Jennifer A Clark
Jennifer A Clark
## Expected behavior ## After creating a universe with multiple trajectory files, and a series of transformations are applied following the protein example. Those transformations are expected to be applied...
Fixes #3847 Changes made in this Pull Request: - Added warning when distance or angle cutoffs produce zero hbonds to clarify a returned value of NaN - Guess_donor uses bonding...
Fixes #3841 Changes made in this Pull Request: - Added dipole and quadrupole moments to AtomGroup topology methods PR Checklist ------------ - [X] Tests? - [X] Docs? - [X] CHANGELOG...
Fixes #3657 Changes made in this Pull Request: - If statement in transform added to ensure that the provided Timestep class is the same used in the Atom Group trajectory....
Fixes ##3843 #3741 Changes made in this Pull Request: - Allow box translation upon importing LAMMPS dump file - Allows coordinates to be unwrapped with dump file image flags -...
## Expected behavior ## - Append to an XYZ file ## Actual behavior ## - The write mode is restricted to "wr" ## Code to reproduce the behavior ## ```...
Fixes #3836 Changes made in this Pull Request: - Add key word argument to XYZWriter to allow users to specify the mode with which to open an XYZ file (default...
## Is your feature request related to a problem? ## LAMMPS trajectories can be written in two way, (1) xu yu zu in dump to allow diffusion coefficients to be...
Fixes #3546 Changes made in this Pull Request: - Added a CONCEPT for how to fix this issue with a base.ReaderBase method. Note that the overwritten method in the LAMMPS...
## Is your feature request related to a problem? ## It would be convenient to obtain the dipole or quadrupole moment of a group or compounds within a group. ##...