Package Pmv :: Module msmsCommands :: Class IdentifyBuriedVertices
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Class IdentifyBuriedVertices

source code

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

This command enables finding out and tagging the vertices of a Solvent excluded surface that are buried by a set of atoms.

    Package : Pmv

    Module  : msmsCommands

    Class   :IdentifyBuriedVertices

    Command name :identifyBuriedVertices

    
Description:

    After running this command the vertices that are buried are tagged in
    the MSMS data structure with the buried flag (which is return by the
    ses.getTriangles() method. Each vertex of the triangulated ses also
    has a member called sesArea and sasArea that hold the surface area
    corresponding to each vertex of the triagulation.

    
Synopsis:

    areas <- identifyBuriedVertices(surfaceName, surfaceMol, nodes)

    
Required Arguments:

      surfaceName ---  name of an MSMS surface computed using MSMS

      surfaceMol --- molecule for which the surface 'surfaceName' has been computed

      nodes --- string or objects that expand into a set of atoms

      



Instance Methods [hide private]
  checkDependencies(self)
make sure the mslib package is available
  doit(self, surfaceName, surfaceMol, nodes)
surfaceName---name of an MSMS surface computed using MSMS surfaceMol---molecule for which the surface 'surfaceName' has been computed nodes---string or objects that expand into a set of atoms which may bury parts of the MSMS surface Return---a dictionary with 2 keys: 'ses' and 'sas'.
  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)
  __call__(self, surfaceName, surfaceMol, nodes, **kw)
areas <- identifyBuriedVertices(surfaceName, surfaceMol, nodes, **kw) Compute the area of the SES and SAS surface buried by a set of atoms Arguments: surfaceName--- name of an MSMS surface computed using MSMS surfaceMol--- molecule for which the surface 'surfaceName' has been computed nodes--- string or objects that expand into a set of atoms Return---a dictionary with 2 keys: 'ses' and 'sas'.

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, nodes)

source code 

        
surfaceName---name of an MSMS surface computed using MSMS
        
surfaceMol---molecule for which the surface 'surfaceName' has been
        computed
        
nodes---string or objects that expand into a set of atoms which may bury
        parts of the MSMS surface

        
Return---a dictionary with 2 keys: 'ses' and 'sas'. The values are
        either lists of buried surface areas for all components considered.
        

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 
None
Overrides: mvCommand.MVCommand.guiCallback

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

source code 
areas <- identifyBuriedVertices(surfaceName, surfaceMol, nodes,
                                           **kw)

        Compute the area of the SES and SAS surface buried by a set of atoms

        
Arguments:

        surfaceName--- name of an MSMS surface computed using MSMS

        surfaceMol--- molecule for which the surface 'surfaceName' has been computed
 
        nodes--- string or objects that expand into a set of atoms

        Return---a dictionary with 2 keys: 'ses' and 'sas'. The values are either
        lists of buried surface areas for all components considered.

        

Overrides: ViewerFramework.VFCommand.Command.__call__