassColors.SYN,
+    ZZ2S_Upr: DefaultClassColors.Z,
+    ZZ2S_Lwr: DefaultClassColors.SYN,
+    ZZS1_Upr: DefaultClassColors.SYN,
+    ZZS1_Lwr: DefaultClassColors.Z,
+    ZZS2_Upr: DefaultClassColors.SYN,
+    ZZS2_Lwr: DefaultClassColors.Z,
+});
+exports.ConfalPyramidsColorThemeParams = {
+    colors: param_definition_1.ParamDefinition.MappedStatic('default', {
+        'default': param_definition_1.ParamDefinition.EmptyGroup(),
+        'custom': param_definition_1.ParamDefinition.Group((0, params_1.getColorMapParams)(PyramidsColors))
+    }),
+};
 function getConfalPyramidsColorThemeParams(ctx) {
-    return exports.ConfalPyramidsColorThemeParams; // TODO return copy
+    return param_definition_1.ParamDefinition.clone(exports.ConfalPyramidsColorThemeParams);
 }
 exports.getConfalPyramidsColorThemeParams = getConfalPyramidsColorThemeParams;
 function ConfalPyramidsColorTheme(ctx, props) {
+    var colorMap = props.colors.name === 'default' ? PyramidsColors : props.colors.params;
     function color(location, isSecondary) {
+        var _a;
         if (types_1.ConfalPyramidsTypes.isLocation(location)) {
-            var _a = location.data, pyramid = _a.pyramid, isLower = _a.isLower;
-            return getConformerColor(pyramid.NtC, isLower);
+            var _b = location.data, pyramid = _b.pyramid, isLower = _b.isLower;
+            var key = pyramid.NtC + "_".concat(isLower ? 'Lwr' : 'Upr');
+            return (_a = colorMap[key]) !== null && _a !== void 0 ? _a : ErrorColor;
         }
-        return DefaultColor;
+        return ErrorColor;
     }
     return {
         factory: ConfalPyramidsColorTheme,
@@ -152,13 +250,7 @@ function ConfalPyramidsColorTheme(ctx, props) {
         color: color,
         props: props,
         description: Description,
-        legend: (0, legend_1.TableLegend)((0, util_1.iterableToArray)(ColorMapping.entries()).map(function (_a) {
-            var conformer = _a[0], color = _a[1];
-            return [conformer, color];
-        }).concat([
-            ['Error', ErrorColor],
-            ['Unknown', DefaultColor]
-        ]))
+        legend: (0, legend_1.TableLegend)((0, type_helpers_1.ObjectKeys)(colorMap).map(function (k) { return [k.replace('_', ' '), colorMap[k]]; }).concat([['Error', ErrorColor]])),
     };
 }
 exports.ConfalPyramidsColorTheme = ConfalPyramidsColorTheme;

package/lib/commonjs/extensions/dnatco/confal-pyramids/property.js

@@ -53,9 +53,9 @@ var ConfalPyramids;
         }
     };
     function fromCif(ctx, model, props) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var info, data, fromCif;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 info = wrapper_1.PropertyWrapper.createInfo();
                 data = getCifData(model);
                 if (data === undefined)
@@ -97,10 +97,10 @@ exports.ConfalPyramidsProvider = custom_model_property_1.CustomModelProperty.cre
     defaultParams: exports.ConfalPyramidsParams,
     getParams: function (data) { return exports.ConfalPyramidsParams; },
     isApplicable: function (data) { return ConfalPyramids.isApplicable(data); },
-    obtain: function (ctx, data, props) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    obtain: function (ctx, data, props) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var p;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(exports.ConfalPyramidsParams)), props);
+        return tslib_1.__generator(this, function (_a) {
+            p = tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(exports.ConfalPyramidsParams)), props);
             return [2 /*return*/, ConfalPyramids.fromCif(ctx, data, p)];
         });
     }); }
@@ -115,10 +115,8 @@ function createPyramidsFromCif(model, steps, stepsSummary) {
         throw new Error('Inconsistent mmCIF data');
     for (var i = 0; i < _rowCount; i++) {
         var model_num = PDB_model_number.value(i);
-        if (model_num !== model.modelNum) {
+        if (model_num !== model.modelNum)
             hasMultipleModels = true;
-            continue; // We are only interested in data for the current model
-        }
         var _a = getNtCAndConfalScore(id.value(i), i, stepsSummary), _NtC = _a._NtC, _confal_score = _a._confal_score;
         var pyramid = {
             PDB_model_number: model_num,

package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.js

@@ -37,7 +37,7 @@ function shiftVertex(vec, ref, scale) {
     linear_algebra_1.Vec3.scale(w, w, scale);
     linear_algebra_1.Vec3.add(vec, vec, w);
 }
-var ConfalPyramidsMeshParams = (0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams);
+var ConfalPyramidsMeshParams = tslib_1.__assign({}, units_visual_1.UnitsMeshParams);
 function createConfalPyramidsIterator(structureGroup) {
     var structure = structureGroup.structure, group = structureGroup.group;
     var instanceCount = group.units.length;
@@ -131,7 +131,7 @@ function ConfalPyramidsVisual(materialId) {
 var ConfalPyramidsVisuals = {
     'confal-pyramids-symbol': function (ctx, getParams) { return (0, representation_2.UnitsRepresentation)('Confal Pyramids Symbol Mesh', ctx, getParams, ConfalPyramidsVisual); },
 };
-exports.ConfalPyramidsParams = (0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams);
+exports.ConfalPyramidsParams = tslib_1.__assign({}, units_visual_1.UnitsMeshParams);
 function getConfalPyramidsParams(ctx, structure) {
     return param_definition_1.ParamDefinition.clone(exports.ConfalPyramidsParams);
 }

package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js

@@ -33,22 +33,17 @@ var ConfalPyramidsUtil;
         return prop.data.hasMultipleModels;
     }
     ConfalPyramidsUtil.hasMultipleModels = hasMultipleModels;
-    function getPossibleAltIdsIndices(eIFirst, eILast, structure, unit) {
-        var loc = structure_1.StructureElement.Location.create(structure, unit, -1);
-        var uIFirst = int_1.OrderedSet.indexOf(unit.elements, eIFirst);
-        var uILast = int_1.OrderedSet.indexOf(unit.elements, eILast);
+    function getPossibleAltIds(residue, structure, unit) {
         var possibleAltIds = [];
-        for (var uI = uIFirst; uI <= uILast; uI++) {
-            loc.element = unit.elements[uI];
+        var loc = structure_1.StructureElement.Location.create(structure, unit, -1);
+        for (var rI = residue.start; rI <= residue.end - 1; rI++) {
+            loc.element = unit.elements[rI];
             var altId = structure_1.StructureProperties.atom.label_alt_id(loc);
             if (altId !== '' && !possibleAltIds.includes(altId))
                 possibleAltIds.push(altId);
         }
         return possibleAltIds;
     }
-    function getPossibleAltIdsResidue(residue, structure, unit) {
-        return getPossibleAltIdsIndices(unit.elements[residue.start], unit.elements[residue.end - 1], structure, unit);
-    }
     var Utility = /** @class */ (function () {
         function Utility(unit) {
             var prop = property_1.ConfalPyramidsProvider.get(unit.model).value;
@@ -78,7 +73,7 @@ var ConfalPyramidsUtil;
         return Utility;
     }());
     var UnitWalker = /** @class */ (function (_super) {
-        (0, tslib_1.__extends)(UnitWalker, _super);
+        tslib_1.__extends(UnitWalker, _super);
         function UnitWalker(structure, unit, handler) {
             var _this = _super.call(this, unit) || this;
             _this.structure = structure;
@@ -89,18 +84,22 @@ var ConfalPyramidsUtil;
             return _this;
         }
         UnitWalker.prototype.getAtomIndices = function (names, residue) {
-            var rI = residue.start;
-            var rILast = residue.end - 1;
             var indices = [];
-            for (; rI !== rILast; rI++) {
-                var eI = this.unit.elements[rI];
-                var loc = structure_1.StructureElement.Location.create(this.structure, this.unit, eI);
+            var loc = structure_1.StructureElement.Location.create(this.structure, this.unit, -1);
+            for (var rI = residue.start; rI <= residue.end - 1; rI++) {
+                loc.element = this.unit.elements[rI];
                 var thisName = structure_1.StructureProperties.atom.label_atom_id(loc);
                 if (names.includes(thisName))
-                    indices.push(eI);
+                    indices.push(loc.element);
+            }
+            if (indices.length === 0) {
+                var namesStr = '';
+                for (var _i = 0, names_1 = names; _i < names_1.length; _i++) {
+                    var n = names_1[_i];
+                    namesStr += "".concat(n, " ");
+                }
+                throw new Error("Element [".concat(namesStr, "] not found on residue ").concat(residue.index));
             }
-            if (indices.length === 0)
-                throw new Error("Element ".concat(name, " not found on residue ").concat(residue.index));
             return indices;
         };
         UnitWalker.prototype.getAtomPositions = function (indices) {
@@ -204,10 +203,10 @@ var ConfalPyramidsUtil;
             return altPos;
         };
         UnitWalker.prototype.step = function (residue) {
-            var firstPossibleAltIds = getPossibleAltIdsResidue(residue, this.structure, this.unit);
+            var firstPossibleAltIds = getPossibleAltIds(residue, this.structure, this.unit);
             var firstAtoms = this.processFirstResidue(residue, firstPossibleAltIds);
             residue = this.residueIt.move();
-            var secondPossibleAltIds = getPossibleAltIdsResidue(residue, this.structure, this.unit);
+            var secondPossibleAltIds = getPossibleAltIds(residue, this.structure, this.unit);
             var secondAtoms = this.processSecondResidue(residue, secondPossibleAltIds);
             return { firstAtoms: firstAtoms, secondAtoms: secondAtoms };
         };

package/lib/commonjs/extensions/g3d/data.js

@@ -12,9 +12,9 @@ var mol_task_1 = require("../../mol-task");
 var zip_1 = require("../../mol-util/zip/zip");
 var HEADER_SIZE = 64000;
 function getG3dHeader(ctx, urlOrData) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var data, last, header;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, getRawData(ctx, urlOrData, { offset: 0, size: HEADER_SIZE })];
                 case 1:
@@ -32,9 +32,9 @@ function getG3dHeader(ctx, urlOrData) {
 }
 exports.getG3dHeader = getG3dHeader;
 function getG3dDataBlock(ctx, header, urlOrData, resolution) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var data, unzipped;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     if (!header.offsets[resolution])
@@ -56,8 +56,8 @@ function getG3dDataBlock(ctx, header, urlOrData, resolution) {
 }
 exports.getG3dDataBlock = getG3dDataBlock;
 function getRawData(ctx, urlOrData, range) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     if (!(typeof urlOrData === 'string')) return [3 /*break*/, 2];

package/lib/commonjs/extensions/g3d/format.js

@@ -26,9 +26,9 @@ exports.G3dProvider = {
     description: 'G3D',
     category: trajectory_1.TrajectoryFormatCategory,
     binaryExtensions: ['g3d'],
-    parse: function (plugin, data) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    parse: function (plugin, data) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var trajectory;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, plugin.state.data.build()
                         .to(data)
@@ -44,9 +44,9 @@ exports.G3dProvider = {
     visuals: defaultStructure
 };
 function defaultStructure(plugin, data) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var builder, model, structure, info, components, repr, _i, _a, h;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     builder = plugin.builders.structure;
@@ -83,7 +83,7 @@ function defaultStructure(plugin, data) {
     });
 }
 var G3dHeaderObject = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(G3dHeaderObject, _super);
+    tslib_1.__extends(G3dHeaderObject, _super);
     function G3dHeaderObject() {
         return _super !== null && _super.apply(this, arguments) || this;
     }
@@ -99,9 +99,9 @@ exports.G3DHeaderFromFile = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a, plugin) {
         var _this = this;
         var a = _a.a;
-        return mol_task_1.Task.create('Parse G3D', function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse G3D', function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var header;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, (0, data_1.getG3dHeader)(plugin, a.data)];
                     case 1:
@@ -122,9 +122,9 @@ exports.G3DHeaderFromUrl = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a, plugin) {
         var _this = this;
         var params = _a.params;
-        return mol_task_1.Task.create('Parse G3D', function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse G3D', function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var header;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, (0, data_1.getG3dHeader)(plugin, params.url)];
                     case 1:
@@ -152,9 +152,9 @@ exports.G3DTrajectory = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a, plugin) {
         var _this = this;
         var a = _a.a, params = _a.params;
-        return mol_task_1.Task.create('G3D Trajectory', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('G3D Trajectory', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var data, traj;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         if (a.data.cache[params.resolution]) {
@@ -180,9 +180,9 @@ exports.LoadG3D = mol_state_1.StateAction.build({
 })(function (_a, ctx) {
     var params = _a.params, state = _a.state;
     return mol_task_1.Task.create('Genome3D', function (taskCtx) {
-        return state.transaction(function () { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+        return state.transaction(function () { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
             var trajectory;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         if (params.url.trim().length === 0) {
@@ -212,7 +212,7 @@ exports.G3DFormat = behavior_1.PluginBehavior.create({
         description: 'G3D Format Support'
     },
     ctor: /** @class */ (function (_super) {
-        (0, tslib_1.__extends)(class_1, _super);
+        tslib_1.__extends(class_1, _super);
         function class_1() {
             return _super !== null && _super.apply(this, arguments) || this;
         }