{"id":1160,"date":"2020-07-15T17:07:16","date_gmt":"2020-07-15T15:07:16","guid":{"rendered":"https:\/\/covid.si\/?page_id=1160"},"modified":"2020-07-18T15:35:44","modified_gmt":"2020-07-18T13:35:44","slug":"ligand-viewer","status":"publish","type":"page","link":"https:\/\/covid.si\/en\/ligand-viewer\/","title":{"rendered":"Ligand Viewer"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-page\" data-elementor-id=\"1160\" class=\"elementor elementor-1160\" data-elementor-post-type=\"page\">\n\t\t\t\t\t\t<section data-particle_enable=\"false\" data-particle-mobile-disabled=\"false\" class=\"elementor-section elementor-top-section elementor-element elementor-element-1eae013 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"1eae013\" data-element_type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-a125aea\" data-id=\"a125aea\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-9fa1b2d elementor-button-align-stretch elementor-widget elementor-widget-form\" data-id=\"9fa1b2d\" data-element_type=\"widget\" data-settings=\"{&quot;step_next_label&quot;:&quot;Next&quot;,&quot;step_previous_label&quot;:&quot;Previous&quot;,&quot;button_width&quot;:&quot;100&quot;,&quot;step_type&quot;:&quot;number_text&quot;,&quot;step_icon_shape&quot;:&quot;circle&quot;}\" data-widget_type=\"form.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<form class=\"elementor-form\" method=\"post\" name=\"TargetSelector\">\n\t\t\t<input type=\"hidden\" name=\"post_id\" value=\"1160\"\/>\n\t\t\t<input type=\"hidden\" name=\"form_id\" value=\"9fa1b2d\"\/>\n\t\t\t<input type=\"hidden\" name=\"referer_title\" value=\"COVID.SI\" \/>\n\n\t\t\t\n\t\t\t<div class=\"elementor-form-fields-wrapper elementor-labels-above\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-field-type-select elementor-field-group elementor-column elementor-field-group-r elementor-col-100\">\n\t\t\t\t\t\t\t\t\t\t\t\t<label for=\"form-field-r\" class=\"elementor-field-label\">\n\t\t\t\t\t\t\t\tTarget\t\t\t\t\t\t\t<\/label>\n\t\t\t\t\t\t\t\t<div class=\"elementor-field elementor-select-wrapper remove-before \">\n\t\t\t<div class=\"select-caret-down-wrapper\">\n\t\t\t\t<i aria-hidden=\"true\" class=\"eicon-caret-down\"><\/i>\t\t\t<\/div>\n\t\t\t<select name=\"form_fields[r]\" id=\"form-field-r\" class=\"elementor-field-textual elementor-size-sm\">\n\t\t\t\t\t\t\t\t\t<option value=\"\"><\/option>\n\t\t\t\t\t\t\t<\/select>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t<div class=\"elementor-field-type-radio elementor-field-group elementor-column elementor-field-group-v1 elementor-col-100\">\n\t\t\t\t\t\t\t\t\t\t\t\t<label for=\"form-field-v1\" class=\"elementor-field-label\">\n\t\t\t\t\t\t\t\tDisplay options\t\t\t\t\t\t\t<\/label>\n\t\t\t\t\t\t<div class=\"elementor-field-subgroup  \"><span class=\"elementor-field-option\"><input type=\"radio\" value=\"0\" id=\"form-field-v1-0\" name=\"form_fields[v1]\"> <label for=\"form-field-v1-0\">Show only skeleton of the protein<\/label><\/span><span class=\"elementor-field-option\"><input type=\"radio\" value=\"1\" id=\"form-field-v1-1\" name=\"form_fields[v1]\"> <label for=\"form-field-v1-1\">Show sidechains of aminoacids<\/label><\/span><span class=\"elementor-field-option\"><input type=\"radio\" value=\"2\" id=\"form-field-v1-2\" name=\"form_fields[v1]\"> <label for=\"form-field-v1-2\">Show target with surface<\/label><\/span><\/div>\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t<div class=\"elementor-field-group elementor-column elementor-field-type-submit elementor-col-100 e-form__buttons\">\n\t\t\t\t\t<button type=\"submit\" class=\"elementor-button elementor-size-sm\" id=\"TargetConfirm\">\n\t\t\t\t\t\t<span >\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-align-icon-left elementor-button-icon\">\n\t\t\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"far fa-eye\"><\/i>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-button-text\">Show<\/span>\n\t\t\t\t\t\t\t\t\t\t\t\t\t<\/span>\n\t\t\t\t\t<\/button>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t<\/form>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section data-particle_enable=\"false\" data-particle-mobile-disabled=\"false\" class=\"elementor-section elementor-top-section elementor-element elementor-element-128c440 elementor-section-full_width elementor-section-height-default elementor-section-height-default\" data-id=\"128c440\" data-element_type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-da7065e\" data-id=\"da7065e\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-b9b94c6 elementor-widget elementor-widget-html\" data-id=\"b9b94c6\" data-element_type=\"widget\" data-widget_type=\"html.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<script src=\"\/res\/ngl.js\"><\/script>\r\n<script src = \"https:\/\/d3js.org\/d3.v4.min.js\"><\/script>\r\n<script>\r\nfunction getQueryVariable(variable)\r\n{\r\n       var query = window.location.search.substring(1);\r\n       var vars = query.split(\"&\");\r\n       for (var i=0;i<vars.length;i++) {\r\n               var pair = vars[i].split(\"=\");\r\n               if(pair[0] == variable){return pair[1];}\r\n       }\r\n       return(false);\r\n}\r\n<\/script>\r\nTarget: <span id=\"r\"><\/span> Ligand : <span id=\"ligid\"><\/span>\r\n<div id=\"viewport\" style=\"overflow: hidden;  width: 100%; height: 500px; left: 10px; border: 2px outset silver;\"><\/div>\r\n<div>Title: <span id=\"title_lig\"><\/span><br>\r\nTotal Score: <span id=\"total\"><\/span><br>\r\nInteraction Score : <span id=\"inter\"><\/span><\/div><br>\r\n<script>\r\nvar r = 2\r\nvar ligid = 0\r\nvar r  =  getQueryVariable(\"r\")\r\nvar v1  =  getQueryVariable(\"v1\")\r\n\r\ndocument.getElementById(\"r\").innerHTML = r\r\ndocument.getElementById(\"ligid\").innerHTML = 0\r\n  \r\nvar target = \"\/res\/r\/rec_\" + r  + \".mol2\"\r\nvar ligands = \"\/res\/l\/l_\" + r  + \".sdf\"\r\nvar scorefile = \"\/res\/c\/l_\" + r + \".csv\"\r\n\r\n\/\/ Create NGL Stage object\r\nvar stage = new NGL.Stage(\"viewport\");\r\nstage.setParameters({ backgroundColor: \"black\" })\r\n\r\nfunction addElement (el) {\r\n  Object.assign(el.style, {\r\n    position: 'absolute',\r\n    zIndex: 50\r\n  })\r\n  stage.viewer.container.appendChild(el)\r\n}\r\n\r\nfunction createElement (name, properties, style) {\r\n  var el = document.createElement(name)\r\n  Object.assign(el, properties)\r\n  Object.assign(el.style, style)\r\n  return el\r\n}\r\n\r\n\r\nstage.loadFile(ligands).then(function (o) {\r\n  o.setSelection('\/' + ligid)\r\n  \/\/o.addRepresentation('hyperball')\r\n  o.addRepresentation(\"surface\", {sele: \"ligand\", color: \"tomato\", surfaceType: \"av\", opacity: 0.7, side: \"front\"})\r\n  document.getElementById(\"ligid\").innerHTML = ligid\r\n  d3.csv(scorefile,function (data) {\r\n        document.getElementById(\"title_lig\").innerHTML = data[ligid]._TITLE1\r\n        document.getElementById(\"total\").innerHTML = data[ligid].TOTAL\r\n        document.getElementById(\"inter\").innerHTML = data[ligid].INTER\r\n  })\r\n  o.autoView()\r\n)\r\n\r\nstage.loadFile(target).then(function (o1) {\r\n  o1.addRepresentation('cartoon', {color: \"white\"})\r\nif (v1==1){\r\n  var sele = \"not _H\"\r\n  var sele2 = \"_C\" \r\n  o1.addRepresentation( \"line\",{sele: sele})\r\n  o1.addRepresentation( \"line\",{sele: sele2, color: \"white\"})\r\n  }\r\nif (v1==2){\r\n  var sele = \"not _H\" \r\n  o1.addRepresentation( \"line\", {sele: sele})\r\n  o1.addRepresentation(\"surface\",{sele: \"polymer\",color: \"white\",surfaceType: \"av\", opacity: 0.9,side: \"front\" })\r\n  }   \r\no1.autoView()\r\n})\r\n\r\n<\/script>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t<div class=\"elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-cd06289\" data-id=\"cd06289\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-7e67442 elementor-widget elementor-widget-text-editor\" data-id=\"7e67442\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p>Welcome to Ligand Viewer.\u00a0<\/p><p>Here you can see how a ligand (red) is docked onto a target (gray). This is essentialy what our missions are all about &#8211; finding ligands that dock onto the target as best as they can.<\/p><p>Ligands that &#8220;fit in&#8221; are the best candidates for further processing and potential laboratory and clinical trials.<\/p><p>When you want to see how another ligand is docked, move the slider above the viewer box.<\/p><p>Commands:<br \/>&#8211; mouse left button hold + mouse move = rotate target<br \/>&#8211; mouse middle button scroll = zoom in\/out of target<br \/>&#8211; mouse right button hold + mouse move = pan target<br \/><br \/>&#8211; &#8220;R&#8221; key = reset view (whole target image displayed)<br \/>&#8211; &#8220;I&#8221; key = slowly rotate target on\/off<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>Target: Ligand : Title: Total Score: Interaction Score : Welcome to Ligand Viewer.\u00a0 Here you can see how a ligand [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-templates\/template_fullwidth.php","meta":{"footnotes":""},"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v22.5 - 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