Building and Docking on CoreHPC - Revision history

Kholland at 15:57, 13 August 2026

2026-08-13T15:57:02Z

← Older revision		Revision as of 15:57, 13 August 2026
Line 10:		Line 10:

	<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
Line 1:		Line 1:
	~~# 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>
	```		```

Kholland at 23:00, 12 August 2026

2026-08-12T23:00:21Z

← Older revision		Revision as of 23:00, 12 August 2026
Line 1:		Line 1:
	3D ~~LIGAND BUILDING~~:		# DOCK 3.8 — 3D Ligand Building & Docking

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

			---

			## 1. 3D Ligand Building

			Source the DOCK environment:

			```bash
	source /home/remote/jirwin3/fac/katiesoft/DOCK3.8/env.sh		source /home/remote/jirwin3/fac/katiesoft/DOCK3.8/env.sh
			```

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

	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		```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
			```

			Launch the array job:

			```bash
	sbatch building_array_job.sh		sbatch building_array_job.sh
			```

			Collect the built bundles into an SDI file:

			```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~~		## 2. Docking

	~~DOCKING:~~		From a directory containing your dockfiles and the SDI file:
	in a directory ~~with~~ your dockfiles and SDI file

			```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
			```

Kholland: Created page with "3D LIGAND BUILDING: source /home/remote/jirwin3/fac/katiesoft/DOCK3.8/env.sh 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 sbatch building_array_job.sh find /path/to/building/output -maxdepth 2 -name "bundle.db2.tgz" > [sdi_file_name}.sdi DOCKING: in a..."

2026-08-12T20:50:31Z

Created page with "3D LIGAND BUILDING: source /home/remote/jirwin3/fac/katiesoft/DOCK3.8/env.sh 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 sbatch building_array_job.sh find /path/to/building/output -maxdepth 2 -name "bundle.db2.tgz" > [sdi_file_name}.sdi DOCKING: in a..."

New page

3D LIGAND BUILDING:
source /home/remote/jirwin3/fac/katiesoft/DOCK3.8/env.sh

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

sbatch building_array_job.sh

find /path/to/building/output -maxdepth 2 -name "bundle.db2.tgz" > [sdi_file_name}.sdi

DOCKING:
in a directory with your dockfiles and SDI file

bash /home/remote/jirwin3/fac/katiesoft/scripts/submit_docking.sh [sdi_file_name].sdi