Need to update README.md explaining webina.zip now in releases.
Need to add grant info, and to update citation.
add Grant number and citation to all web apps. Also licenses?
Good to mmention that all errors interpreted as file not found. For exampmle, when ligand was B (from commmand line):
Output will be ligand_final_out.pdbqt
WARNING: at low exhaustiveness, it may be impossible to utilize all CPUs
Reading input ...
Parse error on line 45 in file "ligand_final.pdbqt": ATOM syntax incorrect: "B" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.
But in browser:
No such file or directory.
Would be good to be able to catch errors better:
Uncaught 5347440 - Exception catching is disabled, this exception cannot be caught. Compile with -s DISABLE_EXCEPTION_CATCHING=0 or DISABLE_EXCEPTION_CATCHING=2 to catch.
this["$bvModal"]["msgBoxOk"]("To convert your file to PDBQT, Webina had to make the following modifications: "+overallMsg,{
...
...
@@ -138,6 +144,8 @@ let methodsFunctions = {
return;
}
// All attempts have failed...
this["$refs"]["convert-modal"].hide();
this["$bvModal"]["msgBoxOk"]("Could not convert your file. Are you sure it is a properly formatted "+this["currentExt"]+" file? If so, it may be too large to convert in the browser.",{
$jscomp.SymbolClass=function(a,c){this.$jscomp$symbol$id_=a;$jscomp.defineProperty(this,"description",{configurable:!0,writable:!0,value:c})};$jscomp.SymbolClass.prototype.toString=function(){returnthis.$jscomp$symbol$id_};$jscomp.Symbol=function(){functiona(b){if(thisinstanceofa)thrownewTypeError("Symbol is not a constructor");returnnew$jscomp.SymbolClass($jscomp.SYMBOL_PREFIX+(b||"")+"_"+c++,b)}varc=0;returna}();
g="\nWEBINA\n======\n\n";void0!==f?("/"!==f.slice(f.length-1)&&(f+="/"),this.WEBINA_BASE_URL=f,g+="User specified baseUrl: "+f+"\n"):g+="No baseUrl specified, so using ./\n\nUse Webina.start() to specify the baseUrl:\n function start(vinaParams, receptorPDBQTTxt, \n ligandPDBQTTxt, onDone, \n onError, baseUrl)\n";g+="\nExpecting files at the following locations:\n";for(varh=0;5>h;h++)g+=""+(void0===f?"./":f)+["Webina.min.min.js","vina.html.mem","vina.min.min.js",
"vina.worker.min.min.js","vina.wasm"][h]+"\n";g+="\n";void0!==f?console.log(g):console.warn(g);void0===e&&(e=function(){console.log("Webina encountered an error! Does your browser support WebAssembly?")});WEBINA_Module={preRun:[],postRun:[],stdOut:"",stdErr:"",print:function(){returnfunction(a){1<arguments.length&&(a=Array.prototype.slice.call(arguments).join(""));window.WEBINA_Module.stdOut+=a+"\n"}}(),printErr:function(a){1<arguments.length&&(a=Array.prototype.slice.call(arguments).join(""));window.WEBINA_Module.stdErr+=
a+"\n"},setStatus:function(a){""===a&&void0!==d&&(a=(newTextDecoder("utf-8")).decode(window.FS.readFile("ligand_out.pdbqt")),d(a,window.WEBINA_Module.stdOut,window.WEBINA_Module.stdErr))},onError:e,catchError:function(a){e(a)},receptorPDBQTTxt:c,ligandPDBQTTxt:b};void0!==a.receptor&&console.warn("Webina does not support Vina's --receptor parameter. Instead, pass the content of the receptor file as a string to the webina.start() function.");void0!==a.receptor&&console.warn("Webina does not support Vina's --ligand parameter. Instead, pass the content of the ligand file as a string to the webina.start() function.");
l.status){vara="Unable to access "+k+'. See JavaScript console for warnings. The "baseUrl" variable passed to Webina is likely incorrect.';WEBINA_Module.catchError({message:a});console.warn(a)}elsea=document.createElement("script"),a.src=m.WEBINA_BASE_URL+"vina.min.js",document.body.appendChild(a)};l.open("GET",k,!0);l.responseType="arraybuffer";l.send(null)},isDataURI:function(a){returnString.prototype.startsWith?a.startsWith(this.WEBINA_DATA_URI_PREFIX):0===a.indexOf(this.WEBINA_DATA_URI_PREFIX)},
$jscomp.defineProperty=$jscomp.ASSUME_ES5||"function"==typeofObject.defineProperties?Object.defineProperty:function(a,c,b){if(a==Array.prototype||a==Object.prototype)returna;a[c]=b.value;returna};$jscomp.getGlobal=function(a){a=["object"==typeofglobalThis&&globalThis,a,"object"==typeofwindow&&window,"object"==typeofself&&self,"object"==typeofglobal&&global];for(varc=0;c<a.length;++c){varb=a[c];if(b&&b.Math==Math)returnb}throwError("Cannot find global object");};$jscomp.global=$jscomp.getGlobal(this);
$jscomp.polyfill("Symbol",function(a){if(a)returna;varc=function(f,l){this.$jscomp$symbol$id_=f;$jscomp.defineProperty(this,"description",{configurable:!0,writable:!0,value:l})};c.prototype.toString=function(){returnthis.$jscomp$symbol$id_};varb="jscomp_symbol_"+(1E9*Math.random()>>>0)+"_",d=0,e=function(f){if(thisinstanceofe)thrownewTypeError("Symbol is not a constructor");returnnewc(b+(f||"")+"_"+d++,f)};returne},"es6","es3");
this,h="\nWEBINA\n======\n\n";void0!==f?("/"!==f.slice(f.length-1)&&(f+="/"),this.WEBINA_BASE_URL=f,h+="User specified baseUrl: "+f+"\n"):h+="No baseUrl specified, so using ./\n\nUse Webina.start() to specify the baseUrl:\n function start(vinaParams, receptorPDBQTTxt, \n ligandPDBQTTxt, onDone, \n onError, baseUrl)\n";h+="\nExpecting files at the following locations:\n";for(vark=0;5>k;k++)h+=""+(void0===f?"./":f)+["Webina.min.min.js","vina.html.mem","vina.min.min.js",
"vina.worker.min.min.js","vina.wasm"][k]+"\n";h+="\n";void0!==f?console.log(h):console.warn(h);void0===e&&(e=function(){console.log("Webina encountered an error! Does your browser support WebAssembly?")});WEBINA_Module={preRun:[],postRun:[],stdOut:"",stdErr:"",print:function(){returnfunction(g){1<arguments.length&&(g=Array.prototype.slice.call(arguments).join(""));window.WEBINA_Module.stdOut+=g+"\n"}}(),printErr:function(g){1<arguments.length&&(g=Array.prototype.slice.call(arguments).join(""));window.WEBINA_Module.stdErr+=
g+"\n"},setStatus:function(g){""===g&&void0!==d&&(g=(newTextDecoder("utf-8")).decode(window.FS.readFile("ligand_out.pdbqt")),d(g,window.WEBINA_Module.stdOut,window.WEBINA_Module.stdErr))},onError:e,catchError:function(g){e(g)},receptorPDBQTTxt:c,ligandPDBQTTxt:b};void0!==a.receptor&&console.warn("Webina does not support Vina's --receptor parameter. Instead, pass the content of the receptor file as a string to the webina.start() function.");void0!==a.receptor&&console.warn("Webina does not support Vina's --ligand parameter. Instead, pass the content of the ligand file as a string to the webina.start() function.");
n.status){varg="Unable to access "+m+'. See JavaScript console for warnings. The "baseUrl" variable passed to Webina is likely incorrect.';WEBINA_Module.catchError({message:g});console.warn(g)}elseg=document.createElement("script"),g.src=l.WEBINA_BASE_URL+"vina.min.js",document.body.appendChild(g)};n.open("GET",m,!0);n.responseType="arraybuffer";n.send(null)},isDataURI:function(a){returnString.prototype.startsWith?a.startsWith(this.WEBINA_DATA_URI_PREFIX):0===a.indexOf(this.WEBINA_DATA_URI_PREFIX)},
intArrayFromBase64:function(a){if("boolean"==typeofthis.WEBINA_ENVIRONMENT_IS_NODE&&this.WEBINA_ENVIRONMENT_IS_NODE){try{varc=Buffer.from(a,"base64")}catch(e){c=newBuffer(a,"base64")}returnnewUint8Array(c.buffer,c.byteOffset,c.byteLength)}try{varb=decodeBase64(a),d=newUint8Array(b.length);for(a=0;a<b.length;++a)d[a]=b.charCodeAt(a);returnd}catch(e){throwError("Converting base64 string to bytes failed.");}},tryParseAsDataURI:function(a){if(this.isDataURI(a))returnthis.intArrayFromBase64(a.slice(this.WEBINA_DATA_URI_PREFIX.length))},
intArrayFromString:function(a,c,b){b=0<b?b:this.WEBINA_lengthBytesUTF8(a)+1;b=Array(b);a=this.WEBINA_stringToUTF8Array(a,b,0,b.length);returnc&&(b.length=a),b},intArrayToString:function(a){for(varc=[],b=0;b<a.length;b++){vard=a[b];255<d&&(this.WEBINA_ASSERTIONS&&this.WEBINA_assert(!1,"Character code "+d+" ("+String.fromCharCode(d)+") at offset "+b+" not in 0x00-0xFF."),d&=255);c.push(String.fromCharCode(d))}returnc.join("")}}}();
