http://wiki.docking.org/index.php?action=history&feed=atom&title=Using_SWAG_to_search_smaller_vendors 2026-05-24T10:24:52Z Revision history for this page on the wiki MediaWiki 1.39.1 http://wiki.docking.org/index.php?title=Using_SWAG_to_search_smaller_vendors&diff=17257&oldid=prev 2026-05-06T19:43:04Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <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 19:43, 6 May 2026</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l18">Line 18:</td> <td colspan="2" class="diff-lineno">Line 18:</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>- The above instructions here make use of SWAG&#039;s local map feature. More detail and uses for local maps can be [[Using SWAG to filter analogs by Graph Edit Distance|found here]].</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 above instructions here make use of SWAG&#039;s local map feature. More detail and uses for local maps can be [[Using SWAG to filter analogs by Graph Edit Distance|found here]].</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 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;">[[Category:Smallworld]] [[Category:SWAG]]</ins></div></td></tr> <!-- diff cache key wikidb:diff::1.12:old-17255:rev-17257 --> </table>

Zdingman http://wiki.docking.org/index.php?title=Using_SWAG_to_search_smaller_vendors&diff=17255&oldid=prev 2026-05-06T19:37:30Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <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 19:37, 6 May 2026</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l6">Line 6:</td> <td colspan="2" class="diff-lineno">Line 6:</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>   source /nfs/home/zdingman/environments/SWAG/bin/activate</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>   source /nfs/home/zdingman/environments/SWAG/bin/activate</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>   cp /nfs/home/zdingman/scripts/<del style="font-weight: bold; text-decoration: none;">SWAG_v1_3_0</del>/SWAG.py .</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>   cp /nfs/home/zdingman/scripts/<ins style="font-weight: bold; text-decoration: none;">SWAG_v1-3-1</ins>/SWAG.py .</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>   ln -s /nfs/db5/newdb/Purchasable/maps/onDemandPlus/onepot-tst.smi.anon.map local.anon.map</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>   ln -s /nfs/db5/newdb/Purchasable/maps/onDemandPlus/onepot-tst.smi.anon.map local.anon.map</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>   ln -s /nfs/db5/newdb/Purchasable/maps/onDemandPlus/onepot-tst.smi.anon.map.blm local.anon.map.blm</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>   ln -s /nfs/db5/newdb/Purchasable/maps/onDemandPlus/onepot-tst.smi.anon.map.blm local.anon.map.blm</div></td></tr> <!-- diff cache key wikidb:diff::1.12:old-17254:rev-17255 --> </table>

Zdingman http://wiki.docking.org/index.php?title=Using_SWAG_to_search_smaller_vendors&diff=17254&oldid=prev 2026-05-06T19:36:02Z

<p>Created page.</p> <p><b>New page</b></p><div>In addition to the included databases that SWAG can search by default ([[How to Use SWAG|see here]]), it is possible to search any other database with a SmallWorld mapping. Recent interest has been expressed by multiple lab members in searching the vendor OnePot&#039;s CORE database for potential compounds to purchase. The below instructions describe how to search OnePot specifically, but can be adapted for any other vendor whose catalog has been mapped with SmallWorld.<br /> <br /> == Instructions ==<br /> <br /> Connect to either epyc or epyc2 on the lab cluster. Make a working directory in the location of your choice, open that directory, and copy query.smi (your SMILES of interest) into the directory. Copy and paste the following code:<br /> <br /> source /nfs/home/zdingman/environments/SWAG/bin/activate<br /> cp /nfs/home/zdingman/scripts/SWAG_v1_3_0/SWAG.py .<br /> ln -s /nfs/db5/newdb/Purchasable/maps/onDemandPlus/onepot-tst.smi.anon.map local.anon.map<br /> ln -s /nfs/db5/newdb/Purchasable/maps/onDemandPlus/onepot-tst.smi.anon.map.blm local.anon.map.blm<br /> python SWAG.py -f query.smi -o lookup -d local -p [0]<br /> <br /> SWAG will begin to lookup your SMILES. The file lookup_responses.csv contains the compounds that were successfully found in the vendor&#039;s catalog. Don&#039;t be surprised if the coverage is subpar for larger compounds; at larger HAC tranches, the overlap between ZINC22 and OnePot is fairly minimal.<br /> <br /> == Notes ==<br /> <br /> - If you&#039;re willing to explore single-atom changes, you can instead specify -p [1] when running SWAG.<br /> <br /> - The above instructions here make use of SWAG&#039;s local map feature. More detail and uses for local maps can be [[Using SWAG to filter analogs by Graph Edit Distance|found here]].</div>

Zdingman