{"id":315,"date":"2013-02-21T12:12:18","date_gmt":"2013-02-21T12:12:18","guid":{"rendered":"http:\/\/blopig.com\/blog\/?p=315"},"modified":"2015-02-19T09:33:30","modified_gmt":"2015-02-19T09:33:30","slug":"how-to-install-rdkit-on-ubuntu-12-04","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2013\/02\/how-to-install-rdkit-on-ubuntu-12-04\/","title":{"rendered":"How to install RDKit on Ubuntu 12.04 \/ 12.10 \/ 13.04 \/ 13.10 \/ 14.04 \/ 14.10 (with InChI support)"},"content":{"rendered":"<p>I make extensive use of this brilliant piece of cheminformatics software <a title=\"RDKit homepage\" href=\"http:\/\/www.rdkit.org\/\" target=\"_blank\">(RD)kit<\/a>, and it has saved me writing my own Molecule, Atom, Bond, Conformer, Fingerprint, SimilarityMetric, Descriptor etc. classes time and time again. \u00a0It is really neat, and works with C++ and python (and Java I think). \u00a0Here are the instructions on how to install it on a relatively recent Ubuntu version (12.04 \/ 12.10 \/ 13.04 \/ 13.10 \/ 14.04 \/ 14.10).<\/p>\n<p><span style=\"line-height: 14px;\">Pre-requisite software (this is why I love Debian based systems)<\/span><\/p>\n<pre class=\"toolbar:2 wrap:true lang:sh decode:true\">sudo apt-get install flex bison build-essential python-numpy cmake python-dev sqlite3 libsqlite3-dev libboost-dev  libboost-python-dev libboost-regex-dev<\/pre>\n<p>Get the latest RDKit goodie from <a title=\"Download RDKit\" href=\"http:\/\/sourceforge.net\/projects\/rdkit\/files\/\" target=\"_blank\">here<\/a>\u00a0(watch out &#8211; version number has been replaced by &#8216;X&#8217; below)<\/p>\n<pre class=\"toolbar:2 lang:sh decode:true\">wget http:\/\/downloads.sourceforge.net\/project\/rdkit\/rdkit\/QX_20XX\/RDKit_20XX_XX_X.tgz<\/pre>\n<p>Unzip the beast, save it to <code>\/opt<\/code><\/p>\n<pre class=\"toolbar:2 wrap:true lang:sh decode:true\">sudo tar xzvf RDKit_20XX_XX_X.tgz -C \/opt<\/pre>\n<p>Add some environment salt, <code>vim ~\/.bashrc<\/code><\/p>\n<pre class=\"toolbar:2 wrap:true lang:sh decode:true\">export RDBASE=\/opt\/RDKit_20XX_XX_X\r\nexport LD_LIBRARY_PATH=$RDBASE\/lib:$LD_LIBRARY_PATH\r\nexport PYTHONPATH=$RDBASE:$PYTHONPATH<\/pre>\n<p>Resource your .bashrc<\/p>\n<pre class=\"toolbar:2 wrap:true lang:sh decode:true\">. ~\/.bashrc<\/pre>\n<p>if you want the InChI stuff (trust me you do), first:<\/p>\n<pre>cd $RDBASE\/External\/INCHI-API\/\r\n.\/download-inchi.sh<\/pre>\n<p><span style=\"line-height: 1.714285714; font-size: 1rem;\">Build (compile), install &amp; test<\/span><\/p>\n<pre class=\"toolbar:2 wrap:true lang:sh decode:true\">cd $RDBASE\r\nmkdir build\r\ncd build\r\ncmake .. # if you do not care for InChI support OR\r\ncmake -DRDK_BUILD_INCHI_SUPPORT=ON .. # to install InChI generation code \r\nmake # -j 4 to use multiple processors\r\nmake install\r\nctest<\/pre>\n<p>If all your tests passed successful you are good to go. \u00a0Otherwise, get in touch via the post comments below.<\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>I make extensive use of this brilliant piece of cheminformatics software (RD)kit, and it has saved me writing my own Molecule, Atom, Bond, Conformer, Fingerprint, SimilarityMetric, Descriptor etc. classes time and time again. \u00a0It is really neat, and works with C++ and python (and Java I think). \u00a0Here are the instructions on how to install [&hellip;]<\/p>\n","protected":false},"author":6,"featured_media":0,"comment_status":"open","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":[14,15],"tags":[],"ppma_author":[40],"class_list":["post-315","post","type-post","status-publish","format-standard","hentry","category-howto","category-technical"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"authors":[{"term_id":40,"user_id":0,"is_guest":1,"slug":"cap-jp","display_name":"jp","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/?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\/315","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\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/comments?post=315"}],"version-history":[{"count":14,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/315\/revisions"}],"predecessor-version":[{"id":2346,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/315\/revisions\/2346"}],"wp:attachment":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media?parent=315"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/categories?post=315"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/tags?post=315"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/ppma_author?post=315"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}