http://wiki.docking.org/index.php?title=Zinc15_curators_notes&feed=atom&action=history
Zinc15 curators notes - Revision history
2024-03-29T01:45:47Z
Revision history for this page on the wiki
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http://wiki.docking.org/index.php?title=Zinc15_curators_notes&diff=9558&oldid=prev
Frodo: asdf
2016-09-06T18:40:14Z
<p>asdf</p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 18:40, 6 September 2016</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> create table target_class2 (like target_class);</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> create table target_class2 (like target_class);</div></td></tr>
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<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">= on postgres vacuuming =</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">I am noticing that, when I am doing major revisions of the protomer, substance and chembl21a.sea tables, where "major revisions" means adding, modifying or deleting multiple millions of rows per week and sometimes even per day, that when these massive changes are being done, I need to vacuum analyze the table at least once a week to prevent autovacuum from kicking in. Autovacuum is slower than a manually executed vacuum verbose analyze, and does not do as good a job. For those tables that are changing less than one million rows a week, vacuuming once a month is probably good enough. </ins></div></td></tr>
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Frodo
http://wiki.docking.org/index.php?title=Zinc15_curators_notes&diff=8252&oldid=prev
Frodo: blah
2015-02-06T00:40:12Z
<p>blah</p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 00:40, 6 February 2015</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>[[Category:Curator]]</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>[[Category:Curator]]</div></td></tr>
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Frodo
http://wiki.docking.org/index.php?title=Zinc15_curators_notes&diff=8251&oldid=prev
Frodo: b;lah
2015-02-05T23:41:26Z
<p>b;lah</p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:41, 5 February 2015</td>
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<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">= cleaning up =</ins></div></td></tr>
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Frodo
http://wiki.docking.org/index.php?title=Zinc15_curators_notes&diff=8184&oldid=prev
Frodo: blah
2014-11-10T20:33:24Z
<p>blah</p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:33, 10 November 2014</td>
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<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>= </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>= <ins style="font-weight: bold; text-decoration: none;">don't forget = </ins></div></td></tr>
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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>[[Category:Curator]]</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>[[Category:Curator]]</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>[[Category:ZINC15]]</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>[[Category:ZINC15]]</div></td></tr>
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Frodo
http://wiki.docking.org/index.php?title=Zinc15_curators_notes&diff=8183&oldid=prev
Frodo: Created page with "Here are the curator's notes for ZINC 15. = protomer (re)build = as xyz: example 1. by catalog python ~/code/ZINC/contrib/fetch.py -t substance -f 'smiles,zinc_id' 'catalog..."
2014-11-10T20:32:04Z
<p>Created page with "Here are the curator's notes for ZINC 15. = protomer (re)build = as xyz: example 1. by catalog python ~/code/ZINC/contrib/fetch.py -t substance -f 'smiles,zinc_id' 'catalog..."</p>
<p><b>New page</b></p><div>Here are the curator's notes for ZINC 15. <br />
<br />
= protomer (re)build =<br />
as xyz: example 1. by catalog<br />
python ~/code/ZINC/contrib/fetch.py -t substance -f 'smiles,zinc_id' 'catalog.short_name = sial' | split -l 1000<br />
example 2. by physical property tranche<br />
python ~/code/ZINC/contrib/fetch.py -t substance -f 'smiles,zinc_id' 'structure.mwt < 200' 'protomer.prot_id is null' | split -a 4 -l 1000<br />
<br />
<br />
# ls -l | wc -l (340)<br />
qsub -t 1-340 ~ts/Code/DOCK/ligand/generate/example-protomer-wrapper.sh ~/work/protomer<br />
<br />
= delta incremental load of smiles from zinc8 = <br />
as jji. based on exported smiles,sub_id from zinc8 since last update.<br />
python ~/code/ZINC/zinc/load/create_substances.py xaa.ism --progress<br />
<br />
= database export by property tranche = <br />
as xyz per ~/zinc14/byproperty/<br />
step1.csh <br />
step2.csh<br />
step3.csh <br />
<br />
= <br />
<br />
<br />
[[Category:Curator]]<br />
[[Category:ZINC15]]</div>
Frodo