Open-source chemistry: still on the frontier
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.
To freedom!
I am a big supporter of open-source software. I love me some Firefox, Thunderbird, Gimp and use them regularly on my PC preferentially over IE, Outlook, and Photoshop (price is the big push for the latter. Why would I pay for Photoshop when Gimp does everything I need). I even refurbished an old Gateway tower and run MythTV on Ubuntu as a free DVR.
Still, both my personal laptop and my office computer run Win7. In my mind, there are two big reasons for not switching to Linux. One is a perception (real for some software, imagined for other (OOo)) that I cant ‘do the same things’ on Linux that I can on Windows/Mac. For the casual email/internet/occasional document or spreadsheet user, this is erroneous. Firefox/Thunderbird are major market pieces of software that even windows/mac users have heard about. As you mentioned OO.o has come a long way in the past few years, and the casual word processing user wouldn’t lack any real functionality in the switch. For the specialty user, this becomes more of a problem. As you noted, chemists are one such specialty user. Gamers would be another. Now that PS3s and Xboxes are essentially personal computers anyway I dont know if people regularly game on computers much or not (clearly I’m not a gamer), but I imagine most major computer games are pc/mac only.
For the first reason, most corporations won’t make the switch because they use specialty software. Thus, most end-users won’t even know there’s an option for casual computing at home.
The second big reason not to switch (often frustratingly not discovered til after the switch) is that drivers are often pc/mac only – especially for more exotic hardware (like, uh, my ATT/Uverse wireless router). As I was setting up my MythTV system, it took several weeks of pretty serious back-hacking to get the tuner card/video card/sound card all talking with the OS and playing nice. Unless you’re somewhat fluent in computer language (and Linux language is completely different from the DOS/Basic/HTML languages) you’re up a creek if some piece of hardware you already own doesn’t want to talk with your Linux OS.
I really hope the open-source platforms gain major cultural support. The free-as-in-beer-ness of most software should be a major draw for people tired of paying exorbitant prices for ‘closed’ software (Windows/OS X/Office Suite/etc).
I personally prefer and love ChemSketch. Its free too.
http://download.cnet.com/ACD-ChemSketch-Freeware/3000-2054_4-10591465.html
I find it much easier to use the ChemDraw. But I do load up my full version of ChemDraw every now and then for the more advanced features not available in the free version of ChemSketch (though, they mostly are available in the full version). Got full version of ChemDraw from institution.
@ Azmanam Yes, I’ve run into driver problems before as well. I count myself lucky in a way that I hold onto old electronics, because now everything on my four-year-old Windows laptop is fully supported.
The gaming issue is just one that I don’t think will ever be fully solved. You will always have rogue game developers doing open source stuff (one game that I loved on linux was Tremulous (http://tremulous.net/about/), but for the most part, games are thin on the ground. The best options you have are games through Wine, which is spotty at best (although World of Warcraft does successfully run under wine, as far as I know, which demonstrates at least that demanding applications aren’t necessarily a barrier).
In rereading my comment, I may have sounded down on OSS. I’m definitely not. If I was at all fluent in programming languages (and if I had any free time) I’d so help out on OSS projects.
I remember hearing at some point about a project to bring computing to developing countries in the form of low-cost laptops running linux OS and using flash memory. Did that ever really get off the ground? I could see this as a major entry into the market for linux software.
Have you tried ChemDoodle? It not open source or free, but only $60, and by buying it you are supporting other open source software like ChemDoodle Web Components. Works in Linux.
I used to use ChemSketch back when it was ISISDraw, and I liked it. But then I got a Mac. And I learned to love MarvinSketch, which was actually quite easy because it rocks.
I had problems installing ChemDoodle on Ubuntu. For whatever reason it does not recognize the Java version, even it is the same one the instructions recommend.
Nice article. I’m at a meeting at PNNL in Washington State (as I write) looking at the new chemical tools that are emerging to allow people to collaborate effectively. One of the advantages of the open source applications you mention is that they can easily be integrated with other tools, such as new electronic lab books that are appearing that “understand” chemistry. i.e. it’s not so much that things like Marvinsketch are meant to work on their own, but what can be done with them in other things. This kind of stuff will be very powerful. Chemdraw cannot be so integrated because it’s not open.
All my life I was a windows user, but then I had several serious online attacks from some (chinese?) hacker (windows security is a joke) and after several firewalls, anti-virus, and Microsoft patches I turned to linux several years ago.
Security and productivity are better and I can do stuff that cannot do in Windows (e.g. I can play to my old DOS games under linux, whereas there is compatibility issues in XP-Vista); I can change/configure everything (e.g. I can switch to completely different windows manager or desktop environment suiting my needs, instead being forced to use the given in Windows/Mac); my software is often more powerful than Windows/Mac analogs (e.g. I can manage two different USB modems at once, including automated PINS entry, which is not possible with the drivers/software that the modems give for Windows/Mac), GIMP has filters that are beyond Photoshop CS capabilities…
I have developed packages for an Unicode extension of LaTeX and abandoned Word and its limitations…
I have dual boot and I only start Windows for using a ‘legacy’ software for a Canon Printer (I did not try to search equivalent for linux but my guess is that there is not), which I use three or four times in a year.
It is curious that someone said that a big reason not to switch to linux is because of lack of drivers support [1]… Precisely this is the reason which most of business continue using the old Windows XP (because the lack of Vista and Windows 7 drivers for their ‘old’ machines)! [2]
[1] In rigor, there is not ‘drivers’ for linux (not in the Windows sense), because devices are supported in linux kernel and so far as I know “ATT UVerse Routers” are.
[2] http://en.wikipedia.org/wiki/Criticism_of_Windows_Vista
Of course, I can print docs, labels, photos… under linux. The Special Canon software that I alluded to is for making printable CD-DVDs using the Canon special CD/DVD printing tray.
Note also that high-performance computational chemistry is done with Unix/Linux not under Windows:
https://www.wiki.ed.ac.uk/display/EaStCHEMresearchwiki/Introduction+to+Computational+Chemistry
http://www.chemistry.montana.edu/facilities/computational.php
http://www.ncsa.illinois.edu/UserInfo/Resources/Software/CHEM/
Another list of chemical software for linux:
http://www.redbrick.dcu.ie/~noel/linux4chemistry/
psi*psi, I don’t think ChemSketch was ever ISIS draw – are you perhaps getting confused with Symyx (or similar)