Package ffx.potential.bonded

Class RelativeSolvation

java.lang.Object

ffx.potential.bonded.RelativeSolvation

public class RelativeSolvation
extends Object

A relative solvation term for chemical perturbations.

Since:

1.0

Author:

Michael J. Schnieders, Jacob M. Litman

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	RelativeSolvation.SolvationLibrary	Citations: Wolfenden et al: Wolfenden, R., Andersson, L., Cullis, P.

Constructor Summary

Constructors

Constructor	Description
RelativeSolvation(RelativeSolvation.SolvationLibrary solvationLibrary, ForceField forceField)	Constructor for RelativeSolvation.

Method Summary

Modifier and Type	Method	Description
double	getSolvationEnergy(Residue residue, boolean checkZeroes)	Gets the solvation energy (de-solvation penalty) for a given residue, allowing for sequence optimization to include an estimate of energy relative to the unfolded state.
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details

RelativeSolvation

public RelativeSolvation(RelativeSolvation.SolvationLibrary solvationLibrary,
 ForceField forceField)

Constructor for RelativeSolvation.

Parameters:

solvationLibrary - a RelativeSolvation.SolvationLibrary object.

forceField - a ForceField object.

Method Details

getSolvationEnergy

public double getSolvationEnergy(Residue residue,
 boolean checkZeroes)
                          throws IllegalArgumentException

Gets the solvation energy (de-solvation penalty) for a given residue, allowing for sequence optimization to include an estimate of energy relative to the unfolded state.

Parameters:

residue - Residue to check

checkZeroes - Throws an error if not in solvation energy library

Returns:

Solvation energy

Throws:

IllegalArgumentException - if any.

IllegalArgumentException - if any.

toString

public String toString()

Overrides:

toString in class Object