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