BioSimSpace provides several tools that provide additional functionality when working interactively. One of these is the
plot function that enables graphing of time series data. This is simply a wrapper around Matplotlib to quickly produce nicely formatted graphs for inclusion in a Jupyter notebook.
(Here we assume that you have initalised a BioSimspace process, see here for details.)
To plot the total energy of the system as a function of time:
import BioSimSpace as BSS # Get the time and energy records. time = process.getTime(time_series=True) energy = process.getTotalEnergy(time_series=True) # Plot the data. BSS.Notebook.plot(x=time, y=energy, xlabel="Time (ns)", ylabel="Energy (kcal/mol")
(Note that in this example we assume that the
process above generates energy record data.)
If you omit the
x keyword argument then the
y data values will be plotted against their list index.
logy keyword arguments can be used to adjust the axis scaling. For example, to use a logarithic axis for the time record data:
BSS.Notebook.plot(x=time, y=energy, xlabel="Time (ns)", ylabel="Energy (kcal/mol", logx=True)
The plot function returns a
matplotlib.pyplot object that can be further customised to your needs.