molview / molview

The code of MolView.org

MolView

This repository holds the code of MolView.org. MolView and the source code of MolView are Copyright of Herman Bergwerf. You are not allowed to redistribute it without written permission.

Build

1. Copy all files to a server with support for: PHP, PHP cURL, mod_rewrite.
2. Make sure the Inkscape and the ImageMagick CLI are installed.
3. Install npm and install local npm modules.
4. Run the build script: ./build.sh fetch jmol
   • Only render images: ./build.sh render
   • Also run bower and grunt: ./build.sh
   • Also download Parsedown (PHP) library: ./build.sh fetch
   • Also download Jmol from sourceforge: ./build.sh fetch jmol
   • Also download Jmol from stolaf.edu: ./build.sh fetch jmol nightly

molview's Issues

2d structures get messed up by the clean function, unless they have defined stereocenters

example:
https://molview.org/?smiles=IC1=CC2S(=O)(=O)N(C3=C(C(N(CCCOC)[H])C=2C=C1)SC=C3)C
https://molview.org/?smiles=IC1C=CC2=C(S(N(C)C3C=CSC=3[C@@]2N([H])CCCOC)(=O)=O)C=1
it's nice that it there's an easy workaround for this (defining the stereocenters), but it took me a long time of using molview to find this out. Chemistry beginners also might not be able to easily go through and mark stereocenters.

P.S: is the molview rewrite still being developed?

How to draw straight with Molview?

I have this graphic:

And would like to transfer it to MolView.

Drawing by hand gives me:

If I click on the button "clean structure", it turns to:

But I would like to keep the positions of the atoms.

How to straighten the lines then?

Unable to load CIF files from the Crystallography Open Database

It seems the php/cif.php scipt that should mirror a given CIF file is broken. It returns Not Found even when the given CIF file does exist. This might be related to get_curl on https://github.com/molview/molview-1st-gen/blob/2d923d3c3ce7d0289c2d98ea6e47bbbae88acf05/php/cif.php#L56.

Multi-touch can only ontouchstart in the target element

When a user uses multi-touch, the second ontouchstart has to be located inside the target element, for example the sketcher. It would be much more convenient if the second ontouchstart can be everywhere in the document.

Partially implement MolView 3 design ideology in final 2.x design

Implement some design rules from MolView 3 in the final 2.x release so that the transition to MolView 3 is more gradually.

NMR spectrum

Hye
Is it possible to re-enable H1-NMR prediction spectrum in molview. That would be great.
Thank you so much.
Gwendal

Image exporting doesn't work on IE11

Automatic bond formation upon clicking to add -CH3 groups

Hi. Wanted to start off by saying that I've been using molview.org for more than 3 years now. It was a great tool in my organic chemistry classes and now it's been a tremendous help at the lab I work at.

Currently, I'm using MolView to add trimethylsilyl (TMS) groups to certain compounds in order to quickly retrieve a formula of a TMS derivative for that compound. It's quick and easy since all I have to do is search for a compound, replace the hydrogen on an alcohol group with Si, and then click the Si three times to add the methyl groups.

However, I noticed that when the groups are too close to another atom, instead of adding methyl groups, bonds begin to form when I click the atom instead. Below is an example: in the first image, 2/3 methyl groups have been added. Upon clicking to add the 3rd, a bond is made instead.


I recognize that this is a feature, not a bug, and that it doesn't seem like the most inconvenient thing in the world. However, when I'm "derivatizing" a complicated compound, it becomes cumbersome to manually hold and position the methyl groups. I also know that MolView is now deprecated, but thought this might be helpful in case anyone picks up this project in the future.

MolPad remove disconnected neighbor atoms should only apply to hydrogen atoms

When you erase an atom, all neighbors which were only connected to this atom are also erased. This is annoying when you didn't want to erase the disconnected atom at all. Therefore this behavior should be restricted to hydrogen atoms.

License

I would like to use this on my site. What are the license terms?

Thanks

NMRdb integration is broken

The API has changed. You now need to supply a script parameter. E.g.: https://script.epfl.ch/script/Service/20160510/vDpGux3hsy?smiles=C1%3DCC%3DCC%3DC1

NIST webpages are no longer parsed correctly

It is possible that there are minor changes in the NIST page format, but that actually seems unlikely.

Redesign MolView logo

The MolView logo must be redesigned to be unique in the cosmos (all that is, or ever was, or ever will be) The current logo will temporarily be replaced with a blank logo.

Brief history

The MolView logo was changed two times so far. From a benzene ring to a ball and stick logo. And from the ball and stick logo to a flatter variant of the ball and stick logo. The ball and stick logo looks too much like the RasMol logo and will therefore, again, be replaced with a new logo.

Where to find the logo's

A list of all places where the MolView logo is currently used.

• MolView 2.x top-left corner
• MolView 2.x shortcut icon
• MolView 2.x splash pop-up
• MolView 2.x info pages
• MolView blog title
• MolView blog shortcut icon
• MolView GitHub wiki page footer
• YouTube branding
• Avatar for several user accounts
  • Chrome Web Store
  • Facebook
  • Google+
  • GitHub
  • GitLab
  • Twitter
  • YouTube
  • Gmail: [email protected]
  • Wordpress: [email protected]

Molview's Backend Seems to Be Overflowed

I'm trying to access molview.com but I am reaching an error:

503 Backend fetch failed

I'd appreciate if you could look into it.

Edit: It seems to be back up now. I was wondering, is there a certain amount of requests that cause it to be overflowed? I love the models, and I wanted to embed some models in my website, and I don't want the server to be overflowed.

Links not rendering in information cards view.

I believe, the text (highlighted) is supposed to be rendered as hyperlinks.

Self-host fonts

By self-hosting FontAwesome and Open Sans we make sure that MolView looks the same everywhere (in China Google Fonts is blocked).

Scalable embedding endpoint

To make the embed API backwards compatible, it needs a more scalable endpoint. The modifications that are required to install the embedding API on such an endpoint have been done already. The current embedding API will be made available under: embed.molview.org/v1/*. This new endpoint still has to be implemented in the embedding dialog.

Trans isomers not resolved correctly when implicit hydrogen atoms are added

A structure diagram of trans-1,2-dichloroethene containing all implicit hydrogen atoms is resolved into in a cis-1,2-dichloroethene molecule instead of the trans isomer. Removing the implicit hydrogen atoms from the structure diagram solves the issue. I suspect this is a bug in the Ketcher SMILES generator which means it cannot be fixed easily.

With implicit hydrogen	Without implicit hydrogen
Produces C(/[H])(/Cl)=C(/[H])\Cl	Produces C(/Cl)=C\Cl
Trans configuration is ignored	Trans configuration if retained

Use Chemical Identifier Resolver via HTTPS

The Chemical Identifier Resolver will move to a new infrastructure during the last week of December 2015 as announced in this note on their website.

The CACTUS web server will move to a significantly reconfigured system on new hardware by the end of the year. This move is planned to take place during the last week of December 2015. This move will also entail a change of the host's IPv4 address. Concurrent with the cut-over, the HTTPS protocol will be enabled for all services. Both HTTP and HTTPS will be supported in parallel for a transition period. We plan to turn off HTTP permanently by end of March 2016. Disruptions to users caused by the move should be minimal. If you encounter any bugs or different behavior starting 1/1/2016, please let us know immediately.

The implementation of the Chemical Identifier Resolver should also start using HTTPS after the CACTUS web server has succesfully enabled it.

Failed to load structure error for COD

Hi Herman

Recently stumbled upon MolView. Very impressive! I have even managed to build (latest from github) without obvious error. Everything seems to be working with one exception. Attemping to load crystal structures (e.g. Pyrite, Halite) from COD throws a 'Failed to load structure' error. All works fine on molview.org.
Any suggestions as to what may be going wrong?
Thanks
Geoff

Not an issue, just need help

Can I ask for help on installing this whole thing. I'm new to coding and I'm definitely stuck because I do not understand the instructions in readme.md. I hope someone could help me because I need the whole thing for our classroom instruction in Chemistry. We are not allowed to use the internet during class instruction, and I believe this thing is the most user-friendly.

Thank you so much!

Description meta with HTML tags breaks page

The description from PubChem for CID=6115 contains HTML tags. This breaks http://molview.org/?cid=6115 To solve this issue the string must be encoded. However, this raises the question whether PubChem descriptions are, at all, suitable for MolView in the future.

Is it possible to flip or rotate 2D molecules?

Hello,

I was wondering if there is a way of rotating ro flipping 2D molecule models.

Best,

Upgrade to PHP 8

It appears an upgrade to PHP 8 is not trivial. I want to remove unneeded PHP components from this repository and make sure it runs on PHP 8.

Export STL files

This is more of a feature request than an issue. Is there any way to export the 3D model in STL format or something similar?

SMILES export for MolView?

This repository ... is not actively maintained due to lacking financial support.

Sad to hear!

I just stumbled over MolView and OpenChemLib: https://cheminfo.github.io/openchemlib-js/examples/Editor.html

MolView's interface is amazing. The only thing missing seems to be a SMILES Export. Could this essential thing be added?

SMILES import exists as I could see in the code.

Update or remove advanced RCSB Search

The legacy RCSB API is no longer available, but it is still used by the advanced search feature in MolView.

Rename this repository to `molview-old`

MolView 3 will be built from the ground up again. Therefore this repository has to be renamed to molview-old so that a new repository can be initialized under https://github.com/molview/molview.git for the development of MolView 3. Please star this new repository if you want to follow the development of MolView 3.

Embedding broken on Chrome

Test site: https://sites.google.com/site/molviewdemo/

Uncaught DOMException: Failed to read the 'localStorage' property from 'Window': Access is denied for this document.

It may be easier to completely replace the embedding page with a new one already, since I'm planning to do so anyway. This could be a separate JS file.

undefined color for some elements in the periodic table causes glitch in MolPad

If you add an element with an undefined color to a molecule in MolPad, the following error will occur:

Uncaught SyntaxError: Failed to execute 'addColorStop' on 'CanvasGradient': The value provided ('undefined') could not be parsed as a color.

The PubChem REST API may return a 404

This only occurs in special cases, for example when trying to match mineral names to PubChem records, so it is not critical. But the loader should handle this gracefully.

Embed 2D Canvas

Hi! I love the work you're doing with this project. I'm thinking about using it for something school related, do you know if its possible to embed 2D diagrams of the molecules?

Use it in combination with python

Hi, I would like to use molview to draw molecules and, at the same time a python script is running in the background (or after finish the draw pressing a submit bottom) calculating some properties of the drawn molecule. How can I do that (if possible) with MolView. Thanks in advance!

Some MIME types and file extension of exported files ignored in Chrome

Google Chrome seems to replace the MIME type and file extension of exported files (you can download the source file of the current 3D model using the Tools > Export menu) In Google Chrome 40.0.2214.111 the .mol and .cif file extensions are replaced with .bin while .pdb is retained. Google Chrome and Firefox 35.0 both seem to replace the chemical/* MIME with plain/text I haven't tested in other browsers yet. This seems to be either a browser dependent issue or a bug in FileSaver.js

PubChem image SVG filter makes image blank on Firefox

On Firefox, the SVG filter that is used to make the background of PubChem images white, causes the entire image to become white.