Update to version 1.0.2.

durrantlab · Apr 22, 2020 · f0ecb33 · f0ecb33
1 parent dfe0591
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,19 @@
 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
 -----
 

diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# Webina 1.0.1 #
+# Webina 1.0.2 #
 
 ## Introduction ##
 

diff --git a/dist/app.3c93c288707c624dc76d.js → dist/app.9f3da2d658e5da75f658.js b/dist/app.3c93c288707c624dc76d.js → dist/app.9f3da2d658e5da75f658.js
diff --git a/dist/index.html b/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>
diff --git a/dist/runtime.3c93c288707c624dc76d.js → dist/runtime.9f3da2d658e5da75f658.js b/dist/runtime.3c93c288707c624dc76d.js → dist/runtime.9f3da2d658e5da75f658.js
diff --git a/dist/styles.3c93c288707c624dc76d.css → dist/styles.9f3da2d658e5da75f658.css b/dist/styles.3c93c288707c624dc76d.css → dist/styles.9f3da2d658e5da75f658.css
diff --git a/dist/styles.3c93c288707c624dc76d.js → dist/styles.9f3da2d658e5da75f658.js b/dist/styles.3c93c288707c624dc76d.js → dist/styles.9f3da2d658e5da75f658.js
diff --git a/dist/styles.css.3c93c288707c624dc76d.js → dist/styles.css.9f3da2d658e5da75f658.js b/dist/styles.css.3c93c288707c624dc76d.js → dist/styles.css.9f3da2d658e5da75f658.js
diff --git a/dist/vendors.3c93c288707c624dc76d.css → dist/vendors.9f3da2d658e5da75f658.css b/dist/vendors.3c93c288707c624dc76d.css → dist/vendors.9f3da2d658e5da75f658.css
diff --git a/dist/vendors.3c93c288707c624dc76d.js → dist/vendors.9f3da2d658e5da75f658.js b/dist/vendors.3c93c288707c624dc76d.js → dist/vendors.9f3da2d658e5da75f658.js
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
     "name": "webina",
-    "version": "1.0.1",
+    "version": "1.0.2",
     "description": "",
     "private": true,
     "scripts": {

diff --git a/src/UI/Modal/ConvertFileModal.ts b/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

diff --git a/src/Version.ts b/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";
diff --git a/docs/assets/css/main.css → technical_docs/assets/css/main.css b/docs/assets/css/main.css → technical_docs/assets/css/main.css
diff --git a/docs/assets/images/icons.png → technical_docs/assets/images/icons.png b/docs/assets/images/icons.png → technical_docs/assets/images/icons.png
diff --git a/docs/assets/images/icons@2x.png → technical_docs/assets/images/icons@2x.png b/docs/assets/images/icons@2x.png → technical_docs/assets/images/icons@2x.png
diff --git a/docs/assets/images/widgets.png → technical_docs/assets/images/widgets.png b/docs/assets/images/widgets.png → technical_docs/assets/images/widgets.png
diff --git a/docs/assets/images/widgets@2x.png → technical_docs/assets/images/widgets@2x.png b/docs/assets/images/widgets@2x.png → technical_docs/assets/images/widgets@2x.png
diff --git a/docs/assets/js/main.js → technical_docs/assets/js/main.js b/docs/assets/js/main.js → technical_docs/assets/js/main.js
diff --git a/docs/assets/js/search.json → technical_docs/assets/js/search.json b/docs/assets/js/search.json → technical_docs/assets/js/search.json
diff --git a/docs/globals.html → technical_docs/globals.html b/docs/globals.html → technical_docs/globals.html
diff --git a/docs/index.html → technical_docs/index.html b/docs/index.html → technical_docs/index.html
@@ -64,8 +64,8 @@ <h1>webina</h1>
 	<div class="row">
 		<div class="col-8 col-content">
 			<div class="tsd-panel tsd-typography">
-				<a href="#webina-101" id="webina-101" style="color: inherit; text-decoration: none;">
-					<h1>Webina 1.0.1</h1>
+				<a href="#webina-102" id="webina-102" style="color: inherit; text-decoration: none;">
+					<h1>Webina 1.0.2</h1>
 				</a>
 				<a href="#introduction" id="introduction" style="color: inherit; text-decoration: none;">
 					<h2>Introduction</h2>

diff --git a/...rfaces/_vue_store_.ifileconvertmodal.html → ...rfaces/_vue_store_.ifileconvertmodal.html b/...rfaces/_vue_store_.ifileconvertmodal.html → ...rfaces/_vue_store_.ifileconvertmodal.html
diff --git a/...terfaces/_vue_store_.iinputfilenames.html → ...terfaces/_vue_store_.iinputfilenames.html b/...terfaces/_vue_store_.iinputfilenames.html → ...terfaces/_vue_store_.iinputfilenames.html
diff --git a/docs/interfaces/_vue_store_.imodal.html → ...l_docs/interfaces/_vue_store_.imodal.html b/docs/interfaces/_vue_store_.imodal.html → ...l_docs/interfaces/_vue_store_.imodal.html
diff --git a/.../interfaces/_vue_store_.iparamaccess.html → .../interfaces/_vue_store_.iparamaccess.html b/.../interfaces/_vue_store_.iparamaccess.html → .../interfaces/_vue_store_.iparamaccess.html
diff --git a/docs/interfaces/_vue_store_.ivuexparam.html → ...cs/interfaces/_vue_store_.ivuexparam.html b/docs/interfaces/_vue_store_.ivuexparam.html → ...cs/interfaces/_vue_store_.ivuexparam.html
diff --git a/...erfaces/_vue_store_.ivuexstoresetvar.html → ...erfaces/_vue_store_.ivuexstoresetvar.html b/...erfaces/_vue_store_.ivuexstoresetvar.html → ...erfaces/_vue_store_.ivuexstoresetvar.html
diff --git a/...aces/_webina_src_webina_.ivinaparams.html → ...aces/_webina_src_webina_.ivinaparams.html b/...aces/_webina_src_webina_.ivinaparams.html → ...aces/_webina_src_webina_.ivinaparams.html
diff --git a/docs/modules/_index_.html → technical_docs/modules/_index_.html b/docs/modules/_index_.html → technical_docs/modules/_index_.html
diff --git a/docs/modules/_ui_forms_checkbox_.html → ...cal_docs/modules/_ui_forms_checkbox_.html b/docs/modules/_ui_forms_checkbox_.html → ...cal_docs/modules/_ui_forms_checkbox_.html
diff --git a/docs/modules/_ui_forms_fileinput_.html → ...al_docs/modules/_ui_forms_fileinput_.html b/docs/modules/_ui_forms_fileinput_.html → ...al_docs/modules/_ui_forms_fileinput_.html
diff --git a/docs/modules/_ui_forms_formbutton_.html → ...l_docs/modules/_ui_forms_formbutton_.html b/docs/modules/_ui_forms_formbutton_.html → ...l_docs/modules/_ui_forms_formbutton_.html
diff --git a/docs/modules/_ui_forms_formgroup_.html → ...al_docs/modules/_ui_forms_formgroup_.html b/docs/modules/_ui_forms_formgroup_.html → ...al_docs/modules/_ui_forms_formgroup_.html
diff --git a/docs/modules/_ui_forms_numericinput_.html → ...docs/modules/_ui_forms_numericinput_.html b/docs/modules/_ui_forms_numericinput_.html → ...docs/modules/_ui_forms_numericinput_.html
diff --git a/docs/modules/_ui_forms_triplenumeric_.html → ...ocs/modules/_ui_forms_triplenumeric_.html b/docs/modules/_ui_forms_triplenumeric_.html → ...ocs/modules/_ui_forms_triplenumeric_.html
diff --git a/.../modules/_ui_modal_convertfilemodal_.html → .../modules/_ui_modal_convertfilemodal_.html b/.../modules/_ui_modal_convertfilemodal_.html → .../modules/_ui_modal_convertfilemodal_.html
@@ -117,7 +117,7 @@ <h3>setup</h3>
 						<li class="tsd-description">
 							<aside class="tsd-sources">
 								<ul>
-									<li>Defined in UI/Modal/ConvertFileModal.ts:226</li>
+									<li>Defined in UI/Modal/ConvertFileModal.ts:250</li>
 								</ul>
 							</aside>
 							<div class="tsd-comment tsd-typography">
@@ -294,7 +294,7 @@ <h3><span class="tsd-flag ts-flagLet">Let</span> methods<wbr>Functions</h3>
 						<a name="methodsfunctions.beginconvert" class="tsd-anchor"></a>
 						<h3>begin<wbr>Convert</h3>
 						<ul class="tsd-signatures tsd-kind-function tsd-parent-kind-object-literal tsd-is-not-exported">
-							<li class="tsd-signature tsd-kind-icon">begin<wbr>Convert<span class="tsd-signature-symbol">(</span>e<span class="tsd-signature-symbol">: </span><span class="tsd-signature-type">any</span>, currentPDBOptimizationLevel<span class="tsd-signature-symbol">?: </span><span class="tsd-signature-type">number</span>, successMsg<span class="tsd-signature-symbol">?: </span><span class="tsd-signature-type">string</span><span class="tsd-signature-symbol">)</span><span class="tsd-signature-symbol">: </span><span class="tsd-signature-type">void</span></li>
+							<li class="tsd-signature tsd-kind-icon">begin<wbr>Convert<span class="tsd-signature-symbol">(</span>e<span class="tsd-signature-symbol">: </span><span class="tsd-signature-type">any</span>, currentPDBOptimizationLevel<span class="tsd-signature-symbol">?: </span><span class="tsd-signature-type">number</span>, successMsgs<span class="tsd-signature-symbol">?: </span><span class="tsd-signature-type">any</span><span class="tsd-signature-symbol">[]</span><span class="tsd-signature-symbol">)</span><span class="tsd-signature-symbol">: </span><span class="tsd-signature-type">void</span></li>
 						</ul>
 						<ul class="tsd-descriptions">
 							<li class="tsd-description">
@@ -326,9 +326,9 @@ <h5><span class="tsd-flag ts-flagDefault value">Default value</span> currentPDBO
 										</div>
 									</li>
 									<li>
-										<h5><span class="tsd-flag ts-flagDefault value">Default value</span> successMsg: <span class="tsd-signature-type">string</span><span class="tsd-signature-symbol"> = &quot;&quot;</span></h5>
+										<h5><span class="tsd-flag ts-flagDefault value">Default value</span> successMsgs: <span class="tsd-signature-type">any</span><span class="tsd-signature-symbol">[]</span><span class="tsd-signature-symbol"> = []</span></h5>
 										<div class="tsd-comment tsd-typography">
-											<p>The message to display
+											<p>The messages to display
 												to the user on success
 											(if any).</p>
 										</div>
@@ -349,7 +349,7 @@ <h3>cancel<wbr>Pressed</h3>
 							<li class="tsd-description">
 								<aside class="tsd-sources">
 									<ul>
-										<li>Defined in UI/Modal/ConvertFileModal.ts:197</li>
+										<li>Defined in UI/Modal/ConvertFileModal.ts:221</li>
 									</ul>
 								</aside>
 								<div class="tsd-comment tsd-typography">
@@ -372,7 +372,7 @@ <h3>pdb<wbr>Optimization</h3>
 							<li class="tsd-description">
 								<aside class="tsd-sources">
 									<ul>
-										<li>Defined in UI/Modal/ConvertFileModal.ts:161</li>
+										<li>Defined in UI/Modal/ConvertFileModal.ts:165</li>
 									</ul>
 								</aside>
 								<div class="tsd-comment tsd-typography">
@@ -407,7 +407,7 @@ <h3>reloadIFrame</h3>
 							<li class="tsd-description">
 								<aside class="tsd-sources">
 									<ul>
-										<li>Defined in UI/Modal/ConvertFileModal.ts:217</li>
+										<li>Defined in UI/Modal/ConvertFileModal.ts:241</li>
 									</ul>
 								</aside>
 								<div class="tsd-comment tsd-typography">

diff --git a/docs/modules/_ui_modal_drawsmilesmodal_.html → ...s/modules/_ui_modal_drawsmilesmodal_.html b/docs/modules/_ui_modal_drawsmilesmodal_.html → ...s/modules/_ui_modal_drawsmilesmodal_.html
diff --git a/docs/modules/_ui_modal_openmodal_.html → ...al_docs/modules/_ui_modal_openmodal_.html b/docs/modules/_ui_modal_openmodal_.html → ...al_docs/modules/_ui_modal_openmodal_.html
diff --git a/docs/modules/_ui_resultstable_.html → ...nical_docs/modules/_ui_resultstable_.html b/docs/modules/_ui_resultstable_.html → ...nical_docs/modules/_ui_resultstable_.html
diff --git a/docs/modules/_ui_subsection_.html → technical_docs/modules/_ui_subsection_.html b/docs/modules/_ui_subsection_.html → technical_docs/modules/_ui_subsection_.html
diff --git a/docs/modules/_ui_tabs_startover_.html → ...cal_docs/modules/_ui_tabs_startover_.html b/docs/modules/_ui_tabs_startover_.html → ...cal_docs/modules/_ui_tabs_startover_.html
diff --git a/...modules/_ui_tabs_vinaexistingoutput_.html → ...modules/_ui_tabs_vinaexistingoutput_.html b/...modules/_ui_tabs_vinaexistingoutput_.html → ...modules/_ui_tabs_vinaexistingoutput_.html
diff --git a/docs/modules/_ui_tabs_vinaoutput_.html → ...al_docs/modules/_ui_tabs_vinaoutput_.html b/docs/modules/_ui_tabs_vinaoutput_.html → ...al_docs/modules/_ui_tabs_vinaoutput_.html
diff --git a/docs/modules/_ui_tabs_vinaparams_.html → ...al_docs/modules/_ui_tabs_vinaparams_.html b/docs/modules/_ui_tabs_vinaparams_.html → ...al_docs/modules/_ui_tabs_vinaparams_.html
diff --git a/docs/modules/_ui_tabs_vinarunning_.html → ...l_docs/modules/_ui_tabs_vinarunning_.html b/docs/modules/_ui_tabs_vinarunning_.html → ...l_docs/modules/_ui_tabs_vinarunning_.html
diff --git a/docs/modules/_ui_threedmol_.html → technical_docs/modules/_ui_threedmol_.html b/docs/modules/_ui_threedmol_.html → technical_docs/modules/_ui_threedmol_.html
diff --git a/docs/modules/_ui_ui_.html → technical_docs/modules/_ui_ui_.html b/docs/modules/_ui_ui_.html → technical_docs/modules/_ui_ui_.html
diff --git a/docs/modules/_ui_vinacommandline_.html → ...al_docs/modules/_ui_vinacommandline_.html b/docs/modules/_ui_vinacommandline_.html → ...al_docs/modules/_ui_vinacommandline_.html
diff --git a/docs/modules/_utils_.html → technical_docs/modules/_utils_.html b/docs/modules/_utils_.html → technical_docs/modules/_utils_.html
diff --git a/docs/modules/_version_.html → technical_docs/modules/_version_.html b/docs/modules/_version_.html → technical_docs/modules/_version_.html
@@ -84,7 +84,7 @@ <h2>Variables</h2>
 				<section class="tsd-panel tsd-member tsd-kind-variable tsd-parent-kind-module">
 					<a name="version" class="tsd-anchor"></a>
 					<h3><span class="tsd-flag ts-flagLet">Let</span> VERSION</h3>
-					<div class="tsd-signature tsd-kind-icon">VERSION<span class="tsd-signature-symbol">:</span> <span class="tsd-signature-type">string</span><span class="tsd-signature-symbol"> = &quot;1.0.1&quot;</span></div>
+					<div class="tsd-signature tsd-kind-icon">VERSION<span class="tsd-signature-symbol">:</span> <span class="tsd-signature-type">string</span><span class="tsd-signature-symbol"> = &quot;1.0.2&quot;</span></div>
 					<aside class="tsd-sources">
 						<ul>
 							<li>Defined in Version.ts:5</li>

diff --git a/docs/modules/_vue_setup_.html → technical_docs/modules/_vue_setup_.html b/docs/modules/_vue_setup_.html → technical_docs/modules/_vue_setup_.html
diff --git a/docs/modules/_vue_store_.html → technical_docs/modules/_vue_store_.html b/docs/modules/_vue_store_.html → technical_docs/modules/_vue_store_.html
diff --git a/docs/modules/_webina_src_webina_.html → ...cal_docs/modules/_webina_src_webina_.html b/docs/modules/_webina_src_webina_.html → ...cal_docs/modules/_webina_src_webina_.html
diff --git a/utils/build/make_docs.sh b/utils/build/make_docs.sh
@@ -1,2 +1,2 @@
-rm -rf docs
-typedoc --out docs --exclude "**/*.js" --ignoreCompilerErrors --mode modules --hideGenerator src
+rm -rf technical_docs
+typedoc --out technical_docs --exclude "**/*.js" --ignoreCompilerErrors --mode modules --hideGenerator src
diff --git a/webina.zip b/webina.zip