ChemPup-0.1.2

I recently had the idea to assemble a Puppy Linux "Puplet" that would be configured with software useful for an undergraduate chemistry student. Considering I know nothing about programming and I am still very new to Linux, this is proving to be a challenge...but I have had success so far.

ChemPup-0.1.2 has been developed from Puppy Linux 4.21 running with 512 MB ram in a VBox machine on Ubuntu-9.04 and so far includes most of the packages I have envisioned in this first generation build. The following is the list of added packages:

Office Productivity Suite:
OpenOffice.org-3.0

General Chemistry:
GElemental - a gtk+ periodic table of the elements with loads of information on each element
MoleCalc - a molecular weight calculator (runs in WINE)

Organic Chemistry:
BKChem - a 2D structure editor with .mol and .odt (openoffice) export capabilities
OpenBabel - a command line molecular file-type converter that handles over a dozen formats
WinDNMR - a dynamic NMR simulator (runs in WINE)

Need:
A suitable 3D molecular viewer (I want Avogadro which includes a force-field minimizer)

Plan to Make:
A slick spreadsheet template (OOCalc) that has useful conversions (mole to gram etc) and equations
Detailed documentation to maximize usage of the system (since most US Students don't know Linux)

Additionally I need to figure out what programs I should cut out to save space, if any, considering OOO is adding most of the extra weight. I will probably remove devx.sfs.

Building in the existing packages (listed above) was fairly straightforward....I needed to install Python, WINE (which I found as a .pet on the Puppy Forum) and a few other package dependencies that I cannot recall.

Update: In order to run BKChem it needs python 2.3 or later and after checking with > python --version <> ./configure; make; make install. Unfortunately these programs must be installed before python so I had to reconfigure python and went ahead and downloaded the upgraded 2.6. Python is a bit large so I removed the old version...2.6 also took several minutues (10 ish) to compile and install. Afterwards bkchem.py runs from command line with > python bkchem.py < in the working directory. I then easily created a bash script to start the program, made it executable with chmod 777 and added it to the desktop with a logo icon to make a simple point and click execution.

The real trouble has been with Avogadro. This is a nice, intuitive 3D molecular viewer and force-field minimizer program that I test-ran on Ubuntu and was quite happy with, however, unlike with Ubuntu, I do not have a prepackaged .deb (.pet) for Puppy and will have to build it from source. Avogadro has several package dependencies, some of which I am having trouble with building as well: Qt4, Eigen2, CMake, and OpenBabel are all required before you can compile and install Avogadro. I installed OpenBabel and CMake okay (I think), and Eigen2 supposedly only need to be unzipped and it is ready to go (although they don't say to which directory it belongs so I stuck it in /usr/local/bin). Qt4 on the other hand has proven very difficult and I also found that I had the wrong version of CMake!! These programs (OpenBabel, Qt4, and even CMake) took a long 20-30 minutes of compiling time each. So long as I can get a user-friendly 3D molecular viewer I will be satisfied with this first release.