Package MolKit :: Package VisionInterface :: Module MolKitNodes :: Class SpheresAsMSMS

Class SpheresAsMSMS

                             object --+                
                                      |                
NetworkEditor.itemBase.NetworkItemsBase --+            
                                          |            
        NetworkEditor.itemBase.NetworkItems --+        
                                              |        
            NetworkEditor.items.NetworkNodeBase --+    
                                                  |    
                    NetworkEditor.items.NetworkNode --+
                                                      |
                                                     SpheresAsMSMS

Compute solvent excluded surface using the MSMS library.

Input ports:
  centers: a set of atoms for which to compute a surface
  radii: optional atomic radii. If they are ommited, we tri to get them
         from the atoms
  seedAtoms: a list of up to 3 atoms that are used to position the rolling
         probe initially. Can be used to compute cavity surfaces.
  density: floating point value describing the number of vertices per
         angstrom square used for triangulating the surface
  probe_radius: floating point value decribing the radius of the rolling
         probe sphere.
  allComp: Boolean value triggering the computation of all components
  
  OutputPort:
    MSMS: outputs an MSMSObject

  The set of atoms used to calculate the surface are stored in the atoms
  attribute of the MSMSobject. By default, the probe_radius and the
  density parameters are bound to dials and allComp is bound to a check-
  button widget located in the parameter panel.

Instance Methods

[hide private]

__init__(self, name='MSMS from spheres', **kw)

beforeAddingToNetwork(self, net)

Inherited from NetworkEditor.items.NetworkNode: addInputPort, addOutputPort, addSpecialPorts, buildNodeIcon, buildSmallIcon, deletePort, deletePortByName, deleteSmallIcon, deselect, editorVisible, getColor, getFont, hideSpecialPorts, isExpanded, refreshInputPortData, resizeIcon, select, setColor, setFont, setModifiedTag, setProgressBar, showSpecialPorts, updatePosXPosY

Inherited from NetworkEditor.items.NetworkNodeBase: addSaveNodeMenuEntries, autoResize, autoResizeX, autoResizeY, buildIcons, checkIfNodeForSavingIsDefined, compareToOrigNodeDescr, computeFunction, configure, cut_cb, delete_cb, edit, editComputeFunction_cb, evalString, getAfterConnectionsSourceCode, getComputeFunctionSourceCode, getConnections, getDescr, getHeaderBlock, getInConnections, getInitBlock, getInputPortByName, getNodeDefinitionSourceCode, getNodeSourceCode, getNodeSourceCodeForDoit, getNodeSourceCodeForInstanciation, getNodeSourceCodeForModifications, getNodeSourceCodeForNode, getNodeSourceCodeForPorts, getNodeSourceCodeForWidgetValue, getNodeSourceCodeForWidgets, getOutConnections, getOutputPortByName, getOutputPortByType, getPortsCreationSourceCode, getSize, getSourceCode, getSpecialInputPortByName, getSpecialOutputPortByName, getStateDefinitionCode, getUniqueNodeName, getWidgetByName, getWidgetsCreationSourceCode, getWidgetsForMaster, getWidthForLabel, getWidthForNodeWidgets, getWidthForPorts, growDown, growRight, hideInNodeWidgets, isMacro, isModified, ischild, move, moveSelectedNodeEnd, outputData, rename, resetModifiedTag, resetTags, safeName, saveSource, saveSource_cb, schedule, scheduleChildren, schedule_cb, setFunction, showInNodeWidgets, startMoveOneNode, toggleNodeExpand_cb, toggleParamPanel_cb, updateCode

Inherited from NetworkEditor.itemBase.NetworkItems: __repr__, afterAddingToNetwork, afterRemovingFromNetwork, beforeRemovingFromNetwork, deleteIcon, editNodeMenu, freeze, gettags, hideParamPanel, highlight, introspect, postItemMenu, run, toggleAutoRun_cb, toggleFrozen_cb, unfreeze, unhighlight

Inherited from NetworkEditor.itemBase.NetworkItems (private): _introspectCB

Inherited from NetworkEditor.itemBase.NetworkItemsBase: delEditor, getEditor, setEditor

Inherited from NetworkEditor.itemBase.NetworkItemsBase (private): _setModified, _setOriginal

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __str__

Properties

[hide private]

Inherited from NetworkEditor.itemBase.NetworkItemsBase: editor

Inherited from object: __class__

Method Details

[hide private]

init(self, name='MSMS from spheres', **kw)
(Constructor)

source code

None

Overrides: NetworkEditor.items.NetworkNode.__init__

beforeAddingToNetwork(self, net)

source code

None

Overrides: NetworkEditor.itemBase.NetworkItems.beforeAddingToNetwork

Class SpheresAsMSMS

__init__(self, name='MSMS from spheres', **kw) (Constructor)

beforeAddingToNetwork(self, net)

init(self, name='MSMS from spheres', **kw)
(Constructor)