Visualisations and trajectories

galaxycomputationalchemistry / galaxy-tools-compchem

:mega: Galaxy Tools for Computational Chemistry

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Visualisations and trajectories #33

Open chrisbarnettster opened 5 years ago

chrisbarnettster commented 5 years ago

We need something to do this, otherwise it is easy to leave galaxy.

An interactive env, tool? what are the options?

@simonbray

simonbray commented 5 years ago

Need to develop NGLviewer further.

Some 2D viewer for chemical structures - something like this -> http://molview.org/

chrisbarnettster commented 5 years ago

Ok great! Also maybe something for docking to view the docking search space box when using autodock.

nglviewer - http://nglviewer.org/ngl/ molview - http://molview.org

chrisbarnettster commented 5 years ago

what about other formats? Current viewer should be able to read pdb, gro, xyz etc/

chrisbarnettster commented 5 years ago

@simonbray Dan Blankenberg's interactive envs also look like a great option. Can you think of any tools that are on docker - e.g. avogadro, autodock tools viewer or similar?

bgruening commented 5 years ago

http://nglviewer.org/ngl/api/manual/file-formats.html#sdf SDF should be supported. Is our version just too old?

chrisbarnettster commented 5 years ago

Yes it is supported. minor mod to Galaxy is needed. https://github.com/galaxyproject/galaxy/issues/8278