Written by Benjamin Roberts, NeSI Application Support Specialist, Manaaki Whenua - Landcare Research Copyright (C) 2019 Landcare Research New Zealand Ltd
For support queries related to this package, please contact the NeSI Support team at:
https://support.nesi.org.nz/hc/requests/new
GOLD is protein-ligand docking software developed and maintained by the Cambridge Crystallographic Data Centre (CCDC) in the United Kingdom. Its web page can be found here:
https://www.ccdc.cam.ac.uk/solutions/csd-discovery/Components/Gold/
The GOLD software itself is proprietary and closed-source, but is licensed by several research groups at universities and other organisations around the world. Some users of GOLD at New Zealand institutions wish to run the software on the NeSI high-performance computers.
In particular, researchers wish to be able to spread out the work to dock large numbers of ligands (thousands or more) over several CPU cores by means of Slurm array jobs. Because of the way the software receives its input data (e.g. ligand molecules in one large file containing many records), we need to be able to detect certain properties.
The gold-functions package contains a single Bash (Bourne Again SHell) resource file consisting of several functions. When this resource file is loaded in a Slurm job submission script, these functions are made available to the script.
The functions are as follows, listed in alphabetical order:
- check_job_status_daemon - a function that obviously existed in earlier (now lost) copies of the gold-functions resource file. GOLD communicates with its licence server by means of daemons, and in some cases it can be necessary to ensure that a daemon has shut down properly.
- clean_up_and_exit - do any necessary cleaning up and exit with the supplied exit code. By convention, the writer of the Slurm script should supply 0 if the script has exited cleanly, or a non-zero exit code if the exit has been triggered by an error condition.
- exit_trap - a function that is called by a trap in the Slurm job submission script. The trap exists to intercept signals caught by the Slurm job.
- get_library_file - parse the GOLD configuration file, looking for a library file containing ligand structures. If the entry exists in the configuration file, parse it to get the name of the library file.
- ligands_total - find the total number of ligands in a file, based solely on record separators. The function assumes a valid MDL SDF file or Tripos Mol2 file.