Depth-First: Tag metamolecular

ChemWriter Now Available for Download

Rich Apodaca — Mon, 14 Jan 2008 10:29:00 +0000

A 2D chemical structure editor is a key component in most cheminformatics systems. With an ever-increasing number of groups using the Web as a cheminformatics platform, the need for a structure editor built specifically around the capabilities and constraints of the Web becomes more apparent.

For the last several months, my company (Metamolecular, LLC) has been developing a 2D structure editor called ChemWriter(TM). It was created specifically to solve the problem of building interactive, chemically-enabled Web applications that look good and load fast.

You can now download a free, fully-functional, non-expiring copy of ChemWriter (the ChemWriter Starter Package) good for development and testing of your chemically-aware Web application. The Metamolecular Company Blog has the details.

ChemWriter, Chemical Structures, and the Web

Rich Apodaca — Tue, 27 Nov 2007 12:09:00 +0000

Of all the components that make up today's cheminformatics systems, the 2D structure editor may be the most widely-used. A 2D structure editor is often a chemist's first and most enduring exposure to cheminformatics, and can be encountered as early as Junior High or High School.

Over time, a good 2D structure editor becomes every bit as important to a chemist as a text editor is to a writer or software developer. At any given ACS organic division symposium, you're likely to find several bench chemists who only casually, if ever, use a 3D molecular modelling program; finding any who don't regularly use a 2D structure editor would be much more challenging.

2D structure editors are ubiquitous. They can be found in one form or another in most cheminformatics systems, ranging from databases, to standalone applications, to property calculators, and even 3D molecular modelling programs.

Despite the importance of structure editors, they don't get much attention among cheminformatics developers. For example, if your bibliography is anything like mine, it contains dozens of papers on molecular descriptors. Yet the number of cheminformatics papers describing the design of ergonomic chemical structure editors is, well, one or maybe two.

About ChemWriter

ChemWriter™ is a new product aimed at making 2D chemical structure editors a lot more interesting, easy to use, and versatile than they have been in the past. Designed specifically as a lightweight, extendable component, ChemWriter is ideal for use in chemically-enabled Web applications.

The second beta version of ChemWriter has recently been released by my company, Metamolecular, LLC. A recent article on the Metamolecular company blog discusses ChemWriter in more detail.

The Structure Editor In-Depth

Because the design and use of 2D chemical structure editors is an unusual subject in cheminformatics, a compilation of articles on the topic from Depth-First and the Metamolecular Web site is provided below. Many of these articles refer to "Firefly", which was ChemWriter's name during early development.

Why the Structure Editor Matters

The Structure Editor: (Forgotten) Link Between Chemistry and Cheminformatics Title says it all.
Four Free 2-D Structure Editors for Web Applications An early look with example code.
Waldorf Salad Why aesthetics matter in chemistry.

Creating ChemWriter

A 2D Chemical Structure Editor for the Web: Embracing Constraints in Firefly Creating remarkable products depends on identifying and embracing constraints.
A Chemical Structure Editor for the Web: Four Screenshots of a Firefly Prototype Some screenshots of an early ChemWriter prototype.
A Chemical Structure Editor for the Web: Firefly's Two Audiences A good structure editor needs to delight both developers and end users.

Using ChemWriter

Open Notebook Science Using InChIMatic ChemWriter in action.
Googling for Molecules with InChIMatic and Firefly One application of InChI using ChemWriter.
Top Ten Best-Selling Drugs Worldwide (2006) - Depth-First Structures courtesy of an early development version of ChemWriter Desktop.
Top Ten Best-Selling Drugs Worldwide With Structures 2006 - Metamolecular ChemWriter can also be used to dynamically render resizable 2D chemical structures in Web pages.
ChemWriter and the Java Deployment Toolkit A simplified method for cross-browser applet deployment using ChemWriter.
Transferring Molecules With ChemWriter Demonstrates how JavaScript can be used to move molecular information into and out of ChemWriter.

Extending ChemWriter

Building a Molecule Preview with Firefly: The Joy of Swing Shows one use for ChemWriter as a Swing GUI component.
Making Your 2D Structures Look Good: Firefly, Styles and Stylesheets Every aspect of ChemWriter's rendering can be customized, as is shown with this early development version of ChemWriter Desktop.
Never Draw the Same Molecule Twice: Viewing Image Metadata Embedding 2D structure information as a molfile in PNG images.
Editable and Searchable 2D Molecular Images Metadata applied in a novel way using a development version of ChemWriter Desktop.

Write Once, Run Anywhere: Simplifying Java Applet Deployment

Rich Apodaca — Tue, 20 Nov 2007 13:31:00 +0000

From the early days, Java has been described by Sun as the "write once, run anywhere" language and platform. And for the most part, Sun has made good on this promise. It's taken some time, but today's Java Virtual Machines (JVMs) enable developers to feel very confident of their code executing as designed (and unmodified) on any computer system. It's easy to forget, but that's a Big Deal.

Unfortunately, one aspect of Java has been saddled with platform-specific issues from the beginning. Ironically, it's the same area for which Java was originally marketed: applets in Web browsers.

The fuzzy boundary between the Web browser and a Java applet is a place where many cross-platform problems can be found. In areas ranging from keyboard focus to state persistence to deployment, developers need to keep on their toes and test on every platform they want to deploy on.

But to be fair, why should we expect all applets to work the same on every browser when even CSS and HTML don't? The "browser wars" exacted a heavy toll on the entire Web user experience that we're only now starting to move past.

As a much-needed step toward making browser applet quirks a lot less interesting, Sun recently introduced its Deployment Toolkit. At its center is a JavaScript library that allows developers to largely forget the differences among browsers when deploying applets on arbitrary clients.

A more technical summary of Sun's Java Deployment Toolkit, including a live example using the ChemWriter™ structure editor can be found on the Metamolecular Company Blog.