What’s New?¶

v1.6.2 (February 19, 2016)¶

• Fix issues and rendering issues with example notebooks (#1049, #1050)

v1.6 (February 15, 2016)¶

MDTraj 1.6 contains a good mix of bug fixes and enhancements. Some highlights include:

• Improved performance for compute_contacts (#995)
• Improved performance for Topology.select_pairs (#1000)
• Fast random access to xtc and trr files (#1038)
• xyz files support the __len__ attribute (#998)
• segment_id is a new residue attribute (#1002)
• Expose FormatRegistry as a public api (#1039)
• Perform a heuristic check for valid unit cells when reading pdb files (#974)
• pdb file parsing uses the last model CONNECT records for bonds, not the first (#980)
• No longer force all warnings to be emitted (#1013 #1030)
• Always respect the force_overwrite argument in save methods (#878)
• Fix interop with scipy.cluster (#997)
• formats.hdf5.ensure_mode was 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_chi4 to 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 (devtools/, setup.py, .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 (compute_nematic_order).
• 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.

v1.3 (February 25, 2015)¶

• New functions to calculate various statistical mechanical properties (unitcell_volumes, dipole_moments, static_dielectric, isothermal_compressability_kappa_T, thermal_expansion_alpha_P, 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)
• New md.compute_neighbors function to efficiently find nearby atoms (Robert T. McGibbon)
• md.shrake_rupley supports 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.
• New md.compute_dssp function 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_distances, compute_angles, compute_dihedrals now accept iterators for the indices argument.
• New Topology.select_atom_indices method.
• Ability to save b factors in PDB files.
• restrict_atoms has been deprecated, and replaced with atom_slice.
• 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)¶

• Brand new nmr library that includes transparent python interfaces to SHIFTX2, PPM and SPARTA+ for chemical shifts, as a library for scalar couplings (J) using the Karplus relation.
• New lprmsd distance metric for linear-programming root mean square deviations which optimizes over the label correspondence between exchangeable atoms in the two conformations.
• New wernet_nilsson function for hydrogen bond identification.
• New parser for mol2 format files.
• Many new convenience methods on md.Topology, including to_bondgraph to create a NetworkX graph from a topology.
• New compute_drid function for calculation of distribution of reciprocal inter-atomic distances (DRID) distance metric
• Core geometry routines compute_angles and compute_dihedrals now 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.rmsd and 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.unit as 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.
• More detailed repr and str on Trajectory.
• 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
• Improvements to DCD seek()
• 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.compute_contacts and md.geometry.squareform for residue-residue contact maps
• Fix segfault in md.rmsd when using the optional atom_indices kwarg
• md.compute_phi, md.compute_psi, and md.compute_omega now return the correct atom indices, as their docstring always said.
• Topology Element instances are now properly immutable
• Small bugfixes to baker_hubbard, and better docstring
• Automatic installation of pandas and simtk.unit via setuptools’ install_requires.
• Small bugfix to mdcrd loading with stride
• superpose now 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 __len__ function.
• Small bugfixes related to vsites.

v0.5.1 (January 4, 2014)¶

• Minor bug fix when no dihedrals match specification
• Add __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 baker_hubbard
• 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 iterload method for chunked trajectory loading