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README.md

WebMolKit

Cheminformatics toolkit built with TypeScript & jQuery. Can be used to carry out some fairly sophisticated cheminformatics tasks on a contemporary web browser, such as rendering molecules for display, format conversions, calculations, interactive sketching, among other things.

License

Copyright © 2010-2016 Molecular Materials Informatics, Inc.

http://molmatinf.com

All rights reserved

  • General availability: The WebMolKit library may be used by anyone under the terms set by the general Gnu Public License (v3.0). The synopsis of this license is that if you use any part of the source code in your own project, you are contractually bound to make the entire project available under a similar license whenever you distribute it, i.e. it's the viral version of the GPL. Not to be confused with the lesser version (LGPL). Also, if you are considering asserting software patents, you'd best read the GPL v3.0 terms very carefully.

  • Special exception 1: An exception to the default licensing is made for Collaborative Drug Discovery, Inc (CDD). CDD is permitted to use this toolkit under the terms of the Apache License 2.0, which is a non-viral license. This exception applies to any version of the toolkit in which this notice appears, i.e. if this exception is ever removed, then CDD may continue to use the version immediately prior to its removal, and is permitted to fork the code under the terms of the Apache License.

  • Special exception 2: An exception to the default licensing is made for Collaborations Pharmaceuticals, Inc (CP). CP is permitted to use this toolkit under the terms of the Apache License 2.0, which is a non-viral license. This exception applies to any version of the toolkit in which this notice appears, i.e. if this exception is ever removed, then CP may continue to use the version immediately prior to its removal, and is permitted to fork the code under the terms of the Apache License.

  • If the copyright owner adds additional exceptions in later releases, they will take effect as of that version.

  • Owner availability: The copyright owner, Molecular Materials Informatics, Inc., can and will exercise the liberty of using this toolkit in proprietary and/or open source software.

Codebase

The framework is written in TypeScript. It requires the TypeScript compiler (tsc) to cross-compile into JavaScript. All development has been done using Visual Studio Code.

Prior to doing anything with the codebase, it needs to be compiled into JavaScript:

$ tsc
$ ls bin
	jquery.js
	webmolkit-build.js
	webmolkit-build.js.map

The compilation creates the file bin/webmolkit-build.js. Once this is generated, the file can be used in a runtime context.

Uses

The framework is designed for use on a standard HTML page and under the NodeJS/Electron framework.

For anyone writing code in TypeScript, the method of choice is to include the src/**.ts files within the main project, and access the classes and functions within the WebMolKit namespace. For using with raw JavaScript, or other derivatives, the cross-compiled output file bin/webmolkit-build.js contains all of the functionality. The class and function names are all the same as for integrating with TypeScript, but the without helpful typing information.

Adding the sketcher to a web page is demonstrated in the example file val/html/sketcher.html.

Importing the necessary content into a web page can be most easily done by inserting lines into the header section of the HTML page, e.g.

<head>
	<script src="../../bin/jquery.js" type="text/javascript"></script>
	<script src="../../bin/webmolkit-build.js" type="text/javascript"></script>
	...
</head>

Note that it is necessary to make sure the JQuery library is also included.

Embedding a blank sketcher instance on the page can be done as:

<script>
	var url = window.location.href.substring(0, window.location.href.lastIndexOf('/'));
	WebMolKit.initWebMolKit(url + '../../../res');

	var mol = WebMolKit.Molecule.fromString($('#moldata').text());

	var sketcher = new WebMolKit.Sketcher();
	sketcher.setSize(800, 700);
	sketcher.defineMolecule(mol);
	let proxy = new WebMolKit.ClipboardProxyWeb();
	sketcher.defineClipboard(proxy);
	sketcher.setup(() => sketcher.render($('#sketcher')));
</script>

There are several things going on here. The first step is to make sure the framework knows where to find its own resources, by calling WebMolKit.initWebMolKit. The example above constructs a URL relative to the current location. The content that it needs to find is located in the res subdirectory of the repository, and contains information such as icons and structure templates.

Starting with a current molecule is optional: the default is blank. To prepopulate, a Molecule object must first be created. The example above creates an instance by unpacking a string that conforms to the SketchEl format, which is the native default. Calling the defineMolecule method for the sketcher class makes that the current molecule.

A sketcher instance requires several other pieces of information, such as predefined size. It also wants something called a "clipboard proxy", which is a way of intermediating between the two very different styles of clipboard access for web vs. desktop targets, and also to provide a way to capture/release clipboard access under scenarios like dialog box creation. For a simple web page, though, the boilerplate code shown above will suffice.

The final rendering and activation of the sketcher is done by chaining the setup and render methods. There is some resource loading that gets done in between the setup and rendering steps, hence the callback.

That is all it takes to embed a sketcher. Interacting with the widget is fairly straightforward, and is done by calling public functions, e.g. getMolecule, defineMolecule, performCopy, etc.

Feedback

If you have any questions, comments or inquiries, feel free to write to aclark@molmatinf.com. Serious people welcome; trolls, spammers and haters not so much.

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Web Molecular Toolkit: cheminformatics functionality in TypeScript + jQuery

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