Support for DTR files

Open jmintser opened this issue 5 years ago • 1 comments

It would be great to support Desmond trajectories. Perhaps this could just be done via VMD's molfiles plugins? Here are some examples trajectories:

MDtraj uses a tiny one in its tests: https://zenodo.org/record/883901/preview/mdtraj/mdtraj-1.9.0.zip#tree_item361

https://zenodo.org/record/3663046#.X141BfL_p24

https://zenodo.org/record/3248885#.X14z9_L_p24

Sep 13 '20 15:09 jmintser

Copy-pasting my comment from gitter:

After digging a bit more in the VMD dtrplugin code, it seems that it support more than what is exported through the VMD API, and it would make sense to extract https://github.com/chemfiles/molfiles/blob/chemfiles/src/dtrplugin.hxx and https://github.com/chemfiles/molfiles/blob/chemfiles/src/dtrplugin.cxx and use them directly. In particular, they support reading only part of the trajectory, which helps reducing the amount of memory required.

This would workaround the issues we have with VMD plugins, cf #370.

Sep 13 '20 15:09 Luthaf