PyMOL CLI Options

This page documents the CLI options for molecular visualization and analysis using PyMOL. Use chemsmart run mol --help for the complete list.

Basic Command Structure

chemsmart run [OPTIONS] mol [MOL_OPTIONS] <SUBCMD> [SUBCMD_OPTIONS]

MOL Options

Option	Type	Description
-f, --filenames	string	Input file(s) for visualization
-d, --directory	string	Directory for batch processing of multiple files
-t, --filetype	string	File type filter for directory processing (gjf, xyz, mol, log, etc.)
-p, --program	string	Computational chemistry program whose output files should be visualized (e.g. gaussian, orca). Used with -d to batch-visualize all output files from that program in one PyMOL session.
-l, --label	string	Custom output filename. For mo/spin/nci, this controls output naming only; processing input files still use the source filename basename.
-a, --append-label	string	String to append to filename
-i, --index	string	Structure index, 1-based (default: -1, last)
--pubchem	string	Query structure from PubChem
-o, --overwrite	bool	Overwrite existing files (default: disabled)

Available Subcommands

Basic Visualization

Subcommand	Description
visualize	Create PyMOL visualization and save as PSE file
movie	Generate rotating molecule movie

Reaction Analysis

Subcommand	Description
irc	Generate IRC movie and trajectory visualization

Electronic Structure Analysis

Subcommand	Description
mo	Generate molecular orbital visualizations
spin	Generate spin density visualizations

Interaction Analysis

Subcommand	Description
nci	Generate non-covalent interaction plots

Next Steps

For detailed information on each visualization type:

• Basic Visualization (PyMOL)

• Reaction Analysis (PyMOL)

• Electronic Structure Analysis (PyMOL)

• Interaction Analysis (PyMOL)