moorhen 0.8.2 → 0.8.4

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "moorhen",
-  "version": "0.8.2",
+  "version": "0.8.4",
   "private": false,
   "main": "moorhen.js",
   "types": "./types/main.d.ts",
@@ -64,12 +64,13 @@
   },
   "dependencies": {},
   "scripts": {
+    "transpile-protobuf": "npx pbjs -t static-module -w es6 -o ./src/protobuf/MoorhenSession.js ./src/protobuf/MoorhenSession.proto",
     "create-version": "npx genversion -e -p ./package.json -d -s ./src/version.js",
     "transpile-ts-worker": "npx tsc --module es2015 --lib webworker --skipLibCheck public/baby-gru/CootWorker.ts && sed -i.bak '/export {}/d' public/baby-gru/CootWorker.js && rm public/baby-gru/CootWorker.js.bak",
     "transpile-ts-worker-jest": "npx tsc --module es2015 --lib webworker --skipLibCheck public/baby-gru/CootWorker.ts && sed -i.bak 's/export {}/export { doCootCommand, setModules }/g' public/baby-gru/CootWorker.js && sed -i.bak '/importScripts.*;/d' public/baby-gru/CootWorker.js && sed -i.bak 's/onmessage/function setModules(arg0, arg1) { molecules_container = arg0; cootModule = arg1 }; let postMessage = () => {}; let onmessage/g' public/baby-gru/CootWorker.js && rm public/baby-gru/CootWorker.js.bak",
-    "prestart": "npm run create-version && npm run transpile-ts-worker",
+    "prestart": "npm run create-version && npm run transpile-ts-worker && npm run transpile-protobuf",
     "start": "vite",
-    "prebuild": "npm run create-version && npm run transpile-ts-worker",
+    "prebuild": "npm run create-version && npm run transpile-ts-worker && npm run transpile-protobuf",
     "build": "vite build",
     "build-release": "npm run prebuild && webpack --mode production --devtool inline-source-map",
     "dev": "concurrently -k \"BROWSER=none npm start\" \"npm:electron\"",
@@ -79,8 +80,8 @@
     "make-linux": "npm run build && electron-forge make --platform linux",
     "make-win32": "npm run build && electron-forge make --platform win32",
     "create-docs": "npm run create-version && npx jsdoc -c jsdoc.json",
-    "test": "npm run create-version && npx tsc && npm run transpile-ts-worker-jest && ln -s ./public/baby-gru/wasm/moorhen.data ./moorhen.data && ln -s ./public/baby-gru ./baby-gru && node --trace-warnings --experimental-vm-modules --experimental-wasm-threads node_modules/jest/bin/jest.js --forceExit",
-    "test-react": "npm run create-version && npx tsc && node --trace-warnings --experimental-vm-modules --experimental-wasm-threads node_modules/jest/bin/jest.js --forceExit --testPathIgnorePatterns=moorhenContainer.test.jsx --selectProjects react-components"
+    "test": "npm run create-version && npm run transpile-protobuf && npx tsc && npm run transpile-ts-worker-jest && ln -s ./public/baby-gru/wasm/moorhen.data ./moorhen.data && ln -s ./public/baby-gru ./baby-gru && node --trace-warnings --experimental-vm-modules --experimental-wasm-threads node_modules/jest/bin/jest.js --forceExit",
+    "test-react": "npm run create-version && npm run transpile-protobuf && npx tsc && node --trace-warnings --experimental-vm-modules --experimental-wasm-threads node_modules/jest/bin/jest.js --forceExit --testPathIgnorePatterns=MoorhenContainer.test.jsx --testPathIgnorePatterns=MoorhenLigandMenu.test.jsx --testPathIgnorePatterns=MoorhenEditMenu.test.jsx --selectProjects react-components"
   },
   "eslintConfig": {
     "extends": [
@@ -162,6 +163,8 @@
     "plotly.js": "^2.12.1",
     "prismjs": "^1.29.0",
     "prop-types": "^15.8.1",
+    "protobufjs": "^7.2.6",
+    "protobufjs-cli": "^1.1.2",
     "protvista-manager": "^3.4.0",
     "protvista-navigation": "^3.5.1",
     "protvista-sequence": "^3.5.1",

package/types/libcoot.d.ts

@@ -429,6 +429,22 @@ export namespace libcootApi {
         psi: number;
         is_pre_pro: boolean;
     }
+    type textureAsFloats = {
+        width: number;
+        height: number;
+        x_size: number;
+        y_size: number;
+        z_position: number;
+        image_data: emscriptem.vector<number>;
+    }
+    type textureAsFloatsJS = {
+        width: number;
+        height: number;
+        x_size: number;
+        y_size: number;
+        z_position: number;
+        image_data: number[];
+    }
     type fitLigandInfo = {
         imol: number;
         cluster_idx: number;

package/types/main.d.ts

@@ -5,6 +5,56 @@ import { gemmi } from "./gemmi";
 import { privateer } from "./privateer";
 
 declare module 'moorhen' {
+    let moleculesReducer: any;
+    module.exports = moleculesReducer
+
+    let mapsReducer: any;
+    module.exports = mapsReducer
+
+    let mouseSettingsReducer: any;
+    module.exports = mouseSettingsReducer
+
+    let backupSettingsReducer: any;
+    module.exports = backupSettingsReducer
+
+    let shortcutSettingsReducer: any;
+    module.exports = shortcutSettingsReducer
+
+    let labelSettingsReducer: any;
+    module.exports = labelSettingsReducer
+
+    let sceneSettingsReducer: any;
+    module.exports = sceneSettingsReducer
+
+    let miscAppSettingsReducer: any;
+    module.exports = miscAppSettingsReducer
+
+    let generalStatesReducer: any;
+    module.exports = generalStatesReducer
+
+    let hoveringStatesReducer: any;
+    module.exports = hoveringStatesReducer
+    
+    let activeModalsReducer: any;
+    module.exports = activeModalsReducer
+    
+    let activePopUpsReducer: any;
+    module.exports = activePopUpsReducer
+    
+    let mapContourSettingsReducer: any;
+    module.exports = mapContourSettingsReducer
+    
+    let moleculeMapUpdateReducer: any;
+    module.exports = moleculeMapUpdateReducer
+    
+    let sharedSessionReducer: any;
+    module.exports = sharedSessionReducer
+    
+    let refinementSettingsReducer: any;
+    module.exports = refinementSettingsReducer
+
+    let MoorhenReduxStore: any;
+    module.exports = MoorhenReduxStore
 
     let MoorhenContainer: any;
     module.exports = MoorhenContainer;
@@ -118,7 +168,8 @@ declare module 'moorhen' {
     module.exports.MoorhenMoleculeRepresentation = MoorhenMoleculeRepresentation
 
     class MoorhenMolecule implements _moorhen.Molecule {
-        constructor(commandCentre: React.RefObject<_moorhen.CommandCentre>, glRef: React.RefObject<webGL.MGWebGL>, monomerLibrary: string)
+        constructor(commandCentre: React.RefObject<_moorhen.CommandCentre>, glRef: React.RefObject<webGL.MGWebGL>, store?: any, monomerLibrary?: string)
+        transferLigandDicts(toMolecule: _moorhen.Molecule, override?: boolean): Promise<void>;
         minimizeEnergyUsingCidAnimated(cid: string, ncyc: number, nIterations: number, useRamaRestraints: boolean, ramaWeight: number, useTorsionRestraints: boolean, torsionWeight: number): Promise<void>;
         addColourRule(ruleType: string, cid: string, color: string, args: (string | number)[], isMultiColourRule?: boolean, applyColourToNonCarbonAtoms?: boolean, label?: string): void;
         splitMultiModels(draw?: boolean): Promise<_moorhen.Molecule[]>;
@@ -208,6 +259,7 @@ declare module 'moorhen' {
         excludedCids: string[];
         commandCentre: React.RefObject<_moorhen.CommandCentre>;
         glRef: React.RefObject<webGL.MGWebGL>;
+        store: any;
         atomsDirty: boolean;
         name: string;
         molNo: number;
@@ -250,7 +302,7 @@ declare module 'moorhen' {
     module.exports.MoorhenMolecule = MoorhenMolecule
     
     class MoorhenMap implements _moorhen.Map {
-        constructor(commandCentre: React.RefObject<_moorhen.CommandCentre>, glRef: React.RefObject<webGL.MGWebGL>)
+        constructor(commandCentre: React.RefObject<_moorhen.CommandCentre>, glRef: React.RefObject<webGL.MGWebGL>, store?: any)
         exportAsGltf(): Promise<ArrayBuffer>;
         getHistogram(nBins?: number, zoomFactor?: number): Promise<libcootApi.HistogramInfoJS>;
         setMapWeight(weight?: number): Promise<_moorhen.WorkerResponse>;
@@ -286,6 +338,7 @@ declare module 'moorhen' {
         setActive(): Promise<void>;
         setupContourBuffers(objects: any[], keepCootColours?: boolean): void;
         setOtherMapForColouring(molNo: number, min?: number, max?: number): void;
+        store: any;
         isEM: boolean;
         suggestedContourLevel: number;
         suggestedRadius: number;
@@ -312,7 +365,7 @@ declare module 'moorhen' {
     }
     module.exports.MoorhenMap = MoorhenMap
 
-    function loadSessionData(
+    function loadSessionFromJsonString(
         sessionDataString: string,
         monomerLibraryPath: string,
         molecules: _moorhen.Molecule[],
@@ -320,6 +373,34 @@ declare module 'moorhen' {
         commandCentre: React.RefObject<_moorhen.CommandCentre>,
         timeCapsuleRef: React.RefObject<_moorhen.TimeCapsule>,
         glRef: React.RefObject<webGL.MGWebGL>,
+        store: any,
+        dispatch: (reduxStoreAction: any) => void,
+    ): Promise<number>;
+    module.exports = loadSessionFromJsonString;
+
+    function loadSessionFromProtoMessage(
+        sessionProtoMessage: any,
+        monomerLibraryPath: string,
+        molecules: _moorhen.Molecule[],
+        maps: _moorhen.Map[],
+        commandCentre: React.RefObject<_moorhen.CommandCentre>,
+        timeCapsuleRef: React.RefObject<_moorhen.TimeCapsule>,
+        glRef: React.RefObject<webGL.MGWebGL>,
+        store: any,
+        dispatch: (reduxStoreAction: any) => void,
+    ): Promise<number>;
+    module.exports = loadSessionFromProtoMessage;
+
+
+    function loadSessionData(
+        sessionData: _moorhen.backupSession,
+        monomerLibraryPath: string,
+        molecules: _moorhen.Molecule[],
+        maps: _moorhen.Map[],
+        commandCentre: React.RefObject<_moorhen.CommandCentre>,
+        timeCapsuleRef: React.RefObject<_moorhen.TimeCapsule>,
+        glRef: React.RefObject<webGL.MGWebGL>,
+        store: any,
         dispatch: (reduxStoreAction: any) => void,
     ): Promise<number>;
     module.exports = loadSessionData;
@@ -578,4 +659,52 @@ declare module 'moorhen' {
 
     function addMapList(arg0: _moorhen.Map[]): any;
     module.exports = addMapList;
+
+    function resetSceneSettings(): any;
+    module.exports = resetSceneSettings;
+
+    function resetBackupSettings(): any;
+    module.exports = resetBackupSettings;
+    
+    function resetDefaultMouseSettings(): any;
+    module.exports = resetDefaultMouseSettings;
+    
+    function resetGeneralStates(): any;
+    module.exports = resetGeneralStates;
+    
+    function resetHoveringStates(): any;
+    module.exports = resetHoveringStates;
+    
+    function resetLabelSettings(): any;
+    module.exports = resetLabelSettings;
+    
+    function resetMapContourSettings(): any;
+    module.exports = resetMapContourSettings;
+    
+    function resetMiscAppSettings(): any;
+    module.exports = resetMiscAppSettings;
+    
+    function resetMoleculeMapUpdates(): any;
+    module.exports = resetMoleculeMapUpdates;
+    
+    function resetRefinementSettings(): any;
+    module.exports = resetRefinementSettings;
+    
+    function resetShortcutSettings(): any;
+    module.exports = resetShortcutSettings;
+    
+    function resetActiveModals(): any;
+    module.exports = resetActiveModals;
+    
+    function focusOnModal(): any;
+    module.exports = focusOnModal;
+    
+    function unFocusModal(): any;
+    module.exports = unFocusModal;
+    
+    function resetActivePopUps(): any;
+    module.exports = resetActivePopUps;
+    
+    function resetSharedSession(): any;
+    module.exports = resetSharedSession;
 }

package/types/mgWebGL.d.ts

@@ -70,6 +70,7 @@ export namespace webGL {
         drawTextLabels(up: vec3, right: vec3) : void;
         drawTriangles(calculatingShadowMap: boolean, invMat: mat4) : void;
         drawImagesAndText(invMat: mat4) : void;
+        drawTexturedShapes(theMatrix: mat4) : void;
         drawTransparent(theMatrix: mat4) : void;
         bindFramebufferDrawBuffers() : void;
         GLrender(calculatingShadowMap: boolean) : mat4;
@@ -104,6 +105,7 @@ export namespace webGL {
         initTextBackgroundShaders(vertexShaderTextBackground : string, fragmentShaderTextBackground : string)  : void;
         initOutlineShaders(vertexShader : string, fragmentShader : string)  : void;
         initShaders(vertexShader : string, fragmentShader : string)  : void;
+        initShadersTextured(vertexShader : string, fragmentShader : string)  : void;
         initGBufferShaders(vertexShader : string, fragmentShader : string)  : void;
         initGBufferShadersInstanced(vertexShader : string, fragmentShader : string)  : void;
         initGBufferShadersPerfectSphere(vertexShader : string, fragmentShader : string)  : void;
@@ -237,6 +239,7 @@ export namespace webGL {
         rttFramebuffer: MGWebGLFrameBuffer;
         doPerspectiveProjection: boolean;
         labelsTextCanvasTexture: TextCanvasTexture;
+        texturedShapes: TexturedShape[];
         currentBufferIdx: number;
         atom_span: number;
         axesColourBuffer: WebGLBuffer;
@@ -267,6 +270,8 @@ export namespace webGL {
         normalThreshold: number;
         scaleDepth: number;
         scaleNormal: number;
+        xPixelOffset: number;
+        yPixelOffset: number;
         occludeDiffuse: boolean;
         doShadowDepthDebug: boolean;
         doSpin: boolean;
@@ -359,6 +364,7 @@ export namespace webGL {
         rttTextureDepth: WebGLTexture;
         rttDepthTexture: WebGLTexture;
         screenZ: number;
+        shaderProgramTextured: MGWebGLTextureQuadShader;
         shaderProgram: ShaderTriangles;
         shaderProgramGBuffers: ShaderGBuffersTriangles;
         shaderProgramGBuffersInstanced: ShaderGBuffersTrianglesInstanced;
@@ -434,5 +440,7 @@ export namespace webGL {
         initializeShaders() : void;
         axesTexture: any;
 
+        hoverSize: number;
+
     }
 }

package/types/moorhen.d.ts

@@ -2,6 +2,8 @@ import React from "react"
 import { emscriptem } from "./emscriptem";
 import { gemmi } from "./gemmi";
 import { webGL } from "./mgWebGL";
+import { MoorhenMolecule } from "../moorhen";
+import { ToolkitStore } from "@reduxjs/toolkit/dist/configureStore";
 
 export namespace moorhen {
 
@@ -121,6 +123,7 @@ export namespace moorhen {
     type coorFormats = 'pdb' | 'mmcif';
     
     interface Molecule {
+        transferLigandDicts(toMolecule: Molecule, override?: boolean): Promise<void>;
         minimizeEnergyUsingCidAnimated(cid: string, ncyc: number, nIterations: number, useRamaRestraints: boolean, ramaWeight: number, useTorsionRestraints: boolean, torsionWeight: number): Promise<void>;
         addColourRule(ruleType: string, cid: string, color: string, args: (string | number)[], isMultiColourRule?: boolean, applyColourToNonCarbonAtoms?: boolean, label?: string): void;
         splitMultiModels(draw?: boolean): Promise<Molecule[]>;
@@ -210,6 +213,7 @@ export namespace moorhen {
         excludedCids: string[];
         commandCentre: React.RefObject<CommandCentre>;
         glRef: React.RefObject<webGL.MGWebGL>;
+        store: ToolkitStore;
         atomsDirty: boolean;
         name: string;
         molNo: number;
@@ -461,6 +465,7 @@ export namespace moorhen {
         setupContourBuffers(objects: any[], keepCootColours?: boolean): void;
         setOtherMapForColouring(molNo: number, min?: number, max?: number): void;
         exportAsGltf(): Promise<ArrayBuffer>;
+        store: ToolkitStore;
         isEM: boolean;
         suggestedContourLevel: number;
         suggestedRadius: number;
@@ -580,8 +585,9 @@ export namespace moorhen {
         removeBackup(key: string): Promise<void>;
         updateDataFiles(): Promise<(string | void)[]>;
         createBackup(keyString: string, sessionString: string): Promise<string>;
-        fetchSession(arg0: boolean): Promise<backupSession>;
+        fetchSession(includeAdditionalMapData: boolean): Promise<backupSession>;
         toggleDisableBackups(): void;
+        store: ToolkitStore;
         moleculesRef: React.RefObject<Molecule[]>;
         mapsRef: React.RefObject<Map[]>;
         glRef: React.RefObject<webGL.MGWebGL>;
@@ -809,7 +815,8 @@ export namespace moorhen {
         extraEditMenuItems: JSX.Element[];
         extraCalculateMenuItems: JSX.Element[];
         aceDRGInstance: AceDRGInstance | null; 
-        includeNavBarMenuNames: string[]
+        includeNavBarMenuNames: string[];
+        store: ToolkitStore;
     }
     
     interface ContainerProps extends Partial<ContainerRefs>, Partial<ContainerOptionalProps> { }