MDAnalysis/mdanalysis

Port Coordinates test to new BaseReader/Writer Test classes 9 days ago

help wanted maintainability testing refactoring GSOC Starter

1.6K

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Python

#computational-chemistry#mdanalysis#molecular-dynamics#molecular-dynamics-simulation#molecular-simulation#python#science#trajectory-analysis

asv: refine tests with PBC/no-PBC 4 months ago

help wanted performance testing PBC benchmarks

MDAnalysis/mdanalysis

1.6K

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Python

#computational-chemistry#mdanalysis#molecular-dynamics#molecular-dynamics-simulation#molecular-simulation#python#science#trajectory-analysis

Add support for @<TRIPOS>CRYSIN MOL2 records 5 months ago

AI Summary: This issue proposes adding support for `@<TRIPOS>CRYSIN` records within MOL2 files to enable the parsing of unit cell dimensions. Currently, the software does not read these crystallographic dimensions from MOL2 files, and this feature would allow for the extraction of such information. The task involves identifying and processing this specific section within the existing MOL2 file parser.

Complexity: 3/5

help wanted Component-Readers Format-MOL2

MDAnalysis/mdanalysis

1.6K

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Python

#computational-chemistry#mdanalysis#molecular-dynamics#molecular-dynamics-simulation#molecular-simulation#python#science#trajectory-analysis

[DOC] doctest MEGA-issue 5 months ago

help wanted Component-Docs Difficulty-easy good-first-issue

MDAnalysis/mdanalysis

1.6K

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Python

#computational-chemistry#mdanalysis#molecular-dynamics#molecular-dynamics-simulation#molecular-simulation#python#science#trajectory-analysis

Mismatch in groupselections for RMSD between target and reference 5 months ago

help wanted Component-Analysis Difficulty-easy GSOC Starter

MDAnalysis/mdanalysis

1.6K

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Python

#computational-chemistry#mdanalysis#molecular-dynamics#molecular-dynamics-simulation#molecular-simulation#python#science#trajectory-analysis

Create `sugar` or `carbohydrate` selection using GLYCAM nomenclature 7 months ago

enhancement help wanted Component-Selections Difficulty-easy

MDAnalysis/mdanalysis

1.6K

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Python

#computational-chemistry#mdanalysis#molecular-dynamics#molecular-dynamics-simulation#molecular-simulation#python#science#trajectory-analysis

`MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel`: Implement parallelization or mark as unparallelizable 7 months ago

help wanted Component-Analysis parallelization

MDAnalysis/mdanalysis

1.6K

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Python

#computational-chemistry#mdanalysis#molecular-dynamics#molecular-dynamics-simulation#molecular-simulation#python#science#trajectory-analysis

missing test for LAMMPS DumpReader for ValueError when missing coordinates 7 months ago

help wanted testing format-LAMMPS

MDAnalysis/mdanalysis

1.6K

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Python

#computational-chemistry#mdanalysis#molecular-dynamics#molecular-dynamics-simulation#molecular-simulation#python#science#trajectory-analysis

Use native scipy periodic KDTree for orthorhombic boxes? 8 months ago

help wanted performance PBC

MDAnalysis/mdanalysis

1.6K

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Python

#computational-chemistry#mdanalysis#molecular-dynamics#molecular-dynamics-simulation#molecular-simulation#python#science#trajectory-analysis

confusing error message from DSSP for too short peptide stretches 8 months ago

help wanted Component-Docs Component-Analysis

MDAnalysis/mdanalysis

1.6K

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Python

#computational-chemistry#mdanalysis#molecular-dynamics#molecular-dynamics-simulation#molecular-simulation#python#science#trajectory-analysis

Issue with `verbose=False` in `EinsteinMSD` 9 months ago

help wanted defect Component-Analysis

MDAnalysis/mdanalysis

1.6K

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Python

#computational-chemistry#mdanalysis#molecular-dynamics#molecular-dynamics-simulation#molecular-simulation#python#science#trajectory-analysis

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