npm - molstar - Versions diffs - 3.8.2 → 3.10.0 - Mend

molstar 3.8.2 → 3.10.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (596) hide show

package/lib/apps/docking-viewer/index.html CHANGED Viewed

@@ -1,37 +1,37 @@
-<!DOCTYPE html>
-<html lang="en">
-    <head>
-        <meta charset="utf-8" />
-        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
-        <title>Mol* Docking Viewer</title>
-        <style>
-            #app {
-                position: absolute;
-                left: 100px;
-                top: 100px;
-                width: 800px;
-                height: 600px;
-            }
-        </style>
-        <link rel="stylesheet" type="text/css" href="molstar.css" />
-    </head>
-    <body>
-        <div id="app"></div>
-        <script type="text/javascript" src="./molstar.js"></script>
-        <script type="text/javascript">
-            function getParam(name, regex) {
-                var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
-                return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
-            }
-            var pdbqt = getParam('pdbqt', '[^&]+').trim() || '../../examples/ace2.pdbqt';
-            var mol2 = getParam('mol2', '[^&]+').trim() || '../../examples/ace2-hit.mol2';
-            DockingViewer.create('app', [0x33DD22, 0x1133EE], true).then(viewer => {
-                viewer.loadStructuresFromUrlsAndMerge([
-                    { url: pdbqt, format: 'pdbqt' },
-                    { url: mol2, format: 'mol2' }
-                ]);
-            });
-        </script>
-    </body>
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+        <title>Mol* Docking Viewer</title>
+        <style>
+            #app {
+                position: absolute;
+                left: 100px;
+                top: 100px;
+                width: 800px;
+                height: 600px;
+            }
+        </style>
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
+    </head>
+    <body>
+        <div id="app"></div>
+        <script type="text/javascript" src="./molstar.js"></script>
+        <script type="text/javascript">
+            function getParam(name, regex) {
+                var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
+                return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
+            }
+            var pdbqt = getParam('pdbqt', '[^&]+').trim() || '../../examples/ace2.pdbqt';
+            var mol2 = getParam('mol2', '[^&]+').trim() || '../../examples/ace2-hit.mol2';
+            DockingViewer.create('app', [0x33DD22, 0x1133EE], true).then(viewer => {
+                viewer.loadStructuresFromUrlsAndMerge([
+                    { url: pdbqt, format: 'pdbqt' },
+                    { url: mol2, format: 'mol2' }
+                ]);
+            });
+        </script>
+    </body>
 </html>

package/lib/apps/viewer/app.d.ts CHANGED Viewed

@@ -18,8 +18,9 @@ import { PluginState } from '../../mol-plugin/state';
 import { StateObjectSelector } from '../../mol-state';
 import { Color } from '../../mol-util/color';
 import '../../mol-util/polyfill';
+import { SaccharideCompIdMapType } from '../../mol-model/structure/structure/carbohydrates/constants';
 export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
-export { setDebugMode, setProductionMode } from '../../mol-util/debug';
+export { setDebugMode, setProductionMode, setTimingMode } from '../../mol-util/debug';
 declare const DefaultViewerOptions: {
     customFormats: [string, DataFormatProvider<any, any, any>][];
     extensions: ("cellpack" | "g3d" | "geo-export" | "model-export" | "mp4-export" | "pdbe-structure-quality-report" | "zenodo-import" | "dnatco-confal-pyramids" | "rcsb-assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "ma-quality-assessment")[];
@@ -43,11 +44,13 @@ declare const DefaultViewerOptions: {
     viewportShowSettings: boolean | undefined;
     viewportShowSelectionMode: boolean | undefined;
     viewportShowAnimation: boolean | undefined;
+    viewportShowTrajectoryControls: boolean | undefined;
     pluginStateServer: string | undefined;
     volumeStreamingServer: string | undefined;
     volumeStreamingDisabled: boolean;
     pdbProvider: "rcsb" | "pdbe" | "pdbj" | undefined;
     emdbProvider: import("../../mol-plugin-state/actions/volume").EmdbDownloadProvider | undefined;
+    saccharideCompIdMapType: SaccharideCompIdMapType;
 };
 declare type ViewerOptions = typeof DefaultViewerOptions;
 export declare class Viewer {
@@ -125,7 +128,7 @@ export declare class Viewer {
      */
     loadTrajectory(params: LoadTrajectoryParams): Promise<{
         model: StateObjectSelector<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, 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>>;
-        coords: StateObjectSelector<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, 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>>;
+        coords: any;
         preset: {
             model: StateObjectSelector<PluginStateObject.Molecule.Model, 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>>;
             modelProperties: StateObjectSelector<PluginStateObject.Molecule.Model, 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>>;

package/lib/apps/viewer/app.js CHANGED Viewed

@@ -35,7 +35,7 @@ import { Asset } from '../../mol-util/assets';
 import '../../mol-util/polyfill';
 import { ObjectKeys } from '../../mol-util/type-helpers';
 export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
-export { setDebugMode, setProductionMode } from '../../mol-util/debug';
+export { setDebugMode, setProductionMode, setTimingMode } from '../../mol-util/debug';
 var CustomFormats = [
     ['g3d', G3dProvider]
 ];
@@ -76,11 +76,13 @@ var DefaultViewerOptions = {
     viewportShowSettings: PluginConfig.Viewport.ShowSettings.defaultValue,
     viewportShowSelectionMode: PluginConfig.Viewport.ShowSelectionMode.defaultValue,
     viewportShowAnimation: PluginConfig.Viewport.ShowAnimation.defaultValue,
+    viewportShowTrajectoryControls: PluginConfig.Viewport.ShowTrajectoryControls.defaultValue,
     pluginStateServer: PluginConfig.State.DefaultServer.defaultValue,
     volumeStreamingServer: PluginConfig.VolumeStreaming.DefaultServer.defaultValue,
     volumeStreamingDisabled: !PluginConfig.VolumeStreaming.Enabled.defaultValue,
     pdbProvider: PluginConfig.Download.DefaultPdbProvider.defaultValue,
     emdbProvider: PluginConfig.Download.DefaultEmdbProvider.defaultValue,
+    saccharideCompIdMapType: 'default',
 };
 var Viewer = /** @class */ (function () {
     function Viewer(plugin) {
@@ -136,6 +138,7 @@ var Viewer = /** @class */ (function () {
                                 [PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
                                 [PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode],
                                 [PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation],
+                                [PluginConfig.Viewport.ShowTrajectoryControls, o.viewportShowTrajectoryControls],
                                 [PluginConfig.State.DefaultServer, o.pluginStateServer],
                                 [PluginConfig.State.CurrentServer, o.pluginStateServer],
                                 [PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
@@ -143,6 +146,7 @@ var Viewer = /** @class */ (function () {
                                 [PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
                                 [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],
                                 [PluginConfig.Structure.DefaultRepresentationPreset, ViewerAutoPreset.id],
+                                [PluginConfig.Structure.SaccharideCompIdMapType, o.saccharideCompIdMapType],
                             ]
                         };
                         element = typeof elementOrId === 'string'
@@ -412,7 +416,7 @@ var Viewer = /** @class */ (function () {
     Viewer.prototype.loadTrajectory = function (params) {
         var _a, _b;
         return __awaiter(this, void 0, void 0, function () {
-            var plugin, model, coords, data, _c, trajectory_1, data, _d, provider, data, _e, provider, trajectory, preset;
+            var plugin, model, data_1, _c, trajectory_1, data_2, _d, provider_1, data, _e, provider, coords, trajectory, preset;
             return __generator(this, function (_f) {
                 switch (_f.label) {
                     case 0:
@@ -428,8 +432,8 @@ var Viewer = /** @class */ (function () {
                         _c = _f.sent();
                         _f.label = 4;
                     case 4:
-                        data = _c;
-                        return [4 /*yield*/, plugin.builders.structure.parseTrajectory(data, (_a = params.model.format) !== null && _a !== void 0 ? _a : 'mmcif')];
+                        data_1 = _c;
+                        return [4 /*yield*/, plugin.builders.structure.parseTrajectory(data_1, (_a = params.model.format) !== null && _a !== void 0 ? _a : 'mmcif')];
                     case 5:
                         trajectory_1 = _f.sent();
                         return [4 /*yield*/, plugin.builders.structure.createModel(trajectory_1)];
@@ -447,9 +451,9 @@ var Viewer = /** @class */ (function () {
                         _d = _f.sent();
                         _f.label = 11;
                     case 11:
-                        data = _d;
-                        provider = plugin.dataFormats.get(params.model.format);
-                        return [4 /*yield*/, provider.parse(plugin, data)];
+                        data_2 = _d;
+                        provider_1 = plugin.dataFormats.get(params.model.format);
+                        return [4 /*yield*/, provider_1.parse(plugin, data_2)];
                     case 12:
                         model = _f.sent();
                         _f.label = 13;

package/lib/apps/viewer/embedded.html CHANGED Viewed

@@ -1,44 +1,44 @@
-<!DOCTYPE html>
-<html lang="en">
-    <head>
-        <meta charset="utf-8" />
-        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
-        <link rel="icon" href="./favicon.ico" type="image/x-icon">
-        <title>Embedded Mol* Viewer</title>
-        <style>
-            #app {
-                position: absolute;
-                left: 100px;
-                top: 100px;
-                width: 800px;
-                height: 600px;
-            }
-        </style>
-        <link rel="stylesheet" type="text/css" href="molstar.css" />
-    </head>
-    <body>
-        <div id="app"></div>
-        <script type="text/javascript" src="./molstar.js"></script>
-        <script type="text/javascript">
-            molstar.Viewer.create('app', {
-                layoutIsExpanded: true,
-                layoutShowControls: false,
-                layoutShowRemoteState: false,
-                layoutShowSequence: true,
-                layoutShowLog: false,
-                layoutShowLeftPanel: true,
-                viewportShowExpand: true,
-                viewportShowSelectionMode: false,
-                viewportShowAnimation: false,
-                pdbProvider: 'rcsb',
-                emdbProvider: 'rcsb',
-            }).then(viewer => {
-                viewer.loadPdb('7bv2');
-                viewer.loadEmdb('EMD-30210', { detail: 6 });
-                // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
-            });
-        </script>
-    </body>
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+        <link rel="icon" href="./favicon.ico" type="image/x-icon">
+        <title>Embedded Mol* Viewer</title>
+        <style>
+            #app {
+                position: absolute;
+                left: 100px;
+                top: 100px;
+                width: 800px;
+                height: 600px;
+            }
+        </style>
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
+    </head>
+    <body>
+        <div id="app"></div>
+        <script type="text/javascript" src="./molstar.js"></script>
+        <script type="text/javascript">
+            molstar.Viewer.create('app', {
+                layoutIsExpanded: true,
+                layoutShowControls: false,
+                layoutShowRemoteState: false,
+                layoutShowSequence: true,
+                layoutShowLog: false,
+                layoutShowLeftPanel: true,
+                viewportShowExpand: true,
+                viewportShowSelectionMode: false,
+                viewportShowAnimation: false,
+                pdbProvider: 'rcsb',
+                emdbProvider: 'rcsb',
+            }).then(viewer => {
+                viewer.loadPdb('7bv2');
+                viewer.loadEmdb('EMD-30210', { detail: 6 });
+                // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
+            });
+        </script>
+    </body>
 </html>

package/lib/apps/viewer/index.html CHANGED Viewed

@@ -1,107 +1,110 @@
-<!DOCTYPE html>
-<html lang="en">
-    <head>
-        <meta charset="utf-8" />
-        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
-        <link rel="icon" href="./favicon.ico" type="image/x-icon">
-        <title>Mol* Viewer</title>
-        <style>
-            * {
-                margin: 0;
-                padding: 0;
-                box-sizing: border-box;
-            }
-            html, body {
-                width: 100%;
-                height: 100%;
-                overflow: hidden;
-            }
-            hr {
-                margin: 10px;
-            }
-            h1, h2, h3, h4, h5 {
-                margin-top: 5px;
-                margin-bottom: 3px;
-            }
-            button {
-                padding: 2px;
-            }
-            #app {
-                position: absolute;
-                left: 100px;
-                top: 100px;
-                width: 800px;
-                height: 600px;
-            }
-        </style>
-        <link rel="stylesheet" type="text/css" href="molstar.css" />
-    </head>
-    <body>
-        <div id="app"></div>
-        <script type="text/javascript" src="./molstar.js"></script>
-        <script type="text/javascript">
-            function getParam(name, regex) {
-                var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
-                return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
-            }
-            var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
-            if (debugMode) molstar.setDebugMode(debugMode, debugMode);
-            var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
-            var collapseLeftPanel = getParam('collapse-left-panel', '[^&]+').trim() === '1';
-            var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
-            var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
-            var mapProvider = getParam('map-provider', '[^&]+').trim().toLowerCase();
-            var pixelScale = getParam('pixel-scale', '[^&]+').trim();
-            var pickScale = getParam('pick-scale', '[^&]+').trim();
-            var pickPadding = getParam('pick-padding', '[^&]+').trim();
-            var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
-            var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
-            molstar.Viewer.create('app', {
-                layoutShowControls: !hideControls,
-                viewportShowExpand: false,
-                collapseLeftPanel: collapseLeftPanel,
-                pdbProvider: pdbProvider || 'pdbe',
-                emdbProvider: emdbProvider || 'pdbe',
-                volumeStreamingServer: (mapProvider || 'pdbe') === 'rcsb'
-                    ? 'https://maps.rcsb.org'
-                    : 'https://www.ebi.ac.uk/pdbe/densities',
-                pixelScale: parseFloat(pixelScale) || 1,
-                pickScale: parseFloat(pickScale) || 0.25,
-                pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
-                enableWboit: disableWboit ? false : void 0, // use default value if disable-wboit is not set
-                preferWebgl1: preferWebgl1,
-            }).then(viewer => {
-                var snapshotId = getParam('snapshot-id', '[^&]+').trim();
-                if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
-                var snapshotUrl = getParam('snapshot-url', '[^&]+').trim();
-                var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj';
-                if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType);
-                var structureUrl = getParam('structure-url', '[^&]+').trim();
-                var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim();
-                var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1';
-                if (structureUrl) viewer.loadStructureFromUrl(structureUrl, structureUrlFormat, structureUrlIsBinary);
-                var pdb = getParam('pdb', '[^&]+').trim();
-                if (pdb) viewer.loadPdb(pdb);
-                var pdbDev = getParam('pdb-dev', '[^&]+').trim();
-                if (pdbDev) viewer.loadPdbDev(pdbDev);
-                var emdb = getParam('emdb', '[^&]+').trim();
-                if (emdb) viewer.loadEmdb(emdb);
-                var afdb = getParam('afdb', '[^&]+').trim();
-                if (afdb) viewer.loadAlphaFoldDb(afdb);
-                var modelArchive = getParam('model-archive', '[^&]+').trim();
-                if (modelArchive) viewer.loadModelArchive(modelArchive);
-            });
-        </script>
-        <!-- __MOLSTAR_ANALYTICS__ -->
-    </body>
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+        <link rel="icon" href="./favicon.ico" type="image/x-icon">
+        <title>Mol* Viewer</title>
+        <style>
+            * {
+                margin: 0;
+                padding: 0;
+                box-sizing: border-box;
+            }
+            html, body {
+                width: 100%;
+                height: 100%;
+                overflow: hidden;
+            }
+            hr {
+                margin: 10px;
+            }
+            h1, h2, h3, h4, h5 {
+                margin-top: 5px;
+                margin-bottom: 3px;
+            }
+            button {
+                padding: 2px;
+            }
+            #app {
+                position: absolute;
+                left: 100px;
+                top: 100px;
+                width: 800px;
+                height: 600px;
+            }
+        </style>
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
+    </head>
+    <body>
+        <div id="app"></div>
+        <script type="text/javascript" src="./molstar.js"></script>
+        <script type="text/javascript">
+            function getParam(name, regex) {
+                var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
+                return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
+            }
+            var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
+            if (debugMode) molstar.setDebugMode(debugMode);
+            var timingMode = getParam('timing-mode', '[^&]+').trim() === '1';
+            if (timingMode) molstar.setTimingMode(timingMode);
+            var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
+            var collapseLeftPanel = getParam('collapse-left-panel', '[^&]+').trim() === '1';
+            var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
+            var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
+            var mapProvider = getParam('map-provider', '[^&]+').trim().toLowerCase();
+            var pixelScale = getParam('pixel-scale', '[^&]+').trim();
+            var pickScale = getParam('pick-scale', '[^&]+').trim();
+            var pickPadding = getParam('pick-padding', '[^&]+').trim();
+            var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
+            var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
+            molstar.Viewer.create('app', {
+                layoutShowControls: !hideControls,
+                viewportShowExpand: false,
+                collapseLeftPanel: collapseLeftPanel,
+                pdbProvider: pdbProvider || 'pdbe',
+                emdbProvider: emdbProvider || 'pdbe',
+                volumeStreamingServer: (mapProvider || 'pdbe') === 'rcsb'
+                    ? 'https://maps.rcsb.org'
+                    : 'https://www.ebi.ac.uk/pdbe/densities',
+                pixelScale: parseFloat(pixelScale) || 1,
+                pickScale: parseFloat(pickScale) || 0.25,
+                pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
+                enableWboit: disableWboit ? false : void 0, // use default value if disable-wboit is not set
+                preferWebgl1: preferWebgl1,
+            }).then(viewer => {
+                var snapshotId = getParam('snapshot-id', '[^&]+').trim();
+                if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
+                var snapshotUrl = getParam('snapshot-url', '[^&]+').trim();
+                var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj';
+                if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType);
+                var structureUrl = getParam('structure-url', '[^&]+').trim();
+                var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim();
+                var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1';
+                if (structureUrl) viewer.loadStructureFromUrl(structureUrl, structureUrlFormat, structureUrlIsBinary);
+                var pdb = getParam('pdb', '[^&]+').trim();
+                if (pdb) viewer.loadPdb(pdb);
+                var pdbDev = getParam('pdb-dev', '[^&]+').trim();
+                if (pdbDev) viewer.loadPdbDev(pdbDev);
+                var emdb = getParam('emdb', '[^&]+').trim();
+                if (emdb) viewer.loadEmdb(emdb);
+                var afdb = getParam('afdb', '[^&]+').trim();
+                if (afdb) viewer.loadAlphaFoldDb(afdb);
+                var modelArchive = getParam('model-archive', '[^&]+').trim();
+                if (modelArchive) viewer.loadModelArchive(modelArchive);
+            });
+        </script>
+        <!-- __MOLSTAR_ANALYTICS__ -->
+    </body>
 </html>

package/lib/cli/cif2bcif/converter.js CHANGED Viewed

@@ -82,7 +82,7 @@ function getCategoryInstanceProvider(cat, fields) {
 function classify(name, field) {
     var type = getCifFieldType(field);
     if (type['@type'] === 'str') {
-        return { name: name, type: 0 /* Str */, value: field.str, valueKind: field.valueKind };
+        return { name: name, type: 0 /* CifWriter.Field.Type.Str */, value: field.str, valueKind: field.valueKind };
     }
     else if (type['@type'] === 'float') {
         var encoder = classifyFloatArray(field.toFloatArray({ array: Float64Array }));

package/lib/commonjs/apps/viewer/app.d.ts CHANGED Viewed

@@ -18,8 +18,9 @@ import { PluginState } from '../../mol-plugin/state';
 import { StateObjectSelector } from '../../mol-state';
 import { Color } from '../../mol-util/color';
 import '../../mol-util/polyfill';
+import { SaccharideCompIdMapType } from '../../mol-model/structure/structure/carbohydrates/constants';
 export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
-export { setDebugMode, setProductionMode } from '../../mol-util/debug';
+export { setDebugMode, setProductionMode, setTimingMode } from '../../mol-util/debug';
 declare const DefaultViewerOptions: {
     customFormats: [string, DataFormatProvider<any, any, any>][];
     extensions: ("cellpack" | "g3d" | "geo-export" | "model-export" | "mp4-export" | "pdbe-structure-quality-report" | "zenodo-import" | "dnatco-confal-pyramids" | "rcsb-assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "ma-quality-assessment")[];
@@ -43,11 +44,13 @@ declare const DefaultViewerOptions: {
     viewportShowSettings: boolean | undefined;
     viewportShowSelectionMode: boolean | undefined;
     viewportShowAnimation: boolean | undefined;
+    viewportShowTrajectoryControls: boolean | undefined;
     pluginStateServer: string | undefined;
     volumeStreamingServer: string | undefined;
     volumeStreamingDisabled: boolean;
     pdbProvider: "rcsb" | "pdbe" | "pdbj" | undefined;
     emdbProvider: import("../../mol-plugin-state/actions/volume").EmdbDownloadProvider | undefined;
+    saccharideCompIdMapType: SaccharideCompIdMapType;
 };
 declare type ViewerOptions = typeof DefaultViewerOptions;
 export declare class Viewer {
@@ -125,7 +128,7 @@ export declare class Viewer {
      */
     loadTrajectory(params: LoadTrajectoryParams): Promise<{
         model: StateObjectSelector<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, 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>>;
-        coords: StateObjectSelector<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, 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>>;
+        coords: any;
         preset: {
             model: StateObjectSelector<PluginStateObject.Molecule.Model, 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>>;
             modelProperties: StateObjectSelector<PluginStateObject.Molecule.Model, 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>>;

package/lib/commonjs/apps/viewer/app.js CHANGED Viewed

@@ -6,7 +6,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.ViewerAutoPreset = exports.Viewer = exports.setProductionMode = exports.setDebugMode = exports.version = void 0;
+exports.ViewerAutoPreset = exports.Viewer = exports.setTimingMode = exports.setProductionMode = exports.setDebugMode = exports.version = void 0;
 var tslib_1 = require("tslib");
 var behavior_1 = require("../../extensions/anvil/behavior");
 var cellpack_1 = require("../../extensions/cellpack");
@@ -42,6 +42,7 @@ Object.defineProperty(exports, "version", { enumerable: true, get: function () {
 var debug_1 = require("../../mol-util/debug");
 Object.defineProperty(exports, "setDebugMode", { enumerable: true, get: function () { return debug_1.setDebugMode; } });
 Object.defineProperty(exports, "setProductionMode", { enumerable: true, get: function () { return debug_1.setProductionMode; } });
+Object.defineProperty(exports, "setTimingMode", { enumerable: true, get: function () { return debug_1.setTimingMode; } });
 var CustomFormats = [
     ['g3d', format_1.G3dProvider]
 ];
@@ -82,11 +83,13 @@ var DefaultViewerOptions = {
     viewportShowSettings: config_1.PluginConfig.Viewport.ShowSettings.defaultValue,
     viewportShowSelectionMode: config_1.PluginConfig.Viewport.ShowSelectionMode.defaultValue,
     viewportShowAnimation: config_1.PluginConfig.Viewport.ShowAnimation.defaultValue,
+    viewportShowTrajectoryControls: config_1.PluginConfig.Viewport.ShowTrajectoryControls.defaultValue,
     pluginStateServer: config_1.PluginConfig.State.DefaultServer.defaultValue,
     volumeStreamingServer: config_1.PluginConfig.VolumeStreaming.DefaultServer.defaultValue,
     volumeStreamingDisabled: !config_1.PluginConfig.VolumeStreaming.Enabled.defaultValue,
     pdbProvider: config_1.PluginConfig.Download.DefaultPdbProvider.defaultValue,
     emdbProvider: config_1.PluginConfig.Download.DefaultEmdbProvider.defaultValue,
+    saccharideCompIdMapType: 'default',
 };
 var Viewer = /** @class */ (function () {
     function Viewer(plugin) {
@@ -142,6 +145,7 @@ var Viewer = /** @class */ (function () {
                                 [config_1.PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
                                 [config_1.PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode],
                                 [config_1.PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation],
+                                [config_1.PluginConfig.Viewport.ShowTrajectoryControls, o.viewportShowTrajectoryControls],
                                 [config_1.PluginConfig.State.DefaultServer, o.pluginStateServer],
                                 [config_1.PluginConfig.State.CurrentServer, o.pluginStateServer],
                                 [config_1.PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
@@ -149,6 +153,7 @@ var Viewer = /** @class */ (function () {
                                 [config_1.PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
                                 [config_1.PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],
                                 [config_1.PluginConfig.Structure.DefaultRepresentationPreset, exports.ViewerAutoPreset.id],
+                                [config_1.PluginConfig.Structure.SaccharideCompIdMapType, o.saccharideCompIdMapType],
                             ]
                         };
                         element = typeof elementOrId === 'string'
@@ -418,7 +423,7 @@ var Viewer = /** @class */ (function () {
     Viewer.prototype.loadTrajectory = function (params) {
         var _a, _b;
         return tslib_1.__awaiter(this, void 0, void 0, function () {
-            var plugin, model, coords, data, _c, trajectory_1, data, _d, provider, data, _e, provider, trajectory, preset;
+            var plugin, model, data_1, _c, trajectory_1, data_2, _d, provider_1, data, _e, provider, coords, trajectory, preset;
             return tslib_1.__generator(this, function (_f) {
                 switch (_f.label) {
                     case 0:
@@ -434,8 +439,8 @@ var Viewer = /** @class */ (function () {
                         _c = _f.sent();
                         _f.label = 4;
                     case 4:
-                        data = _c;
-                        return [4 /*yield*/, plugin.builders.structure.parseTrajectory(data, (_a = params.model.format) !== null && _a !== void 0 ? _a : 'mmcif')];
+                        data_1 = _c;
+                        return [4 /*yield*/, plugin.builders.structure.parseTrajectory(data_1, (_a = params.model.format) !== null && _a !== void 0 ? _a : 'mmcif')];
                     case 5:
                         trajectory_1 = _f.sent();
                         return [4 /*yield*/, plugin.builders.structure.createModel(trajectory_1)];
@@ -453,9 +458,9 @@ var Viewer = /** @class */ (function () {
                         _d = _f.sent();
                         _f.label = 11;
                     case 11:
-                        data = _d;
-                        provider = plugin.dataFormats.get(params.model.format);
-                        return [4 /*yield*/, provider.parse(plugin, data)];
+                        data_2 = _d;
+                        provider_1 = plugin.dataFormats.get(params.model.format);
+                        return [4 /*yield*/, provider_1.parse(plugin, data_2)];
                     case 12:
                         model = _f.sent();
                         _f.label = 13;

package/lib/commonjs/cli/cif2bcif/converter.js CHANGED Viewed

@@ -85,7 +85,7 @@ function getCategoryInstanceProvider(cat, fields) {
 function classify(name, field) {
     var type = (0, cif_1.getCifFieldType)(field);
     if (type['@type'] === 'str') {
-        return { name: name, type: 0 /* Str */, value: field.str, valueKind: field.valueKind };
+        return { name: name, type: 0 /* CifWriter.Field.Type.Str */, value: field.str, valueKind: field.valueKind };
     }
     else if (type['@type'] === 'float') {
         var encoder = (0, binary_cif_1.classifyFloatArray)(field.toFloatArray({ array: Float64Array }));