Jmol visualiser

[subindev-d]

Added a visualizer for molecular structure files, using jsmol library.
Source of the contents in the static directory is from the original source of Jmol, which is part of the pull request but included from the source as it it.
Screenshot of the visualizer:

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  1. upload the follwing files and visualizeit cif file, pdb file

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

[bgruening]

Oh very cool! Thanks a lot @subindev-d!

Do you know Mol* , would that also be interesting for you use-case?

[subindev-d]

Oh very cool! Thanks a lot @subindev-d!

Do you know Mol* , would that also be interesting for you use-case?

This one looks interesting, I'll have a look thanks.

[guerler]

Thank you for working on this. There is one issue with this PR. We recently moved away from committing visualization specific scripts directly into the repo. The Galaxy Visualization XMLs allow installing npm dependencies using the <requirements> tag.

<requirements> <requirement type="npm" version="0.0.1" package="your_npm_package"/> </requirements>

Just make sure that the npm run build command produces a static or dist/static directory with your js-script files. By moving the js-script files out of the Galaxy repo, we ensure proper versioning of visualization plugins and keep the core repo size at bay. Examples for this approach are the msa and ngl viewers.

Please let me know if you have any questions or need further assistance.

[hechth]

@subindev-d this looks very cool, which file types are you supporting?

Also, let me know if you are interested in Mol*.

[subindev-d]

@subindev-d this looks very cool, which file types are you supporting?

Also, let me know if you are interested in Mol*.

@hechth , this pr was for cif and pdb files. As mentioned in the above now thread, Galaxy now only accept npm dependencies, so I am also looking into the alternatives. I'm mainly developing this for CIF files, have not tested Mol* with CIF files, if it works fine, I'm interested to implement the same using Mol*