Updates to docs, replaced CDN urls, etc.

CHANGELOG.md

@@ -8,15 +8,15 @@ WIP
   * Fixed a minor bug that sometimes caused malformed example command lines.
   * Added links so users can save the receptor/ligand PDBQT input files
     generated within the app.
-* Created a separate, independent helper app called PDBQTConvert that can
-  convert files in many other formats (e.g., PDB, XYZ, CAN, SMI) to PDBQT (see
+* Created a separate, independent web app called PDBQTConvert that can convert
+  files in many other formats (e.g., PDB, XYZ, CAN, SMI) to PDBQT (see
   `pdbqt_convert/`). This app uses
-  [openbabel.js](https://github.com/partridgejiang/cheminfo-to-web/)
-  and is GNU GPL licensed. We distribute it alongside Webina, but as a
-  separate program.
+  [openbabel.js](https://github.com/partridgejiang/cheminfo-to-web/) and is
+  GNU GPL licensed. We distribute it alongside Webina, but as a separate
+  program.
 * Added ways to provide/process input PDBQT files.
   * Modified Webina so users can optionally use PDBQTConvert to convert their
-    input files. Webina communicates with PDBQTConvert at "arms length," via
+    input files. Webina communicates with PDBQTConvert at "arm's length," via
     an iframe.
   * Added the ability to draw small-molecule ligands.
   * Added a link to optionally remove non-protein residues from the receptor.

README.md

@@ -38,13 +38,14 @@ Additional browsers are likely to enable SharedArrayBuffer soon.
 
 ## Description of Use ##
 
-### Preparing Receptor/Ligand PDBQT Input Files ###
+### Receptor/Ligand PDBQT Input Files ###
 
 As is the case with command-line Vina, Webina accepts input receptor and
 ligand files in the PDBQT format. The latest version of the Webina app
-interfaces with the PDBQTConvert app (included in the git repository) to
-convert these files from other formats (e.g., PDB) to PDBQT. But some advanced
-users may wish to provide their own PDBQT files. Such users include:
+optionally interfaces with the PDBQTConvert app (included in the git
+repository) to convert these files from other formats (e.g., PDB) to PDBQT.
+But some advanced users may wish to provide their own PDBQT files. Such users
+include:
 
 * Users who wish to have more fine-grained control over the input. For
   example, users who wish to specify protonation states, ring-conformational
@@ -74,7 +75,7 @@ receptor PDBQT files:
   Here is an example command: `obabel -xr -ipqr my_receptor.pqr -O
   my_receptor.pdbqt`
 
-##### Preparing the Ligand PDBQT File #####
+#### Preparing the Ligand PDBQT File ####
 
 We recommend the following steps for those who wish to provide their own
 ligand PDBQT files:
@@ -126,18 +127,33 @@ results. On first visiting the Webina web app, the user encounters the "Input
 Parameters" tab. This tab includes several subsections that are useful for
 setting up a Webina run.
 
-__Input PDBQT Files.__ The "Input PDBQT Files" subsection allows the user to
+__Input PDBQT Files.__ The "Input (PDBQT) Files" 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
 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
-ligand poses.
-
-Some users may wish to test Webina without having to provide their own input
-files. The optional "Use Example Files" button automatically loads in example
-receptor, ligand, and known-pose files.
+ligand poses. In our experience, it is often helpful to first benchmark Webina
+(or Vina) against a known ligand before using the program to evaluate
+compounds with unknown poses and binding affinities.
+
+The "Input (PDBQT) Files" subsection also includes several options to simplify
+the process of preparing/testing protein/ligand input files.
+
+* If users wish only to test Webina without having to provide their own files,
+  they can click the "Use Example Files" button to automatically load example
+  receptor, ligand, and known-pose files.
+* If users specify receptor/ligand input files that are not in the required
+  PDBQT format, the Webina web app will optionally attempt to convert them to
+  PDBQT using the PDBQTConvert app. Interactions between the Webina and
+  PDBQTConvert apps occur at "arm's length" via an iframe.
+* If users' receptor files include non-protein residues that might interfere
+  with docking (e.g., a co-crystallized ligand), they can remove all
+  non-protein atoms.
+* If users do not have a ligand file, they can use a web-based 2D molecular
+  editor to draw their ligand by hand. PDBQTConvert then converts that 2D
+  ligand representation to a 3D PDBQT file for docking.
 
 __Docking Box.__ The "Docking Box" subsection allows users to specify the
 region of the receptor where Webina should attempt to pose the ligand. This
@@ -179,7 +195,9 @@ 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
 to use command-line Vina with the specified parameters. Users can copy this
 example, modify it as needed, and paste it into their command-line terminals
-to run the desired calculation with the standard Vina executable.
+to run the desired calculation with the standard Vina executable. This
+subsection also includes links that allow the user to download the
+receptor/ligand PDBQT files for command-line use.
 
 __Starting the Webina Calculation.__ Once users click the "Start Webina"
 button, the Webina app will switch to the "Running Webina" tab while Webina

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.0e5b3fc3dceab82cde6c.css" rel="stylesheet"><link href="styles.css.0e5b3fc3dceab82cde6c.css" rel="stylesheet"></head>
+    <link rel="shortcut icon" href="favicon.ico"><link href="vendors.6bf864e0e87d872d56ba.css" rel="stylesheet"><link href="styles.6bf864e0e87d872d56ba.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.0e5b3fc3dceab82cde6c.js"></script><script type="text/javascript" src="vendors.0e5b3fc3dceab82cde6c.js"></script><script type="text/javascript" src="app.0e5b3fc3dceab82cde6c.js"></script><script type="text/javascript" src="styles.css.0e5b3fc3dceab82cde6c.js"></script></body>
+    <script type="text/javascript" src="runtime.6bf864e0e87d872d56ba.js"></script><script type="text/javascript" src="vendors.6bf864e0e87d872d56ba.js"></script><script type="text/javascript" src="app.6bf864e0e87d872d56ba.js"></script><script type="text/javascript" src="styles.6bf864e0e87d872d56ba.js"></script><script type="text/javascript" src="styles.css.6bf864e0e87d872d56ba.js"></script></body>
 
     </html>

docs/index.html

@@ -110,8 +110,39 @@
 				<a href="#description-of-use" id="description-of-use" style="color: inherit; text-decoration: none;">
 					<h2>Description of Use</h2>
 				</a>
-				<a href="#preparing-receptorligand-pdbqt-input-files" id="preparing-receptorligand-pdbqt-input-files" style="color: inherit; text-decoration: none;">
-					<h3>Preparing Receptor/Ligand PDBQT Input Files</h3>
+				<a href="#pdbqtconvert-web-app" id="pdbqtconvert-web-app" style="color: inherit; text-decoration: none;">
+					<h3>PDBQTConvert Web App</h3>
+				</a>
+				<p>We created the PDBQTConvert web app to better accomodate novice users. Like
+					Vina, the Webina library accepts receptor/ligand input files only in the PDBQT
+					format, a PDB-like format that additionally includes atom types and partial
+					atomic charges. As described in the &quot;Webina and Vina Benchmarks&quot; section
+					below, a number of command-line and other programs are available for
+					converting receptor/ligand input files from popular formats (e.g., PDB, SDF,
+					etc.) to PDBQT. But PDBQTConvert provides an easier way to prepare these files
+					using a Bootstrap4-powered GUI in the browser. We distribute the PDBQTConvert
+					app alongside Webina, but as an entirely separate program. Unlike the Webina
+				library/app codebase, the PDBQTConvert app is GPLv2 licensed, not Apache-2.0.</p>
+				<p>PDBQTConvert uses the <a href="https://github.com/partridgejiang/cheminfo-to-web/tree/master/OpenBabel/OpenBabel-js">OpenBabel JS
+					library</a>
+					to convert receptor and ligand input files from many common formats (i.e.,
+					CAN, ENT, MCIF, MDL, MMCIF, MOL, MOL2, PDB, PQR, SD, SDF, SMI, SMILES, and
+					XYZ) to the Webina-compatible PDBQT format. The app can optionally include
+					branches and torsion trees, as required to indicate which ligand bonds should
+				be considered rotatable during Webina/Vina docking.</p>
+				<p>A second option instructs PDBQTConvert to add hydrogen atoms per a
+					user-specified pH. This feature is particularly useful because PDB receptor
+					structures derived via X-ray crystallography often lack the resolution
+					required to place hydrogen atoms, and many popular ligand formats (e.g.,
+					SMILES strings) do not enumerate explicit hydrogen atoms. And yet Webina/Vina
+					docking does require that receptor/ligand PDBQT files include polar hydrogen
+				atoms.</p>
+				<p>A third option instructs PDBQTConvert to generate 3D coordinates for the input
+					molecule. Many popular ligand formats (e.g., SMILES strings, flat SDF files,
+					etc.) do not include 3D atomic coordinates, but Webina/Vina docking requires
+				fully 3D models.</p>
+				<a href="#receptorligand-pdbqt-input-files" id="receptorligand-pdbqt-input-files" style="color: inherit; text-decoration: none;">
+					<h3>Receptor/Ligand PDBQT Input Files</h3>
 				</a>
 				<p>As is the case with command-line Vina, Webina accepts input receptor and
 					ligand files in the PDBQT format. The latest version of the Webina app
@@ -201,17 +232,33 @@ ligand.pdbqt</code></li>
 					results. On first visiting the Webina web app, the user encounters the &quot;Input
 					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
+				<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
 					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
-				ligand poses.</p>
-				<p>Some users may wish to test Webina without having to provide their own input
-					files. The optional &quot;Use Example Files&quot; button automatically loads in example
-				receptor, ligand, and known-pose files.</p>
+					ligand poses. In our experience, it is often helpful to first benchmark Webina
+					(or Vina) against a known ligand before using the program to evaluate
+				compounds with unknown poses and binding affinities.</p>
+				<p>The &quot;Input (PDBQT) Files&quot; subsection also includes several options to simplify
+				the process of preparing/testing protein/ligand input files.</p>
+				<ul>
+					<li>If users wish only to test Webina without having to provide their own files,
+						they can click the &quot;Use Example Files&quot; button to automatically load example
+					receptor, ligand, and known-pose files.</li>
+					<li>If users specify receptor/ligand input files that are not in the required
+						PDBQT format, the Webina web app will optionally attempt to convert them to
+						PDBQT using the PDBQTConvert app. Interactions between the Webina and
+					PDBQTConvert apps occur at &quot;arms length&quot; via an iframe.</li>
+					<li>If users&#39; receptor files include non-protein residues that might interfere
+						with docking (e.g., a co-crystallized ligand), they can remove all
+					non-protein atoms.</li>
+					<li>If users do not have a ligand file, they can use a web-based 2D molecular
+						editor to draw their ligand by hand. PDBQTConvert then converts that 2D
+					ligand representation to a 3D PDBQT file for docking.</li>
+				</ul>
 				<p><strong>Docking Box.</strong> The &quot;Docking Box&quot; subsection allows users to specify the
 					region of the receptor where Webina should attempt to pose the ligand. This
 					box-shaped volume is typically centered on a known protein pocket or cavity
@@ -247,7 +294,9 @@ ligand.pdbqt</code></li>
 					docking boxes and user parameters. A text field provides a mock example of how
 					to use command-line Vina with the specified parameters. Users can copy this
 					example, modify it as needed, and paste it into their command-line terminals
-				to run the desired calculation with the standard Vina executable.</p>
+					to run the desired calculation with the standard Vina executable. This
+					subsection also includes links that allow the user to download the
+				receptor/ligand PDBQT files for command-line use.</p>
 				<p><strong>Starting the Webina Calculation.</strong> Once users click the &quot;Start Webina&quot;
 					button, the Webina app will switch to the &quot;Running Webina&quot; tab while Webina
 					executes. When the calculation is complete, the Webina web app will switch to

src/UI/Modal/ConvertFileModal.ts

@@ -182,7 +182,7 @@ export function setup(): void {
                     </span>
                 </p>
 
-                <p>Or click "Convert" below to convert with PDBQTConvert, which should be good enough for most purposes.</p>
+                <p>Or click "Convert" below to convert with the PDBQTConvert app, which should be good enough for most purposes.</p>
 
                 <b-form-checkbox
                     id="babel-add-hydrogens"

src/pdbqt_convert/index.html

@@ -28,35 +28,8 @@
         <meta name="description" content="PDBQT Convert" />
         <meta name="author" content="Jacob D. Durrant" />
 
-        <!-- Latest compiled and minified CSS -->
-        <link
-            rel="stylesheet"
-            href="https://stackpath.bootstrapcdn.com/bootstrap/4.4.1/css/bootstrap.min.css"
-            integrity="sha384-Vkoo8x4CGsO3+Hhxv8T/Q5PaXtkKtu6ug5TOeNV6gBiFeWPGFN9MuhOf23Q9Ifjh"
-            crossorigin="anonymous"
-        />
-
-        <!-- Optional theme -->
-        <link
-            rel="stylesheet"
-            href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap-theme.min.css"
-            integrity="sha384-rHyoN1iRsVXV4nD0JutlnGaslCJuC7uwjduW9SVrLvRYooPp2bWYgmgJQIXwl/Sp"
-            crossorigin="anonymous"
-        />
-
-        <!-- <script
-            src="https://code.jquery.com/jquery-3.4.1.js"
-            integrity="sha256-WpOohJOqMqqyKL9FccASB9O0KwACQJpFTUBLTYOVvVU="
-            crossorigin="anonymous"
-        ></script>
-
-        <script
-            src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
-            integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
-            crossorigin="anonymous"
-        ></script> -->
-
-        <!-- <link rel="stylesheet" href="css/styles.css?v=1.0" /> -->
+        <link rel="stylesheet" href="bootstrap.min.css" />
+        <link rel="stylesheet" href="bootstrap-theme.min.css" />
     </head>
 
     <body>