Package Pmv :: Module amberCommands
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Module amberCommands

source code

Classes [hide private]
  SetupAmber94
This command creates an instance of Amber94 class and enters it in Amber94Config dictionary with specified name as the key.
  SetMinimOptsAmber94
This class allows you to set minimization options of a Amber94 instance These options include cut, nsnb, dield and verbose.
  MinimizeAmber94
This class allows you to select an Amber94 instance from Amber94Config whose keys are ids specified in setup_Amber94 for the Amber94 instances.
  FreezeAtomsAmber94
...
  ConstrainAtomsAmber94
...
  SetMDOptsAmber94
This class allows you to set md options of a Amber94 instance these options include t, dt, tautp, temp0, verbose, vlimit, ntpr_md, zerov,tempi and idum.
  MolecularDynamicsAmber94
This class allows you to select an Amber94 instance from Amber94Config whose keys are ids specified in setup_Amber94 for the Amber94 instances.You can also set md options, freeze atoms, specify constrained atoms and anchor atoms and set maxStep.
  PlayMolecularDynamicsTrjAmber94
This class allows you to select an Amber94 instance from Amber94Config whose keys are ids specified in setup_Amber94 for the Amber94 instances, and a molecular dynamics trajectory file and play the trajectory.
  FixAmberHAtomNamesCommand
This class checks hydrogen atom names and modifies them to conform to Package : Pmv Module : amberCommands Class : FixAmberHAtomNamesCommand Command : fixAmberHAtomNamesCommand Synopsis: None <- fixAmberHNames(nodes, **kw) Arguments: nodes --- TreeNodeSet holding the current selection Amber conventions: Single hydrogen atoms bonded to N are named 'H'.
  FixAmberHAtomNamesGUICommand
This class provides Graphical User Interface to FixAmberHAtomsNameCommand which is invoked by it with the current selection, if there is one.
  FixAmberResNamesAndOrderAtomsCommand
This class reorders atoms to conform to Amber conventions.

Functions [hide private]
  initModule(viewer)

Variables [hide private]
  Amber94Config = {}
  CurrentAmber94 = {}
  SetupAmber94CommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  SetMinimOptsAmber94CommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  MinimizeAmber94CommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  FreezeAtomsAmber94CommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ConstrainAtomsAmber94CommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  SetMDOptsAmber94CommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  MolecularDynamicsAmber94CommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  PlayMolecularDynamicsTrjAmber94CommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  fixAmberHAtomNamesGUICommandGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Hydr...
  FixAmberHAtomNamesGUICommandGUI = <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]

Amber94Config

None
Value:
{}                                                                     
      

CurrentAmber94

None
Value:
{}                                                                     
      

SetupAmber94CommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb310d72c>          
      

SetMinimOptsAmber94CommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb312292c>          
      

MinimizeAmber94CommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb30d3d4c>          
      

FreezeAtomsAmber94CommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb30d3e2c>          
      

ConstrainAtomsAmber94CommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb30d3fec>          
      

SetMDOptsAmber94CommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb305f0cc>          
      

MolecularDynamicsAmber94CommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb305f28c>          
      

PlayMolecularDynamicsTrjAmber94CommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb305f3ac>          
      

fixAmberHAtomNamesGUICommandGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Amber',
 'menuCascadeName': 'Hydrogens',
 'menuEntryLabel': 'Fix Amber Hydrogen Names',
 'widgetType': 'Menu'}                                                 
      

FixAmberHAtomNamesGUICommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb305f46c>          
      

commandList

None
Value:
[{'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb310d72c>
,
  'name': 'setup_Amber94'},
 {'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb312292c>
,
  'name': 'setminimOpts_Amber94'},
...