GChemPaintI am planning on writing a review on different 2D chemical structure editor (CSE) programs that are available to Linux (there is one comprehensive article on this, but it's a bit outdated). In the mean time, I want to say that most of them have made tremendous progress in the last year or so. Big thanks to all the developers!

Here in this article, I want to focus on GChempaint, one of the most prominent CSE's of the day IMHO. The last time I checked, the official deb package for Ubuntu is version 0.6.x. However, thanks to the developer of GChempaint, the current version now is 0.8.3 at the time of writing. One caveat of GChempaint is that it is somewhat difficult to install it from scratch. So here is how:

1. Install Dependencies from Aptitude


sudo aptitude install libglade2-dev libgnomeprintui2.2-dev libgtkglext1-dev gcc libgsf-1-dev libxml++2.6-dev libxml++2.6-dev libpcre3-dev libgnomeui-dev libgettext-ruby1.8 libgettext-ruby-util libintl-gettext-ruby build-essential libgoffice-0-dev


2. Download and Install Openbabel


Get the latest OpenBabel from here and place the .tar.gz file in an appropriate directory within your home directory. I use /home/me/Software/.

First, untar it. At the time of writing, the latest is 2.1.1.
Then go to that directory.
tar -xvzf openbabel-2.1.1.tar.gz
cd openbabel-2.1.1

Now you should have all the dependencies installed and so simply:
./configure
make
sudo make install

Note that each command will take a long time to complete (especially "make").

3. Install chemical-mime-data and bodr


Thanks to the Ubuntu Gutsy team, these 2 packages are now available via Synaptics (or aptitude for that matter). So for now (for GChemPaint 0.8.3), you can simply:

sudo aptitude install chemical-mime-data
sudo aptitude install bodr


If the future versions of GChempaint requires newer versions of the packages, you can easily compile and install them without hitch (I realize I'm making predictions, but I'm pretty sure). Get the source codes from the following sites:

Chemical-MIME-Data
BODR


If you do the above, there is a chance that your MIME system gets disturbed (your icons look funny, etc). In that case, you may have to re-install and re-configure the following packages from Synaptics:
sudo aptitude install gnome-mime-data shared-mime-info mime-support
sudo update-mime-database /usr/share/mime
sudo dpkg-reconfigure shared-mime-info
killall gnome-panel
killall nautilus
And restart the computer

4. Install Gnome Chemistry Utils package


Obtain the latest GCU package from here. Note that if you want the stable and latest, actually get the 0.8.X series as opposed to 0.9.X. This how-to is for 0.8.3.

Just like we installed OpenBabel, untar the package, configure (./configure), make and install (sudo make install) the package. It should go without hitch. If you encounter problems, please post here and we'll figure it out. When you do post a problem, it'd greatly help if you copy and paste the output from the terminal.

5. Install GChemPaint (finally)


Obtain the latest GChemPaint package from here.

Just like we installed OpenBabel and GCU, untar the package, configure (./configure), make and install (sudo make install) the package. It should go without hitch. If you encounter problems, please post here and we'll figure it out. When you do post a problem, it'd greatly help if you copy and paste the output from the terminal.
Since the MIME system may have been altered (I frankly don't quite understand this part of the deal), you may want to reboot the computer (or at least logout/login).

NOTE: I strongly recommend that you KEEP all the directories created here (such as the ones for gnome-chemistry-utils and gchempaint). Since we didn't install these via deb files, the only clean way to uninstall these programs is to do the following from the directory.

sudo make uninstall

6. If GChemPaint or GCU does not start


This happened to me. According to the developer of GChempaint, you can fix the problem by the following command:
sudo ldconfig
This worked for me :)
Enjoy drawing structures!
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Posted by tak, filed under science, linux. Date: October 27, 2007, 11:45 am |

13 Responses

  1. josh Says:
    January 25th, 2008 at 11:53 am

    I got as far as the gnome chemistry utils and got this error when I ran ./config:

    checking for GCU… configure: error: Package requirements (libglade-2.0 >= 2.4.0 gtk+-2.0 >= 2.10.0 gtkglext-1.0 >= 1.0.0 libgnomeprintui-2.2 >= 2.4.0 gnome-vfs-2.0 >= 2.4.0 libgoffice-0.4 >= 0.4.0 libgoffice-0.4 = 0.1.94 shared-mime-info >= 0.12 openbabel-2.0 >= 2.1.0 bodr >= 5) were not met:

    No package ‘openbabel-2.0′ found

    Consider adjusting the PKG_CONFIG_PATH environment variable if you
    installed software in a non-standard prefix.

    Alternatively, you may set the environment variables GCU_CFLAGS
    and GCU_LIBS to avoid the need to call pkg-config.
    See the pkg-config man page for more details.

    The only thing I did differently was that I installed open babel from the synaptic package mananger, but it is the latest version.

    Any ideas?

  2. josh Says:
    January 25th, 2008 at 1:20 pm

    i uninstalled openbabel and reinstalled using the source. this seems to be what the problem was. Odd.

  3. josh Says:
    January 25th, 2008 at 2:22 pm

    now i get the following error when I try to run the program:

    gchempaint: error while loading shared libraries: libgchempaint-0.8.6.so: cannot open shared object file: No such file or directory

    but it does exist in /usr/local/lib/

    any ideas?

  4. josh Says:
    January 25th, 2008 at 2:41 pm

    again - fixed. The lib files needed to be in /usr/lib/, not /usr/local/lib/.

    doh

  5. admin Says:
    January 29th, 2008 at 6:23 pm

    Hi josh,

    Sorry I didn’t get back to you until now :(
    Thanks for posting your efforts to install gchempaint; I’m sure it is useful for other people here.

    I just wanted to let you know that shortly after I wrote this how-to, I found out that an Ubuntu developer started making deb files of Gchempaint. If you’re interested, see:
    http://ubuntuforums.org/showpost.php?p=3689184&postcount=49

    Blessings,
    Tak

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