MDAnalysis/mdanalysis
MDAnalysis is a Python library to analyze molecular dynamics simulations.
PythonNOASSERTION
Issues
- 7
- 5
`H5MDReader/Writer` undocumented limitations
#4561 opened by edisj - 4
Downloading / Streaming Trajectories from MDDB
#4603 opened by BradyAJohnston - 10
- 0
AlignTraj doesn't accept writer kwargs
#4564 opened by ljwoods2 - 9
- 0
Unpin mypy rdkit version
#4581 opened by IAlibay - 3
- 0
Explore solutions for codecov upload failures
#4576 opened by RMeli - 3
- 5
Use a single warning interface.
#4593 opened by mtessmer - 5
- 0
Add example for writing to NamedStream StringIO buffer
#4583 opened by hmacdope - 10
macOS python3.11 fails to install `mdanalysis[all]` from git branch directly (not always though)
#4586 opened by marinegor - 4
- 6
- 1
- 2
Benchmark guessers with asv
#4577 opened by lilyminium - 1
Package tests failing due to normalilzation change
#4573 opened by IAlibay - 3
MAINT: test failures/segfaults against NumPy `main`
#4481 opened by tylerjereddy - 0
- 1
- 10
Incorrect psi values from DCD trajectory that has been rms aligned by cpptraj
#4505 opened by diogomart - 7
Incorrect data points occur when using lineardensity to calculate the linear density of a LAMMPS system.
#4476 opened by Tennisatw - 5
remove analysis.psa in 3.0
#4542 opened by orbeckst - 7
Merge 3.0 pending PRs
#4539 opened by IAlibay - 7
SEQRES writer
#4446 opened by smallfishabc - 1
remove MDAnalysis.visualization in 3.0
#4545 opened by orbeckst - 1
remove LeafletFinder in 3.0
#4544 opened by orbeckst - 2
remove analysis.helanal in 3.0
#4543 opened by orbeckst - 5
Running encores with multiple cores
#4538 opened by kmorisa - 0
remove analysis.waterdynamics in 3.0
#4541 opened by orbeckst - 1
- 4
[CI] Dependency resolution issues MDAnalysis installs
#4492 opened by IAlibay - 8
Aim for SPEC0 adherence over NEP29
#4536 opened by orbeckst - 5
Cannot load LAMMPS NetCDF trajectory files due to "header issue" in scipy.io.netcdf_file
#4444 opened by bbye98 - 2
- 3
Gromacs TPR file `u.atoms.ids` starts from 0
#4450 opened by HankewieDanke - 7
Change API docs logo?
#4430 opened by IAlibay - 0
Replace hole2 imports with mdakit-hole2 imports
#4414 opened by IAlibay - 1
Test timeout on multiprocessing Pool XTC test in CI
#4475 opened by hmacdope - 3
BLD: compile error with NumPy main and Cython 3.0.8
#4460 opened by tylerjereddy - 1
How to Maintain the Integrity of a System Containing Multiple Independent Chains Across PBC in MDAnalysis
#4449 opened by erwusht - 4
Python 3.12 deprecated SafeConfigParser
#4441 opened by nataliyah123 - 0
- 0
analysis.pca.PCA can't be run with `frames=...`
#4425 opened by marinegor - 4
In old `AnalysisBase` subclasses, `self._trajectory` is sometimes used instead of `self._sliced_trajectory`
#4432 opened by marinegor - 0
Electrostatic potential
#4427 opened by hanahg - 0
NEP29 - January 1st 2024 update
#4401 opened by IAlibay - 0
Using MDAnalysis in windows
#4405 opened by hanahg