ketcher-core/dist/domain/entities/DrawingEntitiesManager.d.ts

Web-based molecule sketcher

import { AmbiguousMonomerType, AttachmentPointName, MonomerItemType, MonomerOrAmbiguousType } from "../types";
import { Vec2 } from "./vec2";
import { Command } from "./Command";
import { DrawingEntity } from "./DrawingEntity";
import { PolymerBond } from "./PolymerBond";
import { BaseMonomer, Chem, LinkerSequenceNode, Phosphate, RNABase, Struct, Sugar } from "./";
import { ChainsCollection } from "./monomer-chains/ChainsCollection";
import { Nucleoside } from './Nucleoside';
import { Nucleotide } from './Nucleotide';
import { MACROMOLECULES_BOND_TYPES } from "../../application/editor";
import { CanvasMatrix } from "./canvas-matrix/CanvasMatrix";
import { Matrix } from "./canvas-matrix/Matrix";
import { Cell } from "./canvas-matrix/Cell";
import { AmbiguousMonomer } from "./AmbiguousMonomer";
import { Atom, AtomProperties } from "./CoreAtom";
import { Bond } from "./CoreBond";
import { MonomerToAtomBond } from "./MonomerToAtomBond";
import { AtomLabel } from "../constants";
import { HydrogenBond } from "./HydrogenBond";
export declare const CELL_WIDTH = 60;
export declare const SNAKE_LAYOUT_Y_OFFSET_BETWEEN_CHAINS: number;
export declare const MONOMER_START_X_POSITION: number;
export declare const MONOMER_START_Y_POSITION: number;
declare type RnaPresetAdditionParams = {
    sugar: MonomerItemType;
    sugarPosition: Vec2;
    rnaBase: MonomerItemType | undefined;
    rnaBasePosition: Vec2 | undefined;
    phosphate: MonomerItemType | undefined;
    phosphatePosition: Vec2 | undefined;
    existingNode?: Nucleotide | Nucleoside | LinkerSequenceNode;
};
export declare class DrawingEntitiesManager {
    monomers: Map<number, BaseMonomer>;
    polymerBonds: Map<number, PolymerBond | HydrogenBond>;
    private bondsMonomersOverlaps;
    atoms: Map<number, Atom>;
    bonds: Map<number, Bond>;
    monomerToAtomBonds: Map<number, MonomerToAtomBond>;
    micromoleculesHiddenEntities: Struct;
    canvasMatrix?: CanvasMatrix;
    snakeLayoutMatrix?: Matrix<Cell>;
    get bottomRightMonomerPosition(): Vec2;
    get selectedEntitiesArr(): DrawingEntity[];
    get selectedEntities(): [number, DrawingEntity][];
    get allEntities(): [number, DrawingEntity][];
    get hasDrawingEntities(): boolean;
    get hasMonomers(): boolean;
    get allBondsToMonomers(): ([number, PolymerBond] | [number, MonomerToAtomBond])[];
    deleteSelectedEntities(): Command;
    deleteAllEntities(): Command;
    addMonomerChangeModel(monomerItem: MonomerItemType, position: Vec2, _monomer?: BaseMonomer): BaseMonomer | AmbiguousMonomer;
    createMonomer(monomerItem: MonomerOrAmbiguousType, position: Vec2, generateId?: boolean): AmbiguousMonomer | Chem | Sugar | import("./").Peptide | RNABase | Phosphate;
    updateMonomerItem(monomer: BaseMonomer, monomerItemNew: MonomerItemType): BaseMonomer;
    addMonomer(monomerItem: MonomerItemType, position: Vec2, _monomer?: BaseMonomer): Command;
    deleteDrawingEntity(drawingEntity: DrawingEntity, needToDeleteConnectedEntities?: boolean): Command;
    selectDrawingEntity(drawingEntity: DrawingEntity): Command;
    selectDrawingEntities(drawingEntities: DrawingEntity[]): Command;
    createDrawingEntitySelectionCommand(drawingEntity: DrawingEntity): Command;
    unselectAllDrawingEntities(): Command;
    unselectDrawingEntity(drawingEntity: DrawingEntity): Command;
    selectAllDrawingEntities(): Command;
    addDrawingEntitiesToSelection(drawingEntities: DrawingEntity[]): Command;
    moveDrawingEntityModelChange(drawingEntity: DrawingEntity, offset?: Vec2): DrawingEntity;
    private moveChemAtomsPoint;
    moveSelectedDrawingEntities(partOfMovementOffset: Vec2, fullMovementOffset?: Vec2): Command;
    createDrawingEntityMovingCommand(drawingEntity: DrawingEntity, partOfMovementOffset: Vec2, fullMovementOffset?: Vec2): Command;
    createDrawingEntityRedrawCommand(drawingEntityRedrawModelChange: () => DrawingEntity, invertDrawingEntityRedrawModelChange: () => DrawingEntity): Command;
    private deleteMonomerChangeModel;
    deleteMonomer(monomer: BaseMonomer, needToDeleteConnectedBonds?: boolean): Command;
    modifyMonomerItem(monomer: BaseMonomer, monomerItemNew: MonomerItemType): Command;
    selectIfLocatedInRectangle(rectangleTopLeftPoint: Vec2, rectangleBottomRightPoint: Vec2, previousSelectedEntities: [number, DrawingEntity][], shiftKey?: boolean): Command;
    private checkBondSelectionForSequenceMode;
    startPolymerBondCreationChangeModel(firstMonomer: any, startPosition: any, endPosition: any, bondType?: MACROMOLECULES_BOND_TYPES, _polymerBond?: PolymerBond | HydrogenBond): PolymerBond | HydrogenBond;
    startPolymerBondCreation(firstMonomer: BaseMonomer, startPosition: Vec2, endPosition: Vec2, bondType: MACROMOLECULES_BOND_TYPES): {
        command: Command;
        polymerBond: any;
    };
    deletePolymerBondChangeModel(polymerBond: PolymerBond | HydrogenBond): void;
    deletePolymerBond(polymerBond: PolymerBond | HydrogenBond): Command;
    cancelPolymerBondCreation(polymerBond: PolymerBond, secondMonomer?: BaseMonomer): Command;
    movePolymerBond(polymerBond: PolymerBond, position: Vec2): Command;
    finishPolymerBondCreationModelChange(firstMonomer: BaseMonomer, secondMonomer: BaseMonomer, firstMonomerAttachmentPoint: AttachmentPointName, secondMonomerAttachmentPoint: AttachmentPointName, bondType?: MACROMOLECULES_BOND_TYPES, _polymerBond?: PolymerBond): PolymerBond | HydrogenBond;
    finishPolymerBondCreation(polymerBond: PolymerBond, secondMonomer: BaseMonomer, firstMonomerAttachmentPoint: AttachmentPointName, secondMonomerAttachmentPoint: AttachmentPointName, bondType?: MACROMOLECULES_BOND_TYPES): Command;
    createPolymerBond(firstMonomer: BaseMonomer, secondMonomer: BaseMonomer, firstMonomerAttachmentPoint: AttachmentPointName, secondMonomerAttachmentPoint: AttachmentPointName, bondType?: MACROMOLECULES_BOND_TYPES): Command;
    intendToStartBondCreation(monomer: BaseMonomer): Command;
    intendToStartAttachmenPointBondCreation(monomer: BaseMonomer, attachmentPointName: AttachmentPointName): Command;
    intendToFinishBondCreation(monomer: BaseMonomer, bond: PolymerBond, shouldCalculateBonds: boolean): Command;
    intendToFinishAttachmenPointBondCreation(monomer: BaseMonomer, bond: PolymerBond, attachmentPointName: AttachmentPointName, shouldCalculateBonds: boolean): Command;
    cancelIntentionToFinishBondCreation(monomer: BaseMonomer, polymerBond?: PolymerBond): Command;
    intendToSelectDrawingEntity(drawingEntity: DrawingEntity): Command;
    cancelIntentionToSelectDrawingEntity(drawingEntity: DrawingEntity): Command;
    showPolymerBondInformation(polymerBond: PolymerBond): Command;
    hidePolymerBondInformation(polymerBond: PolymerBond): Command;
    hideAllMonomersHoverAndAttachmentPoints(): Command;
    addRnaPresetFromNode: (node: Nucleotide | Nucleoside | LinkerSequenceNode) => Command;
    addRnaPreset({ sugar, sugarPosition, phosphate, phosphatePosition, rnaBase, rnaBasePosition, }: RnaPresetAdditionParams): {
        command: Command;
        monomers: BaseMonomer[];
    };
    rearrangeChainModelChange(monomer: BaseMonomer, newPosition: Vec2): BaseMonomer;
    private reArrangeChain;
    private reArrangeRnaChain;
    private getNextMonomerPositionForSnakeLayout;
    private addRnaOperations;
    private recalculateCanvasMatrixModelChange;
    recalculateCanvasMatrix(chainsCollection?: ChainsCollection, previousSnakeLayoutMatrix?: Matrix<Cell>): Command;
    private rearrangeAntisenseChain;
    private calculateSnakeLayoutMatrix;
    applySnakeLayout(canvasWidth: number, isSnakeMode: boolean, needRedrawBonds?: boolean, needRepositionMonomers?: boolean): Command;
    private redrawBondsModelChange;
    redrawBonds(): Command;
    getNextPositionAndDistance(lastPosition: Vec2, height: number, canvasWidth: number, width: number | undefined, restOfRowsWithAntisense: number): {
        maxVerticalDistance: number;
        lastPosition: Vec2;
    };
    isNucleosideAndPhosphateConnectedAsNucleotide(nucleoside: Nucleoside, phosphate: Phosphate): boolean;
    setMicromoleculesHiddenEntities(struct: Struct): void;
    clearMicromoleculesHiddenEntities(): void;
    mergeInto(targetDrawingEntitiesManager: DrawingEntitiesManager): {
        command: Command;
        mergedDrawingEntities: DrawingEntitiesManager;
    };
    centerMacroStructure(): void;
    getCurrentCenterPointOfCanvas(): Vec2;
    getMacroStructureCenter(): Vec2;
    applyMonomersSequenceLayout(): ChainsCollection;
    clearCanvas(): void;
    applyFlexLayoutMode(needRedrawBonds?: boolean): Command;
    rerenderBondsOverlappedByMonomers(): void;
    getAllSelectedEntitiesForEntities(drawingEntities: DrawingEntity[]): {
        command: Command;
        drawingEntities: DrawingEntity[];
    };
    getAllSelectedEntitiesForSingleEntity(drawingEntity: DrawingEntity, needToSelectConnectedBonds?: boolean, selectedDrawingEntities?: DrawingEntity[]): {
        command: Command;
        drawingEntities: DrawingEntity[];
    };
    validateIfApplicableForFasta(): boolean;
    moveMonomer(monomer: BaseMonomer, position: Vec2): Command;
    removeHoverForAllMonomers(): Command;
    private reconnectPolymerBondModelChange;
    reconnectPolymerBond(polymerBond: PolymerBond, newFirstMonomerAttachmentPoint: AttachmentPointName, newSecondMonomerAttachmentPoint: AttachmentPointName, initialFirstMonomerAttachmentPoint: AttachmentPointName, initialSecondMonomerAttachmentPoint: AttachmentPointName): Command;
    private addAmbiguousMonomerChangeModel;
    addAmbiguousMonomer(ambiguousMonomerItem: AmbiguousMonomerType, position: Vec2): Command;
    private addAtomChangeModel;
    addAtom(position: Vec2, monomer: BaseMonomer, atomIdInMicroMode: number, label: AtomLabel, properties?: AtomProperties): Command;
    private deleteAtomChangeModel;
    private deleteAtom;
    private addBondChangeModel;
    addBond(firstAtom: Atom, secondAtom: Atom, type: number, stereo: number, bondIdInMicroMode: number): Command;
    private deleteBondChangeModel;
    private deleteBond;
    addMonomerToAtomBondChangeModel(monomer: BaseMonomer, atom: Atom, attachmentPoint: AttachmentPointName, _monomerToAtomBond?: MonomerToAtomBond): MonomerToAtomBond;
    private deleteMonomerToAtomBondChangeModel;
    deleteMonomerToAtomBond(monomerAtomBond: MonomerToAtomBond): Command;
    addMonomerToAtomBond(monomer: BaseMonomer, atom: Atom, attachmentPoint: AttachmentPointName): Command;
    static getStructureBbox(monomers: BaseMonomer[]): {
        left: number;
        right: number;
        top: number;
        bottom: number;
        width: number;
        height: number;
    };
    private static get antisenseChainBasesMap();
    markMonomerAsAntisense(monomer: BaseMonomer): Command;
    markMonomerAsSense(monomer: BaseMonomer): Command;
    recalculateAntisenseChains(): Command;
    get hasAntisenseChains(): boolean;
    private static getAntisenseBaseLabel;
    static createAntisenseNode(node: Nucleoside | Nucleotide, needAddPhosphate?: boolean): {
        modelChanges: Command;
        node: Nucleoside;
    } | {
        modelChanges: Command;
        node: Nucleotide;
    } | undefined;
    createAntisenseChain(): Command;
    get monomersArray(): BaseMonomer[];
    get polymerBondsArray(): (PolymerBond | HydrogenBond)[];
    get molecules(): BaseMonomer[];
    private checkBondForOverlapsByMonomers;
    detectBondsOverlappedByMonomers(polymerBonds?: Array<PolymerBond | HydrogenBond>): void;
}
export {};