{"id":8287,"date":"2022-06-13T08:01:05","date_gmt":"2022-06-13T07:01:05","guid":{"rendered":"https:\/\/www.blopig.com\/blog\/?p=8287"},"modified":"2023-03-03T14:53:28","modified_gmt":"2023-03-03T14:53:28","slug":"viewing-fragment-elaborations-in-rdkit","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2022\/06\/viewing-fragment-elaborations-in-rdkit\/","title":{"rendered":"Viewing fragment elaborations in RDKit"},"content":{"rendered":"\n

As a reasonably new RDKit user, I was relieved to find that using its built-in functionality for generating basic images from molecules is quite easy to use. However, over time I have picked up some additional tricks to make the images generated slightly more pleasing on the eye!<\/p>\n\n\n\n

The first of these (which I definitely stole from another blog post at some point…) is to ask it to produce SVG images rather than png:<\/p>\n\n\n\n

#ensure the molecule visualisation uses svg rather than png format\nIPythonConsole.ipython_useSVG=True<\/pre>\n\n\n\n
Now for something slightly more interesting: as a fragment elaborator, I often need to look at a long list of elaborations that have been made to a starting fragment. As these have usually been docked, these don’t look particularly nice when loaded straight into RDKit and drawn:<\/p>\n\n\n\n
#load several mols from a single sdf file using SDMolSupplier\n#add these to a list\nelabs = [mol for mol in Chem.SDMolSupplier('frag2\/elabsTestNoRefine_Docked_0.sdf')]\n\n#get list of ligand efficiencies so these can be displayed alongside the molecules\nLEs = [(float(mol.GetProp('Gold.PLP.Fitness'))\/mol.GetNumHeavyAtoms()) for mol in elabs]\n\nDraw.MolsToGridImage(elabs, legends = [str(LE) for LE in LEs])<\/pre>\n\n\n\n
\"\"<\/a>
Fig. 1: Images generated without doing any tinkering<\/figcaption><\/figure>\n\n\n\n
Two quick changes that will immediately make this image more useful are aligning the elaborations by a supplied substructure (here I supplied the original fragment so that it’s always in the same place) and calculating the 2D coordinates of the molecules so we don’t see the twisty business happening in the bottom right of Fig. 1:<\/p>\n\n\n\n\n\n\n\n
for elab in elabs:  \n    #view 2D visualisation instead\n    AllChem.Compute2DCoords(elab)\n    #keep fragment section in the same place\n    _=AllChem.GenerateDepictionMatching2DStructure(elab,frag_to_elaborate)  \n\n        \nDraw.MolsToGridImage(elabs,  legends=[str(LE) for LE in LEs])<\/pre>\n\n\n\n
\"\"<\/a>
Fig. 2. Now aren’t they easier to compare!<\/figcaption><\/figure>\n\n\n\n
Now you can scroll through visualizations of your elaborations without even having to touch Pymol. <\/p>\n\n\n\n
<\/p>\n","protected":false},"excerpt":{"rendered":"
As a reasonably new RDKit user, I was relieved to find that using its built-in functionality for generating basic images from molecules is quite easy to use. However, over time I have picked up some additional tricks to make the images generated slightly more pleasing on the eye! The first of these (which I definitely […]<\/p>\n","protected":false},"author":94,"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":[87,477,129,134],"ppma_author":[559],"class_list":["post-8287","post","type-post","status-publish","format-standard","hentry","category-cheminformatics","category-code","category-small-molecules","tag-code-2","tag-fragment-based-drug-discovery","tag-rdkit","tag-small-molecules"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"authors":[{"term_id":559,"user_id":94,"is_guest":0,"slug":"lucy_vost","display_name":"Lucy Vost","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/410b510f70dab77a9fa285069d544f6f8069c1743e6050067edc992e470b551e?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\/8287","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\/94"}],"replies":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/comments?post=8287"}],"version-history":[{"count":4,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/8287\/revisions"}],"predecessor-version":[{"id":8318,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/8287\/revisions\/8318"}],"wp:attachment":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media?parent=8287"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/categories?post=8287"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/tags?post=8287"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/ppma_author?post=8287"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}