Hbonds output formats - Githubissues

uibcdf / MolSysMT

Open source library to work with molecular systems

https://www.uibcdf.org/MolSysMT/

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Hbonds output formats #22

Open dprada opened 3 years ago

dprada commented 3 years ago

What would be the best way to encode the list of hydrogen bonds found in a trajectory?

A dictionary of lists (with frame indices where the bond was formed)
A sparse tensor (3d with the library "Sparse")
An array of arrays with different shape (number of frames x lists of detected hbonds)
A list of sparse matrices (as mdtraj)
A native Hbond class where the info is stored as a sparse tensor with methods to be able to access quickly to different formats.
...

This is not clear now.

dprada commented 3 years ago

Let's take a temporary decision... To postpone this for a MolSysMT version > 1.0.