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PDB reader does not recognize unit cell

bug

Status: Open.

Bug

#2136 In mdtraj/mdtraj;

· k9cdt opened on Feb 9, 2026

Allow mdtraj.load()/SDF loader/CIF loader to directly open files via urls

apiFor changes to the way the user interacts with the codebaseFor changes to the way the user interacts with the codebase

good-first-issueFor changes suited to a first-time contributorFor changes suited to a first-time contributor

wishlist

Status: Open.

Feature

#2118 In mdtraj/mdtraj;

· jeremyleung521 opened on Jan 5, 2026

Reading other properties from mmCIF files (e.g. DSSP predictions)

Status: Open.

#2105 In mdtraj/mdtraj;

· rachitk opened on Nov 19, 2025

Improving Mol2 reader

apiFor changes to the way the user interacts with the codebaseFor changes to the way the user interacts with the codebase

Status: Open.

Feature

#2098 In mdtraj/mdtraj;

· jeremyleung521 opened on Oct 27, 2025

Python Freethreading in future Python versions (3.13+)

dependenciesPull requests that update a dependency filePull requests that update a dependency file

prio-high

Status: Open.

Feature

#2063 In mdtraj/mdtraj;

· jeremyleung521 opened on Jul 25, 2025

Incomplete hash methods in Topology class

Status: Open.

#2039 In mdtraj/mdtraj;

· janash opened on Jun 3, 2025

Topology.delete_atom_by_index can create inconsistency between topology and trajectory data

Status: Open.

#2025 In mdtraj/mdtraj;

· janash opened on May 17, 2025

Revival of the "within" keyword for atom selection

apiFor changes to the way the user interacts with the codebaseFor changes to the way the user interacts with the codebase

wishlist

Status: Open.

Feature

#2024 In mdtraj/mdtraj;

· jeremyleung521 opened on May 16, 2025

Memory not released when reusing Trajectory variable – possible cyclic references or missing explicit cleanup

Status: Open.

#2005 In mdtraj/mdtraj;

· turcinv opened on Mar 22, 2025

Including additional arrays in H5MD trajectory files?

Status: Open.

#1955 In mdtraj/mdtraj;

· orionarcher opened on Dec 2, 2024

_ZSt28__throw_bad_array_new_lengthv

Status: Open.

#1954 In mdtraj/mdtraj;

· weigcdsb opened on Nov 29, 2024

UnicodeEncodeError: 'ascii' codec can't encode characters in position 12-16: ordinal not in range(128)

Status: Open.

#1953 In mdtraj/mdtraj;

· AthenACHY opened on Nov 29, 2024