Ucsfdock - Revision history

Frodo: asdf

2024-05-24T22:56:05Z

asdf

← Older revision		Revision as of 22:56, 24 May 2024
Line 1:		Line 1:
	~~Deprecated.~~ See [[pydock3]].		See [[pydock3]].

			[[Category:Deprecated]]

Ianscottknight: Replaced content with "Deprecated. See pydock3."

2022-09-02T06:40:44Z

Replaced content with "Deprecated. See pydock3."

Show changes

Ianscottknight at 06:26, 2 September 2022

2022-09-02T06:26:37Z

← Older revision		Revision as of 06:26, 2 September 2022
Line 3:		Line 3:
	Scripts included in ''pydock3'':		Scripts included in ''pydock3'':
	* ''blastermaster'': generate a specific docking configuration for a given receptor and ligand		* ''blastermaster'': generate a specific docking configuration for a given receptor and ligand
	* ''dockopt'': generate many different docking configurations ~~and then evaluate & analyze~~ them in parallel using a specified job scheduler (e.g. Slurm)		* ''dockopt'': generate many different docking configurations, perform retrospective docking on them in parallel using a specified job scheduler (e.g. Slurm), and analyze the results.

	A '''docking configuration''' is a unique set of DOCK parameter files (e.g., ''matching_spheres.sph'') and INDOCK parameter values.		A '''docking configuration''' is a unique set of DOCK parameter files (e.g., ''matching_spheres.sph'') and INDOCK parameter values.

Ianscottknight at 06:19, 2 September 2022

2022-09-02T06:19:05Z

← Older revision		Revision as of 06:19, 2 September 2022
Line 1:		Line 1:
	''pydock3'' is a Python package wrapping the [[DOCK\|DOCK Fortran program]] that provides tools to help standardize and automate the computational methods employed in molecular docking.		''pydock3'' is a Python package wrapping the [[DOCK\|DOCK Fortran program]] that provides tools to help standardize and automate the computational methods employed in molecular docking.

	~~Programs~~:		Scripts included in ''pydock3'':
	* ''blastermaster'': generate a specific docking configuration for a given receptor and ligand		* ''blastermaster'': generate a specific docking configuration for a given receptor and ligand
	* ''dockopt'': generate many different docking configurations and then evaluate & analyze them in parallel using a specified job scheduler (e.g. Slurm)		* ''dockopt'': generate many different docking configurations and then evaluate & analyze them in parallel using a specified job scheduler (e.g. Slurm)

Ianscottknight at 06:17, 2 September 2022

2022-09-02T06:17:07Z

← Older revision		Revision as of 06:17, 2 September 2022
Line 34:		Line 34:
	'''Note:''' Invoking ''blastermaster'' commands below will produce a log file called ''blastermaster.log'' in your current working directory.		'''Note:''' Invoking ''blastermaster'' commands below will produce a log file called ''blastermaster.log'' in your current working directory.

	=== ''~~configure~~'' ===		=== ''init'' ===

	First you need to create the file structure for your blastermaster job. To do so, simply type		First you need to create the file structure for your blastermaster job. To do so, simply type

	pydock3 blastermaster - ~~configure~~		pydock3 blastermaster - init

	By default, the job directory is named ''blastermaster_job''. To specify a different name, type		By default, the job directory is named ''blastermaster_job''. To specify a different name, type

	pydock3 blastermaster - ~~configure~~ <JOB_DIR_NAME>		pydock3 blastermaster - init <JOB_DIR_NAME>

	The job directory contains two sub-directories:		The job directory contains two sub-directories:
Line 87:		Line 87:
	'''Note:''' Invoking ''dockopt'' commands will produce a log file called ''dockopt.log'' in your current working directory.		'''Note:''' Invoking ''dockopt'' commands will produce a log file called ''dockopt.log'' in your current working directory.

	=== ''~~configure~~'' ===		=== ''init'' ===
	First you need to create the file structure for your dockopt job. To do so, simply type		First you need to create the file structure for your dockopt job. To do so, simply type

	pydock3 dockopt - ~~configure~~		pydock3 dockopt - init

	By default, the job directory is named ''dockopt_job''. To specify a different name, type		By default, the job directory is named ''dockopt_job''. To specify a different name, type

	pydock3 dockopt - ~~configure~~ <JOB_DIR_NAME>		pydock3 dockopt - init <JOB_DIR_NAME>

	The job directory contains two sub-directories:		The job directory contains two sub-directories:
Line 168:		Line 168:
	=== ''run'' ===		=== ''run'' ===

	Once your job has been configured to your liking, navigate to the the job directory and run dockopt:		Once your job has been configured to your liking, navigate to the the job directory and run ''dockopt'':
	cd <JOB_DIR_NAME>		cd <JOB_DIR_NAME>
	pydock3 dockopt - run <JOB_SCHEDULER_NAME>		pydock3 dockopt - run <JOB_SCHEDULER_NAME>

Ianscottknight at 06:15, 2 September 2022

2022-09-02T06:15:06Z

Show changes

Ianscottknight at 21:12, 12 August 2022

2022-08-12T21:12:11Z

← Older revision		Revision as of 21:12, 12 August 2022
Line 34:		Line 34:
	'''Note:''' Invoking ''blastermaster'' commands below will produce a log file called ''blastermaster.log'' in your current working directory.		'''Note:''' Invoking ''blastermaster'' commands below will produce a log file called ''blastermaster.log'' in your current working directory.

	=== ''~~blastermaster~~ configure'' ===		=== ''configure'' ===

	First you need to create the file structure for your blastermaster job. To do so, simply type		First you need to create the file structure for your blastermaster job. To do so, simply type

	blastermaster configure		ucsfdock blastermaster - configure

	By default, the job directory is named ''blastermaster_job''. To specify a different name, type		By default, the job directory is named ''blastermaster_job''. To specify a different name, type

	blastermaster configure <JOB_DIR_NAME>		ucsfdock blastermaster - configure <JOB_DIR_NAME>

	The job directory contains two sub-directories:		The job directory contains two sub-directories:
Line 71:		Line 71:
	Finally, configure the ''blastermaster_config.yaml'' file in the job directory to your specifications. The parameters in this file govern the behavior of blastermaster.		Finally, configure the ''blastermaster_config.yaml'' file in the job directory to your specifications. The parameters in this file govern the behavior of blastermaster.

	=== ''~~blastermaster~~'' ~~run~~ ===		=== ''run'' ===

	Once your job has been configured to your liking, navigate to the the job directory and run blastermaster:		Once your job has been configured to your liking, navigate to the the job directory and run blastermaster:
	cd <JOB_DIR_NAME>		cd <JOB_DIR_NAME>
	blastermaster run		ucsfdock blastermaster - run

	This will execute the many blastermaster subroutines in sequence. The state of the program will be printed to standard output as it runs.		This will execute the many blastermaster subroutines in sequence. The state of the program will be printed to standard output as it runs.
Line 87:		Line 87:
	'''Note:''' Invoking ''dockmaster'' commands will produce a log file called ''dockmaster.log'' in your current working directory.		'''Note:''' Invoking ''dockmaster'' commands will produce a log file called ''dockmaster.log'' in your current working directory.

	=== ''~~dockmaster~~ configure'' ===		=== ''configure'' ===
	First you need to create the file structure for your dockmaster job. To do so, simply type		First you need to create the file structure for your dockmaster job. To do so, simply type

	dockmaster configure		ucsfdock dockmaster - configure

	By default, the job directory is named ''dockmaster_job''. To specify a different name, type		By default, the job directory is named ''dockmaster_job''. To specify a different name, type

	dockmaster configure <JOB_DIR_NAME>		ucsfdock dockmaster - configure <JOB_DIR_NAME>

	The job directory contains two sub-directories:		The job directory contains two sub-directories:
Line 166:		Line 166:
	export SGE_SETTINGS=/opt/sge/default/common/settings.sh		export SGE_SETTINGS=/opt/sge/default/common/settings.sh

	=== ''~~dockmaster~~ run'' ===		=== ''run'' ===

	Once your job has been configured to your liking, navigate to the the job directory and run dockmaster:		Once your job has been configured to your liking, navigate to the the job directory and run dockmaster:
	cd <JOB_DIR_NAME>		cd <JOB_DIR_NAME>
	dockmaster run <JOB_SCHEDULER_NAME>		ucsfdock dockmaster - run <JOB_SCHEDULER_NAME>

	where <JOB_SCHEDULER_NAME> is one of:		where <JOB_SCHEDULER_NAME> is one of:
Line 179:		Line 179:

	You can also set the following flags to adjust retro docking job submission behavior. This example show the default values:		You can also set the following flags to adjust retro docking job submission behavior. This example show the default values:
	dockmaster run <JOB_SCHEDULER_NAME> --retro_docking_job_max_reattempts=0 --retro_docking_job_timeout_minutes=None		ucsfdock dockmaster - run <JOB_SCHEDULER_NAME> --retro_docking_job_max_reattempts=0 --retro_docking_job_timeout_minutes=None

	Once the dockmaster job is complete, the following files will be generated in the job directory:		Once the dockmaster job is complete, the following files will be generated in the job directory:

Ianscottknight at 23:50, 3 August 2022

2022-08-03T23:50:37Z

← Older revision		Revision as of 23:50, 3 August 2022
Line 125:		Line 125:
	Finally, configure the ''dockmaster_config.yaml'' file in the job directory to your specifications. The parameters in this file govern the behavior of dockmaster.		Finally, configure the ''dockmaster_config.yaml'' file in the job directory to your specifications. The parameters in this file govern the behavior of dockmaster.

	'''Note:''' The ''dockmaster_config.yaml'' file differs from the ''blastermaster_config.yaml'' file in that every parameter of the former may accept either a single value or a ''list of comma-separated values'', which indicates a ~~specific set~~ of ~~configuration parameter~~ values to attempt. Multiple such multi-valued parameters may be provided, and all unique resultant docking configurations will be attempted.		'''Note:''' The ''dockmaster_config.yaml'' file differs from the ''blastermaster_config.yaml'' file in that every parameter of the former may accept either a single value or a ''list of comma-separated values'', which indicates a pool of values to attempt for that parameter. Multiple such multi-valued parameters may be provided, and all unique resultant docking configurations will be attempted.

	Single-valued YAML line format:		Single-valued YAML line format:

Ianscottknight at 20:06, 2 August 2022

2022-08-02T20:06:57Z

← Older revision		Revision as of 20:06, 2 August 2022
Line 62:		Line 62:
	* ''prot.table.ambcrg.ambH''		* ''prot.table.ambcrg.ambH''

	Only the following are required. Default versions / generated versions of the others will be used instead if they are not ~~provided~~.		Only the following are required. Default versions / generated versions of the others will be used instead if they are not detected.
	* ''rec.pdb''		* ''rec.pdb''
	* ''xtal-lig.pdb''		* ''xtal-lig.pdb''
Line 116:		Line 116:
	* ''prot.table.ambcrg.ambH''		* ''prot.table.ambcrg.ambH''

	Only the following are required. Default versions / generated versions of the others will be used instead if they are not ~~provided~~.		Only the following are required. Default versions / generated versions of the others will be used instead if they are not detected.
	* ''rec.pdb''		* ''rec.pdb''
	* ''xtal-lig.pdb''		* ''xtal-lig.pdb''

Ianscottknight: /* Gimel */

2022-07-29T07:44:28Z

Gimel

← Older revision		Revision as of 07:44, 29 July 2022
Line 25:		Line 25:
	Only nodes other than ''gimel'' itself are supported, e.g., ''gimel5''.		Only nodes other than ''gimel'' itself are supported, e.g., ''gimel5''.

			ssh gimel5
	source /nfs/soft/ian/python3.8.5.sh		source /nfs/soft/ian/python3.8.5.sh