Package Pmv :: Module hbondCommands

Module hbondCommands

Classes

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'