cluster_analysis_driver.py Command Help

Command: $SCHRODINGER/run cluster_analysis_gui_dir/cluster_analysis_driver.py

usage: $SCHRODINGER/run cluster_analysis_gui_dir/cluster_analysis_driver.py
       [-h] -cms_file CMS_FILE -trj TRJ [-trj_min TRJ_MIN] [-trj_max TRJ_MAX]
       [-trj_step TRJ_STEP] [-eps Angstroms] [-mol_ids MOL_IDS]
       [-mw_min MW_MIN] [-mw_max MW_MAX] [-rg_com] [-extract]
       [-density_profile] [-resolution RESOLUTION] [-HOST <hostname>] [-D]
       [-JOBNAME JOBNAME]

Script to perform cluster analysis on a desmond trajectory Copyright
Schrodinger, LLC. All rights reserved.

options:
  -h, -help             Show this help message and exit.
  -cms_file CMS_FILE    Input cms file (default: None)
  -trj TRJ              Directory of the trajectory (default: None)
  -trj_min TRJ_MIN      Minimum of trajectory frame to be analysed. (default:
                        0)
  -trj_max TRJ_MAX      Maximum of trajectory frame to be analysed. (default:
                        None)
  -trj_step TRJ_STEP    Use every n-th frame in the trajectory range. The
                        first and last frames in the range will always be
                        included. (default: None)
  -eps Angstroms        The maximum distance between two atoms for them to be
                        considered in the same neighborhood. (default: 3)
  -mol_ids MOL_IDS      Comma separated molecule numbers, one from each
                        molecular species that should be considered in
                        clustering. Cannot be used with -mw_min and -mw_max
                        options. (default: None)
  -mw_min MW_MIN        Minimum weight required for molecules to be considered
                        in clustering. Cannot be used with -mol_ids option.
                        (default: None)
  -mw_max MW_MAX        Maximum weight allowed for molecules to be considered
                        in clustering. Cannot be used with -mol_ids option.
                        (default: None)
  -rg_com               Calculate Rg of clusters using center of mass of each
                        cluster component instead of all atom positions.
                        (default: False)
  -extract              Create and return one structure per cluster in the
                        last trajectory frame (default: False)
  -density_profile      Calculate radial density profile for each cluster and
                        export it to a file. The resolution of the profile can
                        be set with -resolution option. (default: False)
  -resolution RESOLUTION
                        The resolution for radial density profile calculation.
                        (default: 0.1)

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.
                        (default: localhost)
  -D, -DEBUG            Show details of Job Control operation. (default:
                        False)
  -JOBNAME JOBNAME      Provide an explicit name for the job. (default: None)