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SetupAmber94 This command creates an instance of Amber94 class and enters it in Amber94Config dictionary with specified name as the key. |
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SetMinimOptsAmber94 This class allows you to set minimization options of a Amber94 instance These options include cut, nsnb, dield and verbose. |
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MinimizeAmber94 This class allows you to select an Amber94 instance from Amber94Config whose keys are ids specified in setup_Amber94 for the Amber94 instances. |
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FreezeAtomsAmber94 ... |
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ConstrainAtomsAmber94 ... |
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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. |
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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. |
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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. |
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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'. |
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FixAmberHAtomNamesGUICommand This class provides Graphical User Interface to FixAmberHAtomsNameCommand which is invoked by it with the current selection, if there is one. |
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FixAmberResNamesAndOrderAtomsCommand This class reorders atoms to conform to Amber conventions. |
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| initModule(viewer) |
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Amber94Config = {}
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CurrentAmber94 = {}
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SetupAmber94CommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
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SetMinimOptsAmber94CommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
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MinimizeAmber94CommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
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FreezeAtomsAmber94CommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
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ConstrainAtomsAmber94CommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
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SetMDOptsAmber94CommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
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MolecularDynamicsAmber94CommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
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PlayMolecularDynamicsTrjAmber94CommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
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fixAmberHAtomNamesGUICommandGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Hydr...
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FixAmberHAtomNamesGUICommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
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commandList = [{'gui': <ViewerFramework.VFCommand.CommandGUI insta...
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Amber94ConfigNone
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CurrentAmber94None
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SetupAmber94CommandGUINone
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SetMinimOptsAmber94CommandGUINone
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MinimizeAmber94CommandGUINone
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FreezeAtomsAmber94CommandGUINone
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ConstrainAtomsAmber94CommandGUINone
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SetMDOptsAmber94CommandGUINone
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MolecularDynamicsAmber94CommandGUINone
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PlayMolecularDynamicsTrjAmber94CommandGUINone
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fixAmberHAtomNamesGUICommandGuiDescrNone
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FixAmberHAtomNamesGUICommandGUINone
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commandListNone
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