CLI Reference

MDFactory uses a cyclopts CLI. Run mdfactory --help or mdfactory <command> --help for the live command tree.

Build commands

mdfactory prepare-build

Create one hash directory per CSV row plus a summary YAML in the output directory.

mdfactory prepare-build <input.csv> [output_dir]

mdfactory build

Build one simulation from a YAML file into the chosen output directory.

mdfactory build <input.yaml> [output_dir]

mdfactory check-csv

Validate a CSV by converting each row into a BuildInput model and, for bilayers, running the current buildability checks.

mdfactory check-csv <input.csv>

Utility commands

mdfactory clean

Clear cached molecule parameters and or run-database content after confirmation.

mdfactory clean

mdfactory showdb

Show basic information about the molecule or run database.

mdfactory showdb --name mol
mdfactory showdb --name run

Analysis commands

mdfactory analysis run

SOURCE must be either a simulation directory root or a build summary YAML.

mdfactory analysis run SOURCE [options]

Important options:

• --analysis
• --simulation-type
• --hash
• --skip-existing
• --start-ns
• --end-ns
• --last-ns
• --stride
• --max-residues
• --analysis-backend
• --analysis-workers
• --slurm
• --account
• --partition
• --time
• --cpus
• --mem-gb
• --qos
• --constraint
• --log-dir

mdfactory analysis info

Show registered-versus-completed analysis status for discovered simulations.

mdfactory analysis info SOURCE [options]

Important options:

• --simulation-type
• --hash
• --output
• --chemistry-output
• --chemistry-mode

mdfactory analysis preprocess

Run a preprocessing script for each discovered simulation.

mdfactory analysis preprocess SOURCE --script ./script.sh [options]

mdfactory analysis remove

Remove saved analysis outputs after confirmation.

mdfactory analysis remove SOURCE [options]

Artifact commands

mdfactory analysis artifacts run

mdfactory analysis artifacts run SOURCE [options]

Important options:

• --artifact
• --simulation-type
• --hash
• --output-prefix
• --vmd-path
• --ffmpeg-path
• --skip-existing
• --slurm
• --account

mdfactory analysis artifacts info

mdfactory analysis artifacts info SOURCE [options]

mdfactory analysis artifacts remove

mdfactory analysis artifacts remove SOURCE [options]

Sync commands

mdfactory sync init

mdfactory sync init systems [--force]
mdfactory sync init analysis [--force]
mdfactory sync init artifacts [--force]
mdfactory sync init config
mdfactory sync init check

mdfactory sync push

For each push command, provide exactly one of a positional SOURCE or --csv.

mdfactory sync push systems [SOURCE] [options]
mdfactory sync push analysis [SOURCE] [options]
mdfactory sync push artifacts [SOURCE] [options]

Common push options:

• --csv
• --csv-root
• --force
• --diff

Specific options:

• sync push analysis --analysis-name <name>
• sync push artifacts --artifact-name <name>

mdfactory sync pull

mdfactory sync pull systems [options]
mdfactory sync pull analysis [options]
mdfactory sync pull artifacts [options]

Key pull options:

• --status
• --simulation-type
• --parametrization
• --engine
• --hash
• --output
• --full
• --overview
• --analysis-name
• --artifact-name

mdfactory sync clear

mdfactory sync clear systems
mdfactory sync clear analysis [options]
mdfactory sync clear all

sync clear analysis supports:

• --analysis-name
• --artifact-name
• --overview
• --analyses
• --artifacts
• --all

Next steps