moorhen 0.7.2 → 0.7.3

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "moorhen",
-  "version": "0.7.2",
+  "version": "0.7.3",
   "private": false,
   "main": "moorhen.js",
   "types": "./types/main.d.ts",

package/types/libcoot.d.ts

@@ -470,6 +470,10 @@ export namespace libcootApi {
         getRamachandranData(arg0: string, arg1: string): emscriptem.vector<RamaData>
     }
     interface MoleculesContainerJS {
+        set_use_gemmi(arg0: boolean): void;
+        get_use_gemmi(): boolean;
+        export_model_molecule_as_gltf(imol: number, cid: string, mode: string, isDark: boolean, bondWidth: number, atomRadius: number, bondSmoothness: number, drawHydrogens: boolean, drawMissingResidues: boolean, fileName: string): void;
+        export_map_molecule_as_gltf(imol: number, x: number, y: number, z: number, radius: number, contourLevel: number, fileName: string): void;
         set_max_number_of_threads(arg0: number): void;
         set_map_is_contoured_with_thread_pool(arg0: boolean): void;
         close_molecule(molNo: number): number;

package/types/main.d.ts

@@ -49,6 +49,7 @@ declare module 'moorhen' {
 
     class MoorhenMolecule implements _moorhen.Molecule {
         constructor(commandCentre: React.RefObject<_moorhen.CommandCentre>, glRef: React.RefObject<webGL.MGWebGL>, monomerLibrary: string)
+        exportAsGltf(representationId: string): Promise<ArrayBuffer>;
         getNonSelectedCids(cid: string): string[];
         getSecondaryStructInfo(modelNumber?: number): Promise<libcootApi.ResidueSpecJS[]>;
         parseCidIntoSelection(selectedCid: string): Promise<_moorhen.ResidueSelection>;
@@ -108,10 +109,13 @@ declare module 'moorhen' {
         redraw: () => Promise<void>;
         setAtomsDirty: (newVal: boolean) => void;
         isVisible: (excludeBuffers?: string[]) => boolean;
-        centreAndAlignViewOn(selectionCid: string, animate?: boolean): Promise<void>;
+        centreAndAlignViewOn: (selectionCid: string, alignWithCB?: boolean, zoomLevel?: number) => Promise<void>;
         buffersInclude: (bufferIn: { id: string; }) => boolean;
         redrawRepresentation: (id: string) => Promise<void>;
         downloadAtoms(format?: 'mmcif' | 'pdb'): Promise<void>;
+        mergeFragmentFromRefinement(cid: string, fragmentMolecule: _moorhen.Molecule, acceptTransform?: boolean, refineAfterMerge?: boolean): Promise<void>;
+        copyFragmentForRefinement(cid: string[], refinementMap: _moorhen.Map, redraw?: boolean, readrawFragmentFirst?: boolean): Promise<_moorhen.Molecule>;
+        refineResiduesUsingAtomCidAnimated(cid: string, activeMap: moorhen.Map, dist?: number, redraw?: boolean, redrawFragmentFirst?: boolean): Promise<void>;
         isLigand: boolean;
         type: string;
         excludedCids: string[];
@@ -157,6 +161,7 @@ declare module 'moorhen' {
     
     class MoorhenMap implements _moorhen.Map {
         constructor(commandCentre: React.RefObject<_moorhen.CommandCentre>, glRef: React.RefObject<webGL.MGWebGL>)
+        exportAsGltf(): Promise<ArrayBuffer>;
         getHistogram(nBins?: number, zoomFactor?: number): Promise<libcootApi.HistogramInfoJS>;
         setMapWeight(weight?: number): Promise<_moorhen.WorkerResponse>;
         estimateMapWeight(): Promise<void>;
@@ -265,6 +270,9 @@ declare module 'moorhen' {
     function setDefaultBackgroundColor(arg0: [number, number, number, number]): any;
     module.exports = setDefaultBackgroundColor;
     
+    function setDrawScaleBar(arg0: boolean): any;
+    module.exports = setDrawScaleBar;
+    
     function setDrawCrosshairs(arg0: boolean): any;
     module.exports = setDrawCrosshairs;
     

package/types/mgWebGL.d.ts

@@ -35,6 +35,7 @@ export namespace webGL {
         mouseMoveAnimateTrack(force: boolean,count: number) : void;
         drawTextOverlays(invMat: number[]) : void;
         drawAxes(invMat: number[]) : void;
+        drawScaleBar(invMat: number[]) : void;
         drawCrosshairs(invMat: number[]) : void;
         drawMouseTrack() : void;
         reContourMaps() : void;
@@ -360,6 +361,7 @@ export namespace webGL {
         shaderDepthShadowProgramPerfectSpheres: ShaderPerfectSpheres;
         shinyBack: boolean;
         showAxes: boolean;
+        showScaleBar: boolean;
         showCrosshairs: boolean;
         showFPS: boolean;
         silhouetteBufferReady: boolean;

package/types/moorhen.d.ts

@@ -92,6 +92,10 @@ export namespace moorhen {
     type coorFormats = 'pdb' | 'mmcif';
     
     interface Molecule {
+        refineResiduesUsingAtomCidAnimated(cid: string, activeMap: moorhen.Map, dist?: number, redraw?: boolean, redrawFragmentFirst?: boolean): Promise<void>;
+        mergeFragmentFromRefinement(cid: string, fragmentMolecule: moorhen.Molecule, acceptTransform?: boolean, refineAfterMerge?: boolean): Promise<void>;
+        copyFragmentForRefinement(cid: string[], refinementMap: moorhen.Map, redraw?: boolean, readrawFragmentFirst?: boolean): Promise<moorhen.Molecule>;
+        exportAsGltf(representationId: string): Promise<ArrayBuffer>;
         getSecondaryStructInfo(modelNumber?: number): Promise<libcootApi.ResidueSpecJS[]>;
         getNonSelectedCids(cid: string): string[];
         parseCidIntoSelection(selectedCid: string): Promise<ResidueSelection>;
@@ -152,7 +156,7 @@ export namespace moorhen {
         redraw: () => Promise<void>;
         setAtomsDirty: (newVal: boolean) => void;
         isVisible: (excludeBuffers?: string[]) => boolean;
-        centreAndAlignViewOn(selectionCid: string, animate?: boolean): Promise<void>;
+        centreAndAlignViewOn: (selectionCid: string, alignWithCB?: boolean, zoomLevel?: number) => Promise<void>;
         buffersInclude: (bufferIn: { id: string; }) => boolean;
         redrawRepresentation: (id: string) => Promise<void>;
         type: string;
@@ -203,6 +207,7 @@ export namespace moorhen {
     'residueSelection' | 'MetaBalls'
 
     interface MoleculeRepresentation {
+        exportAsGltf(): Promise<ArrayBuffer>;
         setApplyColourToNonCarbonAtoms(newVal: boolean): void;
         setBondOptions(bondOptions: cootBondOptions): void;
         setStyle(style: string): void;
@@ -261,9 +266,11 @@ export namespace moorhen {
         getModifiedMolNo: () => number[];
         lastModifiedMolNo: () => number;
         rebase: (id: string) => void;
+        toggleSkipTracking(): void;
         entries: HistoryEntry[];
         headId: string;
         headIsDetached: boolean;
+        timeCapsule: React.RefObject<TimeCapsule>;
     }
 
     interface HistoryEntry extends cootCommandKwargs{
@@ -398,6 +405,7 @@ export namespace moorhen {
         setActive(): Promise<void>;
         setupContourBuffers(objects: any[], keepCootColours?: boolean): void;
         setOtherMapForColouring(molNo: number, min?: number, max?: number): void;
+        exportAsGltf(): Promise<ArrayBuffer>;
         isEM: boolean;
         suggestedContourLevel: number;
         suggestedRadius: number;
@@ -501,6 +509,7 @@ export namespace moorhen {
         updateDataFiles(): Promise<(string | void)[]>;
         createBackup(keyString: string, sessionString: string): Promise<string>;
         fetchSession(arg0: boolean): Promise<backupSession>;
+        toggleDisableBackups(): void;
         moleculesRef: React.RefObject<Molecule[]>;
         mapsRef: React.RefObject<Map[]>;
         glRef: React.RefObject<webGL.MGWebGL>;
@@ -631,6 +640,7 @@ export namespace moorhen {
         defaultExpandDisplayCards: boolean;
         defaultMapLitLines: boolean;
         enableRefineAfterMod: boolean; 
+        drawScaleBar: boolean; 
         drawCrosshairs: boolean; 
         drawAxes: boolean; 
         drawFPS: boolean; 
@@ -664,6 +674,7 @@ export namespace moorhen {
         defaultUpdatingScores: string[],
         maxBackupCount: number;
         modificationCountBackupThreshold: number;
+        animateRefine: boolean;
         devMode: boolean; 
         shortCuts: string | {
             [label: string]: Shortcut;
@@ -753,6 +764,7 @@ export namespace moorhen {
         };
         sceneSettings: {
             defaultBackgroundColor: [number, number, number, number];
+            drawScaleBar: boolean; 
             drawCrosshairs: boolean; 
             drawAxes: boolean; 
             drawFPS: boolean; 
@@ -781,6 +793,7 @@ export namespace moorhen {
             defaultExpandDisplayCards: boolean; 
             transparentModalsOnMouseOut: boolean; 
             enableRefineAfterMod: boolean; 
+            animateRefine: boolean;
         };
         generalStates: {
             devMode: boolean;