npm - molstar - Versions diffs - 3.0.0-dev.5 → 3.0.0-dev.9 - Mend

molstar 3.0.0-dev.5 → 3.0.0-dev.9

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 (688) hide show

package/lib/examples/proteopedia-wrapper/index.html CHANGED Viewed

@@ -1,236 +1,237 @@
-<!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* Proteopedia Wrapper</title>
-        <style>
-            * {
-                margin: 0;
-                padding: 0;
-                box-sizing: border-box;
-            }
-            #app {
-                position: absolute;
-                left: 160px;
-                top: 100px;
-                width: 600px;
-                height: 600px;
-                border: 1px solid #ccc;
-            }
-            #controls {
-                position: absolute;
-                width: 130px;
-                top: 10px;
-                left: 10px;
-            }
-            #controls > button {
-                display: block;
-                width: 100%;
-                text-align: left;
-            }
-            #controls > hr {
-                margin: 5px 0;
-            }
-            #controls > input, #controls > select {
-                width: 100%;
-                display: block;
-            }
-            #volume-streaming-wrapper {
-                position: absolute;
-                top: 100px;
-                left: 780px;
-                width: 300px;
-            }
-        </style>
-        <link rel="stylesheet" type="text/css" href="molstar.css" />
-        <script type="text/javascript" src="./index.js"></script>
-    </head>
-    <body>
-        <div id='controls'>
-            <h3>Source</h3>
-            <input type='text' id='url' placeholder='url' style='width: 400px' />
-            <input type='text' id='assemblyId' placeholder='assembly id' />
-            <select id='format'>
-                <option value='cif' selected>CIF</option>
-                <option value='pdb'>PDB</option>
-            </select>
-            <input type='checkbox' id='isBinary' style="display: inline-block; width: auto" /> <label for="isBinary"> Binary</label><br />
-        </div>
-        <div id="app"></div>
-        <div id="volume-streaming-wrapper"></div>
-        <script>
-            // it might be a good idea to define these colors in a separate script file
-            var CustomColors = [0x00ff00, 0x0000ff];
-            // create an instance of the plugin
-            var PluginWrapper = new MolStarProteopediaWrapper();
-            console.log('Wrapper version', MolStarProteopediaWrapper.VERSION_MAJOR, MolStarProteopediaWrapper.VERSION_MINOR);
-            function $(id) { return document.getElementById(id); }
-            var pdbId = '1cbs', assemblyId= 'preferred', isBinary = true;
-            var url = 'https://www.ebi.ac.uk/pdbe/entry-files/download/' + pdbId + '.bcif'
-            var format = 'cif';
-            $('url').value = url;
-            $('url').onchange = function (e) { url = e.target.value; }
-            $('assemblyId').value = assemblyId;
-            $('assemblyId').onchange = function (e) { assemblyId = e.target.value; }
-            $('format').value = format;
-            $('format').onchange = function (e) { format = e.target.value; }
-            $('isBinary').checked = isBinary;
-            $('isBinary').onchange = function (e) { isBinary = !!e.target.checked; };
-            function loadAndSnapshot(params) {
-                PluginWrapper.load(params).then(() => {
-                    setTimeout(() => snapshot = PluginWrapper.plugin.state.getSnapshot({ canvas3d: false /* do not save spinning state */ }), 500);
-                });
-            }
-            var representationStyle = {
-                // sequence: { coloring: 'proteopedia-custom' }, // or just { }
-                hetGroups: { kind: 'ball-and-stick' }, // or 'spacefill
-                water: { hide: true },
-                snfg3d: { hide: false }
-            };
-            PluginWrapper.init('app' /** or document.getElementById('app') */, {
-                customColorList: CustomColors
-            });
-            PluginWrapper.setBackground(0xffffff);
-            loadAndSnapshot({ url: url, format: format, isBinary: isBinary, assemblyId: assemblyId, representationStyle: representationStyle });
-            PluginWrapper.toggleSpin();
-            PluginWrapper.events.modelInfo.subscribe(function (info) {
-                console.log('Model Info', info);
-                listHetGroups(info);
-            });
-            addControl('Load Asym Unit', () => loadAndSnapshot({ url: url, format: format, isBinary }));
-            addControl('Load Assembly', () => loadAndSnapshot({ url: url, format: format, isBinary, assemblyId: assemblyId }));
-            addSeparator();
-            addHeader('Representation');
-            addControl('Custom Chain Colors', () => PluginWrapper.updateStyle({ sequence: { coloring: 'proteopedia-custom' } }, true));
-            addControl('Default Chain Colors', () => PluginWrapper.updateStyle({ sequence: { } }, true));
-            addControl('HET Spacefill', () => PluginWrapper.updateStyle({ hetGroups: { kind: 'spacefill' } }, true));
-            addControl('HET Ball-and-stick', () => PluginWrapper.updateStyle({ hetGroups: { kind: 'ball-and-stick' } }, true));
-            addControl('Hide 3DSNFG', () => PluginWrapper.updateStyle({ snfg3d: { hide: true } }, true));
-            addControl('Show 3DSNFG', () => PluginWrapper.updateStyle({ snfg3d: { hide: false } }, true));
-            addControl('Hide Water', () => PluginWrapper.updateStyle({ water: { hide: true } }, true));
-            addControl('Show Water', () => PluginWrapper.updateStyle({ water: { hide: false } }, true));
-            addSeparator();
-            addHeader('Camera');
-            addControl('Reset Position', () => PluginWrapper.camera.resetPosition());
-            addControl('Toggle Spin', () => PluginWrapper.camera.toggleSpin());
-            // Same as "wheel icon" and Viewport options
-            // addControl('Clip', () => PluginWrapper.viewport.setSettings({ clip: [33, 66] }));
-            // addControl('Reset Clip', () => PluginWrapper.viewport.setSettings({ clip: [1, 100] }));
-            addSeparator();
-            addHeader('Animation');
-            // adjust this number to make the animation faster or slower
-            // requires to "restart" the animation if changed
-            PluginWrapper.animate.modelIndex.targetFps = 30;
-            addControl('Play To End', () => PluginWrapper.animate.modelIndex.onceForward());
-            addControl('Play To Start', () => PluginWrapper.animate.modelIndex.onceBackward());
-            addControl('Play Palindrome', () => PluginWrapper.animate.modelIndex.palindrome());
-            addControl('Play Loop', () => PluginWrapper.animate.modelIndex.loop());
-            addControl('Stop', () => PluginWrapper.animate.modelIndex.stop());
-            addSeparator();
-            addHeader('Misc');
-            addControl('Apply Evo Cons Style', () => PluginWrapper.coloring.evolutionaryConservation());
-            addControl('Apply Evo Cons Colors', () => PluginWrapper.coloring.evolutionaryConservation({ sequence: true, het: false, keepStyle: true }));
-            addControl('Default Visuals', () => PluginWrapper.updateStyle());
-            addSeparator();
-            addHeader('HET Groups');
-            addControl('Reset', () => PluginWrapper.hetGroups.reset());
-            addHetGroupsContainer();
-            addSeparator();
-            addHeader('Exp. Data');
-            addControl('Init', () => PluginWrapper.experimentalData.init($('volume-streaming-wrapper')));
-            addControl('Remove', () => PluginWrapper.experimentalData.remove());
-            addSeparator();
-            addHeader('State');
-            var snapshot;
-            addControl('Set Snapshot', () => {
-                // const options = { data: true, behavior: false, animation: false, interactivity: false, canvas3d: false, camera: false, cameraTransition: false };
-                snapshot = PluginWrapper.plugin.state.getSnapshot(/** options */);
-                // console.log(JSON.stringify(snapshot, null, 2));
-            });
-            addControl('Restore Snapshot', () => {
-                if (!snapshot) return;
-                PluginWrapper.snapshot.set(snapshot);
-            });
-            addControl('Download State', () => {
-                PluginWrapper.snapshot.download('molj');
-            });
-            addControl('Download Session', () => {
-                PluginWrapper.snapshot.download('molx');
-            });
-            ////////////////////////////////////////////////////////
-            function addHetGroupsContainer() {
-                var div = document.createElement('div');
-                div.id = 'het-groups';
-                $('controls').appendChild(div);
-            }
-            function addControl(label, action) {
-                var btn = document.createElement('button');
-                btn.onclick = action;
-                btn.innerText = label;
-                $('controls').appendChild(btn);
-            }
-            function addSeparator() {
-                var hr = document.createElement('hr');
-                $('controls').appendChild(hr);
-            }
-            function addHeader(header) {
-                var h = document.createElement('h3');
-                h.innerText = header;
-                $('controls').appendChild(h);
-            }
-            function listHetGroups(info) {
-                var div = $('het-groups');
-                div.innerHTML = '';
-                info.hetResidues.forEach(function (r) {
-                    var l = document.createElement('button');
-                    l.innerText = r.name;
-                    l.onclick = function () {
-                        PluginWrapper.hetGroups.focusFirst(r.name, { doNotLabelWaters: true });
-                    };
-                    div.appendChild(l);
-                });
-            }
-        </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* Proteopedia Wrapper</title>
+        <style>
+            * {
+                margin: 0;
+                padding: 0;
+                box-sizing: border-box;
+            }
+            #app {
+                position: absolute;
+                left: 160px;
+                top: 100px;
+                width: 600px;
+                height: 600px;
+                border: 1px solid #ccc;
+            }
+            #controls {
+                position: absolute;
+                width: 130px;
+                top: 10px;
+                left: 10px;
+            }
+            #controls > button {
+                display: block;
+                width: 100%;
+                text-align: left;
+            }
+            #controls > hr {
+                margin: 5px 0;
+            }
+            #controls > input, #controls > select {
+                width: 100%;
+                display: block;
+            }
+            #volume-streaming-wrapper {
+                position: absolute;
+                top: 100px;
+                left: 780px;
+                width: 300px;
+            }
+        </style>
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
+        <script type="text/javascript" src="./index.js"></script>
+    </head>
+    <body>
+        <div id='controls'>
+            <h3>Source</h3>
+            <input type='text' id='url' placeholder='url' style='width: 400px' />
+            <input type='text' id='assemblyId' placeholder='assembly id' />
+            <select id='format'>
+                <option value='cif' selected>CIF</option>
+                <option value='pdb'>PDB</option>
+            </select>
+            <input type='checkbox' id='isBinary' style="display: inline-block; width: auto" /> <label for="isBinary"> Binary</label><br />
+        </div>
+        <div id="app"></div>
+        <div id="volume-streaming-wrapper"></div>
+        <script>
+            // it might be a good idea to define these colors in a separate script file
+            var CustomColors = [0x00ff00, 0x0000ff];
+            // create an instance of the plugin
+            var PluginWrapper = new MolStarProteopediaWrapper();
+            console.log('Wrapper version', MolStarProteopediaWrapper.VERSION_MAJOR, MolStarProteopediaWrapper.VERSION_MINOR);
+            function $(id) { return document.getElementById(id); }
+            var pdbId = '1cbs', assemblyId= 'preferred', isBinary = true;
+            var url = 'https://www.ebi.ac.uk/pdbe/entry-files/download/' + pdbId + '.bcif'
+            var format = 'cif';
+            $('url').value = url;
+            $('url').onchange = function (e) { url = e.target.value; }
+            $('assemblyId').value = assemblyId;
+            $('assemblyId').onchange = function (e) { assemblyId = e.target.value; }
+            $('format').value = format;
+            $('format').onchange = function (e) { format = e.target.value; }
+            $('isBinary').checked = isBinary;
+            $('isBinary').onchange = function (e) { isBinary = !!e.target.checked; };
+            function loadAndSnapshot(params) {
+                PluginWrapper.load(params).then(() => {
+                    setTimeout(() => snapshot = PluginWrapper.plugin.state.getSnapshot({ canvas3d: false /* do not save spinning state */ }), 500);
+                });
+            }
+            var representationStyle = {
+                // sequence: { coloring: 'proteopedia-custom' }, // or just { }
+                hetGroups: { kind: 'ball-and-stick' }, // or 'spacefill
+                water: { hide: true },
+                snfg3d: { hide: false }
+            };
+            PluginWrapper.init('app' /** or document.getElementById('app') */, {
+                customColorList: CustomColors
+            }).then(() => {
+                PluginWrapper.setBackground(0xffffff);
+                loadAndSnapshot({ url: url, format: format, isBinary: isBinary, assemblyId: assemblyId, representationStyle: representationStyle });
+                PluginWrapper.toggleSpin();
+            });
+            PluginWrapper.events.modelInfo.subscribe(function (info) {
+                console.log('Model Info', info);
+                listHetGroups(info);
+            });
+            addControl('Load Asym Unit', () => loadAndSnapshot({ url: url, format: format, isBinary }));
+            addControl('Load Assembly', () => loadAndSnapshot({ url: url, format: format, isBinary, assemblyId: assemblyId }));
+            addSeparator();
+            addHeader('Representation');
+            addControl('Custom Chain Colors', () => PluginWrapper.updateStyle({ sequence: { coloring: 'proteopedia-custom' } }, true));
+            addControl('Default Chain Colors', () => PluginWrapper.updateStyle({ sequence: { } }, true));
+            addControl('HET Spacefill', () => PluginWrapper.updateStyle({ hetGroups: { kind: 'spacefill' } }, true));
+            addControl('HET Ball-and-stick', () => PluginWrapper.updateStyle({ hetGroups: { kind: 'ball-and-stick' } }, true));
+            addControl('Hide 3DSNFG', () => PluginWrapper.updateStyle({ snfg3d: { hide: true } }, true));
+            addControl('Show 3DSNFG', () => PluginWrapper.updateStyle({ snfg3d: { hide: false } }, true));
+            addControl('Hide Water', () => PluginWrapper.updateStyle({ water: { hide: true } }, true));
+            addControl('Show Water', () => PluginWrapper.updateStyle({ water: { hide: false } }, true));
+            addSeparator();
+            addHeader('Camera');
+            addControl('Reset Position', () => PluginWrapper.camera.resetPosition());
+            addControl('Toggle Spin', () => PluginWrapper.camera.toggleSpin());
+            // Same as "wheel icon" and Viewport options
+            // addControl('Clip', () => PluginWrapper.viewport.setSettings({ clip: [33, 66] }));
+            // addControl('Reset Clip', () => PluginWrapper.viewport.setSettings({ clip: [1, 100] }));
+            addSeparator();
+            addHeader('Animation');
+            // adjust this number to make the animation faster or slower
+            // requires to "restart" the animation if changed
+            PluginWrapper.animate.modelIndex.targetFps = 30;
+            addControl('Play To End', () => PluginWrapper.animate.modelIndex.onceForward());
+            addControl('Play To Start', () => PluginWrapper.animate.modelIndex.onceBackward());
+            addControl('Play Palindrome', () => PluginWrapper.animate.modelIndex.palindrome());
+            addControl('Play Loop', () => PluginWrapper.animate.modelIndex.loop());
+            addControl('Stop', () => PluginWrapper.animate.modelIndex.stop());
+            addSeparator();
+            addHeader('Misc');
+            addControl('Apply Evo Cons Style', () => PluginWrapper.coloring.evolutionaryConservation());
+            addControl('Apply Evo Cons Colors', () => PluginWrapper.coloring.evolutionaryConservation({ sequence: true, het: false, keepStyle: true }));
+            addControl('Default Visuals', () => PluginWrapper.updateStyle());
+            addSeparator();
+            addHeader('HET Groups');
+            addControl('Reset', () => PluginWrapper.hetGroups.reset());
+            addHetGroupsContainer();
+            addSeparator();
+            addHeader('Exp. Data');
+            addControl('Init', () => PluginWrapper.experimentalData.init($('volume-streaming-wrapper')));
+            addControl('Remove', () => PluginWrapper.experimentalData.remove());
+            addSeparator();
+            addHeader('State');
+            var snapshot;
+            addControl('Set Snapshot', () => {
+                // const options = { data: true, behavior: false, animation: false, interactivity: false, canvas3d: false, camera: false, cameraTransition: false };
+                snapshot = PluginWrapper.plugin.state.getSnapshot(/** options */);
+                // console.log(JSON.stringify(snapshot, null, 2));
+            });
+            addControl('Restore Snapshot', () => {
+                if (!snapshot) return;
+                PluginWrapper.snapshot.set(snapshot);
+            });
+            addControl('Download State', () => {
+                PluginWrapper.snapshot.download('molj');
+            });
+            addControl('Download Session', () => {
+                PluginWrapper.snapshot.download('molx');
+            });
+            ////////////////////////////////////////////////////////
+            function addHetGroupsContainer() {
+                var div = document.createElement('div');
+                div.id = 'het-groups';
+                $('controls').appendChild(div);
+            }
+            function addControl(label, action) {
+                var btn = document.createElement('button');
+                btn.onclick = action;
+                btn.innerText = label;
+                $('controls').appendChild(btn);
+            }
+            function addSeparator() {
+                var hr = document.createElement('hr');
+                $('controls').appendChild(hr);
+            }
+            function addHeader(header) {
+                var h = document.createElement('h3');
+                h.innerText = header;
+                $('controls').appendChild(h);
+            }
+            function listHetGroups(info) {
+                var div = $('het-groups');
+                div.innerHTML = '';
+                info.hetResidues.forEach(function (r) {
+                    var l = document.createElement('button');
+                    l.innerText = r.name;
+                    l.onclick = function () {
+                        PluginWrapper.hetGroups.focusFirst(r.name, { doNotLabelWaters: true });
+                    };
+                    div.appendChild(l);
+                });
+            }
+        </script>
+    </body>
 </html>

package/lib/examples/proteopedia-wrapper/index.js CHANGED Viewed

@@ -9,7 +9,7 @@ import { DefaultCanvas3DParams } from '../../mol-canvas3d/canvas3d';
 import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in/model-index';
 import { createStructureRepresentationParams } from '../../mol-plugin-state/helpers/structure-representation-params';
 import { StateTransforms } from '../../mol-plugin-state/transforms';
-import { createPlugin } from '../../mol-plugin-ui';
+import { createPluginUI } from '../../mol-plugin-ui';
 import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
 import { CreateVolumeStreamingInfo, InitVolumeStreaming } from '../../mol-plugin/behavior/dynamic/volume-streaming/transformers';
 import { PluginCommands } from '../../mol-plugin/commands';
@@ -233,21 +233,33 @@ var MolStarProteopediaWrapper = /** @class */ (function () {
         };
     }
     MolStarProteopediaWrapper.prototype.init = function (target, options) {
-        this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target) : target, __assign(__assign({}, DefaultPluginUISpec()), { animations: [
-                AnimateModelIndex
-            ], layout: {
-                initial: {
-                    isExpanded: false,
-                    showControls: false
+        return __awaiter(this, void 0, void 0, function () {
+            var _a, customColoring;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        _a = this;
+                        return [4 /*yield*/, createPluginUI(typeof target === 'string' ? document.getElementById(target) : target, __assign(__assign({}, DefaultPluginUISpec()), { animations: [
+                                    AnimateModelIndex
+                                ], layout: {
+                                    initial: {
+                                        isExpanded: false,
+                                        showControls: false
+                                    }
+                                }, components: {
+                                    remoteState: 'none'
+                                } }))];
+                    case 1:
+                        _a.plugin = _b.sent();
+                        customColoring = createProteopediaCustomTheme((options && options.customColorList) || []);
+                        this.plugin.representation.structure.themes.colorThemeRegistry.add(customColoring);
+                        this.plugin.representation.structure.themes.colorThemeRegistry.add(EvolutionaryConservation.colorThemeProvider);
+                        this.plugin.managers.lociLabels.addProvider(EvolutionaryConservation.labelProvider);
+                        this.plugin.customModelProperties.register(EvolutionaryConservation.propertyProvider, true);
+                        return [2 /*return*/];
                 }
-            }, components: {
-                remoteState: 'none'
-            } }));
-        var customColoring = createProteopediaCustomTheme((options && options.customColorList) || []);
-        this.plugin.representation.structure.themes.colorThemeRegistry.add(customColoring);
-        this.plugin.representation.structure.themes.colorThemeRegistry.add(EvolutionaryConservation.colorThemeProvider);
-        this.plugin.managers.lociLabels.addProvider(EvolutionaryConservation.labelProvider);
-        this.plugin.customModelProperties.register(EvolutionaryConservation.propertyProvider, true);
+            });
+        });
     };
     Object.defineProperty(MolStarProteopediaWrapper.prototype, "state", {
         get: function () {

package/lib/extensions/alpha-orbitals/transforms.d.ts CHANGED Viewed

@@ -72,7 +72,6 @@ export declare const CreateOrbitalDensityVolume: StateTransformer<BasisAndOrbita
     }>, "on">;
 }>>;
 export declare const CreateOrbitalRepresentation3D: StateTransformer<PluginStateObject.Volume.Data, PluginStateObject.Volume.Representation3D, PD.Normalize<{
-    directVolume: boolean;
     relativeIsovalue: number;
     kind: "negative" | "positive";
     color: import("../../mol-util/color").Color;

package/lib/extensions/alpha-orbitals/transforms.js CHANGED Viewed

@@ -176,7 +176,6 @@ export var CreateOrbitalRepresentation3D = PluginStateTransform.BuiltIn({
     from: PluginStateObject.Volume.Data,
     to: PluginStateObject.Volume.Representation3D,
     params: {
-        directVolume: PD.Boolean(false),
         relativeIsovalue: PD.Numeric(1, { min: 0.01, max: 5, step: 0.01 }),
         kind: PD.Select('positive', [['positive', 'Positive'], ['negative', 'Negative']]),
         color: PD.Color(ColorNames.blue),
@@ -249,19 +248,7 @@ function volumeParams(plugin, volume, params) {
     if (!isovalues)
         throw new Error('Isovalues are not computed.');
     var value = isovalues[params.kind];
-    return createVolumeRepresentationParams(plugin, volume.data, params.directVolume ? {
-        type: 'direct-volume',
-        typeParams: {
-            alpha: params.alpha,
-            renderMode: {
-                name: 'isosurface',
-                params: { isoValue: { kind: 'absolute', absoluteValue: (value !== null && value !== void 0 ? value : 1000) * params.relativeIsovalue }, singleLayer: false }
-            },
-            xrayShaded: params.xrayShaded
-        },
-        color: 'uniform',
-        colorParams: { value: params.color }
-    } : {
+    return createVolumeRepresentationParams(plugin, volume.data, {
         type: 'isosurface',
         typeParams: { isoValue: { kind: 'absolute', absoluteValue: (value !== null && value !== void 0 ? value : 1000) * params.relativeIsovalue }, alpha: params.alpha, xrayShaded: params.xrayShaded, tryUseGpu: params.tryUseGpu },
         color: 'uniform',

package/lib/extensions/anvil/behavior.d.ts CHANGED Viewed

@@ -32,6 +32,10 @@ declare const MembraneOrientation3D: StateTransformer<PluginStateObject.Molecule
         roughness: number;
         bumpiness: number;
     }>;
+    clip: PD.Normalize<{
+        variant: any;
+        objects: any;
+    }>;
     sectorOpacity: number;
     doubleSided: boolean;
     flipSided: boolean;