Building and Docking on CoreHPC - Revision history

Kholland at 21:25, 21 September 2026

2026-09-21T21:25:40Z

← Older revision		Revision as of 21:25, 21 September 2026
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	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
	source /mnt/fac/CX900007_DS1/soft/DOCK3.8/~~pydock_env/bin/activate~~		source /mnt/fac/CX900007_DS1/soft/DOCK3.8/env.sh
	</syntaxhighlight>		</syntaxhighlight>

Kholland at 21:19, 21 September 2026

2026-09-21T21:19:41Z

← Older revision		Revision as of 21:19, 21 September 2026
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	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
	source /mnt/fac/CX900007_DS1/soft/DOCK3.8/~~env.sh~~		source /mnt/fac/CX900007_DS1/soft/DOCK3.8/pydock_env/bin/activate
	</syntaxhighlight>		</syntaxhighlight>

Kholland at 21:21, 16 September 2026

2026-09-16T21:21:14Z

← Older revision		Revision as of 21:21, 16 September 2026
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	== Docking ==		== Docking ==

	~~From a~~ directory ~~containing~~ your dockfiles and ~~the~~ SDI file~~, set the environment variables:~~		Run this from your working directory, which must contain your dockfiles and a subdirectory named 'sdi' holding your SDI file:

	~~<syntaxhighlight lang="bash">~~
	~~export DOCKFILES=[path to your dockfiles]~~
	~~export INPUT_FOLDER=[the folder containing your .sdi file(s)]~~
	~~export OUTPUT_FOLDER=[where you want the output]~~
	~~</syntaxhighlight>~~

	~~Then run the docking script~~:

	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
	bash /mnt/fac/CX900007_DS1/soft/super_dock3r.sh		bash /mnt/fac/CX900007_DS1/soft/super_dock3r.sh
	</syntaxhighlight>		</syntaxhighlight>

Kholland at 20:58, 16 September 2026

2026-09-16T20:58:11Z

← Older revision		Revision as of 20:58, 16 September 2026
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	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
	~~export MOLECULES_DIR_TO_BIND=[outermost folder containing the molecules to dock]~~
	export DOCKFILES=[path to your dockfiles]		export DOCKFILES=[path to your dockfiles]
	export INPUT_FOLDER=[the folder containing your .sdi file(s)]		export INPUT_FOLDER=[the folder containing your .sdi file(s)]

Kholland at 19:38, 10 September 2026

2026-09-10T19:38:45Z

← Older revision		Revision as of 19:38, 10 September 2026
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	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
	python $DOCK_INSTALL_PATH/zinc22-3d/submit/submit_building_docker.py --output_folder ~~output~~ --bundle_size ~~5 --skip_name_check~~ --~~schedule~~ slurm --container_software apptainer --container_path_or_name $DOCK_INSTALL_PATH/building_pipeline_oss.sif [smiles].smi		python $DOCK_INSTALL_PATH/zinc22-3d/submit/submit_building_docker.py --output_folder [output_folder_name] --bundle_size [bundle_size] --scheduler slurm --container_software apptainer --container_path_or_name $DOCK_INSTALL_PATH/building_pipeline_oss.sif [smiles].smi
	</syntaxhighlight>		</syntaxhighlight>

Kholland at 19:28, 10 September 2026

2026-09-10T19:28:29Z

← Older revision		Revision as of 19:28, 10 September 2026
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	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
	source /~~home~~/~~remote~~/~~jirwin3~~/~~fac~~/~~katiesoft~~/env.sh		source /mnt/fac/CX900007_DS1/soft/DOCK3.8/env.sh
	</syntaxhighlight>		</syntaxhighlight>

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	== Docking ==		== Docking ==

	From a directory containing your dockfiles and the SDI file:		From a directory containing your dockfiles and the SDI file, set the environment variables:

	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
	bash /~~home/remote/jirwin3~~/fac/~~katiesoft~~/~~scripts~~/~~submit_docking~~.sh ~~[sdi_file_name].sdi~~		export MOLECULES_DIR_TO_BIND=[outermost folder containing the molecules to dock]
			export DOCKFILES=[path to your dockfiles]
			export INPUT_FOLDER=[the folder containing your .sdi file(s)]
			export OUTPUT_FOLDER=[where you want the output]
			</syntaxhighlight>

			Then run the docking script:

			<syntaxhighlight lang="bash">
			bash /mnt/fac/CX900007_DS1/soft/super_dock3r.sh
	</syntaxhighlight>		</syntaxhighlight>
	~~```~~

Kholland at 16:53, 9 September 2026

2026-09-09T16:53:08Z

← Older revision		Revision as of 16:53, 9 September 2026
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	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
	source /home/remote/jirwin3/~~soft~~/~~dock385/DOCK3.8~~/env.sh		source /home/remote/jirwin3/fac/katiesoft/env.sh
	</syntaxhighlight>		</syntaxhighlight>

Kholland at 18:59, 8 September 2026

2026-09-08T18:59:03Z

← Older revision		Revision as of 18:59, 8 September 2026
Line 4:		Line 4:

	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
	source /home/remote/jirwin3/~~fac~~/~~katiesoft~~/DOCK3.8/env.sh		source /home/remote/jirwin3/soft/dock385/DOCK3.8/env.sh
	</syntaxhighlight>		</syntaxhighlight>

Kholland at 15:57, 13 August 2026

2026-08-13T15:57:02Z

← Older revision		Revision as of 15:57, 13 August 2026
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	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
	python $DOCK_INSTALL_PATH/zinc22-3d/submit/submit_building_docker.py --output_folder output --bundle_size 5 --skip_name_check --schedule slurm --container_software apptainer --container_path_or_name $DOCK_INSTALL_PATH/building_pipeline_oss.sif ~~5HT2C_actives~~.smi		python $DOCK_INSTALL_PATH/zinc22-3d/submit/submit_building_docker.py --output_folder output --bundle_size 5 --skip_name_check --schedule slurm --container_software apptainer --container_path_or_name $DOCK_INSTALL_PATH/building_pipeline_oss.sif [smiles].smi
	</syntaxhighlight>		</syntaxhighlight>

Kholland at 23:02, 12 August 2026

2026-08-12T23:02:46Z

← Older revision		Revision as of 23:02, 12 August 2026
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	~~# DOCK 3.8 — 3D Ligand Building & Docking~~		== 3D Ligand Building ==

	~~Workflow for building 3D ligands from a SMILES file and running docking on CoreHPC (SLURM).~~

	~~---~~

	~~## 1.~~ 3D Ligand Building

	Source the DOCK environment:		Source the DOCK environment:

	~~```~~bash		<syntaxhighlight lang="bash">
	source /home/remote/jirwin3/fac/katiesoft/DOCK3.8/env.sh		source /home/remote/jirwin3/fac/katiesoft/DOCK3.8/env.sh
	~~```~~		</syntaxhighlight>

	Submit the building pipeline (Apptainer container, SLURM scheduler):		Submit the building pipeline (Apptainer container, SLURM scheduler):

	~~```~~bash		<syntaxhighlight lang="bash">
	python $DOCK_INSTALL_PATH/zinc22-3d/submit/submit_building_docker.py --output_folder output --bundle_size 5 --skip_name_check --schedule slurm --container_software apptainer --container_path_or_name $DOCK_INSTALL_PATH/building_pipeline_oss.sif 5HT2C_actives.smi		python $DOCK_INSTALL_PATH/zinc22-3d/submit/submit_building_docker.py --output_folder output --bundle_size 5 --skip_name_check --schedule slurm --container_software apptainer --container_path_or_name $DOCK_INSTALL_PATH/building_pipeline_oss.sif 5HT2C_actives.smi
	~~```~~		</syntaxhighlight>

	Launch the array job:		Launch the array job:

	~~```~~bash		<syntaxhighlight lang="bash">
	sbatch building_array_job.sh		sbatch building_array_job.sh
	~~```~~		</syntaxhighlight>

	Collect the built bundles into an SDI file:		Collect the built bundles into an SDI file:

	~~```~~bash		<syntaxhighlight lang="bash">
	find /path/to/building/output -maxdepth 2 -name "bundle.db2.tgz" > [sdi_file_name].sdi		find /path/to/building/output -maxdepth 2 -name "bundle.db2.tgz" > [sdi_file_name].sdi
	~~```~~		</syntaxhighlight>

	~~---~~

	~~## 2.~~ Docking		== Docking ==

	From a directory containing your dockfiles and the SDI file:		From a directory containing your dockfiles and the SDI file:

	~~```~~bash		<syntaxhighlight lang="bash">
	bash /home/remote/jirwin3/fac/katiesoft/scripts/submit_docking.sh [sdi_file_name].sdi		bash /home/remote/jirwin3/fac/katiesoft/scripts/submit_docking.sh [sdi_file_name].sdi
			</syntaxhighlight>
	```		```