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2017-2 Schrodinger Python API
Package schrodinger :: Package application :: Package bioluminate :: Module escomp :: Class ResidualPotential
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Class ResidualPotential

Calculator of the residual potential on the ligand surface. The two components of the residual potential, interaction potential and desolvation potential, can also be reported and visualized on the surface.

Instance Methods [hide private]
 
__init__(self, ct, lig_atoms, jobname='residual')
1D Numpy array
getResidualPotential(self)
return the "residual potential" on the ligand surface.
1D Numpy array
getInteractionPotential(self)
return the "interaction potential" on the ligand surface.
1D Numpy array
getDesolvationPotential(self)
return the "desolvation potential" on the ligand surface.
Dict of lists
getResidualPotentialByAtom(self)
return the residual potential grouped by atom.
Dict of lists
getResidualPotentialByResidue(self)
return the residual potential grouped by residue.
Method Details [hide private]

__init__(self, ct, lig_atoms, jobname='residual')
(Constructor)

 
Parameters:
  • ct (Structure) - the input complex structure
  • atoms1 - atom numbers that define the ligand
  • jobname (String) - the basename for temporary APBS files
  • lig_atoms (list or set)

getResidualPotential(self)

 

return the "residual potential" on the ligand surface.

Returns: 1D Numpy array
a list of potential values on ligand surface points

getInteractionPotential(self)

 

return the "interaction potential" on the ligand surface.

Returns: 1D Numpy array
a list of potential values on ligand surface points

getDesolvationPotential(self)

 

return the "desolvation potential" on the ligand surface.

Returns: 1D Numpy array
a list of potential values on ligand surface points

getResidualPotentialByAtom(self)

 

return the residual potential grouped by atom.

Returns: Dict of lists
dict key is the ligand atom index in the ligand ct, dict value is a list of potential values on the surface points that belong to this atom.

getResidualPotentialByResidue(self)

 

return the residual potential grouped by residue.

Returns: Dict of lists
dict key is the ligand residue string, dict value is a list of potential values on the surface points that belong to this residue.

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2017-2 Schrodinger Python API
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