{"id":3327,"date":"2017-02-08T10:36:58","date_gmt":"2017-02-08T10:36:58","guid":{"rendered":"http:\/\/www.blopig.com\/blog\/?p=3327"},"modified":"2017-02-08T10:36:58","modified_gmt":"2017-02-08T10:36:58","slug":"using-rdkit-to-load-ligand-sdfs-into-pandas-dataframes","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2017\/02\/using-rdkit-to-load-ligand-sdfs-into-pandas-dataframes\/","title":{"rendered":"Using RDKit to load ligand SDFs into Pandas DataFrames"},"content":{"rendered":"

If you have downloaded lots of ligand SDF files from the PDB, then a good way of viewing\/comparing all their properties would be to load it into a Pandas DataFrame.<\/p>\n

RDKit has a very handy function just for this – it\u2019s found under the PandasTool module.<\/a><\/p>\n

I show an example below within Jupypter-notebook, in which I load in the SDF file, view the table of molecules and perform other RDKit functions to the molecules.<\/p>\n

First import the PandasTools module:<\/p>\n

from rdkit.Chem import PandasTools\r\n<\/pre>\n
Read in the SDF file:<\/p>\n
SDFFile\u00a0=\u00a0\".\/Ligands_noHydrogens_noMissing_59_Instances.sdf\"\r\nBRDLigs\u00a0=\u00a0PandasTools.LoadSDF(SDFFile)\r\n<\/pre>\n
You can see the whole table by calling the dataframe:<\/p>\n
BRDLigs<\/pre>\n
\"\"<\/a><\/p>\n
The ligand properties in the SDF file are stored as columns. You can view what these properties are, and in my case I have loaded 59 ligands each having up to 26 properties:<\/p>\n
BRDLigs.info()<\/pre>\n
\"\"<\/a><\/p>\n
It is also very easy to perform other RDKit functions on the dataframe. For instance, I noticed there is no heavy atom column, so I added my own called ‘NumHeavyAtoms’:<\/p>\n
BRDLigs['NumHeavyAtoms']=BRDLigs.apply(lambda x: x['ROMol'].GetNumHeavyAtoms(), axis=1)\r\n\r\n<\/pre>\n
Here is the column added to the table, alongside columns containing the molecules’ SMILES and RDKit molecule:<\/p>\n
BRDLigs[['NumHeavyAtoms','SMILES','ROMol']]\r\n\r\n<\/pre>\n
\"\"<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"
If you have downloaded lots of ligand SDF files from the PDB, then a good way of viewing\/comparing all their properties would be to load it into a Pandas DataFrame. RDKit has a very handy function just for this – it\u2019s found under the PandasTool module. I show an example below within Jupypter-notebook, in which […]<\/p>\n","protected":false},"author":38,"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":[29,10,14],"tags":[154,152,129,134],"ppma_author":[530],"class_list":["post-3327","post","type-post","status-publish","format-standard","hentry","category-code","category-groupmeetings","category-howto","tag-jupyter","tag-python","tag-rdkit","tag-small-molecules"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"authors":[{"term_id":530,"user_id":38,"is_guest":0,"slug":"susan","display_name":"Susan Leung","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/e1a367a2f8d7409be8aa6d2beff2d277525c90331ec34202854a9a5116b4eaa4?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\/3327","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\/38"}],"replies":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/comments?post=3327"}],"version-history":[{"count":6,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/3327\/revisions"}],"predecessor-version":[{"id":3337,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/3327\/revisions\/3337"}],"wp:attachment":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media?parent=3327"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/categories?post=3327"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/tags?post=3327"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/ppma_author?post=3327"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}