meshi.energy.simpleEnergyTerms.compositeTorsions
Class ResidueTorsions

java.lang.Object
  meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions

All Implemented Interfaces:

CompositeTorsionsDefinitions, Attributable, Updateable

public class ResidueTorsions
extends java.lang.Object
implements Updateable, CompositeTorsionsDefinitions, Attributable

Allows easy access to all of a given residue's torsions.

Field Summary

private AttributesRack	attributes
(package private) double	energy
private boolean	isPP
private int	numberOfUpdates
private Residue	residue
private Torsion[]	torsionAngles

Fields inherited from interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions

ALL, CHI_1, CHI_2, CHI_3, CHI_4, COIL, HELIX, NUM_SIDECHAIN_TORSIONS, OMG, OMNI, PHI, POLYNOMIAL_CHI_1, POLYNOMIAL_CHI_1_CHI_2, POLYNOMIAL_CHI_1_CHI_2_TORSIONS, POLYNOMIAL_CHI_1_CHI_3, POLYNOMIAL_CHI_1_CHI_3_TORSIONS, POLYNOMIAL_CHI_1_CHI_4, POLYNOMIAL_CHI_1_CHI_4_TORSIONS, POLYNOMIAL_CHI_1_TORSIONS, POLYNOMIAL_PHI_PSI, POLYNOMIAL_PHI_PSI_CHI_1, POLYNOMIAL_PHI_PSI_CHI_1_TORSIONS, POLYNOMIAL_PHI_PSI_TORSIONS, PREPRO, PSI, SHEET, TOTAL_TORSION_ANGLES, UNIDENTIFIED_TORSION_TYPE

Constructor Summary

ResidueTorsions(Residue residue, TorsionList torsionList)
stores all of the residue's torsion angles.

Method Summary

void	addAttribute(MeshiAttribute attribute)
void	applyForce(int torsionType, double force) Applies force to torsion angles.
double	energy()
AtomList	getAtoms() returns a list of all atoms in this residue torsions
AtomList	getAtoms(int[] whichTorsions)
MeshiAttribute	getAttribute(int key)
Residue	getResidue() returns residue
int	getResidueNumber() returns residue's number
ResidueType	getResidueType() returns residue type
Torsion	getTorsion(int torsionType) returns torsion of type torsionType.
boolean	hasAllTorsions() verifies all the torsions used by this residue are available.
private static boolean	interestingTorsion(Torsion tor) checks whether a given torsion angle is in [PHI,PSI,CHI_1-CHI_4].
boolean	isPP()
void	resetEnergy()
void	setEnergy(double e)
void	setToPP()
private static int	torsionNum(Torsion tor) returns type of given torsion
java.lang.String	toString() Converts attributes of ResidueTorsions to string.
java.lang.String	toStringPhiPsiChi1() Partial conversion to string.
void	update(int numberOfUpdates)

Methods inherited from class java.lang.Object

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

Field Detail

isPP

private boolean isPP

residue

private Residue residue

torsionAngles

private Torsion[] torsionAngles

numberOfUpdates

private int numberOfUpdates

energy

double energy

attributes

private AttributesRack attributes

Constructor Detail

ResidueTorsions

public ResidueTorsions(Residue residue,
                       TorsionList torsionList)

stores all of the residue's torsion angles.

Parameters:

residue - for which torsion angles are stored

torsionList - from where the torsion angles are taken

Method Detail

energy

public double energy()

resetEnergy

public void resetEnergy()

setEnergy

public void setEnergy(double e)

getTorsion

public Torsion getTorsion(int torsionType)

returns torsion of type torsionType.

getResidueType

public ResidueType getResidueType()

returns residue type

getResidueNumber

public int getResidueNumber()

returns residue's number

getResidue

public Residue getResidue()

returns residue

setToPP

public void setToPP()

isPP

public boolean isPP()

hasAllTorsions

public boolean hasAllTorsions()

verifies all the torsions used by this residue are available. This includes phi,psi torsion angles.

applyForce

public void applyForce(int torsionType,
                       double force)

Applies force to torsion angles. Force is applied to each atom of the torsion.

getAtoms

public AtomList getAtoms()

returns a list of all atoms in this residue torsions

getAtoms

public AtomList getAtoms(int[] whichTorsions)

update

public void update(int numberOfUpdates)
            throws UpdateableException

Specified by:

update in interface Updateable

Throws:

UpdateableException

toString

public java.lang.String toString()

Converts attributes of ResidueTorsions to string.

Overrides:

toString in class java.lang.Object

toStringPhiPsiChi1

public java.lang.String toStringPhiPsiChi1()

Partial conversion to string. Convert phi, psi and chi_1 torsion angles.

interestingTorsion

private static boolean interestingTorsion(Torsion tor)

checks whether a given torsion angle is in [PHI,PSI,CHI_1-CHI_4].

torsionNum

private static int torsionNum(Torsion tor)

returns type of given torsion

addAttribute

public final void addAttribute(MeshiAttribute attribute)

Specified by:

addAttribute in interface Attributable

getAttribute

public final MeshiAttribute getAttribute(int key)

Specified by:

getAttribute in interface Attributable