BioSimSpace.Notebook

The Notebook package contains tools that are used when BioSimSpace is run interactively, e.g. within a Jupyter notebook.

Functions

plot([x, y, xerr, yerr, xlabel, ylabel, ...])

A simple function to create x/y plots with matplotlib.

plotContour(x, y, z[, xlabel, ylabel, zlabel])

A simple function to create two-dimensional contour plots with matplotlib.

plotOverlapMatrix(overlap[, ...])

Plot the overlap matrix from a free-energy perturbation analysis.

Examples

Generate a line graph using two lists of data.

../_images/plot_01.png

If no argument is passed for the x data then each y data value is plotted against its list index.

../_images/plot_02.png

Use the xlabel and ylabel arguments to add labels to your plots.

../_images/plot_03.png

Error bars can be added using xerror and yerror.

../_images/plot_04.png

It is possible to generate plots from the output of a real-time simulation. Where functions return time-series data containing BioSimSpace.Types, then axis labels will be automatically generated. (The xlabel and ylabel still take precedence.)

../_images/plot_05.png

Classes

View(handle[, property_map, is_lambda1])

A class for handling interactive molecular visualisations.

Examples

Load and visualise a molecular system.

../_images/view_01.png

Attach a View to a running molecular dynamics Process and visualise the first molecule in the system from the latest configuration in real-time.

../_images/view_02.png