Ucsfdock: Difference between revisions

Revision as of 06:40, 2 September 2022

Deprecated. See pydock3.

@@ Line 1: / Line 1: @@
-''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.
+Deprecated. See [[pydock3]].
-Scripts:
- - 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 ==
-=== blastermaster configure ===
-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
-- rec.pdb
-- xtal-lig.pdb
-- rec.crg.pdb
-- 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 automatically copied into the working directory within the generated blastermaster job directory. If you would like to use
-=== blastermaster run ===
-Now
-== dockamster ==
-# TODO