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Smiles Drawer

Smiles Drawer

Current Version: 1.2.0 (Rumble)

If you use this code or application, please cite the original paper published by the Journal of Chemical Information and Modeling: 10.1021/acs.jcim.7b00425

Demo (Canvas)

Demo (SVG)

### Compatibility

All the current versions of the major browsers are supported and the application has been tested on the following browsers (versions):

  • Chrome (68.0.3440.106)
  • Firefox (61.0.1)
  • Edge (42.17134.167.0)
  • Internet Explorer 11
  • Safari (10.1.2)

SmilesDrawer should also run on older versions of all of these browsers, if you experience any problems on older browsers, please open an issue and it will be tested.

Examples

An example using the light theme can be found here, while one using the dark theme can be found here . The colors of SmilesDrawer are completely configurable.

Examples showing molecules from different databases:

A very simple JSFiddle example can be found here. This example shows the SmilesDrawer.apply() functionality which draws the structure for every canvas element with a data-smiles attribute. E.g. <canvas data-smiles="C1CCCCC1"></canvas>

Experimental Features

If you experience problems with the drawing of complex ring systems (including very long bonds), please enable experimental features (see options).

"Installation"

SmilesDrawer is available from the unpkg content delivery network:

https://unpkg.com/smiles-drawer@1.2.0/dist/smiles-drawer.min.js

You can easily get smiles-drawer using yarn:

yarn add smiles-drawer

or you can just download the files from here.

Building Smiles Drawer

If you decide not to use the ready-to-go scripts in dist, you can (edit and) build the project by running:

npm install
gulp

Getting Started

To get a simple input box which lets the user enter a SMILES and then display it in a canvas, the following minimal example is sufficient. In order to have nice consistent font rendering you have to include the droid sans font from google fonts.

<!DOCTYPE html>
<html>
  <head>
    <meta charset="utf-8" />
    <meta http-equiv="x-ua-compatible" content="ie=edge" />
    <title>Smiles Drawer Example</title>
    <meta name="description" content="A minimal smiles drawer example." />
    <meta name="viewport" content="width=device-width, initial-scale=1" />

    <link
      href="https://fonts.googleapis.com/css?family=Droid+Sans:400,700"
      rel="stylesheet"
    />
  </head>
  <body>
    <input id="example-input" name="example-input" />
    <canvas id="example-canvas" width="500" height="500"></canvas>

    <script src="https://unpkg.com/smiles-drawer@1.0.10/dist/smiles-drawer.min.js"></script>
    <script>
      let input = document.getElementById("example-input");
      let options = {};

      // Initialize the drawer to draw to canvas
      let smilesDrawer = new SmilesDrawer.Drawer(options);
      // Alternatively, initialize the SVG drawer:
      // let svgDrawer = new SmilesDrawer.SvgDrawer(options);

      input.addEventListener("input", function() {
        // Clean the input (remove unrecognized characters, such as spaces and tabs) and parse it
        SmilesDrawer.parse(input.value, function(tree) {
          // Draw to the canvas
          smilesDrawer.draw(tree, "example-canvas", "light", false);
          // Alternatively, draw to SVG:
          // svgDrawer.draw(tree, 'output-svg', 'dark', false);
        });
      });
    </script>
  </body>
</html>

See the example folder for a more complete example.

Options

The options are supplied to the constructor as shown in the example above.

let options = { ... };
let smilesDrawer = new SmilesDrawer(options);

The following options are available:

Option Identifier Data Type Default Value
Drawing width width number 500
Drawing height height number 500
Bond thickness bondThickness number 0.6
Bond length bondLength number 15
Short bond length (e.g. double bonds) in percent of bond length shortBondLength number 0.85
Bond spacing (e.g. space between double bonds) bondSpacing number 0.18 * 15
Atom Visualization atomVisualization string ['default', 'balls', 'none'] 'default'
Large Font Size (in pt for elements) fontSizeLarge number 6
Small Font Size (in pt for numbers) fontSizeSmall number 4
Padding padding number 20.0
Use experimental features experimental boolean false
Show Terminal Carbons (CH3) terminalCarbons boolean false
Show explicit hydrogens explicitHydrogens boolean false
Overlap sensitivity overlapSensitivity number 0.42
# of overlap resolution iterations overlapResolutionIterations number 1
Draw concatenated terminals and pseudo elements compactDrawing boolean true
Draw isometric SMILES if available isometric boolean true
Debug (draw debug information to canvas) debug boolean false
Color themes themes object see below

The default options are defined as follows:

{
    width: 500,
    height: 500,
    bondThickness: 0.6,
    bondLength: 15,
    shortBondLength: 0.85,
    bondSpacing: 0.18 * 15,
    atomVisualization: 'default',
    isomeric: true,
    debug: false,
    terminalCarbons: false,
    explicitHydrogens: false,
    overlapSensitivity: 0.42,
    overlapResolutionIterations: 1,
    compactDrawing: true,
    fontSizeLarge: 5,
    fontSizeSmall: 3,
    padding: 20.0,
    experimental: false,
    themes: {
        dark: {
            C: '#fff',
            O: '#e74c3c',
            N: '#3498db',
            F: '#27ae60',
            CL: '#16a085',
            BR: '#d35400',
            I: '#8e44ad',
            P: '#d35400',
            S: '#f1c40f',
            B: '#e67e22',
            SI: '#e67e22',
            H: '#fff',
            BACKGROUND: '#141414'
        },
        light: {
            C: '#222',
            O: '#e74c3c',
            N: '#3498db',
            F: '#27ae60',
            CL: '#16a085',
            BR: '#d35400',
            I: '#8e44ad',
            P: '#d35400',
            S: '#f1c40f',
            B: '#e67e22',
            SI: '#e67e22',
            H: '#222',
            BACKGROUND: '#fff'
        }
    }
};

Usage

An instance of SmilesDrawer is able to draw to multiple targets. Initialize SmilesDrawer once for each set of options (you would initialize two different objects if you were to draw in two different sizes).

let smilesDrawer = new SmilesDrawer.Drawer({ width: 250, height: 250 });

In order to depict a SMILES string it has to be parsed using SmilesDrawer's SMILES parser, which is encapsulated in the static function SmilesDrawer.parse() where the first argument is the SMILES string and the second argument a callback for a successfull parsing. The third argument provides a way to handle errors using a callback.

SmilesDrawer.parse('C1CCCCC1', function (tree) {
    smilesDrawer.draw(tree, 'output-canvas', 'light', false);
}, function (err) {
    console.log(err);
}

The function smilesDrawer.draw() requires two and accepts up to four arguments. The first argument is the parse tree returned by the parse function (through the callback), the second is the id of a HTML canvas element on which the structure will be drawn. The two optional arguments are whether to use the light or dark theme (defaults to 'light') and whether to only compute properties such as ring count, hac, etc. and not depict the structure (defaults to false).

API

The SmilesDrawer object exposes methods that can be used for purposes other than drawing chemical structures.

Method Description Returns
getMolecularFormula() Returns the molcular formula, eg. C22H30N6O4S, of the currently loaded molecule. String

Bridged Rings

Bridged rings are positioned using the Kamada–Kawai algorithm. If there is a bridged ring in the molecule, explicitly defined aromatic rings are not drawn with a circle inside the ring, but with dashed gray lines where double bonds would be.

Contributors

Thank you for contributing: SRI International's CSE group (For the excellent SVG support) ohardy

About

A small, highly performant JavaScript component for parsing and drawing SMILES strings. Released under the MIT license.

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