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changelog
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Changelog
v0.28
#General
-moved project to github
-contact info
----
v0.27 7. Jan 2013
#readPDB
-Added error message for unsupported pdb files. Example header is now printed to CLI
-bugfixes ...
------------
v0.26 14. Dec 2012
#dxTuber_cmd
-bug /typo for 1D z scanning
-------------
v0.25 22. Oct. 2012
#analysCavity (cmd)
-bug in parameter check block
-------------
v0.24
#analyzecavity
-bug: pore profiles start and end now with values of 0
-multiple zeros in one cavity are now supported AND listet in output files
usefull if disconnected cavites are in forus of a pore profile analysis
-------------
v0.23 20. Jun 2012
#postgroup
+'core_cavities_after_filter.pdb' stores the grouped core cavities
+distcutoff parameter can now be set via cmd
-------------
v0.22 21. Mar 2012
#postgroup
+user can now select either to postgroup ALL cavites or a single cavity
(If '--cid' statement is not given)
-bugfixes
--------------
v0.2 21. Feb 2012
#General
+pdb2dx: Converts previously previously via dxTuber created pdb files back into OpenDX file format. Usefull if cavites shall be represented as 'surface' in VMD
#dxTuber_cmd
+supports now pdb(grid only) files as input
+fill after grouping (Experimental)
+minimum distance keep (mdk) applies an minimum distance filter and stores filtered ISV's separately for grouping // dirty dirty dirty ...
+overlap option, switches if a ISV will be stored during scanning if a protein > protMinDens is located at the very same coordinates.
#scanning / planesearch
+'--mdk' minimum distance keep, new idea to separate cavites inside water water clusters.
-storeOverLappingISV = False <--- switches if ISV will be deleted if a protein Voxels > protMinDens is located at the very same position
#writepdb
-ungrouped cavities now have the (atom)id '0' instead of 'DEN' -> ungrouped cavities can be processed via analyzeCavity.py | dxTuber_gui
-99999'er atom counter bug m( // for some unknown reason code was commented out... "gremlins"?
-densities up to 999999 can now be stored in pdb files
#filter
+filterByDens: filters by voxel density values
+deleteRectangleInside: deletes voxles inside the defined rectangle //Experimental not yet testet
#readPDB
-bugfixes, lots of... do not parse pdb files by column in future *GRML*
#postgroup
+detected cavities can now be devided into subcavities with postgroupcavities.py
----------------
v0.11 12. August 2011
#General
+analyzeCavity.py
-cmd version of the analyze cavity function
----------------
v0.1 10. August 2011
#General
+dxTuber now supports solvent files with smaler dimension than protein input files
-new dependency python-argparse http://code.google.com/p/argparse/ (in standard libs since python 2.7)
#Bugfix
-dx2pdb files can now be imported in dxTuber_gtk
#dxTuber_cmd
+Full parameter support
-completely rewritten
-uses python-argparse (argument parser)
----------------
v0.09 5. July 2011
#General
+dxTuber_cmd <- first command line version of dxTuber
-uses standard parameters
-0.005 prot min dens
-0.01 water min dens
-2D scanning
+version is now stored in ~/.dxTuber/dxTuber.conf
#writepdb
+grouped yes / no entry in PDB output header
#planesearch
-fixed bug if constructor is called using only necessary paramemters
-minDiameter = 0 by default
---------------
v0.085 17. Mar 2011
#General
-default density water 0.01 -> 0
-minimum diameter for cavities during scanning 1A -> 0A
#writepdb
+'CRYST1' entry to enable PBC view in VMD and other molecular viewer
#Readme
+knwon bug's
--------------
v0.0841 14.Mar.2011
+'how to use dxTuber' section in README
--------------
v0.084 4.Mar.2011
#GUI
-changed some labels (typos)
-----------------
v0.083 11.Jan.2011
#general
+Gridsizes !=1 are now supported
#dx2pdb
+filter by residence probabilities stored in minSolventDensity
+settings are now stored in pdb files
#pdbfiles
+reference OpenDX filename is now saved in 'OpenDXFile' (in pdb files)
#README
+tested on Ubuntu Lucid 10.4 LTS (32Bit)
--------------------------
v0.082 22.Sep.2010
#readpdb
+dxTuber now supports previously processed pdb files as full compatible input files
-only files created from version 0.082+ are supported
-all settings including groupes are imported and can be analyzed further
#GUI
+new fields in file tab
+Min Diamemter
+Min Protein density
+Min Solvent density
-made the code little bit 'nicer'
#save to pdb
+dxTuber settings are now stored in pdb files
+version
+ProteinFile (full path)
+SolventFile (full path)
+StepSize
+ScanType
+MinDiameter
+MinProtDens
+MinSolvDens
+Applied Filter (all applied; seperated by ', ')
#filtertube
-minor print to commandline changes
#tubeDx
+tubeDx class has moved into lib/tubedx.py
+lots of new variables
#README
+minor changes
-----------------
v0.08 16.Sep.2010
#new features
+User can adjust solvent minimum density via settings tab
+User can define minimum cavity diameter along priciple axis (1D,2D,3D) [Angstrom]
#GUI-Settings tab
+Solvent density
+Minimum diameter of the cavity
#Scanning
+additional information during scanning is given
+Protein Threshold
+Solvent Threshold
#writepdb.py
-changed the hard coded solvent density
#README
-minor changes
---------------
v0.073 25.Aug.2010
#general
+README file
+Dependencies
+How to install dxTuber
#analyseDx
-all cavity profiles start at (choosen axis = 1)
--------------
v0.072 20.May.2010
#general
+New filter 'Filter by Distance' implemented
-Fixed warnings in analysePopupWindow
-<requires-version lib="gtk+" version="2.12"/> removed
-<requires-version lib="bonobo" version="0.0"/> removed
-<requires-version lib="gnome" version="0.0"/> removed
#GUI-Settings tab
-Filter by plane -> Filter by Distance
+SpinBox 'minimum Distance' in [A]
#filterDx
-Filter by Distance: 2D filtering modified to 3D filtering
--------------
v0.071 17.May.2010
#general
-Modified script description header (hasn't been modified since dxTuber v0.001!)
-Fixed warnings in startup of dxTuber, some deprecated stuff from glade3 were modified in dxTuber.libglade
-<requires-version lib="gtk+" version="2.12"/> removed
-<requires-version lib="bonobo" version="0.0"/> removed
-<requires-version lib="gnome" version="0.0"/> removed
-modified neighborspinbox initialization
-<property name="adjustment">10 1 25 1 10 10</property> -> <property name="adjustment">10 1 25 1 10 0</property>
#GUI
-For 1D scanning all xyz axis are active per default now.
-Renamed two buttons
-Analyse Tube -> Analyze
-Filter Tuber -> Filter
---------------
v0.07 14.Apr.2010
#new features
+fill tubes after grouping (2D & 3D)
#general
-tubeVoxelGroupGrid [x][y][z] = group1 group2 group3
-this effects analyseTube fillTube.
-More than one group is stored here seperated by blanks as string
-Overlapping cavities are possible and still selectable via name (PDB)
#scanning
-user gets a print on console which scan method is currently running
#GUI
+Added checkbox for fill Tubes
#CMD
+Print scanning method while scanning
-----------
v0.067 3.Mar.2010
#GUI
-after opening/saving/scanning 'Files'-Tab will be on focus
-after analysing cavities along princeple axis 'Analyse Tube' window will close
#Scantube
-notification when scanning is "Done"
#grouptube
-print progress while grouping, in percentage
#writedx
-notification when saving is "Done"
#writepdb
+added "TER" + "END" in tail of PDB files