Package Pmv :: Module msmsCommands
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Module msmsCommands

source code

Classes [hide private]
  ReadMSMS
Command reads .face and .vert file, creates the msms surface and links it to the selection if can...
  SaveMSMS
The SaveMSMS commands allows the user to save a chosen MSMS surface (tri-angulated solvant excluded surface) resulting from a calculation.
  ComputeMSMS
The computeMSMS command will compute a triangulated solvent excluded surface for the current selection.
  DisplayMSMS
The displayMSMS command allows the user to display/undisplay or display only the given MSMS surface corresponding to the current selection.
  UndisplayMSMS
The undisplayMSMS command allows the user to undisplay displayedMSMS Package : Pmv Module : msmsCommands Class : UndisplayMSMS Command name : undisplayMSMS Required Arguments: nodes --- TreeNodeSet holding the current selection .
  ComputeMSMSApprox
Computes an approximative molecular surface for a selected set of atoms by molecule.
  MsmsNPR
This command sets colors of MSMS surface to make it look NPR...
  IdentifyBuriedVertices
This command enables finding out and tagging the vertices of a Solvent excluded surface that are buried by a set of atoms.
  DisplayBuriedTriangles
This Command display/Undisplay buried SES as computed with BuriedSurface command.
  DisplayIntermolecularBuriedTriangles
This Command display/Undisplay buried SES between two molecules.
  AssignBuriedAreas
Command to sum the areas of the buried vertices for each atom.

Functions [hide private]
  initModule(viewer)

Variables [hide private]
  ReadMSMSGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  SaveMSMSGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ComputeMSMSGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  DisplayMSMSGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ComputeMSMSApproxGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  msmsNPRGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Compu...
  MsmsNPRGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  identifyBuriedVerticesGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Compu...
  IdentifyBuriedVerticesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  displayBuriedTrianglesGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Displ...
  DisplayBuriedTrianglesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  displayBuriedIntermolecularTrianglesGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Displ...
  DisplayIntermolecularBuriedTrianglesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  assignBuriedSurfaceGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Mole...
  AssignBuriedAreasGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  commandList = [{'gui': <ViewerFramework.VFCommand.CommandGUI insta...

Function Details [hide private]

initModule(viewer)

source code 
None

Variables Details [hide private]

ReadMSMSGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb2c3fd6c>          
      

SaveMSMSGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb2c3fdac>          
      

ComputeMSMSGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb2c3fe6c>          
      

DisplayMSMSGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb2c3fecc>          
      

ComputeMSMSApproxGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb2c3ff4c>          
      

msmsNPRGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Compute',
 'menuEntryLabel': 'NPR MSMS For Selection',
 'widgetType': 'Menu'}                                                 
      

MsmsNPRGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb2c3ff8c>          
      

identifyBuriedVerticesGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Compute',
 'menuEntryLabel': 'Compute Buried Surface',
 'widgetType': 'Menu'}                                                 
      

IdentifyBuriedVerticesGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb2c4c04c>          
      

displayBuriedTrianglesGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Display',
 'menuEntryLabel': 'Buried Surface',
 'widgetType': 'Menu'}                                                 
      

DisplayBuriedTrianglesGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb2c4c10c>          
      

displayBuriedIntermolecularTrianglesGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Display',
 'menuEntryLabel': 'Buried Surface',
 'widgetType': 'Menu'}                                                 
      

DisplayIntermolecularBuriedTrianglesGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb2c4c1ec>          
      

assignBuriedSurfaceGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Compute',
 'menuCascadeName': 'Molecular Surface',
 'menuEntryLabel': 'Assign Buried Surface',
 'widgetType': 'Menu'}                                                 
      

AssignBuriedAreasGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb2c4c2ac>          
      

commandList

None
Value:
[{'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb2c3fd6c>
,
  'name': 'readMSMS'},
 {'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb2c3fe6c>
,
  'name': 'computeMSMS'},
...