/** * A class representing an atom. * * @property {String} element The element symbol of this atom. Single-letter symbols are always uppercase. Examples: H, C, F, Br, Si, ... * @property {Boolean} drawExplicit A boolean indicating whether or not this atom is drawn explicitly (for example, a carbon atom). This overrides the default behaviour. * @property {Object[]} ringbonds An array containing the ringbond ids and bond types as specified in the original SMILE. * @property {String} branchBond The branch bond as defined in the SMILES. * @property {Number} ringbonds[].id The ringbond id as defined in the SMILES. * @property {String} ringbonds[].bondType The bond type of the ringbond as defined in the SMILES. * @property {Number[]} rings The ids of rings which contain this atom. * @property {String} bondType The bond type associated with this array. Examples: -, =, #, ... * @property {Boolean} isBridge A boolean indicating whether or not this atom is part of a bridge in a bridged ring (contained by the largest ring). * @property {Boolean} isBridgeNode A boolean indicating whether or not this atom is a bridge node (a member of the largest ring in a bridged ring which is connected to a bridge-atom). * @property {Number[]} originalRings Used to back up rings when they are replaced by a bridged ring. * @property {Number} bridgedRing The id of the bridged ring if the atom is part of a bridged ring. * @property {Number[]} anchoredRings The ids of the rings that are anchored to this atom. The centers of anchored rings are translated when this atom is translated. * @property {Object} bracket If this atom is defined as a bracket atom in the original SMILES, this object contains all the bracket information. Example: { hcount: {Number}, charge: ['--', '-', '+', '++'], isotope: {Number} }. * @property {Number} plane Specifies on which "plane" the atoms is in stereochemical deptictions (-1 back, 0 middle, 1 front). * @property {Object[]} attachedPseudoElements A map with containing information for pseudo elements or concatinated elements. The key is comprised of the element symbol and the hydrogen count. * @property {String} attachedPseudoElement[].element The element symbol. * @property {Number} attachedPseudoElement[].count The number of occurences that match the key. * @property {Number} attachedPseudoElement[].hyrogenCount The number of hydrogens attached to each atom matching the key. * @property {Boolean} hasAttachedPseudoElements A boolean indicating whether or not this attom will be drawn with an attached pseudo element or concatinated elements. * @property {Boolean} isDrawn A boolean indicating whether or not this atom is drawn. In contrast to drawExplicit, the bond is drawn neither. * @property {Boolean} isConnectedToRing A boolean indicating whether or not this atom is directly connected (but not a member of) a ring. * @property {String[]} neighbouringElements An array containing the element symbols of neighbouring atoms. * @property {Boolean} isPartOfAromaticRing A boolean indicating whether or not this atom is part of an explicitly defined aromatic ring. Example: c1ccccc1. * @property {Number} bondCount The number of bonds in which this atom is participating. * @property {String} chirality The chirality of this atom if it is a stereocenter (R or S). * @property {Number} priority The priority of this atom acording to the CIP rules, where 0 is the highest priority. * @property {Boolean} mainChain A boolean indicating whether or not this atom is part of the main chain (used for chirality). * @property {String} hydrogenDirection The direction of the hydrogen, either up or down. Only for stereocenters with and explicit hydrogen. * @property {Number} subtreeDepth The depth of the subtree coming from a stereocenter. */ declare class Atom { element: any; drawExplicit: any; ringbonds: any; rings: any; bondType: any; branchBond: any; isBridge: any; isBridgeNode: any; originalRings: any; bridgedRing: any; anchoredRings: any; bracket: any; plane: any; attachedPseudoElements: any; hasAttachedPseudoElements: any; hasPseudoElements: any; isDrawn: any; isConnectedToRing: any; neighbouringElements: any; isPartOfAromaticRing: any; bondCount: any; chirality: any; isStereoCenter: any; priority: any; mainChain: any; hydrogenDirection: any; subtreeDepth: any; hasHydrogen: any; /** * The constructor of the class Atom. * * @param {String} element The one-letter code of the element. * @param {String} [bondType='-'] The type of the bond associated with this atom. */ constructor(element: any, bondType?: string); /** * Adds a neighbouring element to this atom. * * @param {String} element A string representing an element. */ addNeighbouringElement(element: any): void; /** * Attaches a pseudo element (e.g. Ac) to the atom. * @param {String} element The element identifier (e.g. Br, C, ...). * @param {String} previousElement The element that is part of the main chain (not the terminals that are converted to the pseudo element or concatinated). * @param {Number} [hydrogenCount=0] The number of hydrogens for the element. * @param {Number} [charge=0] The charge for the element. */ attachPseudoElement(element: any, previousElement: any, hydrogenCount?: number, charge?: number): void; /** * Returns the attached pseudo elements sorted by hydrogen count (ascending). * * @returns {Object} The sorted attached pseudo elements. */ getAttachedPseudoElements(): {}; /** * Returns the number of attached pseudo elements. * * @returns {Number} The number of attached pseudo elements. */ getAttachedPseudoElementsCount(): number; /** * Returns whether this atom is a heteroatom (not C and not H). * * @returns {Boolean} A boolean indicating whether this atom is a heteroatom. */ isHeteroAtom(): boolean; /** * Defines this atom as the anchor for a ring. When doing repositionings of the vertices and the vertex associated with this atom is moved, the center of this ring is moved as well. * * @param {Number} ringId A ring id. */ addAnchoredRing(ringId: any): void; /** * Returns the number of ringbonds (breaks in rings to generate the MST of the smiles) within this atom is connected to. * * @returns {Number} The number of ringbonds this atom is connected to. */ getRingbondCount(): any; /** * Backs up the current rings. */ backupRings(): void; /** * Restores the most recent backed up rings. */ restoreRings(): void; /** * Checks whether or not two atoms share a common ringbond id. A ringbond is a break in a ring created when generating the spanning tree of a structure. * * @param {Atom} atomA An atom. * @param {Atom} atomB An atom. * @returns {Boolean} A boolean indicating whether or not two atoms share a common ringbond. */ haveCommonRingbond(atomA: any, atomB: any): boolean; /** * Check whether or not the neighbouring elements of this atom equal the supplied array. * * @param {String[]} arr An array containing all the elements that are neighbouring this atom. E.g. ['C', 'O', 'O', 'N'] * @returns {Boolean} A boolean indicating whether or not the neighbours match the supplied array of elements. */ neighbouringElementsEqual(arr: any): boolean; /** * Get the atomic number of this atom. * * @returns {Number} The atomic number of this atom. */ getAtomicNumber(): any; /** * Get the maximum number of bonds for this atom. * * @returns {Number} The maximum number of bonds of this atom. */ getMaxBonds(): any; /** * A map mapping element symbols to their maximum bonds. */ static get maxBonds(): { H: number; C: number; N: number; O: number; P: number; S: number; B: number; F: number; I: number; Cl: number; Br: number; }; /** * A map mapping element symbols to the atomic number. */ static get atomicNumbers(): { H: number; He: number; Li: number; Be: number; B: number; b: number; C: number; c: number; N: number; n: number; O: number; o: number; F: number; Ne: number; Na: number; Mg: number; Al: number; Si: number; P: number; p: number; S: number; s: number; Cl: number; Ar: number; K: number; Ca: number; Sc: number; Ti: number; V: number; Cr: number; Mn: number; Fe: number; Co: number; Ni: number; Cu: number; Zn: number; Ga: number; Ge: number; As: number; Se: number; Br: number; Kr: number; Rb: number; Sr: number; Y: number; Zr: number; Nb: number; Mo: number; Tc: number; Ru: number; Rh: number; Pd: number; Ag: number; Cd: number; In: number; Sn: number; Sb: number; Te: number; I: number; Xe: number; Cs: number; Ba: number; La: number; Ce: number; Pr: number; Nd: number; Pm: number; Sm: number; Eu: number; Gd: number; Tb: number; Dy: number; Ho: number; Er: number; Tm: number; Yb: number; Lu: number; Hf: number; Ta: number; W: number; Re: number; Os: number; Ir: number; Pt: number; Au: number; Hg: number; Tl: number; Pb: number; Bi: number; Po: number; At: number; Rn: number; Fr: number; Ra: number; Ac: number; Th: number; Pa: number; U: number; Np: number; Pu: number; Am: number; Cm: number; Bk: number; Cf: number; Es: number; Fm: number; Md: number; No: number; Lr: number; Rf: number; Db: number; Sg: number; Bh: number; Hs: number; Mt: number; Ds: number; Rg: number; Cn: number; Uut: number; Uuq: number; Uup: number; Uuh: number; Uus: number; Uuo: number; }; /** * A map mapping element symbols to the atomic mass. */ static get mass(): { H: number; He: number; Li: number; Be: number; B: number; b: number; C: number; c: number; N: number; n: number; O: number; o: number; F: number; Ne: number; Na: number; Mg: number; Al: number; Si: number; P: number; p: number; S: number; s: number; Cl: number; Ar: number; K: number; Ca: number; Sc: number; Ti: number; V: number; Cr: number; Mn: number; Fe: number; Co: number; Ni: number; Cu: number; Zn: number; Ga: number; Ge: number; As: number; Se: number; Br: number; Kr: number; Rb: number; Sr: number; Y: number; Zr: number; Nb: number; Mo: number; Tc: number; Ru: number; Rh: number; Pd: number; Ag: number; Cd: number; In: number; Sn: number; Sb: number; Te: number; I: number; Xe: number; Cs: number; Ba: number; La: number; Ce: number; Pr: number; Nd: number; Pm: number; Sm: number; Eu: number; Gd: number; Tb: number; Dy: number; Ho: number; Er: number; Tm: number; Yb: number; Lu: number; Hf: number; Ta: number; W: number; Re: number; Os: number; Ir: number; Pt: number; Au: number; Hg: number; Tl: number; Pb: number; Bi: number; Po: number; At: number; Rn: number; Fr: number; Ra: number; Ac: number; Th: number; Pa: number; U: number; Np: number; Pu: number; Am: number; Cm: number; Bk: number; Cf: number; Es: number; Fm: number; Md: number; No: number; Lr: number; Rf: number; Db: number; Sg: number; Bh: number; Hs: number; Mt: number; Ds: number; Rg: number; Cn: number; Uut: number; Uuq: number; Uup: number; Uuh: number; Uus: number; Uuo: number; }; } export declare const getAtomCoefficientForWidth: (atomName: any) => any; export default Atom;