/**
 * Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
 */
import { Table } from '../../mol-data/db.js';
import { mmCIF_Schema } from '../../mol-io/reader/cif/schema/mmcif.js';
import { Mat4, Vec3 } from '../../mol-math/linear-algebra.js';
import { MolstarBondSiteTypeId, MolstarBondSiteValueOrder } from '../../mol-model/structure/export/categories/molstar_bond_site.js';
import { JSONCifDataBlock } from './model.js';
type Atom = Partial<Table.Row<mmCIF_Schema['atom_site']>>;
export interface JSONCifLigandGraphBondProps {
    value_order: MolstarBondSiteValueOrder | undefined;
    type_id: MolstarBondSiteTypeId | undefined;
}
export interface JSONCifLigandGraphAtom {
    key: string;
    final_id: number | undefined;
    row: Atom;
}
export interface JSONCifLigandGraphBond {
    atom_1: JSONCifLigandGraphAtom;
    atom_2: JSONCifLigandGraphAtom;
    props: JSONCifLigandGraphBondProps;
}
export interface JSONCifLigandGraphData {
    block: JSONCifDataBlock;
    atomIdRemapping: Map<number, number>;
    addedAtomIds: number[];
    removedAtomIds: number[];
}
export declare class JSONCifLigandGraph {
    private data;
    readonly atoms: JSONCifLigandGraphAtom[];
    readonly atomsByKey: Map<string, JSONCifLigandGraphAtom>;
    readonly atomsById: Map<number, JSONCifLigandGraphAtom>;
    /** Bond with the provided key is always atom_1 */
    readonly bondByKey: Map<string, JSONCifLigandGraphBond[]>;
    readonly removedAtomIds: Set<number>;
    getAtomAtIndex(index: number): JSONCifLigandGraphAtom;
    getAtom(atomOrId: number | JSONCifLigandGraphAtom): JSONCifLigandGraphAtom | undefined;
    getBonds(atomOrId: number | JSONCifLigandGraphAtom): JSONCifLigandGraphBond[];
    getAtomCoords(atomOrId: number | JSONCifLigandGraphAtom, out?: Vec3): Vec3;
    getBondDirection(bond: JSONCifLigandGraphBond, out?: Vec3): Vec3;
    modifyAtom(atomOrId: number | JSONCifLigandGraphAtom, data: Omit<Atom, 'id'>): void;
    addAtom(data: Omit<Atom, 'id'>): JSONCifLigandGraphAtom;
    removeAtom(atomOrId: number | JSONCifLigandGraphAtom): void;
    addOrUpdateBond(atom1: number | JSONCifLigandGraphAtom, atom2: number | JSONCifLigandGraphAtom, props: JSONCifLigandGraphBondProps): void;
    removeBond(atom1: number | JSONCifLigandGraphAtom, atom2: number | JSONCifLigandGraphAtom): void;
    private transformAtomCoords;
    transformCoords(xform: Mat4, atoms?: (number | JSONCifLigandGraphAtom)[]): void;
    traverse<S>(atomOrId: number | JSONCifLigandGraphAtom, how: 'dfs' | 'bfs', state: S, visitAtom: (atom: JSONCifLigandGraphAtom, state: S, pred: JSONCifLigandGraphBond | undefined, graph: JSONCifLigandGraph) => void): S;
    getData(): JSONCifLigandGraphData;
    constructor(data: JSONCifDataBlock);
}
export {};