Full DR7 API example

cat > run_dr7_prepserver_api_demo.sh <<'EOF'
#!/usr/bin/env bash
set -e

BASE="https://autodockvina.com"
JOB="dr7-example-$(date +%s)"
LIGAND="DR7.sdf"
DR7_URL="https://raw.githubusercontent.com/Joey305/autodock-WEBSERVER/main/Example/Ligand_SDF/DR7.sdf"

echo "=========================================="
echo " AutoDock-Vina PrepServer DR7 API Example"
echo "=========================================="
echo ""
echo "BASE:   $BASE"
echo "JOB:    $JOB"
echo "LIGAND: $LIGAND"
echo ""

echo "0) Download example ligand"
curl -L -o "$LIGAND" "$DR7_URL"
ls -lh "$LIGAND"
echo ""

echo "1) Health check"
curl -sS "$BASE/api/v1/health"
echo ""
echo ""

echo "2) Create workspace"
curl -sS -X POST "$BASE/api/v1/workspaces" \
  -H "Content-Type: application/json" \
  -d "{\"workspace_name\":\"$JOB\"}"
echo ""
echo ""

echo "3) Fetch receptor 3EKY chain A"
curl -sS -X POST "$BASE/api/v1/workspaces/$JOB/receptors/fetch" \
  -H "Content-Type: application/json" \
  -d '{"pdb_id":"3EKY","chains":"A"}'
echo ""
echo ""

echo "4) Save example docking center"
curl -sS -X POST "$BASE/api/v1/workspaces/$JOB/centers/save" \
  -H "Content-Type: application/json" \
  -d '{
    "method":"xyz",
    "receptor":"Receptors/3eky.pdb",
    "center":[10.5, 22.1, -3.4],
    "size":20
  }'
echo ""
echo ""

echo "5) Confirm saved centers"
curl -sS "$BASE/api/v1/workspaces/$JOB/centers"
echo ""
echo ""

echo "6) Prepare receptor"
curl -sS -X POST "$BASE/api/v1/workspaces/$JOB/prep/start" \
  -H "Content-Type: application/json" \
  -d '{
    "remove_hets":"all",
    "remove_chains":"",
    "altloc":"collapse"
  }'
echo ""
echo ""

echo "7) Check receptor-preparation status"
curl -sS "$BASE/api/v1/workspaces/$JOB/prep/status"
echo ""
echo ""

echo "8) Check summary before ligand upload"
curl -sS "$BASE/api/v1/workspaces/$JOB/summary"
echo ""
echo ""

echo "9) Upload DR7 ligand"
curl -sS -X POST "$BASE/api/v1/workspaces/$JOB/ligands/upload" \
  -F "mode=single" \
  -F "file=@$LIGAND"
echo ""
echo ""

echo "10) Confirm ligand upload"
curl -sS "$BASE/api/v1/workspaces/$JOB/ligands"
echo ""
echo ""

echo "11) Build portable docking package"
curl -sS -X POST "$BASE/api/v1/workspaces/$JOB/build" \
  -H "Content-Type: application/json" \
  -d '{
    "package_mode":"portable",
    "vina_poses":20,
    "confgen_poses":64
  }'
echo ""
echo ""

echo "12) List generated artifacts"
curl -sS "$BASE/api/v1/workspaces/$JOB/artifacts"
echo ""
echo ""

echo "13) Download final ZIP"
curl -L -o "${JOB}_docking_package.zip" \
  "$BASE/api/v1/workspaces/$JOB/download"
echo ""
echo ""

echo "14) Confirm local ZIP"
ls -lh "${JOB}_docking_package.zip"
echo ""

echo "Done."
echo "Downloaded package: ${JOB}_docking_package.zip"
EOF

chmod +x run_dr7_prepserver_api_demo.sh
./run_dr7_prepserver_api_demo.sh

Create and upload a simple SMI file

The first column is the SMILES string. The optional second column is a ligand ID. Replace the example SMILES with your molecule of interest.

cat > example_ligand.smi <<'EOF'
CC(=O)Oc1ccccc1C(=O)O aspirin_example
EOF

curl -sS -X POST "$BASE/api/v1/workspaces/$JOB/ligands/upload" \
  -F "mode=single" \
  -F "file=@example_ligand.smi"
echo ""

curl -sS "$BASE/api/v1/workspaces/$JOB/ligands"
echo ""

Heroku Open Babel checklist

# Aptfile
openbabel

# Buildpacks

heroku buildpacks:add --index 1 heroku-community/apt --app autodockvina
heroku buildpacks:add --index 2 heroku/python --app autodockvina

# Verify obabel

heroku run --no-tty "which obabel && obabel -V" --app autodockvina

# Find plugins if needed

heroku run --no-tty "find /app/.apt -type f ( -name 'pdbformat.so' -o -name 'pdbqtformat.so' -o -name 'plugindefines.txt' ) -print" --app autodockvina

# Example plugin path

heroku config:set BABEL_LIBDIR=/app/.apt/usr/lib/x86_64-linux-gnu/openbabel/3.1.1 --app autodockvina
heroku restart --app autodockvina

# Confirm PDB and PDBQT formats

heroku run --no-tty 'echo BABEL_LIBDIR=$BABEL_LIBDIR && which obabel && obabel -V && obabel -L formats | grep -E "pdb|pdbqt"' --app autodockvina