npm - molstar - Versions diffs - 4.0.1 → 4.2.0 - Mend

molstar 4.0.1 → 4.2.0

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 (907) hide show

package/build/viewer/molstar.js.LICENSE.txt CHANGED Viewed

@@ -1,12 +1,3 @@
-/*!
- * The buffer module from node.js, for the browser.
- *
- * @author   Feross Aboukhadijeh <https://feross.org>
- * @license  MIT
- */
-/*! ieee754. BSD-3-Clause License. Feross Aboukhadijeh <https://feross.org/opensource> */
 /*! safe-buffer. MIT License. Feross Aboukhadijeh <https://feross.org/opensource> */
 /**

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/docking-viewer/viewport.d.ts CHANGED Viewed

@@ -24,12 +24,12 @@ export declare const StructurePreset: StructureRepresentationPresetProvider<{
     representations?: undefined;
 } | {
     components: {
-        ligand: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, 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>> | undefined;
-        polymer: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, 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>> | undefined;
+        ligand: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../mol-state").StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>> | undefined;
+        polymer: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../mol-state").StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>> | undefined;
     };
     representations: {
-        ligand: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, 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>>;
-        polymer: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, 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>>;
+        ligand: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../mol-state").StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>>;
+        polymer: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../mol-state").StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>>;
     };
 }>;
 export declare const IllustrativePreset: StructureRepresentationPresetProvider<{
@@ -50,12 +50,12 @@ export declare const IllustrativePreset: StructureRepresentationPresetProvider<{
     representations?: undefined;
 } | {
     components: {
-        ligand: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, 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>> | undefined;
-        polymer: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, 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>> | undefined;
+        ligand: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../mol-state").StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>> | undefined;
+        polymer: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../mol-state").StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>> | undefined;
     };
     representations: {
-        ligand: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, 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>>;
-        polymer: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, 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>>;
+        ligand: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../mol-state").StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>>;
+        polymer: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../mol-state").StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>>;
     };
 }>;
 export declare const ShowButtons: import("../../mol-plugin/config").PluginConfigItem<boolean>;

package/lib/apps/mesoscale-explorer/behavior/camera.d.ts CHANGED Viewed

@@ -6,7 +6,7 @@
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { PluginBehavior } from '../../../mol-plugin/behavior';
 import { Binding } from '../../../mol-util/binding';
-export declare const MesoFocusLoci: import("../../../mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, PD.Values<{
+export declare const MesoFocusLoci: import("../../../mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, PD.Values<{
     minRadius: PD.Numeric;
     extraRadius: PD.Numeric;
     durationMs: PD.Numeric;

package/lib/apps/mesoscale-explorer/behavior/select.d.ts CHANGED Viewed

@@ -6,7 +6,7 @@
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { PluginBehavior } from '../../../mol-plugin/behavior';
 import { Binding } from '../../../mol-util/binding';
-export declare const MesoSelectLoci: import("../../../mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, PD.Values<{
+export declare const MesoSelectLoci: import("../../../mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, PD.Values<{
     bindings: PD.Value<{
         clickToggleSelect: Binding;
         hoverHighlightOnly: Binding;

package/lib/apps/mesoscale-explorer/data/cellpack/model.d.ts CHANGED Viewed

@@ -9,12 +9,12 @@ import { PluginStateObject as PSO } from '../../../../mol-plugin-state/objects';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
 export { CellpackAssembly };
 type CellpackAssembly = typeof CellpackAssembly;
-declare const CellpackAssembly: import("../../../../mol-state/transformer").StateTransformer<PSO.Molecule.Model, PSO.Molecule.Structure, PD.Normalize<{
+declare const CellpackAssembly: import("../../../../mol-state").StateTransformer<PSO.Molecule.Model, PSO.Molecule.Structure, PD.Normalize<{
     id: string;
 }>>;
 export { CellpackStructure };
 type CellpackStructure = typeof CellpackStructure;
-declare const CellpackStructure: import("../../../../mol-state/transformer").StateTransformer<PSO.Root, PSO.Molecule.Structure, PD.Normalize<{
+declare const CellpackStructure: import("../../../../mol-state").StateTransformer<PSO.Root, PSO.Molecule.Structure, PD.Normalize<{
     structureRef: string;
     entityId: string;
 }>>;

package/lib/apps/mesoscale-explorer/data/cellpack/preset.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Ludovic Autin <ludovic.autin@gmail.com>

package/lib/apps/mesoscale-explorer/data/cellpack/preset.js CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Ludovic Autin <ludovic.autin@gmail.com>
@@ -83,11 +83,11 @@ export async function createCellpackHierarchy(plugin, trajectory) {
         .commit();
     const compRoot = await state.build()
         .toRoot()
-        .applyOrUpdateTagged('group:comp:', MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `comp:`, label: 'compartment', color: { type: 'custom', value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1 } }, { tags: 'group:comp:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
+        .applyOrUpdateTagged('group:comp:', MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `comp:`, label: 'compartment', color: { type: 'custom', value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'group:comp:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
         .commit();
     const funcRoot = await state.build()
         .toRoot()
-        .applyOrUpdateTagged('group:func:', MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `func:`, label: 'function', color: { type: 'custom', value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1 } }, { tags: 'group:func:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
+        .applyOrUpdateTagged('group:func:', MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `func:`, label: 'function', color: { type: 'custom', value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'group:func:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
         .commit();
     if (entities._rowCount > 1) {
         for (let i = 0; i < entities._rowCount; i++) {
@@ -137,7 +137,7 @@ export async function createCellpackHierarchy(plugin, trajectory) {
                     parent.cell.state.isCollapsed = false;
                     const group = await state.build()
                         .to(parent)
-                        .applyOrUpdateTagged(`group:comp:${n}`, MesoscaleGroup, { ...groupParams, root: parent === compRoot, index: colorIdx, tag: `comp:${n}`, label, color: { type: 'generate', value: color, variability: 20, shift: 0, lightness: 0, alpha: 1 } }, { tags: `comp:${p}`, state: { isCollapsed: true, isHidden: groupParams.hidden } })
+                        .applyOrUpdateTagged(`group:comp:${n}`, MesoscaleGroup, { ...groupParams, root: parent === compRoot, index: colorIdx, tag: `comp:${n}`, label, color: { type: 'generate', value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `comp:${p}`, state: { isCollapsed: true, isHidden: groupParams.hidden } })
                         .commit({ revertOnError: true });
                     compGroups.set(n, group);
                 }
@@ -148,7 +148,7 @@ export async function createCellpackHierarchy(plugin, trajectory) {
                 const color = colorIdx !== undefined ? baseFuncColors[colorIdx] : ColorNames.white;
                 const group = await state.build()
                     .to(funcRoot)
-                    .applyOrUpdateTagged(`group:func:${f}`, MesoscaleGroup, { ...groupParams, index: colorIdx, tag: `func:${f}`, label: f, color: { type: 'custom', value: color, variability: 20, shift: 0, lightness: 0, alpha: 1 } }, { tags: 'func:', state: { isCollapsed: true, isHidden: groupParams.hidden } })
+                    .applyOrUpdateTagged(`group:func:${f}`, MesoscaleGroup, { ...groupParams, index: colorIdx, tag: `func:${f}`, label: f, color: { type: 'custom', value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'func:', state: { isCollapsed: true, isHidden: groupParams.hidden } })
                     .commit({ revertOnError: true });
                 funcGroups.set(f, group);
             }

package/lib/apps/mesoscale-explorer/data/generic/preset.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/apps/mesoscale-explorer/data/generic/preset.js CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -115,7 +115,7 @@ export async function createGenericHierarchy(plugin, file) {
     async function addGroup(g, cell, parent) {
         const group = await state.build()
             .to(cell)
-            .apply(MesoscaleGroup, { ...groupParams, index: undefined, tag: `${g.root}:${g.id}`, label: g.label || g.id, color: { type: 'custom', value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1 } }, { tags: [`group:${g.root}:${g.id}`, g.root === parent ? `${g.root}:` : `${g.root}:${parent}`], state: { isCollapsed: true, isHidden: groupParams.hidden } })
+            .apply(MesoscaleGroup, { ...groupParams, index: undefined, tag: `${g.root}:${g.id}`, label: g.label || g.id, color: { type: 'custom', value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: [`group:${g.root}:${g.id}`, g.root === parent ? `${g.root}:` : `${g.root}:${parent}`], state: { isCollapsed: true, isHidden: groupParams.hidden } })
             .commit();
         if (g.children) {
             for (const c of g.children) {
@@ -126,7 +126,7 @@ export async function createGenericHierarchy(plugin, file) {
     for (const r of manifest.roots) {
         const root = await state.build()
             .toRoot()
-            .apply(MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `${r.id}:`, label: r.label || r.id, color: { type: 'custom', value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1 } }, { tags: `group:${r.id}:`, state: { isCollapsed: false, isHidden: groupParams.hidden } })
+            .apply(MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `${r.id}:`, label: r.label || r.id, color: { type: 'custom', value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `group:${r.id}:`, state: { isCollapsed: false, isHidden: groupParams.hidden } })
             .commit();
         if (r.children) {
             for (const c of r.children) {

package/lib/apps/mesoscale-explorer/data/mmcif/preset.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/apps/mesoscale-explorer/data/mmcif/preset.js CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -100,7 +100,7 @@ export async function createMmcifHierarchy(plugin, trajectory) {
     const clipVariant = willBeMerged ? 'pixel' : 'instance';
     const entRoot = await state.build()
         .toRoot()
-        .applyOrUpdateTagged('group:ent:', MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `ent:`, label: 'entity', color: { type: 'custom', value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1 } }, { tags: 'group:ent:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
+        .applyOrUpdateTagged('group:ent:', MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `ent:`, label: 'entity', color: { type: 'custom', value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'group:ent:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
         .commit();
     const getEntityType = (i) => {
         if (entities.type.value(i) === 'water')
@@ -130,7 +130,7 @@ export async function createMmcifHierarchy(plugin, trajectory) {
             const color = colorIdx !== undefined ? baseEntColors[colorIdx] : ColorNames.white;
             const group = await state.build()
                 .to(entRoot)
-                .applyOrUpdateTagged(`group:ent:${t}`, MesoscaleGroup, { ...groupParams, index: colorIdx, tag: `ent:${t}`, label: t, color: { type: 'generate', value: color, variability: 20, shift: 0, lightness: 0, alpha: 1 } }, { tags: `ent:`, state: { isCollapsed: true, isHidden: groupParams.hidden } })
+                .applyOrUpdateTagged(`group:ent:${t}`, MesoscaleGroup, { ...groupParams, index: colorIdx, tag: `ent:${t}`, label: t, color: { type: 'generate', value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `ent:`, state: { isCollapsed: true, isHidden: groupParams.hidden } })
                 .commit({ revertOnError: true });
             entGroups.set(t, group);
         }

package/lib/apps/mesoscale-explorer/data/petworld/preset.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2022-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2022-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/apps/mesoscale-explorer/data/petworld/preset.js CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2022-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2022-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -91,11 +91,11 @@ export async function createPetworldHierarchy(plugin, trajectory) {
     const groupParams = getMesoscaleGroupParams(graphicsMode);
     const group = await state.build()
         .toRoot()
-        .applyOrUpdateTagged('group:ent:', MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `ent:`, label: 'entity', color: { type: 'generate', value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1 } }, { tags: 'group:ent:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
+        .applyOrUpdateTagged('group:ent:', MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `ent:`, label: 'entity', color: { type: 'generate', value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'group:ent:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
         .commit({ revertOnError: true });
     await state.build()
         .to(group)
-        .applyOrUpdateTagged(`group:ent:mem`, MesoscaleGroup, { ...groupParams, index: undefined, tag: `ent:mem`, label: 'Membrane', color: { type: 'uniform', value: ColorNames.lightgrey, variability: 20, shift: 0, lightness: 0, alpha: 1 } }, { tags: `ent:`, state: { isCollapsed: true, isHidden: groupParams.hidden } })
+        .applyOrUpdateTagged(`group:ent:mem`, MesoscaleGroup, { ...groupParams, index: undefined, tag: `ent:mem`, label: 'Membrane', color: { type: 'uniform', value: ColorNames.lightgrey, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `ent:`, state: { isCollapsed: true, isHidden: groupParams.hidden } })
         .commit();
     const colors = getDistinctBaseColors(other.length, 0);
     await state.transaction(async () => {

package/lib/apps/mesoscale-explorer/data/state.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -24,6 +24,7 @@ export declare const ColorParams: {
     shift: PD.Numeric;
     lightness: PD.Numeric;
     alpha: PD.Numeric;
+    emissive: PD.Numeric;
 };
 export type ColorProps = PD.Values<typeof ColorParams>;
 export declare const ColorValueParam: PD.Color;
@@ -34,6 +35,7 @@ export declare const RootParams: {
     shift: PD.Numeric;
     lightness: PD.Numeric;
     alpha: PD.Numeric;
+    emissive: PD.Numeric;
 };
 export declare const LightnessParams: {
     lightness: PD.Numeric;
@@ -42,6 +44,9 @@ export declare const DimLightness = 6;
 export declare const OpacityParams: {
     alpha: PD.Numeric;
 };
+export declare const EmissiveParams: {
+    emissive: PD.Numeric;
+};
 export declare const PatternParams: {
     frequency: PD.Numeric;
     amplitude: PD.Numeric;
@@ -122,9 +127,11 @@ export declare const MesoscaleGroupParams: {
         shift: number;
         lightness: number;
         alpha: number;
+        emissive: number;
     }>>;
     lightness: PD.Numeric;
     alpha: PD.Numeric;
+    emissive: PD.Numeric;
     lod: PD.Group<PD.Normalize<{
         lodLevels: PD.Normalize<{
             minDistance: number;
@@ -162,18 +169,18 @@ declare const MesoscaleGroupObject_base: {
         label: string;
         description?: string | undefined;
     } | undefined): {
-        id: import("../../../mol-util/uuid").UUID;
+        id: import("../../../mol-util").UUID;
         type: PSO.TypeInfo;
         label: string;
         description?: string | undefined;
         data: {};
     };
     type: PSO.TypeInfo;
-    is(obj?: import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>> | undefined): obj is import("../../../mol-state/object").StateObject<{}, PSO.TypeInfo>;
+    is(obj?: import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../../mol-state").StateObject<{}, PSO.TypeInfo>;
 };
 export declare class MesoscaleGroupObject extends MesoscaleGroupObject_base {
 }
-export declare const MesoscaleGroup: import("../../../mol-state/transformer").StateTransformer<PSO.Root, MesoscaleGroupObject, PD.Normalize<{
+export declare const MesoscaleGroup: import("../../../mol-state").StateTransformer<PSO.Root, MesoscaleGroupObject, PD.Normalize<{
     root: boolean;
     index: number;
     tag: string;
@@ -186,9 +193,11 @@ export declare const MesoscaleGroup: import("../../../mol-state/transformer").St
         shift: any;
         lightness: any;
         alpha: any;
+        emissive: any;
     }>;
     lightness: number;
     alpha: number;
+    emissive: number;
     lod: PD.Normalize<{
         lodLevels: any;
         cellSize: any;
@@ -235,7 +244,7 @@ declare const MesoscaleStateObject_base: {
         label: string;
         description?: string | undefined;
     } | undefined): {
-        id: import("../../../mol-util/uuid").UUID;
+        id: import("../../../mol-util").UUID;
         type: PSO.TypeInfo;
         label: string;
         description?: string | undefined;
@@ -247,7 +256,7 @@ declare const MesoscaleStateObject_base: {
         }>;
     };
     type: PSO.TypeInfo;
-    is(obj?: import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>> | undefined): obj is import("../../../mol-state/object").StateObject<PD.Values<{
+    is(obj?: import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../../mol-state").StateObject<PD.Values<{
         filter: PD.Value<string>;
         graphics: PD.Select<GraphicsMode>;
         description: PD.Value<string>;
@@ -267,13 +276,13 @@ declare const MesoscaleState: {
 };
 export declare function getRoots(plugin: PluginContext): StateSelection.CellSeq<StateObjectCell<MesoscaleGroupObject>>;
 export declare function getGroups(plugin: PluginContext, tag?: string): StateSelection.CellSeq<StateObjectCell<MesoscaleGroupObject>>;
-export declare function getAllGroups(plugin: PluginContext, tag?: string): StateObjectCell<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/transform").StateTransform<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 function getAllLeafGroups(plugin: PluginContext, tag: string): StateObjectCell<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/transform").StateTransform<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 function getAllGroups(plugin: PluginContext, tag?: string): StateObjectCell<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateTransform<import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>>>[];
+export declare function getAllLeafGroups(plugin: PluginContext, tag: string): StateObjectCell<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateTransform<import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>>>[];
 type EntityCells = StateSelection.CellSeq<StateObjectCell<PSO.Molecule.Structure.Representation3D | PSO.Shape.Representation3D>>;
 export declare function getEntities(plugin: PluginContext, tag?: string): EntityCells;
-export declare function getFilteredEntities(plugin: PluginContext, tag: string, filter: string): StateObjectCell<PSO.Molecule.Structure.Representation3D | PSO.Shape.Representation3D, import("../../../mol-state/transform").StateTransform<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 function getFilteredEntities(plugin: PluginContext, tag: string, filter: string): StateObjectCell<PSO.Molecule.Structure.Representation3D | PSO.Shape.Representation3D, import("../../../mol-state").StateTransform<import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>>>[];
 export declare function getAllEntities(plugin: PluginContext, tag?: string): EntityCells;
-export declare function getAllFilteredEntities(plugin: PluginContext, tag: string, filter: string): StateObjectCell<PSO.Molecule.Structure.Representation3D | PSO.Shape.Representation3D, import("../../../mol-state/transform").StateTransform<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 function getAllFilteredEntities(plugin: PluginContext, tag: string, filter: string): StateObjectCell<PSO.Molecule.Structure.Representation3D | PSO.Shape.Representation3D, import("../../../mol-state").StateTransform<import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>>>[];
 export declare function getEntityLabel(plugin: PluginContext, cell: StateObjectCell): string;
 export declare function updateColors(plugin: PluginContext, values: PD.Values, tag: string, filter: string): Promise<void>;
 export declare function expandAllGroups(plugin: PluginContext): void;

package/lib/apps/mesoscale-explorer/data/state.js CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -99,6 +99,7 @@ export const ColorParams = {
     shift: PD.Numeric(0, { min: 0, max: 100, step: 1 }, { hideIf: p => !p.type.includes('generate') }),
     lightness: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }, { hideIf: p => p.type === 'custom' }),
     alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }, { hideIf: p => p.type === 'custom' }),
+    emissive: PD.Numeric(0, { min: 0, max: 1, step: 0.01 }, { hideIf: p => p.type === 'custom' }),
 };
 export const ColorValueParam = PD.Color(Color(0xFFFFFF));
 export const RootParams = {
@@ -108,6 +109,7 @@ export const RootParams = {
     shift: PD.Numeric(0, { min: 0, max: 100, step: 1 }, { hideIf: p => !p.type.includes('generate') }),
     lightness: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }, { hideIf: p => p.type === 'custom' }),
     alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }, { hideIf: p => p.type === 'custom' }),
+    emissive: PD.Numeric(0, { min: 0, max: 1, step: 0.01 }, { hideIf: p => p.type === 'custom' }),
 };
 export const LightnessParams = {
     lightness: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
@@ -116,6 +118,9 @@ export const DimLightness = 6;
 export const OpacityParams = {
     alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
 };
+export const EmissiveParams = {
+    emissive: PD.Numeric(0, { min: 0, max: 1, step: 0.01 }),
+};
 export const PatternParams = {
     frequency: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
     amplitude: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
@@ -213,6 +218,7 @@ export const MesoscaleGroupParams = {
     color: PD.Group(RootParams),
     lightness: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
     alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
+    emissive: PD.Numeric(0, { min: 0, max: 1, step: 0.01 }),
     lod: PD.Group(LodParams),
     clip: PD.Group(SimpleClipParams),
 };
@@ -440,7 +446,7 @@ export function getEntityLabel(plugin, cell) {
 export async function updateColors(plugin, values, tag, filter) {
     var _a, _b;
     const update = plugin.state.data.build();
-    const { type, value, shift, lightness, alpha } = values;
+    const { type, value, shift, lightness, alpha, emissive } = values;
     if (type === 'group-generate' || type === 'group-uniform') {
         const groups = getAllLeafGroups(plugin, tag);
         const baseColors = getDistinctBaseColors(groups.length, shift);
@@ -460,12 +466,14 @@ export async function updateColors(plugin, values, tag, filter) {
                         old.colorTheme.params.lightness = lightness;
                         old.type.params.alpha = alpha;
                         old.type.params.xrayShaded = alpha < 1 ? 'inverted' : false;
+                        old.type.params.emissive = emissive;
                     }
                     else if (old.coloring) {
                         old.coloring.params.color = c;
                         old.coloring.params.lightness = lightness;
                         old.alpha = alpha;
                         old.xrayShaded = alpha < 1 ? true : false;
+                        old.emissive = emissive;
                     }
                 });
             }
@@ -474,6 +482,7 @@ export async function updateColors(plugin, values, tag, filter) {
                 old.color.value = baseColors[i];
                 old.color.lightness = lightness;
                 old.color.alpha = alpha;
+                old.color.emissive = emissive;
             });
         }
     }
@@ -491,12 +500,14 @@ export async function updateColors(plugin, values, tag, filter) {
                     old.colorTheme.params.lightness = lightness;
                     old.type.params.alpha = alpha;
                     old.type.params.xrayShaded = alpha < 1 ? 'inverted' : false;
+                    old.type.params.emissive = emissive;
                 }
                 else if (old.coloring) {
                     old.coloring.params.color = c;
                     old.coloring.params.lightness = lightness;
                     old.alpha = alpha;
                     old.xrayShaded = alpha < 1 ? true : false;
+                    old.emissive = emissive;
                 }
             });
         }
@@ -507,6 +518,7 @@ export async function updateColors(plugin, values, tag, filter) {
                 old.color.value = value;
                 old.color.lightness = lightness;
                 old.color.alpha = alpha;
+                old.color.emissive = emissive;
             });
         }
     }