Ucsfdock: Difference between revisions

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ucsfdock is a Python package wrapping the [[DOCK|DOCK program]] that provides tools to help standardize and automate the computational methods employed in molecular docking.
See [[pydock3]].


Scripts:
[[Category:Deprecated]]
- blastermaster: given receptor and ligand, generate a specific docking configuration
- dockmaster: evaluate many different docking configurations in parallel using a provided job scheduler (e.g. Slurm)
 
= Installation =
 
# TODO
 
= Quickstart =
 
== blastermaster ==
 
First you need to create the directory for your blastermaster job. To do so, simply type
 
blastermaster configure
 
By default, the job directory is named 'blastermaster_job'. To specify the name, you can do
 
blastermaster configure <JOB_DIR_NAME>
 
If your current working directory contains any of the following files
 
- reduce_wwPDB_het_dict.txt
- filt.params
- radii
- amb.crg.oxt
- vdw.siz
- delphi.def
- vdw.parms.amb.mindock
- prot.table.ambcrg.ambH
 
then they will be copied into the working directory within the generated blastermaster job directory.
 
== dockamster ==
 
# TODO

Latest revision as of 22:56, 24 May 2024

See pydock3.