Package Pmv :: Module msmsCommands

Module msmsCommands

Classes

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'},
...