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Stuff to download
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Here's some of my bits and pieces that you can take. Most of it isn't particularly interesting or useful, but there you go.
Note that the files on this page are unlikely to be the latest, up-to-date, versions - email me if you are really desperate to have those instead.
This stuff is free, so please consider visiting these sponsors:
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SWiM
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 Yet another window manager for X...
There are, literally, hundreds of window managers available for UNIX systems running the X windowing system. The are good window managers and there are bad window managers. Unfortunately the only window managers which had the features I required were huge and bloated monsters. (Sure, enlightenment is nice, but not when you run it on a 166MHz PentiumII laptop.) The lightweight, efficient, window managers tend not to support GNOME, and generally aren't readily themeable or configurable. So, for a laugh, I wrote my own. And a jolly good laugh it was too. Despite being very lightweight, SWiM is still reasonably configurable and easily themeable. It was designed to work alongside the GNOME desktop environment, but may also be used on it's own.
Download the full source-code package, SWIM-0.1-1.tar.gz, under the terms of the GNU General Public License. Download additional themes, swim-themes.tgz. Alternatively, download a RedHat RPM package. More information and the most recent versions are likely to be available from the SWiM homepage.
Features include:
- Themes
- Configurable pointer and keyboard control
- Multi-head (Xinerama) support
- Multi-byte character support
- Multiple desktops
- GNOME compliance
- Low CPU and memory overhead
Whether you find SWiM useful, depends upon what you need. Deliberately excluded features include:
- Session management. (GNOME can do this)
- KDE compliance. (I don't use KDE)
- Embedded scripting engine. (What's the point?)
- Desktop backgrounds. (GNOME can do this)
- Sounds. (Hugely pointless)
- Screenshots. (This is not the window manager's job)
- Desktop icons. (I don't like these)
- Application launcher. (GNOME can do this)
- Graphical configuration tool. (I'm too lazy to write one)
But having given that list, one day I might decide to add one or more of those features. It will just depend on what I feel like coding.
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Lipiddock
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If you have come here looking for lipiddock, then it isn't here yet! I will submit a paper for publication shortly and a soon as I've done that I will also place the lipiddock stuff here.
If you don't know what lipiddock is, then it is a rapid program for automatic generation of a near-equilibrated lipid bilayer with or without integral or bound molecules.
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gVoronoi
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gVoronoi is a tool for two-dimensional Delaunay tesselation and Voronoi decompositions on arbitrary data sets. If you have a need, or interest, in Dirichlet tesselation, Voronoi diagrams, Thiessen polygons, Wigner-Seitz cells or Blum's transform - then you may find this program useful.
This utility is under active development, but is already fully useable. Under the GNOME environment it is has a full graphical interface, yet most of its features are also available directly from the command-line.
The triangulation engine, although not fully optimal, works relatively well. The present interface is a quick prototype of a preview display. I recently added the code necessary to create PNG format graphic files. Future enhancments will include the ability to produce postscript and bitmapped plots as well.
Download the full source-code package, gvoronoi-000609.tgz, under the terms of the GNU General Public License. (Note that this almost certianly isn't the latest version.)
If you want the latest, and greatest version, just send me an email and ask for it.
Development was pretty rapid - until I decided to write a version which could perform the tesselation in an arbitrary number of dimensions. I've written a fairly neat OpenGL visualization program for it. It is a pity that the tesselation is such a nightmare.
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Clusters and Dendrograms
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cluster
A simple utility to perform hierarchical clustering using a number of methods, and plot dendrograms of the result. It is really easy to use, and comes with instructions.
cluster-0.4-2.tgz - C source tarball for UNIX-like operating systems - requires GTK+.
cluster.tgz - Older version - requires g2 instead of GTK+.
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The best program I've ever written ;-)
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FreecivAC
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 Freeciv meets Alpha Centuari
I'm helping (a bit) to add features to Freeciv so that you may play Alpha Centuari-like games.
Further details are available from here.
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Molecular data format converter
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Babel 1.6
Babel is a wee utility for converting between the many, many chemical and protein structure file formats. It's an invaluable tool for computational chemists, modellers and those odd bio-science people.
Unfortunately, it doesn't seem to be actively supported by any one person so (a) it's difficult to find to download, and (b) it has one or two bugs. I'm making available here the version that I use. It is basically Babel version 1.6, with the few fixes I've had to make to it. I use it on a handful of platforms, and it is fairly portable between all UNIX variants.
Tar-gzip'ed code: babel1.6-saa3.tgz
I'm sure you can work out how to get this working. It's not difficult. Just remember that you need to set a couple of environment variables before it will startup, as detailed in the distributed README file.
I think the "offical" Babel download site is at OpenEye Scientific Software. There are versions for that MS Windows thing. There is also a Mac version, which implies there must be a chemist somewhere who uses a Mac. How odd!
A new project has sprung up... OpenBabel... Babel lives on!
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Kohonen Self-organising Networks
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SOM_PAK 3.1 with additional periodic topology
SOM_PAK is a superb set of utilities for using Kohonen self-organising networks, a type of neural network. The official site is ftp://cochlea.hut.fi/pub/som_pak/ where the complete set of original files is available.
My modified version contains a few minor fixes and one significant extra feature. Periodic rectangular (i.e. toroidal) maps are now available by using the topology type "prect".
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Genetic Algorithm Utility Library
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 GAUL: Genetic Algorithm Utility Library
GAUL is a flexible programming library designed to aid in the development of applications that require the use of genetic algorithms. It provides data structures and functions for handling and manipulation of the data required for a genetic algorithm. Additional stochastic algorithms are provided for comparison to the genetic algorithms. Much of the functionality is also available through a simple S-Lang interface. Several example programs are provided, including training a Neural Network using a hybrid GA-Backpropagation approach.
This project is now, gratefully, hosted at SourceForge. The public CVS repository may be found at cvs.gaul.sourceforge.net. Note that if you don't know anything about CVS archives, then GAUL will probably be of no use to you anyway.
The latest and greatest version will always be available at the GAUL home-page.
Downloads for version 0.1844:
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my_crypt
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Legacy UNIX crypt (1) utility replacement
In the dark ages of computing, UNIX had a really dodgy and cyptographically unsound encryption/decryption tool called crypt. Nowadays, most UNIX variants do not include this tool because there are far better alternatives available. That is probably a good thing, and we should be happy. Unfortunately, many files were previously encrypted using this tool, and even some strange people still use it (crypt is still bundled with Silicon Graphics IRIX operating system, for example). That causes a problem, especially since I couldn't find a free version of crypt that worked under Linux when I needed it.
That is no longer a problem because I've now written my own version. Yippee. And you can download it here:
It works exactly as the original UNIX version did:
crypt [-s] passkey < file > encrypted_file
crypt [-s] passkey < encrypted_file > file
Warning:This IS NOT designed to be cryptographically secure. It was solely written as a means to decrypt files which were encrypted using the legacy UNIX crypt utility.
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BB
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Peptide backbone reconstruction
The process of reconstructing an all-atom peptide, or protein, model from a subset of the atomic coordinates is the subject of a considerable body of literature. Numerous applications for this process exist, including enhancement of low-resolution models from crystallography into usable models or conversion of the coarse structures typical of ab initio folding computations or comparative protein modelling techniques into all-atom models.
It is common to split the process of reconstructing all-atom structures into two separate tasks. The first task is to predict the full backbone, and the second is to build side chains onto this. This partitioning of the problem is considered reasonable because it is observed that the backbone geometry of well defined secondary structure elements is mostly invariant to the identity of its amino acid residues.
Previously published backbone reconstruction methods either generate de novo backbone conformations or utilise fragment libraries derived from the PDB to locate possible structures which do not violate the provided Cα trace. These conformations are evaluated using either energetic, homology-based or geometric criteria. BB applies a dead-end elimination procedure, a knowledge-based scoring function and a library of 3-residue fragments to construct all backbone atoms. In a published study, BB was found to produce backbone structures with an average all-backbone atom RMSD of 0.41 Angstroms from the Cα coordinates alone.
- BB - Software download page.
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NN_util
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Peptide backbone reconstruction
"nn_util" is a highly efficient multi-layer perceptron (MLP) neural network programming library with a variety of built-in training protocols. This code is written in highly portable C which has been successfully compiled on numerous computing platforms; Linux with gcc, Compaq's ccc, and Intel's icc, IRIX with MIPSPro C/C++, AIX with gcc and IBM's xlc, Solaris with gcc.
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Links to other peoples stuff
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Here's a weedy collection of other people's bits 'n' pieces that I've liked.
- Freshmeat - Great collection of open source UNIX/Linux apps.
- Molecular Visualization - Pointers to free molecular visualization programs. Obviously none of these are as good as my visualisation program for proteins, compounds and abstract structures... but I haven't released that to the world. ;-)
- SAL - "Scientific Applications on Linux". The name pretty much explains this site.
- Open Science - Directory of scientific open-source software.
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