lambdacasserole / avogadrio Goto Github PK
View Code? Open in Web Editor NEWWorship your favorite molecule by setting it as your wallpaper.
Home Page: https://avogadr.io/
License: MIT License
Worship your favorite molecule by setting it as your wallpaper.
Home Page: https://avogadr.io/
License: MIT License
Bromine atoms seem to disappear by being rendered over each other.
IUPAC name: tri(3,5-di(2,3,4,5,6-pentabromophenyl)phenyl)amine
Render: https://i.imgur.com/XPZGc05.png
Some external APIs won't play nice with +
instead of %20
in URL query strings. This includes the chemical names database currently used on live.
I entered "ethyl cyanoacrylate" into the "Compound Name" box and cleared the SMILES structure box. Longest I've waited is ten minutes, but the displayed molecule doesn't change from the default. There is no error under the compound box like there is with invalid names. Checking it on https://opsin.ch.cam.ac.uk/ brings up the correct result (SMILES C(#N)C(C(=O)OCC)=C
). Entering the SMILES works quickly.
Firefox 100.0.2 on Ubuntu 21.10.
If we search chlorophyll
for example we get a very long SMILES string:
[Mg++].CCc1c(C)c2[n-]c1cc3nc4c([C@@H](C(=O)OC)C(=O)c4c3C)c5nc(cc6[n-]c(c2)c(C=C)c6C)[C@@H](C)[C@@H]5CCC(=O)OC/C=C(C)/CCCC(C)CCCC(C)CCCC(C)C
Which becomes outright monstrous when URL-encoded:
%5BMg%2B%2B%5D.CCc1c%28C%29c2%5Bn-%5Dc1cc3nc4c%28%5BC%40%40H%5D%28C%28%3DO%29OC%29C%28%3DO%29c4c3C%29c5nc%28cc6%5Bn-%5Dc%28c2%29c%28C%3DC%29c6C%29%5BC%40%40H%5D%28C%29%5BC%40%40H%5D5CCC%28%3DO%29OC%2FC%3DC%28C%29%2FCCCC%28C%29CCCC%28C%29CCCC%28C%29C
This breaks sub-requests in Silex as far as I can tell. The only real solution is to avoid passing these strings from action to action and deal with them in the same action they're generated in. This is going to create some redundant code for the time being.
Reported on Twitter. Size of the webpage viewport is used rather than actual screen size.
Hey. I've been bug testing for a while and found a rendering error with bastadin5
Here's what the molecule is supposed to look like: pubchem link
Here's the render: imgur link
IUPAC name: 5,16,21,32,36-Pentabromo-4,20-dihydroxy-2,18-dioxa-10,27-diazapentacyclo(28.2.2.2(14,17).1(3,7).1(19,23))octatriaconta-3,5,7(38),14,16,19,21,23(35),30,32,33,36-dodecaene-11,12,25,26-tetrone 12,25-dioxime
I can't provide a fix as I'm not familiar with web-oriented programming languages, but I'll keep bug testing.
For some reason (K,Na)0-1(Ca,Na,Fe,Mg)2(Mg,Fe,Al)5(Al,Si)8O22(OH)2
doesn't seem to be a valid SMILES structure, and "hornblende" wasn't recognized as a valid mineral name. Tried to google a SMILES structure index for minerals but I couldn't find one.
Forgive me since I'm not an organic-y guy, just a geologist.
It has been pointed out that the presence and function of the burger menu is not always obvious. I agree with this, so what say we roll in a query parameter that will expand it by default?
It was suggested on Twitter that we should introduce a randomize button that will give a random compound and (maybe) random colors. The compound name should probably appear in the custom label as well, so the user actually knows which chemical they're about to set as their desktop background.
We could try to find an external API that will give a random compound name, or just pull from the site cache. I think the latter is the better option to be honest.
Would it be possible to add more ways to input colors to the color selectors. It is hard to generate a specific color with the current setup. I know the default HTML5 input tag with type color lets you do the current method but also has a field for RGB values and hex values.
Just for fun, i tried to let it display Oxygen (O2).
I typed Oxygen into the Compund Name field, and voila, what was displayed there was definitely no oxygen, it was water (H2O)
I hope you can fix that.
P.S.: You website is really nice and sometimes even useful for education!
It shows up almost out of screen instead of center: screenshot
Using firefox 54.0.1 (32-bit)
If you input "deoxyribonucleic acid", the result is a phenolphtalein molecule with an extra ether group connecting the two phenols ¯_(ツ)_/¯
Watching a recent NileRed video I came accross this cool molecule, which doesn't seem to be displayed/rendered correctly.
But it gives seperate molecules. I also tried putting in a custom SMILES structure (from pubchem) but it doesn't seem to work either.
https://pubchem.ncbi.nlm.nih.gov/compound/84567#section=IUPAC-Name
Can you don anything about that or is it the problem of one of the modules you are using?
Hi it's me again, with some strange molecules.
https://en.wikipedia.org/wiki/Octanitrocubane I would imagine it being rendered a bit more like in the image on wikipedia.
https://en.wikipedia.org/wiki/Twistane also a large dissimilarity
https://en.wikipedia.org/wiki/2.2.2-Propellane
https://en.wikipedia.org/wiki/1.1.1-Propellane
https://en.wikipedia.org/wiki/Bicyclo(1.1.1)pentane
https://en.wikipedia.org/wiki/Adamantane displays some CH_2
https://en.wikipedia.org/wiki/Iceane I don't know how you'd render that
https://en.wikipedia.org/wiki/Cubane
I've stumbled across some molecules that don't work. Uranium hexafluoride is apparently an invalid compound name, uranyl nitrate leads to the "backup" molecule.
Using the version on avogadr.io currently, Methylene Blue does not render correctly using "methylthioninium chloride" nor "Methylthionine Chloride" as compound names and gives an "Invalid SMILES structure" error when attempting to render it using "CN(C)C1=CC2=C(C=C1)N=C3C=CC(=N+C)C=C3S2.[Cl-]".
I'm not at my primary computer so I have not attempted to run it myself on XAMP, so all I have to go off of is what's live on avogadr.io.
Feature request
Really nice tool! Been using it on all my monitors as wallpapers.
Unfortunately the API is down for all structures. Here's an example with the default one when you load the site (CCN(CC)C1=CC2=C(C=C1)N=C3C4=CC=CC=C4C(=O)C=C3O2
).
URL: https://avogadr.io/api/smiles/3440/1440/ce3838/CCN(CC)C1%3DCC2%3DC(C%3DC1)N%3DC3C4%3DCC%3DCC%3DC4C(%3DO)C%3DC3O2
GET /api/smiles/3440/1440/ce3838/CCN(CC)C1%3DCC2%3DC(C%3DC1)N%3DC3C4%3DCC%3DCC%3DC4C(%3DO)C%3DC3O2 HTTP/1.1
Host: avogadr.io
Connection: keep-alive
Pragma: no-cache
Cache-Control: no-cache
sec-ch-ua: " Not;A Brand";v="99", "Google Chrome";v="91", "Chromium";v="91"
DNT: 1
sec-ch-ua-mobile: ?0
User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/91.0.4472.77 Safari/537.36
Accept: image/avif,image/webp,image/apng,image/svg+xml,image/*,*/*;q=0.8
Sec-Fetch-Site: same-origin
Sec-Fetch-Mode: no-cors
Sec-Fetch-Dest: image
Referer: https://avogadr.io/?background=5f0000&foreground=ce3838&rotation=0&smiles=CCN(CC)C1%3DCC2%3DC(C%3DC1)N%3DC3C4%3DCC%3DCC%3DC4C(%3DO)C%3DC3O2
Accept-Encoding: gzip, deflate, br
Accept-Language: en,en-CA;q=0.9
HTTP/1.1 500 Internal Server Error
Date: Thu, 10 Jun 2021 08:08:31 GMT
Server: Apache/2.4.18 (Ubuntu)
Cache-Control: no-cache, private
Connection: close
Transfer-Encoding: chunked
Content-Type: text/html; charset=UTF-8
data:text/html,<!DOCTYPE html>
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@media (min-width: 575px) {
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<body>
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<h1 class="break-long-words exception-message">Whoops, looks like something went wrong.</h1>
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1.552.126.56.461.93.908.824.56-.133 1.172-1.006.995-1.795z" fill="#fff" fill-opacity=".6"></path></svg></div>
</div>
</div>
</div>
<div class="container">
<div class="trace trace-as-html">
<table class="trace-details">
<thead class="trace-head"><tr><th>
<h3 class="trace-class">
<span class="text-muted">(1/1)</span>
<span class="exception_title"><abbr title="Intervention\Image\Exception\NotReadableException">NotReadableException</abbr></span>
</h3>
<p class="break-long-words trace-message">Unable to init from given url (http://localhost:8080/molecule/CCN%28CC%29C1%3DCC2%3DC%28C%3DC1%29N%3DC3C4%3DCC%3DCC%3DC4C%28%3DO%29C%3DC3O2?render-stereo-style=none&render-comment-offset=16&render-comment=).</p>
</th></tr></thead>
<tbody><tr><td><span class="block trace-file-path">in <a title="/var/www/avogadr.io/vendor/intervention/image/src/Intervention/Image/AbstractDecoder.php line 83"><strong>AbstractDecoder.php</strong> (line 83)</a></span></td></tr>
<tr><td>at <span class="trace-class"><abbr title="Intervention\Image\AbstractDecoder">AbstractDecoder</abbr></span><span class="trace-type">-></span><span class="trace-method">initFromUrl</span>(<span class="trace-arguments">'http://localhost:8080/molecule/CCN%28CC%29C1%3DCC2%3DC%28C%3DC1%29N%3DC3C4%3DCC%3DCC%3DC4C%28%3DO%29C%3DC3O2?render-stereo-style=none&render-comment-offset=16&render-comment='</span>)<span class="block trace-file-path">in <a title="/var/www/avogadr.io/vendor/intervention/image/src/Intervention/Image/AbstractDecoder.php line 329"><strong>AbstractDecoder.php</strong> (line 329)</a></span></td></tr>
<tr><td>at <span class="trace-class"><abbr title="Intervention\Image\AbstractDecoder">AbstractDecoder</abbr></span><span class="trace-type">-></span><span class="trace-method">init</span>(<span class="trace-arguments">'http://localhost:8080/molecule/CCN%28CC%29C1%3DCC2%3DC%28C%3DC1%29N%3DC3C4%3DCC%3DCC%3DC4C%28%3DO%29C%3DC3O2?render-stereo-style=none&render-comment-offset=16&render-comment='</span>)<span class="block trace-file-path">in <a title="/var/www/avogadr.io/vendor/intervention/image/src/Intervention/Image/AbstractDriver.php line 64"><strong>AbstractDriver.php</strong> (line 64)</a></span></td></tr>
<tr><td>at <span class="trace-class"><abbr title="Intervention\Image\AbstractDriver">AbstractDriver</abbr></span><span class="trace-type">-></span><span class="trace-method">init</span>(<span class="trace-arguments">'http://localhost:8080/molecule/CCN%28CC%29C1%3DCC2%3DC%28C%3DC1%29N%3DC3C4%3DCC%3DCC%3DC4C%28%3DO%29C%3DC3O2?render-stereo-style=none&render-comment-offset=16&render-comment='</span>)<span class="block trace-file-path">in <a title="/var/www/avogadr.io/vendor/intervention/image/src/Intervention/Image/ImageManager.php line 50"><strong>ImageManager.php</strong> (line 50)</a></span></td></tr>
<tr><td>at <span class="trace-class"><abbr title="Intervention\Image\ImageManager">ImageManager</abbr></span><span class="trace-type">-></span><span class="trace-method">make</span>(<span class="trace-arguments">'http://localhost:8080/molecule/CCN%28CC%29C1%3DCC2%3DC%28C%3DC1%29N%3DC3C4%3DCC%3DCC%3DC4C%28%3DO%29C%3DC3O2?render-stereo-style=none&render-comment-offset=16&render-comment='</span>)<span class="block trace-file-path">in <a title="/var/www/avogadr.io/vendor/intervention/image/src/Intervention/Image/ImageManagerStatic.php line 57"><strong>ImageManagerStatic.php</strong> (line 57)</a></span></td></tr>
<tr><td>at <span class="trace-class"><abbr title="Intervention\Image\ImageManagerStatic">ImageManagerStatic</abbr></span><span class="trace-type">::</span><span class="trace-method">make</span>(<span class="trace-arguments">'http://localhost:8080/molecule/CCN%28CC%29C1%3DCC2%3DC%28C%3DC1%29N%3DC3C4%3DCC%3DCC%3DC4C%28%3DO%29C%3DC3O2?render-stereo-style=none&render-comment-offset=16&render-comment='</span>)<span class="block trace-file-path">in <a title="/var/www/avogadr.io/src/MoleculeRenderer.php line 59"><strong>MoleculeRenderer.php</strong> (line 59)</a></span></td></tr>
<tr><td>at <span class="trace-class"><abbr title="Avogadrio\MoleculeRenderer">MoleculeRenderer</abbr></span><span class="trace-type">-></span><span class="trace-method">renderMolecule</span>(<span class="trace-arguments">'CCN(CC)C1=CC2=C(C=C1)N=C3C4=CC=CC=C4C(=O)C=C3O2', 'ce3838'</span>)<span class="block trace-file-path">in <a title="/var/www/avogadr.io/src/MoleculeRenderer.php line 84"><strong>MoleculeRenderer.php</strong> (line 84)</a></span></td></tr>
<tr><td>at <span class="trace-class"><abbr title="Avogadrio\MoleculeRenderer">MoleculeRenderer</abbr></span><span class="trace-type">-></span><span class="trace-method">renderScaledMolecule</span>(<span class="trace-arguments">'CCN(CC)C1=CC2=C(C=C1)N=C3C4=CC=CC=C4C(=O)C=C3O2', 'ce3838', '3440', '1440'</span>)<span class="block trace-file-path">in <a title="/var/www/avogadr.io/web/index.php line 78"><strong>index.php</strong> (line 78)</a></span></td></tr>
<tr><td>at <span class="trace-class"><abbr title=""></abbr></span><span class="trace-type"></span><span class="trace-method">{closure}</span>(<span class="trace-arguments"><em>object</em>(<abbr title="Symfony\Component\HttpFoundation\Request">Request</abbr>), '3440', '1440', 'ce3838', 'CCN(CC)C1=CC2=C(C=C1)N=C3C4=CC=CC=C4C(=O)C=C3O2'</span>)</td></tr>
<tr><td>at <span class="trace-class"><abbr title=""></abbr></span><span class="trace-type"></span><span class="trace-method">call_user_func_array</span>(<span class="trace-arguments"><em>object</em>(<abbr title="Closure">Closure</abbr>), <em>array</em>(<em>object</em>(<abbr title="Symfony\Component\HttpFoundation\Request">Request</abbr>), '3440', '1440', 'ce3838', 'CCN(CC)C1=CC2=C(C=C1)N=C3C4=CC=CC=C4C(=O)C=C3O2')</span>)<span class="block trace-file-path">in <a title="/var/www/avogadr.io/vendor/symfony/http-kernel/HttpKernel.php line 153"><strong>HttpKernel.php</strong> (line 153)</a></span></td></tr>
<tr><td>at <span class="trace-class"><abbr title="Symfony\Component\HttpKernel\HttpKernel">HttpKernel</abbr></span><span class="trace-type">-></span><span class="trace-method">handleRaw</span>(<span class="trace-arguments"><em>object</em>(<abbr title="Symfony\Component\HttpFoundation\Request">Request</abbr>), 1</span>)<span class="block trace-file-path">in <a title="/var/www/avogadr.io/vendor/symfony/http-kernel/HttpKernel.php line 68"><strong>HttpKernel.php</strong> (line 68)</a></span></td></tr>
<tr><td>at <span class="trace-class"><abbr title="Symfony\Component\HttpKernel\HttpKernel">HttpKernel</abbr></span><span class="trace-type">-></span><span class="trace-method">handle</span>(<span class="trace-arguments"><em>object</em>(<abbr title="Symfony\Component\HttpFoundation\Request">Request</abbr>), 1, <em>true</em></span>)<span class="block trace-file-path">in <a title="/var/www/avogadr.io/vendor/silex/silex/src/Silex/Application.php line 496"><strong>Application.php</strong> (line 496)</a></span></td></tr>
<tr><td>at <span class="trace-class"><abbr title="Silex\Application">Application</abbr></span><span class="trace-type">-></span><span class="trace-method">handle</span>(<span class="trace-arguments"><em>object</em>(<abbr title="Symfony\Component\HttpFoundation\Request">Request</abbr>)</span>)<span class="block trace-file-path">in <a title="/var/www/avogadr.io/vendor/silex/silex/src/Silex/Application.php line 477"><strong>Application.php</strong> (line 477)</a></span></td></tr>
<tr><td>at <span class="trace-class"><abbr title="Silex\Application">Application</abbr></span><span class="trace-type">-></span><span class="trace-method">run</span>(<span class="trace-arguments"></span>)<span class="block trace-file-path">in <a title="/var/www/avogadr.io/web/index.php line 152"><strong>index.php</strong> (line 152)</a></span></td></tr>
</tbody>
</table>
</div>
</div>
</body>
</html>
It has been suggested that it should be possible to link to molecules in the preview. For instance:
/?molecule=benzene&color=0000FF&backcolor=FFC0C0
Should pre-populate the relevant fields and display the result. This should be possible to add in client-side (perhaps in conjunction with #11.
Hey so as promised I kept bug testing and found a new rendering bug affecting non-cyclic molecules.
IUPAC name: tri(6-phenylphenyl)amine
Render: https://i.imgur.com/mRAlgtq.png
The problem here just seems to be that there isn't enough room for the external phenyl groups to display so they just overlap.
EDIT: technically, it contains cyclic groups, but the error doesn't seem to come from a massive cyclic chain unlike the previous ones.
Upon feeding C#C to the SMILES input I get a "Invalid SMILES structure!" error.
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