moorhen 0.0.1 → 0.6.2

package/types/main.d.ts

@@ -0,0 +1,428 @@
+import { moorhen as _moorhen } from "./moorhen"
+import { webGL } from "./mgWebGL";
+import { libcootApi } from "./libcoot";
+import { gemmi } from "./gemmi";
+import { emscriptem } from "./emscriptem";
+
+declare module 'moorhen' {
+
+    let MoorhenContainer: any;
+    module.exports = MoorhenContainer;
+
+    let MoorhenDraggableModalBase: any;
+    module.exports = MoorhenDraggableModalBase;
+
+
+    let MoorhenMoleculeSelect: any;
+    module.exports = MoorhenMoleculeSelect;
+
+    let MoorhenQuerySequenceModal: any;
+    module.exports = MoorhenQuerySequenceModal;
+
+    let MoorhenMapSelect: any;
+    module.exports = MoorhenMapSelect;
+
+
+    let MoorhenSlider: any;
+    module.exports = MoorhenSlider;
+
+
+    let MoorhenFetchOnlineSourcesForm: any;
+    module.exports = MoorhenFetchOnlineSourcesForm;
+
+
+    let MoorhenReduxProvider: any;
+    module.exports = MoorhenReduxProvider;
+
+    class MoorhenPreferences implements _moorhen.Preferences {
+        name: string;
+        static defaultPreferencesValues: _moorhen.PreferencesValues;
+        localStorageInstance: {
+            clear: () => void;
+            setItem: (key: string, value: any) => Promise<string>;
+            getItem: (key: string) => Promise<any>;
+        };   
+    }
+    module.exports.MoorhenPreferences = MoorhenPreferences
+
+    class MoorhenMolecule implements _moorhen.Molecule {
+        constructor(commandCentre: React.RefObject<_moorhen.CommandCentre>, glRef: React.RefObject<webGL.MGWebGL>, monomerLibrary: 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<_moorhen.WorkerResponse>;
+        deleteCid(cid: string, redraw?: boolean): Promise<{first: number, second: number}>;
+        getNumberOfAtoms(): Promise<number>;
+        moveMoleculeHere(x: number, y: number, z: number): Promise<void>;
+        checkHasGlycans(): Promise<boolean>;
+        fitLigandHere(mapMolNo: number, ligandMolNo: number, redraw?: boolean, useConformers?: boolean, conformerCount?: number): Promise<_moorhen.Molecule[]>;
+        checkIsLigand(): boolean;
+        removeRepresentation(representationId: string): void;
+        addRepresentation(style: string, cid: string, isCustom?: boolean, colour?: _moorhen.ColourRule[], bondOptions?: _moorhen.cootBondOptions, applyColourToNonCarbonAtoms?: boolean): Promise<_moorhen.MoleculeRepresentation>;
+        getNeighborResiduesCids(selectionCid: string, maxDist: number): Promise<string[]>;
+        drawWithStyleFromMesh(style: string, meshObjects: any[], cid?: string): Promise<void>;
+        updateWithMovedAtoms(movedResidues: _moorhen.AtomInfo[][]): Promise<void>;
+        transformedCachedAtomsAsMovedAtoms(selectionCid?: string): _moorhen.AtomInfo[][];
+        copyFragmentUsingCid(cid: string, doRecentre?: boolean, style?: string): Promise<_moorhen.Molecule>;
+        hideCid(cid: string, redraw?: boolean): Promise<void>;
+        unhideAll(redraw?: boolean): Promise<void>;
+        drawUnitCell(): void;
+        gemmiAtomsForCid: (cid: string, omitExcludedCids?: boolean) => Promise<_moorhen.AtomInfo[]>;
+        mergeMolecules(otherMolecules: _moorhen.Molecule[], doHide?: boolean): Promise<void>;
+        setBackgroundColour(backgroundColour: [number, number, number, number]): void;
+        addDict(fileContent: string): Promise<void>;
+        addDictShim(fileContent: string): void;
+        toggleSymmetry(): Promise<void>;
+        getDict(newTlc: string): string;
+        addLigandOfType(resType: string, fromMolNo?: number): Promise<_moorhen.WorkerResponse>;
+        updateAtoms(): Promise<void>;
+        rigidBodyFit(cidsString: string, mapNo: number, redraw?: boolean): Promise<void>;
+        generateSelfRestraints(cid?: string, maxRadius?: number): Promise<void>;
+        clearExtraRestraints(): Promise<_moorhen.WorkerResponse>;
+        refineResiduesUsingAtomCid(cid: string, mode: string, ncyc?: number, redraw?: boolean): Promise<void>;
+        redo(): Promise<void>;
+        undo(): Promise<void>;
+        show(style: string, cid?: string): void;
+        setSymmetryRadius(radius: number): Promise<void>;
+        drawSymmetry: (fetchSymMatrix?: boolean) => Promise<void>;
+        getUnitCellParams():  { a: number; b: number; c: number; alpha: number; beta: number; gamma: number; };
+        replaceModelWithFile(fileUrl: string, molName: string): Promise<void>
+        delete(): Promise<_moorhen.WorkerResponse> 
+        fetchDefaultColourRules(): Promise<void>;
+        fetchIfDirtyAndDraw(arg0: string): Promise<void>;
+        drawEnvironment: (cid: string, labelled?: boolean) => Promise<void>;
+        centreOn: (selectionCid?: string, animate?: 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<_moorhen.Molecule>;
+        applyTransform: () => Promise<void>;
+        getAtoms(format?: string): Promise<string>;
+        hide: (style: string, cid?: string) => void;
+        redraw: () => Promise<void>;
+        setAtomsDirty: (newVal: boolean) => void;
+        hasVisibleBuffers: (excludeBuffers?: string[]) => boolean;
+        centreAndAlignViewOn(selectionCid: string, animate?: boolean): Promise<void>;
+        buffersInclude: (bufferIn: { id: string; }) => boolean;
+        redrawRepresentation: (id: string) => Promise<void>;
+        isLigand: boolean;
+        type: string;
+        excludedCids: string[];
+        commandCentre: React.RefObject<_moorhen.CommandCentre>;
+        glRef: React.RefObject<webGL.MGWebGL>;
+        atomsDirty: boolean;
+        isVisible: boolean;
+        name: string;
+        molNo: number;
+        gemmiStructure: gemmi.Structure;
+        sequences: _moorhen.Sequence[];
+        ligands: _moorhen.LigandInfo[];
+        atomCount: number;
+        ligandDicts: {[comp_id: string]: string};
+        connectedToMaps: number[];
+        excludedSelections: string[];
+        symmetryOn: boolean;
+        symmetryRadius : number;
+        symmetryMatrices: number[][][];
+        gaussianSurfaceSettings: {
+            sigma: number;
+            countourLevel: number;
+            boxRadius: number;
+            gridScale: number;
+        };
+        isDarkBackground: boolean;
+        representations: _moorhen.MoleculeRepresentation[];
+        defaultBondOptions: _moorhen.cootBondOptions;
+        displayObjectsTransformation: { origin: [number, number, number], quat: any, centre: [number, number, number] }
+        uniqueId: string;
+        defaultColourRules: _moorhen.ColourRule[];
+        restraints: {maxRadius: number, cid: string}[];
+        monomerLibraryPath: string;
+        hoverRepresentation: _moorhen.MoleculeRepresentation;
+        unitCellRepresentation: _moorhen.MoleculeRepresentation;
+        environmentRepresentation: _moorhen.MoleculeRepresentation;
+        selectionRepresentation: _moorhen.MoleculeRepresentation;
+        hasDNA: boolean;
+        hasGlycans: boolean;
+    }
+    module.exports.MoorhenMolecule = MoorhenMolecule
+    
+    class MoorhenMap implements _moorhen.Map {
+        constructor(commandCentre: React.RefObject<_moorhen.CommandCentre>, glRef: React.RefObject<webGL.MGWebGL>)
+        getHistogram(nBins?: number, zoomFactor?: number): Promise<libcootApi.HistogramInfoJS>;
+        setMapWeight(weight?: number): Promise<_moorhen.WorkerResponse>;
+        estimateMapWeight(): Promise<void>;
+        setAlpha(alpha: number, redraw?: boolean): Promise<void>;
+        centreOnMap(): Promise<void>;
+        getSuggestedSettings(): Promise<void>;
+        duplicate(): Promise<_moorhen.Map>;
+        makeCootUnlive(): void;
+        makeCootLive(): void;
+        setColour(r: number, g: number, b: number, redraw?: boolean): Promise<void> ;
+        setDiffMapColour(type: 'positiveDiffColour' | 'negativeDiffColour', r: number, g: number, b: number, redraw?: boolean): Promise<void> ;
+        fetchMapRmsd(): Promise<number>;
+        fetchSuggestedLevel(): Promise<number>;
+        fetchMapCentre(): Promise<[number, number, number]>;
+        replaceMapWithMtzFile(fileUrl: RequestInfo | URL, name: string, selectedColumns: _moorhen.selectedMtzColumns, mapColour?: { [type: string]: {r: number, g: number, b: number} }): Promise<void>;
+        associateToReflectionData (selectedColumns: _moorhen.selectedMtzColumns, reflectionData: Uint8Array | ArrayBuffer): Promise<void>;
+        delete(): Promise<void> 
+        doCootContour(x: number, y: number, z: number, radius: number, contourLevel: number): Promise<void>;
+        fetchReflectionData(): Promise<_moorhen.WorkerResponse<Uint8Array>>;
+        getMap(): Promise<_moorhen.WorkerResponse>;
+        loadToCootFromMtzURL(url: RequestInfo | URL, name: string, selectedColumns: _moorhen.selectedMtzColumns, options?: RequestInit): Promise<_moorhen.Map>;
+        loadToCootFromMapURL(url: RequestInfo | URL, name: string, isDiffMap?: boolean, options?: RequestInit): Promise<_moorhen.Map>;
+        setActive(): Promise<void>;
+        setupContourBuffers(objects: any[], keepCootColours?: boolean): void;
+        setOtherMapForColouring(molNo: number, min?: number, max?: number): void;
+        isEM: boolean;
+        suggestedContourLevel: number;
+        suggestedRadius: number;
+        mapCentre: [number, number, number];
+        type: string;
+        name: string;
+        molNo: number;
+        commandCentre: React.RefObject<_moorhen.CommandCentre>;
+        glRef: React.RefObject<webGL.MGWebGL>;
+        contourLevel: number;
+        mapRadius: number;
+        mapColour: [number, number, number, number];
+        webMGContour: boolean;
+        cootContour: boolean;
+        displayObjects: any;
+        litLines: boolean;
+        solid: boolean;
+        isDifference: boolean;
+        hasReflectionData: boolean;
+        selectedColumns: _moorhen.selectedMtzColumns;
+        associatedReflectionFileName: string;
+        uniqueId: string;
+        otherMapForColouring: {molNo: number, min: number, max: number};
+        mapRmsd: number;
+        suggestedMapWeight: number;
+        rgba: {
+            mapColour: {r: number, g: number, b: number};
+            positiveDiffColour: {r: number, g: number, b: number};
+            negativeDiffColour: {r: number, g: number, b: number};
+            a: number;
+        }
+    }
+    module.exports.MoorhenMap = MoorhenMap
+
+    function getMoleculeBfactors(gemmiStructure: gemmi.Structure): { cid: string, bFactor: number, chainId: string, resNum: number, modelName: string }[];
+    module.exports = getMoleculeBfactors;
+
+    function loadSessionData(
+        sessionDataString: string,
+        monomerLibraryPath: string,
+        molecules: _moorhen.Molecule[],
+        maps: _moorhen.Map[],
+        commandCentre: React.RefObject<_moorhen.CommandCentre>,
+        timeCapsuleRef: React.RefObject<_moorhen.TimeCapsule>,
+        glRef: React.RefObject<webGL.MGWebGL>,
+        dispatch: (reduxStoreAction: any) => void,
+    ): Promise<number>;
+    module.exports = loadSessionData;
+
+    function setDefaultBackgroundColor(arg0: [number, number, number, number]): any;
+    module.exports = setDefaultBackgroundColor;
+    
+    function setDrawCrosshairs(arg0: boolean): any;
+    module.exports = setDrawCrosshairs;
+    
+    function setDrawFPS(arg0: boolean): any;
+    module.exports = setDrawFPS;
+    
+    function setDrawMissingLoops(arg0: boolean): any;
+    module.exports = setDrawMissingLoops;
+    
+    function setDefaultBondSmoothness(arg0: number): any;
+    module.exports = setDefaultBondSmoothness;
+    
+    function setDrawInteractions(arg0: boolean): any;
+    module.exports = setDrawInteractions;
+    
+    function setDoSSAO(arg0: boolean): any;
+    module.exports = setDoSSAO;
+    
+    function setSsaoRadius(arg0: number): any;
+    module.exports = setSsaoRadius;
+    
+    function setSsaoBias(arg0: number): any;
+    module.exports = setSsaoBias;
+    
+    function setResetClippingFogging(arg0: boolean): any;
+    module.exports = setResetClippingFogging;
+    
+    function setClipCap(arg0: boolean): any;
+    module.exports = setClipCap;
+    
+    function setUseOffScreenBuffers(arg0: boolean): any;
+    module.exports = setUseOffScreenBuffers;
+    
+    function setDoShadowDepthDebug(arg0: boolean): any;
+    module.exports = setDoShadowDepthDebug;
+    
+    function setDoShadow(arg0: boolean): any;
+    module.exports = setDoShadow;
+    
+    function setDoSpinTest(arg0: boolean): any;
+    module.exports = setDoSpinTest;
+    
+    function setDoOutline(arg0: boolean): any;
+    module.exports = setDoOutline;
+    
+    function setDepthBlurRadius(arg0: number): any;
+    module.exports = setDepthBlurRadius;
+    
+    function setDepthBlurDepth(arg0: number): any;
+    module.exports = setDepthBlurDepth;
+    
+    function setDrawAxes(arg0: boolean): any;
+    module.exports = setDrawAxes;
+    
+    function setDoPerspectiveProjection(arg0: boolean): any;
+    module.exports = setDoPerspectiveProjection;
+
+    function setEnableTimeCapsule(arg0: boolean): any;
+    module.exports = setEnableTimeCapsule;
+
+    function setMakeBackups(arg0: boolean): any;
+    module.exports = setMakeBackups;
+
+    function setMaxBackupCount(arg0: number): any;
+    module.exports = setMaxBackupCount;
+
+    function setModificationCountBackupThreshold(arg0: number): any;
+    module.exports = setModificationCountBackupThreshold;
+
+    function setHeight(arg0: number): any;
+    module.exports = setHeight;
+
+    function setWidth(arg0: number): any;
+    module.exports = setWidth;
+
+    function setIsDark(arg0: boolean): any;
+    module.exports = setIsDark;
+
+    function setBackgroundColor(arg0: [number, number, number, number]): any;
+    module.exports = setBackgroundColor;
+
+    function setNotificationContent(arg0: JSX.Element): any;
+    module.exports = setNotificationContent;
+
+    function setActiveMap(arg0: _moorhen.Map): any;
+    module.exports = setActiveMap;
+
+    function setCootInitialized(arg0: boolean): any;
+    module.exports = setCootInitialized;
+
+    function setAppTitle(arg0: string): any;
+    module.exports = setAppTitle;
+
+    function setUserPreferencesMounted(arg0: boolean): any;
+    module.exports = setUserPreferencesMounted;
+
+    function setDevMode(arg0: boolean): any;
+    module.exports = setDevMode;
+
+    function setTheme(arg0: string): any;
+    module.exports = setTheme;
+
+    function setViewOnly(arg0: boolean): any;
+    module.exports = setViewOnly;
+
+    function setCursorStyle(arg0: string): any;
+    module.exports = setCursorStyle;
+
+    function setEnableAtomHovering(arg0: boolean): any;
+    module.exports = setEnableAtomHovering;
+
+    function setHoveredAtom(arg0: {molecule: null | _moorhen.Molecule; cid: null | string}): any;
+    module.exports = setHoveredAtom;
+
+    function addAvailableFontList(arg0: string): any;
+    module.exports = addAvailableFontList;
+
+    function setAtomLabelDepthMode(arg0: boolean): any;
+    module.exports = setAtomLabelDepthMode;
+
+    function setGLLabelsFontFamily(arg0: string): any;
+    module.exports = setGLLabelsFontFamily;
+
+    function setGLLabelsFontSize(arg0: number): any;
+    module.exports = setGLLabelsFontSize;
+
+    function setDefaultMapSamplingRate(arg0: number): any;
+    module.exports = setDefaultMapSamplingRate;
+
+    function setDefaultMapLitLines(arg0: boolean): any;
+    module.exports = setDefaultMapLitLines;
+
+    function setMapLineWidth(arg0: number): any;
+    module.exports = setMapLineWidth;
+
+    function setDefaultMapSurface(arg0: boolean): any;
+    module.exports = setDefaultMapSurface;
+
+    function setDefaultExpandDisplayCards(arg0: boolean): any;
+    module.exports = setDefaultExpandDisplayCards;
+
+    function setTransparentModalsOnMouseOut(arg0: boolean): any;
+    module.exports = setTransparentModalsOnMouseOut;
+
+    function setEnableRefineAfterMod(arg0: boolean): any;
+    module.exports = setEnableRefineAfterMod;
+
+    function addMolecule(arg0: _moorhen.Molecule): any;
+    module.exports = addMolecule;
+
+    function removeMolecule(arg0: _moorhen.Molecule): any;
+    module.exports = removeMolecule;
+
+    function emptyMolecules(): any;
+    module.exports = emptyMolecules;
+
+    function addMoleculeList(arg0: _moorhen.Molecule[]): any;
+    module.exports = addMoleculeList;
+
+    function setContourWheelSensitivityFactor(arg0: number): any;
+    module.exports = setContourWheelSensitivityFactor;
+
+    function setZoomWheelSensitivityFactor(arg0: number): any;
+    module.exports = setZoomWheelSensitivityFactor;
+
+    function setMouseSensitivity(arg0: number): any;
+    module.exports = setMouseSensitivity;
+
+    function setShowShortcutToast(arg0: boolean): any;
+    module.exports = setShowShortcutToast;
+
+    function setShortcutOnHoveredAtom(arg0: boolean): any;
+    module.exports = setShortcutOnHoveredAtom;
+
+    function setShortCuts(arg0: string): any;
+    module.exports = setShortCuts;
+
+    function setShowScoresToast(arg0: boolean): any;
+    module.exports = setShowScoresToast;
+
+    function addMapUpdatingScore(arg0: _moorhen.Map): any;
+    module.exports = addMapUpdatingScore;
+
+    function removeMapUpdatingScore(arg0: _moorhen.Map): any;
+    module.exports = removeMapUpdatingScore;
+
+    function overwriteMapUpdatingScores(arg0: _moorhen.Map[]): any;
+    module.exports = overwriteMapUpdatingScores;
+
+    function addMap(arg0: _moorhen.Map): any;
+    module.exports = addMap;
+
+    function removeMap(arg0: _moorhen.Map): any;
+    module.exports = removeMap;
+
+    function emptyMaps(): any;
+    module.exports = emptyMaps;
+
+    function addMapList(arg0: _moorhen.Map[]): any;
+    module.exports = addMapList;
+}