ZINC-22:3D Building - Revision history

Btingle: Changed redirect target from Building the 3D Pipeline ZINC22 to Building The 3D Pipeline ZINC22

2023-03-09T18:06:34Z

Changed redirect target from Building the 3D Pipeline ZINC22 to Building The 3D Pipeline ZINC22

← Older revision		Revision as of 18:06, 9 March 2023
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	#REDIRECT [[Building ~~the~~ 3D Pipeline ZINC22]]		#REDIRECT [[Building The 3D Pipeline ZINC22]]

Btingle: Redirected page to Building the 3D Pipeline ZINC22

2023-03-09T18:06:14Z

Redirected page to Building the 3D Pipeline ZINC22

← Older revision		Revision as of 18:06, 9 March 2023
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	#REDIRECT[Building the 3D Pipeline ZINC22]		#REDIRECT [[Building the 3D Pipeline ZINC22]]

Btingle: Replaced content with "#REDIRECT[Building the 3D Pipeline ZINC22]"

2023-03-09T18:05:53Z

Replaced content with "#REDIRECT[Building the 3D Pipeline ZINC22]"

← Older revision		Revision as of 18:05, 9 March 2023
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	~~= Introduction =~~		#REDIRECT[Building the 3D Pipeline ZINC22]

	~~You can email me to request access to the zinc 3d build repository here:~~

	~~https://github.com/btingle/zinc-3d-build~~

	~~The contents of this github can be found on /nfs/home/xyz/btingle/zinc_deploy/zinc-3d-build. There are two top-level bash scripts in this repository that should be used for the 3d building process:~~

	* build_3d_smiles.bash
	* export_zinc_ids.bash

	~~= export_zinc_ids.bash =~~

	~~This script exports the SMILES for all substances from a chosen TIN database and annotates them with unique ZINC codes.~~

	~~== Example Usage ==~~
	~~<nowiki>~~
	~~export ZINC_PORT=5434~~
	~~export EXPORT_DEST=/local2/3d/export~~
	~~./export_zinc_ids.bash</nowiki>~~

	~~ZINC_PORT is the port number of the database on this machine that should be exported from.~~

	~~EXPORT_DEST is where the annotated smiles/ZINC ID file should be saved.~~

	~~The name of the output file is formatted as follows:~~

	~~<nowiki>~~
	~~$EXPORT_DEST/[PARTITION_RANGE]_[PORT].export</nowiki>~~

	~~= build_3d_smiles.bash =~~

	~~This script submits jobs on the cluster to build the 3d data for the output of export_zinc_ids.bash~~

	~~== Example Usage ==~~
	~~<nowiki>~~
	~~export SMILES_FILE=/local2/3d/export/H30P400_H30P400_5434.export~~
	~~export TEMPDIR=/local2/3d/build/scratch~~
	~~./build_3d_smiles.bash</nowiki>~~

	~~The nodes allocated for these jobs are defined in nodelist.txt.~~

	~~The output of this script will be in $TEMPDIR/~~[~~SMILES].out split into a number of batches. Each batch .tar file contains the output of 5000 jobs. Each job outputs a .tar.gz file containing the results of 3d building for 20 substances.~~


	~~== building on Wynton ==~~
	I have previously built db2 on Wynton, and recently tested with the new script (/build_database_ligand_strain_noH_s.sh). Thought it might be useful to you. The only thing that might not be accessible to you is the ~~python environment I previously installed under my HOME. (Guess Wynton sys admin does not want us to peek other people’s home directory).~~

	~~Here’s the path to my script on Wynton: /wynton/group/bks/work/yingyang/prep_db2/5A_lig/prep_db2.csh~~


	~~== building on LBL ==~~

	~~(space for info for building using docker containers on LBL)~~

	~~== building on AWS ==~~

	~~(space for info about building on aws)~~


	~~[[Category:Curator]]~~
	~~[[Category:DOCK 3.8]]~~
	~~[[Category:ZINC-22]~~]

Frodo: Frodo moved page ZINC 3D Building to ZINC-22:3D Building: rationalize naming

2022-03-15T22:20:33Z

Frodo moved page ZINC 3D Building to ZINC-22:3D Building: rationalize naming

← Older revision	Revision as of 22:20, 15 March 2022
(No difference)

Frodo: asdf

2022-03-15T22:20:05Z

asdf

← Older revision		Revision as of 22:20, 15 March 2022
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	[[Category:Curator]]		[[Category:Curator]]
			[[Category:DOCK 3.8]]
			[[Category:ZINC-22]]

Frodo: asdf

2020-07-13T20:40:58Z

asdf

← Older revision		Revision as of 20:40, 13 July 2020
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	The output of this script will be in $TEMPDIR/[SMILES].out split into a number of batches. Each batch .tar file contains the output of 5000 jobs. Each job outputs a .tar.gz file containing the results of 3d building for 20 substances.		The output of this script will be in $TEMPDIR/[SMILES].out split into a number of batches. Each batch .tar file contains the output of 5000 jobs. Each job outputs a .tar.gz file containing the results of 3d building for 20 substances.


			== building on Wynton ==
			I have previously built db2 on Wynton, and recently tested with the new script (/build_database_ligand_strain_noH_s.sh). Thought it might be useful to you. The only thing that might not be accessible to you is the python environment I previously installed under my HOME. (Guess Wynton sys admin does not want us to peek other people’s home directory).

			Here’s the path to my script on Wynton: /wynton/group/bks/work/yingyang/prep_db2/5A_lig/prep_db2.csh


			== building on LBL ==

			(space for info for building using docker containers on LBL)

			== building on AWS ==

			(space for info about building on aws)


			[[Category:Curator]]

Btingle: /* Introduction */

2020-06-30T18:27:10Z

Introduction

← Older revision		Revision as of 18:27, 30 June 2020
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	= Introduction =		= Introduction =

	You can request access to the zinc 3d build repository here:		You can email me to request access to the zinc 3d build repository here:

	https://github.com/btingle/zinc-3d-build		https://github.com/btingle/zinc-3d-build

Btingle: /* Usage */

2020-06-30T18:25:58Z

Usage

← Older revision		Revision as of 18:25, 30 June 2020
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	This script exports the SMILES for all substances from a chosen TIN database and annotates them with unique ZINC codes.		This script exports the SMILES for all substances from a chosen TIN database and annotates them with unique ZINC codes.

	== Usage ==		== Example Usage ==
	<nowiki>		<nowiki>
	export ZINC_PORT=~~[PORT]~~		export ZINC_PORT=5434
	export EXPORT_DEST=~~[DIR]~~		export EXPORT_DEST=/local2/3d/export
	./export_zinc_ids.bash</nowiki>		./export_zinc_ids.bash</nowiki>

Btingle: /* Example Usage */

2020-06-30T18:24:56Z

Example Usage

← Older revision		Revision as of 18:24, 30 June 2020
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	== Example Usage ==		== Example Usage ==
	<nowiki>		<nowiki>
	export SMILES_FILE=/local2/3d/export/~~[SMILES]~~		export SMILES_FILE=/local2/3d/export/H30P400_H30P400_5434.export
	export TEMPDIR=/local2/3d/build/scratch		export TEMPDIR=/local2/3d/build/scratch
	./build_3d_smiles.bash</nowiki>		./build_3d_smiles.bash</nowiki>

Btingle: /* Usage */

2020-06-30T18:24:26Z

Usage

← Older revision		Revision as of 18:24, 30 June 2020
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	This script submits jobs on the cluster to build the 3d data for the output of export_zinc_ids.bash		This script submits jobs on the cluster to build the 3d data for the output of export_zinc_ids.bash

	== Usage ==		== Example Usage ==
	<nowiki>		<nowiki>
	export SMILES_FILE=/local2/3d/export/[SMILES]		export SMILES_FILE=/local2/3d/export/[SMILES]