Package ffx.algorithms.optimize.manybody

Class EnergyExpansion

java.lang.Object

ffx.algorithms.optimize.manybody.EnergyExpansion

public class EnergyExpansion
extends Object

Constructor Summary

Constructors

Constructor	Description
EnergyExpansion(RotamerOptimization rO, DistanceMatrix dM, EliminatedRotamers eR, MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener, List<Residue> allResiduesList, int[][] resNeighbors, boolean threeBodyTerm, boolean decomposeOriginal, boolean usingBoxOptimization, boolean verbose, boolean pruneClashes, boolean prunePairClashes, boolean master)

Method Summary

Modifier and Type	Method	Description
HashMap<String,Integer>	allocate2BodyJobMap(Residue[] residues, int nResidues, boolean reverseMap)
HashMap<String,Integer>	allocate3BodyJobMap(Residue[] residues, int nResidues, boolean reverseMap)
void	allocate4BodyJobMap(Residue[] residues, int nResidues)
HashMap<String,Integer>	allocateSelfJobMap(Residue[] residues, int nResidues, boolean reverseMap)
double	compute2BodyEnergy(Residue[] residues, int i, int ri, int j, int rj)	Computes a pair energy, defined as energy with all side-chains but two turned off, minus the sum of backbone and component self energies.
double	compute3BodyEnergy(Residue[] residues, int i, int ri, int j, int rj, int k, int rk)	Computes a 3-body energy, defined as the energy with all sidechains but three turned off, minus the sum of backbone and component self/2-Body energies.
double	compute4BodyEnergy(Residue[] residues, int i, int ri, int j, int rj, int k, int rk, int l, int rl)	Computes a 4-body energy, defined as the energy with all sidechains but four turned off, minus the sum of backbone and component self/2-Body/3-body energies.
double	computeSelfEnergy(Residue[] residues, int i, int ri)	Computes a self energy, defined as energy with all side-chains but one turned off, minus the backbone energy.
double	get2Body(int i, int ri, int j, int rj)	Return a previously computed 2-body energy.
double	get3Body(Residue[] residues, int i, int ri, int j, int rj, int k, int rk)	Return a previously computed 3-body energy.
double	getBackboneEnergy()
Map<Integer,Integer[]>	getFourBodyEnergyMap()
double	getSelf(int i, int ri)	Return a previously computed self-energy.
double	getSelf(int i, int ri, Rotamer rot, boolean excludeFMod)	Return a previously computed self-energy.
Map<Integer,Integer[]>	getSelfEnergyMap()
Map<Integer,Integer[]>	getThreeBodyEnergyMap()
double	getTotalRotamerPhBias(List<Residue> residues, int[] rotamers, double pH, double KpH)	Compute the total rotamer Ph bias for an array of residues.
Map<Integer,Integer[]>	getTwoBodyEnergyMap()
int	loadEnergyRestart(File restartFile, Residue[] residues)
int	loadEnergyRestart(File restartFile, Residue[] residues, int boxIteration, int[] cellIndices)
double	lowestPairEnergy(Residue[] residues, int i, int ri, int j)	Return the lowest pair-energy for residue (i,ri) with residue j.
double	lowestSelfEnergy(Residue[] residues, int i)	Return the lowest self-energy for residue i.
boolean	minMaxE2(Residue[] residues, double[] minMax, int i, int ri, int j, int rj)	Calculates the minimum and maximum summations over additional residues for some pair ri-rj.
boolean	minMaxPairEnergy(Residue[] residues, double[] minMax, int i, int ri, int j)	Computes the maximum and minimum energy i,ri might have with j, and optionally (if three-body energies in use) third residues k.
void	set2Body(int i, int ri, int j, int rj, double e)
void	set2Body(int i, int ri, int j, int rj, double e, boolean quiet)	Store a pair energy in the pairs energy matrix.
void	set3Body(Residue[] residues, int i, int ri, int j, int rj, int k, int rk, double e)	set3Body.
void	set3Body(Residue[] residues, int i, int ri, int j, int rj, int k, int rk, double e, boolean quiet)	Stores a triple energy in the triples energy matrix.
void	setBackboneEnergy(double backboneEnergy)
void	setSelf(int i, int ri, double e)
void	setSelf(int i, int ri, double e, boolean quiet)	Stores a self energy in the self energy matrix.
void	turnOffAllResidues(Residue[] residues)
void	turnOffResidue(Residue residue)
void	turnOnAllResidues(Residue[] residues)
void	turnOnResidue(Residue residue, int ri)

Methods inherited from class java.lang.Object

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

Constructor Details

EnergyExpansion

public EnergyExpansion(RotamerOptimization rO,
 DistanceMatrix dM,
 EliminatedRotamers eR,
 MolecularAssembly molecularAssembly,
 Potential potential,
 AlgorithmListener algorithmListener,
 List<Residue> allResiduesList,
 int[][] resNeighbors,
 boolean threeBodyTerm,
 boolean decomposeOriginal,
 boolean usingBoxOptimization,
 boolean verbose,
 boolean pruneClashes,
 boolean prunePairClashes,
 boolean master)

Method Details

allocate2BodyJobMap

public HashMap<String,Integer> allocate2BodyJobMap(Residue[] residues,
 int nResidues,
 boolean reverseMap)

allocate3BodyJobMap

public HashMap<String,Integer> allocate3BodyJobMap(Residue[] residues,
 int nResidues,
 boolean reverseMap)

allocate4BodyJobMap

public void allocate4BodyJobMap(Residue[] residues,
 int nResidues)

allocateSelfJobMap

public HashMap<String,Integer> allocateSelfJobMap(Residue[] residues,
 int nResidues,
 boolean reverseMap)

compute2BodyEnergy

public double compute2BodyEnergy(Residue[] residues,
 int i,
 int ri,
 int j,
 int rj)

Computes a pair energy, defined as energy with all side-chains but two turned off, minus the sum of backbone and component self energies.

Parameters:

residues - Residues under optimization.

i - A residue index.

ri - A rotamer index for residue i.

j - A residue index j!=i.

rj - A rotamer index for residue j.

Returns:

Epair(ri, rj)=E2(ri,rj)-Eself(ri)-Eself(rj)-Eenv/bb.

compute3BodyEnergy

public double compute3BodyEnergy(Residue[] residues,
 int i,
 int ri,
 int j,
 int rj,
 int k,
 int rk)

Computes a 3-body energy, defined as the energy with all sidechains but three turned off, minus the sum of backbone and component self/2-Body energies.

Parameters:

residues - Residues under optimization.

i - A residue index.

ri - A rotamer index for residue i.

j - A residue index j!=i.

rj - A rotamer index for residue j.

k - A residue index k!=j k!=i.

rk - A rotamer index for residue k.

Returns:

Etri(ri, rj)=E3(ri,rj,rk)-Epair(ri,rj)-Epair(ri,rk)-Epair(rj,rk)-Eself(ri)-Eself(rj)-Eself(rk)-Eenv/bb.

compute4BodyEnergy

public double compute4BodyEnergy(Residue[] residues,
 int i,
 int ri,
 int j,
 int rj,
 int k,
 int rk,
 int l,
 int rl)

Computes a 4-body energy, defined as the energy with all sidechains but four turned off, minus the sum of backbone and component self/2-Body/3-body energies.

Parameters:

residues - Residues under optimization.

i - A residue index.

ri - A rotamer index for residue i.

j - A residue index j!=i.

rj - A rotamer index for residue j.

k - A residue index k!=j k!=i.

rk - A rotamer index for residue k.

l - A residue index l!=i l!=j l!=k.

rl - A rotamer index for residue l.

Returns:

The 4-body energy.

computeSelfEnergy

public double computeSelfEnergy(Residue[] residues,
 int i,
 int ri)

Computes a self energy, defined as energy with all side-chains but one turned off, minus the backbone energy.

If a residue has multiple titration states represented by its set of rotamers, then a pH-dependent bias is included.

Parameters:

residues - Residues under optimization.

i - A residue index.

ri - A rotamer index for residue i.

Returns:

Eself(ri)=E1(ri)-Eenv/bb.

getTotalRotamerPhBias

public double getTotalRotamerPhBias(List<Residue> residues,
 int[] rotamers,
 double pH,
 double KpH)

Compute the total rotamer Ph bias for an array of residues.

Parameters:

residues - The array of residues.

rotamers - The array of rotamer indices for each residue.

Returns:

The total Ph bias.

get2Body

public double get2Body(int i,
 int ri,
 int j,
 int rj)

Return a previously computed 2-body energy.

Parameters:

i - Residue i.

ri - Rotamer ri of residue i.

j - Residue j.

rj - Rotamer rj of residue j.

Returns:

The 2-Body energy.

get3Body

public double get3Body(Residue[] residues,
 int i,
 int ri,
 int j,
 int rj,
 int k,
 int rk)

Return a previously computed 3-body energy.

Parameters:

residues - an array of Residue objects.

i - Residue i.

ri - Rotamer ri of residue i.

j - Residue j.

rj - Rotamer rj of residue j.

k - Residue k.

rk - Rotamer rk of residue k.

Returns:

The 3-Body energy.

getBackboneEnergy

public double getBackboneEnergy()

setBackboneEnergy

public void setBackboneEnergy(double backboneEnergy)

getFourBodyEnergyMap

public Map<Integer,Integer[]> getFourBodyEnergyMap()

getSelf

public double getSelf(int i,
 int ri)

Return a previously computed self-energy.

Parameters:

i - Residue i.

ri - Rotamer ri of residue i.

Returns:

The self-energy.

getSelf

public double getSelf(int i,
 int ri,
 Rotamer rot,
 boolean excludeFMod)

Return a previously computed self-energy.

Parameters:

i - Residue i.

ri - Rotamer ri of residue i.

Returns:

The self-energy.

getSelfEnergyMap

public Map<Integer,Integer[]> getSelfEnergyMap()

getThreeBodyEnergyMap

public Map<Integer,Integer[]> getThreeBodyEnergyMap()

getTwoBodyEnergyMap

public Map<Integer,Integer[]> getTwoBodyEnergyMap()

loadEnergyRestart

public int loadEnergyRestart(File restartFile,
 Residue[] residues)

loadEnergyRestart

public int loadEnergyRestart(File restartFile,
 Residue[] residues,
 int boxIteration,
 int[] cellIndices)

lowestPairEnergy

public double lowestPairEnergy(Residue[] residues,
 int i,
 int ri,
 int j)

Return the lowest pair-energy for residue (i,ri) with residue j.

Parameters:

residues - Residue array.

i - Residue i index.

ri - Residue i rotamer index.

j - Residue j index.

Returns:

Lowest pair energy.

lowestSelfEnergy

public double lowestSelfEnergy(Residue[] residues,
 int i)

Return the lowest self-energy for residue i.

Parameters:

residues - Array if residues.

i - Index of residue i.

Returns:

Returns the lowest self-energy for residue i.

minMaxE2

public boolean minMaxE2(Residue[] residues,
 double[] minMax,
 int i,
 int ri,
 int j,
 int rj)
                 throws IllegalArgumentException

Calculates the minimum and maximum summations over additional residues for some pair ri-rj.

Parameters:

residues - Residues under consideration.

minMax - Result array: 0 is min summation, 1 max summation.

i - Residue i.

ri - Rotamer for residue i.

j - Residue j!=i.

rj - Rotamer for residue j.

Returns:

False if ri-rj always clashes with other residues.

Throws:

IllegalArgumentException - If ri, rj, or ri-rj eliminated.

minMaxPairEnergy

public boolean minMaxPairEnergy(Residue[] residues,
 double[] minMax,
 int i,
 int ri,
 int j)

Computes the maximum and minimum energy i,ri might have with j, and optionally (if three-body energies in use) third residues k.

The return value should be redundant with minMax[0] being NaN.

Parameters:

residues - Array of residues under consideration.

minMax - Index 0 to be filled by minimum energy, index 1 filled by maximum energy.

i - Some residue i under consideration.

ri - A rotamer for residue i.

j - Some arbitrary residue i!=j.

Returns:

If a valid configuration between i,ri and j could be found.

set2Body

public void set2Body(int i,
 int ri,
 int j,
 int rj,
 double e)

set2Body

public void set2Body(int i,
 int ri,
 int j,
 int rj,
 double e,
 boolean quiet)

Store a pair energy in the pairs energy matrix.

Parameters:

i - A residue index.

ri - A rotamer for residue i.

j - A residue index j != i.

rj - A rotamer for residue j.

e - Computed energy to store.

quiet - Silence warnings about exceptions.

set3Body

public void set3Body(Residue[] residues,
 int i,
 int ri,
 int j,
 int rj,
 int k,
 int rk,
 double e)

set3Body.

Parameters:

residues - an array of Residue objects.

i - a int.

ri - a int.

j - a int.

rj - a int.

k - a int.

rk - a int.

e - a double.

set3Body

public void set3Body(Residue[] residues,
 int i,
 int ri,
 int j,
 int rj,
 int k,
 int rk,
 double e,
 boolean quiet)
              throws IllegalStateException

Stores a triple energy in the triples energy matrix.

Parameters:

residues - an array of Residue objects.

i - A residue index.

ri - A rotamer for residue i.

j - A residue index j != i.

rj - A rotamer for residue j.

k - A residue index k != j, k != i.

rk - A rotamer for residue k.

e - Computed energy to store.

quiet - Silence warnings about exceptions.

Throws:

IllegalStateException - If threeBodyTerm is false.

setSelf

public void setSelf(int i,
 int ri,
 double e)

setSelf

public void setSelf(int i,
 int ri,
 double e,
 boolean quiet)

Stores a self energy in the self energy matrix.

Parameters:

i - A residue index.

ri - A rotamer for residue i.

e - Computed energy to store.

quiet - Silence warnings about exceptions.

turnOffAllResidues

public void turnOffAllResidues(Residue[] residues)

turnOffResidue

public void turnOffResidue(Residue residue)

turnOnAllResidues

public void turnOnAllResidues(Residue[] residues)

turnOnResidue

public void turnOnResidue(Residue residue,
 int ri)