Structure

Scripts that analyze the structure of the system.

Scripts 

`contact_hist`	Calculate the number of contacts between two MDAnalysis `AtomGroups`.
`densmap`	Compute a 2-dimensional number density map.
`lig_change_at_pos_change_blocks`	Compare the coordination environment of reference compounds before and after they have changed their position.
`lig_change_at_pos_change_blocks_hist`	Compare the coordination environment of reference compounds before and after they have changed their position.
`rmsd_trj_trj`	Calculate the Root Mean Square Deviation (RMSD) between two trajectories for each frame.
`rmsd_vs_time`	Calculate the Root Mean Square Deviation (RMSD) between a reference frame and all other frames in the trajectory.
`subvolume_charge`	Calculate the net charge of cubic subvolumes of the simulation box.

Read up to three matrices from text files and plot them as one RGB matrix with matplotlib.axes.Axes.imshow().