Package ffx.potential.parameters

Class TitrationUtils

java.lang.Object

ffx.potential.parameters.TitrationUtils

public class TitrationUtils
extends Object

Utilities for interpolating between Amino Acid protonation and tautomer states.

Since:

1.0

Author:

Michael Schnieders, Andrew Thiel

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	TitrationUtils.CysStates
static enum	TitrationUtils.CysteineAtomNames	Constant CysteineAtoms
static enum	TitrationUtils.HisStates
static enum	TitrationUtils.HistidineAtomNames	Constant HistidineAtoms
static enum	TitrationUtils.LysineAtomNames	Constant lysineAtoms
static enum	TitrationUtils.LysStates
static enum	TitrationUtils.Titration	Amino acid protonation reactions.

Constructor Summary

Constructors

Constructor	Description
TitrationUtils(ForceField forceField)
TitrationUtils(ForceField forceField, double proteinDielectric, boolean tanhCorrection)

Method Summary

Modifier and Type	Method	Description
double[]	getMultipole(Atom atom, double titrationLambda, double tautomerLambda, double[] multipole)
double[]	getMultipoleTautomerDeriv(Atom atom, double titrationLambda, double tautomerLambda, double[] multipole)
double[]	getMultipoleTitrationDeriv(Atom atom, double titrationLambda, double tautomerLambda, double[] multipole)
double	getPolarizability(Atom atom, double titrationLambda, double tautomerLambda, double defaultPolarizability)
double	getPolarizabilityTautomerDeriv(Atom atom, double titrationLambda, double tautomerLambda)
double	getPolarizabilityTitrationDeriv(Atom atom, double titrationLambda, double tautomerLambda)
double	getRotamerPhBias(AminoAcidUtils.AminoAcid3 AA3)
static int	getTitratingHydrogenDirection(AminoAcidUtils.AminoAcid3 aminoAcid3, Atom atom)
double	getTotalRotamerPhBias(Rotamer[] rotamers)
static boolean	isTitratingHeavy(AminoAcidUtils.AminoAcid3 aminoAcid3, Atom atom)	Used to keep track of heavy atoms with changing polarizability.
static boolean	isTitratingHydrogen(AminoAcidUtils.AminoAcid3 aminoAcid3, Atom atom)
static double[]	predictHillCoeffandPka(double[] pHScale, double[] residueFractions)	Predict pKa from a set of residue fractions (deprotonated / (deprotonated + protonated)).
void	setRotamerPhBias(double temperature, double pH)
boolean	testResidueTypes(Residue residue)
void	updateResidueParameters(Residue residue, Rotamer rotamer)	Update force field parameters for the side-chain atoms of the given residue based on the rotamer amino acid type.

Methods inherited from class java.lang.Object

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

Constructor Details

TitrationUtils

public TitrationUtils(ForceField forceField)

TitrationUtils

public TitrationUtils(ForceField forceField,
 double proteinDielectric,
 boolean tanhCorrection)

Method Details

testResidueTypes

public boolean testResidueTypes(Residue residue)

updateResidueParameters

public void updateResidueParameters(Residue residue,
 Rotamer rotamer)

Update force field parameters for the side-chain atoms of the given residue based on the rotamer amino acid type.

Parameters:

residue - Residue to update.

rotamer - Rotamer that contains the amino acid residue identity.

getMultipole

public double[] getMultipole(Atom atom,
 double titrationLambda,
 double tautomerLambda,
 double[] multipole)

getMultipoleTitrationDeriv

public double[] getMultipoleTitrationDeriv(Atom atom,
 double titrationLambda,
 double tautomerLambda,
 double[] multipole)

getMultipoleTautomerDeriv

public double[] getMultipoleTautomerDeriv(Atom atom,
 double titrationLambda,
 double tautomerLambda,
 double[] multipole)

getPolarizability

public double getPolarizability(Atom atom,
 double titrationLambda,
 double tautomerLambda,
 double defaultPolarizability)

getPolarizabilityTitrationDeriv

public double getPolarizabilityTitrationDeriv(Atom atom,
 double titrationLambda,
 double tautomerLambda)

getPolarizabilityTautomerDeriv

public double getPolarizabilityTautomerDeriv(Atom atom,
 double titrationLambda,
 double tautomerLambda)

isTitratingHydrogen

public static boolean isTitratingHydrogen(AminoAcidUtils.AminoAcid3 aminoAcid3,
 Atom atom)

isTitratingHeavy

public static boolean isTitratingHeavy(AminoAcidUtils.AminoAcid3 aminoAcid3,
 Atom atom)

Used to keep track of heavy atoms with changing polarizability. Only affects carboxylic oxygen and sulfur.

Parameters:

aminoAcid3 - The amino acid type.

atom - The atom to check.

Returns:

True if the atom is a heavy atom with changing polarizability.

getTitratingHydrogenDirection

public static int getTitratingHydrogenDirection(AminoAcidUtils.AminoAcid3 aminoAcid3,
 Atom atom)

setRotamerPhBias

public void setRotamerPhBias(double temperature,
 double pH)

getRotamerPhBias

public double getRotamerPhBias(AminoAcidUtils.AminoAcid3 AA3)

getTotalRotamerPhBias

public double getTotalRotamerPhBias(Rotamer[] rotamers)

predictHillCoeffandPka

public static double[] predictHillCoeffandPka(double[] pHScale,
 double[] residueFractions)

Predict pKa from a set of residue fractions (deprotonated / (deprotonated + protonated)). This method minimizes the L2 loss between the measured residue fractions and various pKa/Hill-coefficient values to get pKa/Hill- coefficient predictions.

Parameters:

pHScale - pH values at which the residue fractions were measured

residueFractions - a sorted array of residue fractions (deprotonated / (deprotonated + protonated))

Returns:

{n, pKa}