-
Notifications
You must be signed in to change notification settings - Fork 94
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Implementing TRR/XTC/NetCDF/DCD support w/o MDTraj #613
Comments
I reached out to the |
Additionally, the two other common trajectory formats, netCDF and DCD, are also supported now with biotraj. |
Biotraj will directly work as a "drop-in replacement" for MDTraj in Biotite, so changes should remain limited |
@JHKru Could you comment in conda-forge/staged-recipes#27312, that I can add you as Conda package maintainer? |
Closed via #627 |
Currently Biotite requires MDTraj as additional dependency only for reading coordinates from trajectory files. However, MDTraj does not support NumPy 2.0, yet, but Biotite 1.0 will require NumPy 2.0. Therefore we could think about removing the dependency by implementing at least the common trajectory file formats
.trr
and.xtc
. Lowering the number of dependencies would also make Biotite more lightweight.To resolve this issue,
TrajectoryFile
classes need to be removed,.trr
and.xtc
(maybe instructure.io.trr
?) andTaking verbatim code from https://github.com/mdtraj/mdtraj is not possible due to the incompatible license.As the
xdrfile
C-library is also GPL licensed, the entire Trajectory code would need to go into a separate extension package, if we decide to drop the MDTraj dependency.The text was updated successfully, but these errors were encountered: