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.
  • 0.3.6
    • 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
    • As for now, the only supported version of MDAnalysis is 0.15.
  • 0.3.4
    • Fixed bug in progress bar updating method causing critical error in some specific circumstances.
  • 0.3.3
    • 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
    • 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
    • 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
    • Stage execution time debug messages.
    • Total execution time debug message.
  • 0.2.25
    • initial public release