free_volume_analysis_driver.py Command Help

Command: $SCHRODINGER/run free_volume_analysis_gui_dir/free_volume_analysis_driver.py

usage: $SCHRODINGER/run free_volume_analysis_gui_dir/free_volume_analysis_driver.py
       [-h] [-grid_max LARGEST_GRID_SPACING] [-grid_min SMALLEST_GRID_SPACING]
       [-grid_step GRID_STEPSIZE] [-radius PROBE_RADIUS] [-cms_file CMS_FILE]
       [-trj TRJ] [-trj_min TRJ_MIN] [-trj_max TRJ_MAX] [-trj_step TRJ_STEP]
       [-all_surfaces] [-HOST <hostname>] [-D] [-VIEWNAME <viewname>]
       [-JOBNAME JOBNAME]
       input_file

Analyzes free volume in a structure Copyright Schrodinger, LLC. All rights
reserved.

positional arguments:
  input_file            Input file

options:
  -h, -help             Show this help message and exit.
  -grid_max LARGEST_GRID_SPACING
                        The largest spacing between grid points. Smaller
                        spacing yields more accurate results. Note that the
                        requested grid spacing is approximate and will be
                        adjusted slightly for even distribution of grid points
                        through the entire system. (default: 1.0)
  -grid_min SMALLEST_GRID_SPACING
                        The smallest spacing between grid points. Smaller
                        spacing yields more accurate results. Note that the
                        requested grid spacing is approximate and will be
                        adjusted slightly for even distribution of grid points
                        through the entire system. (default: 0.25)
  -grid_step GRID_STEPSIZE
                        Free volumes will be calculated at each grid spacing
                        from -grid_max to -grid_min using a step size of
                        -grid_step. (default: 0.25)
  -radius PROBE_RADIUS  The radius of the sphere probing the voids (default:
                        1.4)
  -cms_file CMS_FILE    Input cms file. Multiple cms can be set as input for
                        trajectory analysis. (default: None)
  -trj TRJ              Directory for the trajectory analysis. The order of
                        trajectory inputs should match their corresponding cms
                        input. For example <function type_cms_file at
                        0x14057ba60> A.cms <function type_cms_file at
                        0x14057ba60> B.cms -trj A.trj -trj B.trj. (default:
                        None)
  -trj_min TRJ_MIN      Minimum of trajectory frame to be analyzed. (default:
                        None)
  -trj_max TRJ_MAX      Maximum of trajectory frame to be analyzed. (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)
  -all_surfaces         Will calculate surface of all voids if True. Else will
                        calculate surface of voids with volume greater than 1
                        A^3. (default: False)

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)
  -VIEWNAME <viewname>  Specifies viewname used in job filtering in maestro.
                        (default: False)
  -JOBNAME JOBNAME      Provide an explicit name for the job. (default: None)