meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary
Class SmoothRotamerLibraryEnergy

java.lang.Object
  meshi.energy.AbstractEnergy
      meshi.energy.simpleEnergyTerms.SimpleEnergyTerm
          meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergy

All Implemented Interfaces:

CompositeTorsionsDefinitions, Attributable, Updateable

public class SmoothRotamerLibraryEnergy
extends SimpleEnergyTerm
implements CompositeTorsionsDefinitions

Smooth rotamer library 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 sidechain torsion angles.

Nested Class Summary

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

AbstractEnergy.UpdateableList

Field Summary

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

SmoothRotamerLibraryEnergy(ResidueTorsionsList residueTorsionsList, DistanceMatrix distanceMatrix, SmoothRotamerLibraryParametersList srlpl, double weight, java.lang.String comment)

Method Summary

EnergyElement

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

Methods inherited from class meshi.energy.simpleEnergyTerms.SimpleEnergyTerm

createElementsList, elementsList, evaluate, 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

Constructor Detail

SmoothRotamerLibraryEnergy

public SmoothRotamerLibraryEnergy(ResidueTorsionsList residueTorsionsList,
                                  DistanceMatrix distanceMatrix,
                                  SmoothRotamerLibraryParametersList srlpl,
                                  double weight,
                                  java.lang.String comment)

Method Detail

createElement

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

Specified by:

createElement in class SimpleEnergyTerm