mdtraj/mdtraj 1.11.0

on GitHub

1.11.0 (June 24, 2025)

• Test on Python 3.13 by @jeremyleung521 in #1973
• Set up cibuildwheel by @mattwthompson in #1980
• Remove scipy import in _lprmsd.pyx to make mdtraj submodules importable without scipy by @rjdirisio in #1988
• Run OpenMM tests on CI by @mikemhenry in #1986
• Add flaky/rerun-failures to tests that require pulling off a PDB by @jeremyleung521 in #1987
• Add logo in SVG by @janash in #1989
• Add type annotation to Topology class by @jchen0506 in #1977
• Remove netCDF4 dependency, set up PyPI build variants by @jeremyleung521 in #2000
• Allow ArcTrajectoryFile to optionally take topology by @jeremyleung521 in #2002
• Add formal charge to the to_dataframe() and from_dataframe() methods by @jchen0506 in #2007
• Fix atom_slice resSeq assignment and add HSD/HSE residue names by @huhlim and @jeremyleung521 in #2013
• Unpin sphinx by @janash in #2016
• Move RNG/ptraj generation for distance tests into fixture by @jeremyleung521 in #1999
• Refactor: remove arbitrary arguments from AST module classes by @RobertArbon in #2009
• Update note on project status by @janash in #2019
• Fix Topology double-loading for HDF5 and MOL2 (+ remove false-positive UserWarning) by @jeremyleung521 in #2012
• Feature: calculate Pi-stacking+T-stacking interactions given aromatic groups by @rjdirisio in #1984
• Sort bonds to avoid make_molecules_whole failures by @eruijsena in #1929
• Test Linux aarch64 by @jeremyleung521 in #1974
• Allow mdtraj.rmsd() to calculate without alignment by @jeremyleung521 in #2011
• Update formatters by @mattwthompson in #2022
• Bugfix: delete_atom_by_index updates bond list by @RobertArbon in #2021
• Preserve chain_id when creating topologies by @k9cdt in #2015
• Add nucleic and is_nucleic atom selection PR by @dwhswenson and @janash in #2023
• Remove header option from PDB writer by @cabb99 in #2034
• Port PDBx/mmCIF Reader/Writer from OpenMM to MDTraj by @cabb99 in #2004
• Add formal charge in missing places on topology by @janash in #2038
• Hotfix for numpy 2.3 by @jeremyleung521 in #2045
• Update dcdplugin.c by @reedharrison and @bennybp in #1771
• Update unitcell.py to check if unitcell is valid by @jeremyleung521 in #2029
• Drop Python 3.10 support by @jeremyleung521 in #2046
• Add py3dmol visualization to pi stacking by @janash in #2020
• Allow HDF5TrajectoryFile().topology = None by @jeremyleung521 in #2042
• Limit warnings in tests by @jeremyleung521 in #2047

A total of 14 people contributed to this release.
People with a "+" by their names contributed to MDTraj for the first time.

• Jeremy Leung
• Matt. W. Thompson
• Ryan DiRisio
• Mike M. Henry +
• Jessica A. Nash
• Jing Chen +
• Lim Heo +
• Lex O'brien +
• Enrico Ruijsenaars +
• Da Teng
• David W.H. Swenson
• Carlos Bueno +
• Reed Harrison +
• Benjamin P. Pritchard +