Aqua-Duct changelog
- 0.5.9 (12.03.2018)
- Rewritten module for MD data access. Sandwich mode added.
- Coordinates can be stored in cache directory, in memory or generated on demand.
- Support for long trajectories.
- Passing through paths are supported.
- Improvements in visualization script.
- Coordinates of residues are calculated as center of geometry.
- Recommended MDAnalysis is set to >=0.16 and <0.17. Version 0.17 is supported but not recommended.
- Bug fixes and code cleanup.
- 0.4.0 - 0.4.14 (20.11.2017) unofficial
- Uses newest MDAnalysis (0.16.2).
- Steady improvement of documentation (including API).
- 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.
- Passing through paths are being introduced, WIP.
- Additional tables in the result file.
- CRD is enabled as topology/trajectory format.
- Traced residues are identified by resindices instead of resids; this allows to use weak topologies such as PDB.
- Removed roman dependency.
- In addition to histograms approximate (ConvexHull approximation) areas and volumes of the scope and object can be calculated.
- Bug fixes and reliability fixes.
- 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 documentation.
- 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)
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