olorenrenderer

v1.0.0-c

Published

2 years ago

Render structures; built ontop of smilesDrawer which is licensed under the MIT license

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olorenai

olorenrenderer is a fork of smilesDrawer.

It is meant for us to be able to release our modifications of smilesDrawer onto CDNs as well as to release them under AGPL3.

A substantial part of the codebase is from smilesDrawer which is available under an MIT license. All code written by Oloren AI is given under the AGPL-3.0 license.

Smiles Drawer

Current Version: 2.0.1

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

SmilesDrawer 2.0 is out!

And it now also draws reactions, comes with many new teams and has a cool new website:

smilesdrawer.rocks

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/[email protected]/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/[email protected]/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