2.3.0

dist/declarations/buffer/arrow-buffer.d.ts

@@ -92,9 +92,9 @@ declare class ArrowBuffer {
     cylinderRadius: Float32Array;
     geometry: GeometryGroup;
     picking?: Picker;
-    group: Group;
-    wireframeGroup: Group;
-    pickingGroup: Group;
+    group: Group<import("three").Object3DEventMap>;
+    wireframeGroup: Group<import("three").Object3DEventMap>;
+    pickingGroup: Group<import("three").Object3DEventMap>;
     visible: boolean;
     /**
      * @param {Object} data - buffer data
@@ -113,9 +113,9 @@ declare class ArrowBuffer {
         cylinder: Partial<CylinderBufferData>;
         cone: Partial<ConeBufferData>;
     };
-    getMesh(): Group;
-    getWireframeMesh(): Group;
-    getPickingMesh(): Group;
+    getMesh(): Group<import("three").Object3DEventMap>;
+    getWireframeMesh(): Group<import("three").Object3DEventMap>;
+    getPickingMesh(): Group<import("three").Object3DEventMap>;
     setAttributes(data?: Partial<ArrowBufferData>): void;
     /**
      * Set buffer parameters

dist/declarations/buffer/buffer.d.ts

@@ -4,15 +4,15 @@
  * @private
  */
 import { Vector3, Matrix4, BufferGeometry, Uniform, Group, LineSegments, Points, Mesh, ShaderMaterial } from 'three';
-import { GenericColor, NumberArray } from '../types';
+import { GenericColor, TypedArray } from '../types';
 import { ShaderDefines } from '../shader/shader-utils';
 import { Picker } from '../utils/picker';
 export declare type BufferSide = 'front' | 'back' | 'double';
 export declare type BufferTypes = 'picking' | 'background';
 export declare type BufferMaterials = 'material' | 'wireframeMaterial' | 'pickingMaterial';
 export interface _BufferAttribute {
     type: 'f' | 'v2' | 'v3' | 'c';
-    value?: NumberArray;
+    value?: TypedArray;
 }
 export declare type Uniforms = {
     [k: string]: Uniform | {
@@ -201,12 +201,12 @@ declare class Buffer {
     uniforms: Uniforms;
     pickingUniforms: Uniforms;
     private _positionDataSize;
-    geometry: BufferGeometry;
+    geometry: BufferGeometry<import("three").NormalBufferAttributes>;
     indexVersion: number;
     wireframeIndexVersion: number;
-    group: Group;
-    wireframeGroup: Group;
-    pickingGroup: Group;
+    group: Group<import("three").Object3DEventMap>;
+    wireframeGroup: Group<import("three").Object3DEventMap>;
+    pickingGroup: Group<import("three").Object3DEventMap>;
     vertexShader: string;
     fragmentShader: string;
     isImpostor: boolean;
@@ -245,10 +245,10 @@ declare class Buffer {
     makeWireframeIndex(): void;
     updateWireframeIndex(): void;
     getRenderOrder(): number;
-    _getMesh(materialName: BufferMaterials): LineSegments<BufferGeometry, ShaderMaterial> | Points<BufferGeometry, ShaderMaterial> | Mesh<BufferGeometry, ShaderMaterial>;
-    getMesh(): LineSegments<BufferGeometry, ShaderMaterial> | Points<BufferGeometry, ShaderMaterial> | Mesh<BufferGeometry, ShaderMaterial>;
-    getWireframeMesh(): LineSegments<BufferGeometry, ShaderMaterial>;
-    getPickingMesh(): LineSegments<BufferGeometry, ShaderMaterial> | Points<BufferGeometry, ShaderMaterial> | Mesh<BufferGeometry, ShaderMaterial>;
+    _getMesh(materialName: BufferMaterials): LineSegments<BufferGeometry<import("three").NormalBufferAttributes>, ShaderMaterial> | Points<BufferGeometry<import("three").NormalBufferAttributes>, ShaderMaterial> | Mesh<BufferGeometry<import("three").NormalBufferAttributes>, ShaderMaterial, import("three").Object3DEventMap>;
+    getMesh(): LineSegments<BufferGeometry<import("three").NormalBufferAttributes>, ShaderMaterial> | Points<BufferGeometry<import("three").NormalBufferAttributes>, ShaderMaterial> | Mesh<BufferGeometry<import("three").NormalBufferAttributes>, ShaderMaterial, import("three").Object3DEventMap>;
+    getWireframeMesh(): LineSegments<BufferGeometry<import("three").NormalBufferAttributes>, ShaderMaterial>;
+    getPickingMesh(): LineSegments<BufferGeometry<import("three").NormalBufferAttributes>, ShaderMaterial> | Points<BufferGeometry<import("three").NormalBufferAttributes>, ShaderMaterial> | Mesh<BufferGeometry<import("three").NormalBufferAttributes>, ShaderMaterial, import("three").Object3DEventMap>;
     getShader(name: string, type?: BufferTypes): string;
     getVertexShader(type?: BufferTypes): string;
     getFragmentShader(type?: BufferTypes): string;

dist/declarations/buffer/doublesided-buffer.d.ts

@@ -28,9 +28,9 @@ declare class DoubleSidedBuffer {
     wireframe: boolean;
     geometry: BufferGeometry;
     picking?: Picker;
-    group: Group;
-    wireframeGroup: Group;
-    pickingGroup: Group;
+    group: Group<import("three").Object3DEventMap>;
+    wireframeGroup: Group<import("three").Object3DEventMap>;
+    pickingGroup: Group<import("three").Object3DEventMap>;
     frontMeshes: (Mesh | LineSegments)[];
     backMeshes: (Mesh | LineSegments)[];
     buffer: Buffer;
@@ -71,9 +71,9 @@ declare class DoubleSidedBuffer {
         diffuse: import("../types").GenericColor;
         interiorColor: import("../types").GenericColor;
     };
-    getMesh(picking: boolean): Group;
-    getWireframeMesh(): LineSegments<BufferGeometry, import("three").ShaderMaterial>;
-    getPickingMesh(): Group;
+    getMesh(picking: boolean): Group<import("three").Object3DEventMap>;
+    getWireframeMesh(): LineSegments<BufferGeometry<import("three").NormalBufferAttributes>, import("three").ShaderMaterial>;
+    getPickingMesh(): Group<import("three").Object3DEventMap>;
     setAttributes(data: any): void;
     setParameters(data: any): void;
     setVisibility(value: boolean): void;

dist/declarations/buffer/point-buffer.d.ts

@@ -66,7 +66,7 @@ declare class PointBuffer extends Buffer {
         };
         sortParticles: {};
         alphaTest: {
-            updateShader: boolean;
+            uniform: boolean;
         };
         useTexture: {
             updateShader: boolean;

dist/declarations/buffer/tubemesh-buffer.d.ts

@@ -22,17 +22,7 @@ export declare const TubeMeshBufferDefaultParameters: {
     depthWrite: boolean;
     clipNear: number;
     clipRadius: number;
-    clipCenter: Vector3; /**
-     * @param  {Object} data - attribute object
-     * @param  {Float32Array} data.position - positions
-     * @param  {Float32Array} data.normal - normals
-     * @param  {Float32Array} data.binormal - binormals
-     * @param  {Float32Array} data.tangent - tangents
-     * @param  {Float32Array} data.color - colors
-     * @param  {Float32Array} data.size - sizes
-     * @param  {Picker} data.picking - picking ids
-     * @param  {BufferParameters} params - parameter object
-     */
+    clipCenter: Vector3;
     flatShaded: boolean;
     wireframe: boolean;
     roughness: number;
@@ -68,17 +58,7 @@ declare class TubeMeshBuffer extends MeshBuffer {
         depthWrite: boolean;
         clipNear: number;
         clipRadius: number;
-        clipCenter: Vector3; /**
-         * @param  {Object} data - attribute object
-         * @param  {Float32Array} data.position - positions
-         * @param  {Float32Array} data.normal - normals
-         * @param  {Float32Array} data.binormal - binormals
-         * @param  {Float32Array} data.tangent - tangents
-         * @param  {Float32Array} data.color - colors
-         * @param  {Float32Array} data.size - sizes
-         * @param  {Picker} data.picking - picking ids
-         * @param  {BufferParameters} params - parameter object
-         */
+        clipCenter: Vector3;
         flatShaded: boolean;
         wireframe: boolean;
         roughness: number;

dist/declarations/datasource/pdbe-datasource.d.ts

@@ -0,0 +1,11 @@
+/**
+ * @file PDB Europe Datasource
+ * @author Paul Pillot <paul.pillot@tandemai.com>
+ * @private
+ */
+import Datasource from './datasource';
+declare class PDBeDatasource extends Datasource {
+    getUrl(src: string): string;
+    getExt(src: string): string;
+}
+export default PDBeDatasource;

dist/declarations/ngl.d.ts

@@ -126,7 +126,6 @@ import './parser/mrc-parser';
 import './parser/xplor-parser';
 import './parser/kin-parser';
 import './parser/obj-parser';
-import './parser/ply-parser';
 import './parser/csv-parser';
 import './parser/json-parser';
 import './parser/msgpack-parser';
@@ -142,6 +141,7 @@ import MolecularSurface from './surface/molecular-surface';
 import Volume from './surface/volume';
 import './utils/gzip-decompressor';
 import './datasource/rcsb-datasource';
+import './datasource/pdbe-datasource';
 import './datasource/pubchem-datasource';
 import './datasource/passthrough-datasource';
 import './datasource/alphafold-datasource';

dist/declarations/parser/cif-parser.d.ts

@@ -1,11 +1,13 @@
 /**
  * @file Cif Parser
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Paul Pillot <paul.pillot@tandemai.com>
  * @private
  */
 import StructureParser from './structure-parser';
 declare class CifParser extends StructureParser {
     get type(): string;
-    _parse(): void;
+    get isBinary(): boolean;
+    _parse(): Promise<void>;
 }
 export default CifParser;

dist/declarations/parser/structure-parser.d.ts

@@ -4,6 +4,7 @@
  * @private
  */
 import Parser, { ParserParameters } from './parser';
+import Structure from '../structure/structure';
 import StructureBuilder from '../structure/structure-builder';
 import Streamer from '../streamer/streamer';
 export interface StructureParserParameters extends ParserParameters {
@@ -12,6 +13,7 @@ export interface StructureParserParameters extends ParserParameters {
     cAlphaOnly: boolean;
 }
 declare class StructureParser extends Parser {
+    structure: Structure;
     structureBuilder: StructureBuilder;
     constructor(streamer: Streamer, params?: Partial<StructureParserParameters>);
     get type(): string;

dist/declarations/shader/shader-utils.d.ts

@@ -12,7 +12,7 @@ import './chunk/opaque_back_fragment.glsl';
 import './chunk/radiusclip_vertex.glsl';
 import './chunk/radiusclip_fragment.glsl';
 import './chunk/unpack_color.glsl';
-export declare type ShaderDefine = ('NEAR_CLIP' | 'RADIUS_CLIP' | 'PICKING' | 'NOLIGHT' | 'FLAT_SHADED' | 'OPAQUE_BACK' | 'DIFFUSE_INTERIOR' | 'USE_INTERIOR_COLOR' | 'USE_SIZEATTENUATION' | 'USE_MAP' | 'ALPHATEST' | 'SDF' | 'FIXED_SIZE' | 'CUBIC_INTERPOLATION' | 'BSPLINE_FILTER' | 'CATMULROM_FILTER' | 'MITCHELL_FILTER');
+export declare type ShaderDefine = ('NEAR_CLIP' | 'RADIUS_CLIP' | 'PICKING' | 'NOLIGHT' | 'FLAT_SHADED' | 'OPAQUE_BACK' | 'DIFFUSE_INTERIOR' | 'USE_INTERIOR_COLOR' | 'USE_SIZEATTENUATION' | 'USE_MAP' | 'USE_ALPHATEST' | 'SDF' | 'FIXED_SIZE' | 'CUBIC_INTERPOLATION' | 'BSPLINE_FILTER' | 'CATMULROM_FILTER' | 'MITCHELL_FILTER');
 export declare type ShaderDefines = {
     [k in ShaderDefine]?: number | string;
 };

dist/declarations/stage/stage.d.ts

@@ -31,6 +31,7 @@ import Structure from '../structure/structure';
 import Surface from '../surface/surface';
 import Volume from '../surface/volume';
 import Shape from '../geometry/shape';
+import { GenericColor } from '../types';
 declare global {
     interface Document {
         mozFullScreen: boolean;
@@ -90,7 +91,7 @@ export declare const StageDefaultParameters: {
     quality: RenderQualityType;
     workerDefault: boolean;
     sampleLevel: number;
-    backgroundColor: string | number;
+    backgroundColor: GenericColor;
     rotateSpeed: number;
     zoomSpeed: number;
     panSpeed: number;
@@ -104,9 +105,9 @@ export declare const StageDefaultParameters: {
     cameraFov: number;
     cameraEyeSep: number;
     cameraType: "perspective" | "orthographic" | "stereo";
-    lightColor: string | number;
+    lightColor: GenericColor;
     lightIntensity: number;
-    ambientColor: string | number;
+    ambientColor: GenericColor;
     ambientIntensity: number;
     hoverTimeout: number;
     tooltip: boolean;
@@ -166,7 +167,7 @@ declare class Stage {
         quality: RenderQualityType;
         workerDefault: boolean;
         sampleLevel: number;
-        backgroundColor: string | number;
+        backgroundColor: GenericColor;
         rotateSpeed: number;
         zoomSpeed: number;
         panSpeed: number;
@@ -180,9 +181,9 @@ declare class Stage {
         cameraFov: number;
         cameraEyeSep: number;
         cameraType: "perspective" | "orthographic" | "stereo";
-        lightColor: string | number;
+        lightColor: GenericColor;
         lightIntensity: number;
-        ambientColor: string | number;
+        ambientColor: GenericColor;
         ambientIntensity: number;
         hoverTimeout: number;
         tooltip: boolean;

dist/declarations/store/atom-store.d.ts

@@ -18,7 +18,7 @@ export default class AtomStore extends Store {
     altloc: Uint8Array;
     occupancy: Float32Array;
     partialCharge?: Float32Array;
-    formalCharge?: Uint8Array;
+    formalCharge?: Int8Array;
     get _defaultFields(): StoreField[];
     setAltloc(i: number, str: string): void;
     getAltloc(i: number): string;

dist/declarations/store/chemcomp-map.d.ts

@@ -0,0 +1,26 @@
+/**
+ * @file ChemComp Map
+ * @author Paul Pillot <paul.pillot@tandemai.com>
+ * @private
+ */
+import Structure from "../structure/structure";
+import { ResidueBonds } from "../structure/structure-utils";
+interface ChemCompBonds {
+    atom1: string[];
+    atom2: string[];
+    bondOrders: number[];
+}
+declare class ChemCompMap {
+    readonly structure: Structure;
+    dict: {
+        [resname: string]: {
+            chemCompType: string;
+            bonds?: ChemCompBonds;
+        };
+    };
+    constructor(structure: Structure);
+    add(resname: string, chemCompType: string, bonds?: ChemCompBonds): void;
+    addBond(resname: string, atom1: string, atom2: string, bondOrder: number): void;
+    getBonds(resname: string, atomList: number[]): ResidueBonds | undefined;
+}
+export default ChemCompMap;

dist/declarations/structure/structure.d.ts

@@ -5,6 +5,7 @@
  */
 import { Vector3, Box3 } from 'three';
 import { Signal } from 'signals';
+import { CifBlock } from 'molstar/lib/mol-io/reader/cif';
 import BitArray from '../utils/bitarray';
 import PrincipalAxes from '../math/principal-axes';
 import SpatialHash from '../geometry/spatial-hash';
@@ -31,6 +32,7 @@ import AtomProxy from '../proxy/atom-proxy';
 import ResidueProxy from '../proxy/residue-proxy';
 import ChainProxy from '../proxy/chain-proxy';
 import ModelProxy from '../proxy/model-proxy';
+import ChemCompMap from '../store/chemcomp-map';
 interface Structure {
     signals: StructureSignals;
     name: string;
@@ -65,6 +67,7 @@ interface Structure {
     modelStore: ModelStore;
     atomMap: AtomMap;
     residueMap: ResidueMap;
+    chemCompMap?: ChemCompMap;
     bondHash?: BondHash;
     spatialHash?: SpatialHash;
     atomSet?: BitArray;
@@ -91,7 +94,7 @@ export declare type StructureHeader = {
     experimentalMethods?: string[];
 };
 export declare type StructureExtraData = {
-    cif?: object;
+    cif?: CifBlock;
     sdf?: object[];
 };
 export declare type StructureSignals = {

dist/declarations/surface/surface.d.ts

@@ -3,7 +3,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @private
  */
-import { Vector3, Box3, Geometry, BufferGeometry, Group } from 'three';
+import { Vector3, Box3, BufferGeometry, Group } from 'three';
 import { AtomPicker, SurfacePicker } from '../utils/picker';
 import { ColormakerParameters } from '../color/colormaker';
 import { Structure, Volume } from '../ngl';
@@ -63,7 +63,7 @@ declare class Surface {
      * @return {undefined}
      */
     set(position: Float32Array, index: Uint32Array | Uint16Array | undefined, normal: Float32Array | undefined, color: Float32Array | undefined, atomindex: Int32Array | undefined, contour?: boolean): void;
-    fromGeometry(geometry: Geometry | BufferGeometry | Group): void;
+    fromGeometry(geometry: BufferGeometry | Group): void;
     getPosition(): Float32Array;
     getColor(params: ColormakerParameters & {
         scheme: string;

dist/declarations/surface/volume.d.ts

@@ -38,7 +38,7 @@ declare class Volume {
     data: Float32Array;
     worker: Worker;
     workerPool: WorkerPool;
-    _position: Float32Array;
+    _position: Float32Array | undefined;
     _min: number | undefined;
     _max: number | undefined;
     _mean: number | undefined;
@@ -92,7 +92,7 @@ declare class Volume {
        */
     setAtomindex(atomindex?: Int32Array): void;
     getBox(center: Vector3, size: number, target: Box3): Box3;
-    _getBox(center: Vector3 | undefined, size: number): number[][] | undefined;
+    _getBox(center: Vector3 | undefined, size: number): import("three").Vector3Tuple[] | undefined;
     _makeSurface(sd: any, isolevel: number, smooth: number): Surface;
     getSurface(isolevel: number, smooth: number, center: Vector3, size: number, contour: boolean, wrap?: boolean): Surface;
     getSurfaceWorker(isolevel: number, smooth: number, center: Vector3, size: number, contour: boolean, wrap: boolean, callback: (s: Surface) => void): void;