Aqua-Duct changelog

• devel

  • Uses newest MDAnalysis.
  • Steady improvement of documentation (including API).
  • Added mario script, WIP.
  • If barber is used for clusterization, appropriate radii are displayed. Buggy.
  • Data dumps routines moved to separate module.
  • Tests with netcdf4 for dumping data, WIP.
  • SmartRanges moved to helpers module.
  • Names of traced molecules are returned in the result file and tables are split appropriately.
  • Tables in the result file are split in regard to Object and Passing paths.
  • Small bug in reporting progress in AutoBarber preparation fixed.
  • Passing through paths are being introduced, WIP.

• 0.3.7 (18.07.2017)

  • Enable XTC trajectory format.
  • Reliability fix in progress bar display.

• 0.3.6 (28.06.2017)

  • AQ can be run for given part of trajectory.
  • Fixed bug in passing options to Barber clusterization method.
  • Recursive threshold can be defined as range; no disjoint ranges are supported.

• 0.3.5 (18.04.2017)

  • As for now, the only supported version of MDAnalysis is 0.15.

• 0.3.4 (14.04.2017)

  • Fixed bug in progress bar updating method causing critical error in some specific circumstances.

• 0.3.3 (20.03.2017)

  • AutoBarber default values of maxcut_level and mincut_level changed to True.
  • Improved template configuration file.
  • Number of small improvements in documentaion.

• 0.3.2 (24.02.2017)

  • Major improvement: new auto_barber based clustering method.
  • Clusterization history displayed as simple ascii tree.
  • AutoBarber min and max cut level options added.
  • Barber moved to separate module.
  • Fixed bug in visualization script; if no molecule is kept do not set style and color.

• 0.3.1 (04.02.2017)

  • AutoBarber tovdw option.
  • AutoBarber minimal and maximal cut options.
  • Fixed bug in AutoBarber: some areas were sometimes not cut.
  • Documentation improvements.
  • Valve driver simplified. Most of the functionality moved to separate module.
  • Option for single precision storage.
  • Added Savitzky-Golay smoothing; AQ requires SciPy >= 0.14 now.
  • Improved sorting of CTypes.
  • Raw and Separate paths uses SmartRanges. This allowed for excellent performance improvement of Separate paths calculation.
  • Default display of molecule changed to silver cartoon.
  • Object shape displayed in orange.
  • Fixed several small bugs.

• 0.2.26 (21.01.2017)

  • Stage execution time debug messages.
  • Total execution time debug message.

• 0.2.25 (18.01.2017)

  • initial public release