Commit 26e7d15c authored by Jacob Durrant's avatar Jacob Durrant

Minor bug fixes.

parent 2d23971f
......@@ -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.e79089af6fca69f502b9.css" rel="stylesheet"><link href="styles.css.e79089af6fca69f502b9.css" rel="stylesheet"></head>
<link rel="shortcut icon" href="favicon.ico"><link href="vendors.7fcd84ab12f5b0584040.css" rel="stylesheet"><link href="styles.css.7fcd84ab12f5b0584040.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.e79089af6fca69f502b9.js"></script><script type="text/javascript" src="vendors.e79089af6fca69f502b9.js"></script><script type="text/javascript" src="app.e79089af6fca69f502b9.js"></script><script type="text/javascript" src="styles.css.e79089af6fca69f502b9.js"></script></body>
<script type="text/javascript" src="runtime.7fcd84ab12f5b0584040.js"></script><script type="text/javascript" src="vendors.7fcd84ab12f5b0584040.js"></script><script type="text/javascript" src="app.7fcd84ab12f5b0584040.js"></script><script type="text/javascript" src="styles.css.7fcd84ab12f5b0584040.js"></script></body>
</html>
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......@@ -203,9 +203,8 @@ ligand.pdbqt</code></li>
Parameters&quot; tab. This tab includes several subsections that are useful for
setting up a Webina run.</p>
<p><strong>Input PDBQT Files.</strong> The &quot;Input (PDBQT) Files&quot; subsection allows the user to
select their receptor and ligand files. As is the case with command-line Vina,
these files must be in the PDBQT format. The user can also optionally specify
a known-pose PDB or PDBQT ligand file. This file includes the ligand in its
select their receptor and ligand files. The user can also optionally specify a
known-pose PDB or PDBQT ligand file. This file includes the ligand in its
experimentally determined, correct bound pose (e.g., per X-ray crystallography
or NMR). The known-pose file plays no role in the docking calculation; rather,
it serves as a positive-control reference for evaluating Webina-predicted
......@@ -256,9 +255,9 @@ ligand.pdbqt</code></li>
will wish to adjust these parameters to avoid impacting the performance of
other programs and browser tabs.</p>
<p><strong>Advanced Parameters.</strong> The &quot;Advanced Parameters&quot; subsection allows users to
specify any of the many additional parameters that are also available via
command-line Vina. In our experience, it is rarely necessary to adjust these
parameters, so they are hidden by default.</p>
specify many additional parameters that are also available via command-line
Vina. In our experience, it is rarely necessary to adjust these parameters, so
they are hidden by default.</p>
<p><strong>Run Vina from Command Line.</strong> The &quot;Run Vina from Command Line&quot; subsection
aims to help Vina users who wish to use the Webina web app to setup their
docking boxes and user parameters. A text field provides a mock example of how
......@@ -300,8 +299,8 @@ ligand.pdbqt</code></li>
Webina output files. An associated &quot;Download&quot; button allows users to easily
save those files.</p>
<p><strong>Run Vina from Command Line.</strong> Similar to the &quot;Input Parameters&quot; tab, the
&quot;Output&quot; Tab also includes a &quot;Run Vina from Command Line&quot; Subsection. This
section makes it easy for users to reproduce Webina&#39;s results using
&quot;Output&quot; tab also includes a &quot;Run Vina from Command Line&quot; subsection. This
subsection makes it easy for users to reproduce Webina&#39;s results using
stand-alone Vina. It also reminds users what parameters they selected to
generate the displayed Webina output.</p>
<a href="#start-over-tab" id="start-over-tab" style="color: inherit; text-decoration: none;">
......
......@@ -117,7 +117,7 @@
<li class="tsd-description">
<aside class="tsd-sources">
<ul>
<li>Defined in UI/Modal/ConvertFileModal.ts:146</li>
<li>Defined in UI/Modal/ConvertFileModal.ts:226</li>
</ul>
</aside>
<div class="tsd-comment tsd-typography">
......@@ -294,22 +294,48 @@
<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><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>, 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>
</ul>
<ul class="tsd-descriptions">
<li class="tsd-description">
<aside class="tsd-sources">
<ul>
<li>Defined in UI/Modal/ConvertFileModal.ts:62</li>
<li>Defined in UI/Modal/ConvertFileModal.ts:74</li>
</ul>
</aside>
<div class="tsd-comment tsd-typography">
<div class="lead">
<p>Begin to convert the file to PDBQT.</p>
</div>
</div>
<h4 class="tsd-parameters-title">Parameters</h4>
<ul class="tsd-parameters">
<li>
<h5>e: <span class="tsd-signature-type">any</span></h5>
<div class="tsd-comment tsd-typography">
<p>The click event.</p>
</div>
</li>
<li>
<h5><span class="tsd-flag ts-flagDefault value">Default value</span> currentPDBOptimizationLevel: <span class="tsd-signature-type">number</span><span class="tsd-signature-symbol"> = 1</span></h5>
<div class="tsd-comment tsd-typography">
<p>To what extent the PDB
file should be
optimized (to keep size
low for converting).</p>
</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>
<div class="tsd-comment tsd-typography">
<p>The message to display
to the user on success
(if any).</p>
</div>
</li>
</ul>
<h4 class="tsd-returns-title">Returns <span class="tsd-signature-type">void</span></h4>
<p>void</p>
</li>
</ul>
</section>
......@@ -323,10 +349,51 @@
<li class="tsd-description">
<aside class="tsd-sources">
<ul>
<li>Defined in UI/Modal/ConvertFileModal.ts:122</li>
<li>Defined in UI/Modal/ConvertFileModal.ts:197</li>
</ul>
</aside>
<div class="tsd-comment tsd-typography">
<div class="lead">
<p>The cancel button is pressed.</p>
</div>
</div>
<h4 class="tsd-returns-title">Returns <span class="tsd-signature-type">void</span></h4>
<p>void</p>
</li>
</ul>
</section>
<section class="tsd-panel tsd-member tsd-kind-function tsd-parent-kind-object-literal tsd-is-not-exported">
<a name="methodsfunctions.pdboptimization" class="tsd-anchor"></a>
<h3>pdb<wbr>Optimization</h3>
<ul class="tsd-signatures tsd-kind-function tsd-parent-kind-object-literal tsd-is-not-exported">
<li class="tsd-signature tsd-kind-icon">pdb<wbr>Optimization<span class="tsd-signature-symbol">(</span>level<span class="tsd-signature-symbol">: </span><span class="tsd-signature-type">number</span><span class="tsd-signature-symbol">)</span><span class="tsd-signature-symbol">: </span><span class="tsd-signature-type">string</span></li>
</ul>
<ul class="tsd-descriptions">
<li class="tsd-description">
<aside class="tsd-sources">
<ul>
<li>Defined in UI/Modal/ConvertFileModal.ts:161</li>
</ul>
</aside>
<div class="tsd-comment tsd-typography">
<div class="lead">
<p>PDB files are very common, yet openbabel.js cannot convert them if they
are too large. Here we make efforts to &quot;optimize&quot; the PDB file to
maximize the changes that openbabel.js will succeed.</p>
</div>
</div>
<h4 class="tsd-parameters-title">Parameters</h4>
<ul class="tsd-parameters">
<li>
<h5>level: <span class="tsd-signature-type">number</span></h5>
<div class="tsd-comment tsd-typography">
<p>The optimization level.</p>
</div>
</li>
</ul>
<h4 class="tsd-returns-title">Returns <span class="tsd-signature-type">string</span></h4>
<p>string A message to show the user re. any modifications made
to the PDB file.</p>
</li>
</ul>
</section>
......@@ -340,10 +407,16 @@
<li class="tsd-description">
<aside class="tsd-sources">
<ul>
<li>Defined in UI/Modal/ConvertFileModal.ts:137</li>
<li>Defined in UI/Modal/ConvertFileModal.ts:217</li>
</ul>
</aside>
<div class="tsd-comment tsd-typography">
<div class="lead">
<p>Reload the iframe containing the PDBConvert app.</p>
</div>
</div>
<h4 class="tsd-returns-title">Returns <span class="tsd-signature-type">void</span></h4>
<p>void</p>
</li>
</ul>
</section>
......
......@@ -129,7 +129,7 @@
<li class="tsd-description">
<aside class="tsd-sources">
<ul>
<li>Defined in UI/Tabs/VinaParams.ts:334</li>
<li>Defined in UI/Tabs/VinaParams.ts:316</li>
</ul>
</aside>
<div class="tsd-comment tsd-typography">
......@@ -152,7 +152,7 @@
<li class="tsd-description">
<aside class="tsd-sources">
<ul>
<li>Defined in UI/Tabs/VinaParams.ts:342</li>
<li>Defined in UI/Tabs/VinaParams.ts:324</li>
</ul>
</aside>
<div class="tsd-comment tsd-typography">
......@@ -285,7 +285,7 @@
<li class="tsd-description">
<aside class="tsd-sources">
<ul>
<li>Defined in UI/Tabs/VinaParams.ts:281</li>
<li>Defined in UI/Tabs/VinaParams.ts:263</li>
</ul>
</aside>
<div class="tsd-comment tsd-typography">
......@@ -416,7 +416,7 @@
<li class="tsd-description">
<aside class="tsd-sources">
<ul>
<li>Defined in UI/Tabs/VinaParams.ts:322</li>
<li>Defined in UI/Tabs/VinaParams.ts:304</li>
</ul>
</aside>
<div class="tsd-comment tsd-typography">
......@@ -472,7 +472,7 @@
<li class="tsd-description">
<aside class="tsd-sources">
<ul>
<li>Defined in UI/Tabs/VinaParams.ts:234</li>
<li>Defined in UI/Tabs/VinaParams.ts:216</li>
</ul>
</aside>
<div class="tsd-comment tsd-typography">
......
......@@ -76,6 +76,7 @@
<li class="tsd-kind-function tsd-parent-kind-module"><a href="_utils_.html#curpath" class="tsd-kind-icon">cur<wbr>Path</a></li>
<li class="tsd-kind-function tsd-parent-kind-module"><a href="_utils_.html#getnewobjwithupdate" class="tsd-kind-icon">get<wbr>New<wbr>Obj<wbr>With<wbr>Update</a></li>
<li class="tsd-kind-function tsd-parent-kind-module"><a href="_utils_.html#isfirefox" class="tsd-kind-icon">is<wbr>Firefox</a></li>
<li class="tsd-kind-function tsd-parent-kind-module"><a href="_utils_.html#keeponlyproteinatoms" class="tsd-kind-icon">keep<wbr>Only<wbr>Protein<wbr>Atoms</a></li>
<li class="tsd-kind-function tsd-parent-kind-module"><a href="_utils_.html#replaceext" class="tsd-kind-icon">replace<wbr>Ext</a></li>
<li class="tsd-kind-function tsd-parent-kind-module"><a href="_utils_.html#webassemblysupported" class="tsd-kind-icon">web<wbr>Assembly<wbr>Supported</a></li>
</ul>
......@@ -176,6 +177,38 @@
</li>
</ul>
</section>
<section class="tsd-panel tsd-member tsd-kind-function tsd-parent-kind-module">
<a name="keeponlyproteinatoms" class="tsd-anchor"></a>
<h3>keep<wbr>Only<wbr>Protein<wbr>Atoms</h3>
<ul class="tsd-signatures tsd-kind-function tsd-parent-kind-module">
<li class="tsd-signature tsd-kind-icon">keep<wbr>Only<wbr>Protein<wbr>Atoms<span class="tsd-signature-symbol">(</span>pdbTxt<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">string</span></li>
</ul>
<ul class="tsd-descriptions">
<li class="tsd-description">
<aside class="tsd-sources">
<ul>
<li>Defined in Utils.ts:89</li>
</ul>
</aside>
<div class="tsd-comment tsd-typography">
<div class="lead">
<p>Given some PDB text, keep only those lines that describe protein atoms.</p>
</div>
</div>
<h4 class="tsd-parameters-title">Parameters</h4>
<ul class="tsd-parameters">
<li>
<h5>pdbTxt: <span class="tsd-signature-type">string</span></h5>
<div class="tsd-comment tsd-typography">
<p>The original PDB text.</p>
</div>
</li>
</ul>
<h4 class="tsd-returns-title">Returns <span class="tsd-signature-type">string</span></h4>
<p>string the PDB text containing only the protein atoms.</p>
</li>
</ul>
</section>
<section class="tsd-panel tsd-member tsd-kind-function tsd-parent-kind-module">
<a name="replaceext" class="tsd-anchor"></a>
<h3>replace<wbr>Ext</h3>
......@@ -333,6 +366,9 @@
<li class=" tsd-kind-function tsd-parent-kind-module">
<a href="_utils_.html#isfirefox" class="tsd-kind-icon">is<wbr>Firefox</a>
</li>
<li class=" tsd-kind-function tsd-parent-kind-module">
<a href="_utils_.html#keeponlyproteinatoms" class="tsd-kind-icon">keep<wbr>Only<wbr>Protein<wbr>Atoms</a>
</li>
<li class=" tsd-kind-function tsd-parent-kind-module">
<a href="_utils_.html#replaceext" class="tsd-kind-icon">replace<wbr>Ext</a>
</li>
......
......@@ -89,6 +89,7 @@ let methodsFunctions = {
this["gen3D"] = false;
}
frameWindow.document.querySelector("html").style.overflow = "hidden";
frameWindow["PDBQTConvert"]["convert"](
content,
this["currentExt"].toLowerCase(),
......@@ -121,7 +122,7 @@ let methodsFunctions = {
this.$store.commit("updateFileName", { type: this["currentType"], filename: newFilename });
if (successMsg !== "") {
this["$bvModal"]["msgBoxOk"]("To convert your file, Webina had to make the following modifications: " + successMsg, {
this["$bvModal"]["msgBoxOk"]("To convert your file to PDBQT, Webina had to make the following modifications: " + successMsg, {
"title": "Warning: File Too Big!",
});
}
......@@ -177,7 +178,7 @@ let methodsFunctions = {
// Keep only the first chain.
let chain = pdbTxt.slice(21,22);
pdbTxt = pdbTxt.split("\n").filter(l => l.slice(21,22) === chain).join("\n");
msg += " (1) Keep only the first chain (chain " + chain + ").";
msg += " (2) Keep only the first chain (chain " + chain + ").";
break;
}
......
......@@ -168,7 +168,7 @@ td {
/** Let user know that mobile is no go */
#no-mobile {
position: absolute;
position: fixed;
left: 0px;
top: 0px;
width: 100%;
......
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