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Installation

Quick install (macOS and Linux)

Open a terminal and paste:

curl -fsSL https://moleculedesk.com/install.sh | sh

Then open a new terminal window and run:

moldesk --version
moldesk doctor

You do not need to install anything first: no Node.js, no npm, no Python, and no administrator password. The installer:

  • checks your computer and explains clearly if something is not supported;
  • downloads a private copy of Node.js (checksum verified) only if you do not already have a recent one;
  • installs the MoleculeDesk command into ~/.moldesk, and adds one line to your shell profile so the moldesk command is found in new terminals.

moldesk doctor checks your system and hardware — Python, Docker, CUDA, GPU, RAM, and disk — and explains what's compatible with which models.

Windows: install WSL2, open the Ubuntu terminal, and run the same command there.

Update

Run the same command again. It updates MoleculeDesk and keeps your models.

Remove

rm -rf ~/.moldesk/cli ~/.moldesk/node ~/.moldesk/bin

Then delete the line ending in # MoleculeDesk from ~/.zshrc, ~/.bashrc or ~/.profile. Installed models live in ~/.moldesk/models; delete the whole ~/.moldesk folder to remove them too.

Remote GPU servers

Home folders on cloud GPU machines are often small. Put everything on the large disk by setting MOLDESK_HOME for the installer (and for later commands):

curl -fsSL https://moleculedesk.com/install.sh | MOLDESK_HOME=/workspace/.moldesk sh
export MOLDESK_HOME=/workspace/.moldesk
export PATH="$MOLDESK_HOME/bin:$PATH"
moldesk doctor

Models need disk space: a single model can use 6 to 17 GB, so check moldesk doctor first.

Installer options

Set these before sh as shown above:

  • MOLDESK_HOME=<folder> — install and data location (default ~/.moldesk).
  • MOLDESK_NO_MODIFY_PATH=1 — do not edit your shell profile.
  • MOLDESK_CLI_SPEC=<npm package> — install a specific version, for example @moldesk/cli@0.0.1.

You can read the script before running it: moleculedesk.com/install.sh.

Docker

docker run --rm moldesk/moldesk:latest doctor

From source

git clone https://github.com/pooriyapfn/moldesk.git
cd moldesk
pnpm install
pnpm --filter @moldesk/cli dev -- doctor

Installing models

ProteinMPNN and LigandMPNN have beta installation adapters:

moldesk install proteinmpnn       # review plan, then confirm
moldesk install ligandmpnn --yes  # non-interactive
moldesk list --installed
moldesk install proteinmpnn --reinstall --yes
moldesk uninstall proteinmpnn --yes

Each Python model gets a pinned source checkout and its own uv-managed virtual environment. Checkpoints use a resumable, content-addressed cache and are verified before use. Installation is staged and promoted atomically — a failed reinstall leaves the prior installation intact. uninstall retains shared cached downloads so another model or a later reinstall can reuse them.

Where things are stored

State defaults to ~/.moldesk. Set MOLDESK_HOME to relocate managed models, state, locks, caches, and future run records:

export MOLDESK_HOME=/path/to/moldesk-data

Next steps