ReleaseNotes0161

Max Linke edited this page Jun 4, 2017 · 1 revision

MDAnalysis v0.16.1 release!

release date: 06/03/17

CHANGELOG

Enhancements

  • 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)

Fixes

  • 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)

Changes

  • 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)

Authors

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

Project Information

About
GNU GPL v2 code license
Labels: python, molecular dynamics, analysis, DCD, CHARMM, LAMMPS, NAMD, Gromacs, computer simulation, atoms, coordinates, trajectory, XTC, Library, object-oriented
Core Developers

Essentials

Applications
Downloads
Install
Release Notes
Guide for Developers
Google Summer of Code

Code of Conduct

Links

@mdanalysis on Twitter
Documentation
Tutorials
Downloads (PyPi)
Mailing Lists:
User discussion group
Developer mailing list

Clone this wiki locally
You can’t perform that action at this time.
You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session.
Press h to open a hovercard with more details.