chemplexity/molecules

chemical graph theory library for JavaScript

molecules.js

A chemical graph theory library for JavaScript. Latest demo of molecules.js + d3.js here.

Features

• Import molecules encoded with SMILES chemical line notation.
• Compute various graph matrices of a molecule (e.g. adjacency, degree, distance, Laplacian, Randic, reciprocal).
• Compute several topological indices of a molecule (e.g. Balaban, Harary, Hyper-Wiener, Randic, Wiener).
• Visualize molecules with d3.js force directed graphs.

Getting Started

The Molecules module contains the primary functions for loading, saving, computing graph matrices and computing topological indices.

var Molecules = require('molecules.js');

Introduction

A molecule is a graph comprised of nodes (atoms) and edges (bonds). In molecules.js a molecule is an object with the following schema:

molecule = {
   id : Number,
   name : String,
   atoms : Object,
   bonds : Object,
   properties : {
       mass : Number,
       formula : Object
   } 
}

Loading Molecules

// Create a molecule by parsing a SMILES string 
var molecule = Molecules.load.smiles('NCC(O)O');

// Import a molecule from a JSON file
var molecule = Molecules.load.json(url);

Saving Molecules

// Convert a molecule to JSON format
var data = Molecules.save.json(molecule);

// Convert a molecule to a d3 graph object
var graph = Molecules.save.d3(molecule);

Graph Matrices

// Load a molecule of ethanol ('CCO')
var ethanol = Molecules.load.smiles('CCO');

Adjacency Matrix

// Compute the adjacency matrix of ethanol
var adjacencyMatrix = Molecules.topology.matrix.adjacency(ethanol);

//     C  C  O 
// C [ 0, 1, 0 ]
// C [ 1, 0, 1 ]
// O [ 0, 1, 0 ]

Distance Matrix

// Use the adjacency matrix to compute the distance matrix
var distanceMatrix = Molecules.topology.matrix.distance(adjacencyMatrix);

//     C  C  O
// C [ 0, 1, 2 ]
// C [ 1, 0, 1 ]
// O [ 2, 1, 0 ]

Degree Matrix

// Use the adjacency matrix to compute the degree matrix
var degreeMatrix = Molecules.topology.matrix.degree(adjacencyMatrix);

//     C  C  O
// C [ 1, 0, 0 ] 
// C [ 0, 2, 0 ]
// O [ 0, 0, 1 ]

Reciprocal Matrix

// Use the distance matrix to compute the reciprocal matrix
var reciprocalMatrix = Molecules.topology.matrix.reciprocal(distanceMatrix);

//      C    C    O
// C [ 0.0, 1.0, 0.5 ]
// C [ 1.0, 0.0, 1.0 ]
// C [ 0.5, 1.0, 0.0 ]

Laplacian Matrix

// Use the adjacency and degree matrix to compute the Laplacian matrix
var laplacianMatrix = Molecules.topology.matrix.laplacian(adjacencyMatrix, degreeMatrix);

//      C   C   O
// C [  1, -1,  0 ]
// C [ -1,  2, -1 ]
// C [  0, -1,  1 ]

Randic Matrix

// Use the adjacency and degree matrix to compute the Randic matrix
var randicMatrix = Molecules.topology.matrix.randic(adjacencyMatrix, degreeMatrix);

//       C      C      O
// C [ 0.000, 0.707, 0.000 ]
// C [ 0.707, 0.000, 0.707 ]
// O [ 0.000, 0.707, 0.000 ]

Topological Indices

// Load a molecule of ethanol ('CCO')
var ethanol = Molecules.load.smiles('CCO');

// Compute the following graph matrices
var adjacencyMatrix  = Molecules.topology.matrix.adjacency(ethanol);
var distanceMatrix   = Molecules.topology.matrix.distance(adjacencyMatrix);
var degreeMatrix     = Molecules.topology.matrix.degree(adjacencyMatrix);
var reciprocalMatrix = Molecules.topology.matrix.reciprocal(distanceMatrix);
var randicMatrix     = Molecules.topology.matrix.randic(adjacencyMatrix, degreeMatrix);

Wiener Index

// Use the distance matrix to compute the Wiener index
var wienerIndex = Molecules.topology.index.wiener(distanceMatrix);

// 4.0

Hyper-Wiener Index

// Use the distance matrix to compute the Hyper-Wiener index
var hyperwienerIndex = Molecules.topology.index.hyperwiener(distanceMatrix);

// 5.0

Harary Index

// Use the reciprocal matrix to compute the Harary index
var hararyIndex = Molecules.topology.index.harary(reciprocalMatrix);

// 2.5

Balaban Index

// Use the distance matrix to compute the Balaban index
var balabanIndex = Molecules.topology.index.balaban(distanceMatrix);

// 1.632993

Randic Index

// Use the Randic matrix to compute the Randic index
var randicIndex = Molecules.topology.index.randic(randicMatrix);

// 1.414213

molecules's Issues

Smiles parser fails

c1ccccc1[C@]2(C(=O)N(C)C(N)=[NH+]2)c3cc(ccc3)-c4ccc(cc4)OC

Uncaught TypeError: Cannot read property 'output' of undefined