smiles-drawer
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A SMILES drawer and parser. Generate molecular structure depictions in pure JavaScript.
541 lines (511 loc) • 15.1 kB
JavaScript
//@ts-check
const ArrayHelper = require('./ArrayHelper')
const Vertex = require('./Vertex')
const Ring = require('./Ring')
/**
* 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.
*/
class Atom {
/**
* 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, bondType = '-') {
this.element = element.length === 1 ? element.toUpperCase() : element;
this.drawExplicit = false;
this.ringbonds = Array();
this.rings = Array();
this.bondType = bondType;
this.branchBond = null;
this.isBridge = false;
this.isBridgeNode = false;
this.originalRings = Array();
this.bridgedRing = null;
this.anchoredRings = Array();
this.bracket = null;
this.plane = 0;
this.attachedPseudoElements = {};
this.hasAttachedPseudoElements = false;
this.isDrawn = true;
this.isConnectedToRing = false;
this.neighbouringElements = Array();
this.isPartOfAromaticRing = element !== this.element;
this.bondCount = 0;
this.chirality = '';
this.isStereoCenter = false;
this.priority = 0;
this.mainChain = false;
this.hydrogenDirection = 'down';
this.subtreeDepth = 1;
this.hasHydrogen = false;
}
/**
* Adds a neighbouring element to this atom.
*
* @param {String} element A string representing an element.
*/
addNeighbouringElement(element) {
this.neighbouringElements.push(element);
}
/**
* 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, previousElement, hydrogenCount = 0, charge = 0) {
if (hydrogenCount === null) {
hydrogenCount = 0;
}
if (charge === null) {
charge = 0;
}
let key = hydrogenCount + element + charge;
if (this.attachedPseudoElements[key]) {
this.attachedPseudoElements[key].count += 1;
} else {
this.attachedPseudoElements[key] = {
element: element,
count: 1,
hydrogenCount: hydrogenCount,
previousElement: previousElement,
charge: charge
};
}
this.hasAttachedPseudoElements = true;
}
/**
* Returns the attached pseudo elements sorted by hydrogen count (ascending).
*
* @returns {Object} The sorted attached pseudo elements.
*/
getAttachedPseudoElements() {
let ordered = {};
let that = this;
Object.keys(this.attachedPseudoElements).sort().forEach(function (key) {
ordered[key] = that.attachedPseudoElements[key];
});
return ordered;
}
/**
* Returns the number of attached pseudo elements.
*
* @returns {Number} The number of attached pseudo elements.
*/
getAttachedPseudoElementsCount() {
return Object.keys(this.attachedPseudoElements).length;
}
/**
* Returns whether this atom is a heteroatom (not C and not H).
*
* @returns {Boolean} A boolean indicating whether this atom is a heteroatom.
*/
isHeteroAtom() {
return this.element !== 'C' && this.element !== 'H';
}
/**
* 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) {
if (!ArrayHelper.contains(this.anchoredRings, {
value: ringId
})) {
this.anchoredRings.push(ringId);
}
}
/**
* 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() {
return this.ringbonds.length;
}
/**
* Backs up the current rings.
*/
backupRings() {
this.originalRings = Array(this.rings.length);
for (let i = 0; i < this.rings.length; i++) {
this.originalRings[i] = this.rings[i];
}
}
/**
* Restores the most recent backed up rings.
*/
restoreRings() {
this.rings = Array(this.originalRings.length);
for (let i = 0; i < this.originalRings.length; i++) {
this.rings[i] = this.originalRings[i];
}
}
/**
* 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, atomB) {
for (let i = 0; i < atomA.ringbonds.length; i++) {
for (let j = 0; j < atomB.ringbonds.length; j++) {
if (atomA.ringbonds[i].id == atomB.ringbonds[j].id) {
return true;
}
}
}
return false;
}
/**
* 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) {
if (arr.length !== this.neighbouringElements.length) {
return false;
}
arr.sort();
this.neighbouringElements.sort();
for (var i = 0; i < this.neighbouringElements.length; i++) {
if (arr[i] !== this.neighbouringElements[i]) {
return false;
}
}
return true;
}
/**
* Get the atomic number of this atom.
*
* @returns {Number} The atomic number of this atom.
*/
getAtomicNumber() {
return Atom.atomicNumbers[this.element];
}
/**
* Get the maximum number of bonds for this atom.
*
* @returns {Number} The maximum number of bonds of this atom.
*/
getMaxBonds() {
return Atom.maxBonds[this.element];
}
/**
* A map mapping element symbols to their maximum bonds.
*/
static get maxBonds() {
return {
'H': 1,
'C': 4,
'N': 3,
'O': 2,
'P': 3,
'S': 2,
'B': 3,
'F': 1,
'I': 1,
'Cl': 1,
'Br': 1
};
}
/**
* A map mapping element symbols to the atomic number.
*/
static get atomicNumbers() {
return {
'H': 1,
'He': 2,
'Li': 3,
'Be': 4,
'B': 5,
'b': 5,
'C': 6,
'c': 6,
'N': 7,
'n': 7,
'O': 8,
'o': 8,
'F': 9,
'Ne': 10,
'Na': 11,
'Mg': 12,
'Al': 13,
'Si': 14,
'P': 15,
'p': 15,
'S': 16,
's': 16,
'Cl': 17,
'Ar': 18,
'K': 19,
'Ca': 20,
'Sc': 21,
'Ti': 22,
'V': 23,
'Cr': 24,
'Mn': 25,
'Fe': 26,
'Co': 27,
'Ni': 28,
'Cu': 29,
'Zn': 30,
'Ga': 31,
'Ge': 32,
'As': 33,
'Se': 34,
'Br': 35,
'Kr': 36,
'Rb': 37,
'Sr': 38,
'Y': 39,
'Zr': 40,
'Nb': 41,
'Mo': 42,
'Tc': 43,
'Ru': 44,
'Rh': 45,
'Pd': 46,
'Ag': 47,
'Cd': 48,
'In': 49,
'Sn': 50,
'Sb': 51,
'Te': 52,
'I': 53,
'Xe': 54,
'Cs': 55,
'Ba': 56,
'La': 57,
'Ce': 58,
'Pr': 59,
'Nd': 60,
'Pm': 61,
'Sm': 62,
'Eu': 63,
'Gd': 64,
'Tb': 65,
'Dy': 66,
'Ho': 67,
'Er': 68,
'Tm': 69,
'Yb': 70,
'Lu': 71,
'Hf': 72,
'Ta': 73,
'W': 74,
'Re': 75,
'Os': 76,
'Ir': 77,
'Pt': 78,
'Au': 79,
'Hg': 80,
'Tl': 81,
'Pb': 82,
'Bi': 83,
'Po': 84,
'At': 85,
'Rn': 86,
'Fr': 87,
'Ra': 88,
'Ac': 89,
'Th': 90,
'Pa': 91,
'U': 92,
'Np': 93,
'Pu': 94,
'Am': 95,
'Cm': 96,
'Bk': 97,
'Cf': 98,
'Es': 99,
'Fm': 100,
'Md': 101,
'No': 102,
'Lr': 103,
'Rf': 104,
'Db': 105,
'Sg': 106,
'Bh': 107,
'Hs': 108,
'Mt': 109,
'Ds': 110,
'Rg': 111,
'Cn': 112,
'Uut': 113,
'Uuq': 114,
'Uup': 115,
'Uuh': 116,
'Uus': 117,
'Uuo': 118
};
}
/**
* A map mapping element symbols to the atomic mass.
*/
static get mass() {
return {
'H': 1,
'He': 2,
'Li': 3,
'Be': 4,
'B': 5,
'b': 5,
'C': 6,
'c': 6,
'N': 7,
'n': 7,
'O': 8,
'o': 8,
'F': 9,
'Ne': 10,
'Na': 11,
'Mg': 12,
'Al': 13,
'Si': 14,
'P': 15,
'p': 15,
'S': 16,
's': 16,
'Cl': 17,
'Ar': 18,
'K': 19,
'Ca': 20,
'Sc': 21,
'Ti': 22,
'V': 23,
'Cr': 24,
'Mn': 25,
'Fe': 26,
'Co': 27,
'Ni': 28,
'Cu': 29,
'Zn': 30,
'Ga': 31,
'Ge': 32,
'As': 33,
'Se': 34,
'Br': 35,
'Kr': 36,
'Rb': 37,
'Sr': 38,
'Y': 39,
'Zr': 40,
'Nb': 41,
'Mo': 42,
'Tc': 43,
'Ru': 44,
'Rh': 45,
'Pd': 46,
'Ag': 47,
'Cd': 48,
'In': 49,
'Sn': 50,
'Sb': 51,
'Te': 52,
'I': 53,
'Xe': 54,
'Cs': 55,
'Ba': 56,
'La': 57,
'Ce': 58,
'Pr': 59,
'Nd': 60,
'Pm': 61,
'Sm': 62,
'Eu': 63,
'Gd': 64,
'Tb': 65,
'Dy': 66,
'Ho': 67,
'Er': 68,
'Tm': 69,
'Yb': 70,
'Lu': 71,
'Hf': 72,
'Ta': 73,
'W': 74,
'Re': 75,
'Os': 76,
'Ir': 77,
'Pt': 78,
'Au': 79,
'Hg': 80,
'Tl': 81,
'Pb': 82,
'Bi': 83,
'Po': 84,
'At': 85,
'Rn': 86,
'Fr': 87,
'Ra': 88,
'Ac': 89,
'Th': 90,
'Pa': 91,
'U': 92,
'Np': 93,
'Pu': 94,
'Am': 95,
'Cm': 96,
'Bk': 97,
'Cf': 98,
'Es': 99,
'Fm': 100,
'Md': 101,
'No': 102,
'Lr': 103,
'Rf': 104,
'Db': 105,
'Sg': 106,
'Bh': 107,
'Hs': 108,
'Mt': 109,
'Ds': 110,
'Rg': 111,
'Cn': 112,
'Uut': 113,
'Uuq': 114,
'Uup': 115,
'Uuh': 116,
'Uus': 117,
'Uuo': 118
};
}
}
module.exports = Atom;