molstar
Version:
A comprehensive macromolecular library.
91 lines (90 loc) • 3.97 kB
TypeScript
/**
* Copyright (c) 2017-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Mat3 } from '../linear-algebra/3d/mat3.js';
import { Mat4 } from '../linear-algebra/3d/mat4.js';
import { Vec3 } from '../linear-algebra/3d/vec3.js';
interface SymmetryOperator {
/** Operator name, e.g. 1_555, ASM_1 */
readonly name: string;
/** Canonical operator name, must follow symmetry instance naming rules (https://molstar.org/mol-view-spec-docs/selectors/#instance_id).
* E.g. 1_555, ASM-X0-5 */
readonly instanceId: string;
readonly assembly?: {
/** pointer to `pdbx_struct_assembly.id` or empty string */
readonly id: string;
/** pointers to `pdbx_struct_oper_list.id` or empty list */
readonly operList: string[];
/** (arbitrary) unique id of the operator to be used in suffix */
readonly operId: number;
};
/** pointer to `struct_ncs_oper.id` or -1 */
readonly ncsId: number;
readonly hkl: Vec3;
/** spacegroup symmetry operator index, -1 if not applicable */
readonly spgrOp: number;
/** unique (external) key, -1 if not available */
readonly key: number;
readonly matrix: Mat4;
/** cache the inverse of the transform */
readonly inverse: Mat4;
/** optimize the identity case */
readonly isIdentity: boolean;
/**
* Suffix based on operator type.
* - Assembly: _assembly.operId
* - Crystal: -op_ijk
* - ncs: _ncsId
*/
readonly suffix: string;
}
declare namespace SymmetryOperator {
const DefaultName = "1_555";
const Default: SymmetryOperator;
const RotationTranslationEpsilon = 0.005;
type CreateInfo = {
assembly?: SymmetryOperator['assembly'];
ncsId?: number;
hkl?: Vec3;
spgrOp?: number;
key?: number;
instanceId?: string;
};
function create(name: string, matrix: Mat4, info?: CreateInfo | SymmetryOperator): SymmetryOperator;
/** Create spacegroup symmetry operator name, e.g. getSymmetryOperatorName(0, 0, 0, 0) -> '1_555' */
function getSymmetryOperatorName(spgrOp: number, i: number, j: number, k: number): string;
/** Create assembly symmetry operator name, e.g. getAssemblyOperatorName(['X0', '5']) -> 'X0-5' */
function getAssemblyOperatorName(operatorIds: string[]): string;
function checkIfRotationAndTranslation(rot: Mat3, offset: Vec3): boolean;
function ofRotationAndOffset(name: string, rot: Mat3, offset: Vec3, ncsId?: number): SymmetryOperator;
function lerpFromIdentity(out: Mat4, op: SymmetryOperator, t: number): Mat4;
function slerp(out: Mat4, src: Mat4, tar: Mat4, t: number): Mat4;
/**
* Apply the 1st and then 2nd operator. ( = second.matrix * first.matrix).
* Keep `name`, `assembly`, `ncsId`, `hkl` and `spgrOpId` properties from second.
*/
function compose(first: SymmetryOperator, second: SymmetryOperator): SymmetryOperator;
interface CoordinateMapper<T extends number> {
(index: T, slot: Vec3): Vec3;
}
interface ArrayMapping<T extends number> {
readonly coordinates: Coordinates;
readonly operator: SymmetryOperator;
invariantPosition(this: ArrayMapping<T>, i: T, s: Vec3): Vec3;
position(this: ArrayMapping<T>, i: T, s: Vec3): Vec3;
x(this: ArrayMapping<T>, index: T): number;
y(this: ArrayMapping<T>, index: T): number;
z(this: ArrayMapping<T>, index: T): number;
readonly r: (this: ArrayMapping<T>, index: T) => number;
}
interface Coordinates {
x: ArrayLike<number>;
y: ArrayLike<number>;
z: ArrayLike<number>;
}
function createMapping<T extends number>(operator: SymmetryOperator, coords: Coordinates, radius?: ((index: T) => number)): ArrayMapping<T>;
}
export { SymmetryOperator };