moorhen 0.9.0 → 0.9.2

package/types/moorhen.d.ts

@@ -4,6 +4,7 @@ import { gemmi } from "./gemmi";
 import { webGL } from "./mgWebGL";
 import { MoorhenMolecule } from "../moorhen";
 import { ToolkitStore } from "@reduxjs/toolkit/dist/configureStore";
+import { AnyAction, Dispatch } from "@reduxjs/toolkit";
 
 export namespace moorhen {
 
@@ -81,6 +82,39 @@ export namespace moorhen {
         width: number;
         atomRadiusBondRatio: number;
     }
+
+    type gaussianSurfSettings = {
+        sigma: number;
+        countourLevel: number;
+        boxRadius: number;
+        gridScale: number;
+        bFactor: number;
+    }
+
+    type m2tParameters = {
+        ribbonStyleCoilThickness: number;
+        ribbonStyleHelixWidth: number;
+        ribbonStyleStrandWidth: number;
+        ribbonStyleArrowWidth: number;
+        ribbonStyleDNARNAWidth: number;
+        ribbonStyleAxialSampling: number;
+        cylindersStyleAngularSampling: number;
+        cylindersStyleCylinderRadius: number;
+        cylindersStyleBallRadius: number;
+        surfaceStyleProbeRadius: number;
+        ballsStyleRadiusMultiplier: number;
+        nucleotideRibbonStyle: "StickBases" | "DishyBases";
+        dishStyleAngularSampling: number;
+    }
+
+    type residueEnvironmentOptions = {
+        maxDist: number;
+        backgroundRepresentation: RepresentationStyles;
+        focusRepresentation: RepresentationStyles;
+        labelled: boolean;
+        showHBonds: boolean;
+        showContacts: boolean;
+    }
     
     type ColourRuleObject = {
         cid: string;
@@ -109,6 +143,7 @@ export namespace moorhen {
         uniqueId: string;
         static initFromDataObject(data: ColourRuleObject, commandCentre: React.RefObject<CommandCentre>, molecule: Molecule): ColourRule;
         static initFromString(stringData: string, commandCentre: React.RefObject<CommandCentre>, molecule: Molecule): ColourRule;
+        static parseHexToRgba(hex: string): [number, number, number, number];
         objectify(): ColourRuleObject;
         stringify(): string;
         setLabel(label: string): void;
@@ -116,12 +151,11 @@ export namespace moorhen {
         setParentMolecule(molecule: Molecule): void;
         setParentRepresentation(representation: MoleculeRepresentation): void;    
         setApplyColourToNonCarbonAtoms(newVal: boolean): void;
-        getUserDefinedColours(): { cid: string; rgb: [number, number, number]; applyColourToNonCarbonAtoms: boolean }[];
-        apply(style: string, ruleIndex: number): Promise<void>;
+        getUserDefinedColours(): { cid: string; rgba: [number, number, number, number]; applyColourToNonCarbonAtoms: boolean }[];
+        apply(style?: string, ruleIndex: number): Promise<void>;
     }
 
-    type coorFormats = 'pdb' | 'mmcif';
-    
+    type coorFormats = 'pdb' | 'mmcif' | 'unk' | 'mmjson' | 'xml';
     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>;
@@ -129,7 +163,7 @@ export namespace moorhen {
         splitMultiModels(draw?: boolean): Promise<Molecule[]>;
         getActiveAtom(): Promise<string>;
         setDrawAdaptativeBonds(newValue: boolean): Promise<void>;
-        redrawAdaptativeBonds(selectionString?: string, maxDist?: number): Promise<void>;
+        redrawAdaptativeBonds(selectionString?: string): Promise<void>;
         changeChainId(oldId: string, newId: string, redraw?: boolean, startResNo?: number, endResNo?: number): Promise<number>;
         refineResiduesUsingAtomCidAnimated(cid: string, activeMap: Map, dist?: number, redraw?: boolean, redrawFragmentFirst?: boolean): Promise<void>;
         mergeFragmentFromRefinement(cid: string, fragmentMolecule: Molecule, acceptTransform?: boolean, refineAfterMerge?: boolean): Promise<void>;
@@ -138,12 +172,13 @@ export namespace moorhen {
         getSecondaryStructInfo(modelNumber?: number): Promise<libcootApi.ResidueSpecJS[]>;
         getNonSelectedCids(cid: string): string[];
         parseCidIntoSelection(selectedCid: string): Promise<ResidueSelection>;
-        downloadAtoms(format?: 'mmcif' | 'pdb'): Promise<void>;
+        downloadAtoms(format?: coorFormats, fileName?: string): Promise<void>;
         getResidueBFactors(): { cid: string; bFactor: number; normalised_bFactor: number }[];
         getNcsRelatedChains(): Promise<string[][]>;
         animateRefine(n_cyc: number, n_iteration: number, final_n_cyc?: number): Promise<void>;
         refineResidueRange(chainId: string, start: number, stop: number, ncyc?: number, redraw?: boolean): Promise<void>;
-        SSMSuperpose(movChainId: string, refMolNo: number, refChainId: string): Promise<WorkerResponse>;
+        SSMSuperpose(movChainId: string, refMolNo: number, refChainId: string, redraw?: boolean): Promise<void>;
+        lsqkbSuperpose(refMolNo: number, residueMatches: lskqbResidueRangeMatch[], matchType?: number, redraw?: boolean): Promise<void>;
         refineResiduesUsingAtomCid(cid: string, mode: string, ncyc?: number, redraw?: boolean): Promise<void>;
         deleteCid(cid: string, redraw?: boolean): Promise<{first: number, second: number}>;
         getNumberOfAtoms(): Promise<number>;
@@ -152,7 +187,7 @@ export namespace moorhen {
         fitLigand(mapMolNo: number, ligandMolNo: number, fitRightHere?: boolean, redraw?: boolean, useConformers?: boolean, conformerCount?: number): Promise<Molecule[]>;
         checkIsLigand(): boolean;
         removeRepresentation(representationId: string): void;
-        addRepresentation(style: string, cid: string, isCustom?: boolean, colour?: ColourRule[], bondOptions?: cootBondOptions): Promise<MoleculeRepresentation>;
+        addRepresentation(style: string, cid: string, isCustom?: boolean, colour?: ColourRule[], bondOptions?: cootBondOptions, m2tParams?: m2tParameters, residueEnvOptions?: residueEnvironmentOptions): Promise<MoleculeRepresentation>;
         getNeighborResiduesCids(selectionCid: string, maxDist: number): Promise<string[]>;
         drawWithStyleFromMesh(style: string, meshObjects: any[], cid?: string, fetchAtomBuffers?: boolean): Promise<void>;
         updateWithMovedAtoms(movedResidues: AtomInfo[][]): Promise<void>;
@@ -177,7 +212,7 @@ export namespace moorhen {
         clearExtraRestraints(): Promise<WorkerResponse>;
         redo(): Promise<void>;
         undo(): Promise<void>;
-        show(style: string, cid?: string): void;
+        show(style: string, cid?: string): Promise<MoleculeRepresentation>;
         setSymmetryRadius(radius: number): Promise<void>;
         drawSymmetry: (fetchSymMatrix?: boolean) => Promise<void>;
         drawBiomolecule(fetchSymMatrix?: boolean) : void;
@@ -187,15 +222,15 @@ export namespace moorhen {
         delete(popBackImol?: boolean): Promise<WorkerResponse>;
         fetchDefaultColourRules(): Promise<void>;
         fetchIfDirtyAndDraw(arg0: string): Promise<void>;
-        drawEnvironment: (cid: string, labelled?: boolean) => Promise<void>;
+        drawEnvironment: (cid?: string) => Promise<void>;
         centreOn: (selectionCid?: string, animate?: boolean, setZoom?: boolean) => Promise<void>;
         drawHover: (cid: string) => Promise<void>;
         drawResidueSelection: (cid: string) => Promise<void>;
         clearBuffersOfStyle: (style: string) => void;
         loadToCootFromURL: (inputFile: string, molName: string, options?: RequestInit) => Promise<Molecule>;
         applyTransform: () => Promise<void>;
-        getAtoms(format?: string): Promise<string>;
-        hide: (style: string, cid?: string) => void;
+        getAtoms(format?: coorFormats): Promise<string>;
+        hide: (style: string, cid?: string) => MoleculeRepresentation;
         redraw: () => Promise<void>;
         setAtomsDirty: (newVal: boolean) => void;
         isVisible: (excludeBuffers?: string[]) => boolean;
@@ -205,12 +240,14 @@ export namespace moorhen {
         getPrivateerValidation(useCache?: boolean): Promise<privateer.ResultsEntry[]>;
         getLigandSVG(resName: string, useCache?: boolean): Promise<string>;
         isValidSelection(cid: string): Promise<boolean>;
+        fetchHeaderInfo(useCache?: boolean): Promise<libcootApi.headerInfoJS>;
         type: string;
         adaptativeBondsEnabled: boolean;
         cachedLigandSVGs: {[key: string]: string};
         cachedGemmiAtoms: AtomInfo[];
         cachedPrivateerValidation: privateer.ResultsEntry[];
         isLigand: boolean;
+        isMRSearchModel: boolean;
         excludedCids: string[];
         commandCentre: React.RefObject<CommandCentre>;
         glRef: React.RefObject<webGL.MGWebGL>;
@@ -229,13 +266,9 @@ export namespace moorhen {
         biomolOn: boolean;
         symmetryRadius : number;
         symmetryMatrices: number[][][];
-        gaussianSurfaceSettings: {
-            sigma: number;
-            countourLevel: number;
-            boxRadius: number;
-            gridScale: number;
-            bFactor: number;
-        };
+        gaussianSurfaceSettings: gaussianSurfSettings;
+        defaultM2tParams: m2tParameters;
+        defaultResidueEnvironmentOptions: residueEnvironmentOptions
         isDarkBackground: boolean;
         representations: MoleculeRepresentation[];
         defaultBondOptions: cootBondOptions;
@@ -253,12 +286,20 @@ export namespace moorhen {
         hasGlycans: boolean;
         coordsFormat: coorFormats;
         moleculeDiameter: number;
+        headerInfo: libcootApi.headerInfoJS;
+    }
+
+    type lskqbResidueRangeMatch = {
+        refChainId: string;
+        movChainId: string;
+        refResidueRange: [number, number];
+        movResidueRange: [number, number];
     }
 
     type RepresentationStyles = 'VdwSpheres' | 'ligands' | 'CAs' | 'CBs' | 'CDs' | 'gaussian' | 'allHBonds' | 'rama' | 
     'rotamer' | 'CRs' | 'MolecularSurface' | 'DishyBases' | 'VdWSurface' | 'Calpha' | 'unitCell' | 'hover' | 'environment' | 
     'ligand_environment' | 'contact_dots' | 'chemical_features' | 'ligand_validation' | 'glycoBlocks' | 'restraints' | 
-    'residueSelection' | 'MetaBalls' | 'adaptativeBonds'
+    'residueSelection' | 'MetaBalls' | 'adaptativeBonds' | 'StickBases' | 'residue_environment' | 'transformation'
 
     interface MoleculeRepresentation {
         addColourRule(ruleType: string, cid: string, color: string, args: (string | number)[], isMultiColourRule?: boolean, applyColourToNonCarbonAtoms?: boolean, label?: string): void;
@@ -266,24 +307,31 @@ export namespace moorhen {
         applyColourRules(): Promise<void>;
         exportAsGltf(): Promise<ArrayBuffer>;
         setBondOptions(bondOptions: cootBondOptions): void;
+        setResidueEnvOptions(newOptions: residueEnvironmentOptions): void;
         setStyle(style: string): void;
         setUseDefaultColourRules(arg0: boolean): void;
         setColourRules(ruleList: ColourRule[]): void;
-        buildBuffers(arg0: DisplayObject[]): Promise<void>;
+        buildBuffers(arg0: DisplayObject[]): void;
         setBuffers(meshObjects: DisplayObject[]): void;
         drawSymmetry(): void
         deleteBuffers(): void;
         draw(): Promise<void>;
         redraw(): Promise<void>;
         setParentMolecule(arg0: Molecule): void;
-        show(): void;
+        show(): Promise<void>;
         hide(): void;
         setAtomBuffers(arg0: AtomInfo[]): void;
+        setM2tParams(arg0: m2tParameters): void;
+        static mergeBufferObjects(bufferObj1: libcootApi.InstancedMeshJS[], bufferObj2: libcootApi.InstancedMeshJS[]): libcootApi.InstancedMeshJS[];
         bondOptions: cootBondOptions;
+        m2tParams: m2tParameters;
+        residueEnvironmentOptions: residueEnvironmentOptions;
+        useDefaultM2tParams: boolean;
+        useDefaultResidueEnvironmentOptions: boolean;
         useDefaultColourRules: boolean;
         useDefaultBondOptions: boolean;
         uniqueId: string;
-        style: string;
+        style: RepresentationStyles;
         cid: string;
         visible: boolean;
         buffers: DisplayObject[];
@@ -427,7 +475,7 @@ export namespace moorhen {
         startRecording: () => void;
         isRecording: () => boolean;
         downloadVideo: (blob: Blob) => Promise<void>;
-        takeScreenShot: (fileName: string) => void;
+        takeScreenShot: (fileName: string, doTransparentBackground?: boolean) => void;
     }
 
     interface Map {
@@ -510,17 +558,25 @@ export namespace moorhen {
         name: string;
         molNo: number;
         coordString: string;
+        coordFormat: coorFormats;
         representations: { 
             cid: string;
             style: strin;
             isCustom: boolean;
             colourRules: ColourRuleObject[];
             bondOptions: cootBondOptions;
+            m2tParams: m2tParameters;
+            resEnvOptions: residueEnvironmentOptions;
          }[];
         defaultBondOptions: cootBondOptions;
+        defaultM2tParams: m2tParameters;
+        defaultResEnvOptions: residueEnvironmentOptions;
         defaultColourRules: ColourRuleObject[];
         connectedToMaps: number[];
         ligandDicts: {[comp_id: string]: string};
+        symmetryOn: boolean;
+        biomolOn: boolean;
+        symmetryRadius: number;
     }
     
     type mapDataSession = {
@@ -569,6 +625,7 @@ export namespace moorhen {
             depthThreshold: number;
             normalThreshold: number;
         };
+        doPerspectiveProjection: boolean;
         blur: {enabled: boolean; depth: number; radius: number};
     }
     
@@ -591,6 +648,54 @@ export namespace moorhen {
         createBackup(keyString: string, sessionString: string): Promise<string>;
         fetchSession(includeAdditionalMapData: boolean): Promise<backupSession>;
         toggleDisableBackups(): void;
+        addModification: () =>  Promise<string>;
+        init: () => Promise<void>;
+        retrieveBackup: (arg0: string) => Promise<string | ArrayBuffer>;
+        static getBackupLabel(key: backupKey): string;
+        static loadSessionData(
+            sessionData: backupSession,
+            monomerLibraryPath: string,
+            molecules: Molecule[],
+            maps: Map[],
+            commandCentre: React.RefObject<CommandCentre>,
+            timeCapsuleRef: React.RefObject<TimeCapsule>,
+            glRef: React.RefObject<webGL.MGWebGL>,
+            store: ToolkitStore,
+            dispatch: Dispatch<AnyAction>
+        ): Promise<number>;
+        static loadSessionFromArrayBuffer(
+            sessionArrayBuffer: ArrayBuffer,
+            monomerLibraryPath: string,
+            molecules: Molecule[],
+            maps: Map[],
+            commandCentre: React.RefObject<CommandCentre>,
+            timeCapsuleRef: React.RefObject<TimeCapsule>,
+            glRef: React.RefObject<webGL.MGWebGL>,
+            store: ToolkitStore,
+            dispatch: Dispatch<AnyAction>
+        ): Promise<number>;
+        static loadSessionFromProtoMessage(
+            sessionProtoMessage: any,
+            monomerLibraryPath: string,
+            molecules: Molecule[],
+            maps: Map[],
+            commandCentre: React.RefObject<CommandCentre>,
+            timeCapsuleRef: React.RefObject<TimeCapsule>,
+            glRef: React.RefObject<webGL.MGWebGL>,
+            store: ToolkitStore,
+            dispatch: Dispatch<AnyAction>
+        ): Promise<number>;
+        static loadSessionFromJsonString(
+            sessionDataString: string,
+            monomerLibraryPath: string,
+            molecules: Molecule[],
+            maps: Map[],
+            commandCentre: React.RefObject<CommandCentre>,
+            timeCapsuleRef: React.RefObject<TimeCapsule>,
+            glRef: React.RefObject<webGL.MGWebGL>,
+            store: ToolkitStore,
+            dispatch: Dispatch<AnyAction>
+        ): Promise<number>;
         store: ToolkitStore;
         moleculesRef: React.RefObject<Molecule[]>;
         mapsRef: React.RefObject<Map[]>;
@@ -603,9 +708,6 @@ export namespace moorhen {
         version: string;
         disableBackups: boolean;
         storageInstance: LocalStorageInstance;
-        addModification: () =>  Promise<string>;
-        init: () => Promise<void>;
-        retrieveBackup: (arg0: string) => Promise<string | ArrayBuffer>;
     }
 
     type AtomRightClickEventInfo = {
@@ -730,7 +832,6 @@ export namespace moorhen {
         drawAxes: boolean; 
         drawFPS: boolean; 
         drawMissingLoops: boolean; 
-        drawInteractions: boolean; 
         doPerspectiveProjection: boolean; 
         useOffScreenBuffers: boolean; 
         depthBlurRadius: number; 
@@ -832,6 +933,7 @@ export namespace moorhen {
             moleculeList: Molecule[];
             visibleMolecules: number[];
             customRepresentations: MoleculeRepresentation[];
+            generalRepresentations: MoleculeRepresentation[];
         };
         maps: Map[];
         mouseSettings: {
@@ -863,7 +965,6 @@ export namespace moorhen {
             drawAxes: boolean; 
             drawFPS: boolean; 
             drawMissingLoops: boolean; 
-            drawInteractions: boolean; 
             doPerspectiveProjection: boolean; 
             useOffScreenBuffers: boolean; 
             depthBlurRadius: number; 
@@ -919,27 +1020,10 @@ export namespace moorhen {
             hoveredAtom: HoveredAtom;
             cursorStyle: string;
         };
-        activeModals: {
-            showModelsModal: boolean;
-            showMapsModal: boolean;
-            showCreateAcedrgLinkModal: boolean;
-            showQuerySequenceModal: boolean;
-            showScriptingModal: boolean;
-            showControlsModal: boolean;
-            showFitLigandModal: boolean;
-            showRamaPlotModal: boolean;
-            showDiffMapPeaksModal: boolean;
-            showValidationPlotModal: boolean;
-            showLigandValidationModal: boolean;
-            showCarbohydrateModal: boolean;
-            showPepFlipsValidationModal: boolean;
-            showFillPartialResValidationModal: boolean;
-            showUnmodelledBlobsModal: boolean;
-            showMmrrccModal: boolean;
-            showWaterValidationModal: boolean;
-            showSceneSettingsModal: boolean;
-            showSliceNDiceModal: boolean;
+        modals: {
+            activeModals: string[];
             focusHierarchy: string[];
+            modalsAttachedToSideBar: { key: string; isCollapsed: boolean }[];
         };
         mapContourSettings: {
             visibleMaps: number[];
@@ -971,11 +1055,14 @@ export namespace moorhen {
         };
         refinementSettings: {
             useRamaRefinementRestraints: boolean;
-            useTorsionRefinementRestraints: boolean;        
+            useTorsionRefinementRestraints: boolean;
             enableRefineAfterMod: boolean; 
             animateRefine: boolean;
             refinementSelection: 'SINGLE' | 'TRIPLE' | 'SPHERE';
         };
+        lhasa: {
+            rdkitMoleculePickleList: { cid: string; moleculeMolNo: number; ligandName: string; pickle: string; id: string }[];
+        }
     }
     
     type actionButtonSettings = {

package/baby-gru/CootWorker.js

@@ -1 +0,0 @@
-var cootModule,molecules_container,ccp4Module,__assign=this&&this.__assign||function(){return __assign=Object.assign||function(e){for(var a,r=1,t=arguments.length;r<t;r++)for(var o in a=arguments[r])Object.prototype.hasOwnProperty.call(a,o)&&(e[o]=a[o]);return e},__assign.apply(this,arguments)};importScripts("./moorhen.js"),importScripts("./web_example.js");var guid=function(){var e=Date.now();return"xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx".replace(/[xy]/g,(function(a){var r=(e+16*Math.random())%16|0;return e=Math.floor(e/16),("x"===a?r:3&r|8).toString(16)}))},print=function(e){console.log(e),postMessage({consoleMessage:JSON.stringify(e)})},instancedMeshToMeshData=function(e,a,r,t){void 0===r&&(r=!1),void 0===t&&(t=1e4);for(var o=[],s=[],n=[],i=[],c=[],_=[],l=[],u=[],d=[],m=e.geom,p=e.markup,g=m.size(),h=0;h<g;h++){var f=r,v=[],y=[],S=[],b=[],M=[],z=[],x=[],T=m.get(h);"spherical-atoms"===T.name&&(f=!0);for(var A=T.vertices,F=T.triangles,w=F.size(),k=0;k<w;k++){var I=F.get(k).point_id;a?(v.push(I[0]),v.push(I[2]),v.push(I[1])):(v.push(I[0]),v.push(I[1]),v.push(I[2]))}F.delete();for(var J=A.size(),D=0;D<J;D++){var C=A.get(D),N=C.pos;y.push(N[0]),y.push(N[1]),y.push(N[2]);var R=C.normal;S.push(R[0]),S.push(R[1]),S.push(R[2])}A.delete();var P=T.instancing_data_A,E=P.size();if(E>0)for(var U=0;U<E;U++){var L=(q=P.get(U)).position;z.push(L[0]),z.push(L[1]),z.push(L[2]);var O=q.colour;M.push(O[0]),M.push(O[1]),M.push(O[2]),M.push(O[3]);var B=q.size;b.push(B[0]),b.push(B[1]),b.push(B[2]),x.push.apply(x,[1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1])}P.delete();var j=T.instancing_data_B,V=j.size();if(V>0)for(U=0;U<V;U++){var q;if(!((B=(q=j.get(U)).size)[2]>t)){b.push(B[0]),b.push(B[1]),b.push(B[2]),L=q.position,z.push(L[0]),z.push(L[1]),z.push(L[2]),O=q.colour,M.push(O[0]),M.push(O[1]),M.push(O[2]),M.push(O[3]);var H=q.orientation;x.push(H[0][0]),x.push(H[0][1]),x.push(H[0][2]),x.push(H[0][3]),x.push(H[1][0]),x.push(H[1][1]),x.push(H[1][2]),x.push(H[1][3]),x.push(H[2][0]),x.push(H[2][1]),x.push(H[2][2]),x.push(H[2][3]),x.push(H[3][0]),x.push(H[3][1]),x.push(H[3][2]),x.push(H[3][3])}}j.delete(),n.push(S),s.push(y),o.push(v),i.push(b),_.push(z),l.push(x),c.push(M),u.push(!0),f?d.push("PERFECT_SPHERES"):d.push("TRIANGLES")}m.delete();var K=simpleMeshToMeshData(p);return K.idx_tri.length>0&&K.idx_tri[0].length>0&&K.idx_tri[0][0].length>0?r?{prim_types:[d,K.prim_types[0]],idx_tri:[o,K.idx_tri[0]],vert_tri:[_,K.vert_tri[0]],norm_tri:[n,K.norm_tri[0]],col_tri:[c,K.col_tri[0]],instance_use_colors:[u,null],instance_sizes:[i,null],instance_origins:[_,null],instance_orientations:[l,null]}:{prim_types:[d,K.prim_types[0]],idx_tri:[o,K.idx_tri[0]],vert_tri:[s,K.vert_tri[0]],norm_tri:[n,K.norm_tri[0]],col_tri:[c,K.col_tri[0]],instance_use_colors:[u,null],instance_sizes:[i,null],instance_origins:[_,null],instance_orientations:[l,null]}:{prim_types:[d],idx_tri:[o],vert_tri:[s],norm_tri:[n],col_tri:[c],instance_use_colors:[u],instance_sizes:[i],instance_origins:[_],instance_orientations:[l]}},simpleMeshToMeshData=function(e,a){void 0===a&&(a=!1),performance.now();var r=e.vertices,t=e.triangles,o=r.size(),s=t.size(),n=new Uint32Array(3*s),i=new Float32Array(3*o),c=new Float32Array(3*o),_=new Float32Array(4*o);cootModule.getPositionsFromSimpleMesh2(e,i),cootModule.getColoursFromSimpleMesh2(e,_),a?(cootModule.getReversedNormalsFromSimpleMesh2(e,c),cootModule.getPermutedTriangleIndicesFromSimpleMesh2(e,n)):(cootModule.getNormalsFromSimpleMesh2(e,c),cootModule.getTriangleIndicesFromSimpleMesh2(e,n)),performance.now();var l=i,u=_,d=c,m=n;return r.delete(),t.delete(),{prim_types:[["TRIANGLES"]],idx_tri:[[m]],vert_tri:[[l]],norm_tri:[[d]],col_tri:[[u]]}},SuperposeResultsToJSArray=function(e){for(var a=e.aligned_pairs,r=a.size(),t=[],o=0;o<r;o++){var s=a.get(o),n=s.first,i=n.residue_spec,c=s.second,_=c.residue_spec,l={reference:{chainId:i.chain_id,insCode:i.ins_code,seqNum:i.res_no,restype:"UNK",value:n.function_value,label:n.label},moving:{chainId:_.chain_id,insCode:_.ins_code,seqNum:_.res_no,restype:"UNK",value:c.function_value,label:c.label}};t.push(l)}return a.delete(),{referenceSequence:e.alignment.first,movingSequence:e.alignment.second,supperposeInfo:e.superpose_info,alignedPairsData:t}},colourRulesToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(o)}return e.delete(),a},stringArrayArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){for(var o=e.get(t),s=o.size(),n=[],i=0;i<s;i++){var c=o.get(i);n.push(c)}a.push(n),o.delete()}return e.delete(),a},floatArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(o)}return e.delete(),a},mapMoleculeCentreInfoToJSObject=function(e){var a=e.updated_centre,r={updated_centre:[a.x(),a.y(),a.z()],success:e.success,suggested_radius:e.suggested_radius,suggested_contour_level:e.suggested_contour_level};return a.delete(),r},textureAsFloatsToJSTextureAsFloats=function(e){var a=e.width*e.height,r=new Float32Array(a),t=performance.now();cootModule.getTextureArray(e,r);var o=performance.now();return console.log("Time to convert texture array to JS",o-t),{width:e.width,height:e.height,x_size:e.x_size,y_size:e.y_size,z_position:e.z_position,image_data:r}},fitLigandInfoArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(__assign({},o))}return e.delete(),a},intArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(o)}return e.delete(),a},stringArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(o)}return e.delete(),a},export_map_as_gltf=function(e,a,r,t,o,s){var n="".concat(guid(),".glb");molecules_container.export_map_molecule_as_gltf(e,a,r,t,o,s,n);var i=cootModule.FS.readFile(n,{encoding:"binary"});return cootModule.FS_unlink(n),i.buffer},export_molecular_represenation_as_gltf=function(e,a,r,t){var o="".concat(guid(),".glb");molecules_container.export_molecular_represenation_as_gltf(e,a,r,t,o);var s=cootModule.FS.readFile(o,{encoding:"binary"});return cootModule.FS_unlink(o),s.buffer},export_molecule_as_gltf=function(e,a,r,t,o,s,n,i,c){var _="".concat(guid(),".glb");molecules_container.export_model_molecule_as_gltf(e,a,r,t,o,s,n,i,c,_);var l=cootModule.FS.readFile(_,{encoding:"binary"});return cootModule.FS_unlink(_),l.buffer},symmetryToJSData=function(e){for(var a=[],r=e.first,t=e.second,o=r.symm_trans,s=o.size(),n=0;n<s;n++){var i=o.get(n),c=i.first,_=i.second,l=t.get(n);a.push({x:c.x(),y:c.y(),z:c.z(),asString:c.symm_as_string,isym:c.isym(),us:_.us,ws:_.ws,vs:_.vs,matrix:l}),c.delete()}return o.delete(),t.delete(),a},mmrrccStatsToJSArray=function(e){var a=function(e){for(var a=[],r=e.keys(),t=r.size(),o=0;o<t;o++){var s=r.get(o),n=e.get(s);a.push({resNum:s.res_no,insCode:s.ins_code,modelNumber:s.model_number,chainId:s.chain_id,n:n.n,correlation:n.correlation()}),n.delete()}return r.delete(),a},r=e.first,t=e.second,o={"All atoms":a(r),"Side-chains":a(t)};return r.delete(),t.delete(),o},atomSpecToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({chain_id:o.chain_id,res_no:o.res_no,ins_code:o.ins_code,atom_name:o.atom_name,alt_conf:o.alt_conf,int_user_data:o.int_user_data,float_user_data:o.float_user_data,string_user_data:o.string_user_data,model_number:o.model_number})}return e.delete(),a},residueSpecToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({resNum:o.res_no,insCode:o.ins_code,modelNumber:o.model_number,chainId:o.chain_id,intUserData:o.int_user_data})}return e.delete(),a},stringPairVectorToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({first:o.first,second:o.second})}return e.delete(),a},validationDataToJSArray=function(e,a){void 0===a&&(a=null);for(var r=[],t=e.cviv,o=t.size(),s=0;s<o;s++){var n=t.get(s);if(null!==a&&n.chain_id!==a);else{for(var i=n.rviv,c=i.size(),_=0;_<c;_++){var l=i.get(_),u=l.residue_spec;r.push({chainId:u.chain_id,insCode:u.ins_code,seqNum:u.res_no,restype:"UNK",value:l.function_value})}i.delete()}}return t.delete(),e.delete(),r},linesBoxToJSArray=function(e){for(var a=[],r=e.line_segments,t=r.size(),o=0;o<t;o++){for(var s=[],n=r.get(o),i=n.size(),c=0;c<i;c++){var _=n.get(c),l=_.getStart(),u=_.getFinish(),d=_.amplitude(),m={x:l.x(),y:l.y(),z:l.z()},p={x:u.x(),y:u.y(),z:u.z()};s.push({start:m,end:p,dist:d}),l.delete(),u.delete(),_.delete()}n.delete(),a.push(s)}return r.delete(),a},vectorHBondToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({hb_hydrogen:o.hb_hydrogen,donor:o.donor,acceptor:o.acceptor,donor_neigh:o.donor_neigh,acceptor_neigh:o.acceptor_neigh,angle_1:o.angle_1,angle_2:o.angle_2,angle_3:o.angle_3,dist:o.dist,ligand_atom_is_donor:o.ligand_atom_is_donor,hydrogen_is_ligand_atom:o.hydrogen_is_ligand_atom,bond_has_hydrogen_flag:o.bond_has_hydrogen_flag})}return e.delete(),a},interestingPlaceDataToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t),s=o.residue_spec;a.push({intUserData:s.int_user_data,modelNumber:s.model_number,chainId:s.chain_id,insCode:s.ins_code,resNum:s.res_no,featureType:o.feature_type,featureValue:o.feature_value,buttonLabel:o.button_label,badness:o.badness,coordX:o.x,coordY:o.y,coordZ:o.z})}return e.delete(),a},histogramInfoToJSData=function(e){var a=e.counts;return{counts:intArrayToJSArray(a),bin_width:e.bin_width,base:e.base}},autoReadMtzInfoVectToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({idx:o.idx,F:o.F,phi:o.phi,w:o.w,weights_used:o.weights_used,Rfree:o.Rfree?o.Rfree.split("/")[3]:"",F_obs:o.F_obs?o.F_obs.split("/")[3]:"",sigF_obs:o.sigF_obs?o.sigF_obs.split("/")[3]:""})}if(e.delete(),a.some((function(e){return-1===e.idx}))){var s=a.find((function(e){return-1===e.idx}));s&&s.F_obs&&s.Rfree&&s.sigF_obs&&a.forEach((function(e){e.F_obs=s.F_obs,e.sigF_obs=s.sigF_obs,e.Rfree=s.Rfree})),a=a.filter((function(e){return-1!==e.idx}))}return a},ramachandranDataToJSArray=function(e,a){for(var r=[],t=e.size(),o=0;o<t;o++){var s=e.get(o),n=s.phi_psi;n.chain_id===a&&r.push({chainId:n.chain_id,insCode:n.ins_code,seqNum:n.residue_number,restype:s.residue_name(),isOutlier:!s.is_allowed_flag,phi:n.phi(),psi:n.psi(),is_pre_pro:"PRO"===s.residue_name()}),s.delete(),n.delete()}return e.delete(),r},vectorPairStringIntToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t),s={residue:o.first,slice:o.second};a.push(s)}return e.delete(),a},vectorPairClipperCoordFloatToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t),s=o.second,n=o.first,i={x:n.x(),y:n.y(),z:n.z()};n.delete(),a.push({value:s,coord:i})}return e.delete(),a},simpleMeshToLineMeshData=function(e,a){performance.now();var r=e.vertices,t=e.triangles,o=t.size(),s=r.size(),n=new Uint32Array(6*o),i=new Float32Array(3*s),c=new Float32Array(3*s),_=new Float32Array(4*s);cootModule.getLineIndicesFromSimpleMesh2(e,n),cootModule.getPositionsFromSimpleMesh2(e,i),cootModule.getNormalsFromSimpleMesh2(e,c),cootModule.getColoursFromSimpleMesh2(e,_),performance.now();var l=n,u=i,d=c,m=_;return r.delete(),t.delete(),a?{prim_types:[["NORMALLINES"]],useIndices:[[!0]],idx_tri:[[l]],vert_tri:[[u]],additional_norm_tri:[[d]],norm_tri:[[d]],col_tri:[[m]]}:{prim_types:[["LINES"]],useIndices:[[!0]],idx_tri:[[l]],vert_tri:[[u]],norm_tri:[[d]],col_tri:[[m]]}},auto_read_mtz=function(e){var a=guid(),r=new Uint8Array(e);cootModule.FS_createDataFile(".","".concat(a,".mtz"),r,!0,!0);var t="./".concat(a,".mtz"),o=molecules_container.auto_read_mtz(t);return cootModule.FS_unlink(t),o},replace_map_by_mtz_from_file=function(e,a,r){var t=guid(),o="./".concat(t,".mtz"),s=new Uint8Array(a);cootModule.FS_createDataFile(".",o,s,!0,!0);var n=[e,o,r.F,r.PHI,"",!1],i=molecules_container.replace_map_by_mtz_from_file.apply(molecules_container,n);return cootModule.FS_unlink(o),i},new_positions_for_residue_atoms=function(e,a){var r=0,t=new cootModule.Vectormoved_residue_t;return a.forEach((function(e){if(e.length>0){var a=e[0],r=new cootModule.moved_residue_t(a.chain_id,parseInt(a.res_no),"");e.forEach((function(e){var a=new cootModule.moved_atom_t(e.name,e.alt_loc,e.x,e.y,e.z,-1);r.add_atom(a),a.delete()})),t.push_back(r),r.delete()}})),r+=molecules_container.new_positions_for_atoms_in_residues(e,t),t.delete(),r},read_mtz=function(e,a,r){var t=guid(),o=new Uint8Array(e);cootModule.FS_createDataFile(".","".concat(t,".mtz"),o,!0,!0);var s="./".concat(t,".mtz"),n=[s,r.F,r.PHI,"",!1,r.isDifference],i=molecules_container.read_mtz.apply(molecules_container,n);return cootModule.FS_unlink(s),i},associate_data_mtz_file_with_map=function(e,a,r,t,o){var s=new Uint8Array(a.data);cootModule.FS_createDataFile(".","".concat(a.fileName,".mtz"),s,!0,!0);var n="./".concat(a.fileName,".mtz"),i=[e,n,r,t,o];return molecules_container.associate_data_mtz_file_with_map.apply(molecules_container,i),n},read_ccp4_map=function(e,a,r){var t=guid(),o=new Uint8Array(e),s="";a.endsWith(".map.gz")?s="map.gz":a.endsWith(".mrc.gz")&&(s="mrc.gz"),cootModule.FS_createDataFile(".","".concat(t).concat(s),o,!0,!0);var n="./".concat(t).concat(s),i=[n,r],c=-1;try{c=molecules_container.read_ccp4_map.apply(molecules_container,i)}catch(e){console.warn(e)}finally{cootModule.FS_unlink(n)}return c},setUserDefinedBondColours=function(e,a,r){void 0===r&&(r=!1);var t=new cootModule.MapIntFloat3,o=new cootModule.VectorStringUInt_pair;a.forEach((function(e,a){t.set(a+51,e.rgb);var r={first:e.cid,second:a+51};o.push_back(r)})),molecules_container.set_user_defined_bond_colours(e,t),molecules_container.set_user_defined_atom_colour_by_selection(e,o,r),o.delete(),t.delete()},privateerValidationToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){for(var o=e.get(t),s=[],n=o.torsions,i=n.size(),c=0;c<i;c++)s.push(n.get(c));n.delete();var _={torsions:s,svg:o.svg.replace(/: *32/g,""),id:o.id.replace(/: *32/g,""),chain:o.chain,wurcs:o.wurcs,glyconnect_id:o.glyconnect_id,glytoucan_id:o.glytoucan_id,torsion_err:o.torsion_err,anomer_err:o.anomer_err,conformation_err:o.conformation_err,puckering_err:o.puckering_err,chirality_err:o.chirality_err};a.push(_)}return e.delete(),a},doCootCommand=function(e){var a=e.returnType,r=e.command,t=e.commandArgs,o=e.messageId,s=e.myTimeStamp,n=e.message;try{var i=void 0;switch(r){case"shim_new_positions_for_residue_atoms":i=new_positions_for_residue_atoms.apply(void 0,t);break;case"shim_read_mtz":i=read_mtz.apply(void 0,t);break;case"shim_auto_read_mtz":i=auto_read_mtz.apply(void 0,t);break;case"shim_read_ccp4_map":i=read_ccp4_map.apply(void 0,t);break;case"shim_associate_data_mtz_file_with_map":i=associate_data_mtz_file_with_map.apply(void 0,t);break;case"shim_replace_map_by_mtz_from_file":i=replace_map_by_mtz_from_file.apply(void 0,t);break;case"shim_set_bond_colours":i=setUserDefinedBondColours.apply(void 0,t);break;case"shim_export_map_as_gltf":i=export_map_as_gltf.apply(void 0,t);break;case"shim_export_molecule_as_gltf":i=export_molecule_as_gltf.apply(void 0,t);break;case"shim_export_molecular_represenation_as_gltf":i=export_molecular_represenation_as_gltf.apply(void 0,t);break;default:i=molecules_container[r].apply(molecules_container,t)}var c=void 0;switch(a){case"texture_as_floats_t":c=textureAsFloatsToJSTextureAsFloats(i);break;case"fit_ligand_info_array":c=fitLigandInfoArrayToJSArray(i);break;case"string_array_array":c=stringArrayArrayToJSArray(i);break;case"instanced_mesh_perm":c=instancedMeshToMeshData(i,!0);break;case"histogram_info_t":c=histogramInfoToJSData(i);break;case"symmetry":c=symmetryToJSData(i);break;case"mmrrcc_stats":c=mmrrccStatsToJSArray(i);break;case"colour_rules":c=colourRulesToJSArray(i);break;case"instanced_mesh_perfect_spheres":c=instancedMeshToMeshData(i,!1,!0);break;case"instanced_mesh":c=instancedMeshToMeshData(i,!1,!1,5);break;case"mesh_perm":c=simpleMeshToMeshData(i,!0);break;case"mesh":c=simpleMeshToMeshData(i);break;case"lit_lines_mesh":c=simpleMeshToLineMeshData(i,!0);break;case"lines_mesh":c=simpleMeshToLineMeshData(i,!1);break;case"float_array":c=floatArrayToJSArray(i);break;case"int_array":c=intArrayToJSArray(i);break;case"auto_read_mtz_info_array":c=autoReadMtzInfoVectToJSArray(i);break;case"map_molecule_centre_info_t":c=mapMoleculeCentreInfoToJSObject(i);break;case"string_array":c=stringArrayToJSArray(i);break;case"residue_specs":c=residueSpecToJSArray(i);break;case"atom_specs":c=atomSpecToJSArray(i);break;case"ramachandran_data":c=ramachandranDataToJSArray(i,e.chainID);break;case"validation_data":c=validationDataToJSArray(i,e.chainID);break;case"interesting_places_data":c=interestingPlaceDataToJSArray(i);break;case"superpose_results":c=SuperposeResultsToJSArray(i);break;case"generic_3d_lines_bonds_box":c=linesBoxToJSArray(i);break;case"vector_hbond":c=vectorHBondToJSArray(i);break;case"status_instanced_mesh_pair":c={status:i.first,mesh:instancedMeshToMeshData(i.second,!1,!1,5)};break;case"string_string_pair_vector":c=stringPairVectorToJSArray(i);break;case"void":c=null;break;case"vector_pair_clipper_coord_float":c=vectorPairClipperCoordFloatToJSArray(i);break;case"vector_pair_string_int":c=vectorPairStringIntToJSArray(i);break;case"privateer_results":c=privateerValidationToJSArray(i);break;default:c=i}try{i.delete()}catch(e){}return{messageId:o,messageSendTime:Date.now(),command:r,consoleMessage:"Completed ".concat(r," in ").concat(Date.now()-s," ms"),result:{status:"Completed",result:c}}}catch(e){return console.log(e),{messageId:o,myTimeStamp:s,message:n,consoleMessage:"EXCEPTION RAISED IN ".concat(r,", ").concat(e),result:{status:"Exception"}}}};onmessage=function(e){if("CootInitialize"===e.data.message)createRSRModule({onRuntimeInitialized:function(){},mainScriptUrlOrBlob:"moorhen.js",print,printErr:print}).then((function(a){postMessage({consoleMessage:"Initialized molecules_container",message:e.data.message,messageId:e.data.messageId}),(molecules_container=new(cootModule=a).molecules_container_js(!1)).set_use_gemmi(!1),molecules_container.set_show_timings(!1),molecules_container.set_refinement_is_verbose(!1),molecules_container.fill_rotamer_probability_tables(),molecules_container.set_map_sampling_rate(1.7),molecules_container.set_map_is_contoured_with_thread_pool(!0),molecules_container.set_max_number_of_threads(3),cootModule.FS.mkdir("COOT_BACKUP")})).catch((function(e){console.log(e),print(e)})),createCCP4Module({onRuntimeInitialized:function(){},mainScriptUrlOrBlob:"web_example.js",print,printErr:print}).then((function(e){ccp4Module=e})).catch((function(e){console.log(e),print(e)}));else if("close"===e.data.message)null==molecules_container||molecules_container.delete(),postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,consoleMessage:"Closed molecules container",message:e.data.message,result:{}});else if("get_mtz_data"===e.data.message){var a=cootModule.FS.readFile(e.data.fileName,{encoding:"binary"});postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,consoleMessage:"Fetched mtz data for map ".concat(e.data.molNo),message:e.data.message,result:{molNo:e.data.molNo,mtzData:a}})}else if("get_map"===e.data.message){var r=guid(),t="./".concat(r,".map");molecules_container.writeCCP4Map(e.data.molNo,t);var o=cootModule.FS.readFile(t,{encoding:"binary"});cootModule.FS_unlink(t),postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,consoleMessage:"Fetched map of map ".concat(e.data.molNo),message:e.data.message,result:{molNo:e.data.molNo,mapData:o.buffer}})}else if("delete_file_name"===e.data.message){var s=cootModule.FS_unlink(e.data.fileName);postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,messageTag:"result",result:s})}else if("coot_command_list"===e.data.message){var n=e.data.commandList.map((function(a){return doCootCommand(__assign(__assign({},e.data),a))}));postMessage({messageId:e.data.messageId,resultList:n})}"coot_command"===e.data.message&&(s=doCootCommand(e.data),postMessage(s))};