27 projects
pathsimanalysis
Calculates the geometric similarity of molecular dynamics trajectories using path metrics such as the Hausdorff and Fréchet distances.
MDAnalysis
An object-oriented toolkit to analyze molecular dynamics trajectories.
MDAnalysisTests
MDAnalysis testsuite
basicrta
A package to extract binding kinetics from molecular dynamics simulations
imdclient
Receiver for IMD v2 and v3 data from simulation engines like Gromacs, LAMMPS, and NAMD
propkatraj
Obtain pKas for titreatable residues from a simulation trajectory.
MDPOW
A library for computing solvation/water partitioning coefficients using molecular dynamics simulations
alchemlyb
the simple alchemistry library
GromacsWrapper
A Python wrapper around the GROMACS tools.
numkit
numerical first aid kit
pytng
Minimal Cython wrapper of the TNG trajectory library
kda
Kinetic Diagram Analysis tools
waterdynamics
Analysis of water dynamics in molecular dynamics trajectories and water interactions with other molecules.
pyedr
Read Gromacs EDR files.
mdaencore
Ensemble overlap comparison software for molecular data.
MDAnalysisData
MDAnalysis example data
mdanalysis-sphinx-theme
Modification to sphinx_rtd_theme
GridDataFormats
Reading and writing of data on regular grids in Python
mda-xdrlib
Stand-alone XDRLIB module (from cpython 3.10.8)
alchemtest
the simple alchemistry test set
alchemistry-flamel
A command line interface (CLI) to alchemlyb.
distopia
Fast distance calculations using explicitly vectorised SIMD
multibind
A package to find optimal state free energies from a thermodynamic graph.
pybol
A library for assembling predefined states of files and directories
RotamerConvolveMD
Analysis of spin label distances over structural ensembles
pmda
Parallel Molecular Dynamics Analysis tools
RecSQL
Treat SQLite tables as recarrays
