For most organic chemists (or synthetic chemists in general), if you were to ask them which program they use most on a day-to-day basis, there would be one overwhelmingly popular answer: ChemDraw. The ChemBioOffice suite from CambridgeSoft is like the Excel of the chemistry world: a program so good, and so widely used that thinking of a replacement is often considered folly. While the program is supported on both Mac and Windows, Linux support remains elusive, and likely will for a long time.
About two computers ago (how sad that this can actually be understood as a measurement of time), I had my first encounter with Windows Vista. After about a week, I decided to format the computer and give Ubuntu Linux a go. The version out then was Feisty Fawn (7.04), and while I had to tweak a lot of things to get the OS working the way I wanted, it was actually a very positive experience. I was finishing up my second year of undergrad, and hadn’t had too much experience with chemical drawing, so I figured that the plethora of open-source chemical drawing software would be sufficient. In the long run, it turned out I was wrong.
Simply doing a search in the Ubuntu Software Installer for chemical drawing software turns up quite a few results, often with confusingly similar names (Xdrawchem, GChemPaint, JChemPaint, Chemtool, ChemSketch, Marvinsketch, BKChem, to name a few). There has also been a pretty long-standing effort to get ChemDraw to work under Wine, a windows API emulator for use in Linux systems. This seems to have been mostly unsuccessful, but since I haven’t been using Ubuntu for the past two years, my ear hasn’t exactly been to the ground on this issue.
The main problem with most of these open-source replacements for ChemDraw is that, while they have the basic functionality down (i.e. being able to draw simple chemicals) they lack a lot of the flourishes that make ChemDraw such a pleasure to use. For one, none of the programs I’ve tried has templates like ChemDraw’s (where you can simply load an ACS or RSC template and not have to worry about bond lengths/widths, typeset, or font size at all). Some of them even lack curly arrows, meaning that electron pushing is essentially impossible, unless you were to ink them in by hand (which I admit to doing once or twice). Some have template molecules like carbohydrates and amino acids, most don’t. Some support a vast array of image export formats, some don’t. While some of these aren’t hugely important to, say, an undergrad drawing structures for lab reports, they make writing actual papers a joke because the formatting is never right and small features like aligning objects have to be done by hand (#firstworldproblems).
So what’s an Ubuntu-lover to do? The impetus for this post is that I recently got that four-year-old laptop working again, and threw the latest version of Ubuntu on it. In the past four years, you’d think that the chemistry drawing software would have improved by leaps and bounds. Turns out…not so much. However, there is light at the end of the tunnel.
GChemUtils is an ongoing project that is attempted to provide an open-source suite of chemistry software to Linux users. They recently merged the GChemUtils and GChemPaint projects, and so far it looks like they have a fairly good feature set on the go. The program has been actively developed by one very dedicated programmer, with help, since late 2002. Lately, maintenance releases have been coming out about every month or so, and most of the changes are related to bug fixes as opposed to feature expansion, but the program is still getting stronger all the time.
Marvin is another suite that appears to be getting very good. One excellent feature contained in their drawing program, MarvinSketch, is searching through ChemPub and ChemSpider for drawn structures. Marvin has many of the structure editing features of ChemDraw, including (some) templates, cleanup, and valency checkers. It also comes with a powerful set of visualization tools, and even molecular property calculators (which, while not something to depend too heavily upon, can be great first estimates for medicinal chemists).
One big difference between these two programs is the development team behind each. Marvin is backed by ChemAxon, a company dedicated to the development of an array of cross-platform chemistry software. GChemUtils is developed by a total of seven people, and as far as I know has abolutely no corporate backing. As such, Gchemutils could really use some help. Whether or not you have programming experience, their homepage says they are looking for feature testers, web developers, programmers, bug hunters, translators, help with documentation, and even just brainstorming.
So while open-source and Linux-friendly chemistry software development is ongoing and vibrant, what seems to be missing is that little bit of refinement and feature diversity that many open-source projects seem to lack. Unlike programs such as OpenOffice.org, which are almost perfect mimics of the program suites they replace, most of the chemical drawing software I’ve come across on Linux seems to need a push in the right direction. Being a relatively niche market, it’s my guess that a lot of companies aren’t interested in spending time on an open-source program for (organic) chemists who use the least-popular operating system type on the market. But if more weight gets behind these projects, one of the few remaining barriers to Linux adoption could be torn down.