sscc-visualization

Examples of chemistry data visualization using matplotlib for Spring School in Computational Chemistry

Contents

Simple plotting - subfolder simple

• Typical examples of creating xy-plots from data extracted from log files etc.

Simple plotting - subfolder bar

• Read in the thermodynamic integration data from Tuesday. Integrate and plot with errorbars

Simple contour map - subfolder contour

• Read in an array of potential energy values of a scan of two torsion values and plot it as contour map

Plotting multiple data together and two views to same data - subfolder contact_example

• More examples of creating xy-plots and and example to complement the xy-plot with a histogram

Contact maps - matrix representation of protein residues close to each other - subfolder contacts

• promiximity information provided bt Gromacs filtered and visualized with a color matrix highlighting spatial proximity

1D and 2D density plots - subfolder density

• Time average data from Gromacs MD simulations represented in 1D and 2D plots aiding understanding the numerical data
• Additional analysis to enable estimating uncertainty

Animated graphs - turn a simple plot into an animation

• Uses matplotlib animation tool