molstar 3.3.0 → 3.5.0

package/lib/commonjs/mol-plugin-state/objects.js

@@ -1,6 +1,6 @@
 "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>
@@ -21,15 +21,15 @@ var PluginStateObject;
     }
     PluginStateObject.isBehavior = isBehavior;
     function CreateRepresentation3D(type) {
-        return PluginStateObject.Create((0, tslib_1.__assign)((0, tslib_1.__assign)({}, type), { typeClass: 'Representation3D' }));
+        return PluginStateObject.Create(tslib_1.__assign(tslib_1.__assign({}, type), { typeClass: 'Representation3D' }));
     }
     PluginStateObject.CreateRepresentation3D = CreateRepresentation3D;
     function CreateBehavior(type) {
-        return PluginStateObject.Create((0, tslib_1.__assign)((0, tslib_1.__assign)({}, type), { typeClass: 'Behavior' }));
+        return PluginStateObject.Create(tslib_1.__assign(tslib_1.__assign({}, type), { typeClass: 'Behavior' }));
     }
     PluginStateObject.CreateBehavior = CreateBehavior;
     var Root = /** @class */ (function (_super) {
-        (0, tslib_1.__extends)(Root, _super);
+        tslib_1.__extends(Root, _super);
         function Root() {
             return _super !== null && _super.apply(this, arguments) || this;
         }
@@ -37,7 +37,7 @@ var PluginStateObject;
     }(PluginStateObject.Create({ name: 'Root', typeClass: 'Root' })));
     PluginStateObject.Root = Root;
     var Group = /** @class */ (function (_super) {
-        (0, tslib_1.__extends)(Group, _super);
+        tslib_1.__extends(Group, _super);
         function Group() {
             return _super !== null && _super.apply(this, arguments) || this;
         }
@@ -47,7 +47,7 @@ var PluginStateObject;
     var Data;
     (function (Data) {
         var String = /** @class */ (function (_super) {
-            (0, tslib_1.__extends)(String, _super);
+            tslib_1.__extends(String, _super);
             function String() {
                 return _super !== null && _super.apply(this, arguments) || this;
             }
@@ -55,7 +55,7 @@ var PluginStateObject;
         }(PluginStateObject.Create({ name: 'String Data', typeClass: 'Data', })));
         Data.String = String;
         var Binary = /** @class */ (function (_super) {
-            (0, tslib_1.__extends)(Binary, _super);
+            tslib_1.__extends(Binary, _super);
             function Binary() {
                 return _super !== null && _super.apply(this, arguments) || this;
             }
@@ -63,7 +63,7 @@ var PluginStateObject;
         }(PluginStateObject.Create({ name: 'Binary Data', typeClass: 'Data' })));
         Data.Binary = Binary;
         var Blob = /** @class */ (function (_super) {
-            (0, tslib_1.__extends)(Blob, _super);
+            tslib_1.__extends(Blob, _super);
             function Blob() {
                 return _super !== null && _super.apply(this, arguments) || this;
             }
@@ -74,7 +74,7 @@ var PluginStateObject;
     var Format;
     (function (Format) {
         var Json = /** @class */ (function (_super) {
-            (0, tslib_1.__extends)(Json, _super);
+            tslib_1.__extends(Json, _super);
             function Json() {
                 return _super !== null && _super.apply(this, arguments) || this;
             }
@@ -82,7 +82,7 @@ var PluginStateObject;
         }(PluginStateObject.Create({ name: 'JSON Data', typeClass: 'Data' })));
         Format.Json = Json;
         var Cif = /** @class */ (function (_super) {
-            (0, tslib_1.__extends)(Cif, _super);
+            tslib_1.__extends(Cif, _super);
             function Cif() {
                 return _super !== null && _super.apply(this, arguments) || this;
             }
@@ -90,7 +90,7 @@ var PluginStateObject;
         }(PluginStateObject.Create({ name: 'CIF File', typeClass: 'Data' })));
         Format.Cif = Cif;
         var Cube = /** @class */ (function (_super) {
-            (0, tslib_1.__extends)(Cube, _super);
+            tslib_1.__extends(Cube, _super);
             function Cube() {
                 return _super !== null && _super.apply(this, arguments) || this;
             }
@@ -98,15 +98,31 @@ var PluginStateObject;
         }(PluginStateObject.Create({ name: 'Cube File', typeClass: 'Data' })));
         Format.Cube = Cube;
         var Psf = /** @class */ (function (_super) {
-            (0, tslib_1.__extends)(Psf, _super);
+            tslib_1.__extends(Psf, _super);
             function Psf() {
                 return _super !== null && _super.apply(this, arguments) || this;
             }
             return Psf;
         }(PluginStateObject.Create({ name: 'PSF File', typeClass: 'Data' })));
         Format.Psf = Psf;
+        var Prmtop = /** @class */ (function (_super) {
+            tslib_1.__extends(Prmtop, _super);
+            function Prmtop() {
+                return _super !== null && _super.apply(this, arguments) || this;
+            }
+            return Prmtop;
+        }(PluginStateObject.Create({ name: 'PRMTOP File', typeClass: 'Data' })));
+        Format.Prmtop = Prmtop;
+        var Top = /** @class */ (function (_super) {
+            tslib_1.__extends(Top, _super);
+            function Top() {
+                return _super !== null && _super.apply(this, arguments) || this;
+            }
+            return Top;
+        }(PluginStateObject.Create({ name: 'TOP File', typeClass: 'Data' })));
+        Format.Top = Top;
         var Ply = /** @class */ (function (_super) {
-            (0, tslib_1.__extends)(Ply, _super);
+            tslib_1.__extends(Ply, _super);
             function Ply() {
                 return _super !== null && _super.apply(this, arguments) || this;
             }
@@ -114,7 +130,7 @@ var PluginStateObject;
         }(PluginStateObject.Create({ name: 'PLY File', typeClass: 'Data' })));
         Format.Ply = Ply;
         var Ccp4 = /** @class */ (function (_super) {
-            (0, tslib_1.__extends)(Ccp4, _super);
+            tslib_1.__extends(Ccp4, _super);
             function Ccp4() {
                 return _super !== null && _super.apply(this, arguments) || this;
             }
@@ -122,7 +138,7 @@ var PluginStateObject;
         }(PluginStateObject.Create({ name: 'CCP4/MRC/MAP File', typeClass: 'Data' })));
         Format.Ccp4 = Ccp4;
         var Dsn6 = /** @class */ (function (_super) {
-            (0, tslib_1.__extends)(Dsn6, _super);
+            tslib_1.__extends(Dsn6, _super);
             function Dsn6() {
                 return _super !== null && _super.apply(this, arguments) || this;
             }
@@ -130,7 +146,7 @@ var PluginStateObject;
         }(PluginStateObject.Create({ name: 'DSN6/BRIX File', typeClass: 'Data' })));
         Format.Dsn6 = Dsn6;
         var Dx = /** @class */ (function (_super) {
-            (0, tslib_1.__extends)(Dx, _super);
+            tslib_1.__extends(Dx, _super);
             function Dx() {
                 return _super !== null && _super.apply(this, arguments) || this;
             }
@@ -138,7 +154,7 @@ var PluginStateObject;
         }(PluginStateObject.Create({ name: 'DX File', typeClass: 'Data' })));
         Format.Dx = Dx;
         var Blob = /** @class */ (function (_super) {
-            (0, tslib_1.__extends)(Blob, _super);
+            tslib_1.__extends(Blob, _super);
             function Blob() {
                 return _super !== null && _super.apply(this, arguments) || this;
             }
@@ -149,7 +165,7 @@ var PluginStateObject;
     var Molecule;
     (function (Molecule) {
         var Coordinates = /** @class */ (function (_super) {
-            (0, tslib_1.__extends)(Coordinates, _super);
+            tslib_1.__extends(Coordinates, _super);
             function Coordinates() {
                 return _super !== null && _super.apply(this, arguments) || this;
             }
@@ -157,7 +173,7 @@ var PluginStateObject;
         }(PluginStateObject.Create({ name: 'Coordinates', typeClass: 'Object' })));
         Molecule.Coordinates = Coordinates;
         var Topology = /** @class */ (function (_super) {
-            (0, tslib_1.__extends)(Topology, _super);
+            tslib_1.__extends(Topology, _super);
             function Topology() {
                 return _super !== null && _super.apply(this, arguments) || this;
             }
@@ -165,7 +181,7 @@ var PluginStateObject;
         }(PluginStateObject.Create({ name: 'Topology', typeClass: 'Object' })));
         Molecule.Topology = Topology;
         var Model = /** @class */ (function (_super) {
-            (0, tslib_1.__extends)(Model, _super);
+            tslib_1.__extends(Model, _super);
             function Model() {
                 return _super !== null && _super.apply(this, arguments) || this;
             }
@@ -173,7 +189,7 @@ var PluginStateObject;
         }(PluginStateObject.Create({ name: 'Model', typeClass: 'Object' })));
         Molecule.Model = Model;
         var Trajectory = /** @class */ (function (_super) {
-            (0, tslib_1.__extends)(Trajectory, _super);
+            tslib_1.__extends(Trajectory, _super);
             function Trajectory() {
                 return _super !== null && _super.apply(this, arguments) || this;
             }
@@ -181,7 +197,7 @@ var PluginStateObject;
         }(PluginStateObject.Create({ name: 'Trajectory', typeClass: 'Object' })));
         Molecule.Trajectory = Trajectory;
         var Structure = /** @class */ (function (_super) {
-            (0, tslib_1.__extends)(Structure, _super);
+            tslib_1.__extends(Structure, _super);
             function Structure() {
                 return _super !== null && _super.apply(this, arguments) || this;
             }
@@ -190,7 +206,7 @@ var PluginStateObject;
         Molecule.Structure = Structure;
         (function (Structure) {
             var Representation3D = /** @class */ (function (_super) {
-                (0, tslib_1.__extends)(Representation3D, _super);
+                tslib_1.__extends(Representation3D, _super);
                 function Representation3D() {
                     return _super !== null && _super.apply(this, arguments) || this;
                 }
@@ -198,7 +214,7 @@ var PluginStateObject;
             }(CreateRepresentation3D({ name: 'Structure 3D' })));
             Structure.Representation3D = Representation3D;
             var Representation3DState = /** @class */ (function (_super) {
-                (0, tslib_1.__extends)(Representation3DState, _super);
+                tslib_1.__extends(Representation3DState, _super);
                 function Representation3DState() {
                     return _super !== null && _super.apply(this, arguments) || this;
                 }
@@ -206,7 +222,7 @@ var PluginStateObject;
             }(PluginStateObject.Create({ name: 'Structure 3D State', typeClass: 'Object' })));
             Structure.Representation3DState = Representation3DState;
             var Selections = /** @class */ (function (_super) {
-                (0, tslib_1.__extends)(Selections, _super);
+                tslib_1.__extends(Selections, _super);
                 function Selections() {
                     return _super !== null && _super.apply(this, arguments) || this;
                 }
@@ -218,7 +234,7 @@ var PluginStateObject;
     var Volume;
     (function (Volume) {
         var Data = /** @class */ (function (_super) {
-            (0, tslib_1.__extends)(Data, _super);
+            tslib_1.__extends(Data, _super);
             function Data() {
                 return _super !== null && _super.apply(this, arguments) || this;
             }
@@ -226,7 +242,7 @@ var PluginStateObject;
         }(PluginStateObject.Create({ name: 'Volume', typeClass: 'Object' })));
         Volume.Data = Data;
         var Lazy = /** @class */ (function (_super) {
-            (0, tslib_1.__extends)(Lazy, _super);
+            tslib_1.__extends(Lazy, _super);
             function Lazy() {
                 return _super !== null && _super.apply(this, arguments) || this;
             }
@@ -234,7 +250,7 @@ var PluginStateObject;
         }(PluginStateObject.Create({ name: 'Lazy Volume', typeClass: 'Object' })));
         Volume.Lazy = Lazy;
         var Representation3D = /** @class */ (function (_super) {
-            (0, tslib_1.__extends)(Representation3D, _super);
+            tslib_1.__extends(Representation3D, _super);
             function Representation3D() {
                 return _super !== null && _super.apply(this, arguments) || this;
             }
@@ -245,7 +261,7 @@ var PluginStateObject;
     var Shape;
     (function (Shape) {
         var Provider = /** @class */ (function (_super) {
-            (0, tslib_1.__extends)(Provider, _super);
+            tslib_1.__extends(Provider, _super);
             function Provider() {
                 return _super !== null && _super.apply(this, arguments) || this;
             }
@@ -253,7 +269,7 @@ var PluginStateObject;
         }(PluginStateObject.Create({ name: 'Shape Provider', typeClass: 'Object' })));
         Shape.Provider = Provider;
         var Representation3D = /** @class */ (function (_super) {
-            (0, tslib_1.__extends)(Representation3D, _super);
+            tslib_1.__extends(Representation3D, _super);
             function Representation3D() {
                 return _super !== null && _super.apply(this, arguments) || this;
             }

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

@@ -16,6 +16,8 @@ export { ParseBlob };
 export { ParseCif };
 export { ParseCube };
 export { ParsePsf };
+export { ParsePrmtop };
+export { ParseTop };
 export { ParsePly };
 export { ParseCcp4 };
 export { ParseDsn6 };
@@ -64,6 +66,10 @@ declare type ParseCube = typeof ParseCube;
 declare const ParseCube: StateTransformer<SO.Data.String, SO.Format.Cube, PD.Normalize<{}>>;
 declare type ParsePsf = typeof ParsePsf;
 declare const ParsePsf: StateTransformer<SO.Data.String, SO.Format.Psf, PD.Normalize<{}>>;
+declare type ParsePrmtop = typeof ParsePrmtop;
+declare const ParsePrmtop: StateTransformer<SO.Data.String, SO.Format.Prmtop, PD.Normalize<{}>>;
+declare type ParseTop = typeof ParseTop;
+declare const ParseTop: StateTransformer<SO.Data.String, SO.Format.Top, PD.Normalize<{}>>;
 declare type ParsePly = typeof ParsePly;
 declare const ParsePly: StateTransformer<SO.Data.String, SO.Format.Ply, PD.Normalize<{}>>;
 declare type ParseCcp4 = typeof ParseCcp4;

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

@@ -6,12 +6,12 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.LazyVolume = exports.ParseJson = exports.ImportJson = exports.ImportString = exports.ParseDx = exports.ParseDsn6 = exports.ParseCcp4 = exports.ParsePly = exports.ParsePsf = exports.ParseCube = exports.ParseCif = exports.ParseBlob = exports.ReadFile = exports.RawData = exports.DownloadBlob = exports.Download = void 0;
+exports.LazyVolume = exports.ParseJson = exports.ImportJson = exports.ImportString = exports.ParseDx = exports.ParseDsn6 = exports.ParseCcp4 = exports.ParsePly = exports.ParseTop = exports.ParsePrmtop = exports.ParsePsf = exports.ParseCube = exports.ParseCif = exports.ParseBlob = exports.ReadFile = exports.RawData = exports.DownloadBlob = exports.Download = void 0;
 var tslib_1 = require("tslib");
-var CCP4 = (0, tslib_1.__importStar)(require("../../mol-io/reader/ccp4/parser"));
+var CCP4 = tslib_1.__importStar(require("../../mol-io/reader/ccp4/parser"));
 var cif_1 = require("../../mol-io/reader/cif");
-var DSN6 = (0, tslib_1.__importStar)(require("../../mol-io/reader/dsn6/parser"));
-var PLY = (0, tslib_1.__importStar)(require("../../mol-io/reader/ply/parser"));
+var DSN6 = tslib_1.__importStar(require("../../mol-io/reader/dsn6/parser"));
+var PLY = tslib_1.__importStar(require("../../mol-io/reader/ply/parser"));
 var parser_1 = require("../../mol-io/reader/psf/parser");
 var mol_state_1 = require("../../mol-state");
 var mol_task_1 = require("../../mol-task");
@@ -22,6 +22,9 @@ var assets_1 = require("../../mol-util/assets");
 var parser_2 = require("../../mol-io/reader/cube/parser");
 var parser_3 = require("../../mol-io/reader/dx/parser");
 var names_1 = require("../../mol-util/color/names");
+var type_helpers_1 = require("../../mol-util/type-helpers");
+var parser_4 = require("../../mol-io/reader/prmtop/parser");
+var parser_5 = require("../../mol-io/reader/top/parser");
 var Download = objects_1.PluginStateTransform.BuiltIn({
     name: 'download',
     display: { name: 'Download', description: 'Download string or binary data from the specified URL' },
@@ -36,9 +39,9 @@ var Download = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a, plugin) {
         var _this = this;
         var p = _a.params, cache = _a.cache;
-        return mol_task_1.Task.create('Download', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Download', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var url, asset;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         url = assets_1.Asset.getUrlAsset(plugin.managers.asset, p.url);
@@ -54,9 +57,9 @@ var Download = objects_1.PluginStateTransform.BuiltIn({
         }); });
     },
     dispose: function (_a) {
-        var _b, _c;
+        var _b;
         var cache = _a.cache;
-        (_c = (_b = cache) === null || _b === void 0 ? void 0 : _b.asset) === null || _c === void 0 ? void 0 : _c.dispose();
+        (_b = cache === null || cache === void 0 ? void 0 : cache.asset) === null || _b === void 0 ? void 0 : _b.dispose();
     },
     update: function (_a) {
         var oldParams = _a.oldParams, newParams = _a.newParams, b = _a.b;
@@ -88,9 +91,9 @@ var DownloadBlob = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a, plugin) {
         var _this = this;
         var params = _a.params, cache = _a.cache;
-        return mol_task_1.Task.create('Download Blob', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Download Blob', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var entries, data, assets, i, r, src;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         entries = [];
@@ -116,13 +119,12 @@ var DownloadBlob = objects_1.PluginStateTransform.BuiltIn({
         }); });
     },
     dispose: function (_a, plugin) {
-        var _b;
         var cache = _a.cache;
-        var assets = (_b = cache) === null || _b === void 0 ? void 0 : _b.assets;
+        var assets = cache === null || cache === void 0 ? void 0 : cache.assets;
         if (!assets)
             return;
-        for (var _c = 0, assets_2 = assets; _c < assets_2.length; _c++) {
-            var a = assets_2[_c];
+        for (var _b = 0, assets_2 = assets; _b < assets_2.length; _b++) {
+            var a = assets_2[_b];
             a.dispose();
         }
     }
@@ -151,8 +153,8 @@ var RawData = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var p = _a.params;
-        return mol_task_1.Task.create('Raw Data', function () { 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('Raw Data', function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+            return tslib_1.__generator(this, function (_a) {
                 if (typeof p.data === 'string') {
                     return [2 /*return*/, new objects_1.PluginStateObject.Data.String(p.data, { label: p.label ? p.label : 'String' })];
                 }
@@ -166,7 +168,7 @@ var RawData = objects_1.PluginStateTransform.BuiltIn({
                     return [2 /*return*/, new objects_1.PluginStateObject.Data.Binary(p.data, { label: p.label ? p.label : 'Binary' })];
                 }
                 else {
-                    throw new Error('Supplied binary data must be a plain array, ArrayBuffer, or Uint8Array.');
+                    (0, type_helpers_1.assertUnreachable)(p.data);
                 }
                 return [2 /*return*/];
             });
@@ -221,9 +223,9 @@ var ReadFile = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a, plugin) {
         var _this = this;
         var p = _a.params, cache = _a.cache;
-        return mol_task_1.Task.create('Open File', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Open File', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var asset, o;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         if (p.file === null) {
@@ -243,9 +245,9 @@ var ReadFile = objects_1.PluginStateTransform.BuiltIn({
         }); });
     },
     dispose: function (_a) {
-        var _b, _c;
+        var _b;
         var cache = _a.cache;
-        (_c = (_b = cache) === null || _b === void 0 ? void 0 : _b.asset) === null || _c === void 0 ? void 0 : _c.dispose();
+        (_b = cache === null || cache === void 0 ? void 0 : cache.asset) === null || _b === void 0 ? void 0 : _b.dispose();
     },
     update: function (_a) {
         var _b;
@@ -274,9 +276,9 @@ var ParseBlob = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a, plugin) {
         var _this = this;
         var a = _a.a, params = _a.params;
-        return mol_task_1.Task.create('Parse Blob', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse Blob', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var map, _a, _b, f, entries, _c, _d, e, parsed;
-            return (0, tslib_1.__generator)(this, function (_e) {
+            return tslib_1.__generator(this, function (_e) {
                 switch (_e.label) {
                     case 0:
                         map = new Map();
@@ -328,9 +330,9 @@ var ParseCif = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a;
-        return mol_task_1.Task.create('Parse CIF', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse CIF', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var parsed;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, (objects_1.PluginStateObject.Data.String.is(a) ? cif_1.CIF.parse(a.data) : cif_1.CIF.parseBinary(a.data)).runInContext(ctx)];
                     case 1:
@@ -353,9 +355,9 @@ var ParseCube = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a;
-        return mol_task_1.Task.create('Parse Cube', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse Cube', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var parsed;
-            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.parseCube)(a.data, a.label).runInContext(ctx)];
                     case 1:
@@ -378,9 +380,9 @@ var ParsePsf = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a;
-        return mol_task_1.Task.create('Parse PSF', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse PSF', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var parsed;
-            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.parsePsf)(a.data).runInContext(ctx)];
                     case 1:
@@ -394,6 +396,56 @@ var ParsePsf = objects_1.PluginStateTransform.BuiltIn({
     }
 });
 exports.ParsePsf = ParsePsf;
+var ParsePrmtop = objects_1.PluginStateTransform.BuiltIn({
+    name: 'parse-prmtop',
+    display: { name: 'Parse PRMTOP', description: 'Parse PRMTOP from String data' },
+    from: [objects_1.PluginStateObject.Data.String],
+    to: objects_1.PluginStateObject.Format.Prmtop
+})({
+    apply: function (_a) {
+        var _this = this;
+        var a = _a.a;
+        return mol_task_1.Task.create('Parse PRMTOP', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+            var parsed;
+            return tslib_1.__generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, (0, parser_4.parsePrmtop)(a.data).runInContext(ctx)];
+                    case 1:
+                        parsed = _a.sent();
+                        if (parsed.isError)
+                            throw new Error(parsed.message);
+                        return [2 /*return*/, new objects_1.PluginStateObject.Format.Prmtop(parsed.result)];
+                }
+            });
+        }); });
+    }
+});
+exports.ParsePrmtop = ParsePrmtop;
+var ParseTop = objects_1.PluginStateTransform.BuiltIn({
+    name: 'parse-top',
+    display: { name: 'Parse TOP', description: 'Parse TOP from String data' },
+    from: [objects_1.PluginStateObject.Data.String],
+    to: objects_1.PluginStateObject.Format.Top
+})({
+    apply: function (_a) {
+        var _this = this;
+        var a = _a.a;
+        return mol_task_1.Task.create('Parse TOP', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+            var parsed;
+            return tslib_1.__generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, (0, parser_5.parseTop)(a.data).runInContext(ctx)];
+                    case 1:
+                        parsed = _a.sent();
+                        if (parsed.isError)
+                            throw new Error(parsed.message);
+                        return [2 /*return*/, new objects_1.PluginStateObject.Format.Top(parsed.result)];
+                }
+            });
+        }); });
+    }
+});
+exports.ParseTop = ParseTop;
 var ParsePly = objects_1.PluginStateTransform.BuiltIn({
     name: 'parse-ply',
     display: { name: 'Parse PLY', description: 'Parse PLY from String data' },
@@ -403,9 +455,9 @@ var ParsePly = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a;
-        return mol_task_1.Task.create('Parse PLY', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse PLY', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var parsed;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, PLY.parsePly(a.data).runInContext(ctx)];
                     case 1:
@@ -428,9 +480,9 @@ var ParseCcp4 = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a;
-        return mol_task_1.Task.create('Parse CCP4/MRC/MAP', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse CCP4/MRC/MAP', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var parsed;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, CCP4.parse(a.data, a.label).runInContext(ctx)];
                     case 1:
@@ -453,9 +505,9 @@ var ParseDsn6 = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a;
-        return mol_task_1.Task.create('Parse DSN6/BRIX', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse DSN6/BRIX', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var parsed;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, DSN6.parse(a.data, a.label).runInContext(ctx)];
                     case 1:
@@ -478,9 +530,9 @@ var ParseDx = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a;
-        return mol_task_1.Task.create('Parse DX', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse DX', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var parsed;
-            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.parseDx)(a.data, a.label).runInContext(ctx)];
                     case 1:
@@ -557,9 +609,9 @@ var ParseJson = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a;
-        return mol_task_1.Task.create('Parse JSON', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse JSON', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var json;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, (new Response(a.data)).json()];
                     case 1:
@@ -593,9 +645,9 @@ var LazyVolume = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a, params = _a.params;
-        return mol_task_1.Task.create('Lazy Volume', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Lazy Volume', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var entryId;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 entryId = Array.isArray(params.entryId) ? params.entryId.join(', ') : params.entryId;
                 return [2 /*return*/, new objects_1.PluginStateObject.Volume.Lazy(params, { label: "".concat(entryId || params.url), description: 'Lazy Volume' })];
             });

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

@@ -1,5 +1,5 @@
 /**
- * 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>
@@ -12,7 +12,11 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { PluginStateObject as SO } from '../objects';
 export { CoordinatesFromDcd };
 export { CoordinatesFromXtc };
+export { CoordinatesFromTrr };
+export { CoordinatesFromNctraj };
 export { TopologyFromPsf };
+export { TopologyFromPrmtop };
+export { TopologyFromTop };
 export { TrajectoryFromModelAndCoordinates };
 export { TrajectoryFromBlob };
 export { TrajectoryFromMmCif };
@@ -39,10 +43,18 @@ export { CustomStructureProperties };
 export { ShapeFromPly };
 declare type CoordinatesFromDcd = typeof CoordinatesFromDcd;
 declare const CoordinatesFromDcd: StateTransformer<SO.Data.Binary, SO.Molecule.Coordinates, PD.Normalize<{}>>;
-declare type CoordinatesFromXtc = typeof CoordinatesFromDcd;
+declare type CoordinatesFromXtc = typeof CoordinatesFromXtc;
 declare const CoordinatesFromXtc: StateTransformer<SO.Data.Binary, SO.Molecule.Coordinates, PD.Normalize<{}>>;
+declare type CoordinatesFromTrr = typeof CoordinatesFromTrr;
+declare const CoordinatesFromTrr: StateTransformer<SO.Data.Binary, SO.Molecule.Coordinates, PD.Normalize<{}>>;
+declare type CoordinatesFromNctraj = typeof CoordinatesFromNctraj;
+declare const CoordinatesFromNctraj: StateTransformer<SO.Data.Binary, SO.Molecule.Coordinates, PD.Normalize<{}>>;
 declare type TopologyFromPsf = typeof TopologyFromPsf;
 declare const TopologyFromPsf: StateTransformer<SO.Format.Psf, SO.Molecule.Topology, PD.Normalize<{}>>;
+declare type TopologyFromPrmtop = typeof TopologyFromPrmtop;
+declare const TopologyFromPrmtop: StateTransformer<SO.Format.Prmtop, SO.Molecule.Topology, PD.Normalize<{}>>;
+declare type TopologyFromTop = typeof TopologyFromTop;
+declare const TopologyFromTop: StateTransformer<SO.Format.Top, SO.Molecule.Topology, PD.Normalize<{}>>;
 declare type TrajectoryFromModelAndCoordinates = typeof TrajectoryFromModelAndCoordinates;
 declare const TrajectoryFromModelAndCoordinates: StateTransformer<SO.Root, SO.Molecule.Trajectory, PD.Normalize<{
     modelRef: string;