import { MinimizeRmsd } from 'Molstar/mol-math/linear-algebra/3d/minimize-rmsd';
import { ElementIndex, ResidueIndex } from 'Molstar/mol-model/structure/model/indexing';
import { StructureElement } from 'Molstar/mol-model/structure/structure/element';
import { Structure } from 'Molstar/mol-model/structure';
import { Unit } from 'Molstar/mol-model/structure/structure/unit';
export interface AlignmentResultEntry {
    transform: MinimizeRmsd.Result;
    pivot: number;
    other: number;
}
export interface AlignmentResult {
    entries: AlignmentResultEntry[];
    zeroOverlapPairs: [number, number][];
    failedPairs: [number, number][];
}
type IncludeResidueTest = (traceElementOrFirstAtom: StructureElement.Location<Unit.Atomic>, residueIndex: ResidueIndex, startIndex: ElementIndex, endIndex: ElementIndex) => boolean;
export declare function alignAndSuperposeWithSIFTSMapping(structures: Structure[], options?: {
    traceOnly?: boolean;
    includeResidueTest?: IncludeResidueTest;
    applyTestIndex?: number[];
}): AlignmentResult;
export {};