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

Web-based molecule sketcher

import { type AmbiguousMonomerType, type MonomerItemType, type MonomerOrAmbiguousType, AttachmentPointName } from "../types";
import { Vec2 } from "./vec2";
import { Command } from "./Command";
import type { DrawingEntity } from "./DrawingEntity";
import { PolymerBond } from "./PolymerBond";
import { type KetFileMultitailArrowNode, type LinkerSequenceNode, type RNABase, type RxnArrowMode, BaseMonomer, Chem, Phosphate, Struct, Sugar } from "./";
import type { BondCIP } from "./types";
import { ChainsCollection } from "./monomer-chains/ChainsCollection";
import { Nucleoside } from './Nucleoside';
import { Nucleotide } from './Nucleotide';
import { MACROMOLECULES_BOND_TYPES } from "../../application/editor/tools/types";
import { CanvasMatrix } from "./canvas-matrix/CanvasMatrix";
import { Matrix } from "./canvas-matrix/Matrix";
import { Cell } from "./canvas-matrix/Cell";
import { AmbiguousMonomer } from "./AmbiguousMonomer";
import type { IKetTemplateConnection } from "../../application/formatters";
import { type AtomProperties, Atom } from "./CoreAtom";
import { Bond } from "./CoreBond";
import { MonomerToAtomBond } from "./MonomerToAtomBond";
import { type AtomLabel } from "../constants";
import { HydrogenBond } from "./HydrogenBond";
import type { Chain } from "./monomer-chains/Chain";
import { RxnArrow } from "./CoreRxnArrow";
import { MultitailArrow } from "./CoreMultitailArrow";
import type { KetFileNode } from "../serializers/serializers.types";
import { RxnPlus } from "./CoreRxnPlus";
import type { initiallySelectedType } from "./BaseMicromoleculeEntity";
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;
    connections?: IKetTemplateConnection[];
};
interface MonomerConnectedToSelection {
    monomerFromSelection: BaseMonomer;
    monomerConnectedToSelection: BaseMonomer;
    bond: PolymerBond;
}
export declare class DrawingEntitiesManager {
    monomers: Map<number, BaseMonomer>;
    polymerBonds: Map<number, PolymerBond | HydrogenBond>;
    private readonly bondsMonomersOverlaps;
    atoms: Map<number, Atom>;
    bonds: Map<number, Bond>;
    monomerToAtomBonds: Map<number, MonomerToAtomBond>;
    rxnArrows: Map<number, RxnArrow>;
    multitailArrows: Map<number, MultitailArrow>;
    rxnPluses: Map<number, RxnPlus>;
    micromoleculesHiddenEntities: Struct;
    canvasMatrix?: CanvasMatrix;
    snakeLayoutMatrix?: Matrix<Cell>;
    antisenseMonomerToSenseChain: Map<BaseMonomer, Chain>;
    private nextArrowId;
    private ensureArrowId;
    private resetArrowIdCounter;
    private static normalizeInitiallySelected;
    get bottomRightMonomerPosition(): Vec2;
    get bottomLeftMonomerPosition(): Vec2;
    get selectedEntitiesArr(): DrawingEntity[];
    get selectedEntities(): [number, DrawingEntity][];
    get selectedMonomers(): BaseMonomer[];
    get selectedMicromoleculeEntities(): DrawingEntity[];
    get externalConnectionsToSelection(): MonomerConnectedToSelection[];
    get allEntities(): [number, DrawingEntity][];
    get allEntitiesArray(): DrawingEntity[];
    get hasDrawingEntities(): boolean;
    get hasMonomers(): boolean;
    get allBondsToMonomers(): ([number, PolymerBond] | [number, MonomerToAtomBond])[];
    deleteSelectedEntities(): Command;
    deleteAllEntities(): Command;
    addMonomerChangeModel(monomerItem: MonomerOrAmbiguousType, position: Vec2, _monomer?: BaseMonomer): BaseMonomer | AmbiguousMonomer;
    createMonomer(monomerItem: MonomerOrAmbiguousType, position: Vec2, generateId?: boolean): AmbiguousMonomer | Chem | import("./").Peptide | Phosphate | RNABase | Sugar | import("./").UnresolvedMonomer | import("./").UnsplitNucleotide;
    updateMonomerItem(monomer: BaseMonomer, monomerItemNew: MonomerItemType): BaseMonomer;
    addMonomer(monomerItem: MonomerOrAmbiguousType, position: Vec2, _monomer?: BaseMonomer): Command;
    deleteDrawingEntity(drawingEntity: DrawingEntity, needToDeleteConnectedEntities?: boolean, force?: boolean): Command;
    selectDrawingEntity(drawingEntity: DrawingEntity): Command;
    private selectDrawingEntitiesModelChange;
    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;
    rotateSelectedDrawingEntities(center: Vec2, angleInDegrees: number, isPartialRotation?: boolean): Command;
    flipSelectedDrawingEntities(flipDirection: 'horizontal' | 'vertical'): Command;
    getSelectedEntitiesBoundingBox(): import("./structureBbox").StructureBbox | null;
    getSelectedEntitiesCenter(): Vec2 | null;
    createDrawingEntityMovingCommand(drawingEntity: DrawingEntity, partOfMovementOffset: Vec2, fullMovementOffset?: Vec2): Command;
    createDrawingEntityRedrawCommand(drawingEntityRedrawModelChange: () => DrawingEntity, invertDrawingEntityRedrawModelChange: () => DrawingEntity): Command;
    private deleteMonomerChangeModel;
    deleteMonomer(monomer: BaseMonomer, needToDeleteConnectedBonds?: boolean, force?: boolean): Command;
    modifyMonomerItem(monomer: BaseMonomer, monomerItemNew: MonomerItemType): Command;
    selectIfLocatedInRectangle(rectangleTopLeftPoint: Vec2, rectangleBottomRightPoint: Vec2, previousSelectedEntities: [number, DrawingEntity][], shiftKey?: boolean): Command;
    selectIfLocatedInPolygon(polygonPoints: 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;
    intendToSelectAllConnectedDrawingEntities(startEntity: DrawingEntity): Command;
    cancelIntentionToSelectDrawingEntity(drawingEntity: DrawingEntity): Command;
    cancelIntentionToSelectAllConnectedDrawingEntities(startEntity: DrawingEntity): Command;
    showPolymerBondInformation(polymerBond: PolymerBond): Command;
    hidePolymerBondInformation(polymerBond: PolymerBond): Command;
    hideAllMonomersHoverAndAttachmentPoints(): Command;
    addRnaPresetFromNode: (node: Nucleotide | Nucleoside | LinkerSequenceNode, connections?: IKetTemplateConnection[]) => Command;
    private findGroupTemplateConnection;
    addRnaPreset({ sugar, sugarPosition: _sugarPosition, phosphate, phosphatePosition: _phosphatePosition, rnaBase, rnaBasePosition: _rnaBasePosition, connections, }: RnaPresetAdditionParams): {
        command: Command;
        monomers: BaseMonomer[];
    };
    rearrangeChainModelChange(monomer: BaseMonomer, newPosition: Vec2): BaseMonomer;
    private addRnaOperations;
    private recalculateCanvasMatrixModelChange;
    recalculateCanvasMatrix(chainsCollection?: ChainsCollection, previousSnakeLayoutMatrix?: Matrix<Cell>): Command;
    private calculateSnakeLayoutMatrix;
    private rearrangeSingleMonomerSnakeLayoutNode;
    private rearrangeSugarWithBaseSnakeLayoutNode;
    applySnakeLayout(isSnakeMode: boolean, needRedrawBonds?: boolean, needRepositionMonomers?: boolean, needRecalculateOldAntisense?: boolean, needRepositionMolecules?: boolean): Command;
    private redrawBondsModelChange;
    redrawBonds(): Command;
    isNucleosideAndPhosphateConnectedAsNucleotide(nucleoside: Nucleoside, phosphate: Phosphate): boolean;
    setMicromoleculesHiddenEntities(struct: Struct): void;
    clearMicromoleculesHiddenEntities(): void;
    mergeInto(targetDrawingEntitiesManager: DrawingEntitiesManager): {
        command: Command;
        mergedDrawingEntities: DrawingEntitiesManager;
    };
    filterSelection(): DrawingEntitiesManager;
    centerMacroStructure(): void;
    getCurrentCenterPointOfCanvas(): Vec2;
    getMacroStructureCenter(): Vec2;
    rerenderMolecules(): void;
    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, cip?: BondCIP | null): 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;
    private static antisenseChainBasesMap;
    markMonomerAsAntisense(monomer: BaseMonomer): Command;
    markMonomerAsSense(monomer: BaseMonomer): Command;
    recalculateAntisenseChains(needRecalculateOldAntisense?: boolean): Command;
    get hasAntisenseChains(): boolean;
    static getAntisenseBaseLabel(rnaBaseMonomerOrLabel: RNABase | AmbiguousMonomer | string, isDnaAntisense: boolean): any;
    static createAntisenseNode(node: Nucleoside | Nucleotide, isDnaAntisense: boolean, needAddPhosphate?: boolean): {
        modelChanges: Command;
        node: Nucleotide;
    } | {
        modelChanges: Command;
        node: Nucleoside;
    } | undefined;
    createAntisenseChain(isDnaAntisense: boolean): Command;
    get monomersArray(): BaseMonomer[];
    get polymerBondsArray(): (PolymerBond | HydrogenBond)[];
    get molecules(): BaseMonomer[];
    private checkBondForOverlapsByMonomers;
    detectBondsOverlappedByMonomers(polymerBonds?: Array<PolymerBond | HydrogenBond>): void;
    private deleteRxnArrowModelChange;
    private addRxnArrowModelChange;
    addRxnArrow(type: RxnArrowMode, position: [Vec2, Vec2], height?: number, initiallySelected?: initiallySelectedType, arrowId?: number): Command;
    deleteRxnArrow(rxnArrow: RxnArrow): Command;
    private deleteMultitailArrowModelChange;
    private addMultitailArrowArrowModelChange;
    addMultitailArrow(multitailArrowKetNode: KetFileNode<KetFileMultitailArrowNode>, arrowId?: number): Command;
    deleteMultitailArrow(multitailArrow: MultitailArrow): Command;
    private deleteRxnPlusModelChange;
    private addRxnPlusModelChange;
    addRxnPlus(position: Vec2, initiallySelected?: initiallySelectedType): Command;
    deleteRxnPlus(rxnPlus: RxnPlus): Command;
    selectAllConnectedEntities(startEntity: DrawingEntity): Command;
    private visitAllConnectedEntities;
    getConnectedMolecule(startEntity: DrawingEntity, entitiesToReturn?: Array<typeof Atom | typeof Bond>): (Atom | Bond)[];
    createRotationHistoryCommand(initialPositions: Map<number, Vec2>): Command;
}
export {};