Package Pmv :: Module bondsCommands

Module bondsCommands

Classes

BuildBondsByDistance
This command creates the bonds between atoms of the given set of nodes and connect the residues when necessary.

AddBondsGUICommand
The AddBondGUICommand provides an interactive way of creating bonds between two given atoms by picking on them.

AddBondsCommand
The AddBondsCommand is a command to connect two given atoms.This command will not allow the creation inter-molecular bonds.This command doesn't have a GUI interface and can only be called through the pyShell.

RemoveBondsGUICommand
The RemoveBondsGUICommands provides an interactive way of deleting picked bonds.

RemoveBondsCommand
The RemoveBondsCommand allows the user to remove the bond existing between two given atoms (atom1 and atom2).

Functions

[hide private]

initModule(viewer)

Variables

[hide private]

var = 0
Package: Pmv Module : bondsCommands This module provides a set of commands: - BuildBondsByDistance (buildBondsByDistance) to compute the bonds between atoms of the given nodes and connect the residues when necessary.

buildBondsByDistanceDescr = {'widgeType': 'Menu', 'menuBarName': 'Edit', 'menuCa...

BuildBondsByDistanceGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

AddBondsGUICommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

RemoveBondsGUICommandGUI = <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]

var


Package: Pmv
Module : bondsCommands
This module provides a set of commands:
- BuildBondsByDistance (buildBondsByDistance) to compute the bonds between
  atoms of the given nodes and connect the residues when necessary.
- AddBondsCommands (addBonds) to create a bond instance between two given atoms.
    -no gui
- AddBondsGUICCommands (addBondsGC) to create a bond between two picked
  atoms. If a group of atoms is selected by dragging, it will
  buildBondsByDistance between them.  
  This is an interactive command (ICOM) and the GUI version of addBonds.
- RemoveBondsCommands (removeBonds) to delete an existing bonds between the
  two given atoms.
    -no gui
- RemoveBondsGUICCommands (removeBondsGC) to delete the picked bond. If a
  groups of atoms is selected by dragging, it will remove all the bonds
  between them. 
  This is the GUI command of the removeBonds and it is an ICOM.

The menubuttons for BondsCommands are located under the 'Bonds' entry in the 'Edit' menu.

Value:

buildBondsByDistanceDescr

None

Value:

{'menuBarName': 'Edit',
 'menuButtonName': 'Build By Distance',
 'menuCascadeName': 'Bonds',
 'widgeType': 'Menu'}

BuildBondsByDistanceGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb76ba40c>

AddBondsGUICommandGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb76ba48c>

RemoveBondsGUICommandGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb76ba4ec>

commandList

None

Value:

[{'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb76ba40c>
,
  'name': 'buildBondsByDistance'},
 {'gui': None, 'cmd': self., 'name': 'addBonds'},
 {'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb76ba48c>
,
...