stacker.bottaro_routine

bottaro_routine()

Executes the residue movement routine to generate Bottaro values for a trajectory.

This routine calculates the r, rho, and theta values for each frame of a PDB trajectory between two specified residues and stores them in a CSV file. Optionally, it visualizes the movement using heatmaps or scatter plots.

Parameters:

None

The routine relies on global args, which must be set via command-line arguments or equivalent argument parsing.

Raises:

AtomEmpty

If required atom names or residue indices are not provided.

See also

filter_traj_to_pdb

Filters trajectory and generates an intermediate PDB.

write_bottaro_to_csv

Writes residue movement calculations to a CSV.

visualize_two_residue_movement_heatmap

Creates a heatmap for residue movement.

visualize_two_residue_movement_scatterplot

Creates a scatter plot for residue movement.

Notes

• args.trajectory and args.topology are required for generating an intermediate PDB if one is not already provided.

• Supports heatmap and scatter plot visualizations for residue movement.

• Removes intermediate files (pdb and csv) if –no_inter flag is specified.

Examples

Command-line usage:

$ stacker -s bottaro 
    -trj testing/first10_5JUP_N2_tUAG_aCUA_+1GCU_nowat.mdcrd 
    -top testing/5JUP_N2_tUAG_aCUA_+1GCU_nowat.prmtop 
    -pdb testing/5JUP_N2_tUAG_aCUA_+1GCU_nowat_mdcrd.pdb 
    -o testing/command_line_tests/bottaro/tUAG_aCUA_+1GCU_GC_plot.csv 
    -p 426 
    -v 427 
    -pa C2,C4,C6 
    -va C2,C4,C6 
    -pt scatter

$ stacker -s bottaro 
    -pdb testing/5JUP_N2_tUAG_aCUA_+1GCU_nowat_mdcrd_3200frames.pdb 
    -o testing/command_line_tests/bottaro/tUAG_aCUA_+1GCU_GC_plot_3200frames.csv 
    -p 426 
    -v 427 
    -pa C2,C4,C6 
    -va C2,C4,C6 
    -pt heat