trj_cluster.py Command Help

Command: $SCHRODINGER/run trj_cluster.py

usage: trj_cluster.py [-h] [-HOST <hostname>] [-WAIT] [-LOCAL] [-D] [-NOJOBID]
                      [-VIEWNAME <viewname>] [-OPLSDIR OPLSDIR]
                      [-JOBNAME JOBNAME] [-s START:END:STEP] -rmsd-asl
                      RMSD_ASL [-fit-asl FIT_ASL] [-n N] [-split-trj]
                      [-cutoff CUTOFF] [-rmsd-mat-data]
                      cms trj out

Cluster trajectory frames based on the RMSD on selected atoms.

When passing a cutoff value, a centroid hierarchical clustering with the cutoff
as the threshold will be performed, where the first frame in the trajectory is
used in the output cms file.

Without passing in a cutoff value, 'affinity propagation' clustering, which
calculates the clusters and the corresponding representative members for each
cluster.
For more information, see the reference::

   Brendan J. Frey and Delbert Dueck, "Clustering by Passing Messages Between
   Data Points", Science Feb. 2007, Vol. 315, Issue 5814, pp. 972-976
   DOI: 10.1126/science.1136800

Copyright Schrodinger, LLC. All rights reserved.

positional arguments:
  cms                   Input .cms file name
  trj                   Input trajectory file or dir name, which typically
                        ends with an extension name of '.xtc' (XTC format) or
                        '_trj' (DTR format), e.g., jobname.xtc, jobname_trj
  out                   Output file basename

options:
  -h, --help            show this help message and exit
  -s START:END:STEP, -slice-trj START:END:STEP
                        Use the sliced trajectory. We use Python's slice
                        notation. START, END, and STEP should be integer
                        numbers.
  -rmsd-asl RMSD_ASL    ASL expression to specify atoms to calculate RMSD
  -fit-asl FIT_ASL      ASL expression to specify atoms to superimpose before
                        calculating RMSD. The default value is that of '-rmsd-
                        asl'.
  -n N                  Write output data for the N most populated clusters.
                        Default is 1.
  -split-trj            Saves all members of each cluster as frames of a
                        trajectory. The representative members for each
                        cluster are stored in the CMS files.
  -cutoff CUTOFF        Triggers centroid hierarchical clustering with cutoff
                        as thethreshold
  -rmsd-mat-data        Saves the calculated RMSD matrix as .csv file and
                        plots the RMSD matrix to a .png file

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.
  -WAIT                 Do not return a prompt until the job completes.
  -LOCAL                Do not use a temporary directory for job files. Keep
                        files in the current directory.
  -D, -DEBUG            Show details of Job Control operation.
  -NOJOBID              Run the job directly, without Job Control layer.
  -VIEWNAME <viewname>  Specifies viewname used in job filtering in maestro.
  -OPLSDIR OPLSDIR      Specifies directory for custom forcefield parameters.
  -JOBNAME JOBNAME      Provide an explicit name for the job.