These are new features and improvements of note in each release.
v1.9.4 (May 10, 2020)¶
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)
v1.9.3 (May 17, 2019)¶
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)
[xtc] Fix bugs in striding with atom_indices and seek+stride (#1449)
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)
Ray A. Matsumoto
Robert T. McGibbon
Martin K. Scherer
David W.H. Swenson
Matthew W. Thompson
A total of 12 people contributed to this release. People with a “+” by their names contributed a patch for the first time.
v1.9.2 (July 30, 2018)¶
We’re please 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](https://github.com/pandegroup/openmm/pull/1668) representation into MDTraj. Implements the Bond class to Topology and updates the Mol2 reader to use bond_order field (#1308)
Lester Hedges +
Robert T. McGibbon
Levi Naden +
Justin R. Porter
Martin K. Scherer
Xianqiang Sun +
David W.H. Swenson +
A total of 11 people contributed to this release. People with a “+” by their names contributed a patch for the first time.
v1.9 (September 3, 2017)¶
approx_nframesreturns at least one (#1265)
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)
Fix import of
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
pairsargument 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)
v1.8 (November 9, 2016)¶
mdtraj.htmlhas been removed. We recommend using
nglviewfor 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)
v1.7.2 (May 2, 2016)¶
Small fix to developer tools so docs get uploaded.
v1.7 (May 2, 2016)¶
We’re please to announce the release of MDTraj 1.7. In addition to the usual fixes and improvements, MDTraj has gained the ability to image molecules in trajectories. So far, it’s worked very well even on complicated systems like multi-molecule proteins. Look forward to future enhancements to this new feature! Some other highlights include:
Add option to skip standardization of atom and residue names during
Function for imaging molecules (#1058)
New optional argument
Refresh documentation (#1067, #1074, #1075)
Rewrite geometry code in modern c++ (#1077)
Fix issue with
v1.6 (February 15, 2016)¶
MDTraj 1.6 contains a good mix of bug fixes and enhancements. Some highlights include:
Improved performance for
Improved performance for
Fast random access to xtc and trr files (#1038)
xyz files support the
segment_idis a new residue attribute (#1002)
FormatRegistryas a public api (#1039)
Perform a heuristic check for valid unit cells when reading pdb files (#974)
pdb file parsing uses the last model
CONNECTrecords for bonds, not the first (#980)
No longer force all warnings to be emitted (#1013 #1030)
Always respect the
force_overwriteargument in save methods (#878)
Fix interop with
formats.hdf5.ensure_modewas removed (#990)
v1.5.1 (November 6, 2015)¶
MDTraj 1.5.1 is a small bugfix release to correct two issues introduced in the immediately preceeding 1.5.0 release.
A recent change (merged Nov 5) caused
compute_chi4to compute chi3 angles (#981).
Revert changes in setup.py that resulted in a more confusing error when cython is not installed at build-time (#985).
v1.5 (November 6, 2015)¶
We’re pleased to announce the 1.5 release of MDTraj. It contains new features, improvements, and bug fixes. Highlights of the changes for this version include:
Faster histogramming method in RDF calculations when supported by numpy (#952)
Improved support for mol2 reading (#945)
Support for IPython/Jupyter 4 (#935)
Improved support for Amber NetCDF writing (#939)
Fix handling of periodic boundaries for distance calculations for general triclinic unit cells (#930)
Support different reference and query indices for superposition and RMSD calculation (#915)
Fix dcd reading bug under Windows (#905)
Trajectories have a hash implementation (#898)
Fixes for Hoomd (#900, #885)
Support files (
.travis.yml) are BSD licensed (#891, #893)
Fixes for Lammpstrj (#861)
Support for one letter amino acid codes (#871)
Trajectory smoothing using a Buttersworth filter (#962)
New functions for computing dihedral indices from a topology (#972)
Improvements to build process (#955, #954, #941, #943, #942, #934)
v1.4.2 (June 9, 2015)¶
BUGFIX: Fix pytables inadvertently being moved to a required dependency
v1.4 (June 8, 2015)¶
Version 1.4 is our best release yet! It contains many new features, performance improvements, and bug fixes.
Major highlights include:
New function to calculate nematic order parameters (
Improved efficiency of generating RDF pairs.
Add support for XYZ-format files.
Fix parsing error with certain mol2 files.
Support .pdb.gz files and make loading multiple pdb files more efficient.
Fix use-after-free bug with DCD causing incorrect filenames.
Update IPython-notebook trajectory viewer for IPython 3.0.
Add support for the HOOMD-Blue XML topology format.
Make virtual sites a new “element”.
Add ‘NA’ code to dssp for non-protein residues.
Add support for CHARMM (Chamber) topologies in prmtop loader.
Add methods to calculate more NMR J-couplings.
Fix gro file unitcell handling.
Enable .lammpstrj to parse custom column orders.
Add read_as_traj method to all TrajectoryFile classes, making iterload work for all formats.
A total of 10 people contributed to this release. People with a “+” by their names contributed a patch for the first time.
Kyle A. Beauchamp
Anton Goloborodko +
Robert T. McGibbon
Tim Moore +
Patrick Riley +
Andrea Zonca +
v1.3 (February 25, 2015)¶
New functions to calculate various statistical mechanical properties (
density) (Kyle A. Beauchamp)
Fix for PDB parser to handle more than 100K atoms. (Peter Eastman + ChayaSt)
Include nitrogen atoms as h-bond acceptors in hydrogen bond detection (Gert Kiss)
SSE4.1 support not required. The latest CPU feature now required is SSE3. (Robert T. McGibbon)
New function to calculate radial distribution functions (
compute_rdf) (Christoph Klein)
Assorted bugfixes and improvements to documentation
v1.2 (December 1, 2014)¶
We’re pleased to announce the 1.2 release of MDTraj! This release brings minor changes to support the forthcoming release of MSMBuilder 3.
Refactor RMSD code into a static library (Robert T. McGibbon)
v1.1 (November 10, 2014)¶
We’re pleased to announce the 1.1 release of MDTraj! This release brings support for even more trajectory formats, and some new analysis features.
New loader for CHARMM topology files:
md.load_psf(Jason M. Swails)
New loader for Desmond trajectory files (Teng Lin)
New loader for Amber restart files (Jason M. Swails)
New loader for Gromacs gro files (Robert T. McGibbon)
New loader for LAMMPS trj files (Christoph Klein)
New text-based atom selection domain-specific language allowing natural querying of atoms as well as generation of equivalent python code for embedding in scripts or applications (Matthew P. Harrigan, Robert T. McGibbon)
md.compute_neighborsfunction to efficiently find nearby atoms (Robert T. McGibbon)
md.shrake_rupleysupports a new option to accumulate total SASA by residue (Robert T. McGibbon)
Fix potential segmentation fault when reading corrupted XTC files. (Robert T. McGibbon)
v1.0.0 (September 7, 2014)¶
We’re pleased to announce the 1.0 release of MDTraj! Our 1.0 release indicates that MDTraj is stable enough to be used in production calculations, and that we have a stronger commitment to backward compatibility. Two substantial new features have been added since 0.9, but the API has remained quite stable.
New interactive WebGl-based protein visualization in IPython notebook – this feature is quite new and will continue to evolve throughout the 1.X release cycle.
md.compute_dsspfunction for DSSP secondary structure assignment.
Multiple bugfixes in PDB parsing, including handling of ATOM serial’s CONNECT records, support of .gziped files,
Fix compilation errors on OSX and older linux platforms (gcc-4.1)
compute_dihedralsnow accept iterators for the indices argument.
Ability to save b factors in PDB files.
restrict_atomshas been deprecated, and replaced with
Better support for multi-chain proteins in dihedral methods.
Thanks to Robert T. McGibbon, Kyle A. Beauchamp, Lee-Ping Wang, Jason M. Swails, ag1989, Carlos X. Hernandez, Matthew P. Harrigan and Christian Schwantes for contributions.
v0.9.0 (June 10, 2014)¶
nmrlibrary that includes transparent python interfaces to SHIFTX2, PPM and SPARTA+ for chemical shifts, as a library for scalar couplings (J) using the Karplus relation.
lprmsddistance metric for linear-programming root mean square deviations which optimizes over the label correspondence between exchangeable atoms in the two conformations.
wernet_nilssonfunction for hydrogen bond identification.
New parser for
Many new convenience methods on
to_bondgraphto create a NetworkX graph from a topology.
compute_dridfunction for calculation of distribution of reciprocal inter-atomic distances (DRID) distance metric
Core geometry routines
compute_dihedralsnow respect periodic boundary conditions via a substantial internal refactoring of the geometry library. They also have significantly improved numerical stability.
Numerous bugfixes, including fixing potential segfaults with
md.rmsdand the NetCDF parser as well as increased compliance for AMBER .prmtop and TINKER .arc parsers.
Many internal changes to hardware detection code, ensuring that compiled binaries run appropriately on any platform, including those that don’t support modern CPU features like SSE4.
Major improvements to our automated testing framework. Every pull request and commit to MDTraj is now being tested across a matrix of 4 different python versions on linux as well as python3 on Windows.
A number of brand new example IPython notebooks on the website demonstrating all of these new features!
v0.8.0 (March 10, 2014)¶
New parser for AMBER PRMTOP topology files.
Removed dependency on netCDF4 and the c libnetcdf. We’re now exclusively using the pure python NetCDF3 implementation in
scipy.io, which is now a dependency.
Removed dependency on
simtk.unitas an external package
Fixed a behavior where “default” unit cell dimensions were being saved in trajectories without periodic boundary conditions in XTC, DCD and TRR, which when loaded up later were interpreted as being “real” periodic boundary conditions.
Better ResSeq preservation in HDF5 files.
Load pdb files directly from a URL.
Unicode fixes for python3.
Bugfixes in OpenMM reporters
New theme for the documentation with IPython notebooks for the examples
Reorganized the internal layout of the code for easier navigation, IPython tab completion.
Thanks to everyone who contributed to this release: Robert T. McGibbon, Kyle A. Beauchamp, Carlos Hernandez, TJ Lane, Gert Kiss, and Matt Harrigan.
v0.7.0 (February 21, 2014)¶
New geometry functions
md.geometry.squareformfor residue-residue contact maps
Fix segfault in
md.rmsdwhen using the optional
md.compute_omeganow return the correct atom indices, as their docstring always said.
Elementinstances are now properly immutable
Small bugfixes to
baker_hubbard, and better docstring
Automatic installation of
Small bugfix to mdcrd loading with stride
superposenow correctly translates the final structure, and doesn’t recenter the reference structure
v0.6.1 (February 11, 2014)¶
Trajectory.join(discard_overlapping_frames=True)is criterion for detecting overlapping frames is more realistic
We now support installation via conda, and are supplying conda binaries
md.load()is much faster when loading multiple trajectory files
Bug-fixes for pandas 0.13.0 release, detection of zinc atoms in PDB files
Geometry functions are more resilient to segfaults from bad user parameters
Fix intermittent RMSD segfaults from invalid memory access
Fix RMSD centering bug with memory alignment after restrict_atoms
v0.6.0 (January 21, 2014)¶
md.rmsd()signature changed to be more understandable
All file objects now have a
Small bugfixes related to vsites.
v0.5.1 (January 4, 2014)¶
Minor bug fix when no dihedrals match specification
__str__to Topology parts
More examples sections in docstrings
v0.5.0 (January 3, 2014)¶
Numerous bug fixes
Much improved coverage of the test suite.
Removed cffi dependency for accelerated geometry code
Faster multi-trajectory loading
MSMBuilder2 LH5 format support
Change license from GPL to LGPL
More convenience methods on Topology
PDB writer writes connect records
Hydrogen bond identification with
Rotation/translation to superpose trajectories
New RMSD API. It’s much simpler and much more memory efficient
Full support for computing all of the chi angles
Add seek/tell methods to all of the trajectory file objects
New top level memory efficient
iterloadmethod for chunked trajectory loading