Package ffx.potential.bonded

Class Rotamer

java.lang.Object

ffx.potential.bonded.Rotamer

public class Rotamer
extends Object

The Rotamer Class usually represents one immutable amino acid Rotamer.

It is additionally being extended to represent one nucleic acid Rotamer.

Since:

1.0

Author:

Ava M. Lynn, Jacob M. Litman

Field Summary

Fields

Modifier and Type	Field	Description
AminoAcidUtils.AminoAcid3	aminoAcid3	The A.A. name of this residue (or null for a N.A.).
final double[]	angles	An array of chi angles for this rotamer.
final double	chi1	Torsions chi 1-4 are used for amino acids and nucleic acids.
final double	chi2
final double	chi3
final double	chi4
final double	chi5	Torsions chi 5-7 are only currently used for nucleic acids.
boolean	isState	Flag to indicate the rotamer was initialized from a Residue state.
boolean	isTitrating	If this flag is set, application of a rotamer requires updating force field parameters.
final int	length	Number of chi/sigma values.
NucleicAcidUtils.NucleicAcid3	nucleicAcid3	The N.A. name of this residue (or null for a A.A.).
ResidueState	originalState	Residue state used to initialize the rotamer.
final double[]	sigmas	An array of sigmas for each chi angle.

Constructor Summary

Constructors

Constructor	Description
Rotamer(double... values)	Constructor for unknown residue types.
Rotamer(AminoAcidUtils.AminoAcid3 aminoAcid3, double... values)	Constructor for Rotamer.
Rotamer(AminoAcidUtils.AminoAcid3 aminoAcid3, ResidueState residueState, double... values)	Constructor for Rotamer.
Rotamer(AminoAcidUtils.AminoAcid3 aminoAcid3, ResidueState residueState, TitrationUtils titrationUtils, double... values)	Constructor for Rotamer.
Rotamer(AminoAcidUtils.AminoAcid3 aminoAcid3, TitrationUtils titrationUtils, double... values)	Constructor for Rotamer.
Rotamer(NucleicAcidUtils.NucleicAcid3 nucleicAcid3, double... values)	Constructor for Rotamer.
Rotamer(NucleicAcidUtils.NucleicAcid3 nucleicAcid3, ResidueState residueState, double... values)	Constructor for Rotamer.
Rotamer(NucleicAcidUtils.NucleicAcid3 nucleicAcid3, ResidueState residueState, TitrationUtils titrationUtils, double... values)	Constructor for Rotamer.
Rotamer(ResidueState residueState, double... values)	Constructor for unknown residue types.
Rotamer(ResidueState residueState, TitrationUtils titrationUtils, double... values)	Constructor for unknown residue types.

Method Summary

Modifier and Type	Method	Description
static Rotamer[]	defaultRotamerFactory(Residue residue)	Factory method to construct an original-coordinates Rotamer from a residue.
static Rotamer[]	defaultRotamerFactory(Residue residue, TitrationUtils titrationUtils)	Factory method to construct an original-coordinates Rotamer from a residue.
double[]	getAngles()
String	getName()
double	getRotamerPhBias()
String	toAngleString()	toAngleString.
String	toString()
void	updateParameters(Residue residue)	Update force field parameters for force field dependent rotamers.

Methods inherited from class java.lang.Object

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

Field Details

chi1

public final double chi1

Torsions chi 1-4 are used for amino acids and nucleic acids.

chi2

public final double chi2

chi3

public final double chi3

chi4

public final double chi4

chi5

public final double chi5

Torsions chi 5-7 are only currently used for nucleic acids.

angles

public final double[] angles

An array of chi angles for this rotamer.

sigmas

public final double[] sigmas

An array of sigmas for each chi angle.

length

public final int length

Number of chi/sigma values.

originalState

public ResidueState originalState

Residue state used to initialize the rotamer.

isState

public boolean isState

Flag to indicate the rotamer was initialized from a Residue state.

aminoAcid3

public AminoAcidUtils.AminoAcid3 aminoAcid3

The A.A. name of this residue (or null for a N.A.).

nucleicAcid3

public NucleicAcidUtils.NucleicAcid3 nucleicAcid3

The N.A. name of this residue (or null for a A.A.).

isTitrating

public boolean isTitrating

If this flag is set, application of a rotamer requires updating force field parameters.

Constructor Details

Rotamer

public Rotamer(double... values)

Constructor for unknown residue types.

Parameters:

values - a double.

Rotamer

public Rotamer(AminoAcidUtils.AminoAcid3 aminoAcid3,
 double... values)

Constructor for Rotamer.

Parameters:

aminoAcid3 - a AminoAcidUtils.AminoAcid3 object.

values - a double.

Rotamer

public Rotamer(NucleicAcidUtils.NucleicAcid3 nucleicAcid3,
 double... values)

Constructor for Rotamer.

Parameters:

nucleicAcid3 - a NucleicAcidUtils.NucleicAcid3 object.

values - a double.

Rotamer

public Rotamer(AminoAcidUtils.AminoAcid3 aminoAcid3,
 TitrationUtils titrationUtils,
 double... values)

Constructor for Rotamer.

Parameters:

aminoAcid3 - a AminoAcidUtils.AminoAcid3 object.

titrationUtils - Use to apply rotamer specific force field parameters.

values - a double.

Rotamer

public Rotamer(ResidueState residueState,
 double... values)

Constructor for unknown residue types.

Parameters:

residueState - a ResidueState object.

values - a double.

Rotamer

public Rotamer(ResidueState residueState,
 TitrationUtils titrationUtils,
 double... values)

Constructor for unknown residue types.

Parameters:

residueState - a ResidueState object.

values - a double.

Rotamer

public Rotamer(AminoAcidUtils.AminoAcid3 aminoAcid3,
 ResidueState residueState,
 double... values)

Constructor for Rotamer.

Parameters:

aminoAcid3 - a AminoAcidUtils.AminoAcid3 object.

residueState - a ResidueState object.

values - a double.

Rotamer

public Rotamer(AminoAcidUtils.AminoAcid3 aminoAcid3,
 ResidueState residueState,
 TitrationUtils titrationUtils,
 double... values)

Constructor for Rotamer.

Parameters:

aminoAcid3 - a AminoAcidUtils.AminoAcid3 object.

residueState - a ResidueState object.

values - a double.

Rotamer

public Rotamer(NucleicAcidUtils.NucleicAcid3 nucleicAcid3,
 ResidueState residueState,
 double... values)

Constructor for Rotamer.

Parameters:

nucleicAcid3 - a NucleicAcidUtils.NucleicAcid3 object.

residueState - a ResidueState object.

values - a double.

Rotamer

public Rotamer(NucleicAcidUtils.NucleicAcid3 nucleicAcid3,
 ResidueState residueState,
 TitrationUtils titrationUtils,
 double... values)

Constructor for Rotamer.

Parameters:

nucleicAcid3 - a NucleicAcidUtils.NucleicAcid3 object.

residueState - a ResidueState object.

values - a double.

Method Details

updateParameters

public void updateParameters(Residue residue)

Update force field parameters for force field dependent rotamers.

Parameters:

residue - Residue to update.

defaultRotamerFactory

public static Rotamer[] defaultRotamerFactory(Residue residue)

Factory method to construct an original-coordinates Rotamer from a residue.

Parameters:

residue - Residue to construct a default rotamer for.

Returns:

Rotamer based on the coordinates of the residue.

defaultRotamerFactory

public static Rotamer[] defaultRotamerFactory(Residue residue,
 TitrationUtils titrationUtils)

Factory method to construct an original-coordinates Rotamer from a residue.

Parameters:

residue - Residue to construct a default rotamer for.

Returns:

Rotamer based on the coordinates of the residue.

toAngleString

public String toAngleString()

toAngleString.

Returns:

a String object.

toString

public String toString()

Overrides:

toString in class Object

getName

public String getName()

getRotamerPhBias

public double getRotamerPhBias()

getAngles

public double[] getAngles()