molstar 2.3.2 → 2.3.7

package/lib/mol-plugin-ui/skin/colors/blue.scss

@@ -1,24 +1,24 @@
-$default-background:         #2D3E50;
-$font-color:                 #EDF1F2; 
-$hover-font-color:           #3B9AD9;
-$entity-current-font-color:  #FFFFFF;
-$msp-btn-remove-background:      #BF3A31;
-$msp-btn-remove-hover-font-color:#ffffff;
-$msp-btn-commit-on-font-color:   #ffffff; 
-$entity-badge-font-color:    #ccd4e0;
-
-// used in LOG
-$log-message:          #0CCA5D;
-$log-info:             #5E3673;
-$log-warning:          #FCC937;
-$log-error:            #FD354B;
-
-$logo-background: rgba(0,0,0,0.75);
-
-@function color-lower-contrast($color, $amount) {
-    @return darken($color, $amount);
-}
-
-@function color-increase-contrast($color, $amount) {
-    @return lighten($color, $amount);
+$default-background:         #2D3E50;
+$font-color:                 #EDF1F2; 
+$hover-font-color:           #3B9AD9;
+$entity-current-font-color:  #FFFFFF;
+$msp-btn-remove-background:      #BF3A31;
+$msp-btn-remove-hover-font-color:#ffffff;
+$msp-btn-commit-on-font-color:   #ffffff; 
+$entity-badge-font-color:    #ccd4e0;
+
+// used in LOG
+$log-message:          #0CCA5D;
+$log-info:             #5E3673;
+$log-warning:          #FCC937;
+$log-error:            #FD354B;
+
+$logo-background: rgba(0,0,0,0.75);
+
+@function color-lower-contrast($color, $amount) {
+    @return darken($color, $amount);
+}
+
+@function color-increase-contrast($color, $amount) {
+    @return lighten($color, $amount);
 }

package/lib/mol-plugin-ui/skin/colors/dark.scss

@@ -1,24 +1,24 @@
-$default-background:         #111318;
-$font-color:                 #ccd4e0;
-$hover-font-color:           #51A2FB;
-$entity-current-font-color:  #68BEFD;
-$msp-btn-remove-background:      #DE0A28;
-$msp-btn-remove-hover-font-color:#F2F4F7;
-$msp-btn-commit-on-font-color:   #68BEFD;
-$entity-badge-font-color:    #ccd4e0;
-
-// used in LOG
-$log-message:          #0CCA5D;
-$log-info:             #5E3673;
-$log-warning:          #FCC937;
-$log-error:            #FD354B;
-
-$logo-background: rgba(0,0,0,0.75);
-
-@function color-lower-contrast($color, $amount) {
-    @return darken($color, $amount);
-}
-
-@function color-increase-contrast($color, $amount) {
-    @return lighten($color, $amount);
+$default-background:         #111318;
+$font-color:                 #ccd4e0;
+$hover-font-color:           #51A2FB;
+$entity-current-font-color:  #68BEFD;
+$msp-btn-remove-background:      #DE0A28;
+$msp-btn-remove-hover-font-color:#F2F4F7;
+$msp-btn-commit-on-font-color:   #68BEFD;
+$entity-badge-font-color:    #ccd4e0;
+
+// used in LOG
+$log-message:          #0CCA5D;
+$log-info:             #5E3673;
+$log-warning:          #FCC937;
+$log-error:            #FD354B;
+
+$logo-background: rgba(0,0,0,0.75);
+
+@function color-lower-contrast($color, $amount) {
+    @return darken($color, $amount);
+}
+
+@function color-increase-contrast($color, $amount) {
+    @return lighten($color, $amount);
 }

package/lib/mol-plugin-ui/skin/colors/light.scss

@@ -1,30 +1,30 @@
-// this is complement of the dark theme
-
-@function compl($color) {
-    @return rgb(255 - red($color), 255 - green($color), 255 - blue($color));
-}
-
-$default-background:         compl(#111318);
-$font-color:                 compl(#ccd4e0);
-$hover-font-color:           compl(#51A2FB);
-$entity-current-font-color:  compl(#68BEFD);
-$msp-btn-commit-on-font-color:   compl(#68BEFD);
-$entity-badge-font-color:    lighten(#ccd4e0,10%);
-$msp-btn-remove-background:      #DE0A28;
-$msp-btn-remove-hover-font-color:#F2F4F7;
-
-// used in LOG
-$log-message:          #0CCA5D;
-$log-info:             #5E3673;
-$log-warning:          #FCC937;
-$log-error:            #FD354B;
-
-$logo-background: compl(#111318);
-
-@function color-lower-contrast($color, $amount) {
-    @return lighten($color, $amount);
-}
-
-@function color-increase-contrast($color, $amount) {
-    @return darken($color, $amount);
+// this is complement of the dark theme
+
+@function compl($color) {
+    @return rgb(255 - red($color), 255 - green($color), 255 - blue($color));
+}
+
+$default-background:         compl(#111318);
+$font-color:                 compl(#ccd4e0);
+$hover-font-color:           compl(#51A2FB);
+$entity-current-font-color:  compl(#68BEFD);
+$msp-btn-commit-on-font-color:   compl(#68BEFD);
+$entity-badge-font-color:    lighten(#ccd4e0,10%);
+$msp-btn-remove-background:      #DE0A28;
+$msp-btn-remove-hover-font-color:#F2F4F7;
+
+// used in LOG
+$log-message:          #0CCA5D;
+$log-info:             #5E3673;
+$log-warning:          #FCC937;
+$log-error:            #FD354B;
+
+$logo-background: compl(#111318);
+
+@function color-lower-contrast($color, $amount) {
+    @return lighten($color, $amount);
+}
+
+@function color-increase-contrast($color, $amount) {
+    @return darken($color, $amount);
 }

package/lib/mol-plugin-ui/skin/dark.scss

@@ -1,2 +1,2 @@
-@import 'colors/dark';
+@import 'colors/dark';
 @import 'base/base';

package/lib/mol-plugin-ui/skin/light.scss

@@ -1,2 +1,2 @@
-@import 'colors/light';
+@import 'colors/light';
 @import 'base/base';

package/lib/mol-plugin-ui/structure/measurements.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -36,11 +36,20 @@ export declare class MeasurementControls extends PurePluginUIComponent<{}, {
         action: "options" | "add" | undefined;
     };
     componentDidMount(): void;
+    componentWillUnmount(): void;
+    componentDidUpdate(prevProps: {}, prevState: {
+        isBusy: boolean;
+        action?: 'add' | 'options';
+    }): void;
+    clearOrderLabels(): void;
+    updateOrderLabels(): void;
     get selection(): import("../../mol-plugin-state/manager/structure/selection").StructureSelectionManager;
     measureDistance: () => void;
     measureAngle: () => void;
     measureDihedral: () => void;
     addLabel: () => void;
+    addOrientation: () => void;
+    addPlane: () => void;
     get actions(): ActionMenu.Items;
     selectAction: ActionMenu.OnSelect;
     toggleAdd: () => void;

package/lib/mol-plugin-ui/structure/measurements.js

@@ -3,7 +3,7 @@ import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-run
 import { Loci } from '../../mol-model/loci';
 import { StructureMeasurementParams } from '../../mol-plugin-state/manager/structure/measurement';
 import { PluginCommands } from '../../mol-plugin/commands';
-import { angleLabel, dihedralLabel, distanceLabel, lociLabel } from '../../mol-theme/label';
+import { angleLabel, dihedralLabel, distanceLabel, lociLabel, structureElementLociLabelMany } from '../../mol-theme/label';
 import { CollapsableControls, PurePluginUIComponent } from '../base';
 import { ActionMenu } from '../controls/action-menu';
 import { Button, ExpandGroup, IconButton, ToggleButton } from '../controls/common';
@@ -52,7 +52,7 @@ var MeasurementList = /** @class */ (function (_super) {
     };
     MeasurementList.prototype.render = function () {
         var measurements = this.plugin.managers.structure.measurement.state;
-        return _jsxs("div", __assign({ style: { marginTop: '6px' } }, { children: [this.renderGroup(measurements.labels, 'Labels'), this.renderGroup(measurements.distances, 'Distances'), this.renderGroup(measurements.angles, 'Angles'), this.renderGroup(measurements.dihedrals, 'Dihedrals')] }), void 0);
+        return _jsxs("div", __assign({ style: { marginTop: '6px' } }, { children: [this.renderGroup(measurements.labels, 'Labels'), this.renderGroup(measurements.distances, 'Distances'), this.renderGroup(measurements.angles, 'Angles'), this.renderGroup(measurements.dihedrals, 'Dihedrals'), this.renderGroup(measurements.orientations, 'Orientations'), this.renderGroup(measurements.planes, 'Planes')] }), void 0);
     };
     return MeasurementList;
 }(PurePluginUIComponent));
@@ -78,6 +78,20 @@ var MeasurementControls = /** @class */ (function (_super) {
             var loci = _this.plugin.managers.structure.selection.additionsHistory;
             _this.plugin.managers.structure.measurement.addLabel(loci[0].loci);
         };
+        _this.addOrientation = function () {
+            var locis = [];
+            _this.plugin.managers.structure.selection.entries.forEach(function (v) {
+                locis.push(v.selection);
+            });
+            _this.plugin.managers.structure.measurement.addOrientation(locis);
+        };
+        _this.addPlane = function () {
+            var locis = [];
+            _this.plugin.managers.structure.selection.entries.forEach(function (v) {
+                locis.push(v.selection);
+            });
+            _this.plugin.managers.structure.measurement.addPlane(locis);
+        };
         _this.selectAction = function (item) {
             _this.toggleAdd();
             if (!item)
@@ -92,11 +106,34 @@ var MeasurementControls = /** @class */ (function (_super) {
         var _this = this;
         this.subscribe(this.selection.events.additionsHistoryUpdated, function () {
             _this.forceUpdate();
+            _this.updateOrderLabels();
         });
         this.subscribe(this.plugin.behaviors.state.isBusy, function (v) {
             _this.setState({ isBusy: v });
         });
     };
+    MeasurementControls.prototype.componentWillUnmount = function () {
+        this.clearOrderLabels();
+        _super.prototype.componentWillUnmount.call(this);
+    };
+    MeasurementControls.prototype.componentDidUpdate = function (prevProps, prevState) {
+        if (this.state.action !== prevState.action)
+            this.updateOrderLabels();
+    };
+    MeasurementControls.prototype.clearOrderLabels = function () {
+        this.plugin.managers.structure.measurement.addOrderLabels([]);
+    };
+    MeasurementControls.prototype.updateOrderLabels = function () {
+        if (this.state.action !== 'add') {
+            this.clearOrderLabels();
+            return;
+        }
+        var locis = [];
+        var history = this.selection.additionsHistory;
+        for (var idx = 0; idx < history.length && idx < 4; idx++)
+            locis.push(history[idx].loci);
+        this.plugin.managers.structure.measurement.addOrderLabels(locis);
+    };
     Object.defineProperty(MeasurementControls.prototype, "selection", {
         get: function () {
             return this.plugin.managers.structure.selection;
@@ -108,10 +145,12 @@ var MeasurementControls = /** @class */ (function (_super) {
         get: function () {
             var history = this.selection.additionsHistory;
             var ret = [
-                { kind: 'item', label: "Label " + (history.length === 0 ? ' (1 selection required)' : ' (1st selection)'), value: this.addLabel, disabled: history.length === 0 },
-                { kind: 'item', label: "Distance " + (history.length < 2 ? ' (2 selections required)' : ' (top 2 selections)'), value: this.measureDistance, disabled: history.length < 2 },
-                { kind: 'item', label: "Angle " + (history.length < 3 ? ' (3 selections required)' : ' (top 3 selections)'), value: this.measureAngle, disabled: history.length < 3 },
-                { kind: 'item', label: "Dihedral " + (history.length < 4 ? ' (4 selections required)' : ' (top 4 selections)'), value: this.measureDihedral, disabled: history.length < 4 },
+                { kind: 'item', label: "Label " + (history.length === 0 ? ' (1 selection item required)' : ' (1st selection item)'), value: this.addLabel, disabled: history.length === 0 },
+                { kind: 'item', label: "Distance " + (history.length < 2 ? ' (2 selection items required)' : ' (top 2 selection items)'), value: this.measureDistance, disabled: history.length < 2 },
+                { kind: 'item', label: "Angle " + (history.length < 3 ? ' (3 selection items required)' : ' (top 3 items)'), value: this.measureAngle, disabled: history.length < 3 },
+                { kind: 'item', label: "Dihedral " + (history.length < 4 ? ' (4 selection items required)' : ' (top 4 selection items)'), value: this.measureDihedral, disabled: history.length < 4 },
+                { kind: 'item', label: "Orientation " + (history.length === 0 ? ' (selection required)' : ' (current selection)'), value: this.addOrientation, disabled: history.length === 0 },
+                { kind: 'item', label: "Plane " + (history.length === 0 ? ' (selection required)' : ' (current selection)'), value: this.addPlane, disabled: history.length === 0 },
             ];
             return ret;
         },
@@ -130,7 +169,7 @@ var MeasurementControls = /** @class */ (function (_super) {
     MeasurementControls.prototype.historyEntry = function (e, idx) {
         var _this = this;
         var history = this.plugin.managers.structure.selection.additionsHistory;
-        return _jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsxs(Button, __assign({ noOverflow: true, title: 'Click to focus. Hover to highlight.', onClick: function () { return _this.focusLoci(e.loci); }, style: { width: 'auto', textAlign: 'left' }, onMouseEnter: function () { return _this.highlight(e.loci); }, onMouseLeave: function () { return _this.plugin.managers.interactivity.lociHighlights.clearHighlights(); } }, { children: [idx, ". ", _jsx("span", { dangerouslySetInnerHTML: { __html: e.label } }, void 0)] }), void 0), history.length > 1 && _jsx(IconButton, { svg: ArrowUpwardSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.moveHistory(e, 'up'); }, flex: '20px', title: 'Move up' }, void 0), history.length > 1 && _jsx(IconButton, { svg: ArrowDownwardSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.moveHistory(e, 'down'); }, flex: '20px', title: 'Move down' }, void 0), _jsx(IconButton, { svg: DeleteOutlinedSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.plugin.managers.structure.selection.modifyHistory(e, 'remove'); }, flex: true, title: 'Remove' }, void 0)] }), e.id);
+        return _jsxs("div", __assign({ className: 'msp-flex-row', onMouseEnter: function () { return _this.highlight(e.loci); }, onMouseLeave: function () { return _this.plugin.managers.interactivity.lociHighlights.clearHighlights(); } }, { children: [_jsxs(Button, __assign({ noOverflow: true, title: 'Click to focus. Hover to highlight.', onClick: function () { return _this.focusLoci(e.loci); }, style: { width: 'auto', textAlign: 'left' } }, { children: [idx, ". ", _jsx("span", { dangerouslySetInnerHTML: { __html: e.label } }, void 0)] }), void 0), history.length > 1 && _jsx(IconButton, { svg: ArrowUpwardSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.moveHistory(e, 'up'); }, flex: '20px', title: 'Move up' }, void 0), history.length > 1 && _jsx(IconButton, { svg: ArrowDownwardSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.moveHistory(e, 'down'); }, flex: '20px', title: 'Move down' }, void 0), _jsx(IconButton, { svg: DeleteOutlinedSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.plugin.managers.structure.selection.modifyHistory(e, 'remove'); }, flex: true, title: 'Remove' }, void 0)] }), e.id);
     };
     MeasurementControls.prototype.add = function () {
         var history = this.plugin.managers.structure.selection.additionsHistory;
@@ -244,6 +283,8 @@ var MeasurementEntry = /** @class */ (function (_super) {
                 return selections.triples[0].loci;
             if (selections.quads)
                 return selections.quads[0].loci;
+            if (selections.locis)
+                return selections.locis;
             return [];
         },
         enumerable: false,
@@ -262,6 +303,8 @@ var MeasurementEntry = /** @class */ (function (_super) {
                 return angleLabel(selections.triples[0], { condensed: true });
             if (selections.quads)
                 return dihedralLabel(selections.quads[0], { condensed: true });
+            if (selections.locis)
+                return structureElementLociLabelMany(selections.locis, { countsOnly: true });
             return '<empty>';
         },
         enumerable: false,

package/lib/mol-plugin-ui/structure/measurements.js.map

@@ -1 +1 @@
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package/lib/mol-repr/representation.d.ts

@@ -58,6 +58,7 @@ export declare namespace RepresentationProvider {
     function getDetaultParams<R extends RepresentationProvider<D, any, any>, D>(r: R, ctx: ThemeRegistryContext, data: D): PD.Values<any>;
 }
 export declare type AnyRepresentationProvider = RepresentationProvider<any, {}, Representation.State>;
+export declare const EmptyRepresentationProvider: RepresentationProvider;
 export declare class RepresentationRegistry<D, S extends Representation.State> {
     private _list;
     private _map;

package/lib/mol-repr/representation.js

@@ -5,6 +5,8 @@
  */
 import { __awaiter, __generator } from "tslib";
 import { ParamDefinition as PD } from '../mol-util/param-definition';
+import { ColorTheme } from '../mol-theme/color';
+import { SizeTheme } from '../mol-theme/size';
 import { Theme } from '../mol-theme/theme';
 import { Subject } from 'rxjs';
 import { Task } from '../mol-task';
@@ -24,12 +26,16 @@ export var RepresentationProvider;
     }
     RepresentationProvider.getDetaultParams = getDetaultParams;
 })(RepresentationProvider || (RepresentationProvider = {}));
-var EmptyRepresentationProvider = {
+export var EmptyRepresentationProvider = {
+    name: '',
     label: '',
     description: '',
     factory: function () { return Representation.Empty; },
     getParams: function () { return ({}); },
-    defaultValues: {}
+    defaultValues: {},
+    defaultColorTheme: ColorTheme.EmptyProvider,
+    defaultSizeTheme: SizeTheme.EmptyProvider,
+    isApplicable: function () { return true; }
 };
 function getTypes(list) {
     return list.map(function (e) { return [e.name, e.provider.label]; });

package/lib/mol-repr/representation.js.map

@@ -1 +1 @@
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package/lib/mol-repr/shape/loci/orientation.d.ts

@@ -1,18 +1,19 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-import { Loci } from '../../../mol-model/loci';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { Representation, RepresentationParamsGetter, RepresentationContext } from '../../representation';
+import { StructureElement } from '../../../mol-model/structure';
 export interface OrientationData {
-    locis: Loci[];
+    locis: StructureElement.Loci[];
 }
 export declare const OrientationParams: {
-    visuals: PD.MultiSelect<"box" | "axes" | "ellipsoid">;
+    visuals: PD.MultiSelect<"axes" | "ellipsoid" | "box">;
     color: PD.Color;
-    scale: PD.Numeric;
+    scaleFactor: PD.Numeric;
+    radiusScale: PD.Numeric;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;