molstar 4.1.0 → 4.2.0

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

@@ -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/commonjs/apps/mesoscale-explorer/data/petworld/preset.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
  */
@@ -94,11 +94,11 @@ async function createPetworldHierarchy(plugin, trajectory) {
     const groupParams = (0, state_1.getMesoscaleGroupParams)(graphicsMode);
     const group = await state.build()
         .toRoot()
-        .applyOrUpdateTagged('group:ent:', state_1.MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `ent:`, label: 'entity', color: { type: 'generate', value: names_1.ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1 } }, { tags: 'group:ent:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
+        .applyOrUpdateTagged('group:ent:', state_1.MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `ent:`, label: 'entity', color: { type: 'generate', value: names_1.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`, state_1.MesoscaleGroup, { ...groupParams, index: undefined, tag: `ent:mem`, label: 'Membrane', color: { type: 'uniform', value: names_1.ColorNames.lightgrey, variability: 20, shift: 0, lightness: 0, alpha: 1 } }, { tags: `ent:`, state: { isCollapsed: true, isHidden: groupParams.hidden } })
+        .applyOrUpdateTagged(`group:ent:mem`, state_1.MesoscaleGroup, { ...groupParams, index: undefined, tag: `ent:mem`, label: 'Membrane', color: { type: 'uniform', value: names_1.ColorNames.lightgrey, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `ent:`, state: { isCollapsed: true, isHidden: groupParams.hidden } })
         .commit();
     const colors = (0, state_1.getDistinctBaseColors)(other.length, 0);
     await state.transaction(async () => {

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

@@ -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;
@@ -186,9 +193,11 @@ export declare const MesoscaleGroup: import("../../../mol-state").StateTransform
         shift: any;
         lightness: any;
         alpha: any;
+        emissive: any;
     }>;
     lightness: number;
     alpha: number;
+    emissive: number;
     lod: PD.Normalize<{
         lodLevels: any;
         cellSize: any;

package/lib/commonjs/apps/mesoscale-explorer/data/state.js

@@ -1,11 +1,11 @@
 "use strict";
 /**
- * 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>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.expandAllGroups = exports.updateColors = exports.getEntityLabel = exports.getAllFilteredEntities = exports.getAllEntities = exports.getFilteredEntities = exports.getEntities = exports.getAllLeafGroups = exports.getAllGroups = exports.getGroups = exports.getRoots = exports.MesoscaleState = exports.MesoscaleStateObject = exports.MesoscaleStateParams = exports.setGraphicsCanvas3DProps = exports.getGraphicsModeProps = exports.getLodLevels = exports.getMesoscaleGroupParams = exports.MesoscaleGroup = exports.MesoscaleGroupObject = exports.MesoscaleGroupParams = exports.createClipMapping = exports.getClipObjects = exports.SimpleClipParams = exports.LodParams = exports.PatternParams = exports.OpacityParams = exports.DimLightness = exports.LightnessParams = exports.RootParams = exports.ColorValueParam = exports.ColorParams = exports.getDistinctBaseColors = exports.getDistinctGroupColors = void 0;
+exports.expandAllGroups = exports.updateColors = exports.getEntityLabel = exports.getAllFilteredEntities = exports.getAllEntities = exports.getFilteredEntities = exports.getEntities = exports.getAllLeafGroups = exports.getAllGroups = exports.getGroups = exports.getRoots = exports.MesoscaleState = exports.MesoscaleStateObject = exports.MesoscaleStateParams = exports.setGraphicsCanvas3DProps = exports.getGraphicsModeProps = exports.getLodLevels = exports.getMesoscaleGroupParams = exports.MesoscaleGroup = exports.MesoscaleGroupObject = exports.MesoscaleGroupParams = exports.createClipMapping = exports.getClipObjects = exports.SimpleClipParams = exports.LodParams = exports.PatternParams = exports.EmissiveParams = exports.OpacityParams = exports.DimLightness = exports.LightnessParams = exports.RootParams = exports.ColorValueParam = exports.ColorParams = exports.getDistinctBaseColors = exports.getDistinctGroupColors = void 0;
 const objects_1 = require("../../../mol-plugin-state/objects");
 const param_definition_1 = require("../../../mol-util/param-definition");
 const mol_task_1 = require("../../../mol-task");
@@ -104,6 +104,7 @@ exports.ColorParams = {
     shift: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 100, step: 1 }, { hideIf: p => !p.type.includes('generate') }),
     lightness: param_definition_1.ParamDefinition.Numeric(0, { min: -6, max: 6, step: 0.1 }, { hideIf: p => p.type === 'custom' }),
     alpha: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 1, step: 0.01 }, { hideIf: p => p.type === 'custom' }),
+    emissive: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 1, step: 0.01 }, { hideIf: p => p.type === 'custom' }),
 };
 exports.ColorValueParam = param_definition_1.ParamDefinition.Color((0, color_1.Color)(0xFFFFFF));
 exports.RootParams = {
@@ -113,6 +114,7 @@ exports.RootParams = {
     shift: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 100, step: 1 }, { hideIf: p => !p.type.includes('generate') }),
     lightness: param_definition_1.ParamDefinition.Numeric(0, { min: -6, max: 6, step: 0.1 }, { hideIf: p => p.type === 'custom' }),
     alpha: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 1, step: 0.01 }, { hideIf: p => p.type === 'custom' }),
+    emissive: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 1, step: 0.01 }, { hideIf: p => p.type === 'custom' }),
 };
 exports.LightnessParams = {
     lightness: param_definition_1.ParamDefinition.Numeric(0, { min: -6, max: 6, step: 0.1 }),
@@ -121,6 +123,9 @@ exports.DimLightness = 6;
 exports.OpacityParams = {
     alpha: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 1, step: 0.01 }),
 };
+exports.EmissiveParams = {
+    emissive: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 1, step: 0.01 }),
+};
 exports.PatternParams = {
     frequency: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 1, step: 0.01 }),
     amplitude: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 1, step: 0.01 }),
@@ -220,6 +225,7 @@ exports.MesoscaleGroupParams = {
     color: param_definition_1.ParamDefinition.Group(exports.RootParams),
     lightness: param_definition_1.ParamDefinition.Numeric(0, { min: -6, max: 6, step: 0.1 }),
     alpha: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 1, step: 0.01 }),
+    emissive: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 1, step: 0.01 }),
     lod: param_definition_1.ParamDefinition.Group(exports.LodParams),
     clip: param_definition_1.ParamDefinition.Group(exports.SimpleClipParams),
 };
@@ -462,7 +468,7 @@ exports.getEntityLabel = getEntityLabel;
 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);
@@ -482,12 +488,14 @@ 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;
                     }
                 });
             }
@@ -496,6 +504,7 @@ async function updateColors(plugin, values, tag, filter) {
                 old.color.value = baseColors[i];
                 old.color.lightness = lightness;
                 old.color.alpha = alpha;
+                old.color.emissive = emissive;
             });
         }
     }
@@ -513,12 +522,14 @@ 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;
                 }
             });
         }
@@ -529,6 +540,7 @@ async function updateColors(plugin, values, tag, filter) {
                 old.color.value = value;
                 old.color.lightness = lightness;
                 old.color.alpha = alpha;
+                old.color.emissive = emissive;
             });
         }
     }

package/lib/commonjs/apps/mesoscale-explorer/ui/entities.d.ts

@@ -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>
  */
@@ -170,9 +170,11 @@ export declare class EntityNode extends Node<{}, {
             shift: any;
             lightness: any;
             alpha: any;
+            emissive: any;
         }>;
         lightness: number;
         alpha: number;
+        emissive: number;
         lod: PD.Normalize<{
             lodLevels: any;
             cellSize: any;
@@ -202,6 +204,9 @@ export declare class EntityNode extends Node<{}, {
     get opacityValue(): {
         alpha: number;
     } | undefined;
+    get emissiveValue(): {
+        emissive: number;
+    } | undefined;
     get clipValue(): Clip.Props | undefined;
     get lodValue(): PD.Values<typeof LodParams> | undefined;
     get patternValue(): {
@@ -211,6 +216,7 @@ export declare class EntityNode extends Node<{}, {
     updateColor: ParamOnChange;
     updateLightness: (values: PD.Values) => Promise<void>;
     updateOpacity: (values: PD.Values) => Promise<void>;
+    updateEmissive: (values: PD.Values) => Promise<void>;
     updateClip: (props: Clip.Props) => void;
     updateLod: (values: PD.Values) => void;
     updatePattern: (values: PD.Values) => Promise<void>;

package/lib/commonjs/apps/mesoscale-explorer/ui/entities.js

@@ -4,7 +4,7 @@ exports.EntityNode = exports.GroupNode = exports.EntityControls = exports.Select
 const tslib_1 = require("tslib");
 const jsx_runtime_1 = require("react/jsx-runtime");
 /**
- * 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>
  */
@@ -388,7 +388,7 @@ class GroupNode extends Node {
         };
         this.updateColor = (values) => {
             const update = this.plugin.state.data.build();
-            const { value, type, lightness, alpha } = values;
+            const { value, type, lightness, alpha, emissive } = values;
             const entities = this.filteredEntities;
             let groupColors = [];
             if (type === 'generate') {
@@ -402,12 +402,14 @@ class GroupNode extends Node {
                         old.colorTheme.params.lightness = lightness;
                         old.type.params.alpha = alpha;
                         old.type.params.xrayShaded = alpha < 1 ? 'inverted' : false;
+                        old.type.params.emissive = emissive;
                     }
                     else {
                         old.coloring.params.color = c;
                         old.coloring.params.lightness = lightness;
                         old.alpha = alpha;
                         old.xrayShaded = alpha < 1 ? true : false;
+                        old.emissive = emissive;
                     }
                 });
             }
@@ -679,6 +681,16 @@ class EntityNode extends Node {
                 }
             }).commit();
         };
+        this.updateEmissive = (values) => {
+            return this.plugin.build().to(this.ref).update(old => {
+                if (old.type) {
+                    old.type.params.emissive = values.emissive;
+                }
+                else {
+                    old.emissive = values.emissive;
+                }
+            }).commit();
+        };
         this.updateClip = (props) => {
             const params = this.cell.transform.params;
             const clip = params.type ? params.type.params.clip : params.clip;
@@ -737,6 +749,12 @@ class EntityNode extends Node {
             alpha: (_e = (_c = (_b = (_a = this.cell.transform.params) === null || _a === void 0 ? void 0 : _a.type) === null || _b === void 0 ? void 0 : _b.params.alpha) !== null && _c !== void 0 ? _c : (_d = this.cell.transform.params) === null || _d === void 0 ? void 0 : _d.alpha) !== null && _e !== void 0 ? _e : 1
         };
     }
+    get emissiveValue() {
+        var _a, _b, _c, _d, _e;
+        return {
+            emissive: (_e = (_c = (_b = (_a = this.cell.transform.params) === null || _a === void 0 ? void 0 : _a.type) === null || _b === void 0 ? void 0 : _b.params.emissive) !== null && _c !== void 0 ? _c : (_d = this.cell.transform.params) === null || _d === void 0 ? void 0 : _d.emissive) !== null && _e !== void 0 ? _e : 0
+        };
+    }
     get clipValue() {
         var _a, _b;
         return (_b = (_a = this.cell.transform.params.type) === null || _a === void 0 ? void 0 : _a.params.clip) !== null && _b !== void 0 ? _b : this.cell.transform.params.clip;
@@ -769,6 +787,7 @@ class EntityNode extends Node {
         const colorValue = this.colorValue;
         const lightnessValue = this.lightnessValue;
         const opacityValue = this.opacityValue;
+        const emissiveValue = this.emissiveValue;
         const lodValue = this.lodValue;
         const patternValue = this.patternValue;
         const l = (0, state_1.getEntityLabel)(this.plugin, this.cell);
@@ -776,7 +795,7 @@ class EntityNode extends Node {
         const color = colorValue !== undefined && (0, jsx_runtime_1.jsx)(common_1.Button, { style: { backgroundColor: color_1.Color.toStyle(colorValue), minWidth: 32, width: 32, borderRight: `6px solid ${color_1.Color.toStyle(color_1.Color.lighten(colorValue, (lightnessValue === null || lightnessValue === void 0 ? void 0 : lightnessValue.lightness) || 0))}` }, onClick: this.toggleColor });
         const clip = (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.ContentCutSvg, toggleState: false, disabled: disabled, small: true, onClick: this.toggleClip });
         const visibility = (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: cellState.isHidden ? icons_1.VisibilityOffOutlinedSvg : icons_1.VisibilityOutlinedSvg, toggleState: false, disabled: disabled, small: true, onClick: this.toggleVisible });
-        return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)("div", { className: `msp-flex-row`, style: { margin: `1px 5px 1px ${depth * 10 + 5}px` }, children: [label, color, clip, visibility] }), this.state.action === 'color' && colorValue !== void 0 && (0, jsx_runtime_1.jsx)("div", { style: { marginRight: 5 }, className: 'msp-accent-offset', children: (0, jsx_runtime_1.jsxs)(common_1.ControlGroup, { header: 'Color', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: this.toggleColor, topRightIcon: icons_1.CloseSvg, noTopMargin: true, childrenClassName: 'msp-viewport-controls-panel-controls', children: [(0, jsx_runtime_1.jsx)(color_2.CombinedColorControl, { param: state_1.ColorValueParam, value: colorValue !== null && colorValue !== void 0 ? colorValue : (0, color_1.Color)(0xFFFFFF), onChange: this.updateColor, name: 'color', hideNameRow: true }), (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: state_1.LightnessParams, values: lightnessValue, onChangeValues: this.updateLightness }), (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: state_1.OpacityParams, values: opacityValue, onChangeValues: this.updateOpacity }), patternValue && (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: state_1.PatternParams, values: patternValue, onChangeValues: this.updatePattern })] }) }), this.state.action === 'clip' && (0, jsx_runtime_1.jsx)("div", { style: { marginRight: 5 }, className: 'msp-accent-offset', children: (0, jsx_runtime_1.jsxs)(common_1.ControlGroup, { header: 'Clip', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: this.toggleClip, topRightIcon: icons_1.CloseSvg, noTopMargin: true, childrenClassName: 'msp-viewport-controls-panel-controls', children: [(0, jsx_runtime_1.jsx)(parameters_1.ParameterMappingControl, { mapping: this.clipMapping }), lodValue && (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: state_1.LodParams, values: lodValue, onChangeValues: this.updateLod })] }) })] });
+        return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)("div", { className: `msp-flex-row`, style: { margin: `1px 5px 1px ${depth * 10 + 5}px` }, children: [label, color, clip, visibility] }), this.state.action === 'color' && colorValue !== void 0 && (0, jsx_runtime_1.jsx)("div", { style: { marginRight: 5 }, className: 'msp-accent-offset', children: (0, jsx_runtime_1.jsxs)(common_1.ControlGroup, { header: 'Color', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: this.toggleColor, topRightIcon: icons_1.CloseSvg, noTopMargin: true, childrenClassName: 'msp-viewport-controls-panel-controls', children: [(0, jsx_runtime_1.jsx)(color_2.CombinedColorControl, { param: state_1.ColorValueParam, value: colorValue !== null && colorValue !== void 0 ? colorValue : (0, color_1.Color)(0xFFFFFF), onChange: this.updateColor, name: 'color', hideNameRow: true }), (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: state_1.LightnessParams, values: lightnessValue, onChangeValues: this.updateLightness }), (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: state_1.OpacityParams, values: opacityValue, onChangeValues: this.updateOpacity }), (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: state_1.EmissiveParams, values: emissiveValue, onChangeValues: this.updateEmissive }), patternValue && (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: state_1.PatternParams, values: patternValue, onChangeValues: this.updatePattern })] }) }), this.state.action === 'clip' && (0, jsx_runtime_1.jsx)("div", { style: { marginRight: 5 }, className: 'msp-accent-offset', children: (0, jsx_runtime_1.jsxs)(common_1.ControlGroup, { header: 'Clip', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: this.toggleClip, topRightIcon: icons_1.CloseSvg, noTopMargin: true, childrenClassName: 'msp-viewport-controls-panel-controls', children: [(0, jsx_runtime_1.jsx)(parameters_1.ParameterMappingControl, { mapping: this.clipMapping }), lodValue && (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: state_1.LodParams, values: lodValue, onChangeValues: this.updateLod })] }) })] });
     }
 }
 exports.EntityNode = EntityNode;

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

@@ -187,11 +187,17 @@ export declare class Viewer {
             representation: any;
         } | undefined;
     }>;
-    loadMvsFromUrl(url: string, format: 'mvsj' | 'mvsx'): Promise<void>;
+    loadMvsFromUrl(url: string, format: 'mvsj' | 'mvsx', options?: {
+        replaceExisting?: boolean;
+        keepCamera?: boolean;
+    }): Promise<void>;
     /** Load MolViewSpec from `data`.
      * If `format` is 'mvsj', `data` must be a string or a Uint8Array containing a UTF8-encoded string.
      * If `format` is 'mvsx', `data` must be a Uint8Array or a string containing base64-encoded binary data prefixed with 'base64,'. */
-    loadMvsData(data: string | Uint8Array, format: 'mvsj' | 'mvsx'): Promise<void>;
+    loadMvsData(data: string | Uint8Array, format: 'mvsj' | 'mvsx', options?: {
+        replaceExisting?: boolean;
+        keepCamera?: boolean;
+    }): Promise<void>;
     handleResize(): void;
     dispose(): void;
 }

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

@@ -432,17 +432,17 @@ class Viewer {
         const preset = await plugin.builders.structure.hierarchy.applyPreset(trajectory, (_b = params.preset) !== null && _b !== void 0 ? _b : 'default');
         return { model, coords, preset };
     }
-    async loadMvsFromUrl(url, format) {
+    async loadMvsFromUrl(url, format, options) {
         if (format === 'mvsj') {
             const data = await this.plugin.runTask(this.plugin.fetch({ url, type: 'string' }));
             const mvsData = mvs_data_1.MVSData.fromMVSJ(data);
-            await (0, load_1.loadMVS)(this.plugin, mvsData, { sanityChecks: true, sourceUrl: url });
+            await (0, load_1.loadMVS)(this.plugin, mvsData, { sanityChecks: true, sourceUrl: url, ...options });
         }
         else if (format === 'mvsx') {
             const data = await this.plugin.runTask(this.plugin.fetch({ url, type: 'binary' }));
             await this.plugin.runTask(mol_task_1.Task.create('Load MVSX file', async (ctx) => {
                 const parsed = await (0, formats_1.loadMVSX)(this.plugin, ctx, data);
-                await (0, load_1.loadMVS)(this.plugin, parsed.mvsData, { sanityChecks: true, sourceUrl: parsed.sourceUrl });
+                await (0, load_1.loadMVS)(this.plugin, parsed.mvsData, { sanityChecks: true, sourceUrl: parsed.sourceUrl, ...options });
             }));
         }
         else {
@@ -452,7 +452,7 @@ class Viewer {
     /** Load MolViewSpec from `data`.
      * If `format` is 'mvsj', `data` must be a string or a Uint8Array containing a UTF8-encoded string.
      * If `format` is 'mvsx', `data` must be a Uint8Array or a string containing base64-encoded binary data prefixed with 'base64,'. */
-    async loadMvsData(data, format) {
+    async loadMvsData(data, format, options) {
         if (typeof data === 'string' && data.startsWith('base64')) {
             data = Uint8Array.from(atob(data.substring(7)), c => c.charCodeAt(0)); // Decode base64 string to Uint8Array
         }
@@ -461,7 +461,7 @@ class Viewer {
                 data = new TextDecoder().decode(data); // Decode Uint8Array to string using UTF8
             }
             const mvsData = mvs_data_1.MVSData.fromMVSJ(data);
-            await (0, load_1.loadMVS)(this.plugin, mvsData, { sanityChecks: true, sourceUrl: undefined });
+            await (0, load_1.loadMVS)(this.plugin, mvsData, { sanityChecks: true, sourceUrl: undefined, ...options });
         }
         else if (format === 'mvsx') {
             if (typeof data === 'string') {
@@ -469,7 +469,7 @@ class Viewer {
             }
             await this.plugin.runTask(mol_task_1.Task.create('Load MVSX file', async (ctx) => {
                 const parsed = await (0, formats_1.loadMVSX)(this.plugin, ctx, data);
-                await (0, load_1.loadMVS)(this.plugin, parsed.mvsData, { sanityChecks: true, sourceUrl: parsed.sourceUrl });
+                await (0, load_1.loadMVS)(this.plugin, parsed.mvsData, { sanityChecks: true, sourceUrl: parsed.sourceUrl, ...options });
             }));
         }
         else {

package/lib/commonjs/cli/cifschema/util/cif-dic.js

@@ -40,6 +40,7 @@ function getFieldType(type, description, values, container) {
         case 'pdbx_related_db_id':
         case 'sequence_dep':
         case 'pdb_id':
+        case 'pdb_id_u': // should be case insensitve, but can't express that
         case 'emd_id':
         // todo, consider adding specialised fields
         case 'yyyy-mm-dd':

package/lib/commonjs/extensions/anvil/behavior.d.ts

@@ -36,6 +36,7 @@ declare const MembraneOrientation3D: StateTransformer<PluginStateObject.Molecule
         variant: any;
         objects: any;
     }>;
+    emissive: number;
     instanceGranularity: boolean;
     lod: import("../../mol-math/linear-algebra").Vec3;
     cellSize: number;

package/lib/commonjs/extensions/anvil/representation.d.ts

@@ -38,6 +38,7 @@ declare const BilayerPlanesParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -69,6 +70,7 @@ declare const BilayerRimsParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -101,6 +103,7 @@ export declare const MembraneOrientationParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -142,6 +145,7 @@ export declare function getMembraneOrientationParams(ctx: ThemeRegistryContext,
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -183,6 +187,7 @@ export declare const MembraneOrientationRepresentationProvider: StructureReprese
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

package/lib/commonjs/extensions/assembly-symmetry/behavior.d.ts

@@ -42,6 +42,7 @@ declare const AssemblySymmetry3D: StateTransformer<PluginStateObject.Molecule.St
         variant: any;
         objects: any;
     }>;
+    emissive: number;
     instanceGranularity: boolean;
     lod: import("../../mol-math/linear-algebra").Vec3;
     cellSize: number;

package/lib/commonjs/extensions/assembly-symmetry/representation.d.ts

@@ -36,6 +36,7 @@ export declare const AssemblySymmetryParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.d.ts

@@ -37,6 +37,7 @@ export declare const ConfalPyramidsParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -71,6 +72,7 @@ export declare function getConfalPyramidsParams(ctx: ThemeRegistryContext, struc
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -106,6 +108,7 @@ export declare const ConfalPyramidsRepresentationProvider: StructureRepresentati
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

package/lib/commonjs/extensions/dnatco/ntc-tube/representation.d.ts

@@ -41,6 +41,7 @@ export declare const NtCTubeParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -79,6 +80,7 @@ export declare function getNtCTubeParams(ctx: ThemeRegistryContext, structure: S
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -118,6 +120,7 @@ export declare const NtCTubeRepresentationProvider: StructureRepresentationProvi
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

package/lib/commonjs/extensions/geo-export/glb-exporter.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2021-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

package/lib/commonjs/extensions/geo-export/glb-exporter.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2021-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -132,8 +132,8 @@ class GlbExporter extends mesh_exporter_1.MeshExporter {
         }
         return this.addBuffer(colorBuffer, UNSIGNED_BYTE, 'VEC4', vertexCount, ARRAY_BUFFER, undefined, undefined, true);
     }
-    addMaterial(metalness, roughness, doubleSided, alpha) {
-        const hash = `${metalness}|${roughness}|${doubleSided}`;
+    addMaterial(metalness, roughness, emissive, doubleSided, alpha) {
+        const hash = `${metalness}|${roughness}|${emissive}|${doubleSided}`;
         if (!this.materialMap.has(hash)) {
             this.materialMap.set(hash, this.materials.length);
             this.materials.push({
@@ -142,6 +142,7 @@ class GlbExporter extends mesh_exporter_1.MeshExporter {
                     metallicFactor: metalness,
                     roughnessFactor: roughness
                 },
+                emissiveFactor: [emissive, emissive, emissive],
                 doubleSided,
                 alphaMode: alpha ? 'BLEND' : 'OPAQUE',
             });
@@ -160,9 +161,10 @@ class GlbExporter extends mesh_exporter_1.MeshExporter {
         const instanceCount = values.uInstanceCount.ref.value;
         const metalness = values.uMetalness.ref.value;
         const roughness = values.uRoughness.ref.value;
+        const emissive = values.uEmissive.ref.value;
         const doubleSided = ((_a = values.uDoubleSided) === null || _a === void 0 ? void 0 : _a.ref.value) || values.hasReflection.ref.value;
         const alpha = values.uAlpha.ref.value < 1;
-        const material = this.addMaterial(metalness, roughness, doubleSided, alpha);
+        const material = this.addMaterial(metalness, roughness, emissive, doubleSided, alpha);
         let interpolatedColors;
         if (webgl && mesh && (colorType === 'volume' || colorType === 'volumeInstance')) {
             const stride = isGeoTexture ? 4 : 3;

package/lib/commonjs/extensions/mvs/camera.d.ts

@@ -7,6 +7,8 @@ import { PluginContext } from '../../mol-plugin/context';
 import { StateObjectSelector } from '../../mol-state';
 import { ParamsOfKind } from './tree/generic/tree-schema';
 import { MolstarTree } from './tree/molstar/molstar-tree';
+/** Set the camera position to the current position (thus suppress automatic adjustment). */
+export declare function suppressCameraAutoreset(plugin: PluginContext): Promise<void>;
 /** Set the camera based on a camera node params. */
 export declare function setCamera(plugin: PluginContext, params: ParamsOfKind<MolstarTree, 'camera'>): Promise<void>;
 /** Focus the camera on the bounding sphere of a (sub)structure (or on the whole scene if `structureNodeSelector` is null).

package/lib/commonjs/extensions/mvs/camera.js

@@ -5,7 +5,8 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.setCanvas = exports.setFocus = exports.setCamera = void 0;
+exports.setCanvas = exports.setFocus = exports.setCamera = exports.suppressCameraAutoreset = void 0;
+const canvas3d_1 = require("../../mol-canvas3d/canvas3d");
 const boundary_helper_1 = require("../../mol-math/geometry/boundary-helper");
 const linear_algebra_1 = require("../../mol-math/linear-algebra");
 const loci_1 = require("../../mol-model/loci");
@@ -22,6 +23,14 @@ const DefaultFocusOptions = {
 };
 const DefaultCanvasBackgroundColor = names_1.ColorNames.white;
 const _tmpVec = (0, linear_algebra_1.Vec3)();
+/** Set the camera position to the current position (thus suppress automatic adjustment). */
+async function suppressCameraAutoreset(plugin) {
+    var _a;
+    const snapshot = { ...(_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.camera.state, radius: Infinity }; // `radius: Infinity` avoids clipping when the scene expands
+    adjustSceneRadiusFactor(plugin, snapshot.target);
+    await commands_1.PluginCommands.Camera.SetSnapshot(plugin, { snapshot });
+}
+exports.suppressCameraAutoreset = suppressCameraAutoreset;
 /** Set the camera based on a camera node params. */
 async function setCamera(plugin, params) {
     const target = linear_algebra_1.Vec3.create(...params.target);
@@ -30,7 +39,8 @@ async function setCamera(plugin, params) {
         position = fovAdjustedPosition(target, position, plugin.canvas3d.camera.state.mode, plugin.canvas3d.camera.state.fov);
     const up = linear_algebra_1.Vec3.create(...params.up);
     linear_algebra_1.Vec3.orthogonalize(up, linear_algebra_1.Vec3.sub(_tmpVec, target, position), up);
-    const snapshot = { target, position, up, radius: 10000, 'radiusMax': 10000 };
+    const snapshot = { target, position, up, radius: Infinity }; // `radius: Infinity` avoids clipping (ensures covering the whole scene)
+    adjustSceneRadiusFactor(plugin, snapshot.target);
     await commands_1.PluginCommands.Camera.SetSnapshot(plugin, { snapshot });
 }
 exports.setCamera = setCamera;
@@ -61,10 +71,27 @@ async function setFocus(plugin, structureNodeSelector, params = mvs_defaults_1.M
             up,
             direction,
         });
+        resetSceneRadiusFactor(plugin);
         await commands_1.PluginCommands.Camera.SetSnapshot(plugin, { snapshot });
     }
 }
 exports.setFocus = setFocus;
+/** Adjust `sceneRadiusFactor` property so that the current scene is not cropped */
+function adjustSceneRadiusFactor(plugin, cameraTarget) {
+    var _a;
+    if (!cameraTarget)
+        return;
+    const boundingSphere = getPluginBoundingSphere(plugin);
+    const offset = linear_algebra_1.Vec3.distance(cameraTarget, boundingSphere.center);
+    const sceneRadiusFactor = boundingSphere.radius > 0 ? ((boundingSphere.radius + offset) / boundingSphere.radius) : 1;
+    (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.setProps({ sceneRadiusFactor });
+}
+/** Reset `sceneRadiusFactor` property to the default value */
+function resetSceneRadiusFactor(plugin) {
+    var _a;
+    const sceneRadiusFactor = canvas3d_1.Canvas3DParams.sceneRadiusFactor.defaultValue;
+    (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.setProps({ sceneRadiusFactor });
+}
 /** Return camera snapshot for focusing a sphere with given `center` and `radius`,
  * while ensuring given view `direction` (aligns with vector position->target)
  * and `up` (aligns with screen Y axis). */

package/lib/commonjs/extensions/mvs/components/annotation-label/representation.d.ts

@@ -51,6 +51,7 @@ export declare const MVSAnnotationLabelParams: {
     fontWeight: PD.Select<import("../../../../mol-geo/geometry/text/font-atlas").FontWeight>;
     background: PD.BooleanParam;
     borderWidth: PD.Numeric;
+    emissive: PD.Numeric;
     batchSize: PD.Numeric;
     material: PD.Group<PD.Normalize<{
         metalness: number;
@@ -128,6 +129,7 @@ export declare const MVSAnnotationLabelRepresentationProvider: StructureRepresen
     fontWeight: PD.Select<import("../../../../mol-geo/geometry/text/font-atlas").FontWeight>;
     background: PD.BooleanParam;
     borderWidth: PD.Numeric;
+    emissive: PD.Numeric;
     batchSize: PD.Numeric;
     material: PD.Group<PD.Normalize<{
         metalness: number;