molstar 3.3.0 → 3.5.0

package/lib/commonjs/mol-plugin-state/formats/{structure.d.ts → coordinates.d.ts}

@@ -1,44 +1,48 @@
 /**
- * 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>
  */
-export declare const StructureFormatCategory = "Structure";
-export declare const PsfProvider: {
+export declare const CoordinatesFormatCategory = "Coordinates";
+export { DcdProvider };
+declare const DcdProvider: {
     label: string;
     description: string;
     category: string;
-    stringExtensions: string[];
-    parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<{
-        format: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Format.Psf, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Data.String, import("../objects").PluginStateObject.Format.Psf, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
-        topology: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Format.Psf, import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
-    }>;
+    binaryExtensions: string[];
+    parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Coordinates, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>>;
 };
-export declare const DcdProvider: {
+declare type DcdProvider = typeof DcdProvider;
+export { XtcProvider };
+declare const XtcProvider: {
     label: string;
     description: string;
     category: string;
     binaryExtensions: string[];
     parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Coordinates, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>>;
 };
-export declare const XtcProvider: {
+declare type XtcProvider = typeof XtcProvider;
+export { TrrProvider };
+declare const TrrProvider: {
     label: string;
     description: string;
     category: string;
     binaryExtensions: string[];
     parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Coordinates, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>>;
 };
-export declare const BuiltInStructureFormats: readonly [readonly ["psf", {
+declare type TrrProvider = typeof TrrProvider;
+export { NctrajProvider };
+declare const NctrajProvider: {
     label: string;
     description: string;
     category: string;
-    stringExtensions: string[];
-    parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<{
-        format: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Format.Psf, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Data.String, import("../objects").PluginStateObject.Format.Psf, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
-        topology: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Format.Psf, import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
-    }>;
-}], readonly ["dcd", {
+    binaryExtensions: string[];
+    parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Coordinates, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>>;
+};
+declare type NctrajProvider = typeof NctrajProvider;
+export declare type CoordinatesProvider = DcdProvider | XtcProvider | TrrProvider;
+export declare const BuiltInCoordinatesFormats: readonly [readonly ["dcd", {
     label: string;
     description: string;
     category: string;
@@ -50,5 +54,17 @@ export declare const BuiltInStructureFormats: readonly [readonly ["psf", {
     category: string;
     binaryExtensions: string[];
     parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Coordinates, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>>;
+}], readonly ["trr", {
+    label: string;
+    description: string;
+    category: string;
+    binaryExtensions: string[];
+    parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Coordinates, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>>;
+}], readonly ["nctraj", {
+    label: string;
+    description: string;
+    category: string;
+    binaryExtensions: string[];
+    parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Coordinates, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>>;
 }]];
-export declare type BuildInStructureFormat = (typeof BuiltInStructureFormats)[number][0];
+export declare type BuiltInCoordinatesFormat = (typeof BuiltInCoordinatesFormats)[number][0];

package/lib/commonjs/mol-plugin-state/formats/coordinates.js

@@ -0,0 +1,70 @@
+"use strict";
+/**
+ * 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.BuiltInCoordinatesFormats = exports.NctrajProvider = exports.TrrProvider = exports.XtcProvider = exports.DcdProvider = exports.CoordinatesFormatCategory = void 0;
+var transforms_1 = require("../transforms");
+var provider_1 = require("./provider");
+exports.CoordinatesFormatCategory = 'Coordinates';
+var DcdProvider = (0, provider_1.DataFormatProvider)({
+    label: 'DCD',
+    description: 'DCD',
+    category: exports.CoordinatesFormatCategory,
+    binaryExtensions: ['dcd'],
+    parse: function (plugin, data) {
+        var coordinates = plugin.state.data.build()
+            .to(data)
+            .apply(transforms_1.StateTransforms.Model.CoordinatesFromDcd);
+        return coordinates.commit();
+    }
+});
+exports.DcdProvider = DcdProvider;
+var XtcProvider = (0, provider_1.DataFormatProvider)({
+    label: 'XTC',
+    description: 'XTC',
+    category: exports.CoordinatesFormatCategory,
+    binaryExtensions: ['xtc'],
+    parse: function (plugin, data) {
+        var coordinates = plugin.state.data.build()
+            .to(data)
+            .apply(transforms_1.StateTransforms.Model.CoordinatesFromXtc);
+        return coordinates.commit();
+    }
+});
+exports.XtcProvider = XtcProvider;
+var TrrProvider = (0, provider_1.DataFormatProvider)({
+    label: 'TRR',
+    description: 'TRR',
+    category: exports.CoordinatesFormatCategory,
+    binaryExtensions: ['trr'],
+    parse: function (plugin, data) {
+        var coordinates = plugin.state.data.build()
+            .to(data)
+            .apply(transforms_1.StateTransforms.Model.CoordinatesFromTrr);
+        return coordinates.commit();
+    }
+});
+exports.TrrProvider = TrrProvider;
+var NctrajProvider = (0, provider_1.DataFormatProvider)({
+    label: 'NCTRAJ',
+    description: 'NCTRAJ',
+    category: exports.CoordinatesFormatCategory,
+    binaryExtensions: ['nc', 'nctraj'],
+    parse: function (plugin, data) {
+        var coordinates = plugin.state.data.build()
+            .to(data)
+            .apply(transforms_1.StateTransforms.Model.CoordinatesFromNctraj);
+        return coordinates.commit();
+    }
+});
+exports.NctrajProvider = NctrajProvider;
+exports.BuiltInCoordinatesFormats = [
+    ['dcd', DcdProvider],
+    ['xtc', XtcProvider],
+    ['trr', TrrProvider],
+    ['nctraj', NctrajProvider],
+];

package/lib/commonjs/mol-plugin-state/formats/registry.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -13,10 +13,10 @@ export declare class DataFormatRegistry {
     private _extensions;
     private _binaryExtensions;
     private _options;
-    get types(): [string, string][];
+    get types(): [name: string, label: string][];
     get extensions(): Set<string>;
     get binaryExtensions(): Set<string>;
-    get options(): [string, string, string][];
+    get options(): [name: string, label: string, category: string][];
     constructor();
     private _clear;
     add(name: string, provider: DataFormatProvider): void;

package/lib/commonjs/mol-plugin-state/formats/registry.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -10,7 +10,8 @@ exports.DataFormatRegistry = void 0;
 var trajectory_1 = require("./trajectory");
 var volume_1 = require("./volume");
 var shape_1 = require("./shape");
-var structure_1 = require("./structure");
+var topology_1 = require("./topology");
+var coordinates_1 = require("./coordinates");
 var DataFormatRegistry = /** @class */ (function () {
     function DataFormatRegistry() {
         this._list = [];
@@ -22,16 +23,20 @@ var DataFormatRegistry = /** @class */ (function () {
             var _a = BuiltInVolumeFormats_1[_i], id = _a[0], p = _a[1];
             this.add(id, p);
         }
-        for (var _b = 0, BuiltInStructureFormats_1 = structure_1.BuiltInStructureFormats; _b < BuiltInStructureFormats_1.length; _b++) {
-            var _c = BuiltInStructureFormats_1[_b], id = _c[0], p = _c[1];
+        for (var _b = 0, BuiltInTopologyFormats_1 = topology_1.BuiltInTopologyFormats; _b < BuiltInTopologyFormats_1.length; _b++) {
+            var _c = BuiltInTopologyFormats_1[_b], id = _c[0], p = _c[1];
             this.add(id, p);
         }
-        for (var _d = 0, BuiltInShapeFormats_1 = shape_1.BuiltInShapeFormats; _d < BuiltInShapeFormats_1.length; _d++) {
-            var _e = BuiltInShapeFormats_1[_d], id = _e[0], p = _e[1];
+        for (var _d = 0, BuiltInCoordinatesFormats_1 = coordinates_1.BuiltInCoordinatesFormats; _d < BuiltInCoordinatesFormats_1.length; _d++) {
+            var _e = BuiltInCoordinatesFormats_1[_d], id = _e[0], p = _e[1];
             this.add(id, p);
         }
-        for (var _f = 0, BuiltInTrajectoryFormats_1 = trajectory_1.BuiltInTrajectoryFormats; _f < BuiltInTrajectoryFormats_1.length; _f++) {
-            var _g = BuiltInTrajectoryFormats_1[_f], id = _g[0], p = _g[1];
+        for (var _f = 0, BuiltInShapeFormats_1 = shape_1.BuiltInShapeFormats; _f < BuiltInShapeFormats_1.length; _f++) {
+            var _g = BuiltInShapeFormats_1[_f], id = _g[0], p = _g[1];
+            this.add(id, p);
+        }
+        for (var _h = 0, BuiltInTrajectoryFormats_1 = trajectory_1.BuiltInTrajectoryFormats; _h < BuiltInTrajectoryFormats_1.length; _h++) {
+            var _j = BuiltInTrajectoryFormats_1[_h], id = _j[0], p = _j[1];
             this.add(id, p);
         }
     }

package/lib/commonjs/mol-plugin-state/formats/shape.js

@@ -16,9 +16,9 @@ exports.PlyProvider = (0, provider_1.DataFormatProvider)({
     description: 'PLY',
     category: exports.ShapeFormatCategory,
     stringExtensions: ['ply'],
-    parse: function (plugin, data) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    parse: function (plugin, data) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var format, shape;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     format = plugin.state.data.build()

package/lib/commonjs/mol-plugin-state/formats/topology.d.ts

@@ -0,0 +1,73 @@
+/**
+ * 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>
+ */
+export declare const TopologyFormatCategory = "Topology";
+export { PsfProvider };
+declare const PsfProvider: {
+    label: string;
+    description: string;
+    category: string;
+    stringExtensions: string[];
+    parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<{
+        format: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Format.Psf, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Data.String, import("../objects").PluginStateObject.Format.Psf, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+        topology: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Format.Psf, import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+    }>;
+};
+declare type PsfProvider = typeof PsfProvider;
+export { PrmtopProvider };
+declare const PrmtopProvider: {
+    label: string;
+    description: string;
+    category: string;
+    stringExtensions: string[];
+    parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<{
+        format: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Format.Prmtop, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Data.String, import("../objects").PluginStateObject.Format.Prmtop, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+        topology: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Format.Prmtop, import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+    }>;
+};
+declare type PrmtopProvider = typeof PrmtopProvider;
+export { TopProvider };
+declare const TopProvider: {
+    label: string;
+    description: string;
+    category: string;
+    stringExtensions: string[];
+    parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<{
+        format: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Format.Top, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Data.String, import("../objects").PluginStateObject.Format.Top, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+        topology: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Format.Top, import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+    }>;
+};
+declare type TopProvider = typeof TopProvider;
+export declare type TopologyProvider = PsfProvider;
+export declare const BuiltInTopologyFormats: readonly [readonly ["psf", {
+    label: string;
+    description: string;
+    category: string;
+    stringExtensions: string[];
+    parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<{
+        format: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Format.Psf, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Data.String, import("../objects").PluginStateObject.Format.Psf, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+        topology: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Format.Psf, import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+    }>;
+}], readonly ["prmtop", {
+    label: string;
+    description: string;
+    category: string;
+    stringExtensions: string[];
+    parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<{
+        format: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Format.Prmtop, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Data.String, import("../objects").PluginStateObject.Format.Prmtop, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+        topology: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Format.Prmtop, import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+    }>;
+}], readonly ["top", {
+    label: string;
+    description: string;
+    category: string;
+    stringExtensions: string[];
+    parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<{
+        format: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Format.Top, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Data.String, import("../objects").PluginStateObject.Format.Top, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+        topology: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Format.Top, import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+    }>;
+}]];
+export declare type BuiltInTopologyFormat = (typeof BuiltInTopologyFormats)[number][0];

package/lib/commonjs/mol-plugin-state/formats/topology.js

@@ -0,0 +1,87 @@
+"use strict";
+/**
+ * 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.BuiltInTopologyFormats = exports.TopProvider = exports.PrmtopProvider = exports.PsfProvider = exports.TopologyFormatCategory = void 0;
+var tslib_1 = require("tslib");
+var transforms_1 = require("../transforms");
+var provider_1 = require("./provider");
+exports.TopologyFormatCategory = 'Topology';
+var PsfProvider = (0, provider_1.DataFormatProvider)({
+    label: 'PSF',
+    description: 'PSF',
+    category: exports.TopologyFormatCategory,
+    stringExtensions: ['psf'],
+    parse: function (plugin, data) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
+        var format, topology;
+        return tslib_1.__generator(this, function (_a) {
+            switch (_a.label) {
+                case 0:
+                    format = plugin.state.data.build()
+                        .to(data)
+                        .apply(transforms_1.StateTransforms.Data.ParsePsf, {}, { state: { isGhost: true } });
+                    topology = format.apply(transforms_1.StateTransforms.Model.TopologyFromPsf);
+                    return [4 /*yield*/, format.commit()];
+                case 1:
+                    _a.sent();
+                    return [2 /*return*/, { format: format.selector, topology: topology.selector }];
+            }
+        });
+    }); }
+});
+exports.PsfProvider = PsfProvider;
+var PrmtopProvider = (0, provider_1.DataFormatProvider)({
+    label: 'PRMTOP',
+    description: 'PRMTOP',
+    category: exports.TopologyFormatCategory,
+    stringExtensions: ['prmtop', 'parm7'],
+    parse: function (plugin, data) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
+        var format, topology;
+        return tslib_1.__generator(this, function (_a) {
+            switch (_a.label) {
+                case 0:
+                    format = plugin.state.data.build()
+                        .to(data)
+                        .apply(transforms_1.StateTransforms.Data.ParsePrmtop, {}, { state: { isGhost: true } });
+                    topology = format.apply(transforms_1.StateTransforms.Model.TopologyFromPrmtop);
+                    return [4 /*yield*/, format.commit()];
+                case 1:
+                    _a.sent();
+                    return [2 /*return*/, { format: format.selector, topology: topology.selector }];
+            }
+        });
+    }); }
+});
+exports.PrmtopProvider = PrmtopProvider;
+var TopProvider = (0, provider_1.DataFormatProvider)({
+    label: 'TOP',
+    description: 'TOP',
+    category: exports.TopologyFormatCategory,
+    stringExtensions: ['top'],
+    parse: function (plugin, data) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
+        var format, topology;
+        return tslib_1.__generator(this, function (_a) {
+            switch (_a.label) {
+                case 0:
+                    format = plugin.state.data.build()
+                        .to(data)
+                        .apply(transforms_1.StateTransforms.Data.ParseTop, {}, { state: { isGhost: true } });
+                    topology = format.apply(transforms_1.StateTransforms.Model.TopologyFromTop);
+                    return [4 /*yield*/, format.commit()];
+                case 1:
+                    _a.sent();
+                    return [2 /*return*/, { format: format.selector, topology: topology.selector }];
+            }
+        });
+    }); }
+});
+exports.TopProvider = TopProvider;
+exports.BuiltInTopologyFormats = [
+    ['psf', PsfProvider],
+    ['prmtop', PrmtopProvider],
+    ['top', TopProvider],
+];

package/lib/commonjs/mol-plugin-state/formats/trajectory.js

@@ -28,10 +28,10 @@ exports.MmcifProvider = {
             return (0, provider_1.guessCifVariant)(info, data) === -1;
         return false;
     },
-    parse: function (plugin, data, params) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    parse: function (plugin, data, params) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var state, cif, trajectory;
         var _a, _b;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
                     state = plugin.state.data;
@@ -61,10 +61,10 @@ exports.CifCoreProvider = {
             return (0, provider_1.guessCifVariant)(info, data) === 'coreCif';
         return false;
     },
-    parse: function (plugin, data, params) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    parse: function (plugin, data, params) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var state, cif, trajectory;
         var _a, _b;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
                     state = plugin.state.data;
@@ -86,9 +86,9 @@ exports.CifCoreProvider = {
 };
 function directTrajectory(transformer, transformerParams) {
     var _this = this;
-    return function (plugin, data, params) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return function (plugin, data, params) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var state, trajectory;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     state = plugin.state.data;

package/lib/commonjs/mol-plugin-state/formats/volume.js

@@ -20,18 +20,18 @@ var util_1 = require("../../mol-plugin/behavior/dynamic/volume-streaming/util");
 var mol_task_1 = require("../../mol-task");
 exports.VolumeFormatCategory = 'Volume';
 function tryObtainRecommendedIsoValue(plugin, volume) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var entryId;
         var _this = this;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             if (!volume)
                 return [2 /*return*/];
             entryId = volume.entryId;
             if (!entryId || !entryId.toLowerCase().startsWith('emd'))
                 return [2 /*return*/];
-            return [2 /*return*/, plugin.runTask(mol_task_1.Task.create('Try Set Recommended IsoValue', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+            return [2 /*return*/, plugin.runTask(mol_task_1.Task.create('Try Set Recommended IsoValue', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
                     var absIsoLevel, e_1;
-                    return (0, tslib_1.__generator)(this, function (_a) {
+                    return tslib_1.__generator(this, function (_a) {
                         switch (_a.label) {
                             case 0:
                                 _a.trys.push([0, 2, , 3]);
@@ -60,9 +60,9 @@ function tryGetRecomendedIsoValue(volume) {
     return volume_1.Volume.adjustedIsoValue(volume, recommendedIsoValue.absoluteValue, 'absolute');
 }
 function defaultVisuals(plugin, data) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var typeParams, isoValue, visual;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     typeParams = {};
@@ -84,9 +84,9 @@ exports.Ccp4Provider = (0, provider_1.DataFormatProvider)({
     description: 'CCP4/MRC/MAP',
     category: exports.VolumeFormatCategory,
     binaryExtensions: ['ccp4', 'mrc', 'map'],
-    parse: function (plugin, data, params) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    parse: function (plugin, data, params) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var format, volume;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     format = plugin.build()
@@ -110,9 +110,9 @@ exports.Dsn6Provider = (0, provider_1.DataFormatProvider)({
     description: 'DSN6/BRIX',
     category: exports.VolumeFormatCategory,
     binaryExtensions: ['dsn6', 'brix'],
-    parse: function (plugin, data, params) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    parse: function (plugin, data, params) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var format, volume;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     format = plugin.build()
@@ -137,9 +137,9 @@ exports.DxProvider = (0, provider_1.DataFormatProvider)({
     category: exports.VolumeFormatCategory,
     stringExtensions: ['dx'],
     binaryExtensions: ['dxbin'],
-    parse: function (plugin, data, params) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    parse: function (plugin, data, params) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var format, volume;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     format = plugin.build()
@@ -163,9 +163,9 @@ exports.CubeProvider = (0, provider_1.DataFormatProvider)({
     description: 'Cube',
     category: exports.VolumeFormatCategory,
     stringExtensions: ['cub', 'cube'],
-    parse: function (plugin, data, params) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    parse: function (plugin, data, params) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var format, volume, structure;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     format = plugin.build()
@@ -186,10 +186,10 @@ exports.CubeProvider = (0, provider_1.DataFormatProvider)({
             }
         });
     }); },
-    visuals: function (plugin, data) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    visuals: function (plugin, data) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var surfaces, volumeReprs, volumeData, volumePos, volumeNeg, volume, structure, structureReprs;
         var _a, _b;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
                     surfaces = plugin.build();
@@ -230,7 +230,7 @@ exports.CubeProvider = (0, provider_1.DataFormatProvider)({
                         if (r)
                             structureReprs.push(r);
                     });
-                    return [2 /*return*/, (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], volumeReprs, true), structureReprs, true)];
+                    return [2 /*return*/, tslib_1.__spreadArray(tslib_1.__spreadArray([], volumeReprs, true), structureReprs, true)];
             }
         });
     }); }
@@ -244,9 +244,9 @@ exports.DscifProvider = (0, provider_1.DataFormatProvider)({
     isApplicable: function (info, data) {
         return (0, provider_1.guessCifVariant)(info, data) === 'dscif' ? true : false;
     },
-    parse: function (plugin, data, params) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    parse: function (plugin, data, params) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var cifCell, b, blocks, volumes, i, _i, blocks_1, block, entryId, _a, volumes_1, v;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0: return [4 /*yield*/, plugin.build().to(data).apply(transforms_1.StateTransforms.Data.ParseCif).commit()];
                 case 1:
@@ -282,9 +282,9 @@ exports.DscifProvider = (0, provider_1.DataFormatProvider)({
             }
         });
     }); },
-    visuals: function (plugin, data) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    visuals: function (plugin, data) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var volumes, tree, visuals, isoValue, posParams, negParams;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     volumes = data.volumes;