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jdurrant
webina
Commits
26e7d15c
Commit
26e7d15c
authored
Apr 16, 2020
by
Jacob Durrant
Browse files
Minor bug fixes.
parent
2d23971f
Changes
9
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dist/index.html
View file @
26e7d15c
...
...
@@ -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>
docs/assets/js/search.json
View file @
26e7d15c
This diff is collapsed.
Click to expand it.
docs/index.html
View file @
26e7d15c
...
...
@@ -203,9 +203,8 @@ ligand.pdbqt</code></li>
Parameters
"
tab. This tab includes several subsections that are useful for
setting up a Webina run.
</p>
<p><strong>
Input PDBQT Files.
</strong>
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
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
"
Advanced Parameters
"
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
"
Run Vina from Command Line
"
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
"
Download
"
button allows users to easily
save those files.
</p>
<p><strong>
Run Vina from Command Line.
</strong>
Similar to the
"
Input Parameters
"
tab, the
"
Output
"
T
ab also includes a
"
Run Vina from Command Line
"
S
ubsection. This
section makes it easy for users to reproduce Webina
'
s results using
"
Output
"
t
ab also includes a
"
Run Vina from Command Line
"
s
ubsection. This
sub
section makes it easy for users to reproduce Webina
'
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;"
>
...
...
docs/modules/_ui_modal_convertfilemodal_.html
View file @
26e7d15c
...
...
@@ -117,7 +117,7 @@
<li
class=
"tsd-description"
>
<aside
class=
"tsd-sources"
>
<ul>
<li>
Defined in UI/Modal/ConvertFileModal.ts:
14
6
</li>
<li>
Defined in UI/Modal/ConvertFileModal.ts:
22
6
</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"
>
=
""
</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:1
22
</li>
<li>
Defined in UI/Modal/ConvertFileModal.ts:1
97
</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
"
optimize
"
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:1
3
7
</li>
<li>
Defined in UI/Modal/ConvertFileModal.ts:
2
17
</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>
...
...
docs/modules/_ui_tabs_vinaparams_.html
View file @
26e7d15c
...
...
@@ -129,7 +129,7 @@
<li
class=
"tsd-description"
>
<aside
class=
"tsd-sources"
>
<ul>
<li>
Defined in UI/Tabs/VinaParams.ts:3
34
</li>
<li>
Defined in UI/Tabs/VinaParams.ts:3
16
</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:3
4
2
</li>
<li>
Defined in UI/Tabs/VinaParams.ts:32
4
</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:2
81
</li>
<li>
Defined in UI/Tabs/VinaParams.ts:2
63
</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:3
22
</li>
<li>
Defined in UI/Tabs/VinaParams.ts:3
04
</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:2
34
</li>
<li>
Defined in UI/Tabs/VinaParams.ts:2
16
</li>
</ul>
</aside>
<div
class=
"tsd-comment tsd-typography"
>
...
...
docs/modules/_utils_.html
View file @
26e7d15c
...
...
@@ -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>
...
...
src/UI/Modal/ConvertFileModal.ts
View file @
26e7d15c
...
...
@@ -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
;
}
...
...
src/styles/style.css
View file @
26e7d15c
...
...
@@ -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%
;
...
...
webina.zip
View file @
26e7d15c
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