smiles-drawer
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A SMILES drawer and parser. Generate molecular structure depictions in pure JavaScript.
562 lines (478 loc) • 20.3 kB
JavaScript
//@ts-check
const Graph = require('./Graph')
/** A class encapsulating the functionality to find the smallest set of smallest rings in a graph. */
class SSSR {
/**
* Returns an array containing arrays, each representing a ring from the smallest set of smallest rings in the graph.
*
* @param {Graph} graph A Graph object.
* @returns {Array[]} An array containing arrays, each representing a ring from the smallest set of smallest rings in the group.
*/
static getRings(graph) {
let adjacencyMatrix = graph.getComponentsAdjacencyMatrix();
if (adjacencyMatrix.length === 0) {
return null;
}
let connectedComponents = Graph.getConnectedComponents(adjacencyMatrix);
let rings = Array();
for (var i = 0; i < connectedComponents.length; i++) {
let connectedComponent = connectedComponents[i];
let ccAdjacencyMatrix = graph.getSubgraphAdjacencyMatrix([...connectedComponent]);
let arrBondCount = new Uint16Array(ccAdjacencyMatrix.length);
let arrRingCount = new Uint16Array(ccAdjacencyMatrix.length);
for (var j = 0; j < ccAdjacencyMatrix.length; j++) {
arrRingCount[j] = 0;
arrBondCount[j] = 0;
for (var k = 0; k < ccAdjacencyMatrix[j].length; k++) {
arrBondCount[j] += ccAdjacencyMatrix[j][k];
}
}
// Get the edge number and the theoretical number of rings in SSSR
let nEdges = 0;
for (var j = 0; j < ccAdjacencyMatrix.length; j++) {
for (var k = j + 1; k < ccAdjacencyMatrix.length; k++) {
nEdges += ccAdjacencyMatrix[j][k];
}
}
let nSssr = nEdges - ccAdjacencyMatrix.length + 1;
// console.log(nEdges, ccAdjacencyMatrix.length, nSssr);
// console.log(SSSR.getEdgeList(ccAdjacencyMatrix));
// console.log(ccAdjacencyMatrix);
// If all vertices have 3 incident edges, calculate with different formula (see Euler)
let allThree = true;
for (var j = 0; j < arrBondCount.length; j++) {
if (arrBondCount[j] !== 3) {
allThree = false;
}
}
if (allThree) {
nSssr = 2.0 + nEdges - ccAdjacencyMatrix.length;
}
// All vertices are part of one ring if theres only one ring.
if (nSssr === 1) {
rings.push([...connectedComponent]);
continue;
}
let { d, pe, pe_prime } = SSSR.getPathIncludedDistanceMatrices(ccAdjacencyMatrix);
let c = SSSR.getRingCandidates(d, pe, pe_prime);
let sssr = SSSR.getSSSR(c, d, ccAdjacencyMatrix, pe, pe_prime, arrBondCount, arrRingCount, nSssr);
for (var j = 0; j < sssr.length; j++) {
let ring = Array(sssr[j].size);
let index = 0;
for (let val of sssr[j]) {
// Get the original id of the vertex back
ring[index++] = connectedComponent[val];
}
rings.push(ring);
}
}
return rings;
}
/**
* Creates a printable string from a matrix (2D array).
*
* @param {Array[]} matrix A 2D array.
* @returns {String} A string representing the matrix.
*/
static matrixToString(matrix) {
let str = '';
for (var i = 0; i < matrix.length; i++) {
for (var j = 0; j < matrix[i].length; j++) {
str += matrix[i][j] + ' ';
}
str += '\n';
}
return str;
}
/**
* Returnes the two path-included distance matrices used to find the sssr.
*
* @param {Array[]} adjacencyMatrix An adjacency matrix.
* @returns {Object} The path-included distance matrices. { p1, p2 }
*/
static getPathIncludedDistanceMatrices(adjacencyMatrix) {
let length = adjacencyMatrix.length;
let d = Array(length);
let pe = Array(length);
let pe_prime = Array(length);
var l = 0;
var m = 0;
var n = 0;
var i = length;
while (i--) {
d[i] = Array(length);
pe[i] = Array(length);
pe_prime[i] = Array(length);
var j = length;
while (j--) {
d[i][j] = (i === j || adjacencyMatrix[i][j] === 1) ? adjacencyMatrix[i][j] : Number.POSITIVE_INFINITY;
if (d[i][j] === 1) {
pe[i][j] = [[[i, j]]];
} else {
pe[i][j] = Array();
}
pe_prime[i][j] = Array();
}
}
var k = length;
var j;
while (k--) {
i = length;
while (i--) {
j = length;
while (j--) {
const previousPathLength = d[i][j];
const newPathLength = d[i][k] + d[k][j];
if (previousPathLength > newPathLength) {
var l, m, n;
if (previousPathLength === newPathLength + 1) {
pe_prime[i][j] = [pe[i][j].length];
l = pe[i][j].length
while (l--) {
pe_prime[i][j][l] = [pe[i][j][l].length];
m = pe[i][j][l].length
while (m--) {
pe_prime[i][j][l][m] = [pe[i][j][l][m].length];
n = pe[i][j][l][m].length;
while (n--) {
pe_prime[i][j][l][m][n] = [pe[i][j][l][m][0], pe[i][j][l][m][1]];
}
}
}
} else {
pe_prime[i][j] = Array();
}
d[i][j] = newPathLength;
pe[i][j] = [[]];
l = pe[i][k][0].length;
while (l--) {
pe[i][j][0].push(pe[i][k][0][l]);
}
l = pe[k][j][0].length;
while (l--) {
pe[i][j][0].push(pe[k][j][0][l]);
}
} else if (previousPathLength === newPathLength) {
if (pe[i][k].length && pe[k][j].length) {
var l;
if (pe[i][j].length) {
let tmp = Array();
l = pe[i][k][0].length;
while (l--) {
tmp.push(pe[i][k][0][l]);
}
l = pe[k][j][0].length;
while (l--) {
tmp.push(pe[k][j][0][l]);
}
pe[i][j].push(tmp);
} else {
let tmp = Array();
l = pe[i][k][0].length;
while (l--) {
tmp.push(pe[i][k][0][l]);
}
l = pe[k][j][0].length;
while (l--) {
tmp.push(pe[k][j][0][l]);
}
pe[i][j][0] = tmp
}
}
} else if (previousPathLength === newPathLength - 1) {
var l;
if (pe_prime[i][j].length) {
let tmp = Array();
l = pe[i][k][0].length;
while (l--) {
tmp.push(pe[i][k][0][l]);
}
l = pe[k][j][0].length;
while (l--) {
tmp.push(pe[k][j][0][l]);
}
pe_prime[i][j].push(tmp);
} else {
let tmp = Array();
l = pe[i][k][0].length;
while (l--) {
tmp.push(pe[i][k][0][l]);
}
l = pe[k][j][0].length;
while (l--) {
tmp.push(pe[k][j][0][l]);
}
pe_prime[i][j][0] = tmp;
}
}
}
}
}
return {
d: d,
pe: pe,
pe_prime: pe_prime
};
}
/**
* Get the ring candidates from the path-included distance matrices.
*
* @param {Array[]} d The distance matrix.
* @param {Array[]} pe A matrix containing the shortest paths.
* @param {Array[]} pe_prime A matrix containing the shortest paths + one vertex.
* @returns {Array[]} The ring candidates.
*/
static getRingCandidates(d, pe, pe_prime) {
let length = d.length;
let candidates = Array();
let c = 0;
for (let i = 0; i < length; i++) {
for (let j = 0; j < length; j++) {
if (d[i][j] === 0 || (pe[i][j].length === 1 && pe_prime[i][j] === 0)) {
continue;
} else {
// c is the number of vertices in the cycle.
if (pe_prime[i][j].length !== 0) {
c = 2 * (d[i][j] + 0.5);
} else {
c = 2 * d[i][j];
}
if (c !== Infinity) {
candidates.push([c, pe[i][j], pe_prime[i][j]]);
}
}
}
}
// Candidates have to be sorted by c
candidates.sort(function (a, b) {
return a[0] - b[0];
});
return candidates;
}
/**
* Searches the candidates for the smallest set of smallest rings.
*
* @param {Array[]} c The candidates.
* @param {Array[]} d The distance matrix.
* @param {Array[]} adjacencyMatrix An adjacency matrix.
* @param {Array[]} pe A matrix containing the shortest paths.
* @param {Array[]} pe_prime A matrix containing the shortest paths + one vertex.
* @param {Uint16Array} arrBondCount A matrix containing the bond count of each vertex.
* @param {Uint16Array} arrRingCount A matrix containing the number of rings associated with each vertex.
* @param {Number} nsssr The theoretical number of rings in the graph.
* @returns {Set[]} The smallest set of smallest rings.
*/
static getSSSR(c, d, adjacencyMatrix, pe, pe_prime, arrBondCount, arrRingCount, nsssr) {
let cSssr = Array();
let allBonds = Array();
for (let i = 0; i < c.length; i++) {
if (c[i][0] % 2 !== 0) {
for (let j = 0; j < c[i][2].length; j++) {
let bonds = c[i][1][0].concat(c[i][2][j]);
// Some bonds are added twice, resulting in [[u, v], [u, v]] instead of [u, v].
// TODO: This is a workaround, fix later. Probably should be a set rather than an array, however the computational overhead
// is probably bigger compared to leaving it like this.
for (var k = 0; k < bonds.length; k++) {
if (bonds[k][0].constructor === Array) bonds[k] = bonds[k][0];
}
let atoms = SSSR.bondsToAtoms(bonds);
if (SSSR.getBondCount(atoms, adjacencyMatrix) === atoms.size && !SSSR.pathSetsContain(cSssr, atoms, bonds, allBonds, arrBondCount, arrRingCount)) {
cSssr.push(atoms);
allBonds = allBonds.concat(bonds);
}
if (cSssr.length > nsssr) {
return cSssr;
}
}
} else {
for (let j = 0; j < c[i][1].length - 1; j++) {
let bonds = c[i][1][j].concat(c[i][1][j + 1]);
// Some bonds are added twice, resulting in [[u, v], [u, v]] instead of [u, v].
// TODO: This is a workaround, fix later. Probably should be a set rather than an array, however the computational overhead
// is probably bigger compared to leaving it like this.
for (var k = 0; k < bonds.length; k++) {
if (bonds[k][0].constructor === Array) bonds[k] = bonds[k][0];
}
let atoms = SSSR.bondsToAtoms(bonds);
if (SSSR.getBondCount(atoms, adjacencyMatrix) === atoms.size && !SSSR.pathSetsContain(cSssr, atoms, bonds, allBonds, arrBondCount, arrRingCount)) {
cSssr.push(atoms);
allBonds = allBonds.concat(bonds);
}
if (cSssr.length > nsssr) {
return cSssr;
}
}
}
}
return cSssr;
}
/**
* Returns the number of edges in a graph defined by an adjacency matrix.
*
* @param {Array[]} adjacencyMatrix An adjacency matrix.
* @returns {Number} The number of edges in the graph defined by the adjacency matrix.
*/
static getEdgeCount(adjacencyMatrix) {
let edgeCount = 0;
let length = adjacencyMatrix.length;
var i = length - 1;
while (i--) {
var j = length;
while (j--) {
if (adjacencyMatrix[i][j] === 1) {
edgeCount++;
}
}
}
return edgeCount;
}
/**
* Returns an edge list constructed form an adjacency matrix.
*
* @param {Array[]} adjacencyMatrix An adjacency matrix.
* @returns {Array[]} An edge list. E.g. [ [ 0, 1 ], ..., [ 16, 2 ] ]
*/
static getEdgeList(adjacencyMatrix) {
let length = adjacencyMatrix.length;
let edgeList = Array();
var i = length - 1;
while (i--) {
var j = length;
while (j--) {
if (adjacencyMatrix[i][j] === 1) {
edgeList.push([i, j]);
}
}
}
return edgeList;
}
/**
* Return a set of vertex indices contained in an array of bonds.
*
* @param {Array} bonds An array of bonds. A bond is defined as [ sourceVertexId, targetVertexId ].
* @returns {Set<Number>} An array of vertices.
*/
static bondsToAtoms(bonds) {
let atoms = new Set();
var i = bonds.length;
while (i--) {
atoms.add(bonds[i][0]);
atoms.add(bonds[i][1]);
}
return atoms;
}
/**
* Returns the number of bonds within a set of atoms.
*
* @param {Set<Number>} atoms An array of atom ids.
* @param {Array[]} adjacencyMatrix An adjacency matrix.
* @returns {Number} The number of bonds in a set of atoms.
*/
static getBondCount(atoms, adjacencyMatrix) {
let count = 0;
for (let u of atoms) {
for (let v of atoms) {
if (u === v) {
continue;
}
count += adjacencyMatrix[u][v]
}
}
return count / 2;
}
/**
* Checks whether or not a given path already exists in an array of paths.
*
* @param {Set[]} pathSets An array of sets each representing a path.
* @param {Set<Number>} pathSet A set representing a path.
* @param {Array[]} bonds The bonds associated with the current path.
* @param {Array[]} allBonds All bonds currently associated with rings in the SSSR set.
* @param {Uint16Array} arrBondCount A matrix containing the bond count of each vertex.
* @param {Uint16Array} arrRingCount A matrix containing the number of rings associated with each vertex.
* @returns {Boolean} A boolean indicating whether or not a give path is contained within a set.
*/
static pathSetsContain(pathSets, pathSet, bonds, allBonds, arrBondCount, arrRingCount) {
var i = pathSets.length;
while (i--) {
if (SSSR.isSupersetOf(pathSet, pathSets[i])) {
return true;
}
if (pathSets[i].size !== pathSet.size) {
continue;
}
if (SSSR.areSetsEqual(pathSets[i], pathSet)) {
return true;
}
}
// Check if the edges from the candidate are already all contained within the paths of the set of paths.
// TODO: For some reason, this does not replace the isSupersetOf method above -> why?
let count = 0;
let allContained = false;
i = bonds.length;
while (i--) {
var j = allBonds.length;
while (j--) {
if (bonds[i][0] === allBonds[j][0] && bonds[i][1] === allBonds[j][1] ||
bonds[i][1] === allBonds[j][0] && bonds[i][0] === allBonds[j][1]) {
count++;
}
if (count === bonds.length) {
allContained = true;
}
}
}
// If all the bonds and thus vertices are already contained within other rings
// check if there's one vertex with ringCount < bondCount
let specialCase = false;
if (allContained) {
for (let element of pathSet) {
if (arrRingCount[element] < arrBondCount[element]) {
specialCase = true;
break;
}
}
}
if (allContained && !specialCase) {
return true;
}
// Update the ring counts for the vertices
for (let element of pathSet) {
arrRingCount[element]++;
}
return false;
}
/**
* Checks whether or not two sets are equal (contain the same elements).
*
* @param {Set<Number>} setA A set.
* @param {Set<Number>} setB A set.
* @returns {Boolean} A boolean indicating whether or not the two sets are equal.
*/
static areSetsEqual(setA, setB) {
if (setA.size !== setB.size) {
return false;
}
for (let element of setA) {
if (!setB.has(element)) {
return false;
}
}
return true;
}
/**
* Checks whether or not a set (setA) is a superset of another set (setB).
*
* @param {Set<Number>} setA A set.
* @param {Set<Number>} setB A set.
* @returns {Boolean} A boolean indicating whether or not setB is a superset of setA.
*/
static isSupersetOf(setA, setB) {
for (var element of setB) {
if (!setA.has(element)) {
return false;
}
}
return true;
}
}
module.exports = SSSR;