ReleaseNotes0161

MDAnalysis v0.16.1 release!

release date: 06/03/17

CHANGELOG

Universe now works with StringIO objects for topologies and trajectories.
Residues with the same residue ids are not merged by default now (apply to PDB, GRO) (Issue #1306)
Improved print to screen format in waterdynamics module (using ProgressMeter).
PQRParser now treats insertion codes properly (Issue #1317)
made online docs responsive with the Alabaster Sphinx theme (#378)

In Universe.transfer_to_memory(): dt is now adjusted with step (Issue #1310)
Various documentation sphinx errors (PR #1312)
Bugfix in confdistmatrix.get_distance_matrix; now works on all trajectory types. (issue #1324)
Fixed bug "no molecules in water selection" in waterdynamics analysis module.
Fix hbond_analysis cannot deal with Universe where no two atoms are with 3A. (PR #1325)
Fix PDBParser docs for conect (issue #1246)
Fixed bug where amber topology files would fail to load if number of atoms was exactly divisible by number of atoms per line (issue #1331)
Fixed incorrect handling of residue names with trailing numbers in HydrogenBondAnalysis (issue #801)
Fixed AnalysisBase class provides numerical start,stop,step values (PR #1340)
Fixed PSFParser not creating multiple residues for identical resids in different segments. (Issue #1347, PR #1348)
Add the OC1 and OC2 from amber99sb-ildn to hydrogen bond acceptors (issue #1342)
Fix RMSF run return value (PR #1354)
Fixed documentation in pca (Issue #1378 PR #1379)

Enable various pylint warnings to increase python 3 compatibility
Change Mathjax cdn (Issue #1313)
Change mass_weight to weights for PSA analysis
Move mass_weights deprecation to version 0.18
Docs moved to http://docs.mdanalysis.org (Issue #1315) and made responsive (Alabaster theme with readable-sphinx CSS) (Issue #378)
speed improvements parsing PDB / PDBQT / PQR / XYZ coordinate reader (Issue #1308)

utkbansal, kain88-de, xiki-tempula, kaplajon, wouterboomsma, richardjgowers, Shtkddud123, QuantumEntangledAndy, orbeckst, kaceyreidy