{"id":8456,"date":"2022-08-22T18:48:26","date_gmt":"2022-08-22T17:48:26","guid":{"rendered":"https:\/\/www.blopig.com\/blog\/?p=8456"},"modified":"2022-08-22T18:48:28","modified_gmt":"2022-08-22T17:48:28","slug":"filtering-molecules-with-long-linkers","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2022\/08\/filtering-molecules-with-long-linkers\/","title":{"rendered":"Filtering molecules with long linkers"},"content":{"rendered":"\n<p>Recently I was tasked with filtering out \u2018stringy\u2019 molecules that were being produced with the fragment merging method I\u2019m working on (that is, molecules with lots of consecutive non-ring bonds that weren\u2019t necessarily caught with my rotatable bond filter). While this is quite a niche\/specific task, through this I discovered a couple of RDKit functions that I wasn\u2019t previously aware of but might be helpful for other people regularly looking at small molecules. The demo adapts code from this helpful blogpost on cutting a molecule into rings and linkers from \u2018Is life worth living?\u2019 (which is a useful source of cheminformatics wisdom; <a href=\"https:\/\/iwatobipen.wordpress.com\/2020\/01\/23\/cut-molecule-to-ring-and-linker-with-rdkit-rdkit-chemoinformatics-memo\/\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/iwatobipen.wordpress.com\/2020\/01\/23\/cut-molecule-to-ring-and-linker-with-rdkit-rdkit-chemoinformatics-memo\/<\/a>). Obviously in practice you may be applying lots of different filters to enumerated molecules, but this is just a small example of something I found useful.&nbsp;<\/p>\n\n\n\n<p>The Jupyter Notebook can be found at:&nbsp;<\/p>\n\n\n\n<p><a href=\"https:\/\/github.com\/stephwills\/Demo-removing-stringy-molecules\/blob\/main\/Molecule%20filter.ipynb\">https:\/\/github.com\/stephwills\/Demo-removing-stringy-molecules\/blob\/main\/Molecule%20filter.ipynb<\/a><\/p>\n\n\n\n<p>Happy coding,&nbsp;<\/p>\n\n\n\n<p>Steph&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Recently I was tasked with filtering out \u2018stringy\u2019 molecules that were being produced with the fragment merging method I\u2019m working on (that is, molecules with lots of consecutive non-ring bonds that weren\u2019t necessarily caught with my rotatable bond filter). While this is quite a niche\/specific task, through this I discovered a couple of RDKit functions [&hellip;]<\/p>\n","protected":false},"author":87,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"nf_dc_page":"","wikipediapreview_detectlinks":true,"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"ngg_post_thumbnail":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[187,29,201],"tags":[],"ppma_author":[637],"class_list":["post-8456","post","type-post","status-publish","format-standard","hentry","category-cheminformatics","category-code","category-small-molecules"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"authors":[{"term_id":637,"user_id":87,"is_guest":0,"slug":"steph","display_name":"Stephanie Wills","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/4522454e01b0f43ce1309ba6fdda907c83b6966508817e94a9c4aae112253f01?s=96&d=mm&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/8456","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/users\/87"}],"replies":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/comments?post=8456"}],"version-history":[{"count":1,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/8456\/revisions"}],"predecessor-version":[{"id":8457,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/8456\/revisions\/8457"}],"wp:attachment":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media?parent=8456"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/categories?post=8456"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/tags?post=8456"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/ppma_author?post=8456"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}