Science and software development

Scientific publications on ORCID

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Software

The free programs you will find below are for Windows PCs and are:

• SQLiteHistograms - An SQLite extension library for creating histogram tables, tables of ratio between histograms and interpolation tables of scatter point tables.
• MtzExtInfoTip - A shell extension library enabling Windows Explorer to display the header information present in crystallographic data files of the MTZ file format.
• XCPTLib - an Exception Handler and stack tracer.

SQLiteHistograms

This SQLite extension library is based on the 'ext/misc/series.c example from the SQLite source files. It uses the virtual table feature of SQLite to generate tables on the fly.

The library contains three extensions: HISTO for calculating histograms of data, RATIOHISTO for calculating ratios of two histograms and MEANHISTO for calculating interpolated values of 2D scatter data.

HISTO

A histogram of a table named AllProteins and with the column NumberofResiduesInModel can be computed using the HISTO function like this:
SELECT * FROM HISTO("AllProteins", "NumberofResiduesInModel", 15, 0, 1500);
This produces a histogram with 15 bins between 0 and 1500.

RATIOHISTO

The ratio of two histograms of a table AllProteins with the columns LLGvrms and CCglobal where the LLGvrms values can be grouped into two different subsets depending on whether  CCglobal values is bigger or smaller than 0.2 can be computed with the SQL statement:

SELECT * FROM RATIOHISTO("AllProteins", "LLGvrms", 20, 0, 90, "CCglobal", 0.2);

This produces two histograms of LLGvrms with 20 bins from 0 to 90, one where CCglobal is smaller than 0.2 and one where it is greater than 0.2 as well as a histogram of the total count. In addition the ratio of the first histogram divided by the total count is computed.

MEANHISTO

The interpolated data of a 2-dimensional scatter data can be computed for a table AllProteins with the two columns FracvarVRMS1 and LLGrefl_vrms can be computed with the SQL statement:

SELECT * FROM MEANHISTO("AllProteins", "FracvarVRMS1", "LLGrefl_vrms", 30, 0, 0.6);

This produces a table with 30 bins of FracvarVRMS1 between 0 to 0.6 where each bin contains the average value of LLGrefl_vrms for the corresponding FracvarVRMS value.

Source code

MtzExtInfoTip - a shell extension library for Windows Explorer

Source code

Santorini - a Molecular Viewer

This program is a molecule viewer useful for visualising crystals, molecules or proteins.

Features

• Clipping planes, Tessellation-CPU optimisation algorithm.
• Molecular surface calculation.
• Calculate correlation functions of isotropic neutron scattering structure factor and radial distribution function.
• Supported fileformats: Gaussian cube files, XYZ and protein data bank files PDB (restricted to only interpreting ATOM and HETATM records).
• Show multiple frames in a single file as an animation.

Download Santorini from this link.

History

Patmos - a Molecular Screensaver

This scientific screen saver rotates and bounces your favourite molecules, proteins or crystals. It has almost similar features as Santorini above. If your file contains several frames of atomic coordinates or molecular models then Patmos plays each frame sequentially as an animation. Features Clipping planes, Tessellation-CPU optimisation algorithm. Molecular surface calculation. Supported fileformats: Gaussian cube files, XYZ and protein data bank files PDB (restricted to only interpreting ATOM and HETATM records). Show multiple frames in a single file as an animation.

Download Patmos from this link.

More Screenshots:

History

Correlation Functions

As of version 1.1 the ability to calculate the radial distribution function of atoms as well as the isotropic neutron scattering structure factor has been added. These correlation functions are particularly interesting for people simulating amorphous or glassy bulk materials. The scattering lenghts needed for such calculations are defined in the elements.dat file.

Molecular Surface

As of version 1.2, Santorini can now display a "surface" of the system being considered. One can probably debate until the cows come home exactly which is the proper definition of a molecular surface, let alone its physical significance. The definition employed here is the iso-level contour map satisfying the requirement that the distance to the closest atom equals its van der Waal's radius plus a constant D, which the user can vary but typically is around 1Å. To generate the iso-level contour map I have used Cory Bloyd's version of the Marching Cubes algorithm as detailed here by Paul Bourke.

Tessellation-CPU optimisation algorithm

This algorithm is mostly useful when animating a large molecule, protein or crystal. The problem is that hardware can vary considerably and that there is no prior knowledge of how many atoms the coordinate file contains. Both conditions affect how CPU intensive the screen rendering will be. The algorithm therefore measures the CPU usage during animation and then adjusts the qualilty of the rendering as to avoid hogging the CPU which otherwise could slow down your PC or make it unresponsive. With the algorithm enabled you'd typically see atoms and bonds in small molecules being rendered with quite smooth balls and tubes whereas atoms and bonds in large proteins may only be rendered just with points and lines.

Other molecules and crystals

In addition to the supplied coordinate files you can of course get your own favourite protein molecules from sites such as the Protein Data Bank at RCSB or EBI and mineral crystals from http://rruff.geo.arizona.edu/AMS/amcsd.php to mention but a few.

Drivers

Please note that in order to achieve the best performance for these programs you are advised to install drivers for your graphics card written by your graphics card vendor. The drivers Microsoft supply for PC graphics card with Windows may not be properly optimised for OpenGL unlike the genuine drivers provided by your graphics card vendor. Un-optimised drivers can be the cause of severe reduction in performance of these programs and you should therefore check your graphics card vendor's website for the availability of the latest driver.

XCPTLib is an exceptionhandler library for deployed software that assists the developer with producing a stack trace as well as a crash dump file which can be analysed in WinDbg or Visual Studio for examining where a program failed. It basically overrides Windows default exception handler and presents the user with the choice of emailing a bug report back to the developer. The library can be invoked either statically or dynamically from the faulty application. Once the application crashes the library will catch the exception and ask the user for permission to email crash dump file and stack trace to the developer as shown in the two images above. The source code for the library as well as a test program using it, is hosted at . XCPTLib is partly based on examples by Matt Pietrek and Paul DiLascia found in the MSDN as well as the ZLIB compression algorithm by Jean-loup Gailly and Mark Adler all of whom are due for credit.

Bugs & Comments

Feel free to submit comments and bug reports to

Ph.D thesis

My Ph.D. degree from 1999 was done in theoretical chemistry and the dissertation was titled A Computational Study of Germanium Dioxide.