AQUA-DUCT event

AQUA-DUCT software and its results will be presented during Enzymes, biocatalysis and chemical biology: The new frontiers organised by EMBO in Pavia, Italy 9-12 09 2018.

AQUA-DUCT – Release 0.5.9 is available

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

AQUA-DUCT – Release 0.4.14 is available

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 citation

AQUA-DUCT was cited in VCBM 17: Eurographics Workshop on Visual Computing for Biology and Medicine in article Watergate: Visual Exploration of Water Trajectories in Protein Dynamics by Viktor Vad and co-workers.

Tips and tricks – clustering – new version.

Check out the updated clustering tips and tricks in the Tutorials section Adjusting method of clustering This section will show you how your results can vary from chosen method of clustering ……. For a new PDF file version of the tutorial visit the Download section.

AQUA-DUCT – Release 0.3.6 is available

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/.  

Tips and tricks – clustering.

Check out the clustering tips and tricks in the Tutorials section Adjusting method of clustering This section will show you how your results can vary from chosen method of clustering ……. For a PDF file version of the tutorial visit the Download section.

AQUA-DUCT – Release 0.3.3 is available

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/.

AQUA-DUCT is launched

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