stacker.filter_traj_routine

stacker.filter_traj_routine#

filter_traj_routine()[source]#

Executes the routine for filtering an input trajectory file and converting it to a PDB file.

This function uses provided command-line arguments to call filter_traj_to_pdb() with specified inputs, such as the trajectory file, topology file, output file location, residues to retain, and atom names to retain.

Raises:
ResEmpty

If the –residues argument is not provided.

AtomEmpty

If the –atom_names argument is not provided.

See also

filter_traj_to_pdb

The core function that performs the trajectory filtering and PDB generation.

Notes

  • The args.residues argument should be a list of residue indices to retain.

  • The args.atom_names argument should be a comma-separated string of atom names to retain.

  • Output directories are created automatically if they do not exist.

Examples

Command-line usage with sample arguments:

$ stacker 
    -s filter_traj 
    -trj testing/first10_5JUP_N2_tUAG_aCUA_+1GCU_nowat.mdcrd 
    -top testing/5JUP_N2_tUAG_aCUA_+1GCU_nowat.prmtop 
    -o testing/command_line_tests/filter/5JUP_N2_tUAG_aCUA_+1GCU_nowat_mdcrd.pdb 
    -r 426,427 -a C2,C4,C6