New version of AQUA-DUCT is available (Release 1.0.0) The new version of AQUA-DUCT is combining information from small ligands tracking and from small ligands local distribution. New modes of AQUA-DUCT MD data processing: normal, sandwich, time-window and consolidator mode. Pond module for hot-spots identification facilitating protein engineering and drug design, Energy barrier approximation. Graphical User…
New version of AQUA-DUCT is available (Release 0.5.9) 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…
New version of AQUA-DUCT is available (Release 0.4.14) 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…
New version of AQUA-DUCT is available (Release 0.3.7) Enable XTC trajectory format. Reliability fix in progress bar display. For more specific information on new functionalities see changelog at http://pythonhosted.org/aquaduct/.
New version of AQUA-DUCT is available (Release 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. For more specific information on new functionalities see changelog at http://pythonhosted.org/aquaduct/.
New version of AQUA-DUCT is available (Release 0.3.5) As for now, the only supported version of MDAnalysis is 0.15. For more specific information on new functionalities see changelog at http://pythonhosted.org/aquaduct/.
New version of AQUA-DUCT is available (Release 0.3.4) Fixed bug in progress bar updating method causing critical error in some specific circumstances. For more specific information on new functionalities see changelog at http://pythonhosted.org/aquaduct/.
New version of AQUA-DUCT is available (Release 0.3.3) AutoBarber default values of maxcut_level and mincut_level changed to True. Improved template configuration file. Number of small improvements in documentation. For more specific information on new functionalities see changelog at http://pythonhosted.org/aquaduct/.
Our tool AQUA-DUCT is officially launched (Release 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. New publication…