Aqua-Duct changelog

  • 1.0.2 (29.07.2019)

    • Improvements in GUI configured.

    • Fixed problems with waterfall mode.

  • 1.0.0 (21.07.2019) Aqua-Duct version 1

    • Assorted minor fixes and improvements.

  • 1.0.0b1 (13.07.2019) beta

    • New Waterfall option for analysis of custom sampled simulations.

    • New Kraken GUI tool for facilitating analysis of results.

    • RAM usage optimization in AutoBarber and other procedures.

    • Center of Object and Center of System calculation.

    • Cluster shapes KDE estimation and visualization.

    • New GUI tool for preparing configuration files.

    • Possibility to join clusters by ID and to sort and renumber cluster IDs.

    • Inlets in seleced clusters can be removed.

    • Order of clustering procedures can be altered by user.

    • AutoBarber can be run for different types of traced molecules separately.

    • New driver Pond allows to calculate pockets and master paths energy profiles.

    • Assorted improvements allowing better handling of passing paths.

    • GREAT speedup of Stage I, II, and III calculations: they run in parallel; IO can be a bottleneck though.

    • Substantial speedup of SinglePaths generation: it runs in parallel and uses fastest routines.

    • Substantial speedup of AutoBarber procedures: it runs in parallel; IO can be a bottleneck though.

    • Improvements in analysis stage. Additional info displayed in tables and added progress bar.

    • portal.py script for calculating sizes of selection(s) using convex hull approximation.

    • Improvements in dir-cache handling.

    • Some speedup of master paths calculations, more to come.

    • Paths, SinglePaths and other objects use less memory.

    • Newest MDAnalysis can be used (ie 0.17, 0.18, 0.19) however it is recommended to stay with 0.16.2.

    • Many other minor improvements and bug fixes.

  • 0.5.15 (05.05.2019)

    • Topology residue ID are printed in the analysis files.

  • 0.5.14 (26.09.2018)

    • Recommended MDAnalysis is set to >=0.16 and <0.17. Versions >=0.17 are fully supported.

    • Docs update.

    • Various performance improvements and few minor bug fixes.

  • 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 clustering 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.

    • Clustering 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