moorhen 0.6.1 → 0.6.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "moorhen",
-  "version": "0.6.1",
+  "version": "0.6.2",
   "private": false,
   "main": "moorhen.js",
   "types": "./types/main.d.ts",
@@ -141,6 +141,7 @@
     "gl-matrix": "^3.4.3",
     "html-react-parser": "^1.4.14",
     "html-webpack-plugin": "^5.5.0",
+    "jest": "^27.5.1",
     "jsdoc": "^4.0.2",
     "localforage": "^1.10.0",
     "mini-css-extract-plugin": "^2.7.6",
@@ -159,6 +160,7 @@
     "protvista-sequence": "^3.5.1",
     "protvista-track": "^3.4.0",
     "rc-tree": "4.2.2",
+    "re-resizable": "^6.9.11",
     "react": "^18.1.0",
     "react-bootstrap": "^2.3.1",
     "react-bootstrap-typeahead": "^6.0.0-alpha.11",

package/types/gemmi.d.ts

@@ -3,7 +3,8 @@ import { emscriptem } from "./emscriptem"
 export namespace gemmi {
     interface NeighborSearch extends emscriptem.instance<NeighborSearch> {
         populate: (arg0: boolean) => void;
-        find_atoms: (arg0: Position, arg1: number, arg2: number) => emscriptem.vector<Mark>
+        find_atoms: (arg0: Position, arg1: string, arg2: number) => emscriptem.vector<Mark>;
+        find_neighbors: (arg0: Atom, arg1: number, ag2: number) =>  emscriptem.vector<Mark>;
     }
     interface Mark extends emscriptem.instance<Mark> {
         x: number;
@@ -72,7 +73,7 @@ export namespace gemmi {
         altloc: number;
         charge: number;
         b_iso: number;
-        serial: string;
+        serial: number;
         has_altloc: () => boolean;
     }
     interface ResidueSeqId extends emscriptem.instance<ResidueSeqId> {

package/types/libcoot.d.ts

@@ -2,6 +2,8 @@
 import { emscriptem } from "./emscriptem";
 import { gemmi } from "./gemmi"
 
+// Warning: do not import moorhen namespace otherwise worker code breaks during transpilation
+
 declare global {
     function print(arg0: string): void;
     function createRSRModule(arg0: any): Promise<any>;
@@ -10,6 +12,9 @@ declare global {
 
 export namespace libcootApi {
     type CCP4ModuleType = {
+        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;
         count_residues_in_selection(gemmiStructure: gemmi.Structure, selection: gemmi.Selection): number;
         remove_non_selected_residues(gemmiStructure: gemmi.Structure, selection: gemmi.Selection): gemmi.Structure;
         check_polymer_type(polymerConst: emscriptem.instance<number>): {value: number};
@@ -30,8 +35,20 @@ export namespace libcootApi {
         Fractional: { new(x: number, y: number, z: number): gemmi.Fractional };
         cifDocument: { new(): gemmi.cifDocument }
     }
+    type SequenceResInfo = {
+        resNum: number;
+        resCode: string;
+        cid: string;
+    }
+    type SequenceEntry = {
+        type: number;
+        name: string;
+        chain: string;
+        sequence: emscriptem.vector<SequenceResInfo>;
+    
+    }
+    // We need to define AtomInfo here because we cannot import moorhen namespace otherwise worker code breaks during transpilation
     type AtomInfo = {
-        pos: [number, number, number];
         x: number;
         y: number;
         z: number;
@@ -39,7 +56,7 @@ export namespace libcootApi {
         element: emscriptem.instance<string>;
         symbol: string;
         tempFactor: number;
-        serial: string;
+        serial: number;
         name: string;
         has_altloc: boolean;
         alt_loc: string;
@@ -154,6 +171,18 @@ export namespace libcootApi {
         hydrogen_is_ligand_atom: boolean;
         bond_has_hydrogen_flag: boolean;     
     }
+    interface MMRCCStatsJS {
+        "All atoms": DensityCorrelationStatsInfoJS[];
+        "Side-chains": DensityCorrelationStatsInfoJS[];
+    }
+    interface DensityCorrelationStatsInfoJS {
+        resNum: number;
+        insCode: string;
+        modelNumber: number;
+        chainId: string;
+        n: number;
+        correlation: number;
+    }
     interface DensityCorrelationStatsInfoT extends emscriptem.instance<DensityCorrelationStatsInfoT> {
         n: number;
         sum_xy: number;

package/types/main.d.ts

@@ -47,16 +47,18 @@ declare module 'moorhen' {
 
     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<void>;
+        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[]>;
-        isLigand(): boolean;
+        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, radius: number, minDist: number, maxDist: number): Promise<string[]>;
+        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[][];
@@ -90,8 +92,9 @@ declare module 'moorhen' {
         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) => Promise<_moorhen.Molecule>;
+        loadToCootFromURL: (inputFile: string, molName: string, options?: RequestInit) => Promise<_moorhen.Molecule>;
         applyTransform: () => Promise<void>;
         getAtoms(format?: string): Promise<string>;
         hide: (style: string, cid?: string) => void;
@@ -101,6 +104,7 @@ declare module 'moorhen' {
         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>;
@@ -136,6 +140,7 @@ declare module 'moorhen' {
         hoverRepresentation: _moorhen.MoleculeRepresentation;
         unitCellRepresentation: _moorhen.MoleculeRepresentation;
         environmentRepresentation: _moorhen.MoleculeRepresentation;
+        selectionRepresentation: _moorhen.MoleculeRepresentation;
         hasDNA: boolean;
         hasGlycans: boolean;
     }
@@ -163,8 +168,8 @@ declare module 'moorhen' {
         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): Promise<_moorhen.Map>;
-        loadToCootFromMapURL(url: RequestInfo | URL, name: string, isDiffMap?: boolean): Promise<_moorhen.Map>;
+        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;

package/types/mgWebGL.d.ts

@@ -142,7 +142,8 @@ export namespace webGL {
         resize(width: number, height: number) : void;
         setShadowDepthDebug(doShadowDepthDebug: boolean): void;
         setShadowsOn(doShadow: boolean): void;
-        setSSAOOn(doShadow: boolean): void;
+        setSSAOOn(doSSAO: boolean): void;
+        setOccludeDiffuse(doOccludeDiffuse: boolean): void;
         setOutlinesOn(doOutline: boolean): void;
         setSpinTestState(doSpinTest: boolean): void;
         setBlurSize(blurSize: number): void;
@@ -238,6 +239,7 @@ export namespace webGL {
         diskVertices: number[];
         doShadow: boolean;
         doSSAO: boolean;
+        occludeDiffuse: boolean;
         doShadowDepthDebug: boolean;
         doSpin: boolean;
         doStenciling: boolean;

package/types/moorhen.d.ts

@@ -58,7 +58,7 @@ export namespace moorhen {
         element: emscriptem.instance<string>;
         symbol: string;
         tempFactor: number;
-        serial: string;
+        serial: number;
         name: string;
         has_altloc: boolean;
         alt_loc: string;
@@ -89,17 +89,19 @@ export namespace moorhen {
     }
     
     interface Molecule {
+        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>;
         refineResiduesUsingAtomCid(cid: string, mode: string, ncyc?: number, redraw?: boolean): Promise<void>;
-        deleteCid(cid: string, redraw?: boolean): Promise<void>;
+        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<Molecule[]>;
-        isLigand(): boolean;
+        checkIsLigand(): boolean;
         removeRepresentation(representationId: string): void;
         addRepresentation(style: string, cid: string, isCustom?: boolean, colour?: ColourRule[], bondOptions?: cootBondOptions, applyColourToNonCarbonAtoms?: boolean): Promise<MoleculeRepresentation>;
-        getNeighborResiduesCids(selectionCid: string, radius: number, minDist: number, maxDist: number): Promise<string[]>;
+        getNeighborResiduesCids(selectionCid: string, maxDist: number): Promise<string[]>;
         drawWithStyleFromMesh(style: string, meshObjects: any[], cid?: string): Promise<void>;
         updateWithMovedAtoms(movedResidues: AtomInfo[][]): Promise<void>;
         transformedCachedAtomsAsMovedAtoms(selectionCid?: string): AtomInfo[][];
@@ -132,8 +134,9 @@ export namespace moorhen {
         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) => Promise<Molecule>;
+        loadToCootFromURL: (inputFile: string, molName: string, options?: RequestInit) => Promise<Molecule>;
         applyTransform: () => Promise<void>;
         getAtoms(format?: string): Promise<string>;
         hide: (style: string, cid?: string) => void;
@@ -144,6 +147,7 @@ export namespace moorhen {
         buffersInclude: (bufferIn: { id: string; }) => boolean;
         redrawRepresentation: (id: string) => Promise<void>;
         type: string;
+        isLigand: boolean;
         excludedCids: string[];
         commandCentre: React.RefObject<CommandCentre>;
         glRef: React.RefObject<webGL.MGWebGL>;
@@ -178,13 +182,14 @@ export namespace moorhen {
         hoverRepresentation: MoleculeRepresentation;
         unitCellRepresentation: MoleculeRepresentation;
         environmentRepresentation: MoleculeRepresentation;
+        selectionRepresentation: MoleculeRepresentation;
         hasDNA: boolean;
         hasGlycans: boolean;
     }
 
     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'
+    'ligand_environment' | 'contact_dots' | 'chemical_features' | 'ligand_validation' | 'glycoBlocks' | 'restraints' | 'residueSelection'
 
     interface MoleculeRepresentation {
         setApplyColourToNonCarbonAtoms(newVal: boolean): void;
@@ -220,6 +225,13 @@ export namespace moorhen {
         isCustom: boolean;
         styleHasColourRules: boolean;
     }
+
+    type ResidueSelection = {
+        molecule: null | moorhen.Molecule;
+        first: null | string;
+        second: null | string;
+        cid: null | string;
+    }
     
     type HoveredAtom = {
         molecule: Molecule | null,
@@ -358,8 +370,8 @@ export namespace moorhen {
         doCootContour(x: number, y: number, z: number, radius: number, contourLevel: number): Promise<void>;
         fetchReflectionData(): Promise<WorkerResponse<Uint8Array>>;
         getMap(): Promise<WorkerResponse>;
-        loadToCootFromMtzURL(url: RequestInfo | URL, name: string, selectedColumns: selectedMtzColumns): Promise<Map>;
-        loadToCootFromMapURL(url: RequestInfo | URL, name: string, isDiffMap?: boolean): Promise<Map>;
+        loadToCootFromMtzURL(url: RequestInfo | URL, name: string, selectedColumns: selectedMtzColumns, options?: RequestInit): Promise<Map>;
+        loadToCootFromMapURL(url: RequestInfo | URL, name: string, isDiffMap?: boolean, options?: RequestInit): Promise<Map>;
         setActive(): Promise<void>;
         setupContourBuffers(objects: any[], keepCootColours?: boolean): void;
         setOtherMapForColouring(molNo: number, min?: number, max?: number): void;
@@ -521,6 +533,7 @@ export namespace moorhen {
     type AtomClickedEvent = CustomEvent<{
         buffer: { id: string };
         atom: { label: string };
+        isResidueSelection: boolean;
     }>
 
     type ConnectMapsEvent = CustomEvent<ConnectMapsInfo>
@@ -670,35 +683,6 @@ export namespace moorhen {
         defaultActionButtonSettings: actionButtonSettings;
         setDefaultActionButtonSettings: (arg0: {key: string; value: string}) => void;     
     }
-    
-    type MolChange<T extends Molecule | Map> = {
-        action: 'Add' | 'Remove' | 'AddList' | 'Empty';
-        item?: T;
-        items?: T[];
-    }    
-
-    type EditButtonProps = {
-        mode?: 'edit';
-        monomerLibraryPath: string;
-        backgroundColor: [number, number, number, number];
-        defaultBondSmoothness: number;
-        urlPrefix: string;
-        shortCuts: string | { [label: string]: Shortcut; };
-        selectedButtonIndex: string;
-        setSelectedButtonIndex: React.Dispatch<React.SetStateAction<string>>;
-        setToolTip: React.Dispatch<React.SetStateAction<string>>;
-        setOverlayContents: React.Dispatch<React.SetStateAction<JSX.Element>>;
-        buttonIndex: string;
-        enableRefineAfterMod: boolean;
-        refineAfterMod?: boolean;
-        glRef: React.RefObject<webGL.MGWebGL>;
-        commandCentre: React.RefObject<CommandCentre>;
-        activeMap: Map;
-        molecules: Molecule[];
-        timeCapsuleRef: React.RefObject<TimeCapsule>;
-        windowHeight: number;
-        changeMolecules: (arg0: MolChange<Molecule>) => void
-    }
 
     interface ContainerRefs {
         glRef: React.MutableRefObject<null | webGL.MGWebGL>;
@@ -810,6 +794,7 @@ export namespace moorhen {
             notificationContent: JSX.Element;
             activeMap: Map;
             theme: string;
+            residueSelection: ResidueSelection;
         };
         hoveringStates: {
             enableAtomHovering: boolean;