meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
Class RamachandranSidechainEnergy

java.lang.Object
  meshi.energy.AbstractEnergy
      meshi.energy.simpleEnergyTerms.SimpleEnergyTerm
          meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergy

All Implemented Interfaces:

CompositeTorsionsDefinitions, Attributable, Updateable

public class RamachandranSidechainEnergy
extends SimpleEnergyTerm
implements CompositeTorsionsDefinitions

A Ramachandran plot and sidechain torsions optimization energy term. Statistical analysis of residue backbone and sidechain torsions in a large database of residue observations has been smoothed using polynomial spline interpolation. For a given residue the energy value approximates the percentage of finding its current backbone and sidechain torsion angles.

Nested Class Summary

Nested classes/interfaces inherited from class meshi.energy.AbstractEnergy

AbstractEnergy.UpdateableList

Field Summary

protected static int[]	numberOfResiduesPerType
static double[]	residueEnergies
protected ResidueTorsionsList	residueTorsionsList
protected static double[]	sm2PerResidueType
protected static double[]	sumPerResidueType

Fields inherited from class meshi.energy.simpleEnergyTerms.SimpleEnergyTerm

elementsList, parametersList

Fields inherited from class meshi.energy.AbstractEnergy

comment, filter, INFINITY, NaN, on, updateableResources, weight

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

RamachandranSidechainEnergy(ResidueTorsionsList residueTorsionsList, DistanceMatrix distanceMatrix, RamachandranSidechainParametersList rspl, double weight, java.lang.String comment)

Method Summary

EnergyElement	createElement(java.lang.Object baseElement, Parameters parameters)
double	evaluate() Evaluates the current value of the energy function and update the derivatives.
static int[]	numberOfResiduesPerType()
ResidueTorsionsList	residueTorsionsList()
static double[]	sm2PerResidueType()
static double[]	sumPerResidueType()

Methods inherited from class meshi.energy.simpleEnergyTerms.SimpleEnergyTerm

createElementsList, elementsList, evaluateAtoms, test

Methods inherited from class meshi.energy.AbstractEnergy

addAttribute, comment, getAttribute, handleMissingParameters, isOn, off, on, toArray, toArray, toArray, toArray, toString, update

Methods inherited from class java.lang.Object

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

Field Detail

sumPerResidueType

protected static double[] sumPerResidueType

sm2PerResidueType

protected static double[] sm2PerResidueType

numberOfResiduesPerType

protected static int[] numberOfResiduesPerType

residueEnergies

public static double[] residueEnergies

residueTorsionsList

protected ResidueTorsionsList residueTorsionsList

Constructor Detail

RamachandranSidechainEnergy

public RamachandranSidechainEnergy(ResidueTorsionsList residueTorsionsList,
                                   DistanceMatrix distanceMatrix,
                                   RamachandranSidechainParametersList rspl,
                                   double weight,
                                   java.lang.String comment)

Method Detail

sumPerResidueType

public static double[] sumPerResidueType()

sm2PerResidueType

public static double[] sm2PerResidueType()

numberOfResiduesPerType

public static int[] numberOfResiduesPerType()

residueTorsionsList

public ResidueTorsionsList residueTorsionsList()

evaluate

public double evaluate()

Description copied from class: SimpleEnergyTerm

Evaluates the current value of the energy function and update the derivatives.

Overrides:

evaluate in class SimpleEnergyTerm

createElement

public EnergyElement createElement(java.lang.Object baseElement,
                                   Parameters parameters)

Specified by:

createElement in class SimpleEnergyTerm