View source for Docking to all LSD targets


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

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

=== Options ===

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

=== Notes ===

* Target names and dockfiles paths live in the <code>TARGETS</code> 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 <code>dockfiles</code>, but will refresh a stale symlink.
* The script uses my local copy of SUBDOCK from <code>/nfs/home/ak87/PROGRAMS/SUBDOCK/subdock.bash</code>, let me know if it's inaccessible.

[[Category:Cluster 7]] [[Category:LSD]]