Package Pmv :: Module repairCommands
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Module repairCommands

source code

Classes [hide private]
  CheckForMissingAtomsGUICommand
This class provides Graphical User Interface to CheckForMissingAtomsCommand which is invoked by it with the current selection, if there is one.
  CheckForMissingAtoms
This command compares atoms present in residues with those expected by the dictionary used to assign Kollman charges, qkollua.
  CheckForCloseContactsGUICommand
This class provides Graphical User Interface to CheckForCloseContactsCommand which is invoked by it Package : Pmv Module : repairCommands Class : CheckForCloseContactsGUICommand Command : checkForCloseContactsGC Synopsis: None <--- checkForCloseContactsGC(keynodes,checkNodes, percentCutoff,distanceCutoff, distSelectorString,**kw) Required Arguments: keyNodes --- atoms to use as reference points checkNodes --- atoms to check to see if close to keyNodes Optional Arguments: percentCutoff --- vdw scaling factor distanceCutoff --- distance for DistanceSelector distSelectorString --- name of class of selector to use constant --- possible constant value to be added into selection close is defined as interatomic distance< percentCutoff*(key_radius+check_radius) where the radii depend on atom element .
  CheckForCloseContacts
This command detects atoms which are selected as "close" by a MolKit.distanceSelector.
  RepairMissingAtomsGUICommand
This class provides Graphical User Interface to RepairMissingAtomsCommand which is invoked by it with the current selection, if there is one.
  RepairMissingAtoms
This command compares atoms present in residues with those expected by the dictionary used to assign Kollman charges, qkollua.
  EditHistHydrogensGUICommand
Allows user to call editHistHydrogens on each histidine residue in selection.
  EditHistHydrogens
Allows user to edit hydrogens in histidine residues...
  AddOXTGUICommand
This class provides GUICommand for AddOXT which adds oxygen atom to terminal carbon atom.
  AddOXT
This class uses add_sp2_hydrogen method of the AddHydrogens class from the PyBabel package to compute coordinates of oxygen to be added to carbon atom.The carbon atom is bonded to another oxygen and a CA.
  ModifyCTerminus
This command removes hydrogens from C-atom of internal c-termini residues.
  ModifyNTerminus
This command is used to modify residues which become internal n-termini because some residues are missing within a chain in a crystal structure.
  ModifyTermini
This class detects residues within a chain which are not bonded to a previous residue in the chain and those not bonded to a subsequent residue in the chain.

Functions [hide private]
  check_repair_geoms(VFGUI)
    'name':'attach_nonbonded_fragments','cmd':AttachNonBondedFragments(), 'gui': AttachNonBondedFragmentsGUI},
  initModule(viewer)

Variables [hide private]
  checkForMissingAtomsGUICommandGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Misc...
  CheckForMissingAtomsGUICommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  checkForCloseContactsGUICommandGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Edit'...
  CheckForCloseContactsGUICommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  repairMissingAtomsGUICommandGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Edit'...
  RepairMissingAtomsGUICommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  EditHistHydrogensGUICommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  AddOXTGUICommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ModifyTerminiCommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
    'name':'attach_nonbonded_fragments','cmd':AttachNonBondedFragments(), 'gui': AttachNonBondedFragmentsGUI},
  commandList = [{'gui': <ViewerFramework.VFCommand.CommandGUI insta...

Function Details [hide private]

check_repair_geoms(VFGUI)

source code 
None

initModule(viewer)

source code 
None

Variables Details [hide private]

checkForMissingAtomsGUICommandGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Edit',
 'menuCascadeName': 'Misc',
 'menuEntryLabel': 'Check For Missing Atoms ',
 'widgetType': 'Menu'}                                                 
      

CheckForMissingAtomsGUICommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb77c664c>          
      

checkForCloseContactsGUICommandGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Edit',
 'menuEntryLabel': 'Check For Close Contacts',
 'widgetType': 'Menu'}                                                 
      

CheckForCloseContactsGUICommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb77e008c>          
      

repairMissingAtomsGUICommandGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Edit',
 'menuEntryLabel': 'Repair Missing Atoms ',
 'widgetType': 'Menu'}                                                 
      

RepairMissingAtomsGUICommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb77e012c>          
      

EditHistHydrogensGUICommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb77e024c>          
      

AddOXTGUICommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb77e02ec>          
      

ModifyTerminiCommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb77e03ec>          
      

commandList

None
Value:
[{'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb77e024c>
,
  'name': 'editHist_hGC'},
 {'gui': None, 'cmd': self., 'name': 'editHist_h'},
 {'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb77c664c>
,
...