Action Commands

Commands to perform analysis on frames and topology.

Actions in CPPTRAJ operate on frames read in by the trajin or ensemble commands one at a time and extract derived data, modify the coordinates/topology in some way, or both. Most Actions in CPPTRAJ function exactly the way they do in ptraj and are backwards-compatible. Some Action commands in CPPTRAJ have extra functionality compared to ptraj (such as the per-residue RMSD function of the rmsd Action, or the ability to write out stripped topologies for visualization in the strip Action), while other Actions produce slightly different output (like the hbond/secstruct Actions).

Unlike some other command types, when an Action command is issued it is by default added to the Action queue and is not executed until trajectory processing is started (e.g. by a run or go command). However, Actions can be executed immediately on COORDS data sets via the crdaction command.

When a frame is modified by an Action, it is modified for every Action that follows them during trajectory processing. For example, given a solvated system with water residues  named WAT and the following Action commands:

rmsd R1 first :WAT out water-rmsd.dat
 strip :WAT
 rmsd R2 first :WAT out water-rmsd-2.dat

the first rms command will be valid, but the second rms command will not since all residues named WAT are removed from the state by the strip command. Note that for commands which can use a reference mask as well as a target mask (e.g. rms, drmsd, symmrmsd, etc.) there must be a 1 to 1 correspondence between the atoms in each mask, i.e. the number of atoms and the ordering of selected atoms must be the same.

The following Actions are available. If an Action may modify coordinate/topology information for subsequent Actions it is denoted with an X in the Mod column.