molstar 3.3.1 → 3.6.0

package/lib/commonjs/mol-plugin-state/transforms/model.js

@@ -1,12 +1,12 @@
 "use strict";
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.StructureComplexElementTypes = exports.ShapeFromPly = exports.CustomStructureProperties = exports.CustomModelProperties = exports.StructureComponent = exports.StructureComplexElement = exports.StructureSelectionFromBundle = exports.StructureSelectionFromScript = exports.MultiStructureSelectionFromExpression = exports.StructureSelectionFromExpression = exports.TransformStructureConformation = exports.StructureFromModel = exports.StructureFromTrajectory = exports.ModelFromTrajectory = exports.TrajectoryFromCifCore = exports.TrajectoryFromCube = exports.TrajectoryFromMOL2 = exports.TrajectoryFromSDF = exports.TrajectoryFromMOL = exports.TrajectoryFromXYZ = exports.TrajectoryFromGRO = exports.TrajectoryFromPDB = exports.TrajectoryFromMmCif = exports.TrajectoryFromBlob = exports.TrajectoryFromModelAndCoordinates = exports.TopologyFromPsf = exports.CoordinatesFromXtc = exports.CoordinatesFromDcd = void 0;
+exports.StructureComplexElementTypes = exports.ShapeFromPly = exports.CustomStructureProperties = exports.CustomModelProperties = exports.StructureComponent = exports.StructureComplexElement = exports.StructureSelectionFromBundle = exports.StructureSelectionFromScript = exports.MultiStructureSelectionFromExpression = exports.StructureSelectionFromExpression = exports.TransformStructureConformation = exports.StructureFromModel = exports.StructureFromTrajectory = exports.ModelFromTrajectory = exports.TrajectoryFromCifCore = exports.TrajectoryFromCube = exports.TrajectoryFromMOL2 = exports.TrajectoryFromSDF = exports.TrajectoryFromMOL = exports.TrajectoryFromXYZ = exports.TrajectoryFromGRO = exports.TrajectoryFromPDB = exports.TrajectoryFromMmCif = exports.TrajectoryFromBlob = exports.TrajectoryFromModelAndCoordinates = exports.TopologyFromTop = exports.TopologyFromPrmtop = exports.TopologyFromPsf = exports.CoordinatesFromNctraj = exports.CoordinatesFromTrr = exports.CoordinatesFromXtc = exports.CoordinatesFromDcd = void 0;
 var tslib_1 = require("tslib");
 var parser_1 = require("../../mol-io/reader/dcd/parser");
 var parser_2 = require("../../mol-io/reader/gro/parser");
@@ -42,6 +42,13 @@ var parser_7 = require("../../mol-io/reader/xyz/parser");
 var xyz_1 = require("../../mol-model-formats/structure/xyz");
 var parser_8 = require("../../mol-io/reader/sdf/parser");
 var sdf_1 = require("../../mol-model-formats/structure/sdf");
+var type_helpers_1 = require("../../mol-util/type-helpers");
+var parser_9 = require("../../mol-io/reader/trr/parser");
+var trr_1 = require("../../mol-model-formats/structure/trr");
+var parser_10 = require("../../mol-io/reader/nctraj/parser");
+var nctraj_1 = require("../../mol-model-formats/structure/nctraj");
+var prmtop_1 = require("../../mol-model-formats/structure/prmtop");
+var top_1 = require("../../mol-model-formats/structure/top");
 var CoordinatesFromDcd = objects_1.PluginStateTransform.BuiltIn({
     name: 'coordinates-from-dcd',
     display: { name: 'Parse DCD', description: 'Parse DCD binary data.' },
@@ -51,9 +58,9 @@ var CoordinatesFromDcd = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a;
-        return mol_task_1.Task.create('Parse DCD', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse DCD', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var parsed, coordinates;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, (0, parser_1.parseDcd)(a.data).runInContext(ctx)];
                     case 1:
@@ -79,9 +86,9 @@ var CoordinatesFromXtc = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a;
-        return mol_task_1.Task.create('Parse XTC', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse XTC', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var parsed, coordinates;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, (0, parser_6.parseXtc)(a.data).runInContext(ctx)];
                     case 1:
@@ -98,18 +105,74 @@ var CoordinatesFromXtc = objects_1.PluginStateTransform.BuiltIn({
     }
 });
 exports.CoordinatesFromXtc = CoordinatesFromXtc;
+var CoordinatesFromTrr = objects_1.PluginStateTransform.BuiltIn({
+    name: 'coordinates-from-trr',
+    display: { name: 'Parse TRR', description: 'Parse TRR binary data.' },
+    from: [objects_1.PluginStateObject.Data.Binary],
+    to: objects_1.PluginStateObject.Molecule.Coordinates
+})({
+    apply: function (_a) {
+        var _this = this;
+        var a = _a.a;
+        return mol_task_1.Task.create('Parse TRR', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+            var parsed, coordinates;
+            return tslib_1.__generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, (0, parser_9.parseTrr)(a.data).runInContext(ctx)];
+                    case 1:
+                        parsed = _a.sent();
+                        if (parsed.isError)
+                            throw new Error(parsed.message);
+                        return [4 /*yield*/, (0, trr_1.coordinatesFromTrr)(parsed.result).runInContext(ctx)];
+                    case 2:
+                        coordinates = _a.sent();
+                        return [2 /*return*/, new objects_1.PluginStateObject.Molecule.Coordinates(coordinates, { label: a.label, description: 'Coordinates' })];
+                }
+            });
+        }); });
+    }
+});
+exports.CoordinatesFromTrr = CoordinatesFromTrr;
+var CoordinatesFromNctraj = objects_1.PluginStateTransform.BuiltIn({
+    name: 'coordinates-from-nctraj',
+    display: { name: 'Parse NCTRAJ', description: 'Parse NCTRAJ binary data.' },
+    from: [objects_1.PluginStateObject.Data.Binary],
+    to: objects_1.PluginStateObject.Molecule.Coordinates
+})({
+    apply: function (_a) {
+        var _this = this;
+        var a = _a.a;
+        return mol_task_1.Task.create('Parse NCTRAJ', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+            var parsed, coordinates;
+            return tslib_1.__generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, (0, parser_10.parseNctraj)(a.data).runInContext(ctx)];
+                    case 1:
+                        parsed = _a.sent();
+                        if (parsed.isError)
+                            throw new Error(parsed.message);
+                        return [4 /*yield*/, (0, nctraj_1.coordinatesFromNctraj)(parsed.result).runInContext(ctx)];
+                    case 2:
+                        coordinates = _a.sent();
+                        return [2 /*return*/, new objects_1.PluginStateObject.Molecule.Coordinates(coordinates, { label: a.label, description: 'Coordinates' })];
+                }
+            });
+        }); });
+    }
+});
+exports.CoordinatesFromNctraj = CoordinatesFromNctraj;
 var TopologyFromPsf = objects_1.PluginStateTransform.BuiltIn({
     name: 'topology-from-psf',
-    display: { name: 'PSF Topology', description: 'Parse PSF string data.' },
+    display: { name: 'PSF Topology', description: 'Create topology from PSF.' },
     from: [objects_1.PluginStateObject.Format.Psf],
     to: objects_1.PluginStateObject.Molecule.Topology
 })({
     apply: function (_a) {
         var _this = this;
         var a = _a.a;
-        return mol_task_1.Task.create('Create Topology', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Create Topology', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var topology;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, (0, psf_1.topologyFromPsf)(a.data).runInContext(ctx)];
                     case 1:
@@ -121,10 +184,56 @@ var TopologyFromPsf = objects_1.PluginStateTransform.BuiltIn({
     }
 });
 exports.TopologyFromPsf = TopologyFromPsf;
+var TopologyFromPrmtop = objects_1.PluginStateTransform.BuiltIn({
+    name: 'topology-from-prmtop',
+    display: { name: 'PRMTOP Topology', description: 'Create topology from PRMTOP.' },
+    from: [objects_1.PluginStateObject.Format.Prmtop],
+    to: objects_1.PluginStateObject.Molecule.Topology
+})({
+    apply: function (_a) {
+        var _this = this;
+        var a = _a.a;
+        return mol_task_1.Task.create('Create Topology', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+            var topology;
+            return tslib_1.__generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, (0, prmtop_1.topologyFromPrmtop)(a.data).runInContext(ctx)];
+                    case 1:
+                        topology = _a.sent();
+                        return [2 /*return*/, new objects_1.PluginStateObject.Molecule.Topology(topology, { label: topology.label || a.label, description: 'Topology' })];
+                }
+            });
+        }); });
+    }
+});
+exports.TopologyFromPrmtop = TopologyFromPrmtop;
+var TopologyFromTop = objects_1.PluginStateTransform.BuiltIn({
+    name: 'topology-from-top',
+    display: { name: 'TOP Topology', description: 'Create topology from TOP.' },
+    from: [objects_1.PluginStateObject.Format.Top],
+    to: objects_1.PluginStateObject.Molecule.Topology
+})({
+    apply: function (_a) {
+        var _this = this;
+        var a = _a.a;
+        return mol_task_1.Task.create('Create Topology', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+            var topology;
+            return tslib_1.__generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, (0, top_1.topologyFromTop)(a.data).runInContext(ctx)];
+                    case 1:
+                        topology = _a.sent();
+                        return [2 /*return*/, new objects_1.PluginStateObject.Molecule.Topology(topology, { label: topology.label || a.label, description: 'Topology' })];
+                }
+            });
+        }); });
+    }
+});
+exports.TopologyFromTop = TopologyFromTop;
 function getTrajectory(ctx, obj, coordinates) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var topology, model;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     if (!(obj.type === objects_1.PluginStateObject.Molecule.Topology.type)) return [3 /*break*/, 2];
@@ -155,9 +264,9 @@ var TrajectoryFromModelAndCoordinates = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var params = _a.params, dependencies = _a.dependencies;
-        return mol_task_1.Task.create('Create trajectory from model/topology and coordinates', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Create trajectory from model/topology and coordinates', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var coordinates, trajectory, props;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         coordinates = dependencies[params.coordinatesRef].data;
@@ -181,9 +290,9 @@ var TrajectoryFromBlob = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a;
-        return mol_task_1.Task.create('Parse Format Blob', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse Format Blob', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var models, _i, _a, e, block, xs, i, x, i, props;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         models = [];
@@ -252,9 +361,9 @@ var TrajectoryFromMmCif = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a, params = _a.params;
-        return mol_task_1.Task.create('Parse mmCIF', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse mmCIF', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var header, block, models, props;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         header = params.blockHeader || a.data.blocks[0].header;
@@ -286,9 +395,9 @@ var TrajectoryFromPDB = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a, params = _a.params;
-        return mol_task_1.Task.create('Parse PDB', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse PDB', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var parsed, models, props;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, (0, parser_3.parsePDB)(a.data, a.label, params.isPdbqt).runInContext(ctx)];
                     case 1:
@@ -315,9 +424,9 @@ var TrajectoryFromGRO = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a;
-        return mol_task_1.Task.create('Parse GRO', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse GRO', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var parsed, models, props;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, (0, parser_2.parseGRO)(a.data).runInContext(ctx)];
                     case 1:
@@ -344,9 +453,9 @@ var TrajectoryFromXYZ = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a;
-        return mol_task_1.Task.create('Parse XYZ', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse XYZ', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var parsed, models, props;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, (0, parser_7.parseXyz)(a.data).runInContext(ctx)];
                     case 1:
@@ -373,9 +482,9 @@ var TrajectoryFromMOL = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a;
-        return mol_task_1.Task.create('Parse MOL', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse MOL', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var parsed, models, props;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, (0, parser_4.parseMol)(a.data).runInContext(ctx)];
                     case 1:
@@ -402,9 +511,9 @@ var TrajectoryFromSDF = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a;
-        return mol_task_1.Task.create('Parse SDF', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse SDF', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var parsed, models, _i, _a, compound, traj_1, i, _b, _c, traj, props;
-            return (0, tslib_1.__generator)(this, function (_d) {
+            return tslib_1.__generator(this, function (_d) {
                 switch (_d.label) {
                     case 0: return [4 /*yield*/, (0, parser_8.parseSdf)(a.data).runInContext(ctx)];
                     case 1:
@@ -454,9 +563,9 @@ var TrajectoryFromMOL2 = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a;
-        return mol_task_1.Task.create('Parse MOL2', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse MOL2', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var parsed, models, props;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, (0, parser_5.parseMol2)(a.data, a.label).runInContext(ctx)];
                     case 1:
@@ -483,9 +592,9 @@ var TrajectoryFromCube = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a;
-        return mol_task_1.Task.create('Parse MOL', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse MOL', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var models, props;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, (0, cube_1.trajectoryFromCube)(a.data).runInContext(ctx)];
                     case 1:
@@ -518,9 +627,9 @@ var TrajectoryFromCifCore = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a, params = _a.params;
-        return mol_task_1.Task.create('Parse CIF Core', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse CIF Core', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var header, block, models, props;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         header = params.blockHeader || a.data.blocks[0].header;
@@ -557,9 +666,9 @@ var ModelFromTrajectory = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a, params = _a.params;
-        return mol_task_1.Task.create('Model from Trajectory', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Model from Trajectory', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var modelIndex, model, label, description;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         modelIndex = params.modelIndex % a.data.frameCount;
@@ -594,9 +703,9 @@ var StructureFromTrajectory = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a;
-        return mol_task_1.Task.create('Build Structure', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Build Structure', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var s, props;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, structure_1.Structure.ofTrajectory(a.data, ctx)];
                     case 1:
@@ -627,8 +736,8 @@ var StructureFromModel = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a, plugin) {
         var _this = this;
         var a = _a.a, params = _a.params;
-        return mol_task_1.Task.create('Build Structure', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-            return (0, tslib_1.__generator)(this, function (_a) {
+        return mol_task_1.Task.create('Build Structure', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+            return tslib_1.__generator(this, function (_a) {
                 return [2 /*return*/, root_structure_1.RootStructureDefinition.create(plugin, ctx, a.data, params && params.type)];
             });
         }); });
@@ -1031,7 +1140,7 @@ var StructureComplexElement = objects_1.PluginStateTransform.BuiltIn({
                 query = structure_1.Queries.internal.spheres();
                 label = 'Coarse Spheres';
                 break;
-            default: throw new Error("".concat(params.type, " is a not valid complex element."));
+            default: (0, type_helpers_1.assertUnreachable)(params.type);
         }
         var result = query(new structure_1.QueryContext(a.data));
         var s = structure_1.StructureSelection.unionStructure(result);
@@ -1079,8 +1188,8 @@ var CustomModelProperties = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a, ctx) {
         var _this = this;
         var a = _a.a, params = _a.params;
-        return mol_task_1.Task.create('Custom Props', function (taskCtx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-            return (0, tslib_1.__generator)(this, function (_a) {
+        return mol_task_1.Task.create('Custom Props', function (taskCtx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, attachModelProps(a.data, ctx, taskCtx, params)];
                     case 1:
@@ -1093,9 +1202,9 @@ var CustomModelProperties = objects_1.PluginStateTransform.BuiltIn({
     update: function (_a, ctx) {
         var _this = this;
         var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
-        return mol_task_1.Task.create('Custom Props', function (taskCtx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Custom Props', function (taskCtx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var _i, _a, name_1, property;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         b.data = a.data;
@@ -1123,9 +1232,9 @@ var CustomModelProperties = objects_1.PluginStateTransform.BuiltIn({
 });
 exports.CustomModelProperties = CustomModelProperties;
 function attachModelProps(model, ctx, taskCtx, params) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var propertyCtx, autoAttach, properties, _i, _a, name_2, property, props, e_1;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     propertyCtx = { runtime: taskCtx, assetManager: ctx.managers.asset };
@@ -1174,8 +1283,8 @@ var CustomStructureProperties = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a, ctx) {
         var _this = this;
         var a = _a.a, params = _a.params;
-        return mol_task_1.Task.create('Custom Props', function (taskCtx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-            return (0, tslib_1.__generator)(this, function (_a) {
+        return mol_task_1.Task.create('Custom Props', function (taskCtx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, attachStructureProps(a.data.root, ctx, taskCtx, params)];
                     case 1:
@@ -1190,9 +1299,9 @@ var CustomStructureProperties = objects_1.PluginStateTransform.BuiltIn({
         var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
         if (a.data !== b.data)
             return mol_state_1.StateTransformer.UpdateResult.Recreate;
-        return mol_task_1.Task.create('Custom Props', function (taskCtx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Custom Props', function (taskCtx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var _i, _a, name_3, property;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         b.data = a.data;
@@ -1220,9 +1329,9 @@ var CustomStructureProperties = objects_1.PluginStateTransform.BuiltIn({
 });
 exports.CustomStructureProperties = CustomStructureProperties;
 function attachStructureProps(structure, ctx, taskCtx, params) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var propertyCtx, autoAttach, properties, _i, _a, name_4, property, props, e_2;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     propertyCtx = { runtime: taskCtx, assetManager: ctx.managers.asset };
@@ -1270,9 +1379,9 @@ var ShapeFromPly = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a, params = _a.params;
-        return mol_task_1.Task.create('Create shape from PLY', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Create shape from PLY', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var shape, props;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, (0, ply_1.shapeFromPly)(a.data, params).runInContext(ctx)];
                     case 1:

package/lib/commonjs/mol-plugin-state/transforms/representation.d.ts

@@ -150,6 +150,7 @@ declare const ModelUnitcell3D: StateTransformer<SO.Molecule.Model, SO.Shape.Repr
     flatShaded: boolean;
     ignoreLight: boolean;
     xrayShaded: boolean;
+    allowTransparentBackfaces: boolean;
     bumpFrequency: number;
     bumpAmplitude: number;
     alpha: number;
@@ -172,6 +173,7 @@ declare const StructureBoundingBox3D: StateTransformer<SO.Molecule.Structure, SO
     flatShaded: boolean;
     ignoreLight: boolean;
     xrayShaded: boolean;
+    allowTransparentBackfaces: boolean;
     bumpFrequency: number;
     bumpAmplitude: number;
     alpha: number;
@@ -276,6 +278,7 @@ declare const StructureSelectionsAngle3D: StateTransformer<SO.Molecule.Structure
     flipSided: boolean;
     flatShaded: boolean;
     xrayShaded: boolean;
+    allowTransparentBackfaces: boolean;
     bumpFrequency: number;
     bumpAmplitude: number;
     lineSizeAttenuation: boolean;
@@ -327,6 +330,7 @@ declare const StructureSelectionsDihedral3D: StateTransformer<SO.Molecule.Struct
     flipSided: boolean;
     flatShaded: boolean;
     xrayShaded: boolean;
+    allowTransparentBackfaces: boolean;
     bumpFrequency: number;
     bumpAmplitude: number;
     lineSizeAttenuation: boolean;
@@ -384,6 +388,7 @@ declare const StructureSelectionsOrientation3D: StateTransformer<SO.Molecule.Str
     flatShaded: boolean;
     ignoreLight: boolean;
     xrayShaded: boolean;
+    allowTransparentBackfaces: boolean;
     bumpFrequency: number;
     bumpAmplitude: number;
     alpha: number;
@@ -409,6 +414,7 @@ declare const StructureSelectionsPlane3D: StateTransformer<SO.Molecule.Structure
     flatShaded: boolean;
     ignoreLight: boolean;
     xrayShaded: boolean;
+    allowTransparentBackfaces: boolean;
     bumpFrequency: number;
     bumpAmplitude: number;
     alpha: number;