DISI - Recent changes [en]

Running ChemSTEP with SymDOCK

Kholland — Tue, 07 Jul 2026 17:20:38 GMT

Created page with "last update: july7 2026 katie. ChemSTEP (Chemical Space Traversal and Exploration Procedure) is an open-source, transparent acceleration algorithm for molecular docking capable of dealing with virtual libraries of several trillion compounds. This wiki page is a guide for BKS lab members to run ChemSTEP on Wynton HPC, using a subset of ZINC (22B or 72B) or 13.3B library from Enamine REAL. At a high-level, ChemSTEP is an iterative process that identifies molecules from..."

New page

last update: july7 2026 katie.

ChemSTEP (Chemical Space Traversal and Exploration Procedure) is an open-source, transparent acceleration algorithm for molecular docking capable of dealing with virtual libraries of several trillion compounds. This wiki page is a guide for BKS lab members to run ChemSTEP on Wynton HPC, using a subset of ZINC (22B or 72B) or 13.3B library from Enamine REAL.

At a high-level, ChemSTEP is an iterative process that identifies molecules from the larger virtual library to prioritize for docking. First, we identify a random sample of the total library (termed "seed set", round zero) and dock those molecules to the target of interest. From this seed set, we can calculate total-library pProp values (-log rank percentages) and the number of "virtual hits" in the total library (high-scoring molecules). ChemSTEP will identify a set of maximally diverse molecules that score above the desired pProp threshold ("beacons") from the seed set. These beacons guide prioritization, where molecules chosen and output by ChemSTEP are close in chemical space to the beacons. Prioritized molecules are then built, docked, and returned to ChemSTEP for a second round of prioritization. This process is iterated until you reach desired virtual hit recovery, or you are no longer recovering virtual hits.

= Running ChemSTEP (Auto DOCK and Build with SymDOCK) =

ChemSTEP is configured to run on Wynton with libraries of '''13B''', '''22B''' (HAC 17-26, cLogP <= 3.5), and '''72B''' (HAC4-49, cLogP <=4.0). This page covers the full workflow for running ChemSTEP with automatic submission of docking and building jobs.

__TOC__

== 1. Source Environment ==

<pre>
source /wynton/group/bks/work/shared/kholland/chemstep_auto_symdock/symdock/bin/activate
</pre>

== 2. Dock the Seed Set ==

Copy the <code>.sdi</code> file for the library you want to use into a directory called '''sdi''' at the same level as your dockfiles:

{| class="wikitable"
! Library !! Path
|-
| 13B || <code>/wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/libraries/13B/13M_seeds.wynton.sdi</code>
|-
| 22B || <code>/wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/libraries/22B/22M_seeds.sdi</code>
|-
| 72B || <code>/wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/libraries/72B/72M_seeds.sdi</code>
|}

DOCK the seed set:

<pre>
bash /wynton/group/bks/work/shared/kholland/chemstep_auto_symdock/subScripts/submit_symdock.sh
</pre>

== 3. Gather Scores for the Seed Set ==

Once docking is complete, run the following from the directory '''one level above''' your docking output (where dockfiles and sdi directories are).

'''22B/72B library:'''
<pre>
python /wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/get_scores.py 0
</pre>

'''13B library:'''
<pre>
python /wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/get_scores.py 0 MOL
</pre>

Note: You must specify the molecule ID prefix for the 13B library (<code>MOL</code>)

Verify that <code>scores_round_0.txt</code> was correctly written:
<pre>
wc -l scores_round_0.txt
</pre>

== 4. Convert Scores to .npy Files ==

Convert scores to ChemSTEP-readable <code>.npy</code> files:

<pre>
python /wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/convert_scores_to_npy.py 0 <mol_id_prefix>
</pre>

The <code>mol_id_prefix</code> should match the library:

{| class="wikitable"
! Library !! Prefix
|-
| 22B / 72B || <code>CSLB</code>
|-
| 13B || <code>MOL</code>
|}

== 5. Set Up the ChemSTEP Run Directory ==

Create and enter a ChemSTEP run directory, then copy in the necessary files (with the ChemSTEP SymDOCK environment sourced):

<pre>
mkdir chemstep_run
cd chemstep_run
chemstep-run-new
</pre>

This will populate the directory with <code>params.txt</code>, <code>run_chemstep.py</code>, and <code>launch_chemstep_as_job.sh</code>.

=== Optional: Integrated IFP ===

If running with integrated IFP for beacon selection, also run:

<pre>
chemstep-run-ifp
</pre>

This copies in the additional files <code>ifp_acceptance_criteria.txt</code> and <code>interactions.txt</code>.

== 6. Edit params.txt ==

Add the absolute paths to the ChemSTEP-readable score and indices <code>.npy</code> arrays generated in Step 4.

<pre>
seed_indices_file: /path/to/your/indices_round_0.npy
seed_scores_file: /path/to/your/scores_round_0.npy
hit_pprop: 5.5
n_docked_per_round: 2000000
bundle_size: 1000
max_beacons: 100
max_n_rounds: 250
</pre>

=== Parameter Reference ===

{| class="wikitable"
! Parameter !! Description
|-
| <code>hit_pprop</code> || Defines a "virtual hit." pProp = −log(rank%) within the total library score distribution. E.g., pProp 4 in 13B space ≈ top 0.01% (~1.3M molecules); pProp 5 ≈ 0.001% (~132K). The seed set should contain at least 10<sup>(pProp+2)</sup> molecules.
|-
| <code>n_docked_per_round</code> || Number of molecules prioritized per round. All must be built and docked between rounds. Too many slows throughput and may reduce diversity; too few slows virtual hit recovery. Recommended: 1-2 million
|-
| <code>max_beacons</code> || Diverse, well-scoring molecules used to guide prioritization. All molecules above the pProp threshold are candidates. Too many reduce inter-beacon diversity; too few hinder space exploration. Fewer beacons than specified may be assigned if an insufficient number of molecules clear the threshold. Recommended: 100
|-
| <code>bundle_size</code> || In auto docking mode, number of molecules submitted as a single build job.
|-
| <code>max_n_rounds</code> || No adjustment needed when running ChemSTEP prospectively as described here.
|}

== 7. Edit run_chemstep.py ==

'''Note:''' All paths must be '''absolute paths'''.

=== Required Settings ===

Set <code>lib_path</code> to the library pickle for your library:

{| class="wikitable"
! Library !! Path
|-
| 13B || <code>/wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/libraries/13B/boltz_fplib.pickle</code>
|-
| 22B || <code>/wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/libraries/22B/22B_fplib.pickle</code>
|-
| 72B || <code>/wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/libraries/72B/72B_fplib.pickle</code>
|}

<pre>
lib_path = '/full/path/to/library.pickle'
</pre>

Set <code>dockfiles_path</code>:

<pre>
dockfiles_path="/full/path/to/dockfiles"
</pre>

=== Optional: minTD Exclusion Zone ===

Molecules will not be prioritized from within a specified Tanimoto distance of beacons. Comment in the relevant lines and update the value. Consider also setting <code>enforce_n_docked_per_round = True</code> when using this option:

<pre>
min_td_search=0.5,
enforce_n_docked_per_round=True,
</pre>

=== Optional: Integrated IFP ===

Only selects beacons that satisfy user-defined interaction criteria. Comment in the following lines and update the paths to the necessary files (copied in Step 5 if you ran <code>chemstep-run-ifp</code>):

<pre>
use_IFP=True,
ifp_pdb_path='/full/path/to/rec.crg.pdb',
interactions_file='/full/path/to/interactions.txt',
ifp_acceptance_criteria_file='/full/path/to/ifp_acceptance_criteria.txt',
</pre>

'''<code>interactions.txt</code>''' — one interaction per line, comma-separated. Format: <code>interaction_type, residue_name_and_number</code>. Example:

<pre>
Hydrogen bond, GLY-19
Ionic, ASP-149
</pre>

Supported interaction types include: Proximal, Hydrogen bond, Ionic, Cation-pi, Hydrophobic, Halogen bond, and others. See LUNA and IFP documentation for the full list.

'''<code>ifp_acceptance_criteria.txt</code>''' — defines the number of unsatisfied donors/acceptors/specific interactions required for a molecule to pass IFP and be considered for beacon selection. Example:

<pre>
#_donors
#_acceptors
#_unstatisfied_donors == 0
#_unstatisfied_acceptors <= 4
Ionic/ASP-149 > 0
</pre>

=== Optional: SMARTS exclusion filter ===
Integrated SMARTS filer can exclude problematic chemotypes from being built, docked, or selected as beacons. Multiple SMARTS patterns are tolerated. Comment in the following line in run_chemstep.py:

<pre>
filter_smarts=['n1cncnc1', 'c1cccnc1[SH]']
</pre>

TRIAZINES: 'n1cncnc1'

=== Example: AmpC on 22B with minTD=0.50, No IFP ===

<pre>
lib_path = '/wynton/group/bks/work/shared/kholland/chemstep_auto_v04/scripts/libraries/22B/22B_fplib.pickle'
lib = load_library_from_pickle(lib_path)
algo = CSAlgo(lib, 'params.txt', 'output', 16, verbose=True,
scheduler='sge', smi_id_prefix='CSLB',
python_exec="/wynton/group/bks/work/shared/kholland/chemstep_auto_v04/bin/python",
dockfiles_path="/wynton/group/bks/work/kholland/chemstep_ampc_22B/seed_docking/dockfiles",
min_td_search=0.5,
enforce_n_docked_per_round=True,
#use_IFP=True,
#ifp_pdb_path='/path/to/your/reference/rec.crg.pdb',
#interactions_file='/path/to/your/interactions.txt',
#ifp_acceptance_criteria_file='/path/to/your/ifp_acceptance_criteria.txt',
docking_method="auto", track_beacon_orig=True)
</pre>

== 8. Launch the Job ==

Submit the main ChemSTEP job:

<pre>
qsub launch_chemstep_as_job.sh
</pre>

== 9. Monitor Job Status ==

Check job status with <code>qstat</code>. The main job will run for up to '''2 weeks''' given no errors. ChemSTEP will launch search, building, and docking jobs in successive rounds.

'''Note:''' If any building or docking subjobs hang, the main job will not proceed until those are canceled or finished. Monitor job statuses regularly and occasionally verify that docking output files (<code>scores_round_*.txt</code>) are being populated.

== 10. View Beacon SMILES and IDs ==

From the ChemSTEP running directory, run the following in a '''screen session on a dev node''':

<pre>
python /wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/get_beacon_ids_smiles.py output/complete_info/beacons.df /path/to/fp/library output.txt
</pre>

{| class="wikitable"
! Library !! Path
|-
| 13B || <code>/wynton/group/bks/work/omailhot/chunked_ampc_chemstep_lib</code>
|-
| 22B || <code>/wynton/group/bks/work/kholland/22B_fp_library</code>
|-
| 72B || <code>/wynton/group/bks/work/kholland/72B_fp_library</code>
|}

Use the library pickle path from [[#7. Edit run_chemstep.py|Step 7]].

== 11. Plot Hit Recovery ==

In your ChemSTEP directory containing <code>chemstep_algo.log</code> and score files,
<pre>
bash /wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/submit_hit_recovery.sh
</pre>

== 12. Get Poses After Docking ==

Make a list of <code>test.mol2.gz.0</code> files from docking:

<pre>
find round_*_docking/bundle_paths -maxdepth 2 -name "test.mol2.gz.0" > docked_poses.txt
</pre>

Then extract top poses:

<pre>
python /wynton/group/bks/work/bwhall61/for_beau/top_poses.py -t <pProp_energy_threshold> -s <num_poses_per_file> docked_poses.txt
</pre>

Get poses for Beacons:
<pre> python /wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/get_beacon_poses.py output/complete_info/beacons.df /path/to/fp/library/ docked_poses.txt -o beacon_poses -j 8
</pre>

ADMET Builder

Bromero — Tue, 07 Jul 2026 00:23:52 GMT

← Older revision		Revision as of 00:23, 7 July 2026
Line 2:		Line 2:

	== Introduction ==		== Introduction ==
			[[File:ADMET builder webpage.png\|thumb]]

	As of 7/6/26, '''ADMET Builder''' is an internal Irwin Lab web tool for submitting one or more compounds in SMILES format and receiving OpenADMET prediction results.		As of 7/6/26, '''ADMET Builder''' is an internal Irwin Lab web tool for submitting one or more compounds in SMILES format and receiving OpenADMET prediction results.
Line 18:		Line 19:
	* Human plasma protein binding		* Human plasma protein binding
	* Downloadable CSV output		* Downloadable CSV output

			[[File:Results.png\|thumb]]

	Created by Benjamin "Ben" Romero (Undergrad Northwestern University '29), Summer 2026.<br>		Created by Benjamin "Ben" Romero (Undergrad Northwestern University '29), Summer 2026.<br>

File:Results.png

Bromero — Tue, 07 Jul 2026 00:23:43 GMT

Bromero uploaded File:Results.png

New page

Results

File:ADMET builder webpage.png

Bromero — Tue, 07 Jul 2026 00:22:09 GMT

Bromero uploaded File:ADMET builder webpage.png

New page

interface

ADMET Builder

Bromero — Tue, 07 Jul 2026 00:18:27 GMT

Show changes

ADMET Builder

Bromero — Tue, 07 Jul 2026 00:13:48 GMT

ADMET Builder is a lightweight very modular web interface for running OpenADMET predictions from typed SMILES strings. It was created to make ADMET prediction easier to use for chemists, students, and researchers who may not want to run command-line tools directly.

New page

# ADMET Builder

ADMET Builder is a lightweight web interface for running OpenADMET predictions from typed SMILES strings. It was created to make ADMET prediction easier to use for chemists, students, and researchers who may not want to run command-line tools directly.

---

## What It Does

ADMET Builder lets a user paste one or more SMILES strings into a web interface and run ADMET predictions.

The app returns:

- A clean results table in the browser
- A downloadable CSV file
- Molecular formulas calculated from SMILES
- RDKit-generated 2D structure images
- Click-to-enlarge structure viewing

The current OpenADMET model predicts:

- logD
- Caco-2 A to B permeability
- Caco-2 B to A permeability
- Mouse plasma protein binding
- Human plasma protein binding

---

## How It Works

ADMET Builder has three main parts:

| Layer | Technology | Purpose |
|---|---|---|
| Frontend | HTML, CSS, JavaScript | User interface, SMILES input, results table, structure display |
| Backend API | Flask | Receives SMILES, runs predictions, returns results |
| Prediction Engine | OpenADMET | Generates ADMET predictions from molecular input |

The browser sends SMILES strings to the backend using:

```text
POST /predict-smiles
```

The Flask backend then:

1. Receives the SMILES strings.
2. Converts them into a temporary CSV file.
3. Runs the OpenADMET command-line prediction tool.
4. Reads the prediction output.
5. Generates molecular formulas and structure images using RDKit.
6. Sends results back to the web interface as JSON.
7. Provides the same results as a downloadable CSV file.

---

## Why It Is Modular

ADMET Builder is intentionally modular. The frontend, backend, and prediction engine are separated so each part can be changed or reused.

This means:

- The frontend can be redesigned without changing the model logic.
- The Flask backend can support new endpoints.
- Additional OpenADMET models can be added later.
- Other chemistry tools can be wrapped using the same backend pattern.
- The results table can be adapted for different prediction outputs.
- The SMILES-to-structure display can be reused in other cheminformatics apps.
- The app can serve as a template for future scientific web interfaces.

Because of this structure, ADMET Builder can be used not only as a lab tool, but also as a starting point for other modular research software.

---

## Getting The Code

Clone the repository using HTTPS:

```bash
git clone https://gitlab.docking.org/bromero/admet-builder.git
cd admet-builder
```

Or clone using SSH:

```bash
git clone git@gitlab.docking.org:bromero/admet-builder.git
cd admet-builder
```

---

## Requirements

ADMET Builder expects OpenADMET to already be installed in a working conda environment.

The C7 setup uses:

```bash
module load anaconda3/2025.06.0
source "$(conda info --base)/etc/profile.d/conda.sh"
conda activate openadmet-models
```

Python dependencies include:

- Flask
- pandas
- RDKit
- OpenADMET models package

The app also expects the OpenADMET model directory to be available at:

```text
~/openadmet/permeability-logd-ppb-chemeleon-baseline/anvil_training
```

---

## Running The App

From the repository folder:

```bash
cd ~/openadmet/admet-builder
module load anaconda3/2025.06.0
source "$(conda info --base)/etc/profile.d/conda.sh"
conda activate openadmet-models
python app.py
```

The app runs on:

```text
http://169.230.26.173:8501
```

---

## Running In Screen

For persistent use on C7, run ADMET Builder inside `screen`.

Start a screen session:

```bash
screen -S admet-builder
```

Inside screen, run:

```bash
module load anaconda3/2025.06.0
source "$(conda info --base)/etc/profile.d/conda.sh"
conda activate openadmet-models
cd ~/openadmet/admet-builder
python app.py
```

Detach from screen while keeping the app running:

```text
Ctrl+A
D
```

Reconnect later:

```bash
screen -r admet-builder
```

List running screen sessions:

```bash
screen -ls
```

Stop the app from inside screen:

```text
Ctrl+C
```

---

## Using The Website

1. Open ADMET Builder in the browser.
2. Paste one SMILES string per line.
3. Click `RUN ADMET`.
4. View the results in the table.
5. A CSV file downloads automatically.
6. Click a molecular structure image to enlarge it.

Example input:

```text
CCO
c1ccccc1
CC(=O)Oc1ccccc1C(=O)O
```

---

## Output

The output table includes:

| Column | Meaning |
|---|---|
| Molecule | Molecular formula calculated from the SMILES string |
| SMILES | Input molecule string |
| Structure Image | RDKit-generated 2D molecular structure |
| logD | Predicted distribution coefficient |
| Caco-2 A to B | Predicted apical-to-basolateral permeability |
| Caco-2 B to A | Predicted basolateral-to-apical permeability |
| Mouse PPB | Predicted mouse plasma protein binding |
| Human PPB | Predicted human plasma protein binding |

The CSV download contains the same prediction values in a machine-readable format.

---

## Access Through SwitchyOmega

If using SwitchyOmega, the proxy should be:

```text
SOCKS5
localhost
1074
```

The website itself is opened at:

```text
http://169.230.26.173:8501
```

The ports mean different things:

| Port | Purpose |
|---|---|
| 1074 | Local SOCKS5 proxy used by SwitchyOmega |
| 8501 | ADMET Builder web app running on C7 |

If the SOCKS proxy is not running, start it from a Mac terminal:

```bash
ssh -f -N -D 1074 bromero@epsilon.compbio.ucsf.edu
```

---

## Repository Structure

```text
admet-builder/
├── app.py
├── static/
│ ├── index.html
│ ├── styles.css
│ └── app.js
└── .gitignore
```

### `app.py`

The Flask backend. It receives SMILES input, runs OpenADMET, generates formulas and structure images, and returns results.

### `static/index.html`

The main web page structure.

### `static/styles.css`

The UCSF-style visual design and table layout.

### `static/app.js`

The browser-side logic. It sends SMILES to the backend, renders the results table, downloads CSV output, and handles structure image enlargement.

---

## Current API Endpoint

```text
POST /predict-smiles
```

Example JSON request:

```json
{
"smiles": [
"CCO",
"c1ccccc1",
"CC(=O)Oc1ccccc1C(=O)O"
]
}
```

Example response includes:

```json
{
"csv": "...",
"rows": [],
"columns": []
}
```

The frontend uses this response to display results and download the CSV.

---

## Notes

ADMET Builder is a research tool. Its predictions are intended for screening, comparison, prioritization, and exploration.

Results should not be treated as experimental measurements.

---

## Attribution

Created by Benjamin "Ben" Romero (Undergrad Northwestern University '29), Summer 2026.
Developed in the Irwin Lab at UCSF.
Released as part of an open-source UCSF research tool; please credit the creator and lab when using or adapting this work.

ZINC26:Help

Frodo — Thu, 02 Jul 2026 18:16:40 GMT

asfd

← Older revision		Revision as of 18:16, 2 July 2026
Line 1:		Line 1:
	ZINC26 provides interfaces to search purchasable chemical space and biologically active chemical space.		ZINC26 provides interfaces to search purchasable chemical space and biologically active chemical space.

	~~The interface at zinc26.docking.org features both an~~ interactive ~~batch method to search. The interative approach allows near-instant~~ (~10s) ~~searches of individual databases of up to 5 billion molecules in each transaction. This allows "what~~ if~~" type searches of parts of chemical space, and based on individual vendors~~.		There are two separate interfaces, interactive (10s turnaround time) and batch (3 mins turnaround time if there is no queue).

	~~== Interactive ==~~		The interactive interface searches specific databases subsets you select, from a few to a few billion molecules each. The batch interface searches _all_ purchasable or _all_ bioactive databases in a single transaction.

	~~== Batch ==~~		Anonymous users can search for one molecule at a time in the batch interface, while logged in users may search for up to 10 molecules in a single transaction.

			We throttle usage in other (so far undisclosed) ways that allow us to offer a free public service without overloading.

			Collectively, ZINC26 allows "what if" type searches of purchasable and biologically precedented chemical space. It allows the following questions.

			* what are the most similar molecules I can purchase?
			* what the most most similar molecules I can purchase from a particular vendor (within a particular HAC range)?
			* Does vendor X sell compounds that look like my compound?
			* what is the nearest drug to my compound?
			* what is the nearest chembl bioactive 1uM or better to my compound?
			* what is the nearest ligand for some gene product, say DRD4, 1uM or better, to my compound?
			* what is the nearest natural product to my compound?
			* what is the nearest metabolite to my compound?

	~~== Searching Bioactive chemical space ==~~

	== Updates / Status ==		== Updates / Status ==
			* As of July 2, 2026, zinc26 is in production at zinc26.docking.org and zinc26dev.docking.org. If you cannot get in, write us at jjiteam at googlegroups dot com for access.
			* we have indexed most of the commercially available libraries that are distributed as enumerated libraries. Synthon based libraries will enumerated, but it takes time (ask the vendor to enumerate up to HAC29 and send it to us, and we will index it)
			* We are aiming to offer "all purchasable to HAC29" and "all bioactives" as one-click interactive databases. So far, we are not quiet there, but we are close. Use the batch interface until that is ready. It may turn out that we need to offer
			* all-purchasable-to-HAC25, and then one by one by HAC after that, in order to provide good interactive service. But we are trying to do it to HAC29.

	== how to report suggestions / problems ==		== how to report suggestions / problems ==
			Please use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9

			* Please send us catalogs that you do not see indexed.

SEA26

Frodo — Thu, 02 Jul 2026 17:08:16 GMT

asdf

New page

This is the documentation for the new version of SEA by Yujin Wu and Khanh Tang.

== explanation of all the columns ==

== explanation of all the colors ==

== narration of one or two examples to show how to use it ==

== explanation of all menu items ==

== explanation of how to use compounds vs targets ==

== FAQ ==

== Data sources ==

== Software is open source ==
(link to github?)

[[Category:SEA]]

Group Meeting

Yvonne Munchua — Thu, 02 Jul 2026 16:58:02 GMT

MEETING SCHEDULE

← Older revision		Revision as of 16:58, 2 July 2026
(One intermediate revision by the same user not shown)
Line 25:		Line 25:

	= '''MEETING SCHEDULE =		= '''MEETING SCHEDULE =

	*6/5/26: Katie Holland
	*6/12/26: Brian Dick
	*6/19/26: NO lab mtg (UC Holiday - Juneteenth)
	*6/26/26: Weixiu Xu


Line 53:		Line 48:
	*Xinyu Xu		*Xinyu Xu
	*Joe Pepe		*Joe Pepe
			*Maya Druch (Start Date: 6/22/26 - Will present Oct 2)
	*Andrii Kyrylchuk		*Andrii Kyrylchuk
	*Katie Holland		*Katie Holland
	*Weixiu Xu (Start Date: 2/2/26)		*Weixiu Xu
			*Chris Flores (Start Date: 7/1/26 - Will present Nov 6)
	*Jongbin Kim		*Jongbin Kim
	*Zoey Dingman		*Zoey Dingman

Category:ZINC26

Frodo — Wed, 01 Jul 2026 15:47:05 GMT

asdf

New page

Link all ZINC26 related articles together.

ZINC26:API

Frodo — Wed, 01 Jul 2026 15:46:41 GMT

asdf

New page

Here is how to use the ZINC26 API.

Documentation is at zinc26dev.docking.org/docs/

Examples of how to use it. This may change as it develops, and may change as login/authentication is incorporated.

[[Category:JJI]]
[[Category:ZINC26]]

Looping solution

Frodo — Tue, 30 Jun 2026 22:48:19 GMT

asdf

New page

= Looping Solution =

Here is our approach to running jobs at scale on coreHPC.

* 1. on cluster 7 there is a directory with job control language
* 2. there is a cronjob that runs on corehpc.
* 3. once an hour, it iterates over all jobs in the system, and moves them forward.
* 4. the job status of each job is below.
* 5. the supported job control language is below.

== job status ==
* 0 new job request
* 1 job data has started copying to fac
* 2 job data copy to fac has completed successfully
* 12 job data copy to fac failed (and requires attention)
* 3 job has been submitted on coreHPC
* 4 job is running on coreHPC
* 5 job has completed on coreHPC
* 15 job has failed in coreHPC (and requires attention)
* 6 scp of job results to C7 has started
* 7 scp of job results to C7 has completed normally
* 17 scp of job results to C7 has failed (and requires attention)

== supported job control language (JCL) ==

* Each job has a file. The command syntax is as follows
type: docking, chemstep, other
dockfiles: /nfs/exe/work/jji/projects/target1/dockfiles (includes INDOCK)
tranches: /nfs/exe/work/jji/projects/target1/tranches (one file per jobs, circa 1 TB each)

[[Category:JJI]]

Cluster 8

Frodo — Tue, 30 Jun 2026 22:39:30 GMT

asdf

← Older revision		Revision as of 22:39, 30 June 2026
Line 41:		Line 41:
	https://it.ucsf.edu/how-to/fac-drive-mapping-instructions?check_logged_in=1#linux		https://it.ucsf.edu/how-to/fac-drive-mapping-instructions?check_logged_in=1#linux


			smb://capstorage.fac.ucsf.edu/CX900007_DS1. lab storage
			/mnt/fac/CX900007_DS1 fac

	[[Category:Cluster]]		[[Category:Cluster]]

Standup tuesday

Frodo — Tue, 30 Jun 2026 16:39:38 GMT

asdf

@@ Line 1: / Line 1: @@
-I want to extend our weekly standup as follows:
 * 12 - 12.30  min 1 to max 5 mins per person
 This meeting will be by zoom and in person when possible.
+If you are not available, no worries, but please send me a short email with what you've done in the last week and what you plan for the coming week.
-Please update your own information, and discuss with others to decide priorities.
+[[Category:JJI]]

Chemspace API

Frodo — Mon, 29 Jun 2026 21:54:56 GMT

asdf

← Older revision		Revision as of 21:54, 29 June 2026
Line 60:		Line 60:
	-H "Content-Type: multipart/form-data" \		-H "Content-Type: multipart/form-data" \
	-F "query=CSMB00000000001, CSC000000065, 60-35-5, MFCD06217521, CSC1=NN=NN1C, BBV-32027078"		-F "query=CSMB00000000001, CSC000000065, 60-35-5, MFCD06217521, CSC1=NN=NN1C, BBV-32027078"


			[[Category:JJI]]
			[[Category:API]]

Datagrok

Frodo — Mon, 29 Jun 2026 21:53:27 GMT

asdf

New page

https://github.com/datagrok-ai/public/blob/master/packages/Chem/README.md

figure out how to use this.

[[Category:JJI]]

Category:Huggingface

Frodo — Mon, 29 Jun 2026 21:52:38 GMT

asdf

New page

Links to things we do on huggingface

Category:ADMET

Frodo — Mon, 29 Jun 2026 21:52:21 GMT

asdf

New page

links for ADMET calculations

OpenADMET on huggingface

Frodo — Mon, 29 Jun 2026 21:52:06 GMT

asdf

New page

This page is all about openADMET on huggingface.

https://huggingface.co/spaces/openadmet/prediction_portal

https://huggingface.co/spaces/jir322/prediction_portal

[[Category:JJI]]
[[Category:ADMET]]
[[Category:Huggingface]]

Retro-Blockblaster

Bromero — Mon, 29 Jun 2026 20:49:04 GMT

Environment

← Older revision		Revision as of 20:49, 29 June 2026
(3 intermediate revisions by the same user not shown)
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>

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>

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=abcdefghijklmnop
	FROM_EMAIL=~~benzinc26~~@gmail.com		FROM_EMAIL=retro-blockbalster@gmail.com
	BASE_URL=http://epyc:8001		BASE_URL=http://epyc:8001
	</pre>		</pre>

Retro-Blockblaster

Bromero — Mon, 29 Jun 2026 20:39:33 GMT

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.

File:FinalJobEx.png

Bromero — Mon, 29 Jun 2026 20:36:56 GMT

Bromero uploaded File:FinalJobEx.png

New page

Complete Job

File:Screenshot 2026-06-29 at 1.27.35 PM.png

Bromero — Mon, 29 Jun 2026 20:28:40 GMT

Bromero uploaded File:Screenshot 2026-06-29 at 1.27.35 PM.png

New page

Website Screen

Cluster 9

Frodo — Mon, 29 Jun 2026 17:56:59 GMT

asdf

New page

Off-site experimental cluster.

[[Category:Cluster]]

Cluster exceptions

Frodo — Mon, 29 Jun 2026 17:56:34 GMT

asdf

← Older revision		Revision as of 17:56, 29 June 2026
(One intermediate revision by the same user not shown)
Line 3:		Line 3:
	* UID/GID is shared from [[Cluster 2]] to [[Cluster 3]] but not strictly enforced.		* UID/GID is shared from [[Cluster 2]] to [[Cluster 3]] but not strictly enforced.
	* disks from [[Cluster 2]] are exported read-only to [[Cluster 7]] during the transition from 2 to 7.		* disks from [[Cluster 2]] are exported read-only to [[Cluster 7]] during the transition from 2 to 7.
	* we will experiment with ~~nfs~~ exports from cluster 2/7 to [[Cluster 8]] aka coreHPC. Research only.		* We will experiment with SAMBA (yes, SAMBA) exports from cluster 2/7 to [[Cluster 8]] aka coreHPC. Research only.
	* we tried nfs export from [[Cluster 2]] to [[Cluster 3]] shared/wynton. This was a disaster. Jobs running on wynton overloaded our nfs servers and made them unusable~~. This will probably happen when we export to cluster 8, but it is worth a try~~.		* The DNS server for [[Cluster 2]] is subservient to the DNS server for [[Cluster 0]]. All other DNS servers have zero inter-dependencies.
	* ~~currently~~ all www gateways are hosted on cluster 2. We ~~will~~ establish a www server on cluster 7 ~~as soon as we can~~. We are also investigating hosting some of our www traffic on cluster 8.		* We tried nfs export from [[Cluster 2]] to [[Cluster 3]] shared/wynton. This was a disaster. Jobs running on wynton overloaded our nfs servers and made them unusable.
			* Currently all www gateways are hosted on cluster 2.
			* We plan to establish a www server on cluster 7 and begin migrating services.
			* We are also investigating hosting some of our www traffic on cluster 8.

	No other exceptions known.		No other exceptions known.

User talk:Bromero

Frodo — Wed, 24 Jun 2026 17:48:58 GMT

Welcome!

New page

'''Welcome to ''DISI''!'''
We hope you will contribute much and well.
You will probably want to read the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents help pages].
Again, welcome and have fun! [[User:Frodo|Frodo]] ([[User talk:Frodo|talk]]) 17:48, 24 June 2026 (UTC)

User:Bromero

Frodo — Wed, 24 Jun 2026 17:48:58 GMT

Creating user page for new user.

New page

Hello! My name is Ben Romero, and I am a undergraduate student at Northwestern University. I am super exited to get started working in the lab and I am from SF so I will be coming into the office.

User:Bromero

Frodo — Wed, 24 Jun 2026 17:48:56 GMT

User account Bromero was created by Frodo and password was sent by email welcome!

Create new user

Sstrizhov — Tue, 23 Jun 2026 21:07:01 GMT

← Older revision		Revision as of 21:07, 23 June 2026
(3 intermediate revisions by the same user not shown)
Line 1:		Line 1:
	===Identify a UID===		===Identify a UID===
	'''Check if a uid that is not taken by any other users'''. Start from ~~150~~**		'''Check if a uid that is not taken by any other users'''. Start from 15***
	On CentOS 6		On CentOS 6
	$ getent passwd \| grep ~~150~~**		$ getent passwd \| grep 15***
	On CentOS 7		On CentOS 7
	$ id ~~150~~**		$ id 15***

	===Create users and superuser on the LDAP GUI:===		===Create users and superuser on the LDAP GUI:===
Line 26:		Line 26:

	==== Create User's Home Directory ====		==== Create User's Home Directory ====
	Log in as root on mem		Log in as root on mem
	$ sh /~~nfs~~/home/[create-visitor.sh/create-member.sh] <user_name>		$ sh /export/home/[create-visitor.sh/create-member.sh] <user_name>

	=== Generate ssh for login ===		=== Generate ssh for login ===
Line 35:		Line 35:

	==== Add user's public key to Portal ====		==== Add user's public key to Portal ====
	$ ssh ~~s_khtang@portal.ucsf.bkslab.org~~		$ ssh portal3 (from a different cluster bit like epyc)
	$ sudo -i		$ sudo -i
	$ cd /opt/keys/~~user~~		$ cd /opt/keys/users
	$ vim <username>		$ vim <username>
	Copy the .rsa_key.pub content into the file		Copy the .rsa_key.pub content into the file
Line 43:		Line 43:
	==== Add user into Portal ====		==== Add user into Portal ====
	On LDAP Admin		On LDAP Admin
	Choose ''' dc=bkslab,dc=org (17)''' > '''~~Group~~''' > '''Portal'''		Choose ''' dc=bkslab,dc=org (17)''' > '''Groups''' > '''Portal'''
	Enter <username> in Add Value		Enter <username> in Add Value

	==== Add user into SLURM ====		==== Add user into SLURM ====
			On gimel2 as a super user:
	sudo sacctmgr create user name=<username> account=bks		sudo sacctmgr create user name=<username> account=bks

Blastermaster on C7

Buyan — Mon, 22 Jun 2026 21:42:40 GMT

← Older revision		Revision as of 21:42, 22 June 2026
Line 17:		Line 17:
	rec.pdb		rec.pdb
	xtal-lig.pdb		xtal-lig.pdb
			Some workflows may use xtal-lig.mol2 instead.

			== Outputs ==

			Important output directories:
			working
			dockfiles

			dockfiles is the important directory for later docking.

			For descriptions of the generated files, see [[Blastermaster_files]].


			...

			[Category:Buyan]]

Blastermaster on C7

Buyan — Mon, 22 Jun 2026 21:34:05 GMT

Created page with "This page is for C7-specific notes on running Blastermaster for DOCK 3.8. For general Blastermaster documentation, see Blastermaster, Blastermaster_files, and Blastermaster_(pydock3_script). == What Blastermaster does == Blastermaster prepares a receptor binding site for docking. It takes receptor/ligand input files and creates the dockfiles directory used later by DOCK/SUBDOCK. The final dockfiles directory is what docking needs. The working direc..."

New page

This page is for C7-specific notes on running Blastermaster for [[DOCK 3.8]].

For general Blastermaster documentation, see [[Blastermaster]], [[Blastermaster_files]], and [[Blastermaster_(pydock3_script)]].

== What Blastermaster does ==

Blastermaster prepares a receptor binding site for docking.

It takes receptor/ligand input files and creates the dockfiles directory used later by DOCK/SUBDOCK.

The final dockfiles directory is what docking needs. The working directory contains intermediate files.

== Inputs ==

Typical required input files are:
rec.pdb
xtal-lig.pdb

SUBDOCK DOCK3.8

Buyan — Mon, 22 Jun 2026 21:23:48 GMT

← Older revision		Revision as of 21:23, 22 June 2026
Line 61:		Line 61:
	--use-charity=true</nowiki>		--use-charity=true</nowiki>
	Arguments, respectively		Arguments, respectively

			== C7 users ==

			For C7-specific SUBDOCK notes, see [[SUBDOCK_on_C7]].

			C7 uses SLURM for SUBDOCK jobs.


	==== Using Charity Engine ====		==== Using Charity Engine ====

How to install DOCK 3.8

Buyan — Mon, 22 Jun 2026 21:20:52 GMT

← Older revision		Revision as of 21:20, 22 June 2026
Line 1:		Line 1:
	Many of the tutorials on how to use DOCK software assume you have access to an executable DOCK program- sometimes referred to as DOCKEXEC, or simply DOCK. This page describes how to gain access to this program.		Many of the tutorials on how to use DOCK software assume you have access to an executable DOCK program- sometimes referred to as DOCKEXEC, or simply DOCK. This page describes how to gain access to this program.

			== C7 users ==

			On [[Cluster 7]], DOCK is already installed. Use:
			module load dock

			For a quick C7 test, see [[DOCK_3.8_testing_on_C7]].

			For SUBDOCK on C7, see [[SUBDOCK_on_C7]].

	== Obtaining a License ==		== Obtaining a License ==

SUBDOCK ON C7

Buyan — Mon, 22 Jun 2026 21:15:59 GMT

Buyan moved page SUBDOCK ON C7 to SUBDOCK on C7

New page

SUBDOCK on C7

This page is for C7-specific notes on [[SUBDOCK_DOCK3.8|SUBDOCK]]. For the full SUBDOCK documentation, see [[SUBDOCK_DOCK3.8]].

== C7 setup ==

Load DOCK:

module load dock
echo $DOCK_INSTALL_PATH
echo $DOCKBASE

SUBDOCK is inside the DOCK install:

${DOCK_INSTALL_PATH}/SUBDOCK/subdock.bash
${DOCK_INSTALL_PATH}/SUBDOCK/rundock.bash

`subdock.bash` expects `rundock.bash` to be in the same directory.

== Scheduler ==

C7 runs this workflow through SLURM (`sbatch`). Set the controller explicitly:

export USE_SLURM=true
export USE_SGE=false
export USE_PARALLEL=false
export USE_CHARITY=false

If more than one controller is enabled, SUBDOCK exits with:

cannot select more than one job controller!

== Required variables ==

SUBDOCK needs:

export EXPORT_DEST=/path/to/output
export INPUT_SOURCE=/path/to/split_database_index
export DOCKFILES=/path/to/dockfiles
export DOCKEXEC=${DOCK_INSTALL_PATH}/dock3/dock64

Use paths in your own workspace. Do not write output into the shared DOCK install, e.g. avoid:

${DOCK_INSTALL_PATH}/test/docking/output

== Run ==

Example:

mkdir -p output
export EXPORT_DEST="$(pwd)/output"
export INPUT_SOURCE="$(pwd)/split_database_index"
export DOCKFILES="$(pwd)/dockfiles"
export DOCKEXEC="${DOCK_INSTALL_PATH}/dock3/dock64"
bash ${DOCK_INSTALL_PATH}/SUBDOCK/subdock.bash

Successful submission looks like:

submitting N out of N jobs
Submitted batch job <jobid>

== Check jobs ==

squeue -u $USER
squeue -j <jobid>

`sacct` may not work on C7 if SLURM accounting is disabled. Check logs after completion:

ls output/logs
less output/logs/1.out

Success usually includes:

starting DOCK vers=3.8
finished!

== Related pages ==

* [[SUBDOCK_DOCK3.8]]
* [[DOCK_3.8_testing_on_C7]]
* [[DOCK 3.8]]

[[Category:DOCK_3.8]]
[[Category:Cluster 7]]

C7 SUBDOCK DOCK 3.8

Buyan — Mon, 22 Jun 2026 21:15:04 GMT

Buyan moved page C7 SUBDOCK DOCK 3.8 to SUBDOCK ON C7

New page

DOCK 3.8

Buyan — Mon, 22 Jun 2026 21:14:02 GMT

← Older revision		Revision as of 21:14, 22 June 2026
Line 40:		Line 40:
	== Availability ==		== Availability ==
	DOCK 3.8 is installed on our cluster and on Wynton. It is available on AWS and OCI as a docker container. The software has never been easier to install (low bar!). It should be runnable on any modern HPC platform. We recommend using an OS were python 3.8 or later is installed by default, however, you should be able to install python 3.8 or later on older equipment.		DOCK 3.8 is installed on our cluster and on Wynton. It is available on AWS and OCI as a docker container. The software has never been easier to install (low bar!). It should be runnable on any modern HPC platform. We recommend using an OS were python 3.8 or later is installed by default, however, you should be able to install python 3.8 or later on older equipment.

			== C7 Usage ==
			DOCK 3.8 is available on [[Cluster 7]] through the dock module.

			For a C7 smoke test of the installed DOCK 3.8 setup, see [[DOCK_3.8_testing_on_C7]].

			For C7-specific SUBDOCK notes, see [[SUBDOCK_on_C7]].

	== General Use ==		== General Use ==

C7 SUBDOCK DOCK 3.8

Buyan — Mon, 22 Jun 2026 21:10:57 GMT

← Older revision		Revision as of 21:10, 22 June 2026
(2 intermediate revisions by the same user not shown)
Line 1:		Line 1:
	notes ~~for c7 users:~~		SUBDOCK on C7
	on [[~~Cluster 7~~]], ~~use~~ path /~~nfs~~/~~software~~/~~dock~~/~~versions~~/~~dock385~~/~~DOCK3~~.8/
			This page is for C7-specific notes on [[SUBDOCK_DOCK3.8\|SUBDOCK]]. For the full SUBDOCK documentation, see [[SUBDOCK_DOCK3.8]].

			== C7 setup ==

			Load DOCK:

			module load dock
			echo $DOCK_INSTALL_PATH
			echo $DOCKBASE

			SUBDOCK is inside the DOCK install:

			${DOCK_INSTALL_PATH}/SUBDOCK/subdock.bash
			${DOCK_INSTALL_PATH}/SUBDOCK/rundock.bash

			`subdock.bash` expects `rundock.bash` to be in the same directory.

			== Scheduler ==

			C7 runs this workflow through SLURM (`sbatch`). Set the controller explicitly:

			export USE_SLURM=true
			export USE_SGE=false
			export USE_PARALLEL=false
			export USE_CHARITY=false

			If more than one controller is enabled, SUBDOCK exits with:

			cannot select more than one job controller!

			== Required variables ==

			SUBDOCK needs:

			export EXPORT_DEST=/path/to/output
			export INPUT_SOURCE=/path/to/split_database_index
			export DOCKFILES=/path/to/dockfiles
			export DOCKEXEC=${DOCK_INSTALL_PATH}/dock3/dock64

			Use paths in your own workspace. Do not write output into the shared DOCK install, e.g. avoid:

			${DOCK_INSTALL_PATH}/test/docking/output

			== Run ==

			Example:

			mkdir -p output
			export EXPORT_DEST="$(pwd)/output"
			export INPUT_SOURCE="$(pwd)/split_database_index"
			export DOCKFILES="$(pwd)/dockfiles"
			export DOCKEXEC="${DOCK_INSTALL_PATH}/dock3/dock64"
			bash ${DOCK_INSTALL_PATH}/SUBDOCK/subdock.bash

			Successful submission looks like:

			submitting N out of N jobs
			Submitted batch job <jobid>

			== Check jobs ==

			squeue -u $USER
			squeue -j <jobid>

			`sacct` may not work on C7 if SLURM accounting is disabled. Check logs after completion:

			ls output/logs
			less output/logs/1.out

			Success usually includes:

			starting DOCK vers=3.8
			finished!

			== Related pages ==

			* [[SUBDOCK_DOCK3.8]]
			* [[DOCK_3.8_testing_on_C7]]
			* [[DOCK 3.8]]

			[[Category:DOCK_3.8]]
			[[Category:Cluster 7]]

C7 SUBDOCK DOCK 3.8

Buyan — Mon, 22 Jun 2026 19:52:24 GMT

Created page with "notes for c7 users: on Cluster 7, use path /nfs/software/dock/versions/dock385/DOCK3.8/"

New page

notes for c7 users:
on [[Cluster 7]], use path /nfs/software/dock/versions/dock385/DOCK3.8/

DOCK 3.8 testing on C7

Buyan — Mon, 22 Jun 2026 19:34:57 GMT

← Older revision		Revision as of 19:34, 22 June 2026
Line 1:		Line 1:
	These are instructions to run the [[DOCK 3.8]] test on [[Cluster 7]].		These are instructions to run the [[DOCK 3.8]] test on [[Cluster 7]]. This is only a C7 quick test, not a full DOCK tutorial. For general DOCK 3.8 usage, see [[DOCK 3.8]] and [[SUBDOCK_DOCK3.8]].

	== 1. Log in and start screen ==		== 1. Log in and start screen ==
	Log in to [[Cluster 7]] first. The exact SSH command may depend on whether you are onsite, on VPN, or going through a portal/jump host. Once you are on C7, start a screen or tmux session so the job keeps running if your SSH disconnects.		Log in to [[Cluster 7]] first. The exact SSH command may depend on whether you are onsite, on VPN, or going through a portal/jump host. Once you are on C7, start a screen or tmux session so the job keeps running if your SSH disconnects.

DOCK 3.8 C7

Buyan — Mon, 22 Jun 2026 19:33:28 GMT

Buyan moved page DOCK 3.8 C7 to DOCK 3.8 testing on C7 testing page

New page

These are instructions to run the [[DOCK 3.8]] test on [[Cluster 7]].

== 1. Log in and start screen ==
Log in to [[Cluster 7]] first. The exact SSH command may depend on whether you are onsite, on VPN, or going through a portal/jump host. Once you are on C7, start a screen or tmux session so the job keeps running if your SSH disconnects.
Start a screen or tmux session so the job keeps running if your SSH disconnects:
Screen:
screen -S dock_test
Tmux alternative:
tmux new -s dock_test

== 2. Make a working folder ==

Use your own writable space, not the shared DOCK install directory.

Example:

cd /nfs/home/xyz/hdd02
mkdir -p docking
cd docking

== 3. Load DOCK ==

module load dock

Check the DOCK paths:

echo $DOCK_INSTALL_PATH
echo $DOCKBASE

== 4. Copy the test files ==

cp -r ${DOCK_INSTALL_PATH}/test/docking test
cd test

Remove old copied output. The shared test folder may already contain someone else's old results:

rm -rf output
rm -f split_database_index

== 5. Edit test_subdock.sh ==

The copied test_subdock.sh may still point back to the shared DOCK install. Edit it so it writes to your local test folder.

Change:

find test_ligs -name '*.db2.tgz' -exec realpath {} \; > ${DOCK_INSTALL_PATH}/test/docking/split_database_index

to:

find test_ligs -name '*.db2.tgz' -exec realpath {} \; > split_database_index

Change:

export EXPORT_DEST="${DOCK_INSTALL_PATH}/test/docking/output"
export INPUT_SOURCE="${DOCK_INSTALL_PATH}/test/docking/split_database_index"
export DOCKFILES="${DOCK_INSTALL_PATH}/test/docking/dockfiles"

to:

export EXPORT_DEST="$(pwd)/output"
export INPUT_SOURCE="$(pwd)/split_database_index"
export DOCKFILES="$(pwd)/dockfiles"

Keep:

export DOCKEXEC="${DOCK_INSTALL_PATH}/dock3/dock64"

== 6. Run with SLURM ==

C7 uses SLURM, not SGE.

export USE_SLURM=true
export USE_SGE=false
mkdir -p output
./test_subdock.sh

Successful submission looks like:

submitting 4 out of 4 jobs
Submitted batch job <jobid>

== 7. Check the job ==

squeue -u $USER

Check logs:

ls output/logs
less output/logs/1.out

Success looks like:

user=<your_username>
starting DOCK vers=3.8
finished!

If the log shows another user or paths under /nfs/software/dock/..., you are looking at old copied output, not your run.

[[Category:Buyan]]