Mdtraj Versions Save

An open library for the analysis of molecular dynamics trajectories

1.9.9

9 months ago

v1.9.9 (July 22, 2023)

  • Pin Cython~=0.29 in pyproject.toml (#1801)
  • Remove "stale" bot (#1758)
  • Announce maintainer update (#1795)
  • Use oldest-supported-numpy in pyproject.toml (#1751)

A total of 4 people contributed to this release, including three new contributors. People with a "+" by their names contributed a patch for the first time.

In-Ho Yi+ Sukrit Singh+ Jeremy Leung+ Matthew W. Thompson

1.9.8

10 months ago

v1.9.8 (July 2, 2023)

  • Patch util_arm.h for M1 (#1694)
  • Avoid side effects in mdtraj.load (#1706)
  • Add PDB chainID support (#1715)
  • Remove imports from simtk namespace (#1698)
  • Implement reading and writing PDBx/mmCIF (#1718)
  • Fix compute_inertia_tensor docstring (#1721)
  • Fix typo in docs (#1725)
  • Adds lower-level compute_distances_core function (#1728)
  • Implement generic C code paths for non-accelerated architectures (#1727)
  • Add note about project maintinance status (#1738)
  • Force new residue when creating new chain (#1740)
  • Warn if atom_indices are not monotonically increasing (#1766)
  • Delete notes in issue-template by (#1778)
  • Fix hashing when unitcell data is not present (#1781)
  • Test on Python 3.11 (#1758)
  • Constrain GSD to version 2 (#1790)

A total of 10 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

  • Robert T. McGibbon
  • Sander Roet
  • Peter Eastman
  • Charlie Laughton
  • Christoph Klein
  • Luca Naef +
  • Jacob Lumpkins +
  • Ray A. Matsumoto
  • Matthew W. Thompson
  • Moritz Hoffmann +
  • German P. Barletta +
  • Masataka Yamauchi +
  • Samuel Lotz +
  • Toni G +
  • Bojun Liu +

1.9.7

2 years ago

v1.9.7 (November 12, 2021)

  • Replace discourse link with gitter link (904338b799842c103dcb9e306e6878a739a4d39f)
  • Faster load function and more homogenous file parser interface (#1648)
  • Reduce memory usage of rdf_t (#1661)
  • Update to new OpenMM namespace (#1668)
  • Fix compute_contact bug with glycine sidechains (#1674)
  • Fix errors in RMSF documentation (#1676)
  • Handle path-like objects in place of filenames (#1680)
  • Pin NumPy in pyproject.toml for Python 3.10 (#1681)
  • Fix compilation errors on M1 Macs (#1684)
  • Update Python versions in CI (#1686)
  • Fix jupyter runners in CI (#1687)

A total of 10 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

  • Robert T. McGibbon
  • Sander Roet
  • Charlie Laughton +
  • Alexander Matthew Payne +
  • Tucker Burgin +
  • Maurice Karrenbrock
  • Luca Naef +
  • Jacob Lumpkins +
  • Ray A. Matsumoto
  • Matthew W. Thompson

1.9.6

2 years ago

v1.9.6

  • Fix compatibility with all versions of astunparse (03753d736e30f15f8f210434e689e9ff664bb611)
  • Rework CI to be simpler and more maintainable
  • Fix deployment of the documentation to the website
  • Don't use serials for more than 1 chain (#1612)
  • Added enforcePeriodicBox option for HDF5Reporter (#1622)
  • Add time-dependent distance and RDF functions (#1633)
  • Add select option to compute_center_of_mass() (#1640)
  • Topology.join() can optionally updates resSeq of new residues (#1639)

A total of 7 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

  • Robert T. McGibbon
  • Sander Roet
  • Ray A. Matsumoto
  • Maurice Karrenbrock +
  • Kirill Shmilovich
  • Heyi Liang +
  • Matthew W. Thompson

(Special thank you to Matthew W. Thompson for putting together these release notes)

1.9.5

3 years ago
  • Fix memory allocation when opening XTC trajectory on OSX Catalina (#1594)
  • Write out serial instead of index in pdbs (#1584)
  • Fix residue idx sliced traj (#1586)
  • Update shift_wrappers.py (#1579)
  • Rsmd atom_indices checks fix (#1571)
  • Port to aarch64 (#1562)
  • Add compatibility with pandas 1.0

1.9.4

4 years ago
  • Update some pandas calls for v1.0 (#1536)
  • Fix TRR file offset (#1534)
  • Update selection for Python 3.8 compatibility (#1523)
  • Ensure bonds exist before using them (#1512, #1513)
  • Let compute_displacements handle empty atom_pairs (#1515)
  • Add GSD reader and writer (#1494)
  • Fix stride parameter for .netcdf files (#1501)
  • Ensure that the license file is packaged in the sdist (#1498)
  • Right-justify atom symbol when writing PDB files (#1459)
  • Add calculations for shape metrics (#1471)
  • Fix residue parsing in MOL2 reader (#1490)
  • Set up "stale" bot
  • Use AZP for CI (#1484, #1536)
  • Fix leaving malformed TRR files open (#1482)
  • Fix various OpenMP issues (#1476, #1477, #1488, #1508, #1529)
  • Add gyration tensor calculation (#1467)
  • Fix some type conversions (#1466, #1511)
  • Remove bundled dependencies astor and pyparsing (#1452)
  • Correct ordering in hoomdxml files (#1453)

1.9.3

4 years ago

  • Fix CI (#1416, #1420, #1444)

  • Add compute_center_of_geometry (#1405)

  • Fix a test failure in test_reporters.py caused by merge of #1431 (#1443)

  • Reporters no longer override user request to write unit cell information (#1431)

  • Add XTCReporter for OpenMM (#1403)

  • Avoid infinite recursion error in mol2 parser (#1426)

  • [formats/mol2] add more checks to element parsing (#1407)

  • Replace strip() with split() in mol2.py (#1378)

  • Use and set resSeq attribute in Topology.to_openmm() and from_openmm() (#1424)

  • fix parallel reduction error (#1419)

  • Fixes 'Buffer dtype mismatch' error on 64-bit Windows (#1409)

  • add RMSF analysis (#1414)

  • allow RMSD calls when ref_atom_indices and atom_indices are used (#1392)

  • Notebook tests: from __future__ must come first (#1401)

  • [setup] do not enforce clang/std++ on osx (#1400)

  • silence cython related numpy warnings (#1391)

  • Prep py37, some bugfixes (#1388)

  • Ensure 'bond_value' is a string (#1382)

  • fix typo in docs (#1381)

Authors

  • Carlos Hernández
  • John Chodera +
  • Jack Greisman +
  • jgilaber +
  • Sunhwan Jo +
  • Ray A. Matsumoto +
  • Robert T. McGibbon
  • João Rodrigues +
  • Shyam Saladi
  • Martin K. Scherer
  • David W.H. Swenson
  • Matthew W. Thompson +
  • Lee-Ping Wang

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

1.9.2

5 years ago

We're pleased to announce the release of MDTraj 1.9.2. This version has a number of bug fixes and improvements for trajectory parsing and conversion.

  • Fix bug in TINKER ARC reader (#1371)
  • Improved mdconvert error message (#1368)
  • Striding relative to current position in XTC and TRR (#1364)
  • Return last successful read frame for DCD (#1358)
  • Handle stride like numpy for DCDs (#1352)
  • Fix pickling of virtual site's element field (#1350)
  • Compile geometry extension with OpenMP (#1349)
  • Ensure correct dtype in neighborlist box vectors (#1344)
  • Added support for prm7 topology file extension (#1334)
  • Added efficient stride handling fo TRR (#1332)
  • Use byte offsets between frames for stride of XTCs (#1331)
  • Updated the calculation of chi5 (#1322, #1323)
  • Added testing against conda-forge channel (#1310)
  • Port OpenMM bond order representation into MDTraj. Implements the Bond class to Topology and updates the Mol2 reader to use bond_order field (#1308)

Authors

  • Carlos Hernández
  • Guillermo Pérez-Hernández +
  • Matthew Harrigan
  • Lester Hedges +
  • Robert T. McGibbon
  • Levi Naden +
  • Fabian Paul
  • Justin R. Porter
  • Martin K. Scherer
  • Xianqiang Sun +
  • David W.H. Swenson +
  • Lee-Ping Wang

A total of 12 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

1.9.0

6 years ago
  • [xtc] approx_nframes returns at least one (#1265)
  • Make compute_directors user-facing (#1260)
  • Add differentiable contacts option (#1247)
  • Remove link to forum (#1237)
  • Skip renumbering if no bonds in mol2 (#1238)
  • Add a bunch of Van Der Waals values (#1174)
  • [geometry] Fix compatibility with old visual studio for Python 2.7 (#1233)
  • Implement compute_average_structure (#1221)
  • Fix import of load_stk (#1231)
  • Fix bugs in load with atom_indices and frame args (#1227)
  • Fix conda test running (#1228)
  • Amber restart file convention (#1223)
  • Install path for zlib on linux too (#1208)
  • Fix transform calculation and Transform object to be more general (#1254)
  • Add O1 as alternative definition for water oxygen (#1257)
  • Fix precentering overflow error in center.c (#1283)
  • Add chi5 angle computation (#1291)
  • Fix the build bug caused by incorrect plumbing of the numpy include path into cflags (#1290)
  • Make RDF pairs argument required (#1288)
  • Refresh tests (#1266)
  • Remove PyPI downloads badge (#1293)
  • Extracting velocities/forces from TRR files (hidden API) (#1294)
  • Add "in" selection to selection language (#1268)
  • Handle a single frame being passed to sparta+ (#1295)

1.8.0

7 years ago
  • PR #1202: mdtraj.html has been removed. We recommend using nglview for visualizing MDTraj trajectory objects.
  • PR #1204: Fix search functionality with docs
  • PR #1167: Fix corner case in distancekernel.h
  • PR #1190: Fix issue with rmsd precentered = True and atom_indices != None
  • PR #1106: Speed up image_molecules
  • PR #1182: Add 'sidechain' and 'sidechain-heavy' options to compute_contacts
  • PR #1180: Handle unexpected keyword arguments gracefully in psf and prmtop parsers
  • PR #1171: Remove unnecessary restriction on iterload
  • PR #1170: Load single-element path lists without a copy
  • PR #1165: There should never be zero bins in Voxels class
  • PR #1158: Update deprecated use of scipy.stats.nanmean
  • PR #1153: [formats/XTC] in case of an out of bounds seek, raise IOError
  • PR #1161: Fix typos in examples
  • PR #1130: Automatically test examples to make sure they work
  • PR #1155: Update wording for simulation-with-openmm.ipynb
  • PR #1146: Ensure box vectors have right dtype
  • PR #1145: Check that file exists before trying to open it
  • PR #1139: Optimize baker_hubbard and wernet_nilsson functions
  • PR #1137: Allow standard_names as a keyword argument to md.load()
  • PR #1132: Fix bug in hoomdxml reader
  • PR #1125: Support Gromacs TNG files
  • PR #1123: Add md.join(trajs)