import * as DG from 'datagrok-api/dg';
import { RDModule } from '@datagrok-libraries/chem-meta/src/rdkit-api';
import { ALPHABET } from '../utils/macromolecule/consts';
import { IMonomerLib, IMonomerLibBase, Monomer } from '../types/monomer-library';
import { Bonds, MolGraph, MonomerMolGraphMap, NucleotideRole } from './types';
import { ISeqHelper, ToAtomicLevelRes } from '../utils/seq-helper';
import { ISeqMonomer, PolymerType } from '../helm/types';
/** Convert Macromolecule column into Molecule column storing molfile V3000 with the help of a monomer library
 * @param {DG.DataFrame} df - DataFrame containing the column to be converted
 * @param {DG.Column} seqCol - Column containing the macromolecule sequence
 * @param {IMonomerLib} monomerLib - Monomer library
 */
export declare function _toAtomicLevel(df: DG.DataFrame, seqCol: DG.Column<string>, monomerLib: IMonomerLib, seqHelper: ISeqHelper, rdKitModule: RDModule): Promise<ToAtomicLevelRes>;
/** Get jagged array of monomer symbols for the dataframe
 * @param {DG.Column} macroMolCol - Column with macro-molecules
 * @return {string[]} - Jagged array of monomer symbols for the dataframe */
export declare function getMonomerSequencesArray(macroMolCol: DG.Column<string>, seqHelper: ISeqHelper): ISeqMonomer[][];
/** Get a mapping of monomer symbols to MolGraph objects. Notice, the
 * transformation from molfile V2000 to V3000 takes place,
 * with the help of async function call from Chem (RdKit module)
 * @param {ISeqMonomer[][]} monomerSequencesArray - Jagged array of monomer symbols for the dataframe
 * @param {Array} rolesArray - Per-row NucleotideRole tags (undefined for legacy bases-only rows)
 * @param {PolymerType} polymerType - Polymer type
 * @param {ALPHABET} alphabet - Alphabet
 * @param {IMonomerLibBase} monomerLib - Monomer library
 * @param {RDModule} rdKitModule - RDKit module
 * @return {MonomerMolGraphMap} - Mapping of monomer symbols to MolGraph objects */
export declare function getMonomersDictFromLib(monomerSequencesArray: ISeqMonomer[][], rolesArray: (NucleotideRole[] | undefined)[], polymerType: PolymerType, alphabet: ALPHABET, monomerLib: IMonomerLibBase, rdKitModule: RDModule): MonomerMolGraphMap;
/** Parse element symbols for R-groups from the HELM monomer library R-group field
 * @param {any[]} rGroupObjList - R-group object list
 * @return {Map<number, number>} - Cap group index map*/
export declare function parseCapGroups(rGroupObjList: any[]): string[];
/** V2000 to V3000 converter
 * @param {string} molfileV2K - V2000 molfile
 * @param {any} moduleRdkit - RDKit module
 * @return {string} - V3000 molfile*/
export declare function convertMolfileToV3K(molfileV2K: string, moduleRdkit: any): string;
/** fixes the r lines of the molblock. rdkit sometimes gives v2000 with weird numbers in r atom lines,
 * that can be interpreted as isotopes or cause downstream weirdness
 * @param {string} molfileV2K
 * @return {string} */
export declare function fixV2000MolfileRAtomLines(molfileV2K: string): string;
/** Parse V3000 bond block and construct the Bonds object
 * @param {string} molfileV3K - V3000 molfile
 * @param {number} bondCount - Number of bonds
 * @return {Bonds} - Bonds object*/
export declare function parseBondBlock(molfileV3K: string, bondCount: number): Bonds;
/** Constructs mapping of r-group nodes to default capGroups, all numeration starting from 1.
 * According to https://pubs.acs.org/doi/10.1021/ci3001925, R1 and R2 are the chain extending attachment points,
 * while R3 is the branching attachment point.
 * @param {string} molfile - V2000 or V3000 molfile
 * @return {Map<number, number>} - Map of r-group nodes to default capGroups*/
export declare function parseCapGroupIdxMap(molfile: string): Map<number, number>;
export declare function parseCapGroupIdxMapV2K(molfileV2K: string): Map<number, number>;
export declare function parseCapGroupIdxMapV3K(molfileV3K: string): Map<number, number>;
export declare function parseAtomAndBondCounts(molfileV3K: string): {
    atomCount: number;
    bondCount: number;
};
export declare function convertMolGraphToMolfileV3K(molGraph: MolGraph): string;
export declare function getSymbolToCappedMolfileMap(monomersLibList: any[]): Promise<Map<string, string> | undefined>;
/** Get the V3K molfile corresponding to the capped Monomer (default cap groups)
 * @param {Monomer} monomer
 * @return {string} V3K molfile*/
export declare function capPeptideMonomer(monomer: Monomer): string;
//# sourceMappingURL=to-atomic-level.d.ts.map