moorhen 0.6.7 → 0.7.0

package/types/moorhen.d.ts

@@ -2,7 +2,6 @@ import React from "react"
 import { emscriptem } from "./emscriptem";
 import { gemmi } from "./gemmi";
 import { webGL } from "./mgWebGL";
-import { MoorhenCommandCentre } from "../moorhen";
 
 export namespace moorhen {
 
@@ -29,6 +28,7 @@ export namespace moorhen {
         modelName: string;
         cid: string;
         svg?: string;
+        chem_comp_info?: {first: string; second: string}[];
     }
     
     type Sequence = {
@@ -88,8 +88,15 @@ export namespace moorhen {
         ruleType: string;
         label: string;
     }
+
+    type coorFormats = 'pdb' | 'mmcif';
     
     interface Molecule {
+        getNonSelectedCids(cid: string): string[];
+        parseCidIntoSelection(selectedCid: string): Promise<ResidueSelection>;
+        downloadAtoms(format?: 'mmcif' | 'pdb'): 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>;
@@ -128,12 +135,12 @@ export namespace moorhen {
         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>
+        replaceModelWithFile(fileUrl: string): Promise<void>
         delete(): Promise<WorkerResponse> 
         fetchDefaultColourRules(): Promise<void>;
         fetchIfDirtyAndDraw(arg0: string): Promise<void>;
         drawEnvironment: (cid: string, labelled?: boolean) => Promise<void>;
-        centreOn: (selectionCid?: string, animate?: boolean) => 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;
@@ -143,7 +150,7 @@ export namespace moorhen {
         hide: (style: string, cid?: string) => void;
         redraw: () => Promise<void>;
         setAtomsDirty: (newVal: boolean) => void;
-        hasVisibleBuffers: (excludeBuffers?: string[]) => boolean;
+        isVisible: (excludeBuffers?: string[]) => boolean;
         centreAndAlignViewOn(selectionCid: string, animate?: boolean): Promise<void>;
         buffersInclude: (bufferIn: { id: string; }) => boolean;
         redrawRepresentation: (id: string) => Promise<void>;
@@ -153,7 +160,6 @@ export namespace moorhen {
         commandCentre: React.RefObject<CommandCentre>;
         glRef: React.RefObject<webGL.MGWebGL>;
         atomsDirty: boolean;
-        isVisible: boolean;
         name: string;
         molNo: number;
         gemmiStructure: gemmi.Structure;
@@ -171,6 +177,7 @@ export namespace moorhen {
             countourLevel: number;
             boxRadius: number;
             gridScale: number;
+            bFactor: number;
         };
         isDarkBackground: boolean;
         representations: MoleculeRepresentation[];
@@ -186,6 +193,7 @@ export namespace moorhen {
         selectionRepresentation: MoleculeRepresentation;
         hasDNA: boolean;
         hasGlycans: boolean;
+        coordsFormat: coorFormats
     }
 
     type RepresentationStyles = 'VdwSpheres' | 'ligands' | 'CAs' | 'CBs' | 'CDs' | 'gaussian' | 'allHBonds' | 'rama' | 
@@ -234,6 +242,7 @@ export namespace moorhen {
         second: null | string;
         cid: null | string | string[];
         isMultiCid: boolean;
+        label: string;
     }
     
     type HoveredAtom = {
@@ -270,7 +279,8 @@ export namespace moorhen {
         unhook: () => void;
         onCootInitialized: null | ( () => void );
         onConsoleChanged: null | ( (msg: string) => void );
-        onNewCommand : null | ( (kwargs: any) => void );
+        onCommandStart : null | ( (kwargs: any) => void );
+        onCommandExit : null | ( (kwargs: any) => void );
         onActiveMessagesChanged: null | ( (activeMessages: WorkerMessage[]) => void );
         cootCommandList(commandList: cootCommandKwargs[]): Promise<WorkerResponse>;
         cootCommand: (kwargs: cootCommandKwargs, doJournal?: boolean) => Promise<WorkerResponse>;
@@ -356,21 +366,30 @@ export namespace moorhen {
         getHistogram(nBins?: number, zoomFactor?: number): Promise<libcootApi.HistogramInfoJS>;
         setMapWeight(weight?: number): Promise<WorkerResponse>;
         estimateMapWeight(): Promise<void>;
-        setAlpha(alpha: number, redraw?: boolean): Promise<void>;
+        fetchMapAlphaAndRedraw(): Promise<void>;
         centreOnMap(): Promise<void>;
         getSuggestedSettings(): Promise<void>;
-        duplicate(): Promise<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> ;
+        copyMap(): Promise<Map>;
+        getMapContourParams(): { 
+            mapRadius: number; 
+            contourLevel: number; 
+            mapAlpha: number; 
+            mapStyle: "lines" | "solid" | "lit-lines"; 
+            mapColour: {r: number; g: number; b: number}; 
+            positiveMapColour: {r: number; g: number; b: number}; 
+            negativeMapColour: {r: number; g: number; b: number}
+        };
+        hideMapContour(): void;
+        drawMapContour(): Promise<void>;
+        fetchColourAndRedraw(): Promise<void> ;
+        fetchDiffMapColourAndRedraw(type: 'positiveDiffColour' | 'negativeDiffColour'): Promise<void> ;
         fetchMapRmsd(): Promise<number>;
         fetchSuggestedLevel(): Promise<number>;
         fetchMapCentre(): Promise<[number, number, number]>;
         replaceMapWithMtzFile(fileUrl: RequestInfo | URL, selectedColumns: selectedMtzColumns): Promise<void>;
         associateToReflectionData (selectedColumns: selectedMtzColumns, reflectionData: Uint8Array | ArrayBuffer): Promise<void>;
         delete(): Promise<void> 
-        doCootContour(x: number, y: number, z: number, radius: number, contourLevel: number): Promise<void>;
+        doCootContour(x: number, y: number, z: number, radius: number, contourLevel: number, style: "lines" | "lit-lines" | "solid"): Promise<void>;
         fetchReflectionData(): Promise<WorkerResponse<Uint8Array>>;
         getMap(): Promise<WorkerResponse>;
         loadToCootFromMtzURL(url: RequestInfo | URL, name: string, selectedColumns: selectedMtzColumns, options?: RequestInit): Promise<Map>;
@@ -387,14 +406,9 @@ export namespace moorhen {
         molNo: number;
         commandCentre: React.RefObject<CommandCentre>;
         glRef: React.RefObject<webGL.MGWebGL>;
-        contourLevel: number;
-        mapRadius: number;
-        mapColour: [number, number, number, number];
         webMGContour: boolean;
-        isVisible: boolean;
+        showOnLoad: boolean;
         displayObjects: any;
-        litLines: boolean;
-        solid: boolean;
         isDifference: boolean;
         hasReflectionData: boolean;
         selectedColumns: selectedMtzColumns;
@@ -403,12 +417,9 @@ export namespace moorhen {
         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;
-        }
+        defaultMapColour: {r: number, g: number, b: number};
+        defaultPositiveMapColour: {r: number, g: number, b: number};
+        defaultNegativeMapColour: {r: number, g: number, b: number};
     }
     
     interface backupKey {
@@ -425,7 +436,7 @@ export namespace moorhen {
     type moleculeSessionData = {
         name: string;
         molNo: number;
-        pdbData: string;
+        coordString: string;
         representations: { cid: string, style: string, isCustom: boolean, colourRules: ColourRule[], bondOptions: cootBondOptions }[];
         defaultBondOptions: cootBondOptions;
         defaultColourRules: ColourRule[];
@@ -439,11 +450,16 @@ export namespace moorhen {
         uniqueId: string;
         mapData: Uint8Array;
         reflectionData: Uint8Array;
-        isVisible: boolean;
+        showOnLoad: boolean;
         contourLevel: number;
         radius: number;
-        colour: [number, number, number, number];
-        litLines: boolean;
+        rgba: {
+            mapColour: {r: number, g: number, b: number};
+            positiveDiffColour: {r: number, g: number, b: number};
+            negativeDiffColour: {r: number, g: number, b: number};
+            a: number;
+        };
+        style: "solid" | "lit-lines" | "lines";
         isDifference: boolean;
         selectedColumns: selectedMtzColumns;
         hasReflectionData: boolean;
@@ -724,12 +740,6 @@ export namespace moorhen {
     interface State {
         molecules: Molecule[];
         maps: Map[];
-        mapSettings: {
-            defaultMapSamplingRate: number;
-            defaultMapLitLines: boolean;
-            mapLineWidth: number;
-            defaultMapSurface: boolean;
-        };
         mouseSettings: {
             contourWheelSensitivityFactor: number;
             zoomWheelSensitivityFactor: number;
@@ -799,6 +809,8 @@ export namespace moorhen {
             isChangingRotamers: boolean;
             isDraggingAtoms: boolean;
             isRotatingAtoms: boolean;
+            newCootCommandAlert: boolean;
+            showResidueSelection: boolean;
         };
         hoveringStates: {
             enableAtomHovering: boolean;
@@ -809,11 +821,37 @@ export namespace moorhen {
             showModelsModal: boolean;
             showMapsModal: boolean;
             showCreateAcedrgLinkModal: boolean;
-            showValidationModal: boolean;
             showQuerySequenceModal: boolean;
             showScriptingModal: boolean;
             showControlsModal: boolean;
             showFitLigandModal: boolean;
+            showRamaPlotModal: boolean;
+            showDiffMapPeaksModal: boolean;
+            showValidationPlotModal: boolean;
+            showLigandValidationModal: boolean;
+            showPepFlipsValidationModal: boolean;
+            showFillPartialResValidationModal: boolean;
+            showUnmodelledBlobsModal: boolean;
+            showMmrrccModal: boolean;
+            showWaterValidationModal: boolean;
+            focusHierarchy: string[];
+        };
+        mapContourSettings: {
+            visibleMaps: number[];
+            contourLevels: { molNo: number; contourLevel: number }[];
+            mapRadii: { molNo: number; radius: number }[];
+            mapAlpha: { molNo: number; alpha: number }[];
+            mapStyles: { molNo: number; style: "solid" | "lit-lines" | "lines" }[];
+            defaultMapSamplingRate: number;
+            defaultMapLitLines: boolean;
+            mapLineWidth: number;
+            defaultMapSurface: boolean;
+            mapColours: { molNo: number; rgb: {r: number, g: number, b: number} }[];
+            negativeMapColours: { molNo: number; rgb: {r: number, g: number, b: number} }[];
+            positiveMapColours: { molNo: number; rgb: {r: number, g: number, b: number} }[];
+        };
+        moleculeRepresentations: {
+            visibleMolecules: number[];
         };
     }