import * as DG from 'datagrok-api/dg';
import { ISeqSplitted } from '../utils/macromolecule/types';
import { ISeqHelper } from '../utils/seq-helper';
export declare function encodeMonomers(col: DG.Column, seqHelper: ISeqHelper): DG.Column | null;
export declare function getMolfilesFromSeq(col: DG.Column, monomersLibObject: any[], seqHelper: ISeqHelper): any[][] | null;
export declare function getMolfilesFromSingleSeq(cell: DG.Cell, monomersLibObject: any[], seqHelper: ISeqHelper): any[][] | null;
export declare function createMomomersMolDict(lib: any[]): {
    [key: string]: string | any;
};
export declare function createJsonMonomerLibFromSdf(table: DG.DataFrame): any;
/** Calculates chemical similarity between reference sequence and list of sequences.
 * Similarity is computed as a sum of monomer similarities on corresponding positions. Monomer similarity is calculated
 * based on Morgan fingerprints.
 * @param {DG.Column<string>[]} positionColumns List of position columns containing monomers.
 * @param {string[]} referenceSequence Reference sequence.
 * @returns {Promise<DG.Column<number>>} Column with similarity values. */
export declare function sequenceChemSimilarity(sequenceCol: DG.Column<string>, referenceSequence: ISeqSplitted, seqHelper: ISeqHelper): Promise<DG.Column<number>>;
export declare function sequenceChemSimilarity(positionColumns: DG.Column<string>[], referenceSequence: ISeqSplitted, seqHelper: ISeqHelper): Promise<DG.Column<number>>;
/** Calculates chemical similarity between each pair of monomers.
 * @param {string[]} monomerSet Set of unique monomers.
 * @returns {Promise<{scoringMatrix: number[][], alphabetIndexes: {[monomerId: string]: number}}>} Ojbect containing similarity scoring matrix and monomer to index mapping. */
export declare function calculateMonomerSimilarity(monomerSet: string[]): Promise<{
    scoringMatrix: number[][];
    alphabetIndexes: {
        [monomerId: string]: number;
    };
}>;
export declare function getMonomerSubstitutionMatrix(monomerSet: string[], fingerprintType?: string): Promise<{
    scoringMatrix: number[][];
    alphabetIndexes: {
        [monomerId: string]: number;
    };
}>;
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