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Worship your favorite molecule by setting it as your wallpaper.

Home Page: https://avogadr.io/

License: MIT License

JavaScript 35.17% CoffeeScript 17.68% CSS 11.24% HTML 12.47% PHP 23.44%

molecule wallpaper chemical php api

avogadrio's People

Contributors

Stargazers

Watchers

Forkers

klotztech dinkin hkilter adevelopers erdincay laviee nanxiaolei immortalin angelomedeiros czechbol nakedlitttlezombie

avogadrio's Issues

Deoxyribonucleic acid displayed incorrectly

If you input "deoxyribonucleic acid", the result is a phenolphtalein molecule with an extra ether group connecting the two phenols ¯_(ツ)_/¯

avogadr.io API down

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

Request headers

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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

Response headers

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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

Response content:

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data:text/html,<!DOCTYPE html>
<html>
    <head>
        <meta charset="UTF-8" />
        <meta name="robots" content="noindex,nofollow" />
        <style>            body { background-color: #F9F9F9; color: #222; font: 14px/1.4 Helvetica, Arial, sans-serif; margin: 0; padding-bottom: 45px; }

            a { cursor: pointer; text-decoration: none; }
            a:hover { text-decoration: underline; }
            abbr[title] { border-bottom: none; cursor: help; text-decoration: none; }

            code, pre { font: 13px/1.5 Consolas, Monaco, Menlo, "Ubuntu Mono", "Liberation Mono", monospace; }

            table, tr, th, td { background: #FFF; border-collapse: collapse; vertical-align: top; }
            table { background: #FFF; border: 1px solid #E0E0E0; box-shadow: 0px 0px 1px rgba(128, 128, 128, .2); margin: 1em 0; width: 100%; }
            table th, table td { border: solid #E0E0E0; border-width: 1px 0; padding: 8px 10px; }
            table th { background-color: #E0E0E0; font-weight: bold; text-align: left; }

            .hidden-xs-down { display: none; }
            .block { display: block; }
            .break-long-words { -ms-word-break: break-all; word-break: break-all; word-break: break-word; -webkit-hyphens: auto; -moz-hyphens: auto; hyphens: auto; }
            .text-muted { color: #999; }

            .container { max-width: 1024px; margin: 0 auto; padding: 0 15px; }
            .container::after { content: ""; display: table; clear: both; }

            .exception-summary { background: #B0413E; border-bottom: 2px solid rgba(0, 0, 0, 0.1); border-top: 1px solid rgba(0, 0, 0, .3); flex: 0 0 auto; margin-bottom: 30px; }

            .exception-message-wrapper { display: flex; align-items: center; min-height: 70px; }
            .exception-message { flex-grow: 1; padding: 30px 0; }
            .exception-message, .exception-message a { color: #FFF; font-size: 21px; font-weight: 400; margin: 0; }
            .exception-message.long { font-size: 18px; }
            .exception-message a { text-decoration: none; }
            .exception-message a:hover { text-decoration: underline; }

            .exception-illustration { flex-basis: 111px; flex-shrink: 0; height: 66px; margin-left: 15px; opacity: .7; }

            .trace + .trace { margin-top: 30px; }
            .trace-head .trace-class { color: #222; font-size: 18px; font-weight: bold; line-height: 1.3; margin: 0; position: relative; }

            .trace-message { font-size: 14px; font-weight: normal; margin: .5em 0 0; }

            .trace-file-path, .trace-file-path a { margin-top: 3px; color: #999; color: #795da3; color: #B0413E; color: #222; font-size: 13px; }
            .trace-class { color: #B0413E; }
            .trace-type { padding: 0 2px; }
            .trace-method { color: #B0413E; color: #222; font-weight: bold; color: #B0413E; }
            .trace-arguments { color: #222; color: #999; font-weight: normal; color: #795da3; color: #777; padding-left: 2px; }

            @media (min-width: 575px) {
                .hidden-xs-down { display: initial; }
            }</style>
    </head>
    <body>
                    <div class="exception-summary">
                <div class="container">
                    <div class="exception-message-wrapper">
                        <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>
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            </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&amp;render-comment-offset=16&amp;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&amp;render-comment-offset=16&amp;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&amp;render-comment-offset=16&amp;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&amp;render-comment-offset=16&amp;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&amp;render-comment-offset=16&amp;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&amp;render-comment-offset=16&amp;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>

Response content render:

Sub-requests for large molecules causing issue

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.

Bastadin 5 rendering error

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.

The function of the burger menu is not always obvious

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?

Ability to replace "Chiral" with custom text

Feature request

Needs minerals

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.

Custom label + rotation = error

I just filled the "Custom label" field and changed the rotation to a value other than 0. Also, a strange artifact appeared in the label, which might be a clue to the origin of the issue.

Rendering error (not a cyclic molecule)

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.

Ferroin not displayed correctly

Watching a recent NileRed video I came accross this cool molecule, which doesn't seem to be displayed/rendered correctly.

I assumed something like

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?

Incorrect method used to get screen size

Reported on Twitter. Size of the webpage viewport is used rather than actual screen size.

Add hex code or RGB input to the color selectors.

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.

Methylene Blue not rendering correctly (And "Invalid SMILES structure")

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.

Invalid SMILES for C#C the SMILES for Acetylene.

Upon feeding C#C to the SMILES input I get a "Invalid SMILES structure!" error.

Uranium hexafluoride invalid compound name

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.

Displaying molecules with a 3d shape

Atoms not displaying

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

Handle spaces correctly in URLs

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.

Molecule out of screen

It shows up almost out of screen instead of center: screenshot

Using firefox 54.0.1 (32-bit)

Oxygen is displayed as Water

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!

There is no way to link to molecules in the preview

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.

backup when using Vescalagin

by inputting Vescalagin, (a complex molecule,) a backup is caused somewhere.
I'd guess that a string "Backup" is returned and falsely interpreted.

Ethyl cyanoacrylate hangs indefinitely

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.

Octacyclooctylcyclooctane is displayed in a combobulated fashion, while a simple display is found by OPSIN

For comparison:
Avogadr.io result:

OPSIN result:

Randomize button

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.

Porphin rendering oddly

Originally raised in #21 by @sgitkene, the compound porphin renders very oddly:

No idea about this one, might be a Sourire or even Indigo issue.

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