{"id":3128,"date":"2016-09-26T21:03:55","date_gmt":"2016-09-26T20:03:55","guid":{"rendered":"http:\/\/www.blopig.com\/blog\/?p=3128"},"modified":"2016-09-26T21:03:55","modified_gmt":"2016-09-26T20:03:55","slug":"physical-chemical-property-predictors-as-command-line-tools","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2016\/09\/physical-chemical-property-predictors-as-command-line-tools\/","title":{"rendered":"Physical-chemical property predictors as command line tools"},"content":{"rendered":"<p>The <a href=\"https:\/\/www.chemaxon.com\/products\/instant-jchem-suite\/instant-jchem\/\">Instant JChem Suite<\/a>, from ChemAxon, is a fantastic set of software designed for Chemists. It allows easy and simple database management to store both chemical and non-chemical data. It also contains a plethora of physical-chemical prediction and visualisation tools that can be utilised by chemists and computational based scientists alike.<\/p>\n<p>I personally believe that the hidden gem within the suite is the availability of these predictive tools in the command line, found within the <a href=\"https:\/\/www.chemaxon.com\/marvin-archive\/5_2_0\/marvin\/help\/applications\/calc.html\">ChemAxon Calculator (cxcalc)<\/a>. In addition, calculator plug ins have also been developed by external developers. This allows you to incorporate the powerful predictive tools of ChemAxon into your larger workflows, with a little scripting.<\/p>\n<p>For example, it can be used to predict the dominant protonation state of a ligand before use in MD or docking studies, with the <code>majormicrospecies<\/code> tool. You can input and output all major file types including SDF, PDB and MOL2 using commands such as:<\/p>\n<p><code>cxcalc [Input_File].sdf -o [Output_File].sdf majormicrospecies -H [pH] -f [Output_File_Type]:H<\/code><\/p>\n<p>You can easily find the <a href=\"https:\/\/www.chemaxon.com\/marvin-archive\/5_2_0\/marvin\/help\/applications\/cxcalc-calculations.html\">calculator plugins available<\/a> and how to construct input commands using the <code>cxcalc \u2013h<\/code> command, or the available <a href=\"https:\/\/www.chemaxon.com\/marvin-archive\/5_2_0\/marvin\/help\/applications\/calc.html\">online information<\/a>. I would thoroughly recommend looking at the tools available and how you could incorporate them into your workflows.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>The Instant JChem Suite, from ChemAxon, is a fantastic set of software designed for Chemists. It allows easy and simple database management to store both chemical and non-chemical data. It also contains a plethora of physical-chemical prediction and visualisation tools that can be utilised by chemists and computational based scientists alike. I personally believe that [&hellip;]<\/p>\n","protected":false},"author":37,"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],"tags":[],"ppma_author":[525],"class_list":["post-3128","post","type-post","status-publish","format-standard","hentry","category-code"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"authors":[{"term_id":525,"user_id":37,"is_guest":0,"slug":"joe","display_name":"Joseph Bluck","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/83982ffcf500f0fe47fec340fcf3c1c396ae844739c03da6c069f0a4552641bd?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\/3128","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\/37"}],"replies":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/comments?post=3128"}],"version-history":[{"count":1,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/3128\/revisions"}],"predecessor-version":[{"id":3129,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/3128\/revisions\/3129"}],"wp:attachment":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media?parent=3128"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/categories?post=3128"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/tags?post=3128"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/ppma_author?post=3128"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}