Package edu.duke.cs.osprey.kstar.emat

Class ReducedEnergyMatrix

java.lang.Object

edu.duke.cs.osprey.confspace.AbstractTupleMatrix<Double>

edu.duke.cs.osprey.confspace.TupleMatrixDouble

edu.duke.cs.osprey.ematrix.EnergyMatrix

edu.duke.cs.osprey.kstar.emat.ReducedEnergyMatrix

All Implemented Interfaces:

FragmentEnergies, TupleMatrix<Double>, Serializable

public class ReducedEnergyMatrix
extends EnergyMatrix

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected KSSearchProblem	sp

Constructor Summary

Constructors

Constructor	Description
ReducedEnergyMatrix(KSSearchProblem sp, EnergyMatrix emat)

Method Summary

Modifier and Type	Method	Description
HigherTupleFinder<Double>	getHigherOrderTerms(int res1, int index1, int res2, int index2)
int	getNumConfAtPos(int pos)
int	getNumPos()
Double	getOneBody(int res, int index)
Double	getPairwise(int res1, int index1, int res2, int index2)

Methods inherited from class edu.duke.cs.osprey.ematrix.EnergyMatrix

confE, diff, getConstTerm, getEnergy, getEnergy, geteRefMat, getHigherOrderEnergy, getInternalEnergy, getInternalEnergyAtPos, rcContribAtPos, read, read, setConstTerm, seteRefMat, topPairwiseInteractions, write, write

Methods inherited from class edu.duke.cs.osprey.confspace.TupleMatrixDouble

allocate, fill, negate, setOneBody, setOneBody, setPairwise, setPairwise, sum, toString, toString, toStringScientific

Methods inherited from class edu.duke.cs.osprey.confspace.AbstractTupleMatrix

equals, equals, fill, fill, getDefaultHigherInteraction, getHigherOrderTuples, getNumConfAtPos, getNumOneBody, getNumPairwise, getOneBodyIndex, getOrMakeHigherOrderTuples, getPairwiseIndex, getPairwiseIndex, getPruningInterval, hasHigherOrderTermFor, hasHigherOrderTerms, hasHigherOrderTuples, matches, setHigherOrder, setHigherOrderTerms, setPruningInterval, setTupleValue, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface edu.duke.cs.osprey.confspace.FragmentEnergies

getEnergy, getEnergy

Methods inherited from interface edu.duke.cs.osprey.confspace.TupleMatrix

forEachHigherOrderTupleIn, forEachHigherOrderTupleIn, forEachHigherOrderTupleIn, getOneBody, getPairwise, getTuple, setOneBody, setPairwise, setTuple

Field Details

sp

protected KSSearchProblem sp

Constructor Details

ReducedEnergyMatrix

public ReducedEnergyMatrix(KSSearchProblem sp,
 EnergyMatrix emat)

Method Details

getOneBody

public Double getOneBody(int res,
 int index)

Specified by:

getOneBody in interface TupleMatrix<Double>

Overrides:

getOneBody in class TupleMatrixDouble

getPairwise

public Double getPairwise(int res1,
 int index1,
 int res2,
 int index2)

Specified by:

getPairwise in interface TupleMatrix<Double>

Overrides:

getPairwise in class TupleMatrixDouble

getHigherOrderTerms

public HigherTupleFinder<Double> getHigherOrderTerms(int res1,
 int index1,
 int res2,
 int index2)

Specified by:

getHigherOrderTerms in interface TupleMatrix<Double>

Overrides:

getHigherOrderTerms in class AbstractTupleMatrix<Double>

getNumConfAtPos

public int getNumConfAtPos(int pos)

Specified by:

getNumConfAtPos in interface TupleMatrix<Double>

Overrides:

getNumConfAtPos in class AbstractTupleMatrix<Double>

getNumPos

public int getNumPos()

Specified by:

getNumPos in interface TupleMatrix<Double>

Overrides:

getNumPos in class AbstractTupleMatrix<Double>