- 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.
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.
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