pdbe-molstar/lib/extensions/complexes/index.d.ts

Molstar implementation for PDBe

/** Helper functions to allow superposition of complexes */
import { Structure } from 'molstar/lib/mol-model/structure';
import { PDBeMolstarPlugin } from '../..';
import { QueryParam } from '../../helpers';
import { SuperpositionResult } from './superpose-by-biggest-chain';
export * as Coloring from './coloring';
export interface LoadComplexSuperpositionParams {
    /** PDB identifier of complex structure */
    pdbId: string;
    /** Assembly identifier */
    assemblyId: string;
    /** Arbitrary string identifier to refer to the newly loaded structure later */
    id?: string;
    /** Duration of camera transition, in milliseconds. Default: 250. Do not use 0 (won't work because of bugs in Molstar), but you can use 1. */
    animationDuration?: number;
    /** Apply coloring to the base structure and newly loaded structure.
     * 'subcomplex' = color the common components by unique entities (UniProt/Rfam accession); color remaining components by base color (gray).
     * 'supercomplex' = color the common components by base color (gray); color additional components in the new structure (supercomplex) by unique entities. */
    coloring?: 'subcomplex' | 'supercomplex' | undefined;
    /** List of Uniprot/Rfam accessions in the base complex. Mandatory when `coloring` is not `undefined`. */
    baseComponents?: string[];
    /** List of Uniprot/Rfam accessions in the newly loaded complex. Mandatory when `coloring` is not `undefined`. */
    otherComponents?: string[];
    /** Base color for coloring "uninteresting" parts of structures (i.e. subcomplexes: additional components, supercomplexes: common components). Default: gray. */
    coreColor?: string;
    /** Color for coloring unmapped additional components for supercomplexes. */
    unmappedColor?: string;
    /** List of colors for coloring unique entities. */
    componentColors?: string[];
    /** Optional specification of which parts of the base complex structure belong to individual Uniprot/Rfam accessions (will be inferred from mmCIF atom_site if not provided) */
    baseMappings?: {
        [accession: string]: QueryParam[];
    };
    /** Optional specification of which parts of the other complex structure belong to individual Uniprot/Rfam accessions (will be inferred from mmCIF atom_site if not provided) */
    otherMappings?: {
        [accession: string]: QueryParam[];
    };
    /** Superposition method */
    method?: 'biggest-matched-chain' | 'molstar-builtin';
}
/** Load a structure, superpose onto the main structure based on Uniprot residue numbers, and optionally apply coloring to show common/additional components. */
export declare function loadComplexSuperposition(viewer: PDBeMolstarPlugin, params: LoadComplexSuperpositionParams): Promise<{
    /** Structure identifier of the newly loaded complex structure, to refer to this structure later */
    id: string;
    /** Status of pairwise superposition ('success' / 'zero-overlap' / 'failed') */
    status: "success" | "zero-overlap" | "failed";
    /** Superposition RMSD and tranform (if status is 'success') */
    superposition: (import("molstar/lib/mol-math/linear-algebra/3d/minimize-rmsd").MinimizeRmsd.Result & {
        nAlignedElements: number;
    }) | undefined;
    /** Function that deletes the newly loaded complex structure */
    delete: () => Promise<void>;
}>;
/** Superpose mobile structure onto static structure, based on Uniprot residue numbers. */
export declare function superposeStructuresByMolstarDefault(staticStruct: Structure, mobileStruct: Structure): SuperpositionResult;