api.ts

/**
 * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
 */

import { Queries, Structure, StructureQuery, StructureSymmetry } from 'mol-model/structure';
import { getAtomsTests } from '../query/atoms';

export enum QueryParamType {
    JSON,
    String,
    Integer,
    Float
}

export interface QueryParamInfo {
    name: string,
    type: QueryParamType,
    description?: string,
    required?: boolean,
    defaultValue?: any,
    exampleValues?: any[],
    validation?: (v: any) => void
}

export interface QueryDefinition<Params = any> {
    name: string,
    niceName: string,
    exampleId: string, // default is 1cbs
    query: (params: any, structure: Structure) => StructureQuery,
    description: string,
    params: QueryParamInfo[],
    structureTransform?: (params: any, s: Structure) => Promise<Structure>,
    '@params': Params
}

export interface AtomSiteSchema {
    label_entity_id?: string,

    label_asym_id?: string,
    auth_asym_id?: string,

    label_comp_id?: string,
    auth_comp_id?: string,
    label_seq_id?: string,
    auth_seq_id?: string,
    pdbx_PDB_ins_code?: string,

    label_atom_id?: string,
    auth_atom_id?: string,
    type_symbol?: string
}

const AtomSiteTestParams: QueryParamInfo = {
    name: 'atom_site',
    type: QueryParamType.JSON,
    description: 'Object or array of objects describing atom properties. Names are same as in wwPDB mmCIF dictionary of the atom_site category.',
    exampleValues: [{ label_comp_id: 'ALA' }, { label_seq_id: 123, label_asym_id: 'A' }]
};

const RadiusParam: QueryParamInfo = {
    name: 'radius',
    type: QueryParamType.Float,
    defaultValue: 5,
    exampleValues: [5],
    description: 'Value in Angstroms.',
    validation(v: any) {
        if (v < 1 || v > 10) {
            throw `Invalid radius for residue interaction query (must be a value between 1 and 10).`;