DISI - User contributions [en]

How to be Kyle

2025-07-29T09:13:25Z

Kyle: /* Development Resources */

== Stuff I did ==

This section contains links to repositories for projects I worked on.

=== Wiki Pages ===

* [[How to edit dock website]] - Guide for making changes to the DOCK website
* [[Add major version]] - Instructions for adding a new major version to DOCK

=== Database Management ===

==== Arthor and SmallWorld Indexing ====
* [https://docs.google.com/spreadsheets/d/1hqvj7hH2ylpVIyAcAlzzLK21DQxfQ0CmkJCRzTpQpfY/edit?gid=0#gid=0 Arthor and SmallWorld Indexing Spreadsheet] - Tracking sheet for Arthor and SmallWorld database indexing

=== GitLab Repositories ===

==== DOCK License ====
* '''Repository:''' https://gitlab.docking.org/kylep/dock-admin
* '''Website:''' https://license.docking.org
* '''Purpose:''' Manages DOCK license requests

==== DOCK Website ====
* '''Repository:''' https://gitlab.docking.org/kylep/dock
* '''Website:''' https://dock.docking.org
* '''Purpose:''' Main DOCK website

==== IrwinLab Website ====
* '''Repository:''' https://gitlab.docking.org/kylep/IrwinLab
* '''Website:''' https://irwinlab.compbio.ucsf.edu
* '''Purpose:''' John Irwin Laboratory website

==== IrwinLab Template Site ====
* '''Repository:''' https://gitlab.docking.org/kylep/irwinlab-template-site
* '''Purpose:''' Next.js template for lab websites

==== BKSLab ====
* '''Repository:''' https://gitlab.docking.org/kylep/BKSLab
* '''Website:''' https://bkslab.org
* '''Purpose:''' BKS Laboratory resources

=== Setup Notes ===

* All repositories have CI/CD set up via docker deployments. Any changes pushed the repos will be automatically built and deployed. For building locally the <code>dockerfile</code>s have all the instructions for making the docker container so you can run those commands.
* Running the docker compose file for DOCK License will also create the pgsql database. Prod database is on mem2.

How to be Kyle

2025-07-29T09:04:53Z

Kyle: Clarify how to run stuff

== Development Resources ==

This section contains links to various resources and repositories for DOCK development and maintenance.

=== Wiki Pages ===

* [[How to edit dock website]] - Guide for making changes to the DOCK website
* [[Add major version]] - Instructions for adding a new major version to DOCK

=== Database Management ===

==== Arthor and SmallWorld Indexing ====
* [https://docs.google.com/spreadsheets/d/1hqvj7hH2ylpVIyAcAlzzLK21DQxfQ0CmkJCRzTpQpfY/edit?gid=0#gid=0 Arthor and SmallWorld Indexing Spreadsheet] - Tracking sheet for Arthor and SmallWorld database indexing

=== GitLab Repositories ===

==== DOCK License ====
* '''Repository:''' https://gitlab.docking.org/kylep/dock-admin
* '''Website:''' https://license.docking.org
* '''Purpose:''' Manages DOCK license requests

==== DOCK Website ====
* '''Repository:''' https://gitlab.docking.org/kylep/dock
* '''Website:''' https://dock.docking.org
* '''Purpose:''' Main DOCK website

==== IrwinLab Website ====
* '''Repository:''' https://gitlab.docking.org/kylep/IrwinLab
* '''Website:''' https://irwinlab.compbio.ucsf.edu
* '''Purpose:''' John Irwin Laboratory website

==== IrwinLab Template Site ====
* '''Repository:''' https://gitlab.docking.org/kylep/irwinlab-template-site
* '''Purpose:''' Next.js template for lab websites

==== BKSLab ====
* '''Repository:''' https://gitlab.docking.org/kylep/BKSLab
* '''Website:''' https://bkslab.org
* '''Purpose:''' BKS Laboratory resources

=== Setup Notes ===

* All repositories have CI/CD set up via docker deployments. Any changes pushed the repos will be automatically built and deployed. For building locally the <code>dockerfile</code>s have all the instructions for making the docker container so you can run those commands.
* Running the docker compose file for DOCK License will also create the pgsql database. Prod database is on mem2.

How to be me

2025-07-29T08:59:03Z

Kyle: Add how to be Kyle page

This is where we collect all the documents that are self-created job descriptions.

The purpose of these documents is to allow us to take over from you when you are on holiday or sick.

* how to be JJ
https://docs.google.com/document/d/1hGKjXUnCZHaxRNeuxli6XcMjd0StCpAnieSj2DtnfeA/edit?tab=t.0#heading=h.cdgaj7hju176

* how to be Khanh
https://docs.google.com/document/d/1eXA3VFOZSBDlYlrbp7xKp7WQaRSXLSO2W40ufzokoN8/edit?tab=t.0#heading=h.9jtvguku2mp1

* how to be Mar
https://docs.google.com/document/d/1NhO4DcAuqCYVMjF_AB3KB4qBgwqP13LL/edit

* how to be Max

[[How to be Max]]

* how to be Kyle

[[How to be Kyle]]

* how to be Roman

* how to be John

[[How to be John]]

[[Category:Internal]]

How to be Kyle

2025-07-29T08:56:05Z

Kyle: create how to be Kyle page

== Development Resources ==

This section contains links to various resources and repositories for DOCK development and maintenance.

=== Wiki Pages ===

* [[How to edit dock website]] - Guide for making changes to the DOCK website
* [[Add major version]] - Instructions for adding a new major version to DOCK

=== Database Management ===

==== Arthor and SmallWorld Indexing ====
* [https://docs.google.com/spreadsheets/d/1hqvj7hH2ylpVIyAcAlzzLK21DQxfQ0CmkJCRzTpQpfY/edit?gid=0#gid=0 Arthor and SmallWorld Indexing Spreadsheet] - Tracking sheet for Arthor and SmallWorld database indexing

=== GitLab Repositories ===

==== DOCK Admin Panel ====
* '''Repository:''' https://gitlab.docking.org/kylep/dock-admin
* '''Website:''' https://license.docking.org
* '''Purpose:''' Manages DOCK license requests

==== DOCK Website ====
* '''Repository:''' https://gitlab.docking.org/kylep/dock
* '''Website:''' https://dock.docking.org
* '''Purpose:''' Main DOCK website

==== IrwinLab Website ====
* '''Repository:''' https://gitlab.docking.org/kylep/IrwinLab
* '''Website:''' https://irwinlab.compbio.ucsf.edu
* '''Purpose:''' John Irwin Laboratory website

==== IrwinLab Template Site ====
* '''Repository:''' https://gitlab.docking.org/kylep/irwinlab-template-site
* '''Purpose:''' Next.js template for lab websites

==== BKSLab ====
* '''Repository:''' https://gitlab.docking.org/kylep/BKSLab
* '''Website:''' https://bkslab.org
* '''Purpose:''' BKS Laboratory resources

=== Setup Notes ===

* All repositories have CI/CD set up via docker deployments. Any changes pushed the repos will be automatically built and deployed.

DOCKovalent 3.7

2025-07-15T20:09:54Z

Kyle: Update dock licensing website

DOCKovalent is the covalent docking version of DOCK. Originally implemented within DOCK 3.6, it was ported over to DOCK 3.7 on March 2015. The most current publication to cite DOCKovalent is:

[http://www.nature.com/nchembio/journal/v10/n12/full/nchembio.1666.html "Covalent docking of large libraries for the discovery of chemical probes" Nir London, Rand M Miller, Shyam Krishnan, Kenji Uchida, John J Irwin, Oliv Eidam, Lucie Gibold, Peter Cimermančič, Richard Bonnet, Brian K Shoichet & Jack Taunton. Nature Chemical Biology 10, 1066–1072 (2014) doi:10.1038/nchembio.1666]

Below are instructions on various aspects related to using this version of DOCKovalent. The running example for usage would be docking of cyanoacrylamides (doubly activated Michael's acceptors) to an active site cysteine in RSK2 kinase (PDB ID: 4d9t)

== General setup ==

* Apply for a DOCK3.7 license:
** go here: [[https://license.docking.org/application dock Academic License]]
** select version DOCK3.7
** fill in the required information
** be patient because a real person approve the license and also get your e-mails.
** Download the tar.gz file and copy it to your desired location on the cluster.
** tar -zxvf [file name].tar.gz

* You have checked out DOCK3.7.x and have it under /path/to/DOCK
** setenv DOCKBASE /path/to/DOCK
The rest of the tutorial will assume DOCKBASE is set.

* you need an amsol binary, you can get amsol 7.1<ref>[http://comp.chem.umn.edu/amsol/ Get amsol 7.1]</ref> and apply a patch to make it comparable with our docking methods [[amsol 7 patch]]. Or if '''you are in the lab''' make a symbolic link to this amsol version:
ln -s /nfs/home/londonir/code/git_trunk/DOCK/ligand/amsol/amsol7.1 .

== Custom Ligand / Library Generation ==
'''To generate a single / few ligands:'''
* make a directory to generate the db2 files:
<code> mkdir lig_db2 </code>
* make a smiles file containing the ligands you wish to DOCK. The Covalent attachment point should be marked with a [SiH3] group that would be removed during the ligand preparation. You can read more on how to generate such smiles for a specific subset and reaction scheme using the new ZINC api [link required].
* For our example docking, this is the smiles of the crystal ligand with the covalent attachment point marked (lig.smi):
<code>COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO xtal-lig</code>

<code>cp lig.smi lig_db2</code>
* run the ligand generation script with a covalent flag (must be second argument)
<code> cd lig_db2 </code>

<code>$DOCKBASE/ligand/generate/build_smiles_ligand.sh lig.smi --covalent </code>

The output of the script should be a lig.db2.gz file. You can step out of the db2 generation dir.

'''To generate a large library of ligands for covalent docking:'''
* First get the smiles file of the library, where the covalent attachment point should be marked by an [SiH3] dummy atom.
Important - make sure the smiles explicitly notes [SiH3] and not just [Si]. Eventually the [SiH3] would be removed and replaced by the covalently attached atom from the protein side.
* This command will send the library preparation scripts to the cluster (run on gimel). First argument is the smiles file, Second is how many directories you wish to make (chunks). Third is a prefix name for the dirs.
<code> $DOCKBASE/ligand/generate/build_covalent_lib.csh example.ism 100 prefix </code>
* After all compounds are done, combine the db2 gz files to one directory, if everything went well, you can later delete all intermediate files and just keep the gz_files/ dir.
<code> $DOCKBASE/ligand/generate/combine_gz_files.sh </code>

'''Currently available covalent libraries (At the Shoichet lab / cluster 2)'''
[to be added]

== Protein preparation ==

For covalent docking we need the structure (or a model) of a protein, a crystal ligand to define the binding site, and the identity of the residue for which we want to covalently dock.

* Download 4d9t.pdb
* Extract the protein (e.g. grep ^ATOM 4d9t.pdb > rec.pdb)
* Extract the crystal ligand (e..g grep "0JG A" 4d9t.pdb > xtal-lig.pdb)
* Execute the protein preparation script while indicating the covalent attachment point, in this case CYS 436
<code> $DOCKBASE/proteins/blastermaster/blastermaster.py --covalentResNum 436 --covalentResName CYS --covalentResAtoms HG </code>

Note 1: the default receptor and ligand file names are rec.pdb and xtal-lig.pdb but you can specify other names using -r and -l

Note 2 if you want to dock to a Serine residue you also need to de-protonate the HG atom but for Lysine for instance you should remove all three protons: <code> --covalentResNum 123 --covalentResName LYS --covalentResAtoms HZ1,HZ2,HZ3 </code>

The output of this script is an INDOCK file (see below), a "working" dir which contains temporary files that were generated during the preparation and a "dockfiles" dir that is required for the docking run (containing e.g. the scoring grids).
One of the files that were automatically generated is dockfiles/matching_spheres.sph which for a covalent run would contain only three spheres corresponding to the three atoms in the protein preceding the covalent attachment point. E.g. for CYS these will be CA,CB,SG. Currently this is automatically generated for CYS/SER/LYS if you wish to dock to a different residue edit this file and input the coordinates of the corresponding atoms.

== INDOCK parameters ==

By default covalent docking is turned off (weird right?)
* Edit the INDOCK file to turn it on by changing dockovalent no -> yes
* chemical_matching should be set to "no" as a) there is no need for matching when only sampling around the covalent bond and b) the covalent code overrides the coloring code.

Description of covalent docking related parameters:

'''bond_len''' - the 'ideal' covalent bond length

'''len_range''' - what range around the ideal length should be sampled.

'''len_step''' - at what increments should the bond length be sampled.

So. e.g. for bond_len=1.8, len_range=0.1, len_step=0.05, the following lengths will be sampled: 1.7,1.75,1.8,1.85,1.9

Note that due to steric hindrance of 1-3 interactions DOCK will most of the time prefer the longest bond length possible, for this reason, currently it's advised to use len_range=0, len_step=0.1 (to avoid division by zero) and just set the ideal length correctly. With better modeling of the covalent energy this might be fixed.

'''bond_ang1''' - the 'ideal' bond angle for CB-SG-Lig1 (look at length explantation above for '''ang1_range''', and '''ang1_step''')

'''bond_ang2''' - the 'ideal' bond angle for SG-Lig1-Lig2 (look at length explantation above for '''ang2_range''', and '''ang2_step''')

The default parameters for sampling (bond length and two bond angles are suitable for thioethers (e.g. when docking acrylamides to cysteines) these should be changed for different electrophile/nucleophile combinations.
Some parameters you might want to use are listed below, but more work is being done in this vein as you read these lines.

* It is also (highly) recommended to allow bumping in a covalent run, especially of the rigid part.
Set '''bump_rigid''' to 100.0 and '''bump_maximum''' to 100.0 - one can play around with these to balance speed and sampling.
* Change '''check_clashes''' to '''no'''.

== Sending a run ==

* First setup the directory structure for docking:
<code>$DOCKBASE/docking/setup/setup_db2.csh /path/to/ligand/lig_db2/ </code>
tip: use FULL path to the db files (and not ../../etc)

For each .db2.gz file this will create a separate running dir

* Setting up directory structure for docking of pre-computed ligand libraries (here we use alkylhalides as an example):
mkdir run.alkylhalides
cd run.alkylhalides/
cp ../INDOCK .
ln -s ../dockfiles/ .
<code>$DOCKBASE/docking/setup/setup_db2.csh path/to/ligand/gz_files/ </code>

Path to commercially available pre-computed ligand libraries:

Alkyl-halides:
/mnt/nfs/work/londonir/CovalentLibs/alkyl-halides/fragments/gz_files/
/mnt/nfs/work/londonir/CovalentLibs/alkyl-halides/lead-like/gz_files/

Unsaturated carbonyls:
/mnt/nfs/work/londonir/CovalentLibs/alpha-sub-acrylate-esters/fragments/gz_files/
/mnt/nfs/work/londonir/CovalentLibs/alpha-sub-acrylate-esters/lead-like/gz_files/
/mnt/nfs/work/londonir/CovalentLibs/beta-sub-acrylate-esters/fragments/gz_files/
/mnt/nfs/work/londonir/CovalentLibs/beta-sub-acrylate-esters/lead-like/gz_files/
/mnt/nfs/work/londonir/CovalentLibs/ketone-based-enones/fragments/gz_files/
/mnt/nfs/work/londonir/CovalentLibs/ketone-based-enones/lead-like/gz_files/
/mnt/nfs/work/londonir/CovalentLibs/unsubstituted-acrylamides/fragments/gz_files/
/mnt/nfs/work/londonir/CovalentLibs/unsubstituted-acrylamides/lead-like/gz_files/

Heterocyclic nitriles:
/mnt/nfs/work/londonir/CovalentLibs/heterocyclic-nitriles/fragments/gz_files/
/mnt/nfs/work/londonir/CovalentLibs/heterocyclic-nitriles/lead-like/gz_files/

* Submit the docking job:
- locally:

cd lig
<code>$DOCKBASE/docking/DOCK/bin/dock64 </code>

- on cluster2:

ssh to cluster2
cd run.alkylhalides
<code>$DOCKBASE/docking/submit/submit.csh </code>

== Analysis and interpretation of the results ==

<code> cd .. </code>
* Combine the docking results and make a scores file:
<code> $DOCKBASE/analysis/extract_all.py </code>
* Extract the docked poses:
<code> $DOCKBASE/analysis/getposes.py </code>

Congratulations you've now successfully docked covalently. A couple of pointers for compound selection for testing:

* Due to the ignorance of the scoring function to the covalent bond, scores tend to be higher than non covalent docking scores, even positive at times. As an example just covalently docking a methyl on to a cysteine without it clashing with anything will give a VDW score of ~+10. So positive VDW scores should not deter you from choosing what may look by eye like a good pose.

* Different electrophiles have different inherent reactivity. This is not taken into account in any way during the docking. The docked library should be matched to the application you are interested in. If you are looking for a non-toxic compound that may be active in cells you might consider unsubstituted acrylamides that are considered mild. If on the other hand you are looking for something that can label your protein in-vitro for crystallization studies Bromo-acetamide is very very reactive. Most of the covalent docking libraries were designed with fairly mild electrophiles but keep this consideration in mind when selecting which library to dock and which compounds to test.
==Notes==
<references />

Back to [[:Category:Covalent]]

[[Category:Covalent]]

How to install DOCK 3.8

2025-07-15T20:09:12Z

Kyle: Update dock license website

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.

== Obtaining a License ==

Please obtain a license via the DOCK license server [[https://license.docking.org/application]] and download the software.

== Compiling from source ==

See this page: [[How_to_compile_DOCK]]

If you are a BKS cluster member, you should follow the instructions for compiling via pgf. The DOCK 3.8 source can be found on github:

<nowiki>git clone https://github.com/docking-org/dock3.git</nowiki>

For any others without a PGF license, follow the gfortran instructions.

== Prebuilt Executable ==

DOCK is constantly being modified & fine-tuned, sometimes there may be a special version of DOCK floating around you want to use, or perhaps you have a special version of your own you'd like to share. We collect all custom DOCK executables on the BKS cluster at this location (which is world-writable):

<nowiki>/nfs/soft/dock/versions/dock38/executables</nowiki>

Here is a brief description of the various executables here at the time of writing:
<nowiki>
dock37_vanilla : standard DOCK 3.7 executable
dock38_vanilla : standard DOCK 3.8 executable
dock37_matchcap : DOCK 3.7 executable that more strictly caps the number of matches DOCK generates - slightly faster!
dock38_matchcap : Same as above, but for 3.8
dock38_nogist : DOCK 3.8 sans error messages that sometimes occur when using recently built ligand libraries</nowiki>

You are encouraged to also included the source code in this directory as a tar.gz file with the same base name as your executable.

[[Category:DOCK 3.8]]
[[Category:Developers]]

DOCK 3.8:How to build a release

2025-07-15T20:06:20Z

Kyle: /* Distribution */

This page describes the formal definition of a release of the [https://dock.compbio.ucsf.edu/ ''UCSF DOCK''] software suite

= Build [[pydock3]] Python package =
* (e.g., build pip-installable wheel file using [[Python Poetry|poetry]]).
* this can all be done on gimel2
* git clone https://github.com/docking-org/pydock3.git
* cd pydock3
* git submodule update --init --recursive. #why? dock3 is a submodule of pydock3. We need to tell git this.
( you need to authenticate, and you need to have generated token)
* use the generated token as your password
* run poetry, e.g.
* ~isknight/.local/bin/poetry build
* if there is a general python venv ready, use it. Else create new python venv (see below)
* e.g. source myvenv/bin/activate
* pip install dist/pydock3-0.1.0rc1-py3-none-any.whl

== (optional) create new python venv ==
* https://wiki.docking.org/index.php/Create_venv

= Make a fresh and clean [[dock3]] executable =
* git clone https://github.com/docking-org/dock3.git
* ssh psi
* bash
* export PATH=/nfs/soft/pgi/current/linux86-64/12.10/bin:$PATH
* source /nfs/home/tbalius/zzz.virtualenvs/virtualenv-1.9.1/myVEonGimel/bin/activate
* source /nfs/soft/pgi/env.sh
* verify that compiler set to pgf95 in Makefiles
* cd into libfgz
* make clean; make
* cd into i386
* make clean; make

= Get the 3D building pipeline =
* git clone https://github.com/docking-org/zinc22-3d.git
* instructions: https://wiki.docking.org/index.php/Building_The_3D_Pipeline_ZINC22
* git clone https://github.com/docking-org/zinc22-3d-submit.git
* mv zinc22-3d-submit zinc22-3d/bin
* yeah, ok, this is funky, we will clean it up
* git clone https://github.com/docking-org/SUBDOCK.git
* mv SUBDOCK DOCK3.8/bin

= Incorporate the fruits of (1), (2) and (3) into [[DOCK3.8]] repository housing an arsenal of scripts =

* (e.g., 3D build scripts, post-processing scripts) that are essential for following the [https://www.nature.com/articles/s41596-021-00597-z published Nature protocol].
* mkdir DOCK3.8 # create an empty shell
* cp pydock3/dist/pydock3-0.1.0rc1-py3-none-any.whl DOCK3.8 # copy in pointer to scripts
* cp dock3/src/i386/dock64 DOCK3.8 # copy in optimized executable
* tar czf DOCK3.8/zinc22-3d.tgz zinc22-3d
* the release is now ready. create a tarball.
* tar czf dock_3.8.x.tar.gz DOCK3.8

= Distribution =
* [[Add_major_version#Adding_new_DOCK_Versions_to_licensing.docking.org|Put on licensing.docking.org]]
* copy dock3.8.x.tar.gz to dock server. test download and install
* put on gimel
* same
* put on wynton
* same
* put in dockingorg/awsdock
* bin and dock64

= Testing at point of installation =
* test on DOCK license server (download, install, follow instructions)
* installation instructions....
* test on gimel2
* test on wynton
* test on AWS

= once tested, clean up old versions so the correct version to use is unambiguous. =

A particular commit of the DOCK3.8 repository formally becomes a particular distribution of [https://dock.compbio.ucsf.edu/ ''UCSF DOCK''] software when the commit is tagged with the distribution's [https://semver.org/ semantic version (e.g., DOCK3.8 v1.2.0)]. Note that ''pydock3'' and ''dock3'' are separately versioned from ''DOCK3.8''.

[[Category:DOCK 3.8]]

Add major version

2025-07-15T20:04:35Z

Kyle: /* Adding new DOCK Versions to licensing.docking.org */

= Adding new DOCK Versions to licensing.docking.org =
* DOCK-License code is on https://gitlab.docking.org/kylep/dock-admin request access from [[sysadmin]]
* All the dock versions are in <code>/nfs/soft/dock/packages</code> on <code>nfs-soft</code>
* Add the new DOCK file and then replace the relevant <code>dockx-latest.tgz</code> with the new DOCK release
** For example, if there is a new minor version of DOCK 6 like DOCK 6.15 (<code>dock.6.15.tgz</code>), copy the .tgz into the <code>/nfs/soft/dock/packages</code> folder. Remove <code>dock6-latest.tgz</code> and then <code>ln -s dock.6.15.tgz dock6-latest.tgz</code>. You should now have dock6-latest.tgz as a symlink pointing to dock.6.15.tgz.
** If you are getting permission errors change to the <code>www</code> user: <code>sudo su</code> and then <code>su - www</code>

= Adding new Major Dock version =
* Major dock versions are listed in <code>dock-admin/lib/constants.ts</code>
* Add the name of the new DOCK version to <code>MAIN_VERSIONS</code>, the same name to <code>MainVersions</code>, and a mapping of that name to a <code>.tgz</code> file in <code>/nfs/soft/dock/packages</code> in <code>dockVersions</code>.
* For example, if adding DOCK 7 as a new major version:

== Change constants.ts From ==
<pre>
// These DOCK versions will be shown on the application screen and highlighted when creating / editing a user
export type MainVersion = 'DOCK 3.7' | 'DOCK 3.8' | 'DOCK 4' | 'DOCK 6';

export const MAIN_VERSIONS: MainVersion[] = [
'DOCK 3.7',
'DOCK 3.8',
'DOCK 4',
'DOCK 6'
];

const dockVersions: AllowedFiles = {
'DOCK 3.7': 'dock3.7-latest.tgz',
'DOCK 3.8': 'dock3.8-latest.tgz',
'DOCK 4': 'dock4-latest.tgz',
'DOCK 6': 'dock6-latest.tgz',

// Old Versions imported from old db
...
};
</pre>

== Change constants.ts To ==
<pre>
// These DOCK versions will be shown on the application screen and highlighted when creating / editing a user
export type MainVersion = 'DOCK 3.7' | 'DOCK 3.8' | 'DOCK 4' | 'DOCK 6' | 'DOCK 7'; // <- The new major DOCK version

export const MAIN_VERSIONS: MainVersion[] = [
'DOCK 3.7',
'DOCK 3.8',
'DOCK 4',
'DOCK 6',
'DOCK 7' // <- The new major DOCK version
];

const dockVersions: AllowedFiles = {
'DOCK 3.7': 'dock3.7-latest.tgz',
'DOCK 3.8': 'dock3.8-latest.tgz',
'DOCK 4': 'dock4-latest.tgz',
'DOCK 6': 'dock6-latest.tgz',
'DOCK 7': 'dock7-latest.tgz', // <- The new major Dock versions latest.tgz in `/nfs/soft/dock/packages`

// Old Versions imported from old db
...
};
</pre>

= Testing Changes =
* <code>git clone https://gitlab.docking.org/kylep/dock-admin</code>
* <code>cd dock-admin</code>
* <code>npm install</code> to install all required packages
* <code>docker compose up -d</code> is required as it will build and create the docker container for the database and initialize a default admin account.
* While the postgress db is running you can use <code>npm run dev</code> to run the dev server without needing to rebuild the entire container every time. If ran locally it will use the downloads folder in the repo instead of <code>/nfs/soft/dock/packages</code>. If ran with docker it will use <code>/nfs/soft/dock/packages</code>. You can change <code>.env.docker</code> to modify the directory the server looks in for serving downloads.

= Committing Changes =
* <code>git add</code> the changed files, make a new commit, and push
* The CI/CD pipeline will automatically deploy the new changes. Use the admin dashboard to test the new changes!

How to edit dock website

2025-07-15T20:03:32Z

Kyle: Link to how to update dock versions that license manager uses

=How to update DOCK Website=

==Via gitlab.docking.org==
* 1. request an account on gitlab.docking.org from [[sysadmin]]

* 2. login to gitlab.docking.org

* 3. request "maintainer" access ("developer" will require pull requests) to the DOCK Website repo from [[sysadmin]]

* 4. browse to change files and commit. All the files (probably) are in html/kuntz/. If you are only editing text files, you have our permission to push directly to main.

* 5. it should push to the public website automatically. (you may need to refresh cache on your browser to see the change)

* 6. If any problems or questions contact Kyle Petkovic or [[sysadmin]]. We are happy to talk to you about making this as easy as we can.

==Via git==

It works mostly the same as it did on the old DOCK site

===Running DOCK===
<syntaxhighlight lang="bash">
git clone https://gitlab.docking.org/kylep/dock
cd dock/html/kuntz/
python3 -m http.server 8023
</syntaxhighlight>
''Note: It's all html + bootstrap so no special packages are needed''

===Adding a New Minor DOCK Version===
'''File Location:''' <code>dock/html/kuntz/DOCK_6/index.htm</code> is where the DOCK 6 html file is located.

You can edit the HTML to add new release note links. In the DOCK_6 folder you can add a new <code>changelog.txt</code> file and then link to it from DOCK_6 using an <code><nowiki><a></nowiki></code> with an <code>href</code> in the ''Release Notes:'' section of <code>DOCK_6/index.htm</code>.

===Adding a New Major DOCK Version===
# Duplicate the <code>DOCK_6</code> folder and give it a new name
# Edit the files inside the new folder
# To add the new version to the navigation bar:
#* Go to <code>dock/html/kuntz/components/components.js</code>
#* Search for an existing DOCK version (e.g., "DOCK 6")
#* Duplicate its list item
#* Update the name and href to point to your new DOCK version page

===Committing Changes===
When your changes are done:
# Use <code>git add</code> to stage your modified files
# Commit the changes to the repository
# The CI/CD pipeline will automatically run and push the changes to public

=How to update DOCK Files that are served to users=
[[Add_major_version#Adding_new_DOCK_Versions_to_licensing.docking.org|Adding new DOCK Versions to licensing.docking.org]]

[[Category:Sysadmin]]

Add major version

2025-07-15T20:02:20Z

Kyle: /* Adding new DOCK Versions to DOCK-Admin */

= Adding new DOCK Versions to licensing.docking.org =
* DOCK-License code is on https://gitlab.docking.org/kylep/dock-admin request access from [[sysadmin]]
* All the dock versions are in <code>/nfs/soft/dock/packages</code> on <code>nfs-soft</code>
* Add the new DOCK file and then replace the relevant <code>dockx-latest.tgz</code> with the new DOCK release
** For example, if there is a new minor version of DOCK 6 like DOCK 6.15 (<code>dock.6.15.tgz</code>), copy the .tgz into the <code>/nfs/soft/dock/packages</code> folder. Remove <code>dock6-latest.tgz</code> and then <code>ln -s dock.6.15.tgz dock6-latest.tgz</code>.
** If you are getting permission errors change to the <code>www</code> user: <code>sudo su</code> and then <code>su - www</code>

= Adding new Major Dock version =
* Major dock versions are listed in <code>dock-admin/lib/constants.ts</code>
* Add the name of the new DOCK version to <code>MAIN_VERSIONS</code>, the same name to <code>MainVersions</code>, and a mapping of that name to a <code>.tgz</code> file in <code>/nfs/soft/dock/packages</code> in <code>dockVersions</code>.
* For example, if adding DOCK 7 as a new major version:

== Change constants.ts From ==
<pre>
// These DOCK versions will be shown on the application screen and highlighted when creating / editing a user
export type MainVersion = 'DOCK 3.7' | 'DOCK 3.8' | 'DOCK 4' | 'DOCK 6';

export const MAIN_VERSIONS: MainVersion[] = [
'DOCK 3.7',
'DOCK 3.8',
'DOCK 4',
'DOCK 6'
];

const dockVersions: AllowedFiles = {
'DOCK 3.7': 'dock3.7-latest.tgz',
'DOCK 3.8': 'dock3.8-latest.tgz',
'DOCK 4': 'dock4-latest.tgz',
'DOCK 6': 'dock6-latest.tgz',

// Old Versions imported from old db
...
};
</pre>

== Change constants.ts To ==
<pre>
// These DOCK versions will be shown on the application screen and highlighted when creating / editing a user
export type MainVersion = 'DOCK 3.7' | 'DOCK 3.8' | 'DOCK 4' | 'DOCK 6' | 'DOCK 7'; // <- The new major DOCK version

export const MAIN_VERSIONS: MainVersion[] = [
'DOCK 3.7',
'DOCK 3.8',
'DOCK 4',
'DOCK 6',
'DOCK 7' // <- The new major DOCK version
];

const dockVersions: AllowedFiles = {
'DOCK 3.7': 'dock3.7-latest.tgz',
'DOCK 3.8': 'dock3.8-latest.tgz',
'DOCK 4': 'dock4-latest.tgz',
'DOCK 6': 'dock6-latest.tgz',
'DOCK 7': 'dock7-latest.tgz', // <- The new major Dock versions latest.tgz in `/nfs/soft/dock/packages`

// Old Versions imported from old db
...
};
</pre>

= Testing Changes =
* <code>git clone https://gitlab.docking.org/kylep/dock-admin</code>
* <code>cd dock-admin</code>
* <code>npm install</code> to install all required packages
* <code>docker compose up -d</code> is required as it will build and create the docker container for the database and initialize a default admin account.
* While the postgress db is running you can use <code>npm run dev</code> to run the dev server without needing to rebuild the entire container every time. If ran locally it will use the downloads folder in the repo instead of <code>/nfs/soft/dock/packages</code>. If ran with docker it will use <code>/nfs/soft/dock/packages</code>. You can change <code>.env.docker</code> to modify the directory the server looks in for serving downloads.

= Committing Changes =
* <code>git add</code> the changed files, make a new commit, and push
* The CI/CD pipeline will automatically deploy the new changes. Use the admin dashboard to test the new changes!

Add major version

2025-07-15T19:55:49Z

Kyle: Make DOCK update instructions more clear

= Adding new DOCK Versions to DOCK-Admin =
* DOCK-License code is on https://gitlab.docking.org/kylep/dock-admin request access from [[sysadmin]]
* All the dock versions are in <code>/nfs/soft/dock/packages</code> on <code>nfs-soft</code>
* Add the new DOCK file and then replace the relevant <code>dockx-latest.tgz</code> with the new DOCK release
** For example, if there is a new minor version of DOCK 6 like DOCK 6.15 (<code>dock.6.15.tgz</code>), copy the .tgz into the <code>/nfs/soft/dock/packages</code> folder. Remove <code>dock6-latest.tgz</code> and then <code>ln -s dock.6.15.tgz dock6-latest.tgz</code>.
** If you are getting permission errors change to the <code>www</code> user: <code>sudo su</code> and then <code>su - www</code>

= Adding new Major Dock version =
* Major dock versions are listed in <code>dock-admin/lib/constants.ts</code>
* Add the name of the new DOCK version to <code>MAIN_VERSIONS</code>, the same name to <code>MainVersions</code>, and a mapping of that name to a <code>.tgz</code> file in <code>/nfs/soft/dock/packages</code> in <code>dockVersions</code>.
* For example, if adding DOCK 7 as a new major version:

== Change constants.ts From ==
<pre>
// These DOCK versions will be shown on the application screen and highlighted when creating / editing a user
export type MainVersion = 'DOCK 3.7' | 'DOCK 3.8' | 'DOCK 4' | 'DOCK 6';

export const MAIN_VERSIONS: MainVersion[] = [
'DOCK 3.7',
'DOCK 3.8',
'DOCK 4',
'DOCK 6'
];

const dockVersions: AllowedFiles = {
'DOCK 3.7': 'dock3.7-latest.tgz',
'DOCK 3.8': 'dock3.8-latest.tgz',
'DOCK 4': 'dock4-latest.tgz',
'DOCK 6': 'dock6-latest.tgz',

// Old Versions imported from old db
...
};
</pre>

== Change constants.ts To ==
<pre>
// These DOCK versions will be shown on the application screen and highlighted when creating / editing a user
export type MainVersion = 'DOCK 3.7' | 'DOCK 3.8' | 'DOCK 4' | 'DOCK 6' | 'DOCK 7'; // <- The new major DOCK version

export const MAIN_VERSIONS: MainVersion[] = [
'DOCK 3.7',
'DOCK 3.8',
'DOCK 4',
'DOCK 6',
'DOCK 7' // <- The new major DOCK version
];

const dockVersions: AllowedFiles = {
'DOCK 3.7': 'dock3.7-latest.tgz',
'DOCK 3.8': 'dock3.8-latest.tgz',
'DOCK 4': 'dock4-latest.tgz',
'DOCK 6': 'dock6-latest.tgz',
'DOCK 7': 'dock7-latest.tgz', // <- The new major Dock versions latest.tgz in `/nfs/soft/dock/packages`

// Old Versions imported from old db
...
};
</pre>

= Testing Changes =
* <code>git clone https://gitlab.docking.org/kylep/dock-admin</code>
* <code>cd dock-admin</code>
* <code>npm install</code> to install all required packages
* <code>docker compose up -d</code> is required as it will build and create the docker container for the database and initialize a default admin account.
* While the postgress db is running you can use <code>npm run dev</code> to run the dev server without needing to rebuild the entire container every time. If ran locally it will use the downloads folder in the repo instead of <code>/nfs/soft/dock/packages</code>. If ran with docker it will use <code>/nfs/soft/dock/packages</code>. You can change <code>.env.docker</code> to modify the directory the server looks in for serving downloads.

= Committing Changes =
* <code>git add</code> the changed files, make a new commit, and push
* The CI/CD pipeline will automatically deploy the new changes. Use the admin dashboard to test the new changes!

Install DOCK 3.7

2025-07-10T08:46:04Z

Kyle: Update licensing link to the new page

If you do not already have a cluster with middleware, see: [[So you want to set up a lab]].

'''Now you are ready for the installation'''
= Installing third-party softwares =
This section is for building your own databases. If you use ZINC, you do not need OpenEye, Jchem, Corina or AMSOL.)
* OpenEye (OEChem, Omega)
** More information [http://www.eyesopen.com/oechem-tk here for OEChem TK]
** More information [http://www.eyesopen.com/omega here for Omega]
Apply for academic license [http://www.eyesopen.com/academic here]
* JChemBase (Chemaxon)
** Definitely need marvin, molconvert, molcharge . . .
** Academic license [http://www.chemaxon.com/my-chemaxon/my-academic-license/ here]
* Corina ([https://www.mn-am.com/products/corina here])
* [http://www.cgl.ucsf.edu/chimera/ Chimera]
* AMSOL
** A '''modified''' version of AMSOL6.5.3 is required for DOCK 3.5.54, 3.6, and 3.7
** [http://comp.chem.umn.edu/amsol/ AMSOL7.1] is need for DOCK 3.7.1. For install and path instruction, see [[AMSOL]]
*PYTHON
**numpy
**scipy
**matplotlib
**biopython (this is need for only one or two scripts, beblasti.py )
** virtual environments are very helpful.
**see $DOCKBASE/install/environ/python/requirements.txt for more information.
* RDkit (not required but useful, see $DOCKBASE/install/environ/python/rdkit.sh for help building rdkit.)
* msms (only need for using beblasti.py) see [[installing msms]]

The DOCK Environment is a collection of scripts, programs and 3rd party programs.

= Our software =
Here we install a private copy under a user's account. It is easy to generalize this to a global location, e.g. /nfs/software . You can request a license and a copy (free to academics, a bargain for for-profits) at

[https://license.docking.org/application license.docking.org/application]

mkdir -p ~/code
cd ~/code
tar xzf dock37_source.tar.gz
ln -s dock-3.7-release DOCK

= set up .cshrc (or .bashrc equivalent) =
You need to create something like this, depending on your exact circumstances.
setenv DOCKBASE /raid4/people/mattchu/code/DOCK
set path = ($path $DOCKBASE/bin)
setenv AMSOLEXE $DOCKBASE/bin/amsol-mod4
setenv OE_DIR /raid3/software/openeye/current
alias pymol ~/pymol/pymol
if ( $?PYTHONPATH ) then
if ( `echo $PYTHONPATH | grep -c 'openeye/python'` == 0 ) then
setenv PYTHONPATH $OE_DIR/python:${PYTHONPATH}
endif
else
setenv PYTHONPATH $OE_DIR/python
endif

= Test 1: Basic tests =
Before you test our software, test that all third party software is correctly installed.
cd ~/$DOCKBASE/test
./third-party-test.sh

This will tell you quick what you forgot to install or if there is any obvious problem with your installation. Once the above works without error, you are ready to test our software.
cd ~/$DOCKBASE/test
./all-test.sh
This should run about 10-30 minutes depending on your hardware.
If you can pass the tests without error, congratulations! You are ready to get started with docking: [[Getting started with DOCK 3.7]].

== Possible problems and solutions during installation ==

* OpenEye missing or problem

* Python missing or problem

* AMSOL missing or problem

* Chemaxon missing or problem

* SGE or problem

[[Category:Sysadmin]]
[[Category:DOCK 3.7]]
[[Category:Setup]]

Arthor Documentation for Future Developer

2025-06-12T18:47:18Z

Kyle: Update arthor version to 4.2.4

== Introduction ==
[https://www.nextmovesoftware.com/downloads/arthor/documentation/Arthor.pdf Here is the link to Arthor's manual]
* Username: ucsf@nextmovesoftware.com
* Password: <Ask jjiteam@googlegroups.com>

Arthor configurations and the frontend files are consolidated in '''/nfs/soft2/arthor_configs/'''.

'''/nfs/soft2/arthor_configs/start_arthor_script.sh''' can start/restart Arthor instances on respective machines.

Launch the script to see the options available.

== How To Download Arthor ==
# Ssh to nfs-soft2 and become root. Prepare directory
#: <source> mkdir /export/soft2/arthor_configs/arthor-<version> && cd /export/soft2/arthor_configs/arthor-<version> </source>
# [https://www.nextmovesoftware.com/downloads/arthor/ Download Software with this link]
#* Username: ucsf@nextmovesoftware.com
#* Password: <Ask jjiteam@googlegroups.com>
# Go to releases. Look for ''' smallworld-java-<version>.tar.gz ''' and copy the link address.
# Download using wget
#: <source> wget --user ucsf@nextmovesoftware.com --password <Ask jjiteam@googlegroups.com> <link address> </source>
# Decompress the file
#* <source> tar -xvf <file_name> </source>

== How To Launch Arthor For The First Time ==
=== Prepare Files and Directories ===
# Ssh to nfs-exc and become root
# Open a port in the firewall
#: <source>firewall-cmd --permanent --add-port=<port_number>/tcp
firewall-cmd --reload
</source>
# Go to Arthor Config directory
#: <source>cd /export/soft2/arthor_configs/arthor-<latest_version></source>
# Create an Arthor config file
#: <source>vim <name_of_file>.cfg</source>
#* Add these lines in the file. Check the manual for more options.
#: <source>
DataDir=/local2/public_arthor
MaxConcurrentSearches=6
MaxThreadsPerSearch=8
AutomaticIndex=false
AsyncHitCountMax=20000
Depiction=./depict/bot/svg?w=%w&h=%h&svgunits=px&smi=%s&zoom=0.8&sma=%m&smalim=1
Resolver=https://sw.docking.org/util/smi2mol?smi=%s
</source>
=== Start Arthor Instance ===
# Now ssh into a machine you wish to run an Arthor instance on and become root
# Change your shell to bash if you havn't already
#: <source>bash</source>
# Create a screen
#: <source>screen -S <screen_name></source>
# Prepare Arthor Config Path
#: <source>export ARTHOR_CONFIG="/nfs/soft2/arthor_configs/arthor-<version>/<name_of_config_file>.cfg"</source>
# Launch java
#: <source>java -jar -Dserver.port=<port_number> /nfs/soft2/arthor_configs/arthor-<version>/arthor-server-<version>.war</source>

=== Configuration Details ===

*'''DataDir''': This is the directory where the Arthor data files live. Location where the index files will be created and loaded from.

*'''MaxConcurrentSearches''': Controls the maximum number of searches that can be run concurrently by setting the database pool size. When switching between a large number of databases it can be useful to have a larger pool size, the only trade off is keeping file pointers open.

*'''MaxThreadsPerSearch''': The number of threads to use for both ATDB and ATFP searches

*Set '''AutomaticIndex''' to false if you don't want new smiles files added to the data directory to be indexed automatically

*'''AsyncHitCountMax''': The upper-bound for the number of hits to retrieve in background searches.

*'''Resolver''': Using Smallworld API, allows input box to take in a SMILE format and automatically draw on the board.

'''Check Arthor manual for more configuration options'''

== How to Build Arthor Databases==
We can build Arthor Databases anywhere. Consolidate smiles into one directory so you can index them all one by one.

Just use the script located at '''/nfs/home/jjg/scripts/arthor_index_script.sh''' at the directory where you stored the smiles.

Here is the content of the script:
<source>
#!/bin/bash

target="*.smi"
threads='48'
version="4.2.4"

export ARTHOR_DIR=/nfs/soft2/arthor_configs/arthor-$version/arthor-$version-centos8/
export PATH=$ARTHOR_DIR/bin/:$PATH

for j in $target
do
echo 'smi2atdb -v -r -j '$threads' -p '$j' '${j}'.atdb |& tee -a '${j}'_log'
time smi2atdb -v -r -j $threads -p $j ${j}.atdb |& tee -a ${j}_log
echo 'smi2atfp -j '$threads' -p '$j' '${j}.atfp' |& tee -a '${j}'_log'
time smi2atfp -j $threads -p $j ${j}.atfp |& tee -a ${j}_log
done

for i in $target*atdb
do
echo 'atdb2fp -j '$threads' '$i
time atdb2fp -j $threads $i
chmod 744 $i.fp
done
</source>

If errors about smi2atdb and atdb2fp show up after running the script make sure '''ARTHOR_DIR''' is a folder that exists and double check '''version'''.

=== Command Details ===
'''smi2atdb''' creates the atdb files needed for Substructure searching.
*'''-v''' verbose
*'''-r''' Compute and store ring size information in the index allowing ring size (3-10) expressions ([r6] and [Z5])
*'''-j''' is the amount of threads to use to index the smiles file
*'''-p''' stores the position of the original file
'''atdb2fp''' makes substructure searching faster

'''smi2atfp''' creates atfp files for similarity searching

==Setting up Round Table==
"Round Table allows you to serve and split chemical searches across multiple host machines. The implementation provides a lightweight proxy that forwards requests to other Arthor host servers that do the actual search. Communication is done using the existing Web APIs.
===Setting up Host Server===
# Ssh to nfs-soft2 and become root
# Open a port in the firewall
#: <source>firewall-cmd --permanent --add-port=<port_number>/tcp
firewall-cmd --reload
</source>
# Go to Arthor Config Directory
#: <source>cd /export/soft2/arthor_configs/arthor-<version></source>
# Create Round Table Head configuration file. Here is an example:
# <source>
[RoundTable]
RemoteClient=http://10.20.0.41:8008
RemoteClient=http://10.20.5.19:8008
Resolver=https://sw.docking.org/util/smi2mol?smi=%s
</source>
# Now ssh into a machine you wish to run the round table head on and become root
# Change your shell to bash if you havn't already
#: <source>bash</source>
# Create a screen
#: <source>screen -S <screen_name></source>
# Prepare Arthor Config Path
#: <source>export ARTHOR_CONFIG="/nfs/soft2/arthor_configs/arthor-<version>/<round_table_head>.cfg"</source>
# Launch java
#: <source>java -jar /nfs/soft2/arthor_configs/arthor-<version>/arthor-<version>-centos7/java/arthor.jar --httpPort=<port_number></source>

== Active Arthor Instances ==
===Public Arthor===
{| class="wikitable"
|-
! Rocky Linux Machine
! Port
! Data Directory
! Which Arthor
|-
| arthor
| 10.20.200.100:8080
| /local3/public_arthor/
| Public Arthor
|-
|}

===Private Arthor===
{| class="wikitable"
|-
! Rocky Linux Machine
! Port
! Data Directory
! Which Arthor
|-
| arthor
| 10.20.200.100:8081
| /local3/private_arthor/
| Private Arthor
|-
|}

===Super Private Arthor===
{| class="wikitable"
|-
! Rocky Linux Machine
! Port
! Data Directory
! Which Arthor
|-
| arthor
| 10.20.200.100:8082
| /local3/super_private_arthor/
| Private Arthor
|-
|}

===Arthor BB, CC, and Covalent===
{| class="wikitable"
|-
! CentOS 7 Machine
! Port
! Data Directory
! Which Arthor
|-
| epyc-A40
| 10.20.200.92:8081
| /local2/arthorbb
| ArthorBB
|-
| epyc-A40
| 10.20.200.92:8082
| /local2/arthorcc
| ArthorCC
|-
| epyc-A40
| 10.20.200.92:8080
| /local2/arthorcovalent
| Arthor Covalent
|-
|}

== Customizing Arthor Frontend To Our Needs (Arthor 4.1) ==
'''These instructions only worked and compiled for me in the machine called epyc which is running Rocky 8 Linux operating system.'''

Summary of changes in index.html:
*Add contact info
*Advertise TLDR
*Remove button for Formula
*Database Information Link

Summary of changes in index.js:
*Hyperlink the results to zinc20 or cartblanche22
*Copy SMILES with clipboard button

Summary of changes in sketcher.js:
*Input box should be updated as user draws molecule

Summary of changes in arthor-swagger.yaml.js:
*Make API point to "/"

=== Install Prerequisite Packages ===
# Install Apache Maven
#* <source>dnf install maven -y</source>
# Install Node Package Manager (NPM)
#* <source>dnf install npm -y</source>
# In your home directory, create a new directory to hold the files for the upcoming procedures
#* <source>mkdir /mnt/nfs/home/jjg/arthor_build_from_source</source>
# Download these latest Arthors and store them in 'arthor_build_from_source/'. [[Arthor Documentation for Future Developer#How To Download Arthor|Here's how to download Arthor.]]
#* arthor-4.1-source.tar.gz
#* arthor-4.1-centos8.tar.gz
# Extract contents from the tar.gz files
#* <source>tar -xvf arthor-4.1-source.tar.gz
tar -xvf arthor-4.1-centos8.tar.gz</source>
# Install Apache Maven Arthor dependencies through this script located at '''nfs/home/jjg/arthor_build_from_source/mvn_build.sh'''
#* <source>
#!/bin/bash

version=4.1

export ARTHOR_DIR=/mnt/nfs/home/jjg/arthor_build_from_source/arthor-$version/arthor-$version-centos8/java/
export OS=linux
export VERSION=$version

mvn install:install-file -Dfile=$ARTHOR_DIR/arthor-jni-${OS}.jar \
-Dpackaging=jar \
-DgeneratePom=true \
-DartifactId=arthor-jni-${OS} \
-DgroupId=com.nextmovesoftware.arthor \
-Dversion=$VERSION
mvn install:install-file -Dfile=$ARTHOR_DIR/arthor-jni.jar \
-Dpackaging=jar \
-DgeneratePom=true \
-DartifactId=arthor-jni \
-DgroupId=com.nextmovesoftware.arthor \
-Dversion=$VERSION
</source>

=== Customizing Index.html ===
Location: /nfs/home/jjg/arthor_build_from_source/arthor-4.1/arthor-4.1-source/server-ui/src/index.html

==== Add contact info and tldr ====
# vim /nfs/home/jjg/arthor_build_from_source/arthor-4.1/arthor-4.1-source/server-ui/src/index.html
# Search for 'arthor_table_list'
#: <source>?arthor_table_list</source>
# Add contact info, a plug to tldr.docking.org, and database link after the div block where arthor_table_list is inside of. It should look like this
#: <source lang="html">
<div class="opt-box-border">
<label>Databases</label>

<ul id="arthor_table_list">
<li class="placeholder">Please select a search type</li>
</ul>
</div>
<div class="opt-box-border">
<label>Ask Questions</label>
Email us: jjiteam@googlegroups.com
</div>
<div class="opt-box-border">
<label> To Download 100K+ Results</label>
Sign up for <a href="http://tldr.docking.org/">tldr.docking.org</a> and use arthorbatch
</div>
<div class="opt-box-border">
<label> Database Information</label>
<a href="https://wiki.docking.org/index.php?title=Arthor_Databases" target="_blank">Database Information Link</a>
</div>
</source>

==== Remove Similarity and Formula Buttons ====
# vim /mnt/nfs/home/jjg/arthor_build_from_source/arthor-4.1/arthor-4.1-source/server-ui/src/index.html
# Search for 'arthor_search_list'
#: <source> ?arthor_search_list </source>
# Delete and Replace the whole 'ul' element block with this
#: <source lang="html">
<li value="Similarity" onclick="setSearchType(this)" class="first">
Similarity
</li><li value="Substructure" onclick="setSearchType(this)">
Substructure
</li><li value="SMARTS" onclick="setSearchType(this)" class="last">
SMARTS
</li>

</source>

=== Customize Index.js ===
==== Conditional Hyperlinks ====
Location /mnt/nfs/home/jjg/arthor_build_from_source/arthor-4.1-source/server-ui/src/index.js

# Add the zinc20 hyperlink to the Arthor results. Search for this
#: <source lang="javascript">
$info.append($("<tr>").append($('<td class="identifier">').append(id)));
</source>
# Delete the contents of the whole else block and replace it with this
#: <source lang="javascript">
if (id.substring(0, 6) == "ZINC00") {
$info.append(
$('<tr>').append(
$('<td class="identifier">').append("<b><a target='_blank' href='https://zinc20.docking.org/substances/"+id+"'>" + id + "</a></b>")));
$info.append(
$("<tr>").append(
$("<td>").append(
"<span class='table_name'>" + table_name + "</span>",
),
),
);
} else if (id.substring(0,4) == "ZINC" && id.substring(4,6) != "00") {
$info.append(
$('<tr>').append(
$('<td class="identifier">').append("<b><a target='_blank' href='https://cartblanche22.docking.org/substance/"+id+"'>" + id + "</a></b>")));
$info.append(
$("<tr>").append(
$("<td>").append(
"<span class='table_name'>" + table_name + "</span>",
),
),
);
} else {
$info.append($("<tr>").append($('<td class="identifier">').append(id)));
$info.append(
$("<tr>").append(
$("<td>").append(
"<span class='table_name'>" + table_name + "</span>",
),
),
);
}
</source>
==== Copy SMILES Clipboard ====
# Search this
#: <source>?parser</source>
# At the end of the the try block add this
#: <source lang="javascript">
$info.append(
$('<tr>').append(
$('<td>').append('Copy SMILES: <a href="#" onclick="navigator.clipboard.writeText(\'' + parser.smi + '\');" ><i class="fa fa-clipboard" aria-hidden="true"></i></a>')));
</source>
# The whole try and catch block should look like this
#: <source lang="javascript">
try {
var parser = new SmiJs.Parser(data);
if (parser.parse()) {
$info.append(
$('<tr>').append(
$('<td>').append(parser.mf(true))));
$info.append(
$('<tr>').append(
$('<td>').append(parser.mw())));
$info.append(
$('<tr>').append(
$('<td>').append('Copy SMILES: <a href="#" onclick="navigator.clipboard.writeText(\'' + parser.smi + '\');" ><i class="fa fa-clipboard" aria-hidden="true"></i></a>')));
}
} catch(err) {
console.log(err);
}
</source>

=== Customize Sketcher.js ===
Location: /mnt/nfs/home/jjg/arthor_build_from_source/arthor-4.1-source/server-ui/src/sketcher.js

==== Input Box Updates as User Draws ====
#vim /mnt/nfs/home/jjg/arthor_build_from_source/arthor-4.1-source/server-ui/src/sketcher.js
#Search for this line "var smiles = event.src.smiles();"
#* <source>?var smiles = event.src.smiles();</source>
#Add this new line below it
#* <source lang="javascript">$('#ar_text_input').val(smiles);</source>

=== Customize arthor-swagger.yaml ===
Location: /mnt/nfs/home/jjg/arthor_build_from_source/arthor-4.1/arthor-4.1-source/server/src/main/webapp/WEB-INF/static/swagger/arthor-swagger.yaml

==== Change URL Base Path for API Call ====
# vim /mnt/nfs/home/jjg/arthor_build_from_source/arthor-4.1/arthor-4.1-source/server/src/main/webapp/WEB-INF/static/swagger/arthor-swagger.yaml
# Search for "servers"
#* <source>?basePath</source>
# Remove "arthor" and keep argument as "/"

=== Compile/Minify Code through NPM ===
# Install NPM packages and Minify Code
#* <source>
cd /nfs/home/jjg/arthor_build_from_source/arthor-4.1/arthor-4.1-source/server-ui
npm install
npx webpack-dev-server
npx webpack --mode=production
</source>
# If the npx commands don't work, try updating node and npm version to the latest one.
# Build the war file
#* <source>
cd /nfs/home/jjg/arthor_build_from_source/arthor-4.1/arthor-4.1-source/server
mvn install -Pbootable
</source>
# If it works, then the path to new war file is at /mnt/nfs/home/jjg/arthor_build_from_source/arthor-4.1/arthor-4.1-source/server/target/arthor-server-4.1.war

== Adding Arthor to Systemd (example) ==
# Create service files
#: <source>
touch /etc/systemd/system/arthor.service
</source>
# Add this code block in the service file
#: <source>

[Unit]
Description=Arthor Public Instance
After=network.target

[Service]
Type=exec
Restart=always
RestartSec=3
User=root
ExecStart=/usr/bin/bash /nfs/soft2/arthor_configs/start_arthor_service.sh -arthor
ExecStop=/bin/kill -15 $MAINPID

[Install]
WantedBy=multi-user.target
</source>
# Change "ExecStart" to other Arthor Instances

== Restarting Arthor Instance(s) Instructions ==
=== Public, Private Arthor, and Super Private Arthor ===
# ssh to "arthor" server and run
#: <source>
systemctl <start|stop|restart> <arthor|arthorp|arthorc>
</source>

=== ArthorBB, ArthorCC, and ArthorCovalent ===
# ssh to "epyc-a40" server and run
#: <source>
systemctl <start|stop|restart> <arthorbb|arthorcc|arthorcovalent>
</source>

[[Category:Arthor]]
[[Category:Developer]]

Smallworld Databases

2025-05-31T00:51:08Z

Kyle: Add Accessible-BB-94M-25Q1 to SWP database info table

== Introduction ==
This page details the databases on Smallworld

{{TOCright}}

== Smallworld slides/presentations ==

https://www.slideshare.net/NextMoveSoftware/smallworld-efficient-maximum-common-substructure-searching-of-large-databases

https://www.nextmovesoftware.com/products/SmallWorld.pdf <--- very good, more detailed overview of how the technology works

https://www.nextmovesoftware.com/talks/Sayle_InterestingApplicationsOfChemicalGraphEditDistance_ACS_202303.pdf <--- random slides i found not that interesting

== Smallworld Databases ==
Tables of the five smallworld instances running on '''abacus'''.

=== sw.docking.org ===
{| class="wikitable"
|-
! Database !! Description (Always latest version available, shows number when available)
|-
| ChemSpace-SC-Stock-Mar2022 || Screening compounds sold by ChemSpace.
|-
| In-Stock-2020Q2-13.8M.anon || All ZINC in stock compounds.
|-
| Informer-Set-22Q3-4M || The ZINC "informer set" (compounds that can be purchased quickly, within a week or so).
|-
| Mcule-22Q1-8.7M || Mcule screening compounds.
|-
| Mcule-Full-22Q1-56M || Mcule, all compounds
|-
| Mcule-V-22Q1-47M || Mcule, make-on-demand.
|-
| MculeUltimate_20Q2_126M || Mcule "Ultimate" library.
|-
| REAL-Database-22Q1-4.5B || Enamine REAL database. (publicly available)
|-
| Wait-OK-2020Q2-1.2B.anon || ZINC compounds, in stock combined with make-on-demand.
|-
| WuXi-20Q4-2.2B || WuXi compounds, almost all make-on-demand.
|-
| ZINC-All-2020Q2-1.46B.anon || All compounds in ZINC20, including annotated only (not purchasable) compounds.
|-
| ZINC-Interesting-2020Q2-300K.anon || Drugs, bioactive, natural products, biogenic, or otherwise annotated for activity.
|-
|}

=== swp.docking.org ===
{| class="wikitable"
|-
! Database !! Description (version, number of molecules)
|-
| Chembridge On Demand 23Q4 22B
|-
| Macrocycles Make on Demand 23Q4. 9.9K
|-
| REAL-Space-22Q1-21B || Enamine private library
|-
| zinc22-All || ZINC-22
|-
| Accessible-BB-94M-25Q1 || 2 Component reaction enumerated product list from Fe Library
|-
|}

=== swbb.docking.org ===
{| class="wikitable"
|-
! Database !! Description
|-
| ChemSpace-BB-Stock-Mar2022 || Building blocks for sale from ChemSpace
|-
| BB-All-2020Q2-26.7M.anon || ZINC20 Building blocks for sale
|-
| BB-Now-2020Q2-1.6M.anon || ZINC20 Building blocks for rapid delivery (in-stock).
|-
| Mcule stock BB 23Q1 3.5M || can't be true, but try ordering and let us know
|-
| Mcule-BB-22Q1-2.1M || Mcule building blocks
|-
|}

=== swcc.docking.org ===
{| class="wikitable"
|-
! Database !! Description
|-
| el2_22Q1_290K || Ellman library 2. isoquinuclidines
|-
| y1-22Q3-57M || Damien Young library #1, substituted piperidines.
|}

[[Category:Smallworld]]
[[Category:Databases]]
[[Category:ZINC]]

Arthor Databases

2025-05-30T21:58:46Z

Kyle: Update arthorBB table with the new BB databases. May 2025

== Arthor Databases ==
Tables of the arthor instances.
=== arthor.docking.org ===
{| class="wikitable"
|-
! Database !! Description
|-
| BB-50-22Q1 || ZINC20 Building blocks, best price/delivery-speed combination
|-
| BB-40-22Q1 || ZINC20 building blocks, second tier in stock.
|-
| BB-30-22Q1 || ZINC20 building blocks, third tier in stock
|-
| BB-20-22Q1 || ZINC20 make-on-demand building blocks. Likely >> $500 . Likely 6 weeks or more.
|-
| BB-10-22Q1 || ZINC20 make-on-demand or expensive building blocks. Like >> $1000. Likely 6 weeks or more.
|-
| BB-ForSale-22Q1 || ZINC20 building blocks (50+40+30+20+10)
|-
| BB-InStock-22Q1 || ZINC20 building blocks (50+40+30)
|-
| ChemSpace-BB-Stock-Mar2022-712K || ChemSpace building blocks
|-
| ChemSpace-SC-Stock-Mar2022-346K || ChemSpace screening compounds
|-
| HMDBMetabolites-20Q1-585 || HMDB Metabolites
|-
| In-Stock-19Q4-13.8M || ZINC20 in stock
|-
| Informer-Set-22Q3-4M || ZINC20 informer set (fast delivery, modest prices)
|-
| Mcule-22Q1-8.7M || Mcule Screening compounds
|-
| Mcule-V-22Q1-51M || Mcule make on demand
|-
| Mcule-BB-22Q1-2.1M || some description
|-
| Mcule-Full-22Q1-60M || Mcule SC+BB
|-
| Mcule_ultimate_20Q2-126M || Mcule Ultimate
|-
| REAL-Database-22Q1-00 || Enamine REAL one part
|-
| REAL-Database-22Q1-01 || Enamine REAL another part
|-
| TCNMP-20Q1-37K || Traditional Chinese Medicine database
|-
| Wait-OK-19Q4-1.1B || ZINC20 in stock and make on demand
|-
| World-Drugs-20Q1-3K || ZINC20 drugs
|-
| WuXi-19Q4-339M || WuXi make-on-demand
|-
| ZINC-All-19Q4-1.4B || All ZINC20
|-
| ZINC-Interesting-2019Q4-307K || ZINC20 annotated, bioactive
|-
| ZINC-On-Demand-19Q4-311M || ZINC20 make on demand
|-
| ZINC20-ForSale-22Q1 || ZINC20 for sale
|-
|}

=== arthorp.docking.org ===
{| class="wikitable"
|-
! Database !! Description
|-
| el2_22Q1 || some description
|-
| REAL-Space-22Q1-00 ||
|-
| REAL-Space-22Q1-01 ||
|-
| REAL-Space-22Q1-02 ||
|-
| REAL-Space-22Q1-03 ||
|-
| REAL-Space-22Q1-04 ||
|-
| REAL-Space-22Q1-05 ||
|-
| REAL-Space-22Q1-06 ||
|-
| REAL-Space-22Q1-07 ||
|-
| zinc22-22Q1(H01~H25) ||
|-
|}
=== arthorbb.docking.org ===
{| class="wikitable"
|-
! Database !! Description
|-
| BB-10-22Q1 ||
|-
| BB-20-22Q1 ||
|-
| BB-30-22Q1 ||
|-
| BB-40-22Q1 ||
|-
| BB-50-22Q1 ||
|-
| BB-ForSale-22Q1 ||
|-
| BB-InStock-22Q1 ||
|-
| ChemSpace-BB-Stock-Mar2022-712K ||
|-
| Mcule-BB-22Q1-2.1M ||
|-
| 1-CSeconstock || Chemspace Economical Building Blocks Chiral & Achiral
|-
| 2-CSstock || Chemspace Building Blocks Full Stock Chiral & Achiral
|-
| 3-CS+fastMADE || Chemspace Building Blocks Full Stock and FastMade Building Blocks Chiral & Achiral
|-
| 4-CS+MADE || Chemspace Building Blocks Full Stock and Made Building Blocks Chiral & Achiral
|-
| 5-achCSeconstock || Chemspace Economical Building Blocks Achiral ONLY
|-
| 6-achCSstock || Chemspace Building Blocks Full Stock Achiral ONLY
|-
| 7-achCS+fastMADE || Chemspace Building Blocks Full Stock and FastMade Building Blocks Achiral ONLY
|-
| 8-achCS+MADE || Chemspace Building Blocks Full Stock and Made Building Blocks Achiral ONLY
|-
|}
=== arthorcc.docking.org ===
{| class="wikitable"
|-
! Database !! Description
|-
| el2_22Q1 || some description
|-
|}

[[Category:Arthor]]
[[Category:Databases]]
[[Category:ZINC]]

Smallworld and Arthor Databases

2025-05-28T22:49:43Z

Kyle: Create a redirect so the DB page on SW websites actually goes somehwere

#REDIRECT [[Smallworld Databases]]

Create dock release

2025-03-18T08:52:38Z

Kyle: Add page for adding major version to dock license

[[DOCK 3.8:How to build a release]]

[[How to update dock website]]

===Adding a major version to the DOCK licensing application===
[[Add major version]]

Add major version

2025-03-18T08:51:01Z

Kyle: How to add in major versions of DOCK to DOCK-license

= Adding new DOCK Versions to DOCK-Admin =
* DOCK-License code is on https://gitlab.docking.org/kylep/dock-admin request access from [[sysadmin]]
* All the dock versions are in <code>/nfs/soft/dock/packages</code> on <code>nfs-soft</code>
* Add the new DOCK file and then replace the relevant <code>dockx-latest.tgz</code> with the new DOCK release
** For example, if there is a new minor version of DOCK 6 like DOCK 6.15 (<code>dock.6.15.tgz</code>), copy the .tgz into the <code>/nfs/soft/dock/packages</code> folder. Remove <code>dock6-latest.tgz</code> and then <code>ln dock.6.15.tgz dock6-latest.tgz</code>.

= Adding new Major Dock version =
* Major dock versions are listed in <code>dock-admin/lib/constants.ts</code>
* Add the name of the new DOCK version to <code>MAIN_VERSIONS</code>, the same name to <code>MainVersions</code>, and a mapping of that name to a <code>.tgz</code> file in <code>/nfs/soft/dock/packages</code> in <code>dockVersions</code>.
* For example, if adding DOCK 7 as a new major version:

== Change constants.ts From ==
<pre>
// These DOCK versions will be shown on the application screen and highlighted when creating / editing a user
export type MainVersion = 'DOCK 3.7' | 'DOCK 3.8' | 'DOCK 4' | 'DOCK 6';

export const MAIN_VERSIONS: MainVersion[] = [
'DOCK 3.7',
'DOCK 3.8',
'DOCK 4',
'DOCK 6'
];

const dockVersions: AllowedFiles = {
'DOCK 3.7': 'dock3.7-latest.tgz',
'DOCK 3.8': 'dock3.8-latest.tgz',
'DOCK 4': 'dock4-latest.tgz',
'DOCK 6': 'dock6-latest.tgz',

// Old Versions imported from old db
...
};
</pre>

== Change constants.ts To ==
<pre>
// These DOCK versions will be shown on the application screen and highlighted when creating / editing a user
export type MainVersion = 'DOCK 3.7' | 'DOCK 3.8' | 'DOCK 4' | 'DOCK 6' | 'DOCK 7'; // <- The new major DOCK version

export const MAIN_VERSIONS: MainVersion[] = [
'DOCK 3.7',
'DOCK 3.8',
'DOCK 4',
'DOCK 6',
'DOCK 7' // <- The new major DOCK version
];

const dockVersions: AllowedFiles = {
'DOCK 3.7': 'dock3.7-latest.tgz',
'DOCK 3.8': 'dock3.8-latest.tgz',
'DOCK 4': 'dock4-latest.tgz',
'DOCK 6': 'dock6-latest.tgz',
'DOCK 7': 'dock7-latest.tgz', // <- The new major Dock versions latest.tgz in `/nfs/soft/dock/packages`

// Old Versions imported from old db
...
};
</pre>

= Testing Changes =
* <code>git clone https://gitlab.docking.org/kylep/dock-admin</code>
* <code>cd dock-admin</code>
* <code>npm install</code> to install all required packages
* <code>docker compose up -d</code> is required as it will build and create the docker container for the database and initialize a default admin account.
* While the postgress db is running you can use <code>npm run dev</code> to run the dev server without needing to rebuild the entire container every time. If ran locally it will use the downloads folder in the repo instead of <code>/nfs/soft/dock/packages</code>. If ran with docker it will use <code>/nfs/soft/dock/packages</code>. You can change <code>.env.docker</code> to modify the directory the server looks in for serving downloads.

= Committing Changes =
* <code>git add</code> the changed files, make a new commit, and push
* The CI/CD pipeline will automatically deploy the new changes. Use the admin dashboard to test the new changes!

How to edit dock website

2025-03-18T08:30:14Z

Kyle: Added instructions on how to change the DOCK website with git

=How to update DOCK=

==Via gitlab.docking.org==
* 1. request an account on gitlab.docking.org from [[sysadmin]]

* 2. login to gitlab.docking.org

* 3. request "maintainer" access ("developer" will require pull requests) to the DOCK Website repo from [[sysadmin]]

* 4. browse to change files and commit. All the files (probably) are in html/kuntz/. If you are only editing text files, you have our permission to push directly to main.

* 5. it should push to the public website automatically. (you may need to refresh cache on your browser to see the change)

* 6. If any problems or questions contact Kyle Petkovic or [[sysadmin]]. We are happy to talk to you about making this as easy as we can.

==Via git==

It works mostly the same as it did on the old DOCK site

===Running DOCK===
<syntaxhighlight lang="bash">
git clone https://gitlab.docking.org/kylep/dock
cd dock/html/kuntz/
python3 -m http.server 8023
</syntaxhighlight>
''Note: It's all html + bootstrap so no special packages are needed''

===Adding a New Minor DOCK Version===
'''File Location:''' <code>dock/html/kuntz/DOCK_6/index.htm</code> is where the DOCK 6 html file is located.

You can edit the HTML to add new release note links. In the DOCK_6 folder you can add a new <code>changelog.txt</code> file and then link to it from DOCK_6 using an <code><nowiki><a></nowiki></code> with an <code>href</code> in the ''Release Notes:'' section of <code>DOCK_6/index.htm</code>.

===Adding a New Major DOCK Version===
# Duplicate the <code>DOCK_6</code> folder and give it a new name
# Edit the files inside the new folder
# To add the new version to the navigation bar:
#* Go to <code>dock/html/kuntz/components/components.js</code>
#* Search for an existing DOCK version (e.g., "DOCK 6")
#* Duplicate its list item
#* Update the name and href to point to your new DOCK version page

===Committing Changes===
When your changes are done:
# Use <code>git add</code> to stage your modified files
# Commit the changes to the repository
# The CI/CD pipeline will automatically run and push the changes to public

[[Category:Sysadmin]]