pdbe-molstar 3.6.0 → 3.7.1

package/lib/ui/pdbe-viewport-controls.js

@@ -2,31 +2,15 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PDBeViewportControls = void 0;
 const jsx_runtime_1 = require("react/jsx-runtime");
+const common_1 = require("molstar/lib/mol-plugin-ui/controls/common");
 const viewport_1 = require("molstar/lib/mol-plugin-ui/viewport");
-const names_1 = require("molstar/lib/mol-util/color/names");
-const helpers_1 = require("../helpers");
 const plugin_custom_state_1 = require("../plugin-custom-state");
 class PDBeViewportControls extends viewport_1.ViewportControls {
-    isBlack() {
-        var _a;
-        const bgColor = (_a = (0, plugin_custom_state_1.PluginCustomState)(this.plugin).initParams) === null || _a === void 0 ? void 0 : _a.bgColor;
-        return bgColor !== undefined && (0, helpers_1.normalizeColor)(bgColor) === names_1.ColorNames.black;
-    }
     render() {
         const initParams = (0, plugin_custom_state_1.PluginCustomState)(this.plugin).initParams;
         const showPDBeLink = (initParams === null || initParams === void 0 ? void 0 : initParams.moleculeId) && (initParams === null || initParams === void 0 ? void 0 : initParams.pdbeLink) && !(initParams === null || initParams === void 0 ? void 0 : initParams.superposition);
-        const pdbeLinkColor = this.isBlack() ? '#fff' : '#555';
-        const pdbeLink = {
-            containerStyle: { position: 'absolute', right: '10px', top: '10px', padding: '6px', paddingRight: '3px', paddingLeft: '18px' },
-            bgStyle: { position: 'absolute', height: '32px', width: '54px', marginLeft: '-33px' },
-            style: { display: 'inline-block', fontSize: '14px', color: pdbeLinkColor, borderBottom: 'none', cursor: 'pointer', textDecoration: 'none', position: 'absolute', right: '5px' },
-            pdbeImg: {
-                src: 'https://www.ebi.ac.uk/pdbe/entry/static/images/logos/PDBe/logo_T_64.png',
-                alt: 'PDBe logo',
-                style: { height: '12px', width: '12px', border: 0, position: 'absolute', margin: '4px 0 0 -13px' },
-            },
-        };
-        return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [showPDBeLink && (0, jsx_runtime_1.jsxs)("div", { className: 'msp-viewport-controls-buttons', style: pdbeLink.containerStyle, children: [(0, jsx_runtime_1.jsx)("div", { className: 'msp-semi-transparent-background', style: pdbeLink.bgStyle }), (0, jsx_runtime_1.jsxs)("a", { className: 'msp-pdbe-link', style: pdbeLink.style, target: "_blank", href: `https://pdbe.org/${initParams.moleculeId}`, children: [(0, jsx_runtime_1.jsx)("img", { src: pdbeLink.pdbeImg.src, alt: pdbeLink.pdbeImg.alt, style: pdbeLink.pdbeImg.style }), initParams.moleculeId] })] }), (0, jsx_runtime_1.jsx)("div", { style: { position: 'absolute', top: showPDBeLink ? (32 + 4) : 0, right: 0 }, children: super.render() })] });
+        return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [showPDBeLink &&
+                    (0, jsx_runtime_1.jsx)("div", { className: 'msp-viewport-controls', children: (0, jsx_runtime_1.jsx)("div", { className: 'msp-viewport-controls-buttons', children: (0, jsx_runtime_1.jsxs)("div", { className: 'pdbemolstar-pdbe-link-box', children: [(0, jsx_runtime_1.jsx)("div", { className: 'msp-semi-transparent-background' }), (0, jsx_runtime_1.jsx)("a", { target: '_blank', href: `https://pdbe.org/${initParams.moleculeId}`, style: { textDecoration: 'none', color: 'initial' }, children: (0, jsx_runtime_1.jsxs)(common_1.Button, { className: 'msp-btn-link-toggle-on pdbemolstar-pdbe-link', title: 'Go to PDBe Pages', children: [(0, jsx_runtime_1.jsx)("img", { className: 'pdbemolstar-pdbe-logo', alt: 'PDBe logo', src: 'https://www.ebi.ac.uk/pdbe/entry/static/images/logos/PDBe/logo_T_64.png' }), initParams.moleculeId] }) })] }) }) }), (0, jsx_runtime_1.jsx)("div", { className: showPDBeLink ? 'pdbemolstar-viewport-controls-shifted' : 'pdbemolstar-viewport-controls-normal', children: super.render() })] });
     }
 }
 exports.PDBeViewportControls = PDBeViewportControls;

package/lib/ui/split-ui/components.d.ts

@@ -1,5 +1,6 @@
 import { ControlsWrapper, Log } from 'molstar/lib/mol-plugin-ui/plugin';
 import { SequenceView } from 'molstar/lib/mol-plugin-ui/sequence';
+import { FullLayoutNoControlsUnlessExpanded } from '../layout-no-controls-unless-expanded';
 export declare const UIComponents: {
     /** Component containing 3D canvas, button in top left and top right corners, and tooltip box (center panel in default layout). Changes to fullscreen view by "Toggle Expanded Viewport" button, or "expanded" option. */
     readonly PDBeViewport: import("react").ComponentClass<{}, any>;
@@ -13,4 +14,6 @@ export declare const UIComponents: {
     readonly DefaultLeftPanelControls: import("react").ComponentClass<{}, any>;
     /** Component containing right panel controls (contents depend on PDBeMolstar init params (superposition/ligand/default view)) */
     readonly DefaultRightPanelControls: typeof ControlsWrapper;
+    /** Component containing only `PDBeViewport` when not in fullscreen view, but shows full UI layout when in fullscreen view. */
+    readonly FullLayoutNoControlsUnlessExpanded: typeof FullLayoutNoControlsUnlessExpanded;
 };

package/lib/ui/split-ui/components.js

@@ -3,6 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.UIComponents = void 0;
 const plugin_1 = require("molstar/lib/mol-plugin-ui/plugin");
 const sequence_1 = require("molstar/lib/mol-plugin-ui/sequence");
+const layout_no_controls_unless_expanded_1 = require("../layout-no-controls-unless-expanded");
 const pdbe_left_panel_1 = require("../left-panel/pdbe-left-panel");
 const pdbe_viewport_1 = require("../pdbe-viewport");
 exports.UIComponents = {
@@ -18,5 +19,7 @@ exports.UIComponents = {
     DefaultLeftPanelControls: pdbe_left_panel_1.DefaultLeftPanelControls,
     /** Component containing right panel controls (contents depend on PDBeMolstar init params (superposition/ligand/default view)) */
     DefaultRightPanelControls: plugin_1.ControlsWrapper,
+    /** Component containing only `PDBeViewport` when not in fullscreen view, but shows full UI layout when in fullscreen view. */
+    FullLayoutNoControlsUnlessExpanded: layout_no_controls_unless_expanded_1.FullLayoutNoControlsUnlessExpanded,
     // TODO add all meaningful components,
 };

package/lib/viewer.d.ts

@@ -232,6 +232,7 @@ export declare class PDBeMolstarPlugin {
         readonly PDBeLeftPanelControls: import("react").ComponentClass<{}, any>;
         readonly DefaultLeftPanelControls: import("react").ComponentClass<{}, any>;
         readonly DefaultRightPanelControls: typeof import("molstar/lib/mol-plugin-ui/plugin").ControlsWrapper;
+        readonly FullLayoutNoControlsUnlessExpanded: typeof import("./ui/layout-no-controls-unless-expanded").FullLayoutNoControlsUnlessExpanded;
     };
     static MAIN_STRUCTURE_ID: string;
 }

package/lib/viewer.js

@@ -431,8 +431,6 @@ class PDBeMolstarPlugin {
                 if (this.initParams.customData && this.initParams.customData.url && !this.initParams.customData.format)
                     return false;
                 (0, plugin_custom_state_1.PluginCustomState)(this.plugin).initParams = this.initParams;
-                // Update layout
-                commands_1.PluginCommands.Layout.Update(this.plugin, { state: (0, helpers_1.pluginLayoutStateFromInitParams)(this.initParams) });
                 // Show/hide buttons in the viewport control panel
                 this.plugin.config.set(config_1.PluginConfig.Viewport.ShowScreenshotControls, !this.initParams.hideCanvasControls.includes('screenshot'));
                 this.plugin.config.set(config_1.PluginConfig.Viewport.ShowExpand, !this.initParams.hideCanvasControls.includes('expand'));
@@ -441,6 +439,8 @@ class PDBeMolstarPlugin {
                 this.plugin.config.set(config_1.PluginConfig.Viewport.ShowSelectionMode, !this.initParams.hideCanvasControls.includes('selection'));
                 this.plugin.config.set(config_1.PluginConfig.Viewport.ShowAnimation, !this.initParams.hideCanvasControls.includes('animation'));
                 this.plugin.config.set(config_1.PluginConfig.Viewport.ShowTrajectoryControls, !this.initParams.hideCanvasControls.includes('trajectory'));
+                // Update layout
+                commands_1.PluginCommands.Layout.Update(this.plugin, { state: (0, helpers_1.pluginLayoutStateFromInitParams)(this.initParams) });
                 // Set background colour
                 if (this.initParams.bgColor || this.initParams.lighting) {
                     yield this.canvas.applySettings({ color: this.initParams.bgColor, lighting: this.initParams.lighting });
@@ -776,7 +776,7 @@ class PDBeMolstarPlugin {
                             return;
                         const asm = this.state.select(this.assemblyRef)[0].obj;
                         const defaultMapParams = transformers_1.InitVolumeStreaming.createDefaultParams(asm, this.plugin);
-                        const pdbeMapParams = helpers_1.PDBeVolumes.mapParams(defaultMapParams, this.initParams.mapSettings, '');
+                        const pdbeMapParams = helpers_1.PDBeVolumes.mapParams(defaultMapParams, this.initParams.mapSettings);
                         if (pdbeMapParams) {
                             yield this.plugin.runTask(this.state.applyAction(transformers_1.InitVolumeStreaming, pdbeMapParams, this.assemblyRef));
                             if (pdbeMapParams.method !== 'em' && !this.initParams.ligandView)

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "pdbe-molstar",
-  "version": "3.6.0",
+  "version": "3.7.1",
   "description": "Molstar implementation for PDBe",
   "main": "index.js",
   "scripts": {

package/lib/superposition-sifts-mapping.d.ts

@@ -1,22 +0,0 @@
-import { MinimizeRmsd } from 'molstar/lib/mol-math/linear-algebra/3d/minimize-rmsd';
-import { Structure } from 'molstar/lib/mol-model/structure';
-import { ElementIndex, ResidueIndex } from 'molstar/lib/mol-model/structure/model/indexing';
-import { StructureElement } from 'molstar/lib/mol-model/structure/structure/element';
-import { Unit } from 'molstar/lib/mol-model/structure/structure/unit';
-export interface AlignmentResultEntry {
-    transform: MinimizeRmsd.Result;
-    pivot: number;
-    other: number;
-}
-export interface AlignmentResult {
-    entries: AlignmentResultEntry[];
-    zeroOverlapPairs: [number, number][];
-    failedPairs: [number, number][];
-}
-type IncludeResidueTest = (traceElementOrFirstAtom: StructureElement.Location<Unit.Atomic>, residueIndex: ResidueIndex, startIndex: ElementIndex, endIndex: ElementIndex) => boolean;
-export declare function alignAndSuperposeWithSIFTSMapping(structures: Structure[], options?: {
-    traceOnly?: boolean;
-    includeResidueTest?: IncludeResidueTest;
-    applyTestIndex?: number[];
-}): AlignmentResult;
-export {};

package/lib/superposition-sifts-mapping.js

@@ -1,153 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.alignAndSuperposeWithSIFTSMapping = alignAndSuperposeWithSIFTSMapping;
-const int_1 = require("molstar/lib/mol-data/int");
-const minimize_rmsd_1 = require("molstar/lib/mol-math/linear-algebra/3d/minimize-rmsd");
-const element_1 = require("molstar/lib/mol-model/structure/structure/element");
-const sifts_mapping_1 = require("./sifts-mapping");
-function alignAndSuperposeWithSIFTSMapping(structures, options) {
-    var _a, _b;
-    const indexMap = new Map();
-    for (let i = 0; i < structures.length; i++) {
-        let includeResidueTest = (_a = options === null || options === void 0 ? void 0 : options.includeResidueTest) !== null && _a !== void 0 ? _a : _includeAllResidues;
-        if ((options === null || options === void 0 ? void 0 : options.applyTestIndex) && !options.applyTestIndex.includes(i))
-            includeResidueTest = _includeAllResidues;
-        buildIndex(structures[i], indexMap, i, (_b = options === null || options === void 0 ? void 0 : options.traceOnly) !== null && _b !== void 0 ? _b : true, includeResidueTest);
-    }
-    const index = Array.from(indexMap.values());
-    // TODO: support non-first structure pivots
-    const pairs = findPairs(structures.length, index);
-    const zeroOverlapPairs = [];
-    const failedPairs = [];
-    const entries = [];
-    for (const p of pairs) {
-        if (p.count === 0) {
-            zeroOverlapPairs.push([p.i, p.j]);
-        }
-        else {
-            const [a, b] = getPositionTables(index, p.i, p.j, p.count);
-            const transform = minimize_rmsd_1.MinimizeRmsd.compute({ a, b });
-            if (Number.isNaN(transform.rmsd)) {
-                failedPairs.push([p.i, p.j]);
-            }
-            else {
-                entries.push({ transform, pivot: p.i, other: p.j });
-            }
-        }
-    }
-    return { entries, zeroOverlapPairs, failedPairs };
-}
-function getPositionTables(index, pivot, other, N) {
-    const xs = minimize_rmsd_1.MinimizeRmsd.Positions.empty(N);
-    const ys = minimize_rmsd_1.MinimizeRmsd.Positions.empty(N);
-    let o = 0;
-    for (const { pivots } of index) {
-        const a = pivots[pivot];
-        const b = pivots[other];
-        if (!a || !b)
-            continue;
-        const l = Math.min(a[2] - a[1], b[2] - b[1]);
-        // TODO: check if residue types match?
-        for (let i = 0; i < l; i++) {
-            let eI = (a[1] + i);
-            xs.x[o] = a[0].conformation.x(eI);
-            xs.y[o] = a[0].conformation.y(eI);
-            xs.z[o] = a[0].conformation.z(eI);
-            eI = (b[1] + i);
-            ys.x[o] = b[0].conformation.x(eI);
-            ys.y[o] = b[0].conformation.y(eI);
-            ys.z[o] = b[0].conformation.z(eI);
-            o++;
-        }
-    }
-    return [xs, ys];
-}
-function findPairs(N, index) {
-    const pairwiseCounts = [];
-    for (let i = 0; i < N; i++) {
-        pairwiseCounts[i] = [];
-        for (let j = 0; j < N; j++)
-            pairwiseCounts[i][j] = 0;
-    }
-    for (const { pivots } of index) {
-        for (let i = 0; i < N; i++) {
-            if (!pivots[i])
-                continue;
-            const lI = pivots[i][2] - pivots[i][1];
-            for (let j = i + 1; j < N; j++) {
-                if (!pivots[j])
-                    continue;
-                const lJ = pivots[j][2] - pivots[j][1];
-                pairwiseCounts[i][j] = pairwiseCounts[i][j] + Math.min(lI, lJ);
-            }
-        }
-    }
-    const ret = [];
-    for (let j = 1; j < N; j++) {
-        ret[j - 1] = { i: 0, j, count: pairwiseCounts[0][j] };
-    }
-    // TODO: support non-first structure pivots
-    // for (let i = 0; i < N - 1; i++) {
-    //     let max = 0, maxJ = i;
-    //     for (let j = i + 1; j < N; j++) {
-    //         if (pairwiseCounts[i][j] > max) {
-    //             maxJ = j;
-    //             max = pairwiseCounts[i][j];
-    //         }
-    //     }
-    //     ret[i] = { i, j: maxJ, count: max };
-    // }
-    return ret;
-}
-function _includeAllResidues() { return true; }
-function buildIndex(structure, index, sI, traceOnly, includeTest) {
-    const loc = element_1.StructureElement.Location.create(structure);
-    for (const unit of structure.units) {
-        if (unit.kind !== 0 /* Unit.Kind.Atomic */)
-            continue;
-        const { elements, model } = unit;
-        loc.unit = unit;
-        const map = sifts_mapping_1.SIFTSMapping.Provider.get(model).value;
-        if (!map)
-            return;
-        const { dbName, accession, num } = map;
-        const chainsIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
-        const residuesIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
-        const traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex;
-        while (chainsIt.hasNext) {
-            const chainSegment = chainsIt.move();
-            residuesIt.setSegment(chainSegment);
-            while (residuesIt.hasNext) {
-                const residueSegment = residuesIt.move();
-                const rI = residueSegment.index;
-                if (!dbName[rI])
-                    continue;
-                const traceElement = traceElementIndex[rI];
-                let start, end;
-                if (traceOnly) {
-                    start = traceElement;
-                    if (start === -1)
-                        continue;
-                    end = start + 1;
-                }
-                else {
-                    start = elements[residueSegment.start];
-                    end = elements[residueSegment.end - 1] + 1;
-                }
-                loc.element = (traceElement >= 0 ? traceElement : start);
-                if (!includeTest(loc, rI, start, end))
-                    continue;
-                const key = `${dbName[rI]}-${accession[rI].split('-')[0]}-${num[rI]}`;
-                if (!index.has(key)) {
-                    index.set(key, { key, pivots: { [sI]: [unit, start, end] } });
-                }
-                else {
-                    const entry = index.get(key);
-                    if (!entry.pivots[sI]) {
-                        entry.pivots[sI] = [unit, start, end];
-                    }
-                }
-            }
-        }
-    }
-}