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Installation

Stanza is a Go server that shells out to Python (RDKit, PDBFixer/OpenMM) and to three scientific binaries (AutoDock Vina, OpenBabel, fpocket), with a React frontend and an optional Postgres database. This guide sets up all of it.

The versions below are the ones the project is verified against. Newer point releases are generally fine; the scientific binaries are the ones worth pinning if you hit trouble.

Component Verified version Required?
Go 1.25+ yes (server)
Python 3.11+ (tested on 3.14) yes (helper scripts)
RDKit 2026.03 yes
OpenMM 8.5 yes (mutagenesis)
PDBFixer current yes (mutagenesis)
AutoDock Vina 1.2.7 yes (docking)
OpenBabel 3.1.1 yes (ligand/receptor prep)
fpocket current yes (pocket detection)
Node.js / npm 22 / 10 yes (frontend)
PostgreSQL 14+ (tested on 18) optional (falls back to in-memory)

1. The scientific stack (recommended: conda)

RDKit, OpenMM, PDBFixer, OpenBabel and Vina all live on conda-forge, and fpocket on bioconda, so one environment is the least painful way to get a consistent toolchain:

conda create -n stanza -c conda-forge -c bioconda \
    python=3.12 rdkit openmm pdbfixer openbabel vina fpocket
conda activate stanza

If you prefer native installs, each tool builds independently (Vina and fpocket ship release binaries; OpenBabel is in most package managers). Whatever route you take, verify:

vina --version          # AutoDock Vina v1.2.7
obabel -V               # Open Babel 3.1.1
fpocket -h              # prints usage
python3 -c "import rdkit, openmm, pdbfixer; print('scientific stack OK')"

If you did not use the conda environment above, install the Python packages directly:

pip install -r scripts/requirements.txt      # rdkit, openmm, pdbfixer

The synthetic-accessibility score is an optional RDKit Contrib script. If it is not importable the pipeline simply reports sa_score = null; nothing else is affected.

2. The Go server

go build ./...      # or: go run .

Go modules are fetched automatically on first build. go test ./... runs the unit tests; the tests that need RDKit or a database skip cleanly when those are absent.

3. The frontend

cd app
npm install
npm run build       # production build, or `npm run dev` for the Vite dev server

4. Environment

Variable Purpose Required?
ANTHROPIC_API_KEY molecule generation (Stage 6) required to generate; docking works without it
DATABASE_URL Postgres connection, e.g. postgres://user:pass@127.0.0.1:5432/stanza?sslmode=disable optional
STANZA_TEST_DATABASE_URL Postgres for the store integration tests test-only

Without DATABASE_URL the server runs in-memory: fully functional for a session, but run history is lost on restart. With it set, the schema is created and migrated automatically on startup, so you only need an empty database:

createdb stanza
export DATABASE_URL='postgres://<user>:<pass>@127.0.0.1:5432/stanza?sslmode=disable'

5. A writable ./tmp, run from the repo root

fpocket writes into ./tmp relative to the server's working directory, so run the server from the repository root and make sure ./tmp is writable. It is created automatically if missing. The docking stages use the system temp dir and clean up after themselves.

6. Run it

export ANTHROPIC_API_KEY=sk-ant-...            # for generation
export DATABASE_URL='postgres://...'           # optional
go run .                                        # serves on :8080
# in another shell:
cd app && npm run dev                           # frontend dev server

7. Verify the toolchain end to end

The reproducible controls exercise the whole scientific stack (fetch, mutate, dock, covalent assessment) without needing the server, the API key, or a database. If this runs, your Vina + OpenBabel + RDKit/PDBFixer install is sound:

scripts/controls/abl_t315i.sh                   # ~8 min; ends in PASS