BFedder

AuxReader for EDR Files

7

Fixes #3629 With ~~panedrlite now closer to~~ pyedr now being a thing, and the actual code itself less likely to still change, I have now finally started work on the...

## Is your feature request related to a problem? ## Many of the analysis tools MDAnalysis provides return their results in the form of NumPy arrays. Linking these results to...

Add energy readers to the Auxiliary module

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## Is your feature request related to a problem? ## In molecular dynamics simulations, users frequently have to inspect energy-like terms such as potential or kinetic energy, temperature, or pressure....

Implement an AuxReader that supports GROMACS EDR files

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## Is your feature request related to a problem? ## When running MD simulations, it is often desirable to plot 'energy' terms like the potential energy, temperature, pressure, etc. of...

LinearDensity should have more reliable tests

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## Is your feature request related to a problem? ## Currently, some of the tests in test_lineardensity.py are basically tautologies because the expected values the tests check against were obtained...

[WIP] NumPy AuxReader

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Fixes #3750 This is very much a work in progress, so far only the very barest of skeletons is present. PR Checklist ------------ - [ ] Tests? - [ ]...

define method calc_representative() for averages of auxiliary data in the AUXReader

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## Is your feature request related to a problem? ## The AuxReaders have a `calc_representative` method which returns a representative value of the auxiliary data for any given time step....

Change order of arguments for adding auxiliary data for 3.0 release

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## Is your feature request related to a problem? ## Currently, auxiliary data is added as such: ```python aux = mda.auxiliary.EDR.EDRReader(edr_file) u.trajectory.add_auxiliary(aux_spec, aux) ``` i.e. ```python u.trajectory.add_auxiliary({"temp": "Temperature"}, aux) ```...