ReleaseNotes0180

MDAnalysis 0.18.0 release

• release date: 04/15/18
• release announcement
• CHANGELOG

CHANGELOG

Enhancements

• Added flatten_dict function that flattens nested dicts into shallow dicts with tuples as keys.
• Can now pass multiple attributes as a list to groupby function. Eg ag.groupby(["masses","charges"]) (Issue #1839)
• Added reading of record types (ATOM/HETATM) for PDB, PDBQT and PQR formats (Issue #1753)
• Added Universe.copy to allow creation of an independent copy of a Universe (Issue #1029)
• Added copy method to various core classes including Reader, TransTable, Topology, TopologyAttr (Issue #1029)
• Added reindex option to GROWriter to preserve original atom ids when set to False (Issue #1777)
• Can now pass 'atom_style' keyword argument when parsing Lammps Data files to specify what is on each line. Eg atom_style = 'id type charge x y z' (Issue #1791)
• Added periodic boundary condition option to HydrogenBondAnalysis (Issue #1188)
• Added duecredit to prepare a summary of the citations, when a user uses MDAnalysis (Issue #412)
• Added AtomGroup, ResidueGroup and SegmentGroup to the top module namespace

Fixes

• Fixed MPI fork() warning when importing MDAnalysis in an Infiniband-enabled MPI environment (PR #1794)
• Fixed waterdynamics SurvivalProbability ignoring the t0 start time (Issue #1759)
• AtomGroup.dimensions now strictly returns a copy (Issue #1582)
• lib.distances.transform_StoR now checks input type (Issue #1699)
• libdcd now writes correct length of remark section (Issue #1701)
• DCDReader now reports the correct time based on istart information (PR #1767)
• added requirement scipy >= 1.0.0 (absolutely needed: >= 0.19) (Issue #1775)
• Universe.empty now warns about empty Residues and Segmnets (Issue #1771)
• AMBER netcdf reader now defaults to mmap=None as described in the docs (meaning mmap=True for files and NOT in memory), thus avoiding memory problems on big trajectories (Issue #1807)
• analysis.align: fixed output and catch more cases with SelectionError when selections are incompatible (Issue #1809)
• fix cython 0.28 compiler error
• DCD istart was wrongly interpreted as frames (only in 0.17.0) instead of integrator timesteps, which lead to large time-offsets when reading and writing DCD files; now istart is correctly interpreted when reading and when writing, istart=None will set it to the CHARMM default nsavc but the default is istart=0, which will make the DCD start at frame 0 (Issue #1819)
• Can now parse PDB files without resids (Issue #1854)
• Fixed periodic KDTree, now requires Biopython version 1.71 onwards (Issue #1857)
• fixed a bug in visualization.streamlines (Issue #1617)
• Updated TPR parser for GROMACS 2018 (Issue #1796)
• Fixed reading of PQR files generated by Gromacs (Issue #1804)

Changes

• scipy >= 1.0.0 is now required (issue #1775 because of PR #1758)

Deprecations

• undeprecated creating Groups from list of Components (Issue #1847)

Authors

tylerjereddy, richardjgowers, palnabarun, bieniekmateusz, kain88-de, orbeckst, xiki-tempula, navyakhare, zemanj, ayushsuhane, davidercruz, jbarnoud