Docking to all LSD targets

From DISI
Revision as of 23:11, 15 September 2026 by Iamkaant (talk | contribs) (first commit)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search

Sets up the ten LSD_Website DOCK run directories in the current directory and submits them.

Runs on Cluster 7 only so far.

Usage

cd /path/to/where/you/want/the/folders
python3 /nfs/hdd02/work/ak87/SCRIPTS/DOCK/DOCK2LSD/setup_launch_lsd_run.py my.sdi

What it does

For each target (EP4R, SERT, 5HT2A, CB1R, MT1R, Sigma2, D4, AmpC, NSP3_Mac1, Alpha2AR):

  • creates <TARGET>/
  • symlinks dockfiles to the target's dockfiles dir under /nfs/cluster_2/exf/LSD_Website/
  • writes the SDI into <TARGET>/sdi/ — as-is if ≤ 5000 lines, otherwise split into 5000-line chunks
  • copies run_subdock.sh and checks USE_DB2_TGZ_BATCH_SIZE against the SLURM array limit (10001 per SDI file), raising it only if the array would be rejected
  • runs sh run_subdock.sh in the folder

Failures are reported at the end; one bad target does not stop the others.

Options

  • --dry-run — print the plan, change nothing
  • --no-submit — set up but do not run run_subdock.sh
  • --targets D4 AmpC — restrict to a subset
  • --chunk-size N — lines per SDI chunk (default 5000)
  • --batch-size N — force USE_DB2_TGZ_BATCH_SIZE=N in every copy
  • --max-array N — SLURM MaxArraySize (default 10001)
  • --run-subdock PATH — alternative run_subdock.sh

Notes

  • Target names and dockfiles paths live in the TARGETS dict at the top of the script — edit there to add or change a screen.
  • The script refuses to replace an existing real directory named dockfiles, but will refresh a stale symlink.
  • The script uses my local copy of SUBDOCK from /nfs/home/ak87/PROGRAMS/SUBDOCK/subdock.bash, let me know if it's inaccessible.
Retrieved from "http://wiki.docking.org/index.php?title=Docking_to_all_LSD_targets&oldid=17523"