Update dependency mdtraj to v1.11.1

[renovate]

This PR contains the following updates:

Package	Update	Change
mdtraj (source)	patch	1.11.0 → 1.11.1

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Release Notes

mdtraj/mdtraj (mdtraj)

v1.11.1

Compare Source

1.11.1 (January 15, 2026)

• Update pypi upload trigger by @​janash in #​2054
• Speedup some cython functions by enforcing nogil for exceptions (add return code) by @​jeremyleung521 in #​2049
• Minor bug fix for documentation equations by @​shehan807 in #​2060
• Drop numpy1 from testing/support, not building freethreading wheels, build linux-arm64 wheels by @​jeremyleung521 in #​2066
• Add support for "standard_names" keyword argument to Amber prmtop reader by @​CharlieLaughton in #​2057
• Fix docstring typo in compute_directors by @​ctk3b in #​2073
• Update dependabot weekly and pre-commit monthly by @​jeremyleung521 in #​2081
• Fixed typos and did minor reorganization in hdf5 docs by @​MrMultiMediator in #​2082
• Avoid linear search in topology subsetting by @​jgullingsrud in #​2085
• Updating macos-13 runner to macos-15-intel by @​jeremyleung521 in #​2088
• Python3.14 testing and building by @​jeremyleung521 in #​2089
• Official release of python 3.14 by @​jeremyleung521 in #​2090
• Fix pyparsing Deprecations by @​jeremyleung521 in #​2097
• Formal Charge from Mol2 Files by @​jeremyleung521 in #​2093
• Rewrite trajectory.py topology parsing with match/case by @​jeremyleung521 in #​2094
• Use repeated bonds in PDB CONECT records to increase bond orders (REMAKE of #​1848) by @​jeremyleung521 in #​2083
• Simplify testing on python 3.14 (with openmm) by @​jeremyleung521 in #​2091
• Move all rcsb url downloads to https by @​jeremyleung521 in #​2106
• Add bond metadata (order and type) and formal charge to HDF5 by @​janash in #​2101
• Addressing some issues with save_cif by @​darianyang in #​2103
• Fix to allow mdtraj.load() to load urls ending with pdb file extensions by @​jeremyleung521 in #​2115
• Update PyParsing deprecations by @​mattwthompson in #​2117

A total of 9 people contributed to this release.
People with a "+" by their names contributed to MDTraj for the first time.

• Jeremy Leung
• Jessica A. Nash
• Shehan Parmar +
• Charlie Laughton
• Christoph Klein
• MrMultiMediator +
• Justin Gullingsrud +
• Darian Yang +
• Matt. W. Thompson

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