stacker.system_routine

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stacker.system_routine#

system_routine()[source]#

Runs the System Stacking Fingerprint (SSF) routine to generate a single SSF for a specified frame or range of frames.

This routine processes a trajectory to create SSFs based on inter-residue distances and outputs either visualizations or raw data for further analysis. The user can provide input fingerprints or generate them from trajectory files.

Parameters:
None

The routine relies on global args for all input values.

Raises:
FileNotFoundError

If the specified trajectory or topology file does not exist.

ValueError

If the provided input files have incompatible dimensions or unexpected formatting.

See also

filter_traj

Filters the trajectory for the specified residues.

get_residue_distance_for_trajectory

Computes inter-residue distances for a trajectory.

combine_frames

Combines two SSFs into a single array for comparison.

display_arrays_as_video

Visualizes SSF arrays and saves them as video files.

Notes

  • If args.input is provided, the routine will use pre-calculated fingerprint data.

  • If args.residues is specified, only those residues are considered in the calculation.

  • SSFs can be created for individual frames, a list of frames, or all frames in the trajectory.

  • If args.input_B is provided, two SSFs are combined for analysis.

Examples

Command-line usage:

$ stacker -s system 
    -trj testing/first10_5JUP_N2_tUAG_aCUA_+1GCU_nowat.mdcrd 
    -top testing/5JUP_N2_tUAG_aCUA_+1GCU_nowat.prmtop 
    -r 90-215 
    -fl 1-2 

$ stacker -s ssf 
    -trj testing/first10_5JUP_N2_tUAG_aCUA_+1GCU_nowat.mdcrd 
    -top testing/5JUP_N2_tUAG_aCUA_+1GCU_nowat.prmtop 
    -r 90-215 
    -fl 1-2 
    -g 10 
    -o testing/command_line_tests/pairwise/5JUP_N2_tUAG_aCUA_+1GCU_nowat_pairwise_avg_1to2.png 
    -d testing/command_line_tests/pairwise/5JUP_N2_tUAG_aCUA_+1GCU_data_1to2.txt.gz
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