Update to version 1.0.2.

CHANGELOG.md

 Changes
 =======
 
+1.0.2
+-----
+
+* Renamed the `docs/` directory to `technical_docs/` so end users won't
+  confuse it with the user manual found in the `README.md` file.
+* Improved Webina's ability to convert large PDB files to PDBQT. PDBQTConvert
+  cannot convert large PDB files, so Webina reduces the input file size if it
+  encounters an error. In addition to the previous steps, it now does the
+  following:
+  * keeps only the first frame of multi-frame PDB files
+  * removes existing hydrogen atoms
+  * removes beta/occupancy/element columns
+
 1.0.1
 -----
 

README.md

-# Webina 1.0.1 #
+# Webina 1.0.2 #
 
 ## Introduction ##
 

dist/app.3c93c288707c624dc76d.js → dist/app.9f3da2d658e5da75f658.js

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  */
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 props:{}})})();(function(){Vue.component("draw-smiles-modal",{computed:B,methods:F,data:function(){return{}},template:'\n            <b-modal\n              size="xl" ok-title="Convert to PDBQT" v-model="drawSmilesModalShow"\n              id="draw-structure-modal" title="Draw Ligand Structure"\n              @ok="startConversion">\n                <p class="my-4">\n                    <iframe id="draw-widget" style="border:0; width:100%; height:350px; margin-left:auto; margin-right:auto; display:block;" src="mol_editor/index.html"></iframe>\n                </p>\n            </b-modal>',
@@ -45,8 +46,8 @@ props:{label:String,id:String,description:String,placeholder:String,required:Boo
 props:{hide:Boolean,label:String,id1:String,id2:String,id3:String,styl:String,description:String,min:{type:Number,"default":void 0}},methods:{}})})();(function(){Vue.component("check-box",{data:function(){return{}},computed:k,template:'\n            <b-form-checkbox\n                :id="id"\n                v-model="val"\n                :name="id"\n                :value="true"\n                :unchecked-value="false"\n            >\n                {{label}}\n            </b-form-checkbox>\n        ',
 props:{label:String,id:String}})})();r.a();(function(){Vue.component("results-table",{data:function(){return{}},computed:a,template:'\n            <b-table\n                striped hover small\n                :items="items"\n                :fields="fields"\n                @row-clicked="rowClicked">\n            </b-table>\n        ',props:{},methods:p})})();g.a();(function(){Vue.component("vina-running",{template:'\n            <div class="text-center">\n                <b-spinner style="width: 4rem; height: 4rem;" label="Working"></b-spinner>\n                <br /><br />\n                <p>Running Webina in your browser. Docking may take some minutes.</p>\n                <p>This page may become unresponsive while performing calculations.\n                   Need to stop Webina but can\'t close this tab? Use your browser or\n                   operating-system Task Manager.</p>\n            </div>\n        ',
 props:{},computed:{},data:function(){return{msg:"",aa:0}},methods:{}})})();c.a();e.a();(function(){Vue.component("vina-existing-output",{template:'\n            <b-form>\n                <b-card\n                    class="mb-2 text-center"\n                    style="margin-bottom:1.4rem !important;"\n                >\n                    <b-card-text>\n                        Use this tab if you\'ve already run Webina or Vina and\n                        have an existing docked-ligand PDBQT output file.\n                    </b-card-text>\n                </b-card>\n\n                <sub-section title="Existing Output Files">\n                    <file-input\n                        label="Receptor"\n                        id="receptor"\n                        description="The rigid part of the receptor (PDBQT or PDB)."\n                        accept=".pdbqt, .pdb"\n                    ></file-input>\n\n                    <file-input\n                        label="Docked Output"\n                        id="output"\n                        description="The Webina/Vina output file (PDBQT, OUT, VINA, or TXT) containing docked ligand poses."\n                        accept=".pdbqt, .out, .vina, .txt"\n                    ></file-input>\n\n                    <file-input\n                        label="Correct Pose"\n                        id="crystal"\n                        :required="false"\n                        description="The correct ligand pose, if known from experiment. This PDBQT or PDB file is optional."\n                        accept=".pdbqt, .pdb"\n                    ></file-input>\n                </sub-section>\n\n                <form-button cls="float-right mb-4" @click.native="onSubmitClick" variant="primary">Load Files</form-button>\n                <form-button @click.native="useExampleOutputFiles" cls="float-right mr-2">Use Example Files</form-button>\n            </b-form>\n        ',
-props:{},computed:{},data:function(){return{}},methods:d})})();(function(){new Vue({el:"#app",store:z.a,template:'\n            <div class="container-fluid">\n                <open-modal></open-modal>\n                <convert-file-modal></convert-file-modal>\n                <draw-smiles-modal></draw-smiles-modal>\n                <div id="no-mobile">\n                    <b-jumbotron class="jumbo" header="Webina 1.0.1" lead="AutoDock Vina Ported to WebAssembly">\n                        <p>Webina 1.0.1 is not designed to work on mobile phones. Please use a device with a larger screen.</p>\n                    </b-jumbotron>\n                </div>\n\n                <b-jumbotron class="jumbo" style="background-image:url('+
-A.a()+'webina_logo.jpg);" header="Webina 1.0.1" lead="AutoDock Vina Ported to WebAssembly">\n                    <p>Brought to you by the <a target="_blank" href="http://durrantlab.com">Durrant Lab</a>.</p>\n                    <b-button variant="primary" target="_blank" href="http://durrantlab.com">More Info</b-button>\n                </b-jumbotron>\n\n                <b-card no-body class="mb-3">\n                    <b-tabs v-model="tabIdx" card fill pills vertical content-class="mt-3"> \x3c!-- vertical --\x3e\n                        <b-tab title="Input Parameters" active :disabled="parametersTabDisabled">\n                            <b-card-text>\n                                <vina-params></vina-params>\n                            </b-card-text>\n                        </b-tab>\n                        <b-tab title="Existing Vina Output" :disabled="existingVinaOutputTabDisabled">\n                            <b-card-text>\n                                <vina-existing-output></vina-existing-output>\n                            </b-card-text>\n                        </b-tab>\n                        <b-tab title="Running Webina" :disabled="runningTabDisabled">\n                            <b-card-text>\n                                <vina-running></vina-running>\n                            </b-card-text>\n                        </b-tab>\n                        <b-tab title="Output" :disabled="outputTabDisabled">\n                            <b-card-text>\n                                <vina-output></vina-output>\n                            </b-card-text>\n                        </b-tab>\n                        <b-tab title="Start Over" :disabled="startOverTabDisabled">\n                            <b-card-text>\n                                <start-over></start-over>\n                            </b-card-text>\n                        </b-tab>\n                    </b-tabs>\n                </b-card>\n            </div>\n        ',
+props:{},computed:{},data:function(){return{}},methods:d})})();(function(){new Vue({el:"#app",store:z.a,template:'\n            <div class="container-fluid">\n                <open-modal></open-modal>\n                <convert-file-modal></convert-file-modal>\n                <draw-smiles-modal></draw-smiles-modal>\n                <div id="no-mobile">\n                    <b-jumbotron class="jumbo" header="Webina 1.0.2" lead="AutoDock Vina Ported to WebAssembly">\n                        <p>Webina 1.0.2 is not designed to work on mobile phones. Please use a device with a larger screen.</p>\n                    </b-jumbotron>\n                </div>\n\n                <b-jumbotron class="jumbo" style="background-image:url('+
+A.a()+'webina_logo.jpg);" header="Webina 1.0.2" lead="AutoDock Vina Ported to WebAssembly">\n                    <p>Brought to you by the <a target="_blank" href="http://durrantlab.com">Durrant Lab</a>.</p>\n                    <b-button variant="primary" target="_blank" href="http://durrantlab.com">More Info</b-button>\n                </b-jumbotron>\n\n                <b-card no-body class="mb-3">\n                    <b-tabs v-model="tabIdx" card fill pills vertical content-class="mt-3"> \x3c!-- vertical --\x3e\n                        <b-tab title="Input Parameters" active :disabled="parametersTabDisabled">\n                            <b-card-text>\n                                <vina-params></vina-params>\n                            </b-card-text>\n                        </b-tab>\n                        <b-tab title="Existing Vina Output" :disabled="existingVinaOutputTabDisabled">\n                            <b-card-text>\n                                <vina-existing-output></vina-existing-output>\n                            </b-card-text>\n                        </b-tab>\n                        <b-tab title="Running Webina" :disabled="runningTabDisabled">\n                            <b-card-text>\n                                <vina-running></vina-running>\n                            </b-card-text>\n                        </b-tab>\n                        <b-tab title="Output" :disabled="outputTabDisabled">\n                            <b-card-text>\n                                <vina-output></vina-output>\n                            </b-card-text>\n                        </b-tab>\n                        <b-tab title="Start Over" :disabled="startOverTabDisabled">\n                            <b-card-text>\n                                <start-over></start-over>\n                            </b-card-text>\n                        </b-tab>\n                    </b-tabs>\n                </b-card>\n            </div>\n        ',
 data:function(){return{receptorFile:!1,ligandFile:!1}},computed:{tabIdx:{get:function(){return this.$store.state.tabIdx},set:function(l){this.$store.commit("setVar",{name:"tabIdx",f:l})}},parametersTabDisabled:function(){return this.$store.state.parametersTabDisabled},runningTabDisabled:function(){return this.$store.state.runningTabDisabled},outputTabDisabled:function(){return this.$store.state.outputTabDisabled},existingVinaOutputTabDisabled:function(){return this.$store.state.existingVinaOutputTabDisabled},
 startOverTabDisabled:function(){return this.$store.state.startOverTabDisabled}},methods:{},mounted:function(){}})})();-1!==window.location.href.indexOf("durrantlab")&&setTimeout(function(){(function(l,n,y,w,x,C,D){l.GoogleAnalyticsObject=x;l[x]=l[x]||function(){(l[x].q=l[x].q||[]).push(arguments)};l[x].$=(new Date).getTime();C=n.createElement(y);D=n.getElementsByTagName(y)[0];C.async=1;C.src=w;D.parentNode.insertBefore(C,D)})(window,document,"script","https://www.google-analytics.com/analytics.js",
 "ga");ga("create","UA-144382730-1",{name:"webina"});ga("webina.send",{hitType:"event",eventCategory:"webina",eventAction:"pageview",eventLabel:window.location.href})},0)},"/dHQ":function(r,g,m){(function(t){function z(){void 0===this.$store.state.validation[this.id]&&this.$store.commit("setValidationParam",{name:this.id,f:!1});!1===this.required&&(this.$store.commit("setValidationParam",{name:this.id,f:!0}),t("."+this.id).find("input").removeClass("is-invalid"))}function A(){Vue.component("file-input",

dist/index.html

@@ -10,7 +10,7 @@
         <meta charset="utf-8">
         <meta content="text/html; charset=utf-8" http-equiv="Content-Type">
         <title>Webina</title>
-    <link rel="shortcut icon" href="favicon.ico"><link href="vendors.3c93c288707c624dc76d.css" rel="stylesheet"><link href="styles.3c93c288707c624dc76d.css" rel="stylesheet"></head>
+    <link rel="shortcut icon" href="favicon.ico"><link href="vendors.9f3da2d658e5da75f658.css" rel="stylesheet"><link href="styles.9f3da2d658e5da75f658.css" rel="stylesheet"></head>
 
     <body>
         <div id="app"></div>
@@ -24,6 +24,6 @@
         <script src="vue.min.js"></script>
         <script src="vuex.min.js"></script>
         <script src="bootstrap-vue.min.js"></script>
-    <script type="text/javascript" src="runtime.3c93c288707c624dc76d.js"></script><script type="text/javascript" src="vendors.3c93c288707c624dc76d.js"></script><script type="text/javascript" src="app.3c93c288707c624dc76d.js"></script><script type="text/javascript" src="styles.3c93c288707c624dc76d.js"></script><script type="text/javascript" src="styles.css.3c93c288707c624dc76d.js"></script></body>
+    <script type="text/javascript" src="runtime.9f3da2d658e5da75f658.js"></script><script type="text/javascript" src="vendors.9f3da2d658e5da75f658.js"></script><script type="text/javascript" src="app.9f3da2d658e5da75f658.js"></script><script type="text/javascript" src="styles.9f3da2d658e5da75f658.js"></script><script type="text/javascript" src="styles.css.9f3da2d658e5da75f658.js"></script></body>
 
     </html>

package-lock.json

 {
   "name": "webina",
-  "version": "1.0.1",
+  "version": "1.0.2",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {

package.json

 {
     "name": "webina",
-    "version": "1.0.1",
+    "version": "1.0.2",
     "description": "",
     "private": true,
     "scripts": {

src/UI/Modal/ConvertFileModal.ts

@@ -66,12 +66,12 @@ let methodsFunctions = {
      *                                                 file should be
      *                                                 optimized (to keep size
      *                                                 low for converting).
-     * @param  {string=""} successMsg                  The message to display
+     * @param  {string[]} successMsgs                  The messages to display
      *                                                 to the user on success
      *                                                 (if any).
      * @returns void
      */
-    "beginConvert"(e, currentPDBOptimizationLevel=1, successMsg=""): void {
+    "beginConvert"(e, currentPDBOptimizationLevel=1, successMsgs=[]): void {
         let frameWindow = document.getElementById("convert-frame")["contentWindow"];
         frameWindow["startSpinner"]();
         let content: string = this.$store.state["convertFile"];
@@ -80,7 +80,10 @@ let methodsFunctions = {
         }
 
         if (this["currentExt"].toUpperCase() === "PDB") {
-            successMsg += this.pdbOptimization(currentPDBOptimizationLevel);
+            let msg = this.pdbOptimization(currentPDBOptimizationLevel);
+            if (msg !== "") {
+                successMsgs.push(msg);
+            }
         }
 
         if (this["currentType"]!=="ligand") {
@@ -121,16 +124,17 @@ let methodsFunctions = {
             let newFilename = Utils.replaceExt(this.$store.state[this["currentType"] + "FileName"], "converted.pdbqt");
             this.$store.commit("updateFileName", { type: this["currentType"], filename: newFilename });
 
-            if (successMsg !== "") {
-                this["$bvModal"]["msgBoxOk"]("To convert your file to PDBQT, Webina had to make the following modifications: " + successMsg, {
+            if (successMsgs.length !== 0) {
+                let overallMsg = successMsgs.map((m, i) => { return "(" + (i + 1).toString() + ") " + m; }).join(" ");
+                this["$bvModal"]["msgBoxOk"]("To convert your file to PDBQT, Webina had to make the following modifications: " + overallMsg, {
                     "title": "Warning: File Too Big!",
                 });
             }
         }).catch((msg) => {
             // The conversion failed. But if it's a PDB file, it might be
             // worth trying to optimize it further.
-            if (currentPDBOptimizationLevel <= 3) {
-                this["beginConvert"](e, currentPDBOptimizationLevel + 1, successMsg);
+            if (currentPDBOptimizationLevel <= 4) {  // one less than max number in pdbOptimization.
+                this["beginConvert"](e, currentPDBOptimizationLevel + 1, successMsgs);
                 return;
             }
 
@@ -166,22 +170,42 @@ let methodsFunctions = {
         switch (level) {
             case 1:
                 // Always run this optimization. Just removes lines that don't
-                // start with ATOM and HETATM.
+                // start with ATOM and HETATM. Also keeps only the first frame
+                // if it's a multi-frame PDB.
+
+                if (pdbTxt.indexOf("\nEND") !== -1) {
+                    // Perhaps a multi-frame PDB.
+                    pdbTxt = pdbTxt.split("\nEND")[0];
+                    msg = "Keep only the first frame."
+                }
+
                 pdbTxt = pdbTxt.split("\n").filter(l => l.slice(0, 5) === "ATOM " || l.slice(0, 7) === "HETATM ").join("\n");
                 break;
             case 2:
                 // Try removing everything but protein atoms.
                 pdbTxt = Utils.keepOnlyProteinAtoms(pdbTxt);
-                msg += " (1) Discard non-protein atoms."
+                msg = "Discard non-protein atoms."
                 break;
             case 3:
                 // Keep only the first chain.
-                let chain = pdbTxt.slice(21,22);
+                let chain = pdbTxt.slice(21,22);  // first chain
                 pdbTxt = pdbTxt.split("\n").filter(l => l.slice(21,22) === chain).join("\n");
-                msg += " (2) Keep only the first chain (chain " + chain + ").";
+                msg = "Keep only the first chain (chain " + chain + ").";
+                break;
+            case 4:
+                // Remove existing hydrogen atoms.
+                pdbTxt = pdbTxt.split("\n").filter(l => l.substr(12,4).replace(/ /g, "").substr(0, 1) !== "H").join("\n");
+                msg = "Remove original hydrogen atoms.";
+                break;
+            case 5:
+                // Remove beta, occupancy, etc. columns.
+                pdbTxt = pdbTxt.split("\n").map(l => l.substr(0,54)).join("\n");
+                msg = "Remove original occupancy, beta, and element columns.";
                 break;
         }
 
+        // console.log("HHHHH>>> " + msg + " >>>> " + pdbTxt.length.toString());
+
         this.$store.commit("setVar", {
             name: "convertFile",
             val: pdbTxt

src/Version.ts

@@ -2,4 +2,4 @@
 // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
 // details. Copyright 2020 Jacob D. Durrant.
 
-export let VERSION = "1.0.1";
+export let VERSION = "1.0.2";