Category Archives: New version

12Mar/18

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 is set to >=0.16 and <0.17. Version 0.17 is supported but not recommended.
  • Bug fixes and code cleanup.

For more specific information on new functionalities see changelog at http://pythonhosted.org/aquaduct/.

 

20Nov/17

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 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.

For more specific information on new functionalities see changelog at http://pythonhosted.org/aquaduct/.

03Mar/17

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 in “Bioinformatics”: AQUA-DUCT a ligand tracking tool