Updated readme

reymond-group · Aug 28, 2018 · 7d89e47 · 7d89e47
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-![Smiles Drawer](https://github.com/reymond-group/smilesDrawer/blob/master/logo.png?raw=true)
-# Smiles Drawer
-Current Version: 1.0.9 ([Ballroom Blitz](https://www.youtube.com/watch?v=ewFBuYHldeY))
-
-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](http://dx.doi.org/10.1021/acs.jcim.7b00425)
-
-<img src="http://doc.gdb.tools/smilesDrawer/structures.png"></img>
-
-<h3><a href="http://doc.gdb.tools/smilesDrawer/sd/example/index_light.html">Demo</a></h3>
-
-### Examples
-An example using the light theme can be found [here](http://doc.gdb.tools/smilesDrawer/sd/example/index_light.html), while one using the dark theme can be found [here](http://doc.gdb.tools/smilesDrawer/sd/example/index.html) . The colors of SmilesDrawer are completely configurable.
-
-Examples showing molecules from different databases:
-- [Drugbank](http://doc.gdb.tools/smilesDrawer/sd/test/browser.html?set=drugbank)
-- [GDB-17](http://doc.gdb.tools/smilesDrawer/sd/test/browser.html?set=gdb17)
-- [FDB-17](http://doc.gdb.tools/smilesDrawer/sd/test/browser.html?set=fdb)
-- [SureChEMBL](http://doc.gdb.tools/smilesDrawer/sd/test/browser.html?set=schembl)
-- [ChEMBL](http://doc.gdb.tools/smilesDrawer/sd/test/browser.html?set=chembl)
-
-A very simple JSFiddle example can be found [here](https://jsfiddle.net/zjdtkL57/1/). 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>`
-### "Installation"
-SmilesDrawer is available from the unpkg content delivery network:
-```
-https://unpkg.com/smiles-drawer@1.0.2/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:
-```bash
-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.
-```html
-<!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@1.0.2/dist/smiles-drawer.min.js"></script>
-        <script>
-            let input = document.getElementById('example-input');
-            let options = {};
-            
-            // Initialize the drawer
-            let smilesDrawer = new SmilesDrawer.Drawer(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);
-                });
-            });
-        </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.
-```javascript
-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 |
-| 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:
-```javascript
-{
-    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,
-    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).
-
-```javascript
-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.
-
-```javascript
-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.
-
-### [Documentation](/doc/all.md)
-The documentation can be found in the docs folder. A markdown version is available [here](/doc/all.md).
-
-### Contributors
-Thank you for contributing:
-[ohardy](https://github.com/ohardy)
-=======
 ![Smiles Drawer](https://github.com/reymond-group/smilesDrawer/blob/master/logo.png?raw=true)
 # Smiles Drawer
 Current Version: 1.0.10 ([Ballroom Blitz](https://www.youtube.com/watch?v=ewFBuYHldeY))
@@ -207,6 +8,16 @@ If you use this code or application, please cite the original paper published by
 
 <h3><a href="http://doc.gdb.tools/smilesDrawer/sd/example/index_light.html">Demo</a></h3>
 
+### 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](http://doc.gdb.tools/smilesDrawer/sd/example/index_light.html), while one using the dark theme can be found [here](http://doc.gdb.tools/smilesDrawer/sd/example/index.html) . The colors of SmilesDrawer are completely configurable.
 
@@ -394,4 +205,3 @@ The documentation can be found in the docs folder. A markdown version is availab
 ### Contributors
 Thank you for contributing:
 [ohardy](https://github.com/ohardy)
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