DOCK3.8:Pydock3: Difference between revisions

From DISI
Jump to navigation Jump to search
m (Frodo moved page Pydock3 to DOCK3.8:Pydock3: package naming convention)
No edit summary
 
(10 intermediate revisions by 2 users not shown)
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. 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'':
* ''blastermaster'': generate a specific docking configuration for a given receptor and ligand
* ''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.  
* ''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|'''docking configuration''']] is a unique set of DOCK parameter files (e.g., ''matching_spheres.sph'') and INDOCK parameter values.
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 =


See: [[How to install pydock3]].
See: [[DOCK 3.8:How to install pydock3]].


= Instructions =
= Instructions =
== ''blastermaster'' ==
See: [[blastermaster (pydock3 script)]].
== ''dockopt'' ==
See: [[dockopt (pydock3 script)]].


== Note for UCSF Shoichet Lab members ==
== Note for UCSF Shoichet Lab members ==
Line 19: Line 31:
=== Wynton ===
=== Wynton ===


source /wynton/home/irwin/isknight/envs/python3.8.5.sh
  source /wynton/group/bks/soft/python_envs/python3.8.5.sh


=== Gimel ===
=== Gimel ===
Line 28: Line 40:
  source /nfs/soft/ian/python3.8.5.sh
  source /nfs/soft/ian/python3.8.5.sh


== ''blastermaster'' ==
See: [[blastermaster (pydock3 script)]].
== ''dockopt'' ==


See: [[dockopt (pydock3 script)]].
[[Category:DOCK 3.8]]
[[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.

Pydock3 logo.png

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