Guillaume Fraux

Trajectory NG

1

| File Type | binary | | --- | --- | | Topological information | ??? | | Positions | Yes | | Velocities | Yes | Reference http://dx.doi.org/10.1002/jcc.23495

Using a selection like `water or name Na` could be nice. This need to predefine a group of atoms as "water". I do not know how to do this, it...

Remove need for a miniconda installation ?

21

It could be feasible to parse directly the metadata in the `info` folder to resolve the dependencies directly in Julia. Pro: - Remove the need for a full miniconda installation,...

Use template classe for extraction of values ?

2

The interface would be nicer if we could do ``` cpp auto out = args["--output"].as(); auto num = args["--num"].as(); ``` instead of ``` cpp auto out = args["--output"].asString(); auto num...

This also requires julia>=1.6 to enable Apple ARM64 CPU (https://github.com/chemfiles/Chemfiles.jl/issues/56)

Write an example/recipe for going from structure to chemiscope input

1

There should be an example (maybe in https://github.com/cosmo-epfl/kernel-tutorials/) on how to go from structure to chemiscope, using SOAP and PCA (maybe KPCovR).

There are a lot of ML applications working with topological description of molecules (only atoms & bonds between them), an it would be nice to allow them to use chemiscope...

Add ribbon representation in structure viewer

2

This is a popular representation for bio-molecules, in particular proteins, supported by both JSmol and 3Dmol.js. Two separate people asked for us to support this! This kind of representation requires...

This would allow to look at the evolution of a property in a dataset, in particular trajectories from simulations. This is already achievable by adding a `index` property, and then...

The idea would be to add the ability to show vector properties as arrows, and rank-2 tensorial properties as ellipsoïds, à-la shiftml.org. Additionally, we could represent scalar properties using colors...