Command Line Interface

MoloVol provides a command line interface (CLI). The CLI allows users to use MoloVol from the command line and can be used to automate workflows, conduct many calculations in succession, and communicate with other programs.

Examples shown on this page work on Mac, but syntax may differ slightly between operating systems.

Operating the CLI

The CLI can be "enabled" simply by calling the executable file from the command line, followed by any switch. To verify that the CLI is working you can, for instance, simply use the --version switch:

$ MoloVol --version

If the output displays the version, then the CLI works as intended. Each switch has a verbose and a short name. The verbose switch is preceded by two dash symbols, while the short name is preceded by one. The --version switch can therefore also be called like this:

$ MoloVol -v

To run a calculation three arguments are required at least: Probe radius -r, grid resolution -g, and structure file fs. An example command would look as such:

$ MoloVol -r 1.2 -g 0.2 -fs ./inputfiles/exampleC60.xyz

All file path arguments can be either absolute or relative to the place where the command is run. In the above case a relative path is used. All valid command line switches are listed in the table below.

Switch	Verbose	Description	Argument
-h	--help	Display help for CLI	none
-v	--version	Display the app version	none
-r	--radius	(Small) probe radius	Decimal number
-g	--grid	Spatial resolution of the underlying grid	Integer
-fs	--file-structure	Path to the structure file	Path
-fe	--file-elements	Path to the elements file	Path
-do	--dir-output	Path to the directory output	Path
-r2	--radius2	Large probe radius, also enables two-probe mode	Decimal number
-d	--depth	Octree depth	Integer
-ht	--hetatm	Include HETATM from pdb file	none
-uc	--unitcell	Analyze unit cell	none
-sf	--surface	Calculate surface areas	none
-xr	--export-report	Export report (requires:-do)	none
-xt	--export-total	Export total surface map (requires:-do)	none
-xc	--export-cavities	Export surface maps for all cavities (requires:-do)	none
-o	--output	Control what parts of the output to display (default:all)	none
-q	--quiet	Silence progress resporting	none
-un	--unicode	Allows unicode output (only works for some shells)	none

Display options

You can suppress parts of the output. By default, the app will give updates on the calculation progress and display all results. If you would like to disable progress reporting you can use the --quiet switch. It is also possible to suppress parts, or all of the output by using the --output option followed by comma-separated arguments. For instance:

$ MoloVol -r 1.2 -g 0.2 -fs ./inputfiles/exampleC60.xyz -q -o time,vol

This command will only display the calculation time and the volume values. It is important to make sure that the list of arguments is only comma-separated, not separated by spaces.

A list of --output arguments is given in the table below. The bold entries group multiple options together.

Option	Display
none	Suppress all output
inputfile	Display structure file path
resolution	Display grid resolution
depth	Display octree depth
radius_small	Display (small) probe radius
radius_large	Display large probe radius
input	Display all user input parameters
hetatm	Display "Include HETATM" option
unitcell	Display "Analyze unit cell" option
probemode	Display whether two-probe mode enabled
surface	Display whether surface area calculation is enabled
options	Display all binary user options
formula	Display sum formula of molecule/structure
time	Display calculation time
vol_vdw	Display van der Waals volume
vol_inaccessible	Display inaccessible volume
vol_core_s	Display core volume of small probe
vol_shell_s	Display shell volume of small probe
vol_core_l	Display core volume of large probe
vol_shell_l	Display shell volume of large probe
vol	Display all volumes
surf_vdw	Display van der Waals surface
surf_mol	Display molecular surface
surf_excluded_s	Display (small) probe excluded surface
surf_accessible_s	Display (small) probe accessible surface
surf	Display all surfaces
cavities	Display cavity data
all	Display all, default option