DOCK3.8:Pydock3: Difference between revisions
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''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. It is a natural successor to DOCK Blaster, originally published in 2009, and blastermaster.py, part of the [[DOCK 3.7]] release in 2012. | ''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. It is a natural successor to DOCK Blaster, originally published in 2009, and blastermaster.py, part of the [[DOCK 3.7]] release in 2012. | ||
[[File:Pydock3 logo.png|thumb]] | |||
Scripts included in ''pydock3'': | Scripts included in ''pydock3'': | ||
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* ''blastermaster'': generate a specific docking configuration for a given receptor and ligand, intended for use by experts who wish to tune the docking model themselves. This is a direct successor of blastermaster.py from DOCK 3.7. | * ''blastermaster'': generate a specific docking configuration for a given receptor and ligand, intended for use by experts who wish to tune the docking model themselves. This is a direct successor of blastermaster.py from DOCK 3.7. | ||
A [[docking configuration|'''docking configuration''']] | A [[docking configuration|'''docking configuration''']] is a unique set of (1) DOCK parameter files (e.g., ''matching_spheres.sph''), (2) an INDOCK file, and (3) a DOCK executable. | ||
= Installation = | = Installation = | ||
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= Instructions = | = Instructions = | ||
== ''blastermaster'' == | |||
See: [[blastermaster (pydock3 script)]]. | |||
== ''dockopt'' == | |||
See: [[dockopt (pydock3 script)]]. | |||
== Note for UCSF Shoichet Lab members == | == Note for UCSF Shoichet Lab members == | ||
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ssh gimel5 | ssh gimel5 | ||
source /nfs/soft/ian/python3.8.5.sh | source /nfs/soft/ian/python3.8.5.sh | ||
[[Category:DOCK 3.8]] | [[Category:DOCK 3.8]] | ||
[[Category:DOCK Blaster]] | [[Category:DOCK Blaster]] | ||
Latest revision as of 01:51, 24 August 2023
pydock3 is a Python package wrapping the DOCK Fortran program that provides tools to help standardize and automate the computational methods employed in molecular docking. It is a natural successor to DOCK Blaster, originally published in 2009, and blastermaster.py, part of the DOCK 3.7 release in 2012.
Scripts included in pydock3:
- 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.
- blastermaster: generate a specific docking configuration for a given receptor and ligand, intended for use by experts who wish to tune the docking model themselves. This is a direct successor of blastermaster.py from DOCK 3.7.
A docking configuration is a unique set of (1) DOCK parameter files (e.g., matching_spheres.sph), (2) an INDOCK file, and (3) a DOCK executable.
Installation
See: DOCK 3.8:How to install pydock3.
Instructions
blastermaster
See: blastermaster (pydock3 script).
dockopt
See: dockopt (pydock3 script).
Note for UCSF Shoichet Lab members
pydock3 is already installed on the following clusters. You can source the provided Python environment scripts to expose the pydock3 executable:
Wynton
source /wynton/group/bks/soft/python_envs/python3.8.5.sh
Gimel
Only nodes other than gimel itself are supported, e.g., gimel5.
ssh gimel5 source /nfs/soft/ian/python3.8.5.sh