molstar 3.4.0 → 3.6.1

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/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/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;

package/lib/mol-canvas3d/canvas3d.d.ts

@@ -166,6 +166,7 @@ export declare const Canvas3DParams: {
             flipSided: any;
             flatShaded: any;
             xrayShaded: any;
+            allowTransparentBackfaces: any;
             bumpFrequency: any;
             bumpAmplitude: any;
             quality: any;
@@ -319,6 +320,7 @@ export declare const DefaultCanvas3DParams: PD.Values<{
             flipSided: any;
             flatShaded: any;
             xrayShaded: any;
+            allowTransparentBackfaces: any;
             bumpFrequency: any;
             bumpAmplitude: any;
             quality: any;

package/lib/mol-canvas3d/helper/camera-helper.d.ts

@@ -22,6 +22,7 @@ export declare const CameraHelperParams: {
         flipSided: boolean;
         flatShaded: boolean;
         xrayShaded: boolean;
+        allowTransparentBackfaces: boolean;
         bumpFrequency: number;
         bumpAmplitude: number;
         quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";

package/lib/mol-canvas3d/helper/handle-helper.d.ts

@@ -24,6 +24,7 @@ export declare const HandleHelperParams: {
         flipSided: boolean;
         flatShaded: boolean;
         xrayShaded: boolean;
+        allowTransparentBackfaces: boolean;
         bumpFrequency: number;
         bumpAmplitude: number;
         quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";

package/lib/mol-canvas3d/helper/helper.d.ts

@@ -33,6 +33,7 @@ export declare const HelperParams: {
             flipSided: any;
             flatShaded: any;
             xrayShaded: any;
+            allowTransparentBackfaces: any;
             bumpFrequency: any;
             bumpAmplitude: any;
             quality: any;
@@ -65,6 +66,7 @@ export declare const DefaultHelperProps: PD.Values<{
             flipSided: any;
             flatShaded: any;
             xrayShaded: any;
+            allowTransparentBackfaces: any;
             bumpFrequency: any;
             bumpAmplitude: any;
             quality: any;

package/lib/mol-canvas3d/passes/image.d.ts

@@ -60,6 +60,7 @@ export declare const ImageParams: {
             flipSided: any;
             flatShaded: any;
             xrayShaded: any;
+            allowTransparentBackfaces: any;
             bumpFrequency: any;
             bumpAmplitude: any;
             quality: any;