Uses of Class
ffx.potential.bonded.Residue

Packages that use Residue

Package	Description
ffx.algorithms.cli	The Algorithms CLI package defines options for PicoCLI command line scripts.
ffx.algorithms.mc	The MC package implements a variety of Monte Carlo moves for optimization and simulation algorithms.
ffx.algorithms.misc	The Misc package contains a few miscellaneous algorithms.
ffx.algorithms.optimize	The Optimize package contains local and global optimization algorithms using pure Java and OpenMM code paths.
ffx.algorithms.optimize.manybody	The manybody package implements many-body rotamer optimization infrastructure, including distance matrices, an energy expansion (self, two-body, three-body, and four-body), Dead-end elimination criteria, Goldstein elimination criteria, and supporting data structures for efficient optimization.
ffx.potential	The Potential package implements molecular mechanics force fields with shared memory Parallel Java and via OpenMM.
ffx.potential.bonded	The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions, etc.
ffx.potential.extended	The Extended package is progress toward support for constant pH molecular dynamics using extended system variables (i.e. lambda dynamics on protonation).
ffx.potential.nonbonded.implicit	The implicit package implements implicit solvent models and related terms, including Generalized Kirkwood (GK) electrostatics, surface area terms, dispersion/cavitation contributions, and supporting parallel regions for Born radii and field evaluation.
ffx.potential.parameters	The Parameters package stores force field atom types, bond types, etc, and keywords that define the potential.
ffx.potential.parsers	The Parsers package handles reading/writing files to/from the internal data structure.
ffx.potential.utils	The Utils package implements core functionality needed for using the Potential package, such as opening and closing structure files, basic force field energy evaluations, etc.
ffx.realspace	The Real Space package implements real space structure refinement.
ffx.xray	The X-ray package implements support for X-ray and Neutron refinement.

Uses of Residue in ffx.algorithms.cli

Methods in ffx.algorithms.cli that return types with arguments of type Residue

Modifier and Type	Method	Description
List<Residue>	ManyBodyOptions.collectResidues(MolecularAssembly activeAssembly)	Collect residues based on residue selection flags.

Method parameters in ffx.algorithms.cli with type arguments of type Residue

Modifier and Type	Method	Description
String	ManyBodyOptions.selectInclusionResidues(List<Residue> residueList, int mutatingResidue, boolean onlyTitration, double inclusionCutoff)

Uses of Residue in ffx.algorithms.mc

Constructor parameters in ffx.algorithms.mc with type arguments of type Residue

Modifier	Constructor	Description
	RosenbluthCBMC(MolecularAssembly molecularAssembly, ForceFieldEnergy ffe, Thermostat thermostat, List<Residue> targets, int mcFrequency, int trialSetSize, boolean writeSnapshots)	RRMC constructor.
	RosenbluthOBMC(MolecularAssembly molecularAssembly, ForceFieldEnergy forceFieldEnergy, Thermostat thermostat, List<Residue> targets, int mcFrequency, int trialSetSize)	RRMC constructor.
	RosenbluthOBMC(MolecularAssembly molecularAssembly, ForceFieldEnergy forceFieldEnergy, Thermostat thermostat, List<Residue> targets, int mcFrequency, int trialSetSize, boolean writeSnapshots)	Constructor for RosenbluthOBMC.

Uses of Residue in ffx.algorithms.misc

Constructors in ffx.algorithms.misc with parameters of type Residue

Modifier	Constructor	Description
	GenerateRotamers(MolecularAssembly molecularAssembly, Potential potential, Residue residue, File file, int nChi, AlgorithmListener listener)	Intended to create rotamer sets for nonstandard amino acids.
	GenerateRotamers(MolecularAssembly molecularAssembly, Potential potential, Residue residue, File file, int nChi, AlgorithmListener listener, RotamerLibrary library)	Intended to create rotamer sets for nonstandard amino acids.

Uses of Residue in ffx.algorithms.optimize

Methods in ffx.algorithms.optimize that return types with arguments of type Residue

Modifier and Type	Method	Description
List<Residue>	RotamerOptimization.getResidues()	Return the residue list.

Methods in ffx.algorithms.optimize with parameters of type Residue

Modifier and Type	Method	Description
double	RotamerOptimization.computeBackboneEnergy(Residue[] residues)	Computes the environment/backbone energy, defined as energy with all sidechains under consideration turned off in their 0th rotamer.
double	RotamerOptimization.computeEnergy(Residue[] residues, int[] rotamers, boolean print)	Uses existing backbone, self, 2-Body, and 3-body energies from rotamerEnergies() to calculate an approximate energy for a rotamer permutation.
double	RotamerOptimization.currentEnergy(Residue[] resArray)	Calculates the energy at the current state.
void	RotamerOptimization.getFractions(Residue[] residues, int i, int[] currentRotamers)	Calculate population of each rotamer for residues in the system
void	RotamerOptimization.getFractions(Residue[] residues, int i, int[] currentRotamers, boolean usingBoxOptimization)	Return population of each rotamer for residues in the system
double[][]	RotamerOptimization.getProtonationPopulations(Residue[] residues)	Return the populations of the titratable residue states and print
double	RotamerOptimization.goldsteinPairSumOverK(Residue[] residues, int lb, int ub, int i, int riA, int riB, int j, int rjC, int rjD, List<Residue> blockedResidues, int[] possK)
void	RotamerOptimization.partitionFunction(Residue[] residues, int i, int[] currentRotamers)	A global optimization over side-chain rotamers using a recursive algorithm and information about eliminated rotamers, rotamer pairs and rotamer triples.
double	RotamerOptimization.rotamerOptimization(MolecularAssembly molecularAssembly, Residue[] residues, int i, double lowEnergy, int[] optimum)	A brute-force global optimization over side-chain rotamers using a recursive algorithm.
void	RotamerOptimization.turnOffAllResidues(Residue[] residues)
void	RotamerOptimization.turnOffResidue(Residue residue)
void	RotamerOptimization.turnOnAllResidues(Residue[] residues)
void	RotamerOptimization.turnOnResidue(Residue residue, int ri)

Method parameters in ffx.algorithms.optimize with type arguments of type Residue

Modifier and Type	Method	Description
double	RotamerOptimization.currentEnergyWrapper(List<Residue> resList)	Wrapper intended for use with RotamerMatrixMC.
boolean	TitrationManyBody.excludeExcessAtoms(Set<Atom> excludeAtoms, int[] optimalRotamers, MolecularAssembly molecularAssembly, List<Residue> residueList)
boolean	TitrationManyBody.excludeExcessAtoms(Set<Atom> excludeAtoms, int[] optimalRotamers, List<Residue> residueList)
protected double	RotamerOptimization.globalOptimization(List<Residue> residueList)	The main driver for optimizing a block of residues using DEE.
double	RotamerOptimization.goldsteinPairSumOverK(Residue[] residues, int lb, int ub, int i, int riA, int riB, int j, int rjC, int rjD, List<Residue> blockedResidues, int[] possK)
void	RotamerOptimization.initFraction(List<Residue> residueList)	Init fraction array
void	RotamerOptimization.setResidues(List<Residue> residueList)	Set the residue list.
void	RotamerOptimization.setResiduesIgnoreNull(List<Residue> residues)	Accepts a list of residues but throws out null residues.
double	RotamerOptimization.slidingWindowCentered(List<Residue> residueList)

Uses of Residue in ffx.algorithms.optimize.manybody

Methods in ffx.algorithms.optimize.manybody that return types with arguments of type Residue

Modifier and Type	Method	Description
ArrayList<Residue>	GoldsteinPairRegion.getMissedResidues()
ArrayList<Residue>	ManyBodyCell.getResiduesAsList()	Returns a copy of the ArrayList of residues.

Methods in ffx.algorithms.optimize.manybody with parameters of type Residue

Modifier and Type	Method	Description
void	ManyBodyCell.addResidue(Residue residue)	Add a residue to the box.
HashMap<String,Integer>	EnergyExpansion.allocate2BodyJobMap(Residue[] residues, int nResidues, boolean reverseMap)
HashMap<String,Integer>	EnergyExpansion.allocate3BodyJobMap(Residue[] residues, int nResidues, boolean reverseMap)
void	EnergyExpansion.allocate4BodyJobMap(Residue[] residues, int nResidues)
HashMap<String,Integer>	EnergyExpansion.allocateSelfJobMap(Residue[] residues, int nResidues, boolean reverseMap)
boolean	ManyBodyCell.anyRotamerInsideCell(Residue residue, Crystal crystal, SymOp symOp, boolean variableOnly)	Checks if any rotamer of a Residue is inside this BoxOptCell.
double	EnergyExpansion.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	EnergyExpansion.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	EnergyExpansion.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	EnergyExpansion.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.
boolean	EliminatedRotamers.eliminateRotamer(Residue[] residues, int i, int ri, boolean verbose)	Safe method to eliminate a rotamer: will not eliminate if there are no alternate rotamers for residue i, or if i-ri is already eliminated.
boolean	EliminatedRotamers.eliminateRotamerPair(Residue[] residues, int i, int ri, int j, int rj, boolean verbose)
int	EliminatedRotamers.eliminateRotamerPairs(Residue[] residues, int i, int ri, boolean verbose)
double	EnergyExpansion.get3Body(Residue[] residues, int i, int ri, int j, int rj, int k, int rk)	Return a previously computed 3-body energy.
void	DistanceRegion.init(DistanceMatrix dM, MolecularAssembly molecularAssembly, Residue[] allResiduesArray, AlgorithmListener algorithmListener, DistanceMatrix.NeighborDistances[][] distanceMatrix)
void	EnergyRegion.init(EnergyExpansion eE, Residue[] residues, int[] rotamers, boolean threeBodyTerm)
void	GoldsteinPairRegion.init(Residue[] residues, int i, int riA, int riB, int j, int rjC, int rjD, int[][] bidiResNeighbors, RotamerOptimization rotamerOptimization)	Initializes a ParallelRegion to attempt the elimination of riA,rjC by riB,rjD.
int	EnergyExpansion.loadEnergyRestart(File restartFile, Residue[] residues)
int	EnergyExpansion.loadEnergyRestart(File restartFile, Residue[] residues, int boxIteration, int[] cellIndices)
double	EnergyExpansion.lowestPairEnergy(Residue[] residues, int i, int ri, int j)	Return the lowest pair-energy for residue (i,ri) with residue j.
double	EnergyExpansion.lowestSelfEnergy(Residue[] residues, int i)	Return the lowest self-energy for residue i.
boolean	EnergyExpansion.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	EnergyExpansion.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.
boolean	EliminatedRotamers.pairsToSingleElimination(Residue[] residues, int i, int j)	Method to check if pairs elimination for some residue pair has enabled a singles rotamer elimination by eliminating all ri-rj for some ri or some rj.
void	EliminatedRotamers.prePrunePairs(Residue[] residues)	Pre-prunes any pairs that have a pair-energy of Double.NaN before pruning and eliminations happen.
void	EliminatedRotamers.prePruneSelves(Residue[] residues)	Pre-prunes any selves that have a self-energy of Double.NaN before pruning and eliminations happen.
void	EliminatedRotamers.prunePairClashes(Residue[] residues)	Prunes rotamer ri of residue i if all ri-j pair energies are worse than the best i-j pair by some threshold value; additionally prunes ri-rj pairs if they exceed the best i-j pair by a greater threshold value; additionally performs this in reverse (searches over j-i).
void	EliminatedRotamers.pruneSingleClashes(Residue[] residues)	Uses calculated energies to prune rotamers based on a threshold distance from that residue's minimum energy rotamer (by default 20 kcal/mol).
boolean	ManyBodyCell.residueInsideCell(Residue residue, Crystal crystal, SymOp symOp, boolean variableOnly)	Checks if a Residue is inside this BoxOptCell.
void	EnergyExpansion.set3Body(Residue[] residues, int i, int ri, int j, int rj, int k, int rk, double e)	set3Body.
void	EnergyExpansion.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	EnergyExpansion.turnOffAllResidues(Residue[] residues)
void	EnergyExpansion.turnOffResidue(Residue residue)
void	EnergyExpansion.turnOnAllResidues(Residue[] residues)
void	EnergyExpansion.turnOnResidue(Residue residue, int ri)
boolean	EliminatedRotamers.validateDEE(Residue[] residues)

Method parameters in ffx.algorithms.optimize.manybody with type arguments of type Residue

Modifier and Type	Method	Description
double	EnergyExpansion.getTotalRotamerPhBias(List<Residue> residues, int[] rotamers, double pH, double KpH)	Compute the total rotamer Ph bias for an array of residues.

Constructors in ffx.algorithms.optimize.manybody with parameters of type Residue

Modifier	Constructor	Description
	DistanceMatrix(MolecularAssembly molecularAssembly, AlgorithmListener algorithmListener, Residue[] allResiduesArray, List<Residue> allResiduesList, RotamerOptimization.DistanceMethod distanceMethod, double distance, double twoBodyCutoffDist, double threeBodyCutoffDist)
	EliminatedRotamers(RotamerOptimization rO, DistanceMatrix dM, List<Residue> allResiduesList, int maxRotCheckDepth, double clashThreshold, double pairClashThreshold, double multiResClashThreshold, double nucleicPruningFactor, double nucleicPairsPruningFactor, double multiResPairClashAddn, boolean pruneClashes, boolean prunePairClashes, boolean print, Residue[] residues)
	FourBodyEnergyRegion(RotamerOptimization rotamerOptimization, DistanceMatrix dM, EnergyExpansion eE, EliminatedRotamers eR, Residue[] residues, List<Residue> allResiduesList, double superpositionThreshold)
	RotamerMatrixMC(int[] rotamers, Residue[] residues, boolean useFullAMOEBAEnergy, RotamerOptimization rotamerOptimization)	The Rotamers array must be the same array as passed to any MCMove objects used (and not a copy).
	RotamerMatrixMove(boolean useAllElims, int[] rotamers, Residue[] residues, RotamerOptimization rotamerOptimization, EliminatedRotamers eliminatedRotamers, boolean monteCarloTesting)	Constructs the RotamerMatrixMove set; at present, a new object must be made if rotamers or residues are changed outside the scope of this class.
	SelfEnergyRegion(RotamerOptimization rO, EnergyExpansion eE, EliminatedRotamers eR, Residue[] residues, BufferedWriter energyWriter, Comm world, int numProc, boolean pruneClashes, boolean master, int rank, boolean verbose, boolean writeEnergyRestart, boolean printFiles)
	ThreeBodyEnergyRegion(RotamerOptimization rotamerOptimization, DistanceMatrix dM, EnergyExpansion eE, EliminatedRotamers eR, Residue[] residues, List<Residue> allResiduesList, BufferedWriter energyWriter, Comm world, int numProc, double superpositionThreshold, boolean master, int rank, boolean verbose, boolean writeEnergyRestart, boolean printFiles)
	TwoBodyEnergyRegion(RotamerOptimization rotamerOptimization, DistanceMatrix dM, EnergyExpansion eE, EliminatedRotamers eR, Residue[] residues, List<Residue> allResiduesList, BufferedWriter energyWriter, Comm world, int numProc, boolean prunePairClashes, double superpositionThreshold, boolean master, int rank, boolean verbose, boolean writeEnergyRestart, boolean printFiles)

Constructor parameters in ffx.algorithms.optimize.manybody with type arguments of type Residue

Modifier	Constructor	Description
	DistanceMatrix(MolecularAssembly molecularAssembly, AlgorithmListener algorithmListener, Residue[] allResiduesArray, List<Residue> allResiduesList, RotamerOptimization.DistanceMethod distanceMethod, double distance, double twoBodyCutoffDist, double threeBodyCutoffDist)
	EliminatedRotamers(RotamerOptimization rO, DistanceMatrix dM, List<Residue> allResiduesList, int maxRotCheckDepth, double clashThreshold, double pairClashThreshold, double multiResClashThreshold, double nucleicPruningFactor, double nucleicPairsPruningFactor, double multiResPairClashAddn, boolean pruneClashes, boolean prunePairClashes, boolean print, Residue[] residues)
	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)
	FourBodyEnergyRegion(RotamerOptimization rotamerOptimization, DistanceMatrix dM, EnergyExpansion eE, EliminatedRotamers eR, Residue[] residues, List<Residue> allResiduesList, double superpositionThreshold)
	ThreeBodyEnergyRegion(RotamerOptimization rotamerOptimization, DistanceMatrix dM, EnergyExpansion eE, EliminatedRotamers eR, Residue[] residues, List<Residue> allResiduesList, BufferedWriter energyWriter, Comm world, int numProc, double superpositionThreshold, boolean master, int rank, boolean verbose, boolean writeEnergyRestart, boolean printFiles)
	TwoBodyEnergyRegion(RotamerOptimization rotamerOptimization, DistanceMatrix dM, EnergyExpansion eE, EliminatedRotamers eR, Residue[] residues, List<Residue> allResiduesList, BufferedWriter energyWriter, Comm world, int numProc, boolean prunePairClashes, double superpositionThreshold, boolean master, int rank, boolean verbose, boolean writeEnergyRestart, boolean printFiles)

Uses of Residue in ffx.potential

Methods in ffx.potential that return types with arguments of type Residue

Modifier and Type	Method	Description
List<Residue>	MolecularAssembly.getResidueList()	getResidueList

Uses of Residue in ffx.potential.bonded

Subclasses of Residue in ffx.potential.bonded

Modifier and Type	Class	Description
class	MultiResidue	The MultiResidue class allows switching between residues for uses such as sequence optimization.

Fields in ffx.potential.bonded declared as Residue

Modifier and Type	Field	Description
final Residue	BondedUtils.MissingAtomTypeException.residue

Methods in ffx.potential.bonded that return Residue

Modifier and Type	Method	Description
static Residue	AminoAcidUtils.buildAIB(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildAIB.
static Residue	AminoAcidUtils.buildAlanine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildAlanine.
static Residue	AminoAcidUtils.buildArginine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildArginine.
static Residue	AminoAcidUtils.buildAsparagine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildAsparagine.
static Residue	AminoAcidUtils.buildAspartate(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildAspartate.
static Residue	AminoAcidUtils.buildCysteine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildCysteine.
static Residue	AminoAcidUtils.buildCystine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildCystine.
static Residue	AminoAcidUtils.buildDeprotonatedCysteine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildDeprotonatedCysteine.
static Residue	AminoAcidUtils.buildDeprotonatedLysine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildDeprotonatedLysine.
static Residue	AminoAcidUtils.buildDeprotonatedTyrosine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildDeprotonatedTyrosine.
static Residue	AminoAcidUtils.buildGlutamate(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildGlutamate.
static Residue	AminoAcidUtils.buildGlutamine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildGlutamine.
static Residue	AminoAcidUtils.buildGlycine(Residue res, Atom CA, Atom N, Atom C, AminoAcidUtils.ResiduePosition position, ForceField ff, List<Bond> bonds)	buildGlycine.
static Residue	AminoAcidUtils.buildHistidine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildHistidine.
static Residue	AminoAcidUtils.buildIsoleucine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildIsoleucine.
static Residue	AminoAcidUtils.buildLeucine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildLeucine.
static Residue	AminoAcidUtils.buildLysine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildLysine.
static Residue	AminoAcidUtils.buildMethionine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bond)	buildMethionine.
static Residue	AminoAcidUtils.buildNeutralAsparticAcid(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildNeutralAsparticAcid.
static Residue	AminoAcidUtils.buildNeutralGlutamicAcid(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildNeutralGlutamicAcid.
static Residue	AminoAcidUtils.buildNeutralHistidineD(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildNeutralHistidineD.
static Residue	AminoAcidUtils.buildNeutralHistidineE(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildNeutralHistidineE.
static Residue	AminoAcidUtils.buildOrnithine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildOrnithine.
static Residue	AminoAcidUtils.buildPCA(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildPCA.
static Residue	AminoAcidUtils.buildPhenylalanine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildPhenylalanine.
static Residue	AminoAcidUtils.buildProline(Residue res, Atom CA, Atom N, Atom C, AminoAcidUtils.ResiduePosition position, ForceField ff, List<Bond> bonds)	buildProline.
static Residue	AminoAcidUtils.buildSerine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildSerine.
static Residue	AminoAcidUtils.buildThreonine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildThreonine.
static Residue	AminoAcidUtils.buildTryptophan(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bond)	buildTryptophan.
static Residue	AminoAcidUtils.buildTwoProtonAsparticAcid(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildTwoProtonAsparticAcid.
static Residue	AminoAcidUtils.buildTwoProtonGlutamicAcid(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildTwoProtonGlutamicAcid.
static Residue	AminoAcidUtils.buildTyrosine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildTyrosine.
static Residue	AminoAcidUtils.buildValine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildValine.
Residue	MultiResidue.getActive()	getActive.
Residue	Polymer.getFirstResidue()	getFirstResidue
Residue	Residue.getNextResidue()	Returns the Residue bonded to this Residue at this Residue's 3' or C-terminal end.
Residue	ResidueState.getParent()	Getter for the field parent.
Residue	Residue.getPreviousResidue()	Returns the Residue bonded to this Residue at this Residue's 5' or N-terminal end.
Residue	Polymer.getResidue(int resNum)	getResidue
Residue	Polymer.getResidue(String resName, int resNum, boolean create)	getResidue
Residue	Polymer.getResidue(String resName, int resNum, boolean create, Residue.ResidueType defaultRT)	getResidue
Residue	RotamerLibrary.RotamerGuess.getResidue()

Methods in ffx.potential.bonded that return types with arguments of type Residue

Modifier and Type	Method	Description
static List<List<Residue>>	PolymerUtils.findChainBreaks(List<Residue> residues, double cutoff)
List<Residue>	MultiResidue.getConsideredResidues()	Returns a copy of this MultiResidue's consideredResidues array.
List<Residue>	MultiResidue.getInactive()	Returns a list of this MultiResidue's inactive residues.
List<Residue>	Polymer.getResidues()	getResidues

Methods in ffx.potential.bonded with parameters of type Residue

Modifier and Type	Method	Description
void	MultiResidue.addResidue(Residue newResidue)	addResidue.
static void	RotamerLibrary.applyRotamer(Residue residue, Rotamer rotamer)	Applies a Rotamer to a Residue by calling applyAARotamer or applyNARotamer.
static void	RotamerLibrary.applyRotamer(Residue residue, Rotamer rotamer, boolean independent)	Version of applyRotamer which allows for chain context-independent drawing of nucleic acid Rotamers.
static double[]	RotamerLibrary.applySugarPucker(Residue residue, RotamerLibrary.NucleicSugarPucker pucker, boolean isDeoxy, boolean place)	If place is true, builds C2', C3', and O3' based on delta(i) and returns an empty double[]; if place is false, returns a double[] filled with the coordinates at which O3' would be placed by the specified pucker.
static void	AminoAcidUtils.assignAminoAcidAtomTypes(Residue residue, Residue previousResidue, Residue nextResidue, ForceField forceField, List<Bond> bondList)	assignAminoAcidAtomTypes.
static Residue	AminoAcidUtils.buildAIB(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildAIB.
static Residue	AminoAcidUtils.buildAlanine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildAlanine.
static Residue	AminoAcidUtils.buildArginine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildArginine.
static Residue	AminoAcidUtils.buildAsparagine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildAsparagine.
static Residue	AminoAcidUtils.buildAspartate(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildAspartate.
static Residue	AminoAcidUtils.buildCysteine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildCysteine.
static Residue	AminoAcidUtils.buildCystine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildCystine.
static Residue	AminoAcidUtils.buildDeprotonatedCysteine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildDeprotonatedCysteine.
static Residue	AminoAcidUtils.buildDeprotonatedLysine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildDeprotonatedLysine.
static Residue	AminoAcidUtils.buildDeprotonatedTyrosine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildDeprotonatedTyrosine.
static Residue	AminoAcidUtils.buildGlutamate(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildGlutamate.
static Residue	AminoAcidUtils.buildGlutamine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildGlutamine.
static Residue	AminoAcidUtils.buildGlycine(Residue res, Atom CA, Atom N, Atom C, AminoAcidUtils.ResiduePosition position, ForceField ff, List<Bond> bonds)	buildGlycine.
static Residue	AminoAcidUtils.buildHistidine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildHistidine.
static Residue	AminoAcidUtils.buildIsoleucine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildIsoleucine.
static Residue	AminoAcidUtils.buildLeucine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildLeucine.
static Residue	AminoAcidUtils.buildLysine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildLysine.
static Residue	AminoAcidUtils.buildMethionine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bond)	buildMethionine.
static Residue	AminoAcidUtils.buildNeutralAsparticAcid(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildNeutralAsparticAcid.
static Residue	AminoAcidUtils.buildNeutralGlutamicAcid(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildNeutralGlutamicAcid.
static Residue	AminoAcidUtils.buildNeutralHistidineD(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildNeutralHistidineD.
static Residue	AminoAcidUtils.buildNeutralHistidineE(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildNeutralHistidineE.
static Residue	AminoAcidUtils.buildOrnithine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildOrnithine.
static Residue	AminoAcidUtils.buildPCA(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildPCA.
static Residue	AminoAcidUtils.buildPhenylalanine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildPhenylalanine.
static Residue	AminoAcidUtils.buildProline(Residue res, Atom CA, Atom N, Atom C, AminoAcidUtils.ResiduePosition position, ForceField ff, List<Bond> bonds)	buildProline.
static Residue	AminoAcidUtils.buildSerine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildSerine.
static Residue	AminoAcidUtils.buildThreonine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildThreonine.
static Residue	AminoAcidUtils.buildTryptophan(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bond)	buildTryptophan.
static Residue	AminoAcidUtils.buildTwoProtonAsparticAcid(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildTwoProtonAsparticAcid.
static Residue	AminoAcidUtils.buildTwoProtonGlutamicAcid(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildTwoProtonGlutamicAcid.
static Residue	AminoAcidUtils.buildTyrosine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildTyrosine.
static Residue	AminoAcidUtils.buildValine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildValine.
static void	NamingUtils.checkHydrogenAtomNames(Residue residue, PDBFilter.PDBFileStandard fileStandard)	Ensures proper naming of hydrogen according to latest PDB format.
int	Residue.compareTo(Residue o)
static void	AminoAcidUtils.copyResidue(Residue fromResidue, Residue toResidue)	copyResidue.
Joint	Polymer.createJoint(Residue residue1, Residue residue2, ForceField forceField)	Form a Joint between two residues.
static Rotamer[]	Rotamer.defaultRotamerFactory(Residue residue)	Factory method to construct an original-coordinates Rotamer from a residue.
static Rotamer[]	Rotamer.defaultRotamerFactory(Residue residue, TitrationUtils titrationUtils)	Factory method to construct an original-coordinates Rotamer from a residue.
static List<Atom>	BondedUtils.findAtomsOfElement(Residue residue, int element)	Finds all Atoms belonging to a Residue of a given atomic number.
static Atom	BondedUtils.findNitrogenAtom(Residue residue)	Finds the backbone nitrogen of a residue.
static Optional<Atom>	BondedUtils.findNucleotideO4s(Residue residue)	Find the O4' of a nucleic acid Residue.
static Atom	BondedUtils.getAlphaCarbon(Residue residue, Atom N)	Finds the alpha carbon of a residue, and handles any C-terminal ACE caps while at it.
double	RelativeSolvation.getSolvationEnergy(Residue residue, boolean checkZeroes)	Gets the solvation energy (de-solvation penalty) for a given residue, allowing for sequence optimization to include an estimate of energy relative to the unfolded state.
RotamerLibrary.RotamerGuess	RotamerLibrary.guessRotamer(Residue residue)	Guess at what rotamer a residue is currently in.
static int	RotamerLibrary.measureAARotamer(Residue residue, double[] chi, boolean print)	Measures the torsions of an amino acid Residue's current configuration.
static double	RotamerLibrary.measureDelta(Residue residue)	Measures the delta torsion (sugar pucker) of a nucleic acid Residue.
static double[]	RotamerLibrary.measureRotamer(Residue residue, boolean print)	Measures the torsional angles of a residue's side chain.
static int	RotamerLibrary.measureRotamer(Residue residue, double[] chi, boolean print)	Measures the torsion angles of a Residue.
static void	NamingUtils.nameAcetylCap(Residue residue, Atom aceC)	Names the atoms in an N-terminal acetyl ACE capping group.
static void	AminoAcidUtils.removeH1_H2_H3(AminoAcidUtils.AminoAcid3 aminoAcid, Residue residue)	Only the first nitrogen should have H1, H2 and H3 atoms, unless it's an NME cap.
static void	AminoAcidUtils.removeOXT_OT2(Residue residue)	Only the last residue in a chain should have an OXT/OT2 atom.
static boolean	NamingUtils.renameAminoAcidToPDBStandard(Residue residue)	Renames the Atoms in an amino acid to PDB standard.
static void	NamingUtils.renameArginineHydrogen(Residue residue, List<Atom> resAtoms)	renameArginineHydrogen.
static void	NamingUtils.renameAsparagineHydrogen(Residue residue, List<Atom> resAtoms)	renameAsparagineHydrogen.
static void	NamingUtils.renameBetaHydrogen(Residue residue, List<Atom> resAtoms, int indexes)	renameBetaHydrogen.
static void	NamingUtils.renameCommonAminoAcids(Residue residue, AminoAcidUtils.AminoAcid3 aa3, Atom CA, Atom CB)	Renames atoms in common amino acids to PDB standard.
static void	NamingUtils.renameCommonNucleicAcid(Residue residue, NucleicAcidUtils.NucleicAcid3 na3)	Renames atoms in common nucleic acids to PDB standard.
static void	NamingUtils.renameDeltaHydrogen(Residue residue, List<Atom> resAtoms, int indexes)	renameDeltaHydrogen.
static void	NamingUtils.renameEpsilonHydrogen(Residue residue, List<Atom> resAtoms, int indexes)	renameEpsilonHydrogen.
static void	NamingUtils.renameGammaHydrogen(Residue residue, List<Atom> resAtoms, int indexes)	renameGammaHydrogen.
static void	NamingUtils.renameGlutamineHydrogen(Residue residue, List<Atom> resAtoms)	renameGlutamineHydrogen.
static void	NamingUtils.renameGlycineAlphaHydrogen(Residue residue, List<Atom> resAtoms)	renameGlycineAlphaHydrogen.
static void	NamingUtils.renameIsoleucineHydrogen(Residue residue, List<Atom> resAtoms)	renameIsoleucineHydrogen.
static void	NamingUtils.renameNTerminusHydrogen(Residue residue)	renameNTerminusHydrogen.
static void	NamingUtils.renameNucleicAcidToPDBStandard(Residue residue)	Renames the Atoms in a nucleic acid to PDB standard.
static void	NamingUtils.renameZetaHydrogen(Residue residue, List<Atom> resAtoms, int indexes)	renameZetaHydrogen.
boolean	MultiResidue.setActiveResidue(Residue residue)	Setter for the field activeResidue.
static ResidueState[]	ResidueState.storeAllCoordinates(Residue[] residues)	storeAllCoordinates.
void	Rotamer.updateParameters(Residue residue)	Update force field parameters for force field dependent rotamers.

Method parameters in ffx.potential.bonded with type arguments of type Residue

Modifier and Type	Method	Description
static void	AminoAcidUtils.assignAminoAcidAtomTypes(List<Residue> residues, ForceField forceField, List<Bond> bondList)	Assign atom types to an amino acid polymer.
static void	NucleicAcidUtils.assignNucleicAcidAtomTypes(List<Residue> residues, ForceField forceField, List<Bond> bondList)	Assign atom types for a nucleic acid polymer.
static List<List<Residue>>	PolymerUtils.findChainBreaks(List<Residue> residues, double cutoff)
static void	RotamerLibrary.measureRotamers(List<Residue> residueList, boolean print)	Measures the torsions in a list of Residues.
static void	ResidueState.revertAllCoordinates(List<Residue> residueList, ResidueState[] states)	revertAllCoordinates.
static ResidueState[]	ResidueState.storeAllCoordinates(List<Residue> residueList)	storeAllCoordinates.

Constructors in ffx.potential.bonded with parameters of type Residue

Modifier	Constructor	Description
	MissingAtomTypeException(Residue residue, Atom atom)
	MultiResidue(Residue residue, ForceField forceField)	Constructor for MultiResidue.
	ResidueState(Residue residue)	Constructor for ResidueState.
	ResidueState(Residue parent, Residue residue)	Constructor for ResidueState.

Uses of Residue in ffx.potential.extended

Methods in ffx.potential.extended that return types with arguments of type Residue

Modifier and Type	Method	Description
List<Residue>	ExtendedSystem.getExtendedResidueList()	Return the List of Extended Residues which = TitratingResidueList + TautomerizingResidueList
List<Residue>	ExtendedSystem.getTautomerizingResidueList()	Return the List of Tautomerizing Residues
List<Residue>	ExtendedSystem.getTitratingResidueList()	Return the List of Titrating Residues

Methods in ffx.potential.extended with parameters of type Residue

Modifier and Type	Method	Description
double	ExtendedSystem.getTautomerLambda(Residue residue)	Gets the tautomer lambda for the input residue if the residue is tautomerizing
double	ExtendedSystem.getTitrationLambda(Residue residue)	Gets the titration lambda for the input residue if the residue is titrating
boolean	ExtendedSystem.isTautomer(Residue residue)	Returns the tautomerizibility of a residue
boolean	ExtendedSystem.isTitratable(Residue residue)	Returns the titratibility of the passed residue
void	ExtendedSystem.setTautomerLambda(Residue residue, double lambda)	Set the tautomer lambda of a residue and update corresponding theta
void	ExtendedSystem.setTautomerLambda(Residue residue, double lambda, boolean changeThetas)	Set the tautomer lambda of a residue and update corresponding theta if desired
void	ExtendedSystem.setTitrationLambda(Residue residue, double lambda)	Set the titration lambda of a residue and update corresponding theta
void	ExtendedSystem.setTitrationLambda(Residue residue, double lambda, boolean changeThetas)	Set the titration lambda of a residue and update corresponding theta if desired

Uses of Residue in ffx.potential.nonbonded.implicit

Methods in ffx.potential.nonbonded.implicit with parameters of type Residue

Modifier and Type	Method	Description
double	SurfaceAreaRegion.getResidueSurfaceArea(Residue residue)

Uses of Residue in ffx.potential.parameters

Methods in ffx.potential.parameters with parameters of type Residue

Modifier and Type	Method	Description
boolean	TitrationUtils.testResidueTypes(Residue residue)
void	TitrationUtils.updateResidueParameters(Residue residue, Rotamer rotamer)	Update force field parameters for the side-chain atoms of the given residue based on the rotamer amino acid type.

Uses of Residue in ffx.potential.parsers

Method parameters in ffx.potential.parsers with type arguments of type Residue

Modifier and Type	Method	Description
String	ESVFilter.getLambdaHistogram(List<Residue> titratingResidueList, int[][][] esvHistogram, double pH)
boolean	ESVFilter.writeESV(File dynFile, double[] x, double[] v, double[] a, List<Residue> titrResList, int[][][] esvHist, double pH)	Write the extended system variables to a file.

Uses of Residue in ffx.potential.utils

Methods in ffx.potential.utils with parameters of type Residue

Modifier and Type	Method	Description
double	GetProteinFeatures.getConfidenceScore(Residue currentRes)	Get the alphafold confidence score or b-factor from an X-ray model.
void	GetProteinFeatures.getOmega(Residue currentRes)	Get the omega angle of a residue
void	GetProteinFeatures.getPhi(Residue currentRes)	Get the phi angle of a residue
String	GetProteinFeatures.getPPI(Residue residue)
void	GetProteinFeatures.getPsi(Residue currentRes)	Get the psi angle of a residue
String[]	GetProteinFeatures.saveFeatures(Residue residue, double surfaceArea, boolean includeAngles, boolean includeStructure, boolean includePPI)	Make a string array of surface area and additional selected features (phi,psi,omega,and structure annotations)

Uses of Residue in ffx.realspace

Methods in ffx.realspace that return types with arguments of type Residue

Modifier and Type	Method	Description
List<List<Residue>>	RealSpaceData.getAltResidues()	getAltResidues

Uses of Residue in ffx.xray

Methods in ffx.xray that return types with arguments of type Residue

Modifier and Type	Method	Description
List<List<Residue>>	DataContainer.getAltResidues()	getAltResidues
List<List<Residue>>	DiffractionData.getAltResidues()	getAltResidues
List<List<Residue>>	RefinementModel.getAltResidues()	Getter for the field altResidues.