http://wiki.docking.org/index.php?action=history&feed=atom&title=Docking_to_all_LSD_targetsDocking to all LSD targets - Revision history2026-09-19T18:29:19ZRevision history for this page on the wikiMediaWiki 1.39.1http://wiki.docking.org/index.php?title=Docking_to_all_LSD_targets&diff=17524&oldid=prevIamkaant: added categories2026-09-15T23:14:40Z<p>added categories</p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:14, 15 September 2026</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* The script refuses to replace an existing real directory named <code>dockfiles</code>, but will refresh a stale symlink.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* The script refuses to replace an existing real directory named <code>dockfiles</code>, but will refresh a stale symlink.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* 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.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* 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.</div></td></tr>
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</table>Iamkaanthttp://wiki.docking.org/index.php?title=Docking_to_all_LSD_targets&diff=17523&oldid=prevIamkaant: first commit2026-09-15T23:11:41Z<p>first commit</p>
<p><b>New page</b></p><div><br />
Sets up the ten LSD_Website DOCK run directories in the current directory and submits them.<br />
<br />
Runs on Cluster 7 only so far.<br />
<br />
=== Usage ===<br />
<br />
cd /path/to/where/you/want/the/folders<br />
python3 /nfs/hdd02/work/ak87/SCRIPTS/DOCK/DOCK2LSD/setup_launch_lsd_run.py my.sdi<br />
<br />
=== What it does ===<br />
<br />
For each target (EP4R, SERT, 5HT2A, CB1R, MT1R, Sigma2, D4, AmpC, NSP3_Mac1, Alpha2AR):<br />
<br />
* creates <code><TARGET>/</code><br />
* symlinks <code>dockfiles</code> to the target's dockfiles dir under <code>/nfs/cluster_2/exf/LSD_Website/</code><br />
* writes the SDI into <code><TARGET>/sdi/</code> — as-is if ≤ 5000 lines, otherwise split into 5000-line chunks<br />
* 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<br />
* runs <code>sh run_subdock.sh</code> in the folder<br />
<br />
Failures are reported at the end; one bad target does not stop the others.<br />
<br />
=== Options ===<br />
<br />
* <code>--dry-run</code> — print the plan, change nothing<br />
* <code>--no-submit</code> — set up but do not run <code>run_subdock.sh</code><br />
* <code>--targets D4 AmpC</code> — restrict to a subset<br />
* <code>--chunk-size N</code> — lines per SDI chunk (default 5000)<br />
* <code>--batch-size N</code> — force <code>USE_DB2_TGZ_BATCH_SIZE=N</code> in every copy<br />
* <code>--max-array N</code> — SLURM MaxArraySize (default 10001)<br />
* <code>--run-subdock PATH</code> — alternative <code>run_subdock.sh</code><br />
<br />
=== Notes ===<br />
<br />
* 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.<br />
* The script refuses to replace an existing real directory named <code>dockfiles</code>, but will refresh a stale symlink.<br />
* 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.</div>Iamkaant