Retro-Blockblaster - Revision history

Bromero at 22:09, 13 July 2026

2026-07-13T22:09:47Z

← Older revision		Revision as of 22:09, 13 July 2026
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	[[File:Web-interface.png\|thumb]]		[[File:Web-interface.png\|thumb]]
			[[File:Ex._Results_.png\|thumb]]
			[[File:Example results.png\|thumb]]
			[[File:Ex results with building blocks.png\|thumb]]

	As of 7/13/26, Retro-Blockbalster is an internal Irwin Lab web tool for submitting a compound in SMILES format and receiving retro/analoging reaction results (also enumeration)--all info is from Chemistry Commons and uses RDKit.		As of 7/13/26, Retro-Blockbalster is an internal Irwin Lab web tool for submitting a compound in SMILES format and receiving retro/analoging reaction results (also enumeration)--all info is from Chemistry Commons and uses RDKit.

Bromero at 22:05, 13 July 2026

2026-07-13T22:05:43Z

← Older revision		Revision as of 22:05, 13 July 2026
Line 3:		Line 3:
	== Introduction ==		== 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 (also enumeration)--all info is from Chemistry Commons and uses RDKit.		[[File:Web-interface.png\|thumb]]

			As of 7/13/26, Retro-Blockbalster is an internal Irwin Lab web tool for submitting a compound in SMILES format and receiving retro/analoging reaction results (also enumeration)--all info is from Chemistry Commons and uses RDKit.

	The current backend runs on Cluster 2 using epyc (port 8001)		The current backend runs on Cluster 2 using epyc (port 8001)

	== How to ~~Login~~ ==		== How to Open Website (MUST USE) With SwitchyOmega ==

	Start the portal SSH/SOCKS tunnel from your laptop:		Start the portal SSH/SOCKS tunnel from your laptop:
Line 16:		Line 18:

	Leave this terminal open.		Leave this terminal open.

	~~In a second terminal, log into gimel:~~

	~~<pre>~~
	~~ssh -p 2222 USER@localhost~~
	~~</pre>~~

	~~Then log into epyc:~~

	~~<pre>~~
	~~ssh epyc~~
	~~</pre>~~


	~~== How to Open Website (MUST USE) With SwitchyOmega ==~~

	In Chrome, set SwitchyOmega to:		In Chrome, set SwitchyOmega to:
Line 178:		Line 165:
	</pre>		</pre>

	RDKit works on epyc. ~~RDKit may fail on gimel.~~		RDKit works on epyc.

	~~== Final Result ==~~

	~~Web interface~~

	~~[[File:Screenshot 2026-06-29 at 1.27.35 PM.png\|thumb]]~~

	~~Finished job~~

	~~[[File:FinalJobEx.png\|thumb]]~~

	== Troubleshooting ==		== Troubleshooting ==

Bromero at 21:29, 10 July 2026

2026-07-10T21:29:37Z

← Older revision		Revision as of 21:29, 10 July 2026
Line 3:		Line 3:
	== Introduction ==		== 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.		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 (also enumeration)--all info is from Chemistry Commons and uses RDKit.

	The current backend runs on Cluster 2 using epyc.		The current backend runs on Cluster 2 using epyc (port 8001)

	== How to Login ==		== How to Login ==

	~~=== Off Site ===~~

	Start the portal SSH/SOCKS tunnel from your laptop:		Start the portal SSH/SOCKS tunnel from your laptop:
Line 31:		Line 29:
	</pre>		</pre>

	~~Confirm location:~~

	~~<pre>~~
	~~hostname~~
	~~</pre>~~

	~~=== On Site ===~~

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

	~~<pre>~~
	~~ssh -o HostKeyAlgorithms=+ssh-rsa bromero@gimel.compbio.ucsf.edu~~
	~~ssh epyc~~
	~~</pre>~~

	== How to Open Website (MUST USE) With SwitchyOmega ==		== How to Open Website (MUST USE) With SwitchyOmega ==

	~~Start the portal SSH/SOCKS tunnel:~~

	~~<pre>~~
	~~ssh -vNL localhost:2222:gimel:22 -D1080 USER@portal3.ucsf.bkslab.org~~
	~~</pre>~~

	In Chrome, set SwitchyOmega to:		In Chrome, set SwitchyOmega to:
Line 67:		Line 45:
	http://epyc:8001		http://epyc:8001
	</pre>		</pre>

	~~When finished, switch SwitchyOmega back to Direct.~~

	== Where The Website Lives ==		== Where The Website Lives ==
Line 247:		Line 223:
	* SMTP_USER and FROM_EMAIL are the same account.		* SMTP_USER and FROM_EMAIL are the same account.
	* The app password belongs to that 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.~~

Bromero: /* Environment */

2026-06-29T20:49:04Z

Environment

← Older revision		Revision as of 20:49, 29 June 2026
Line 183:		Line 183:
	SMTP_PORT=587		SMTP_PORT=587
	SMTP_USER=retro-blockbalster@gmail.com		SMTP_USER=retro-blockbalster@gmail.com
	SMTP_PASSWORD=~~GOOGLE_APP_PASSWORD~~		SMTP_PASSWORD=abcdefghijklmnop
	FROM_EMAIL=retro-blockbalster@gmail.com		FROM_EMAIL=retro-blockbalster@gmail.com
	BASE_URL=http://epyc:8001		BASE_URL=http://epyc:8001

Bromero: /* Environment */

2026-06-29T20:47:49Z

Environment

← Older revision		Revision as of 20:47, 29 June 2026
Line 182:		Line 182:
	SMTP_HOST=smtp.gmail.com		SMTP_HOST=smtp.gmail.com
	SMTP_PORT=587		SMTP_PORT=587
	SMTP_USER=~~benzinc26~~@gmail.com		SMTP_USER=retro-blockbalster@gmail.com
	SMTP_PASSWORD=GOOGLE_APP_PASSWORD		SMTP_PASSWORD=GOOGLE_APP_PASSWORD
	FROM_EMAIL=~~benzinc26~~@gmail.com		FROM_EMAIL=retro-blockbalster@gmail.com
	BASE_URL=http://epyc:8001		BASE_URL=http://epyc:8001
	</pre>		</pre>

Bromero: /* How to Open Website (MUST USE) With SwitchyOmega */

2026-06-29T20:46:56Z

How to Open Website (MUST USE) With SwitchyOmega

← Older revision		Revision as of 20:46, 29 June 2026
Line 51:		Line 51:

	<pre>		<pre>
	ssh -vNL localhost:2222:gimel:22 -D1080 ~~bromero~~@portal3.ucsf.bkslab.org		ssh -vNL localhost:2222:gimel:22 -D1080 USER@portal3.ucsf.bkslab.org
	</pre>		</pre>

Bromero: /* Off Site */

2026-06-29T20:46:38Z

Off Site

← Older revision		Revision as of 20:46, 29 June 2026
Line 14:		Line 14:

	<pre>		<pre>
	ssh -vNL localhost:2222:gimel:22 -D1080 ~~bromero~~@portal3.ucsf.bkslab.org		ssh -vNL localhost:2222:gimel:22 -D1080 USER@portal3.ucsf.bkslab.org
	</pre>		</pre>

Line 22:		Line 22:

	<pre>		<pre>
	ssh -p 2222 ~~bromero~~@localhost		ssh -p 2222 USER@localhost
	</pre>		</pre>

Bromero: Retro-Blockblaster is an internal UCSF Irwin Lab web tool for submitting compounds in SMILES format and identifying possible Chemistry Commons retro/analoging reactions. The site runs on Cluster 2 using epyc, processes jobs with an RDKit-enabled environment, generates downloadable result files, and emails users when their job is complete.

2026-06-29T20:39:33Z

Retro-Blockblaster is an internal UCSF Irwin Lab web tool for submitting compounds in SMILES format and identifying possible Chemistry Commons retro/analoging reactions. The site runs on Cluster 2 using epyc, processes jobs with an RDKit-enabled environment, generates downloadable result files, and emails users when their job is complete.

New page

= 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:

<pre>
ssh -vNL localhost:2222:gimel:22 -D1080 bromero@portal3.ucsf.bkslab.org
</pre>

Leave this terminal open.

In a second terminal, log into gimel:

<pre>
ssh -p 2222 bromero@localhost
</pre>

Then log into epyc:

<pre>
ssh epyc
</pre>

Confirm location:

<pre>
hostname
</pre>

=== On Site ===

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

<pre>
ssh -o HostKeyAlgorithms=+ssh-rsa bromero@gimel.compbio.ucsf.edu
ssh epyc
</pre>

== How to Open Website (MUST USE) With SwitchyOmega ==

Start the portal SSH/SOCKS tunnel:

<pre>
ssh -vNL localhost:2222:gimel:22 -D1080 bromero@portal3.ucsf.bkslab.org
</pre>

In Chrome, set SwitchyOmega to:

<pre>
Protocol: SOCKS5
Host: localhost
Port: 1080
</pre>

Then open:

<pre>
http://epyc:8001
</pre>

When finished, switch SwitchyOmega back to Direct.

== Where The Website Lives ==

Project directory on epyc:

<pre>
~/Initial-BenZinc26-website
</pre>

Important files:

<pre>
index.html
run_job.py
backend/server_old.py
.env
</pre>

== .env Setup ==

<pre>
SMTP_HOST=smtp.gmail.com
SMTP_PORT=587
SMTP_USER=...@...com
SMTP_PASSWORD=....(GOOGLE_APP_PASSWORD)
FROM_EMAIL=...@....com
</pre>

== How to Start Backend ==

On epyc:

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

The backend currently runs on:

<pre>
http://0.0.0.0:8001
</pre>

Test from epyc:

<pre>
curl http://127.0.0.1:8001
</pre>

== How to Keep Backend Running ==

Use screen:

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

Detach:

<pre>
Ctrl-A
D
</pre>

Reconnect:

<pre>
screen -r benzinc26
</pre>

List screens:

<pre>
screen -ls
</pre>

Stop backend:

<pre>
screen -r benzinc26
Ctrl-C
exit
</pre>

== Test Input ==

A test molecule that returns reaction rows:

<pre>
CN(C)C(=O)NC1=CC=CC=C1
</pre>

Test with curl from epyc:

<pre>
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"}'
</pre>

== Environment ==

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

Do not commit `.env` to GitHub.

Example:

<pre>
SMTP_HOST=smtp.gmail.com
SMTP_PORT=587
SMTP_USER=benzinc26@gmail.com
SMTP_PASSWORD=GOOGLE_APP_PASSWORD
FROM_EMAIL=benzinc26@gmail.com
BASE_URL=http://epyc:8001
</pre>

== RDKit Environment ==

The retro reaction script uses RDKit through:

<pre>
/nfs/exj/Fe/scripts/common_db/arthor-env/bin/python
</pre>

Test on epyc:

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

RDKit works on epyc. RDKit may fail on gimel.

== Final Result ==

Web interface

[[File:Screenshot 2026-06-29 at 1.27.35 PM.png|thumb]]

Finished job

[[File:FinalJobEx.png|thumb]]

== 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:

<pre>
ss -ltnp | grep 8001
</pre>

Only kill processes owned by you:

<pre>
kill PID_NUMBER
</pre>

=== 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.