change CI process

.gitignore

 .vscode
 .mypy_cache
-node_modules
\ No newline at end of file
+node_modules
+
+build/*.js*
\ No newline at end of file

.gitlab-ci.yml

-image: alpine:3.8
+image: docker:latest
+
+before_script:
+  - npm install
+  - npm install --save-dev webpack
+  - webpack --mode=production
+  - npm run build
 
 pages:
   script:

build/app.d.ts

-declare namespace Model {
-    class UIParameters {
-        reinitialize: boolean;
-        downloadImage: boolean;
-        downloadData: boolean;
-        center: boolean;
-        help: boolean;
-        residueLabel: boolean;
-        tooltip: boolean;
-        constructor();
-    }
-    /**
-     *
-     *
-     * @export
-     * @enum {number}
-     */
-    enum InteractionType {
-        AtomAtom = 0,
-        AtomPlane = 1,
-        PlanePlane = 2,
-        GroupPlane = 3,
-        GroupGroup = 4
-    }
-    class InteractionTypeUtil {
-        static parse(value: string): InteractionType;
-    }
-    class Interaction {
-        sourceAtoms: string[];
-        targetAtoms: string[];
-        interactionType: InteractionType;
-        interactionsClases: string[];
-        distance: number;
-        constructor(srcAtoms: string[], targetAtoms: string[], type: InteractionType, intClasses: string[], d: number);
-    }
-    /**
-     * Data model representing a single residue, which is a part of the
-     * bound molecule. This residue is unique in the entire binding site.
-     */
-    class Residue {
-        id: string;
-        chainId: string;
-        authorResidueNumber: number;
-        chemCompId: string;
-        authorInsertionCode: string;
-        isLigand: boolean;
-        constructor(data: any, isLigand: boolean);
-        /**
-         * Infer type of the residue, which is then used as a CSS source
-         * for proper residue aesthetics.
-         */
-        getResidueType(): string;
-        equals(other: Residue): boolean;
-        toString(): string;
-    }
-    class InteractionNode implements d3.SimulationNodeDatum {
-        id: string;
-        residue: Residue;
-        scale: number;
-        index?: number;
-        x?: number;
-        y?: number;
-        vx?: number;
-        vy?: number;
-        fx?: number;
-        fy?: number;
-        constructor(r: Residue, scale: number, id: string, x?: number, y?: number);
-        equals(other: InteractionNode): boolean;
-        toString(): string;
-        toTooltip(): string;
-    }
-    interface Link {
-        source: InteractionNode;
-        target: InteractionNode;
-        getLinkClass(): string;
-        toTooltip(): string;
-    }
-    class ResidueResidueLink implements Link {
-        target: InteractionNode;
-        source: InteractionNode;
-        interactions: Map<InteractionType, Array<string>>;
-        constructor(source: InteractionNode, target: InteractionNode, interactions: any);
-        /**
-         * Checks if the link contains a given node.
-         */
-        containsNode(n: InteractionNode): boolean;
-        /**
-         * Shorthand to check if the link contains particular underlying
-         * residue.
-         */
-        containsResidue(n: Residue): boolean;
-        isBoundMoleculeLink(): boolean;
-        toTooltip(): string;
-        /**
-         * Check all the interactions, which are a part of the contact
-         * and determine their class. This is later on used for selection
-         * of the correct aesthetics with CSS.
-         */
-        getLinkClass(): string;
-    }
-    class LigandResidueLink implements Link {
-        source: InteractionNode;
-        target: InteractionNode;
-        interaction: Array<Interaction>;
-        constructor(begin: InteractionNode, end: InteractionNode, beginAtoms: string[], endAtoms: string[], interactionType: string, interactionDetails: string[], distance: number);
-        containsBothNodes(a: InteractionNode, b: InteractionNode): boolean;
-        addInteraction(beginAtoms: string[], endAtoms: string[], interactionType: string, interactionDetails: string[], distance: number): void;
-        /**
-         * Check all the interactions, which are a part of the contact
-         * and determine their class. This is later on used for selection
-         * of the correct aesthetics with CSS.
-         */
-        getLinkClass(): string;
-        containsInteractionNode(node: InteractionNode): boolean;
-        hasClash(): boolean;
-        toTooltip(): string;
-    }
-    /**
-     * DataObject representing the entire binding site with the bound
-     * molecule and all its interactions.
-     */
-    class BindingSite {
-        pdbId: string;
-        bmId: string;
-        residues: Residue[];
-        interactionNodes: InteractionNode[];
-        links: Link[];
-        constructor();
-        fromBoundMolecule(pdbId: string, data: any): BindingSite;
-        private processResidueInteractionPartner;
-        private processLigandInteractionPartner;
-        fromLigand(pdbId: string, data: any, ligand: Depiction): BindingSite;
-    }
-}
-/**
- * Provider of glycan depictions for a given hetcode. Uses two external
- * resources. One configuration XML with the glycan classes and their
- * depictions and a file providing mapping between glycan class and het
- * codes.
- *
- * @class VisualsMapper
- */
-declare class VisualsMapper {
-    glycanImages: Map<string, SVGElement>;
-    glycanMapping: Map<string, string>;
-    graphicsPromise: Promise<void>;
-    mappingPromise: Promise<void>;
-    constructor();
-    /**
-     * Gets proper glycan in the SVG format based on teh glycan class.
-     *
-     * @param {string} compId Class id.
-     * @returns {SVGElement} glycan representation in the SVG format.
-     * @memberof GlycanMapper
-     */
-    getGlycanImage(compId: string): SVGElement;
-    /**
-     * Parse external file with glycan representation and stores it for
-     * further use.
-     *
-     * @private
-     * @param {string} symbolsLink external link to the XML mapping file.
-     * @returns {Promise} To check later if it has been processed.
-     * @memberof GlycanMapper
-     */
-    private parseSymbols;
-    /**
-     * Parses an external JSON configuration file which provides a mapping
-     * between glycan id (e.g. GlcA) and het codes.
-     */
-    private parseGlycanMapping;
-}
-/**
- * This class contains all the details which are necessary for redrawing
- * RDKIt style 2D molecule depiction on a client side as well as some
- * other logic which should hopefully help with the initial placement of
- * binding partners in the residue-level view.
- *
- * @author Lukas Pravda <lpravda@ebi.ac.uk>
- * @class Depiction
- * @param {string} ccdId PDB CCD id.
- * @param {Atom[]} atoms List of atoms.
- * @param {Bond[]} bonds Visual representation of bonds.
- * They do not correlate 1:1 with a number of bonds!
- * @param {Vector2D} resolution x,y dimension of the image. Needs to be used
- * for a scene shift, so it is centered.
- */
-declare class Depiction {
-    ccdId: string;
-    atoms: Atom[];
-    bonds: Bond[];
-    resolution: Vector2D;
-    constructor(data: any);
-    /**
-     * Returns an initial position of Residue node bound to a list of
-     * atom.
-     *
-     * Present implementation sorts all the partners based on the atom
-     * degree and then gets the one with the lovest degree and places
-     * the initial residue position along the vector pointing from it.
-     *
-     * @param {string[]} atomNames list of atom names the bound residue
-     * has a contact with.
-     * @returns {Vector2D} Returns an initial placement of the residue in contact.
-     * @memberof Depiction
-     */
-    getInitalNodePosition(atomNames: string[]): Vector2D;
-    /**
-     * Appends to a given selection the visual representation of bonds as svg:path elements.
-     *
-     * @param {d3.Selection<d3.BaseType, {}, HTMLElement, any>} selection where to append SVG
-     * representation of the bond visuals.
-     * @memberof Depiction
-     */
-    appendBondVisualsTo(root: d3.Selection<d3.BaseType, {}, HTMLElement, any>): void;
-    /**
-     * Append depiction labels to the visualization. Because RDKIt places
-     * the labels slightly differently this information needs to be
-     * consumed too, because we cannot use just atom position directly.
-     * Also there are all sorts of colorful subscripts and superscripts,
-     * so it is much easier to use it this way.
-     *
-     * @param {d3.Selection<d3.BaseType, {}, HTMLElement, any>} root where to append SVG
-     * representation of compounds' labels.
-     * @memberof Depiction
-     */
-    appendTextsTo(root: any): void;
-    /**
-     * Add small white circle on the background of atoms with label
-     * just to make the interaction lines pretty.
-     *
-     * @param {*} root
-     * @memberof Depiction
-     */
-    appendClarityNodes(root: any): void;
-    getCenter(ids: string[]): Vector2D;
-    /**
-     *
-     *
-     * @param {Map<string, number>} map
-     * @returns
-     * @memberof Depiction
-     */
-    sortMap(map: Map<string, number>): Map<string, number>;
-}
-/**
- * Atom from the depiction
- *
- * @class Atom
- * @param {string} name Unique atom name.
- * @param {any} label Atom label
- * @param {Vector2D} position Position of the atom in 2D coordinate system.
- */
-declare class Atom {
-    name: string;
-    label: any;
-    position: Vector2D;
-    constructor(item: any);
-    /**
-     *
-     *
-     * @param {Atom} other
-     * @returns true if the atoms are equal
-     * @memberof Atom
-     */
-    equals(other: Atom): boolean;
-}
-/**
- * 2D point definition
- *
- * @class Point
- * @param {number} x coordinate
- * @param {number} y coordinate
- */
-declare class Vector2D {
-    x: number;
-    y: number;
-    constructor(x: number, y: number);
-    /**
-     * Returns a string representation of the object in a format: [x, y]
-     *
-     * @returns {string} String representation of the object
-     * @memberof Point
-     */
-    toString(): string;
-    /**
-     * Checks whether or not two Vector2D objects are equal.
-     *
-     * @param {Vector2D} other instance of an object to check.
-     * @returns {boolean} whether or not the objects are equal.
-     * @memberof Point
-     */
-    equals(other: Vector2D): boolean;
-    /**
-     * Measures a distance between this atom and another atom.
-     *
-     * @param {Vector2D} other atom to measure a distance to.
-     * @returns {number} Returns the distance to another object.
-     * @memberof Point
-     */
-    distanceTo(other: Vector2D): number;
-    /**
-     * Composes vectors to a single one. This is used in infering the
-     * original placement of the residue nodes.
-     *
-     * @static
-     * @param {Vector2D[]} points Vectors to be composed.
-     * @returns {Vector2D} Result of a vector composition.
-     * @memberof Point
-     */
-    static composeVectors(points: Vector2D[]): Vector2D;
-}
-/**
- * Represents a bond in a 2D depiction.
- *
- * @class Bond
- * @param {Atom} bgn one side of the bond.
- * @param {Atom} end the other side of the bond.
- * @param {string} coords coordinates of the bonds graphical primitive.
- * @param {string} style Style of the bonds graphical primitive.
- */
-declare class Bond {
-    bgn: Atom;
-    end: Atom;
-    coords: string;
-    style: string;
-    /**
-     *Creates an instance of the bond.
-     * @param {Atom} a
-     * @param {Atom} b
-     * @memberof Bond
-     */
-    constructor(a: Atom, b: Atom, coords: string, style: string);
-    /**
-     * Get the other atom for a given bond.
-     *
-     * @param {Atom} other
-     * @returns {Atom} The other atom from the bond.
-     * @throws {Error} if the atom is not part of that bond at all.
-     * @memberof Bond
-     */
-    getOtherAtom(other: Atom): Atom;
-    /**
-     * Check whether or not a bond contains the atom.
-     *
-     * @param {Atom} other The other side of the bond
-     * @returns True if the atom is a part of the bond, false otherwise.
-     * @memberof Bond
-     */
-    containsAtom(other: Atom): boolean;
-    /**
-     * Hide bond from the representation.
-     *
-     * @memberof Bond
-     */
-    hide(): void;
-}
-declare const server: string;
-declare const clickEvent = "PDB.interactions.click";
-declare const mouseoverEvent = "PDB.interactions.mouseover";
-declare const mouseoutEvent = "PDB.interactions.mouseout";
-declare class Visualization {
-    private parent;
-    private canvas;
-    private simulation;
-    private svg;
-    private visualization;
-    private nodes;
-    private links;
-    private residueLabel;
-    private tooltip;
-    private pdbId;
-    private bindingSite;
-    private depiction;
-    private visualsMapper;
-    private interactionsData;
-    private selectedResidueHash;
-    constructor(element: HTMLElement);
-    private nodeMouseEnterEventHandler;
-    private nodeMouseLeaveEventHandler;
-    private linkMouseClickEventHandler;
-    private linkMouseOverEventHandler;
-    private linkMouseOutEventHandler;
-    private zoom_handler;
-    private drag_handler;
-    initialiseBoundMolecule(pdbid: string, bmId: string): Promise<void>;
-    initialiseLigand(pdbId: string, resId: number, chainId: string): Promise<void>;
-    saveSvg(ctx: Visualization): void;
-    downloadInteractionsData(ctx: Visualization): void;
-    reinitialize(ctx: Visualization): void;
-    private resize;
-    centerScene(ctx: Visualization): void;
-    private fireNodeMouseEnterEvent;
-    private fireNodeMouseLeaveEvent;
-    private fireLinkEvent;
-    private fireNodeEvent;
-    private fireLinkLeaveEvent;
-    private showLabel;
-    private selectLigand;
-    private setupLigandScene;
-    private setupScene;
-    private simulationStep;
-    private nodeHighlight;
-    private nodeDim;
-    private addMarkers;
-}
-declare let helpLigands: string;
-declare let helpBonds: string;
-declare class UI {
-    private root;
-    private display;
-    private residueLabel;
-    private tooltip;
-    constructor(element: HTMLElement, vis: Visualization);
-    register(params: Model.UIParameters): void;
-    private saveSVG;
-    private reinitialize;
-    private download;
-    private center;
-    private changeHelp;
-    showHelp(): void;
-    displayToolbarPanel(show: boolean): void;
-}