mdanalysis

mdanalysis copied to clipboard

Adding Appending Functionality to Writers

1

## Current Writer API ## ```python # option 1 AtomGroup.write(filename,..., **kwargs) # option 2 with mda.Writer(filename, n_atoms) as w: for ts in Universe.trajectory: w.write(AtomGroup) ``` ## New API (`append=False` in...

yuxuanzhuang

Is there anyway to specify the frame slicing range when creating a Universe object?

lucl13

As noticed recently, the 32bit windows azure runner has been failing. This appears to stem from a mix of the recent scipy 1.9.2 release which no longer providing win32 wheels,...

IAlibay

Hbond update

3

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...

jaclark5

Add dipole and quadrupole caclulation in AtomGroup

2

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...

jaclark5

Ensure Timestep in ChainReader is updated for multiple trajectory files

4

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....

jaclark5

Lammps Dump Parser

1

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 -...

jaclark5

hanging while reading in gromacs trr trajectory

9

## Expected behavior ## quick loading of GROMACS universe with trr trajectory into MDAnalysis ## Actual behavior ## it hangs indefinitely in some internal process and is resistant to Ctrl^C...

dkonstan

WIP, CI: 3.11rc2 check

6

* Python 3.11rc2 is guaranteed ABI stable with the final release per: https://www.python.org/downloads/release/python-3110rc2/ * the final release is about two weeks away, so let's see what goes wrong with `3.11`...

tylerjereddy

MAINT: Cython lint

3

I saw [`cython-lint`](https://github.com/MarcoGorelli/cython-lint) [used successfully upstream](https://github.com/scipy/scipy/pull/17014) and ran it on MDAnalysis out of curiosity (below). Maybe some straightforward fixups we could accept. `cython-lint MDAnalysis/lib/*.pyx MDAnalysis/coordinates/*.pyx MDAnalysis/analysis/encore/*.pyx` ``` MDAnalysis/lib/c_distances.pyx:38:24: 'fabs' imported...

tylerjereddy