molstar 3.3.1 → 3.6.0

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

@@ -6,141 +6,239 @@
  */
 import { ConfalPyramids, ConfalPyramidsProvider } from './property';
 import { ConfalPyramidsTypes as CPT } from './types';
-import { Color } from '../../../mol-util/color';
+import { Color, ColorMap } from '../../../mol-util/color';
+import { getColorMapParams } from '../../../mol-util/color/params';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { TableLegend } from '../../../mol-util/legend';
-import { iterableToArray } from '../../../mol-data/util';
-var DefaultColor = Color(0xCCCCCC);
+import { ObjectKeys } from '../../../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 = Color(0xFFA10A);
-var ColorMapping = new Map([
-    ['A', Color(0xFFC1C1)],
-    ['B', Color(0xC8CFFF)],
-    ['BII', Color(0x0059DA)],
-    ['miB', Color(0x3BE8FB)],
-    ['Z', Color(0x01F60E)],
-    ['IC', Color(0xFA5CFB)],
-    ['OPN', Color(0xE90000)],
-    ['SYN', Color(0xFFFF01)],
-    ['N', 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;
-}
-export var ConfalPyramidsColorThemeParams = {};
+var PyramidsColors = 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,
+});
+export var ConfalPyramidsColorThemeParams = {
+    colors: PD.MappedStatic('default', {
+        'default': PD.EmptyGroup(),
+        'custom': PD.Group(getColorMapParams(PyramidsColors))
+    }),
+};
 export function getConfalPyramidsColorThemeParams(ctx) {
-    return ConfalPyramidsColorThemeParams; // TODO return copy
+    return PD.clone(ConfalPyramidsColorThemeParams);
 }
 export function ConfalPyramidsColorTheme(ctx, props) {
+    var colorMap = props.colors.name === 'default' ? PyramidsColors : props.colors.params;
     function color(location, isSecondary) {
+        var _a;
         if (CPT.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,
@@ -148,13 +246,7 @@ export function ConfalPyramidsColorTheme(ctx, props) {
         color: color,
         props: props,
         description: Description,
-        legend: TableLegend(iterableToArray(ColorMapping.entries()).map(function (_a) {
-            var conformer = _a[0], color = _a[1];
-            return [conformer, color];
-        }).concat([
-            ['Error', ErrorColor],
-            ['Unknown', DefaultColor]
-        ]))
+        legend: TableLegend(ObjectKeys(colorMap).map(function (k) { return [k.replace('_', ' '), colorMap[k]]; }).concat([['Error', ErrorColor]])),
     };
 }
 export var ConfalPyramidsColorThemeProvider = {

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

@@ -112,10 +112,8 @@ 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/extensions/dnatco/confal-pyramids/representation.d.ts

@@ -17,6 +17,7 @@ export declare const ConfalPyramidsParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -46,6 +47,7 @@ export declare function getConfalPyramidsParams(ctx: ThemeRegistryContext, struc
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -76,6 +78,7 @@ export declare const ConfalPyramidsRepresentationProvider: StructureRepresentati
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

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

@@ -6,7 +6,7 @@
  */
 import { __extends } from "tslib";
 import { ConfalPyramidsProvider } from './property';
-import { OrderedSet, Segmentation } from '../../../mol-data/int';
+import { Segmentation } from '../../../mol-data/int';
 import { Vec3 } from '../../../mol-math/linear-algebra';
 import { StructureElement, StructureProperties } from '../../../mol-model/structure';
 export var ConfalPyramidsUtil;
@@ -30,22 +30,17 @@ export var ConfalPyramidsUtil;
         return prop.data.hasMultipleModels;
     }
     ConfalPyramidsUtil.hasMultipleModels = hasMultipleModels;
-    function getPossibleAltIdsIndices(eIFirst, eILast, structure, unit) {
-        var loc = StructureElement.Location.create(structure, unit, -1);
-        var uIFirst = OrderedSet.indexOf(unit.elements, eIFirst);
-        var uILast = 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 = StructureElement.Location.create(structure, unit, -1);
+        for (var rI = residue.start; rI <= residue.end - 1; rI++) {
+            loc.element = unit.elements[rI];
             var altId = 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 = ConfalPyramidsProvider.get(unit.model).value;
@@ -86,18 +81,22 @@ export 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 = StructureElement.Location.create(this.structure, this.unit, eI);
+            var loc = 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 = 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) {
@@ -201,10 +200,10 @@ export 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/extensions/geo-export/ui.js

@@ -91,8 +91,8 @@ var GeometryExporterUI = /** @class */ (function (_super) {
             this.isARSupported = !!((_b = (_a = document.createElement('a').relList) === null || _a === void 0 ? void 0 : _a.supports) === null || _b === void 0 ? void 0 : _b.call(_a, 'ar'));
         }
         var ctrl = this.controls;
-        return _jsxs(_Fragment, { children: [_jsx(ParameterControls, { params: GeometryParams, values: ctrl.behaviors.params.value, onChangeValues: function (xs) { return ctrl.behaviors.params.next(xs); }, isDisabled: this.state.busy }, void 0), _jsx(Button, __assign({ icon: GetAppSvg, onClick: this.save, style: { marginTop: 1 }, disabled: this.state.busy || !((_c = this.plugin.canvas3d) === null || _c === void 0 ? void 0 : _c.reprCount.value) }, { children: "Save" }), void 0), this.isARSupported && ctrl.behaviors.params.value.format === 'usdz' &&
-                    _jsx(Button, __assign({ icon: CubeScanSvg, onClick: this.viewInAR, style: { marginTop: 1 }, disabled: this.state.busy || !((_d = this.plugin.canvas3d) === null || _d === void 0 ? void 0 : _d.reprCount.value) }, { children: "View in AR" }), void 0)] }, void 0);
+        return _jsxs(_Fragment, { children: [_jsx(ParameterControls, { params: GeometryParams, values: ctrl.behaviors.params.value, onChangeValues: function (xs) { return ctrl.behaviors.params.next(xs); }, isDisabled: this.state.busy }), _jsx(Button, __assign({ icon: GetAppSvg, onClick: this.save, style: { marginTop: 1 }, disabled: this.state.busy || !((_c = this.plugin.canvas3d) === null || _c === void 0 ? void 0 : _c.reprCount.value) }, { children: "Save" })), this.isARSupported && ctrl.behaviors.params.value.format === 'usdz' &&
+                    _jsx(Button, __assign({ icon: CubeScanSvg, onClick: this.viewInAR, style: { marginTop: 1 }, disabled: this.state.busy || !((_d = this.plugin.canvas3d) === null || _d === void 0 ? void 0 : _d.reprCount.value) }, { children: "View in AR" }))] });
     };
     GeometryExporterUI.prototype.componentDidMount = function () {
         var _this = this;

package/lib/extensions/model-export/ui.js

@@ -26,7 +26,7 @@ var ModelExportUI = /** @class */ (function (_super) {
         };
     };
     ModelExportUI.prototype.renderControls = function () {
-        return _jsx(ExportControls, { plugin: this.plugin }, void 0);
+        return _jsx(ExportControls, { plugin: this.plugin });
     };
     return ModelExportUI;
 }(CollapsableControls));
@@ -69,5 +69,5 @@ function ExportControls(_a) {
             }
         });
     }); };
-    return _jsxs(_Fragment, { children: [_jsx(ParameterControls, { params: Params, values: params, onChangeValues: setParams, isDisabled: isBusy || exporting }, void 0), _jsx(Button, __assign({ onClick: onExport, style: { marginTop: 1 }, disabled: isBusy || hierarchy.structures.length === 0 || exporting, commit: hierarchy.structures.length ? 'on' : 'off' }, { children: label }), void 0)] }, void 0);
+    return _jsxs(_Fragment, { children: [_jsx(ParameterControls, { params: Params, values: params, onChangeValues: setParams, isDisabled: isBusy || exporting }), _jsx(Button, __assign({ onClick: onExport, style: { marginTop: 1 }, disabled: isBusy || hierarchy.structures.length === 0 || exporting, commit: hierarchy.structures.length ? 'on' : 'off' }, { children: label }))] });
 }

package/lib/extensions/mp4-export/ui.js

@@ -59,7 +59,7 @@ var Mp4EncoderUI = /** @class */ (function (_super) {
     };
     Mp4EncoderUI.prototype.downloadControls = function () {
         var _this = this;
-        return _jsxs(_Fragment, { children: [_jsx("div", __assign({ className: 'msp-control-offset msp-help-text' }, { children: _jsx("div", __assign({ className: 'msp-help-description', style: { textAlign: 'center' } }, { children: "Rendering successful!" }), void 0) }), void 0), _jsx(Button, __assign({ icon: GetAppSvg, onClick: this.save, style: { marginTop: 1 } }, { children: "Save Animation" }), void 0), _jsx(Button, __assign({ onClick: function () { return _this.setState({ data: void 0 }); }, style: { marginTop: 6 } }, { children: "Clear" }), void 0)] }, void 0);
+        return _jsxs(_Fragment, { children: [_jsx("div", __assign({ className: 'msp-control-offset msp-help-text' }, { children: _jsx("div", __assign({ className: 'msp-help-description', style: { textAlign: 'center' } }, { children: "Rendering successful!" })) })), _jsx(Button, __assign({ icon: GetAppSvg, onClick: this.save, style: { marginTop: 1 } }, { children: "Save Animation" })), _jsx(Button, __assign({ onClick: function () { return _this.setState({ data: void 0 }); }, style: { marginTop: 6 } }, { children: "Clear" }))] });
     };
     Mp4EncoderUI.prototype.renderControls = function () {
         var _a;
@@ -70,7 +70,7 @@ var Mp4EncoderUI = /** @class */ (function (_super) {
         var current = ctrl.behaviors.current.value;
         var info = ctrl.behaviors.info.value;
         var canApply = ctrl.behaviors.canApply.value;
-        return _jsxs(_Fragment, { children: [_jsx(ParameterControls, { params: ctrl.behaviors.animations.value, values: { current: current === null || current === void 0 ? void 0 : current.anim.name }, onChangeValues: function (xs) { return ctrl.setCurrent(xs.current); }, isDisabled: this.state.busy }, void 0), current && _jsx(ParameterControls, { params: current.params, values: current.values, onChangeValues: function (xs) { return ctrl.setCurrentParams(xs); }, isDisabled: this.state.busy }, void 0), _jsx("div", __assign({ className: 'msp-control-offset msp-help-text' }, { children: _jsxs("div", __assign({ className: 'msp-help-description', style: { textAlign: 'center' } }, { children: ["Resolution: ", info.width, "x", info.height, _jsx("br", {}, void 0), "Adjust in viewport using ", _jsx(Icon, { svg: CameraOutlinedSvg, inline: true }, void 0)] }), void 0) }), void 0), _jsx(ParameterControls, { params: Mp4AnimationParams, values: ctrl.behaviors.params.value, onChangeValues: function (xs) { return ctrl.behaviors.params.next(xs); }, isDisabled: this.state.busy }, void 0), _jsx(Button, __assign({ onClick: this.generate, style: { marginTop: 1 }, disabled: this.state.busy || !canApply.canApply, commit: canApply.canApply ? 'on' : 'off' }, { children: canApply.canApply ? 'Render' : (_a = canApply.reason) !== null && _a !== void 0 ? _a : 'Invalid params/state' }), void 0)] }, void 0);
+        return _jsxs(_Fragment, { children: [_jsx(ParameterControls, { params: ctrl.behaviors.animations.value, values: { current: current === null || current === void 0 ? void 0 : current.anim.name }, onChangeValues: function (xs) { return ctrl.setCurrent(xs.current); }, isDisabled: this.state.busy }), current && _jsx(ParameterControls, { params: current.params, values: current.values, onChangeValues: function (xs) { return ctrl.setCurrentParams(xs); }, isDisabled: this.state.busy }), _jsx("div", __assign({ className: 'msp-control-offset msp-help-text' }, { children: _jsxs("div", __assign({ className: 'msp-help-description', style: { textAlign: 'center' } }, { children: ["Resolution: ", info.width, "x", info.height, _jsx("br", {}), "Adjust in viewport using ", _jsx(Icon, { svg: CameraOutlinedSvg, inline: true })] })) })), _jsx(ParameterControls, { params: Mp4AnimationParams, values: ctrl.behaviors.params.value, onChangeValues: function (xs) { return ctrl.behaviors.params.next(xs); }, isDisabled: this.state.busy }), _jsx(Button, __assign({ onClick: this.generate, style: { marginTop: 1 }, disabled: this.state.busy || !canApply.canApply, commit: canApply.canApply ? 'on' : 'off' }, { children: canApply.canApply ? 'Render' : (_a = canApply.reason) !== null && _a !== void 0 ? _a : 'Invalid params/state' }))] });
     };
     Mp4EncoderUI.prototype.componentDidMount = function () {
         var _this = this;

package/lib/extensions/rcsb/assembly-symmetry/behavior.d.ts

@@ -24,6 +24,7 @@ declare const AssemblySymmetry3D: StateTransformer<PluginStateObject.Molecule.St
     flatShaded: boolean;
     ignoreLight: boolean;
     xrayShaded: boolean;
+    allowTransparentBackfaces: boolean;
     bumpFrequency: number;
     bumpAmplitude: number;
     alpha: number;

package/lib/extensions/rcsb/assembly-symmetry/representation.d.ts

@@ -16,6 +16,7 @@ export declare const AssemblySymmetryParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

package/lib/extensions/rcsb/assembly-symmetry/ui.js

@@ -69,10 +69,10 @@ var AssemblySymmetryControls = /** @class */ (function (_super) {
         var pivot = this.pivot;
         if (!pivot.cell.parent)
             return null;
-        return _jsx(ApplyActionControl, { state: pivot.cell.parent, action: EnableAssemblySymmetry3D, initiallyCollapsed: true, nodeRef: pivot.cell.transform.ref, simpleApply: { header: 'Enable', icon: CheckSvg } }, void 0);
+        return _jsx(ApplyActionControl, { state: pivot.cell.parent, action: EnableAssemblySymmetry3D, initiallyCollapsed: true, nodeRef: pivot.cell.transform.ref, simpleApply: { header: 'Enable', icon: CheckSvg } });
     };
     AssemblySymmetryControls.prototype.renderNoSymmetries = function () {
-        return _jsx("div", __assign({ className: 'msp-row-text' }, { children: _jsx("div", { children: "No Symmetries for Assembly" }, void 0) }), void 0);
+        return _jsx("div", __assign({ className: 'msp-row-text' }, { children: _jsx("div", { children: "No Symmetries for Assembly" }) }));
     };
     Object.defineProperty(AssemblySymmetryControls.prototype, "params", {
         get: function () {
@@ -180,7 +180,7 @@ var AssemblySymmetryControls = /** @class */ (function (_super) {
         configurable: true
     });
     AssemblySymmetryControls.prototype.renderParams = function () {
-        return _jsx(_Fragment, { children: _jsx(ParameterControls, { params: this.params, values: this.values, onChangeValues: this.paramsOnChange }, void 0) }, void 0);
+        return _jsx(_Fragment, { children: _jsx(ParameterControls, { params: this.params, values: this.values, onChangeValues: this.paramsOnChange }) });
     };
     AssemblySymmetryControls.prototype.renderControls = function () {
         if (!this.pivot)

package/lib/extensions/rcsb/validation-report/representation.d.ts

@@ -31,6 +31,7 @@ export declare const IntraUnitClashParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -73,6 +74,7 @@ export declare const InterUnitClashParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -116,6 +118,7 @@ export declare const ClashesParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -158,6 +161,7 @@ export declare function getClashesParams(ctx: ThemeRegistryContext, structure: S
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -201,6 +205,7 @@ export declare const ClashesRepresentationProvider: StructureRepresentationProvi
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;