meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
Class RamachandranSidechainEnergyElement

java.lang.Object
  meshi.energy.EnergyElement
      meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElement

Direct Known Subclasses:

RamachandranSidechainEnergyElementChi0, RamachandranSidechainEnergyElementChi1, RamachandranSidechainEnergyElementChi2, RamachandranSidechainEnergyElementChi3, RamachandranSidechainEnergyElementChi4

public abstract class RamachandranSidechainEnergyElement
extends EnergyElement

Encapsulation of RamachandranSidechain energy value for a single residue. Much like the parameters for this energy function, each residue type has its own class of energy element.

Field Summary

protected ResidueTorsions	residueTorsions
protected int	residueTypeIndex
protected RamachandranSidechainParameters	rsp
protected double	weight

Fields inherited from class meshi.energy.EnergyElement

atoms, dFormatSrt, dFormatStd, DX, frozen, relativeDiffTolerance, VERY_SMALL, XYZ

Constructor Summary

RamachandranSidechainEnergyElement(ResidueTorsions residueTorsions, RamachandranSidechainParameters rsp, double weight)

Method Summary

protected abstract boolean	legalResidueType() verifies residue type is a legal residue types for class.
protected void	monitor(double energy, double... derivs) Reports energy values.
protected void	setAtoms()

Methods inherited from class meshi.energy.EnergyElement

atoms, evaluate, evaluateAtoms, frozen, test, updateFrozen

Methods inherited from class java.lang.Object

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

Field Detail

residueTorsions

protected ResidueTorsions residueTorsions

rsp

protected RamachandranSidechainParameters rsp

weight

protected double weight

residueTypeIndex

protected int residueTypeIndex

Constructor Detail

RamachandranSidechainEnergyElement

public RamachandranSidechainEnergyElement(ResidueTorsions residueTorsions,
                                          RamachandranSidechainParameters rsp,
                                          double weight)

Method Detail

setAtoms

protected void setAtoms()

Specified by:

setAtoms in class EnergyElement

monitor

protected void monitor(double energy,
                       double... derivs)

Reports energy values. Currently switched off.

legalResidueType

protected abstract boolean legalResidueType()

verifies residue type is a legal residue types for class.