List of extensions

Max Linke edited this page Nov 10, 2017 · 10 revisions

MDAnalysis uses lots of extensions, below is a list of them and their readiness for Python 3

Extension Description Language Python 3 ready? Solved in
coordinates._dcd DCD format reader CPython No (Cpython api changed) done
coordinates.dcdtimeseries Timeseries for DCD Cpython No (as above) removed
lib._distances Distance calculations C / Cython Yes? done
lib._distances_openmp Parallel of above C / Cython Yes? done
lib.parallel.distances More parallel distances Cython Yes?? #530
lib.qcprot RMSD via QCP Cython Yes? done
lib._transformations Coordinate transformations C/CPython Probably (#401) done
lib.KDTree._KDTree KDTree for distance searches CPP/SWIG yes (originally no #383) 395 (now using Biophyton)
coordinates.xdrfile Gromacs format reader C/Swig No (#211) 441

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Labels: python, molecular dynamics, analysis, DCD, CHARMM, LAMMPS, NAMD, Gromacs, computer simulation, atoms, coordinates, trajectory, XTC, Library, object-oriented
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