Mdtraj Versions Save

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:

• New compute_neighborlist() function (#1057)
• Add option to skip standardization of atom and residue names during load_pdb (#1061)
• Function for imaging molecules (#1058)
• New optional argument periodic for compute_contacts (#1072)
• Refresh documentation (#1067, #1074, #1075)
• Rewrite geometry code in modern c++ (#1077)
• Fix issue with Topoplogy.from_openmm (#1089)

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)

Many thanks to our contributors for making this release possible.

This release includes important bugfixes identified in the 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).

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)

Thanks to all the contributors for making this release possible.

• Fix pytables inadvertently being moved to a required dependency

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.

Authors:

• Kyle A. Beauchamp
• Anton Goloborodko +
• Matthew Harrigan
• Christoph Klein
• Robert T. McGibbon
• Tim Moore +
• Patrick Riley +
• Jason Swails
• Lee-Ping Wang
• Andrea Zonca +

We're pleased to announce the 1.3 release of MDTraj!

• 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

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 (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)

We're happy to announce a new release of MDTraj. Our 1.0 release indicates that MDTraj is stable, 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. Binary installers for conda will be available shortly!

• 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 Kyle A. Beauchamp, Lee-Ping Wang, Jason M. Swails, ag1989, Carlos X. Hernandez, Matthew P. Harrigan and Christian Schwantes for contributions.