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Trent scripts - Revision history
2026-05-27T05:23:45Z
Revision history for this page on the wiki
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http://wiki.docking.org/index.php?title=Trent_scripts&diff=8755&oldid=prev
TBalius at 16:22, 18 June 2015
2015-06-18T16:22:51Z
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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 16:22, 18 June 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> >> pwd</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> >> pwd</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> /mnt/nfs/work/tbalius/Water_Project_all_in_the_same_frame_ph4/vs_frags</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> /mnt/nfs/work/tbalius/Water_Project_all_in_the_same_frame_ph4/vs_frags</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;"></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> >> python /nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number.py ./ vs_frag /nfs/work/tbalius/database_ph4/frags.txt 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 /nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number.py ./ vs_frag /nfs/work/tbalius/database_ph4/frags.txt 500 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><del style="font-weight: bold; text-decoration: none;"> ## </del>this will make 500 subdirectories<del style="font-weight: bold; text-decoration: none;">. </del>with approximately the same number of databases.</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> </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>this will make 500 subdirectories with approximately the same number of databases<ins style="font-weight: bold; text-decoration: none;">. If "number" is grater than number of databases it will make have a directory for each database</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;"><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 /nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number.py ./ vs_frag /nfs/work/tbalius/database_ph4/frags.txt 500 size</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 /nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number.py ./ vs_frag /nfs/work/tbalius/database_ph4/frags.txt 500 size</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>this will give more or less the behavior now, It will limit the size of the database contain in each chunk to the maximum sized chunk. (however, biggest databases are submitted first, before they were submitted last.) </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>this will give more or less the behavior now <ins style="font-weight: bold; text-decoration: none;">($DOCKBASE/docking/setup/setup_db2_zinc15.py)</ins>, It will limit the size of the database contain in each chunk to the maximum sized chunk. (however, biggest databases are submitted first, before they were submitted last.) </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;"><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 /nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number.py ./ vs_frag /nfs/work/tbalius/database_ph4/frags.txt 500 both</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 /nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number.py ./ vs_frag /nfs/work/tbalius/database_ph4/frags.txt 500 both</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>this will make > 500 <del style="font-weight: bold; text-decoration: none;">subdirectory</del>. with approximately the same number of databases, and will also limit the size of the database contain in each chunk.</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>this will make > 500 <ins style="font-weight: bold; text-decoration: none;">subdirectories</ins>. with approximately the same number of databases, and will also limit the size of the database contain in each chunk.</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>Please test it and let me know if it works for you. </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>Please test it and let me know if it works for you. </div></td></tr>
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TBalius
http://wiki.docking.org/index.php?title=Trent_scripts&diff=8754&oldid=prev
Frodo: asdf
2015-06-18T16:07:12Z
<p>asdf</p>
<p><b>New page</b></p><div>This is how to use Trent's scripts for preparing to dock. <br />
<br />
/nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number.py<br />
<br />
Usage: setup_db2_zinc15.py dir name filename number typr<br />
dir: The full path of the directory where docking will be performed, subdirectorys will be created and contain databases.<br />
name: The idenifying 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 subdiretorys to create, this devides the databases into ~ equal docking chunks to be submited.<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.<br />
<br />
Here are examples of how to run it:<br />
<br />
>> pwd<br />
/mnt/nfs/work/tbalius/Water_Project_all_in_the_same_frame_ph4/vs_frags<br />
>> python /nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number.py ./ vs_frag /nfs/work/tbalius/database_ph4/frags.txt 500 count<br />
## this will make 500 subdirectories. with approximately the same number of databases.<br />
<br />
>> python /nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number.py ./ vs_frag /nfs/work/tbalius/database_ph4/frags.txt 500 size<br />
this will give more or less the behavior now, It will limit the size of the database contain in each chunk to the maximum sized chunk. (however, biggest databases are submitted first, before they were submitted last.) <br />
<br />
<br />
>> python /nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number.py ./ vs_frag /nfs/work/tbalius/database_ph4/frags.txt 500 both<br />
this will make > 500 subdirectory. with approximately the same number of databases, and will also limit the size of the database contain in each chunk.<br />
<br />
Please test it and let me know if it works for you. <br />
<br />
[[Category:Tutorials]]<br />
[[Category:DOCK]]</div>
Frodo