Package Pmv :: Module editCommands
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Module editCommands

source code

Classes [hide private]
  TypeAtomsCommand
This class uses the AtomHybridization class to assign atom types.
  EditAtomTypeGUICommand
This class provides the GUI to EditAtom Type which allows the user to change assigned atom types.
  EditAtomTypeCommand
This class allows the user to change assigned atom types.
  EditAtomChargeGUICommand
This class provides the GUI to EditAtomCharge which allows the user to change atom charge.
  TypeBondsCommand
This class uses the BondOrder class to compute bond order.
  AddHydrogensGUICommand
This GUICOMMAND class calls the AddHydrogenCommand class.
  AddHydrogensCommand
This command adds hydrogen atoms to all atoms in all molecules that have at least one member (i.e atom, residue, chain, base-pair etc..) specified in the first argument.
  FixHydrogenAtomNamesGUICommand
This class provides Graphical User Interface to FixHydrogenAtomsNameCommand which is invoked by it with the current selection, if there is one.
  FixHydrogenAtomNamesCommand
This class checks hydrogen atom names and modifies them to conform to 'IUPAC-IUB' conventions Package:Pmv Module :editCommands Class:FixHydrogenAtomNamesCommand Command:fixHNames Synopsis: None <- fixHNames(nodes, **kw) Required Arguments: nodes --- TreeNodeSet holding the current selection Hydrogen names have 4 spaces:'H _ _ _', (here referred to as 1-4).
  SplitNodesGUICommand
This class presents GUI for SplitNodesCommand ...
  SplitNodesCommand
This class allows the user to split current selection from unselected nodes.
  MergeFieldsCommand
This class allows the user to change the fields of one set by the values of another set.
  MergeSetsCommand
This class allows the user to merge two sets into one.
  MergeNPHsGUICommand
This class implements GUICommand for MergeNPHsCommand below...
  MergeNPHsCommand
This class merges non-polar hydrogens and the carbons to which they are attached.
  MergeLonePairsGUICommand
This class presents GUI for MergeLonePairsCommand...
  MergeLonePairsCommand
This class merges lone-pairs and the sulfur atoms to which they are attached.There are three parts to the process:the charges of lone-pairs, if any, are added to those of the sulfurs the bond between the lone-pair and its sulfur is removed from the sulfur's bonds the lone-pair 'atoms' are deleted Package:Pmv Module :editCommands Class:MergeLonePairsCommand Command:mergeLPS Synopsis: None<---mergeLPS(nodes, **kw) Required Arguments: nodes --- TreeNodeSet holding the current selection NB: the lone pairs are identified by these criteria: the element field of the lone pair 'atom' is 'Xx' and its name has a 'L' in the first or second position.
  ComputeGasteigerGUICommand
Calls computeGasteiger which does work of computing gasteiger partial charges for each atom and entering each atom's charge in its _charges dictionary.
  ComputeGasteigerCommand
Does work of computing gasteiger partial charges for each atom and entering each atom's charge in its '_charges' dictionary as value for key 'gasteiger' (rounded to 4 decimal places).
  AddKollmanChargesGUICommand
Kollman united atom charges are added to atoms in peptides by looking up each atom's parent and name in table in Pmv.qkollua.
  AddKollmanChargesCommand
Kollman united atom partial charges are added to atoms by looking up each atom's parent's type to get a dictionary of charges for specific atom names (from Pmv.qkollua).
  AverageChargeErrorCommand
Adjusts the charge on each atom in residue with non-integral overall charge so that the sum of the charge on all the atoms in the residue is an integer.
  CheckChargesGUICommand
Allows user to call checkResCharges on each residue in selection...
  SetChargeCommand
allows user to set string used to index into _charges dictionary Package:Pmv Module :editCommands Class:SetChargeCommand Command:setChargeSet Synopsis: None<---setChargeSet(nodes, key, **kw) Required Arguments: nodes --- TreeNodeSet holding the current selection key --- what charges (keyword of the _charges dictionary).
  CheckResidueChargesCommand
Allows user to check charges on each residue + whole molecule ...
  AssignAtomsRadiiCommand
This commands adds radii to all the atoms loaded so far in the application.

Functions [hide private]
  check_edit_geoms(VFGUI)
    'name':'mergeSets','cmd':MergeSetsCommand(),
  initModule(viewer)

Variables [hide private]
  typeAtomsCommandGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Atom...
  TypeAtomsCommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  editAtomTypeGUICommandGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Atom...
  EditAtomTypeGUICommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  editAtomChargeGUICommandGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Atom...
  EditAtomChargeGUICommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  typeBondsCommandGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Bond...
  TypeBondsCommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  addHydrogensGUICommandGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Hydr...
  AddHydrogensGUICommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  fixHydrogenAtomNamesGUICommandGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Hydr...
  FixHydrogenAtomNamesGUICommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  splitNodesGUICommandGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Misc...
  SplitNodesGUICommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  mergeFieldsCommandGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Misc...
  MergeFieldsCommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  mergeSetsCommandGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Misc...
  MergeSetsCommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  mergeNPHsGUICommandGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Hydr...
  MergeNPHsGUICommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  mergeLonePairsCommandGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Misc...
  MergeLonePairsGUICommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  computeGasteigerGUICommandGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Char...
  ComputeGasteigerGUICommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  addKollmanChargesGUICommandGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Char...
  AddKollmanChargesGUICommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  checkChargesGUICommandGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Char...
  CheckChargesGUICommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  setChargeGUICommandGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Char...
  SetChargeCommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  assignAtomsRadiiGUICommandGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Atom...
  AssignAtomsRadiiCommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
    'name':'mergeSets','cmd':MergeSetsCommand(),
  commandList = [{'gui': <ViewerFramework.VFCommand.CommandGUI insta...

Function Details [hide private]

check_edit_geoms(VFGUI)

source code 
None

initModule(viewer)

source code 
None

Variables Details [hide private]

typeAtomsCommandGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Edit',
 'menuCascadeName': 'Atoms',
 'menuEntryLabel': 'Type',
 'widgetType': 'Menu'}                                                 
      

TypeAtomsCommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb766b3ec>          
      

editAtomTypeGUICommandGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Edit',
 'menuCascadeName': 'Atoms',
 'menuEntryLabel': 'Edit Type',
 'widgetType': 'Menu'}                                                 
      

EditAtomTypeGUICommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb766b46c>          
      

editAtomChargeGUICommandGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Edit',
 'menuCascadeName': 'Atoms',
 'menuEntryLabel': 'Edit Charge',
 'widgetType': 'Menu'}                                                 
      

EditAtomChargeGUICommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb766b4ec>          
      

typeBondsCommandGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Edit',
 'menuCascadeName': 'Bonds',
 'menuEntryLabel': 'Type',
 'widgetType': 'Menu'}                                                 
      

TypeBondsCommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb766b70c>          
      

addHydrogensGUICommandGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Edit',
 'menuCascadeName': 'Hydrogens',
 'menuEntryLabel': 'Add',
 'widgetType': 'Menu'}                                                 
      

AddHydrogensGUICommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb7673eac>          
      

fixHydrogenAtomNamesGUICommandGuiDescr

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

FixHydrogenAtomNamesGUICommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb7673f6c>          
      

splitNodesGUICommandGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Edit',
 'menuCascadeName': 'Misc',
 'menuEntryLabel': 'Split Selection',
 'widgetType': 'Menu'}                                                 
      

SplitNodesGUICommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb767f04c>          
      

mergeFieldsCommandGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Edit',
 'menuCascadeName': 'Misc',
 'menuEntryLabel': 'Fields',
 'widgetType': 'Menu'}                                                 
      

MergeFieldsCommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb767f10c>          
      

mergeSetsCommandGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Edit',
 'menuCascadeName': 'Misc',
 'menuEntryLabel': 'Sets',
 'widgetType': 'Menu'}                                                 
      

MergeSetsCommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb767f16c>          
      

mergeNPHsGUICommandGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Edit',
 'menuCascadeName': 'Hydrogens',
 'menuEntryLabel': 'Merge Non-Polar Hs',
 'widgetType': 'Menu'}                                                 
      

MergeNPHsGUICommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb767f20c>          
      

mergeLonePairsCommandGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Edit',
 'menuCascadeName': 'Misc',
 'menuEntryLabel': 'Merge Lone Pairs',
 'widgetType': 'Menu'}                                                 
      

MergeLonePairsGUICommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb767f2ec>          
      

computeGasteigerGUICommandGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Edit',
 'menuCascadeName': 'Charges',
 'menuEntryLabel': 'Compute Gasteiger',
 'widgetType': 'Menu'}                                                 
      

ComputeGasteigerGUICommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb767f3ac>          
      

addKollmanChargesGUICommandGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Edit',
 'menuCascadeName': 'Charges',
 'menuEntryLabel': 'Add Kollman Charges',
 'widgetType': 'Menu'}                                                 
      

AddKollmanChargesGUICommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb767f46c>          
      

checkChargesGUICommandGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Edit',
 'menuCascadeName': 'Charges',
 'menuEntryLabel': 'Check Charges',
 'widgetType': 'Menu'}                                                 
      

CheckChargesGUICommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb767f62c>          
      

setChargeGUICommandGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Edit',
 'menuCascadeName': 'Charges',
 'menuEntryLabel': 'Set Charge Field',
 'widgetType': 'Menu'}                                                 
      

SetChargeCommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb767f6ac>          
      

assignAtomsRadiiGUICommandGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Edit',
 'menuCascadeName': 'Atoms',
 'menuEntryLabel': 'Assign Radii',
 'widgetType': 'Menu'}                                                 
      

AssignAtomsRadiiCommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb767f76c>          
      

commandList

None
Value:
[{'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb766b46c>
,
  'name': 'editAtomTypeGC'},
 {'gui': None, 'cmd': self., 'name': 'editAtomChargeGC'},
 {'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb766b3ec>
,
...