fastfold-agent-cli 0.0.1

Fastfold CLI — An autonomous agent for drug discovery research

Fastfold Agent CLI

Where scientists and AI agents work together doing real science.

Ask questions in natural language. Fastfold CLI plans the analysis, selects the right tools, executes them, validates results, and returns data-backed conclusions. Integrates with Fastfold AI Cloud for GPU compute, protein folding, workflow orchestration, and team collaboration.

Built on top of Claude Agent SDK and CellType CLI.

Installation

Quick install (recommended)

curl -fsSL https://raw.githubusercontent.com/fastfold-ai/fastfold-agent-cli/main/install.sh | bash

Detects Python 3.10+, installs via uv, pipx, or pip, and launches an interactive setup wizard.

Install from source with uv

# Clone the repo
git clone https://github.com/fastfold-ai/fastfold-agent-cli.git
cd fastfold-agent-cli

# Install uv if you don't have it
curl -LsSf https://astral.sh/uv/install.sh | sh

# Create a virtual environment with Python 3.12 and install all dependencies
uv venv --python 3.12
uv sync

# Run the setup wizard
uv run fastfold setup

# Or activate the venv and use fastfold directly
source .venv/bin/activate
fastfold setup

Install from PyPI

# With uv (recommended)
uv tool install fastfold-agent-cli

# With pipx
pipx install fastfold-agent-cli

# With pip
pip install fastfold-agent-cli

# With all optional scientific stacks (RDKit, scanpy, etc.)
pip install "fastfold-agent-cli[all]"

Authentication

# Interactive setup wizard (recommended — configures Anthropic + Fastfold AI Cloud keys)
fastfold setup

# Or set directly
export ANTHROPIC_API_KEY="sk-ant-..."
export FASTFOLD_API_KEY="sk-..."

# Non-interactive (CI/scripting)
fastfold setup --api-key sk-ant-... --fastfold-api-key sk-...

Getting Started

# Start interactive session
fastfold

# Single query
fastfold "What are the top degradation targets for this compound?"

# Validate setup
fastfold doctor

# List available tools
fastfold tool list

# List loaded skills
fastfold skill list

Interactive commands

Inside fastfold interactive mode:

• /help — command reference + examples
• /tools — list all tools with status
• /agents N <query> — run N parallel research agents
• /sessions, /resume — session lifecycle
• /copy, /export — save/share outputs
• /usage — token and cost tracking

Quick examples

Target prioritization

fastfold "I have a CRBN molecular glue. Proteomics shows it degrades
          IKZF1, GSPT1, and CK1α. Which target should I prioritize?"

Protein folding

fastfold "Fold this sequence with boltz-2 and find the binding pockets: MALWMRLLPLL..."

Combination strategy

fastfold "My lead compound is immune-cold. What combination strategy should I use?"

Key Features

190+ Domain Tools

Category	Examples
Target	Neosubstrate scoring, degron prediction, co-essentiality networks
Chemistry	SAR analysis, fingerprint similarity, scaffold clustering
Expression	L1000 signatures, pathway enrichment, TF activity, immune scoring
Viability	Dose-response modeling, PRISM screening, therapeutic windows
Biomarker	Mutation sensitivity, resistance profiling, dependency validation
Clinical	Indication mapping, population sizing, TCGA stratification
Safety	Anti-target flagging, multi-modal profiling, SALL4 risk
Structure	AlphaFold fetch, docking, binding sites, MD simulation
Folding	Fastfold AI Cloud: boltz-2, monomer, multimer, simplefold_*
Literature	PubMed, OpenAlex, ChEMBL search
DNA	ORF finding, codon optimization, primer design, Gibson/Golden Gate assembly

Agent Skills

Fastfold CLI ships with a bundled skill catalog and supports user-installed skills:

fastfold skill list          # see loaded skills

# Install additional skills (requires npx), check https://skills.sh
npx skills addd <owner/repo>

Data Management

fastfold data pull depmap    # DepMap CRISPR, mutations, expression
fastfold data pull prism     # PRISM cell viability
fastfold data pull msigdb    # Gene sets

# Or point to existing data
fastfold config set data.depmap /path/to/depmap/

Reports

fastfold report list         # list reports
fastfold report publish      # convert latest .md to .html
fastfold report show         # open in browser

Troubleshooting

Symptom	Fix
fastfold fails at startup	fastfold doctor
No API key	fastfold setup or export ANTHROPIC_API_KEY=...
Data not found	fastfold data pull <dataset>
Missing dependency	pip install "fastfold-agent-cli[all]"
Session lost	fastfold --continue

Contributing

git clone https://github.com/fastfold-ai/fastfold-agent-cli.git
cd fastfold-agent-cli
uv venv --python 3.12 && uv sync
fastfold setup
pytest tests/

License

MIT — see LICENSE

Credits

Based on CellType CLI