Ucsfdock: Difference between revisions

Latest revision as of 22:56, 24 May 2024

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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 job directory 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