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Package AutoDockTools :: Module autoanalyzeCommands
[hide private]
[frames] | no frames]

Module autoanalyzeCommands

source code


This Module facilitates analyzing results of autodock jobs. 

    * The first step is 'Read Docking Log'  The selected file is parsed 
    which sets mv.docked to a new Docking instance.  The Docking class 
    has attributes:

        o dlgParser

            x 'dlg': full pathname of dlg

        o dpo 

        o ch:a conformation handler.

            x 'clusterNum': 

            x 'clusterList': 

            x 'modelList': a list of docked conformations 

        o macroFile: the Macromolecule file used

        o 'macro': filename of macromolecule (eg '1hvrCorr.pdbqt')

        o 'macroStem': name of macromolecule up to last '.' (eg '1hvrCorr')

        o ligand:  the original ligand 

        o output: lines containing summary of docking

    The new Docking is also entered in the dictionary 'dockings' as a separate item 
    whose key is the file and whose value is the Docking.


After the selected docking log file is parsed, the user can:

    * select a displayed docked conformation using the 'Choose A Docked Conformation' menubutton.  This opens a DockingChooser widget which is a ListChooser allowing selection either in the widget or in the viewer of any of the displayed docking. Information about each docked conformation is displayed in the information window of the DockingChooser as different entries are high-lighted.  

    * display the macromolecule via the "Show Macromolecule" menubutton.  This menubutton is linked to a file browsers in case the macromolecule whose name is parsed from the docking log file is not in the current directory. (FIX THIS: what if the macromolecule is in a different directory but there is a molecule with the same name here???). The user can change the visibility, sampling, isovalue, renderMode and visibility of bounding box  for each of  the displayed grids

    * display the autogrids used in the docking via the "Show Grids Used For Calc" menubutton.  This menubutton is linked to a ListChooser which lets the user select whether to load all or some of the grids. The user can interactively change the visibility of each grid's isosurface, its sampling value, its isovalue, its rendermode (LINE or FILL) and the visibility of its bounding box. 

    * The user is able to visualize extra grid maps using the "Show Grid" button. 

    * If the current docking has clusters, the user is able to visualize a results histogram for it with 'Show Histogram'. The histogram can be printed.

    * Result Summaries for docking(s) can be viewed, edited and saved with 'Get Output'

    * Dockings can be deleted via 'Delete Docking Log'


Classes [hide private]
  ADChooseMacro
This class is used to choose the macromolecule from molecules already present in the viewer...
  ADReadMacro
This class is used to load the macromolecule specified in the docking log...
  ADEPDBMol
This class is used to run AutoDock in the cmd mode, epdb a molecule in...
  ADSeeSpots
This class is used to display all docked conformations as spheres...
  ADShowBindingSite
This class is used to display docked ligand and surrounding atoms in macromolecule...
  ADMakeAllGrids
toplevel GUI with one row per grid_type allowing:loading a grid (first, then->),toggling the visiblity of its isosurface,changing sampling rate,changing isocontour isovalue,changing the render mode between LINE and FILL visibility of the grid's bounding box...
  ADGetOutput
When the docking log is parsed, summary lines are detected and saved in ...
  ADGetAGrid
Adds a row to the toplevel GUI of ADMakeAllGrids enabling:loading a USER grid (first, then->),toggling its visiblity,changing sampling rate,changing isocontour value,changing the render mode between lines and fill.
  ADSelectDLG
Allows the user to change current docking ...
  ADDeleteDLG
Allows the user to delete docking ...
  ADGetDirDLGs
Allows the user to read all the docking logs in a chosen directory Package : AutoDockTools Module : autoanalyzeCommands Class : ADGetDirDLGs Command : ADanalyze_readAllDLGinDirectory Synopsis: None<---ADanalyze_readAllDLGinDirectory(dlgDir, makeOneDocking) Required Arguments: dlgDir --- directory containing any number of docking log files Optional Arguments: makeOneDocking --- whether to compile all dlg results into one Docking object with 1 list of conformations and ability to do clustering if not, a separate Docking is created for each docking logfile.
  ADGetDLG
Allows the user to select a filename for the docking log...
  ClusterDockingChooser
  ModelDockingChooser
  ADDrawHistogram
  ADMacroLigandChart
  ADDockingChooser
  ReadAutoDockStates
  StatesPlayerWidget
  ShowAutoDockStatesBaseCmd
base cmd for cmds allowing user to show different docked states of a ligand
  ShowAutoDockStates
allows user to show different docked states of a ligand
  ShowAutoDockStatesByEnergy
allows user to show docked states of a ligand ordered by energy
  ShowAutoDockPopulation
allows user to show population created in autodock
  ShowAutoDockStatesHISTOGRAM
allows user to show histogram of docked states of a ligand
  ShowAutoDockClusteringStates
allows user to show states in a CLUSTERING of docked states of a ligand
  ReadAutoDockClusteringStates
allows user to read in a CLUSTERING from a 'clust' file
  WriteAutoDockStates
allows user to write Entropia type clustered docking results
  WriteAutoDockClustering
allows user to write Clustering results
  MakeAutoDockCLUSTERING
allows user to make clustering of docking results at specified rms tolerances
  MakeAutoDockSubsetCLUSTERING
allows user to make clustering of docking results at specified rms tolerances using a subset of the atoms in the docked ligand

Functions [hide private]
  checkHasInitializedDockings(vf)
  hideShowHide(vf, mol)
  toggleShowHide(vf, molname)
  checkNameStr(molname)
  getCoords_subset(conf)
Return coordinates of conf's current subset, if there is one.
  getRMSD_subset(conf, refCoords=None)
Return RMSD of conf's subset relative to refCoords.
  get_distance_subset(clusterer, a, b)
return RMSD between subsets of atoms in two conformations, a and b.
  initModule(vf)

Variables [hide private]
  menuText = {'seeSpots': 'Show as Spheres...', 'DockingLogMB': '...
  ADChooseMacroGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ADReadMacroGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ADEPDBMolGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ADSeeSpotsGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ADShowBindingSiteGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ADMakeAllGridsGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ADGetOutputGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ADGetAGridGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ADSelectDLGGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ADDeleteDLGGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ADGetDirDLGsGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ADGetDLGGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  colorsList = ['black', 'brown', 'blue', 'red']
  ADDrawHistogramGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ADMacroLigandChartGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ADDockingChooserGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ReadAutoDockStatesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ShowAutoDockStatesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ShowAutoDockStatesByEnergyGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ShowAutoDockPopulationGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ShowAutoDockStatesHISTOGRAMGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ShowAutoDockStatesCLUSTERINGGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ReadAutoDockStatesCLUSTERINGGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  WriteAutoDockStatesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  WriteAutoDockClusteringGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  MakeAutoDockCLUSTERINGGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  MakeAutoDockSubsetCLUSTERINGGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  commandList = [{'gui': <ViewerFramework.VFCommand.CommandGUI insta...
  i = {'gui': <ViewerFramework.VFCommand.CommandGUI instan...

Function Details [hide private]

checkHasInitializedDockings(vf)

source code 
None

hideShowHide(vf, mol)

source code 
None

toggleShowHide(vf, molname)

source code 
None

checkNameStr(molname)

source code 
None

getCoords_subset(conf)

source code  
Return coordinates of conf's current subset, if there is one.

If the coordinates haven't been computed yet,
    then compute, save, and return them.
Otherwise, return the previously-computed coordinates.

getRMSD_subset(conf, refCoords=None)

source code 

Return RMSD of conf's subset relative to refCoords.

If refCoords is not given, the original coordinates for the subset will be used as the reference.

get_distance_subset(clusterer, a, b)

source code 
return RMSD between subsets of atoms in two conformations, a and b.

initModule(vf)

source code 
None

Variables Details [hide private]

menuText

None
Value:
{'AnalyzeMB': 'Analyze',
 'ClusteringMB': 'Clusterings',
 'DockingLogMB': 'Dockings',
 'GridsMB': 'Grids',
 'MoleculesMB': 'Macromolecule',
 'ResultsMB': 'Other Results',
 'StatesMB': 'Conformations',
 'addGridMB': 'Open Other...',
...

ADChooseMacroGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6e3c7ec>

ADReadMacroGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6ebfeec>

ADEPDBMolGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6ebfe0c>

ADSeeSpotsGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6eb530c>

ADShowBindingSiteGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6e5a3ac>

ADMakeAllGridsGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6e5a42c>

ADGetOutputGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6e5a46c>

ADGetAGridGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6e5a4ac>

ADSelectDLGGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6e5a4ec>

ADDeleteDLGGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6e5a52c>

ADGetDirDLGsGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6e5a58c>

ADGetDLGGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6e5a5ec>

colorsList

None
Value:
['black', 'brown', 'blue', 'red']

ADDrawHistogramGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6e5a78c>

ADMacroLigandChartGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6e5a8ec>

ADDockingChooserGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6e5a9ac>

ReadAutoDockStatesGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6e5aa2c>

ShowAutoDockStatesGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6e5acac>

ShowAutoDockStatesByEnergyGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6e5ad2c>

ShowAutoDockPopulationGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6e5adac>

ShowAutoDockStatesHISTOGRAMGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6e5ae8c>

ShowAutoDockStatesCLUSTERINGGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6e5af6c>

ReadAutoDockStatesCLUSTERINGGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6e5afec>

WriteAutoDockStatesGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6e6f08c>

WriteAutoDockClusteringGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6e6f10c>

MakeAutoDockCLUSTERINGGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6e6f1cc>

MakeAutoDockSubsetCLUSTERINGGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6e6f28c>

commandList

None
Value:
[{'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb6e5a5ec>
,
  'name': 'ADanalyze_readDLG'},
 {'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb6e5a58c>
,
  'name': 'ADanalyze_readAllDLGInDirectory'},
...

i

None
Value:
{'cmd': self.,
 'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb6e5a42c>,
 'name': 'ADanalyze_showGridIsocontours'}

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