Package AutoDockTools :: Module pyAutoDockCommands

Module pyAutoDockCommands

source code

This Module contains commands which allow the user to compute various component pair-wise energies of the autodock305 forcefield and assign the results to individual atoms.

Classes

[hide private]

PyADCalcClosestPairs
For each atom in one AtomSet, determine the index of closest atom in a second AtomSet and the distance between them.

PyADCalcVDWEnergies
For each atom in one AtomSet, determine the vdw energy vs all the atoms in a second AtomSet

PyAD4CalcVDWEnergies
For each atom in one AtomSet, determine the vdw energy vs all the atoms in a second AtomSet

PyADCalcHBONDEnergies
For each atom in one AtomSet, determine the hydrogen bonding energy vs all the atoms in a second AtomSet

PyAD4CalcHBONDEnergies
For each atom in one AtomSet, determine the hydrogen bonding energy vs all the atoms in a second AtomSet

PyADCalcESTATEnergies
For each atom in one AtomSet, determine the electrostatics energy vs all the atoms in a second AtomSet

PyAD4CalcESTATEnergies
For each atom in one AtomSet, determine the electrostatics energy vs all the atoms in a second AtomSet

PyADCalcDSOLVEnergies
For each atom in one AtomSet, determine the hydrogen bonding energy vs all the atoms in a second AtomSet

PyAD4CalcDSOLVEnergies
For each atom in one AtomSet, determine the hydrogen bonding energy vs all the atoms in a second AtomSet

PyADCalcAD3Energies
For each atom in one AtomSet, determine the autodock3 energy vs all the atoms in a second AtomSet

PyAD4CalcAD4Energies
For each atom in one AtomSet, determine the autodock4 energy vs all the atoms in a second AtomSet

PyAD4CalcInternalEnergies
For one AtomSet, determine the autodock4 energy of all the non-bond interactions:exclude 1-1, 1-2, 1-3, 1-4 and weedbonds in the same rigid piece.

PyAD305CalcInternalEnergies
For one AtomSet, determine the autodock3 energy of all the non-bond interactions:exclude 1-1, 1-2, 1-3, 1-4 and weedbonds in the same rigid piece.

Functions

[hide private]

initModule(vf)

Variables

[hide private]

parentGeom = <DejaVu.Geom.Geom> pyADGeoms with 0 vertices

pep_aromList = ['PHE_CD1', 'PHE_CG', 'PHE_CD2', 'PHE_CE1', 'PHE_CE2...

PyADCalcClosestPairsGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

PyADCalcVDWEnergiesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

PyAD4CalcVDWEnergiesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

PyADCalcHBONDEnergiesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

PyAD4CalcHBONDEnergiesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

PyADCalcESTATEnergiesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

PyAD4CalcESTATEnergiesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

PyADCalcDSOLVEnergiesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

PyAD4CalcDSOLVEnergiesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

PyADCalcAD3EnergiesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

PyAD4CalcAD4EnergiesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

PyAD4CalcInternalEnergiesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

PyAD305CalcInternalEnergiesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...

commandList = [{'gui': <ViewerFramework.VFCommand.CommandGUI insta...

Function Details

[hide private]

initModule(vf)

source code

None

Variables Details

[hide private]

parentGeom

None

Value:

<DejaVu.Geom.Geom> pyADGeoms with 0 vertices

pep_aromList

None

Value:

['PHE_CD1',
 'PHE_CG',
 'PHE_CD2',
 'PHE_CE1',
 'PHE_CE2',
 'PHE_CZ',
 'TYR_CD1',
 'TYR_CG',
...

PyADCalcClosestPairsGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb74a202c>

PyADCalcVDWEnergiesGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb74a212c>

PyAD4CalcVDWEnergiesGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb74a21ac>

PyADCalcHBONDEnergiesGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb74a224c>

PyAD4CalcHBONDEnergiesGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb74a22ec>

PyADCalcESTATEnergiesGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb74a238c>

PyAD4CalcESTATEnergiesGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb74a242c>

PyADCalcDSOLVEnergiesGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb74a24cc>

PyAD4CalcDSOLVEnergiesGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb74a256c>

PyADCalcAD3EnergiesGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb74a260c>

PyAD4CalcAD4EnergiesGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb74a268c>

PyAD4CalcInternalEnergiesGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb74a272c>

PyAD305CalcInternalEnergiesGUI

None

Value:

<ViewerFramework.VFCommand.CommandGUI instance at 0xb74a27ac>

commandList

None

Value:

[{'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb74a202c>
,
  'name': 'PyAD_calcClosestPairs'},
 {'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb74a212c>
,
  'name': 'PyAD_calcVDWEnergies'},
...