Package Pmv :: Module hbondCommands
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Module hbondCommands

source code

Classes [hide private]
  GetHydrogenBondDonors
This class allows user to get AtomSets of sp2 hydridized and sp3 hybridized hydrogenBond Donors able.
  GetHydrogenBondAcceptors
This class allows user to get AtomSets of sp2 hydridized and sp3 hybridized hydrogenBond Acceptors.
  GetHydrogenBondEnergies
This class allows user to get a list of energies of HydrogenBonds.
  ShowHBDonorsAcceptors
This class allows user to show AtomSets of HydrogenBond donors and acceptors.
  ShowHydrogenBonds
This class allows user to visualize pre-existing HydrogenBonds between ...
  BuildHydrogenBondsGUICommand
This class provides Graphical User Interface to BuildHydrogenBonds which is invoked by it.
  BuildHydrogenBonds
This command finds hydrogen donor atoms within 2.4*percentCutoff angstrom distance of hydrogen acceptor atoms.
  AddHBondHydrogensGUICommand
This class provides Graphical User Interface to AddHBondHydrogens which is invoked by it.
  AddHBondHydrogens
This command adds hydrogen atoms to preexisting hydrogen bonds...
  LimitHydrogenBonds
This class allows user to detect pre-existing HydrogenBonds with energy values 'lower' than a designated cutoff.
  DisplayHBonds
Base class to allow user to visualize pre-existing HydrogenBonds between ...
  DisplayHBondsAsSpheres
This class allows user to visualize pre-existing HydrogenBonds between ...
  DisplayHBondsAsCylinders
This class allows user to visualize pre-existing HydrogenBonds between ...
  ExtrudeHydrogenBonds
This class allows user to visualize pre-existing HydrogenBonds between ...
  WriteAssemblyHBonds
Command to write a file specifying >1 chain with hydrogen bonds.
  WriteIntermolHBonds
Command to write files specifying intermolecular hydrogen bonds...
  ReadIntermolHBonds
Command to read files specifying intermolecular hydrogen bonds...
  AddHBondCommandGUICommand
GUI command wrapper for AddHBondCommand which allows user to add hbonds between selected atoms.
  AddHBondCommand
AddHBondCommand allows user to add hydrogen bonds between pairs of atoms.
  RemoveHBondCommandGUICommand
RemoveHBondCommandGUICommand allows user to remove hbonds between picked atoms.
  RemoveHBondCommand
RemoveHBondCommand allows user to remove hydrogen bonds between specified atoms.

Functions [hide private]
  check_hbond_geoms(VFGUI)
  dist(c1, c2)
  getAngle(ac, hat, don)
  applyTransformation(pt, mat)
  getTransformedCoords(atom)
  initModule(viewer)

Variables [hide private]
  sp2Donors = ['Nam', 'Ng+', 'Npl']
  sp3Donors = ['N3+', 'O3', 'S3']
  allDonors = ['Nam', 'Ng+', 'Npl', 'N3+', 'O3', 'S3']
  sp2Acceptors = ['O2', 'O-', 'Npl', 'Nam']
  sp3Acceptors = ['S3', 'O3']
  allAcceptors = ['O2', 'O-', 'Npl', 'Nam', 'S3', 'O3']
  a_allAcceptors = ['aO2', 'aO-', 'aNpl', 'aNam', 'aS3', 'aO3']
  ShowHBDonorsAcceptorsGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Buil...
  ShowHBDonorsAcceptorsGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ShowHydrogenBondsGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Disp...
  ShowHydrogenBondsGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  BuildHydrogenBondsGUICommandGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Buil...
  BuildHydrogenBondsGUICommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  AddHBondHydrogensGUICommandGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Buil...
  AddHBondHydrogensGUICommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  LimitHydrogenBondsGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Edit...
  LimitHydrogenBondsGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  DisplayHBondsAsSpheresGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Disp...
  DisplayHBondsAsSpheresGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  DisplayHBondsAsCylindersGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Disp...
  DisplayHBondsAsCylindersGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ExtrudeHydrogenBondsGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Disp...
  ExtrudeHydrogenBondsGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  WriteAssemblyHBondsGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Asse...
  WriteAssemblyHBondsGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  WriteIntermolHBondsGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Asse...
  WriteIntermolHBondsGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ReadIntermolHBondsGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Asse...
  ReadIntermolHBondsGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  AddHBondGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Edit...
  AddHBondCommandGUICommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  RemoveHBondGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'Edit...
  RemoveHBondCommandGUICommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  commandList = [{'gui': None, 'cmd': self., 'name': 'getHBDonors'},...
  n = 'O3'

Function Details [hide private]

check_hbond_geoms(VFGUI)

source code 
None

dist(c1, c2)

source code 
None

getAngle(ac, hat, don)

source code 
None

applyTransformation(pt, mat)

source code 
None

getTransformedCoords(atom)

source code 
None

initModule(viewer)

source code 
None

Variables Details [hide private]

sp2Donors

None
Value:
['Nam', 'Ng+', 'Npl']                                                  
      

sp3Donors

None
Value:
['N3+', 'O3', 'S3']                                                    
      

allDonors

None
Value:
['Nam', 'Ng+', 'Npl', 'N3+', 'O3', 'S3']                               
      

sp2Acceptors

None
Value:
['O2', 'O-', 'Npl', 'Nam']                                             
      

sp3Acceptors

None
Value:
['S3', 'O3']                                                           
      

allAcceptors

None
Value:
['O2', 'O-', 'Npl', 'Nam', 'S3', 'O3']                                 
      

a_allAcceptors

None
Value:
['aO2', 'aO-', 'aNpl', 'aNam', 'aS3', 'aO3']                           
      

ShowHBDonorsAcceptorsGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Hydrogen Bonds',
 'menuCascadeName': 'Build',
 'menuEntryLabel': 'Show Donors + Acceptors',
 'widgetType': 'Menu'}                                                 
      

ShowHBDonorsAcceptorsGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb703d40c>          
      

ShowHydrogenBondsGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Hydrogen Bonds',
 'menuCascadeName': 'Display',
 'menuEntryLabel': 'As Lines',
 'widgetType': 'Menu'}                                                 
      

ShowHydrogenBondsGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb703d54c>          
      

BuildHydrogenBondsGUICommandGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Hydrogen Bonds',
 'menuCascadeName': 'Build',
 'menuEntryLabel': 'Set Params + Build',
 'widgetType': 'Menu'}                                                 
      

BuildHydrogenBondsGUICommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb703d6cc>          
      

AddHBondHydrogensGUICommandGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Hydrogen Bonds',
 'menuCascadeName': 'Build',
 'menuEntryLabel': 'Add Hydrogens to Hbonds',
 'widgetType': 'Menu'}                                                 
      

AddHBondHydrogensGUICommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb703d7ac>          
      

LimitHydrogenBondsGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Hydrogen Bonds',
 'menuCascadeName': 'Edit',
 'menuEntryLabel': 'Limit Existing Hbonds',
 'widgetType': 'Menu'}                                                 
      

LimitHydrogenBondsGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb703d9ac>          
      

DisplayHBondsAsSpheresGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Hydrogen Bonds',
 'menuCascadeName': 'Display',
 'menuEntryLabel': 'As Spheres',
 'widgetType': 'Menu'}                                                 
      

DisplayHBondsAsSpheresGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb703dbec>          
      

DisplayHBondsAsCylindersGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Hydrogen Bonds',
 'menuCascadeName': 'Display',
 'menuEntryLabel': 'As Cylinders',
 'widgetType': 'Menu'}                                                 
      

DisplayHBondsAsCylindersGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb703dc8c>          
      

ExtrudeHydrogenBondsGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Hydrogen Bonds',
 'menuCascadeName': 'Display',
 'menuEntryLabel': 'As Extruded Shapes',
 'widgetType': 'Menu'}                                                 
      

ExtrudeHydrogenBondsGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb703de6c>          
      

WriteAssemblyHBondsGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Hydrogen Bonds',
 'menuCascadeName': 'Assemblies',
 'menuEntryLabel': 'Write Assembly with Hbonds',
 'widgetType': 'Menu'}                                                 
      

WriteAssemblyHBondsGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb703decc>          
      

WriteIntermolHBondsGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Hydrogen Bonds',
 'menuCascadeName': 'Assemblies',
 'menuEntryLabel': 'Write Intermolecular Hbonds',
 'widgetType': 'Menu'}                                                 
      

WriteIntermolHBondsGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb703df2c>          
      

ReadIntermolHBondsGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Hydrogen Bonds',
 'menuCascadeName': 'Assemblies',
 'menuEntryLabel': 'Read Intermolecular Hbonds',
 'widgetType': 'Menu'}                                                 
      

ReadIntermolHBondsGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb703df8c>          
      

AddHBondGuiDescr

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

AddHBondCommandGUICommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb70720ac>          
      

RemoveHBondGuiDescr

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

RemoveHBondCommandGUICommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb704f06c>          
      

commandList

None
Value:
[{'gui': None, 'cmd': self., 'name': 'getHBDonors'},
 {'gui': None, 'cmd': self., 'name': 'getHBAcceptors'},
 {'gui': None, 'cmd': self., 'name': 'getHBondEnergies'},
 {'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb703d40c>
,
  'name': 'showHBDA'},
 {'cmd': self.,
...                                                                    
      

n

None
Value:
'O3'