Package Pmv :: Module repairCommands :: Class CheckForCloseContacts
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Class CheckForCloseContacts

source code

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

This command detects atoms which are selected as "close" by a MolKit.distanceSelector.  These selectors use criteria such as closer than combined atomic radii distance of nodes or closer than a specific distance.
   
Package : Pmv
   
Module  : repairCommands
   
Class   : CheckForCloseContacts
   
Command : checkForCloseContacts
   
Synopsis:
   
        closeAts <--- checkForCloseContacts(keyNodes, nodesToCheck, percentCutoff, **kw)
   
Required Arguments:

        keyNodes --- nodes to use as centers for selectInSphere of distance keyNode.radius + radius nodes in nodesToCheck
        
nodesToCheck --- nodes to test to see if within sumRadii distance of keyNodes. 
   
Optional Arguments:
     
        percentCutoff ---  each sum of radii * this number is used to pick close contacts
        
distSelectorClass=None --- optional distanceSelector Class.default class is CloserThanVDWSelector
    



Instance Methods [hide private]
  onAddCmdToViewer(self)
method called when an instance of this command is added to the viewer.
  doit(self, keyAts, checkAts, percentCutoff, distanceCutoff, **kw)
virtual method.
  cleanupDicts(self, atDict, distDict)
  __call__(self, keyNodes, nodesToCheck, percentCutoff=1.0, distanceCutoff=3.0, distSelectorClass=None, **kw)
closeAts <- checkForCloseContacts(keyNodes, nodesToCheck, percentCutoff, **kw) Required Arguments: keyNodes --- nodes to use as centers for selectInSphere of distance keyNode.radius + radius nodes in nodesToCheck nodesToCheck --- nodes to test to see if within sumRadii distance of keyNodes.

Inherited from mvCommand.MVCommand: __init__, guiCallback, strArg

Inherited from mvCommand.MVCommand (private): _strArg

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


Class Variables [hide private]

Inherited from ViewerFramework.VFCommand.Command: negateKw, objArgOnly


Method Details [hide private]

onAddCmdToViewer(self)

source code 
method called when an instance of this command is added to the viewer. This enable viewer-addition time initializations
Overrides: ViewerFramework.VFCommand.Command.onAddCmdToViewer
(inherited documentation)

doit(self, keyAts, checkAts, percentCutoff, distanceCutoff, **kw)

source code 
virtual method. Has to be implemented by the sub classes
Overrides: ViewerFramework.VFCommand.Command.doit
(inherited documentation)

cleanupDicts(self, atDict, distDict)

source code 
None

__call__(self, keyNodes, nodesToCheck, percentCutoff=1.0, distanceCutoff=3.0, distSelectorClass=None, **kw)
(Call operator)

source code 
closeAts <- checkForCloseContacts(keyNodes, nodesToCheck, percentCutoff, **kw)
        
Required Arguments:

        keyNodes --- nodes to use as centers for selectInSphere of distance keyNode.radius + radius nodes in nodesToCheck

        nodesToCheck --- nodes to test to see if within sumRadii distance of keyNodes.
 
        
Optional Arguments:

        percentCutoff --- each sum of radii * this number is used to pick close contacts

        distSelectorClass=None --- optional distanceSelector Class

        

Overrides: ViewerFramework.VFCommand.Command.__call__