stacker.stack_events_routine

stacker.stack_events_routine#

stack_events_routine()[source]#

Identifies residue pairs with the most π-stacking interactions.

This routine analyzes a molecular dynamics trajectory and identifies residue pairs with the smallest center of geometry (COG) distances, typically indicating strong π-stacking. It outputs the top n_events residue pairings based on user input.

Parameters:
None

This function relies on global args for input values.

Raises:
FileNotFoundError

If the trajectory or topology files are not found.

ValueError

If input parameters are invalid or incompatible with the data.

See also

filter_traj

Filters trajectory data based on residue selection.

get_top_stacking

Extracts top stacking events from a trajectory.

Examples

Command-line usage:

$ stacker -s stack_events 
    -trj testing/first10_5JUP_N2_tUAG_aCUA_+1GCU_nowat.mdcrd 
    -top testing/5JUP_N2_tUAG_aCUA_+1GCU_nowat.prmtop 
    -r 90-215 
    -f 1 
    -n 5

$ stacker -s stack_events 
    -trj testing/first10_5JUP_N2_tUAG_aCUA_+1GCU_nowat.mdcrd 
    -top testing/5JUP_N2_tUAG_aCUA_+1GCU_nowat.prmtop 
    -r 90-100 
    -fl 1-10 
    -n 5

$ stacker -s stack_events 
    -trj testing/first10_5JUP_N2_tUAG_aCUA_+1GCU_nowat.mdcrd 
    -top testing/5JUP_N2_tUAG_aCUA_+1GCU_nowat.prmtop 
    -r 90-215 
    -n 5 
    -i testing/command_line_tests/pairwise/5JUP_N2_tUAG_aCUA_+1GCU_data_1to2.txt