moorhen 0.6.7 → 0.6.8

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "moorhen",
-  "version": "0.6.7",
+  "version": "0.6.8",
   "private": false,
   "main": "moorhen.js",
   "types": "./types/main.d.ts",
@@ -62,7 +62,7 @@
       ]
     }
   },
-  "dependencies": { },
+  "dependencies": {},
   "scripts": {
     "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",
@@ -142,7 +142,8 @@
     "gl-matrix": "^3.4.3",
     "html-react-parser": "^1.4.14",
     "html-webpack-plugin": "^5.5.0",
-    "iris-validation": "^0.1.8",
+    "iris-validation": "^0.1.10",
+    "iris-validation-backend": "^0.0.8",
     "jest": "^27.5.1",
     "jsdoc": "^4.0.2",
     "localforage": "^1.10.0",

package/types/libcoot.d.ts

@@ -12,6 +12,15 @@ declare global {
 
 export namespace libcootApi {
     type CCP4ModuleType = {
+        get_ligand_info_for_structure(gemmiStructure: gemmi.Structure): emscriptem.vector<{
+            resName: string;
+            chainName: string;
+            resNum: string;
+            modelName: string;
+            cid: string;
+        }>;
+        guess_coord_data_format(coordDataString: string): number;
+        get_structure_bfactors(gemmiStructure: gemmi.Structure): emscriptem.vector<{ cid: string; bFactor: number }>;
         get_sequence_info(gemmiStructure: gemmi.Structure, molName: string): emscriptem.vector<SequenceEntry>;
         get_atom_info_for_selection(gemmiStructure: gemmi.Structure, arg1: string, arg2: string): emscriptem.vector<AtomInfo>;
         structure_is_ligand(gemmiStructure: gemmi.Structure): boolean;
@@ -20,9 +29,10 @@ export namespace libcootApi {
         check_polymer_type(polymerConst: emscriptem.instance<number>): {value: number};
         remove_ligands_and_waters_chain(chain: gemmi.Chain): void;
         gemmi_setup_entities(gemmiStructure: gemmi.Structure): void;
+        gemmi_add_entity_types(gemmiStructure: gemmi.Structure, overWrite: boolean): void;
         remove_ligands_and_waters_structure(gemmiStructure: gemmi.Structure): void;
         remove_hydrogens_structure(gemmiStructure: gemmi.Structure): void;
-        read_structure_from_string(pdbData: string | ArrayBuffer, molName: string): gemmi.Structure;
+        read_structure_from_string(coordData: string | ArrayBuffer, molName: string): gemmi.Structure;
         get_mtz_columns(fileName: string): emscriptem.vector<string>;
         FS_createDataFile(arg0: string, fileName: string, byteArray: Uint8Array, arg3: boolean, arg4: boolean): void;
         getElementNameAsString: (arg0: emscriptem.instance<string>) => string;
@@ -66,7 +76,7 @@ export namespace libcootApi {
         res_name: string;
         label: string;
     }
-    interface AutoReadMtzInfo extends emscriptem.instance<AutoReadMtzInfo> {
+    interface AutoReadMtzInfo {
         idx: number;
         F: string;
         phi: string;
@@ -88,7 +98,7 @@ export namespace libcootApi {
         is_allowed_flag: boolean;
         residue_name: () => string;
     }
-    interface InterestingPlaceT extends emscriptem.instance<InterestingPlaceT> {
+    interface InterestingPlaceT {
         feature_type: string;
         residue_spec: ResidueSpecT;
         x: number;
@@ -203,7 +213,7 @@ export namespace libcootApi {
         amplitude: () => number;
         size: number;
     }
-    interface Generic3dLinesBondsBoxT extends emscriptem.instance<Generic3dLinesBondsBoxT> {
+    interface Generic3dLinesBondsBoxT {
         line_segments: emscriptem.vector<emscriptem.vector<CootCartesianPair>>;
     }
     type Generic3dLinesBondsBoxJS = {
@@ -217,7 +227,7 @@ export namespace libcootApi {
         status: string;
         richardson_probability: number;
     }
-    interface SimpleMeshT extends emscriptem.instance<SimpleMeshT> {
+    interface SimpleMeshT {
         vertices: emscriptem.vector<VncVertex>;
         triangles: emscriptem.vector<gTriangle>;
     }
@@ -230,7 +240,7 @@ export namespace libcootApi {
         norm_tri: [[number[]]];
         col_tri: [[number[]]];
     }
-    interface SymmetryData extends emscriptem.instance<SymmetryData> {
+    interface SymmetryData {
         cell: CellTranslation;
         symm_trans: emscriptem.vector<PairType<SymmetryTransT, CellTranslation>>;
     }
@@ -270,7 +280,7 @@ export namespace libcootApi {
         suggested_contour_level: number;
         suggested_radius: number;
     }
-    interface ResidueSpecT extends emscriptem.instance<ResidueSpecT> {
+    interface ResidueSpecT {
         model_number: number;
         chain_id: string;
         res_no: number;
@@ -282,7 +292,7 @@ export namespace libcootApi {
         modelNumber: number;
         chainId: string;
     }
-    interface AtomSpecT extends emscriptem.instance<ResidueSpecT> {
+    interface AtomSpecT {
         chain_id: string;
         res_no: number;
         ins_code: string;
@@ -304,12 +314,12 @@ export namespace libcootApi {
         string_user_data: string;
         model_number: number;
     }
-    interface ResidueValidationInformationT extends emscriptem.instance<ResidueValidationInformationT> {
+    interface ResidueValidationInformationT {
         label: string;
         residue_spec: ResidueSpecT;
         function_value: number;
     }
-    interface ChainValidationInformationT extends emscriptem.instance<ChainValidationInformationT> {
+    interface ChainValidationInformationT {
         chain_id: string;
         rviv: emscriptem.vector<ResidueValidationInformationT>;
     }
@@ -345,22 +355,22 @@ export namespace libcootApi {
         colour: [number, number, number, number];
         orientation: [[number, number, number, number], [number, number, number, number], [number, number, number, number], [number, number, number, number]];
     }
-    interface gTriangle extends emscriptem.instance<gTriangle> {
+    interface gTriangle {
         point_id: [number, number, number];
     }
-    interface VncVertex extends emscriptem.instance<VncVertex> {
+    interface VncVertex {
         pos: [number, number, number];
         normal: [number, number, number];
         color: [number, number, number, number];
     }
-    interface InstancedGeomT extends emscriptem.instance<InstancedGeomT> {
+    interface InstancedGeomT {
         vertices: emscriptem.vector<VncVertex>;
         triangles: emscriptem.vector<gTriangle>;
         name: string;
         instancing_data_A: emscriptem.vector<InstancedDataType>;
         instancing_data_B: emscriptem.vector<InstancedDataType>;
     }
-    interface InstancedMeshT extends emscriptem.instance<InstancedMeshT> {
+    interface InstancedMeshT {
         geom: emscriptem.vector<InstancedGeomT>;
         markup: SimpleMeshT;
     }

package/types/main.d.ts

@@ -82,18 +82,20 @@ declare module 'moorhen' {
         generateSelfRestraints(cid?: string, maxRadius?: number): Promise<void>;
         clearExtraRestraints(): Promise<_moorhen.WorkerResponse>;
         refineResiduesUsingAtomCid(cid: string, mode: string, ncyc?: number, redraw?: boolean): Promise<void>;
+        getNcsRelatedChains(): Promise<string[][]>;
+        getResidueBFactors(): { cid: string, bFactor: number }[];
         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>
+        replaceModelWithFile(fileUrl: 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>;
+        centreOn: (selectionCid?: string, animate?: boolean, setZoom?: boolean) => Promise<void>;
         drawHover: (cid: string) => Promise<void>;
         drawResidueSelection: (cid: string) => Promise<void>;
         clearBuffersOfStyle: (style: string) => void;
@@ -107,6 +109,7 @@ declare module 'moorhen' {
         centreAndAlignViewOn(selectionCid: string, animate?: boolean): Promise<void>;
         buffersInclude: (bufferIn: { id: string; }) => boolean;
         redrawRepresentation: (id: string) => Promise<void>;
+        downloadAtoms(format?: 'mmcif' | 'pdb'): Promise<void>;
         isLigand: boolean;
         type: string;
         excludedCids: string[];
@@ -131,6 +134,7 @@ declare module 'moorhen' {
             countourLevel: number;
             boxRadius: number;
             gridScale: number;
+            bFactor: number;
         };
         isDarkBackground: boolean;
         representations: _moorhen.MoleculeRepresentation[];
@@ -146,6 +150,7 @@ declare module 'moorhen' {
         selectionRepresentation: _moorhen.MoleculeRepresentation;
         hasDNA: boolean;
         hasGlycans: boolean;
+        coordsFormat: _moorhen.coorFormats;
     }
     module.exports.MoorhenMolecule = MoorhenMolecule
     
@@ -210,9 +215,6 @@ declare module 'moorhen' {
     }
     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,

package/types/mgWebGL.d.ts

@@ -18,7 +18,11 @@ export namespace webGL {
         createIndexBuffer(tri: number[]) : void;
         createSizeBuffer(tri: number[]) : void;
         addSupplementaryInfo(info: any, name: string) : void;
-
+        calculateOriginDelta(newOrigin: [number, number, number], oldOrigin: [number, number, number], nFrames: number): [number, number, number];
+        setOriginAndZoomAnimated(newOrigin: [number, number, number], newZoom: number): void;
+        drawOriginAndZoomFrame(oldOrigin: [number, number, number], oldZoom: number, deltaOrigin: [number, number, number], deltaZoom: number, iframe: number): void;
+        setZoomAnimated(newZoom: number): void;
+        drawZoomFrame(oldZoom: number, newZoom: number, iframe: number): void;
         createInstanceSizesBuffer(tri: number[]) : void;
         createVertexBuffer(tri: number[]) : void;
         createRealNormalBuffer(tri: number[]) : void;
@@ -115,7 +119,7 @@ export namespace webGL {
         appendOtherData(jsondata: any, skipRebuild?: boolean, name?: string) : any;
         setZoom(z: number, drawScene?: boolean);
         setOriginOrientationAndZoomAnimated(o: number[],q: quat4,z: number) : void;
-        setOriginAnimated(o: number[], doDrawScene=true) : void;
+        setOriginAnimated(o: number[]) : void;
         initTextureFramebuffer() : void;
         clearMeasureCylinderBuffers() : void;
         getFrontAndBackPos(event: KeyboardEvent) : [number[], number[], number, number];

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 {
 
@@ -88,8 +87,13 @@ export namespace moorhen {
         ruleType: string;
         label: string;
     }
+
+    type coorFormats = 'pdb' | 'mmcif';
     
     interface Molecule {
+        downloadAtoms(format?: 'mmcif' | 'pdb'): Promise<void>;
+        getResidueBFactors(): { cid: string, 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 +132,12 @@ 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;
@@ -171,6 +175,7 @@ export namespace moorhen {
             countourLevel: number;
             boxRadius: number;
             gridScale: number;
+            bFactor: number;
         };
         isDarkBackground: boolean;
         representations: MoleculeRepresentation[];
@@ -186,6 +191,7 @@ export namespace moorhen {
         selectionRepresentation: MoleculeRepresentation;
         hasDNA: boolean;
         hasGlycans: boolean;
+        coordsFormat: coorFormats
     }
 
     type RepresentationStyles = 'VdwSpheres' | 'ligands' | 'CAs' | 'CBs' | 'CDs' | 'gaussian' | 'allHBonds' | 'rama' | 
@@ -270,7 +276,8 @@ 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>;
@@ -425,7 +432,7 @@ 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[];
@@ -799,6 +806,7 @@ export namespace moorhen {
             isChangingRotamers: boolean;
             isDraggingAtoms: boolean;
             isRotatingAtoms: boolean;
+            newCootCommandAlert: boolean;
         };
         hoveringStates: {
             enableAtomHovering: boolean;