/** * @file Atom Proxy * @author Alexander Rose * @private */ import { Vector3 } from 'three'; import { NumberArray } from '../types'; import { Elements } from '../structure/structure-constants'; import Structure from '../structure/structure'; import ChainStore from '../store/chain-store'; import ResidueStore from '../store/residue-store'; import AtomStore from '../store/atom-store'; import AtomMap from '../store/atom-map'; import ResidueMap from '../store/residue-map'; import BondProxy from '../proxy/bond-proxy'; import AtomType from '../store/atom-type'; import ResidueType from '../store/residue-type'; import ResidueProxy from './residue-proxy'; import Entity from '../structure/entity'; import BondHash from '../store/bond-hash'; /** * Atom proxy */ declare class AtomProxy { readonly structure: Structure; index: number; chainStore: ChainStore; residueStore: ResidueStore; atomStore: AtomStore; residueMap: ResidueMap; atomMap: AtomMap; /** * @param {Structure} structure - the structure * @param {Integer} index - the index */ constructor(structure: Structure, index?: number); /** * @type {BondHash} */ get bondHash(): BondHash | undefined; /** * Molecular enity * @type {Entity} */ get entity(): Entity; get entityIndex(): number; get modelIndex(): number; get chainIndex(): number; /** * @type {ResidueProxy} */ get residue(): ResidueProxy; get residueIndex(): number; set residueIndex(value: number); /** * Secondary structure code * @type {String} */ get sstruc(): string; /** * Insertion code * @type {String} */ get inscode(): string; /** * Residue number/label * @type {Integer} */ get resno(): number; /** * Chain name * @type {String} */ get chainname(): string; /** * Chain id * @type {String} */ get chainid(): string; /** * @type {ResidueType} */ get residueType(): ResidueType; /** * @type {AtomType} */ get atomType(): AtomType; get residueAtomOffset(): number; /** * Residue name */ get resname(): string; /** * Hetero flag */ get hetero(): number; /** * Atom name */ get atomname(): string; /** * Atomic number */ get number(): number; /** * Element */ get element(): string; /** * Van-der-Waals radius */ get vdw(): number; /** * Covalent radius */ get covalent(): number; /** * X coordinate */ get x(): number; set x(value: number); /** * Y coordinate */ get y(): number; set y(value: number); /** * Z coordinate */ get z(): number; set z(value: number); /** * Serial number */ get serial(): number; set serial(value: number); /** * B-factor value */ get bfactor(): number; set bfactor(value: number); /** * Occupancy value */ get occupancy(): number; set occupancy(value: number); /** * Alternate location identifier */ get altloc(): string; set altloc(value: string); /** * Partial charge */ get partialCharge(): number | null; set partialCharge(value: number | null); /** * Explicit radius */ get radius(): any; set radius(value: any); /** * Formal charge */ get formalCharge(): number | null; set formalCharge(value: number | null); /** * Aromaticity flag */ get aromatic(): number; set aromatic(value: number); get bondCount(): number; /** * Iterate over each bond * @param {function(bond: BondProxy)} callback - iterator callback function * @param {BondProxy} [bp] - optional target bond proxy for use in the callback * @return {undefined} */ eachBond(callback: (bp: BondProxy) => void, bp?: BondProxy): void; /** * Iterate over each bonded atom * @param {function(atom: AtomProxy)} callback - iterator callback function * @param {AtomProxy} [ap] - optional target atom proxy for use in the callback * @return {undefined} */ eachBondedAtom(callback: (ap: AtomProxy) => void, _ap?: AtomProxy): void; /** * Check if this atom is bonded to the given atom, * assumes both atoms are from the same structure * @param {AtomProxy} ap - the given atom * @return {Boolean} whether a bond exists or not */ hasBondTo(ap: AtomProxy): boolean; bondToElementCount(element: Elements): number; hasBondToElement(element: Elements): boolean; /** * If atom is part of a backbone * @return {Boolean} flag */ isBackbone(): boolean; /** * If atom is part of a polymer * @return {Boolean} flag */ isPolymer(): boolean; /** * If atom is part of a sidechin * @return {Boolean} flag */ isSidechain(): boolean; /** * If atom is part of a coarse-grain group * @return {Boolean} flag */ isCg(): boolean; isTrace(): boolean; /** * If atom is part of a hetero group * @return {Boolean} flag */ isHetero(): boolean; /** * If atom is part of a protein molecule * @return {Boolean} flag */ isProtein(): boolean; /** * If atom is part of a nucleic molecule * @return {Boolean} flag */ isNucleic(): boolean; /** * If atom is part of a rna * @return {Boolean} flag */ isRna(): boolean; /** * If atom is part of a dna * @return {Boolean} flag */ isDna(): boolean; /** * If atom is part of a water molecule * @return {Boolean} flag */ isWater(): boolean; /** * If atom is part of an ion * @return {Boolean} flag */ isIon(): boolean; /** * If atom is part of a saccharide * @return {Boolean} flag */ isSaccharide(): boolean; /** * If atom is part of a helix * @return {Boolean} flag */ isHelix(): boolean; /** * If atom is part of a sheet * @return {Boolean} flag */ isSheet(): boolean; /** * If atom is part of a turn * @return {Boolean} flag */ isTurn(): boolean; isBonded(): boolean; /** * If atom is part of a ring * @return {Boolean} flag */ isRing(): boolean; isAromatic(): boolean; isMetal(): boolean; isNonmetal(): boolean; isMetalloid(): boolean; isHalogen(): boolean; isDiatomicNonmetal(): boolean; isPolyatomicNonmetal(): boolean; isAlkaliMetal(): boolean; isAlkalineEarthMetal(): boolean; isNobleGas(): boolean; isTransitionMetal(): boolean; isPostTransitionMetal(): boolean; isLanthanide(): boolean; isActinide(): boolean; getDefaultValence(): number; getValenceList(): number[]; getOuterShellElectronCount(): number; /** * Distance to another atom * @param {AtomProxy} atom - the other atom * @return {Number} the distance */ distanceTo(atom: AtomProxy): number; /** * If connected to another atom * @param {AtomProxy} atom - the other atom * @return {Boolean} flag */ connectedTo(atom: AtomProxy): boolean; /** * Set atom position from array * @param {Array|TypedArray} array - input array * @param {Integer} [offset] - the offset * @return {AtomProxy} this object */ positionFromArray(array: NumberArray, offset?: number): this; /** * Write atom position to array * @param {Array|TypedArray} [array] - target array * @param {Integer} [offset] - the offset * @return {Array|TypedArray} target array */ positionToArray(array?: NumberArray, offset?: number): NumberArray; /** * Write atom position to vector * @param {Vector3} [v] - target vector * @return {Vector3} target vector */ positionToVector3(v: Vector3): Vector3; /** * Set atom position from vector * @param {Vector3} v - input vector * @return {AtomProxy} this object */ positionFromVector3(v: Vector3): this; /** * Add vector to atom position * @param {Vector3} v - input vector * @return {AtomProxy} this object */ positionAdd(v: Vector3 | AtomProxy): this; /** * Subtract vector from atom position * @param {Vector3} v - input vector * @return {AtomProxy} this object */ positionSub(v: Vector3 | AtomProxy): this; /** * Get intra group/residue bonds * @param {Boolean} firstOnly - immediately return the first connected atomIndex * @return {Integer[]|Integer|undefined} connected atomIndices */ getResidueBonds(firstOnly?: boolean): number | number[] | undefined; qualifiedName(noResname?: boolean): string; /** * Clone object * @return {AtomProxy} cloned atom */ clone(): AtomProxy; toObject(): { index: number; residueIndex: number; resname: string; x: number; y: number; z: number; element: string; chainname: string; resno: number; serial: number; vdw: number; covalent: number; hetero: number; bfactor: number; altloc: string; atomname: string; modelIndex: number; }; } export default AtomProxy;