[*Feature request*] output pairwise vectors between two groups of coordinates

[ruihao99]

Hello, MDAnalysis development team.

In the MDAnalysis package, function 'calc_bonds' in 'MDAnalysis.lib.distances' provides an excellent way to calculate distances between two groups of coordinates. However, the vector of each coordinate pair is also useful for angle calculations, but the original function does't output these vectors. Would you like to add this feature to future release of MDAnalysis or distopia?

[hmacdope]

Hi @ruihao69! Welcome to distopia!

If you are looking to calculate angles the MDAnalysis.lib.distances.calc_angles function at https://docs.mdanalysis.org/1.1.1/documentation_pages/lib/distances.html is your best friend. We are currently working on a fast version of the angle code for distopia.

To obtain the vectors themselves, you can use a setup similar to https://www.mdanalysis.org/MDAnalysisTutorial/trajectories.html

In terms of outputting the vectors, they are not useful per se apart from calculating bond, angle and dihedral values. If you need to use the vectors in your own work, you will need to write a similar function to the one in the tutorial above and use some linear algebra!

Let me know if you have any questions :)