Package Pmv :: Module msmsCommands :: Class AssignBuriedAreas
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Class AssignBuriedAreas

source code

ViewerFramework.VFCommand.Command --+    
                                    |    
                  mvCommand.MVCommand --+
                                        |
                                       AssignBuriedAreas

Command to sum the areas of the buried vertices for each atom.

    Package : Pmv

    Module  : msmsCommands

    Class   : AssignBuriedAreas

    Command name : assignBuriedAreas

    
Description:

    This command assumes that a command to find buried vertices has been run
previousely

    
Synopsis :

    None <- assignBuriedAreas(surfaceName, surfaceMol)

    
Required Arguments:

    surfaceName---name of an MSMS surface computed using msms. (string)

    surfaceMol---molecule for which the surface 'surfaceName' has been computed. (string, TreeNode or TreeNodeSet)

    
Optional Arguments:

     attributes---buriedSES and buriedSAS.



Instance Methods [hide private]
  checkDependencies(self)
make sure the mslib package is available
  doit(self, surfaceName, surfaceMol)
surfaceName---name of an MSMS surface computed using MSMS surfaceMol: molecule for which the surface 'surfaceName' has been computed Return: None after the command is executed each atom and residue has a 2 attributes: buriedSES and buriedSAS.
  selectMolecule_cb(self, event=None)
  OK_cb(self, event=None)
call back for OK button
  buildFormDescr(self, formName)
descr <- buildFormDescr(self, formName): this virtual method is implemented in the classes derived from Command.
  guiCallback(self, event=None)
Default callback function called by the gui
  __call__(self, surfaceName, surfaceMol, **kw)
None <- assignBuriedAreas(surfaceName, surfaceMol, **kw) Assign buried surface areas to atoms and residues.

Inherited from mvCommand.MVCommand: __init__, strArg

Inherited from mvCommand.MVCommand (private): _strArg

Inherited from ViewerFramework.VFCommand.Command: __repr__, addCallbackAfter, addCallbackBefore, addUndoCall, afterDoit, beforeDoit, buildLogArgList, cleanup, customizeGUI, doitWrapper, getArguments, getHelp, getLastUsedValues, getLogArgs, getValNamedArgs, log, logString, onAddCmdToViewer, onAddNewCmd, onCmdRun, setLastUsedValues, setupUndoAfter, setupUndoBefore, showForm, tkCb, updateGeom, warningMsg


Class Variables [hide private]

Inherited from ViewerFramework.VFCommand.Command: negateKw, objArgOnly


Method Details [hide private]

checkDependencies(self)

source code 
make sure the mslib package is available
Overrides: ViewerFramework.VFCommand.Command.checkDependencies

doit(self, surfaceName, surfaceMol)

source code 

surfaceName---name of an MSMS surface computed using MSMS
        
surfaceMol: molecule for which the surface 'surfaceName' has been computed
        
Return: None
        
after the command is executed each atom and residue has a 2 attributes:
        buriedSES and buriedSAS.

Overrides: ViewerFramework.VFCommand.Command.doit

selectMolecule_cb(self, event=None)

source code 
None

OK_cb(self, event=None)

source code 
call back for OK button

buildFormDescr(self, formName)

source code 
descr <- buildFormDescr(self, formName): this virtual method is implemented in the classes derived from Command. This is where the inputFormDescr is created and the description of the widgets appended. If a command has several inputForm buildFormDescr should build all the inputFormDescr and you do a if / elif check to know which one to create. formName : string name of the form corresponding to this descr.
Overrides: ViewerFramework.VFCommand.Command.buildFormDescr
(inherited documentation)

guiCallback(self, event=None)

source code 
Default callback function called by the gui
Overrides: mvCommand.MVCommand.guiCallback

__call__(self, surfaceName, surfaceMol, **kw)
(Call operator)

source code 
None <- assignBuriedAreas(surfaceName, surfaceMol, **kw)       
        
Assign buried surface areas to atoms and residues.

        
Arguments:

        surfaceName--- name of an MSMS surface computed using msms. (string)

        surfaceMol--- molecule for which the surface 'surfaceName' has been computed. (string, TreeNode or TreeNodeSet)

        After the command is executed all atoms and residues have 2 new

        attributes--- buriedSES and buriedSAS.

        

Overrides: ViewerFramework.VFCommand.Command.__call__