Retro-Blockblaster

Retro-Blockbalster (BenZinc26)

Introduction

As of 6/29/26, Retro-Blockbalster is an internal Irwin Lab web tool for submitting a compound in SMILES format and receiving retro/analoging reaction results.

The current backend runs on Cluster 2 using epyc.

How to Login

Off Site

Start the portal SSH/SOCKS tunnel from your laptop:

ssh -vNL localhost:2222:gimel:22 -D1080 USER@portal3.ucsf.bkslab.org

Leave this terminal open.

In a second terminal, log into gimel:

ssh -p 2222 USER@localhost

Then log into epyc:

ssh epyc

Confirm location:

hostname

On Site

If on the UCSF/lab network, direct login may work:

ssh -o HostKeyAlgorithms=+ssh-rsa bromero@gimel.compbio.ucsf.edu
ssh epyc

How to Open Website (MUST USE) With SwitchyOmega

Start the portal SSH/SOCKS tunnel:

ssh -vNL localhost:2222:gimel:22 -D1080 USER@portal3.ucsf.bkslab.org

In Chrome, set SwitchyOmega to:

Protocol: SOCKS5
Host: localhost
Port: 1080

Then open:

http://epyc:8001

When finished, switch SwitchyOmega back to Direct.

Where The Website Lives

Project directory on epyc:

~/Initial-BenZinc26-website

Important files:

index.html
run_job.py
backend/server_old.py
.env

.env Setup

SMTP_HOST=smtp.gmail.com
SMTP_PORT=587
SMTP_USER=...@...com
SMTP_PASSWORD=....(GOOGLE_APP_PASSWORD)
FROM_EMAIL=...@....com

How to Start Backend

On epyc:

cd ~/Initial-BenZinc26-website
python3 backend/server_old.py

The backend currently runs on:

http://0.0.0.0:8001

Test from epyc:

curl http://127.0.0.1:8001

How to Keep Backend Running

Use screen:

cd ~/Initial-BenZinc26-website
screen -S benzinc26
python3 backend/server_old.py

Detach:

Ctrl-A
D

Reconnect:

screen -r benzinc26

List screens:

screen -ls

Stop backend:

screen -r benzinc26
Ctrl-C
exit

Test Input

A test molecule that returns reaction rows:

CN(C)C(=O)NC1=CC=CC=C1

Test with curl from epyc:

curl -X POST http://127.0.0.1:8001/hello-job \
  -H "Content-Type: application/json" \
  -d '{"user_input":"CN(C)C(=O)NC1=CC=CC=C1 urea_test","email":"your_email@gmail.com"}'

Environment

The backend needs a `.env` file in the project root.

Do not commit `.env` to GitHub.

Example:

SMTP_HOST=smtp.gmail.com
SMTP_PORT=587
SMTP_USER=retro-blockbalster@gmail.com
SMTP_PASSWORD=abcdefghijklmnop
FROM_EMAIL=retro-blockbalster@gmail.com
BASE_URL=http://epyc:8001

RDKit Environment

The retro reaction script uses RDKit through:

/nfs/exj/Fe/scripts/common_db/arthor-env/bin/python

Test on epyc:

/nfs/exj/Fe/scripts/common_db/arthor-env/bin/python -c "from rdkit import Chem; print('rdkit works')"

RDKit works on epyc. RDKit may fail on gimel.

Final Result

Web interface

Finished job

Troubleshooting

Site Cannot Be Reached

Check that:

• Backend is running on epyc.
• The SSH/SOCKS tunnel is running.
• SwitchyOmega is set to SOCKS5 localhost port 1080.
• The browser is using http://epyc:8001.

Port Already In Use

Check port 8001:

ss -ltnp | grep 8001

Only kill processes owned by you:

kill PID_NUMBER

Email Not Sending

Check that:

• `.env` exists.
• Gmail app password is correct.
• SMTP_USER and FROM_EMAIL are the same account.
• The app password belongs to that same account.

Notes

For office-wide use without SSH/SOCKS tunnels, Retro-Blockblaster will eventually be placed behind an internal hostname or proxy.