How to install DOCK 3.8 - Revision history

Kyle: Update dock license website

2025-07-15T20:09:12Z

Update dock license website

← Older revision		Revision as of 20:09, 15 July 2025
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	== Obtaining a License ==		== Obtaining a License ==

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

	== Compiling from source ==		== Compiling from source ==

Btingle: /* Compiling from source */

2023-03-03T04:52:32Z

Compiling from source

← Older revision		Revision as of 04:52, 3 March 2023
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	See this page: [[How_to_compile_DOCK]]		See this page: [[How_to_compile_DOCK]]

	If you are a BKS ~~or Wynton~~ cluster member, you should follow the instructions for compiling via pgf. The DOCK 3.8 source can be found on github:		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>		<nowiki>git clone https://github.com/docking-org/dock3.git</nowiki>

	For any others without ~~access to our clusters or~~ a PGF license, follow the gfortran instructions.		For any others without a PGF license, follow the gfortran instructions.

	== Prebuilt Executable ==		== Prebuilt Executable ==

Btingle at 04:51, 3 March 2023

2023-03-03T04:51:29Z

← Older revision		Revision as of 04:51, 3 March 2023
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			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://dock.docking.org/Online_Licensing/dock_license_application.html]] and download the software.

	== Compiling from source ==		== Compiling from source ==

Btingle: /* Prebuilt Executable */

2023-03-03T04:46:22Z

Prebuilt Executable

← Older revision		Revision as of 04:46, 3 March 2023
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	dock38_matchcap : Same as above, but for 3.8		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>		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:DOCK 3.8]]
	[[Category:Developers]]		[[Category:Developers]]

Btingle: /* Prebuilt Executable */

2023-03-03T04:44:25Z

Prebuilt Executable

← Older revision		Revision as of 04:44, 3 March 2023
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	dock37_matchcap : DOCK 3.7 executable that more strictly caps the number of matches DOCK generates - slightly faster!		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_matchcap : Same as above, but for 3.8
	dock38_nogist : DOCK 3.8 sans error messages that sometimes occur when using recently built libraries</nowiki>		dock38_nogist : DOCK 3.8 sans error messages that sometimes occur when using recently built ligand libraries</nowiki>


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

Btingle at 20:55, 2 March 2023

2023-03-02T20:55:48Z

← Older revision		Revision as of 20:55, 2 March 2023
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	== Prebuilt Executable ==		== 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:		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>		<nowiki>/nfs/soft/dock/versions/dock38/executables</nowiki>

Btingle at 20:54, 2 March 2023

2023-03-02T20:54:25Z

← Older revision		Revision as of 20:54, 2 March 2023
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	== ~~install~~ ==		== Compiling from source ==
	* get a computer
	* go to dock.compbio.ucsf.edu. get a license.
	~~[https://dock.docking.org/Online_Licensing/dock_license_application.html dock.compbio.ucsf.edu]~~

	* download tarball		See this page: [[How_to_compile_DOCK]]
	* unpack tarball: ~~tar xzf dock.3.8_source.tar.gz~~
	~~you now have a directory pydock3-0.1.0 (or so)~~

	* make sure you ~~have python~~ 3.8 ~~or later.~~		If you are a BKS or Wynton cluster member, you should follow the instructions for compiling via pgf. The DOCK 3.8 source can be found on github:
	* bash
	* source ~~/nfs/soft/python/python3.8.5.sh~~
	* (some command to install)

	== ~~access for developers ==~~		<nowiki>git clone https://github.com/docking-org/dock3.git</nowiki>

	* https://github.~~com/docking-org/pydock3~~		For any others without access to our clusters or a PGF license, follow the gfortran instructions.

	~~<nowiki>~~		== Prebuilt Executable ==
	~~git clone https://github.com/docking-org/pydock3~~
	~~cd DOCK~~
	~~DOCKBASE~~=~~$PWD</nowiki>~~

	~~And retrieve the scripts from~~ DOCK~~/docking/submit/sge and~~ DOCK~~/docking/submit/slurm~~.		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:

	~~If you don't have the repository already cloned to your machine, you just need to clone it first:~~		<nowiki>/nfs/soft/dock/versions/dock38/executables</nowiki>

			Here is a brief description of the various executables here at the time of writing:
	<nowiki>		<nowiki>
	~~git clone https~~:~~//github.com/docking-org/~~DOCK.~~git~~		dock37_vanilla : standard DOCK 3.7 executable
	cd DOCK		dock38_vanilla : standard DOCK 3.8 executable
	~~DOCKBASE=$PWD</nowiki>~~		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
	~~If you're on BKS, you can find~~ DOCK 3.~~8 @ /nfs/soft/dock/versions/dock38/~~DOCK-~~current~~		dock38_nogist : DOCK 3.8 sans error messages that sometimes occur when using recently built libraries</nowiki>

	~~<nowiki>~~
	~~DOCKBASE=/nfs/soft/dock/versions/dock38/~~DOCK~~-current~~</nowiki>



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

Frodo: sdsfg

2022-11-02T23:28:06Z

sdsfg

← Older revision		Revision as of 23:28, 2 November 2022
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	== ~~Installation/Download~~ ==		== install ==
			* get a computer
			* go to dock.compbio.ucsf.edu. get a license.
			[https://dock.docking.org/Online_Licensing/dock_license_application.html dock.compbio.ucsf.edu]

	~~These instructions are only for developers. To install DOCK 3.8 for non-developers, please obtain a license via the DOCK license server [https~~://dock.~~docking~~.~~org/Online_Licensing/dock_license_application~~.~~html dock~~.~~compbio~~.~~ucsf.edu] and download the software~~.		* download tarball
			* unpack tarball: tar xzf dock.3.8_source.tar.gz
			you now have a directory pydock3-0.1.0 (or so)

	~~The up-to-date docking scripts for DOCK~~ 3.8 ~~are hosted primarily on github~~. ~~https:~~//~~github.com~~/~~docking-org~~/~~DOCK/tree/dev~~		* make sure you have python 3.8 or later.
			* bash
			* source /nfs/soft/python/python3.8.5.sh
			* (some command to install)

	~~If you already have a~~ docking-org ~~repository cloned to your machine, simply do the following:~~		== access for developers ==

			* https://github.com/docking-org/pydock3

	<nowiki>		<nowiki>
	git ~~pull~~		git clone https://github.com/docking-org/pydock3
	cd DOCK		cd DOCK
	DOCKBASE=$PWD</nowiki>		DOCKBASE=$PWD</nowiki>
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	<nowiki>		<nowiki>
	DOCKBASE=/nfs/soft/dock/versions/dock38/DOCK-current</nowiki>		DOCKBASE=/nfs/soft/dock/versions/dock38/DOCK-current</nowiki>



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

Frodo: asd

2022-08-31T17:48:58Z

asd

← Older revision		Revision as of 17:48, 31 August 2022
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	== Installation/Download ==		== Installation/Download ==

	These instructions are only for developers. To install DOCK 3.8 for non-developers, please obtain a license via the DOCK license server [https://dock.docking.org/Online_Licensing/dock_license_application.html \| dock.compbio.ucsf.edu] and download the software.		These instructions are only for developers. To install DOCK 3.8 for non-developers, please obtain a license via the DOCK license server [https://dock.docking.org/Online_Licensing/dock_license_application.html dock.compbio.ucsf.edu] and download the software.

	The up-to-date docking scripts for DOCK 3.8 are hosted primarily on github. https://github.com/docking-org/DOCK/tree/dev		The up-to-date docking scripts for DOCK 3.8 are hosted primarily on github. https://github.com/docking-org/DOCK/tree/dev

Frodo: asdf

2022-08-31T17:48:42Z

asdf

← Older revision		Revision as of 17:48, 31 August 2022
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	== Installation/Download ==		== Installation/Download ==

	These instructions are only for developers. To install DOCK 3.8 for non-developers, please obtain a license via the DOCK license server [https://dock.docking.org/Online_Licensing/dock_license_application.html] and download the software.		These instructions are only for developers. To install DOCK 3.8 for non-developers, please obtain a license via the DOCK license server [https://dock.docking.org/Online_Licensing/dock_license_application.html \| dock.compbio.ucsf.edu] and download the software.

	The up-to-date docking scripts for DOCK 3.8 are hosted primarily on github. https://github.com/docking-org/DOCK/tree/dev		The up-to-date docking scripts for DOCK 3.8 are hosted primarily on github. https://github.com/docking-org/DOCK/tree/dev