http://wiki.docking.org/index.php?title=March2019_protocol&feed=atom&action=history
March2019 protocol - Revision history
2024-03-28T19:36:03Z
Revision history for this page on the wiki
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http://wiki.docking.org/index.php?title=March2019_protocol&diff=11611&oldid=prev
Dudenko at 02:11, 6 April 2019
2019-04-06T02:11:35Z
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 02:11, 6 April 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l10">Line 10:</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> sub_number = 500 <- this is the number of subdirectories </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> sub_number = 500 <- this is the number of subdirectories </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> runtype = count</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> runtype = count</div></td></tr>
<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> out_number = <del style="font-weight: bold; text-decoration: none;">100 </del><- this is the number of outer directories ( calculated from tot_number/sub_number)</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> out_number = <ins style="font-weight: bold; text-decoration: none;">60 </ins><- this is the number of outer directories ( calculated from tot_number/sub_number)</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;"><br/></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;"><br/></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>Here is a description of the inputs to the script:</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>Here is a description of the inputs to the script:</div></td></tr>
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Dudenko
http://wiki.docking.org/index.php?title=March2019_protocol&diff=11610&oldid=prev
Dudenko at 23:28, 5 April 2019
2019-04-05T23:28:28Z
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:28, 5 April 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l7">Line 7:</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> name = leads</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> name = leads</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> infile = ZINC-downloader-3D-db2.gz.wait-ok_new.database_index</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> infile = ZINC-downloader-3D-db2.gz.wait-ok_new.database_index</div></td></tr>
<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> tot_number = <del style="font-weight: bold; text-decoration: none;">50000</del></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> tot_number = <ins style="font-weight: bold; text-decoration: none;">30000</ins></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> sub_number = 500 <- this is the number of subdirectories </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> sub_number = 500 <- this is the number of subdirectories </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> runtype = count</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> runtype = count</div></td></tr>
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Dudenko
http://wiki.docking.org/index.php?title=March2019_protocol&diff=11609&oldid=prev
Dudenko at 23:28, 5 April 2019
2019-04-05T23:28:07Z
<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:28, 5 April 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1">Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</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>Here is the tutorial for the setup script for DOCK3</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>Here is the tutorial for the setup script for DOCK3</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;"><br/></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;"><br/></td></tr>
<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> python /mnt/nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number_newstruc.py <del style="font-weight: bold; text-decoration: none;">'</del>.<del style="font-weight: bold; text-decoration: none;">' </del>leads ZINC-downloader-3D-db2.gz.wait-ok_new.database_index <del style="font-weight: bold; text-decoration: none;">50000 </del>500 count</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> python /mnt/nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number_newstruc.py .<ins style="font-weight: bold; text-decoration: none;">/ </ins>leads ZINC-downloader-3D-db2.gz.wait-ok_new.database_index <ins style="font-weight: bold; text-decoration: none;">30000 </ins>500 count</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;"><br/></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;"><br/></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>In this example, the parameter values are as follows: </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>In this example, the parameter values are as follows: </div></td></tr>
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Dudenko
http://wiki.docking.org/index.php?title=March2019_protocol&diff=11542&oldid=prev
Jklyu at 23:20, 15 March 2019
2019-03-15T23:20:10Z
<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:20, 15 March 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1">Line 1:</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><del style="font-weight: bold; text-decoration: none;">ere </del>is the tutorial for the setup script for DOCK3</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;">Here </ins>is the tutorial for the setup script for DOCK3</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;"><br/></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;"><br/></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> python /mnt/nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number_newstruc.py '.' leads ZINC-downloader-3D-db2.gz.wait-ok_new.database_index 50000 500 count</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> python /mnt/nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number_newstruc.py '.' leads ZINC-downloader-3D-db2.gz.wait-ok_new.database_index 50000 500 count</div></td></tr>
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Jklyu
http://wiki.docking.org/index.php?title=March2019_protocol&diff=11541&oldid=prev
Frodo: asdf
2019-03-15T23:18:45Z
<p>asdf</p>
<p><b>New page</b></p><div>ere is the tutorial for the setup script for DOCK3<br />
<br />
python /mnt/nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number_newstruc.py '.' leads ZINC-downloader-3D-db2.gz.wait-ok_new.database_index 50000 500 count<br />
<br />
In this example, the parameter values are as follows: <br />
workdir = .<br />
name = leads<br />
infile = ZINC-downloader-3D-db2.gz.wait-ok_new.database_index<br />
tot_number = 50000<br />
sub_number = 500 <- this is the number of subdirectories <br />
runtype = count<br />
out_number = 100 <- this is the number of outer directories ( calculated from tot_number/sub_number)<br />
<br />
Here is a description of the inputs to the script:<br />
<br />
Usage:<br />
setup_db2_zinc15_file_number_newstruc.py dir name filename number subnumber type<br />
dir: The full path of the directory where docking will be performed, subdirectoriss will be created and contain databases.<br />
name: The identifying name of subdirectorys (these are created in the "dir" directory).<br />
filename: the file that contains the full paths where dbs are located,<br />
this you can download from zinc15.<br />
number: number of total diretories to create, this devides the databases into ~ equal docking chunks to be submited.<br />
subnumber: number of subdiretories to create, this will make listing files much easer.<br />
type: size, count, or both<br />
* size will make dirs equal chunks in terms of size,<br />
* "count" option will put equal numbers of database files in the number directory spesified, <br />
* the option "both" will try and satisfy both size and count options.</div>
Frodo