# Index

A C D E F G H I J L M P R S T U W X
All Classes and Interfaces|All Packages|Constant Field Values

## A

addAtom(Atom) - Method in class jgromacs.data.Residue
  Adds a new atom to the residue
addAtomToResidue(int, Atom) - Method in class jgromacs.data.Structure
  Adds the given atom to residue #i
addAtomToResidueOfIndex(int, Atom) - Method in class jgromacs.data.Structure
  Adds the given atom to the residue of given index
addFrame(int) - Method in class jgromacs.data.FrameIndexSet
  Adds a new frame to the frame index set
addFrame(PointList) - Method in class jgromacs.data.Trajectory
  Adds a new frame to the trajectory
addGap() - Method in class jgromacs.data.Sequence
  Adds a new gap to the sequence
addIndex(int) - Method in class jgromacs.data.IndexSet
  Adds a new index to the index set
addIndexSet(IndexSet) - Method in class jgromacs.data.IndexSetList
  Adds a new index set to the list
addIndexSet(IndexSet, String) - Method in class jgromacs.data.IndexSetList
  Adds a new index set of given name to the list
addPoint(Point3D) - Method in class jgromacs.data.PointList
  Adds a new point to the point list
addPosition(int, ResidueType) - Method in class jgromacs.data.Sequence
  Adds a new position of given index and residue type to the sequence
addPosition(int, ResidueType, String) - Method in class jgromacs.data.Sequence
  Adds a new position of given index, residue type and annotation to the sequence
addPosition(SequencePosition) - Method in class jgromacs.data.Sequence
  Adds a new position to the sequence
addPosition(ResidueType, String) - Method in class jgromacs.data.Sequence
  Adds a new position of given residue type and annotation to the sequence
addPositionsFromString(String) - Method in class jgromacs.data.Sequence
  Adds a series of new positions to the sequence taken from a String object
addResidue(Residue) - Method in class jgromacs.data.Structure
  Adds a new residue to the structure
addSequence(Sequence) - Method in class jgromacs.data.Alignment
  Adds a new sequence to the alignment
Alignment - Class in jgromacs.data
  Objects of this class represent a sequence alignment
Alignment() - Constructor for class jgromacs.data.Alignment
  Constructs a new Alignment object
ALPHACARBON - Static variable in class jgromacs.analysis.Distances
Angle - Class in jgromacs.data
  Objects of this class represent an angle
Angle() - Constructor for class jgromacs.data.Angle
  Constructs a new Angle object
Angle(double) - Constructor for class jgromacs.data.Angle
  Constructs a new Angle object of given value in degrees
Angles - Class in jgromacs.analysis
  Collection of methods for analysing angles
Angles() - Constructor for class jgromacs.analysis.Angles
Application - Class in jgromacs.ui
  Parent class of JGromacs applications.
Application() - Constructor for class jgromacs.ui.Application
  Constructor
askIndexSetFromUser(IndexSetList) - Method in class jgromacs.ui.Application
  Asks the user which index set is to be selected from the index set list
askIndexSetFromUser(IndexSetList, String) - Method in class jgromacs.ui.Application
  Asks the user which index set is to be selected from the index set list
Atom - Class in jgromacs.data
  Objects of this class represent a single atom
Atom() - Constructor for class jgromacs.data.Atom
  Constructs a new Atom object
AtomType - Class in jgromacs.db
  Objects of this class represent an atom type
AtomType() - Constructor for class jgromacs.db.AtomType
  Constructs a new AtomType object
AtomType(int) - Constructor for class jgromacs.db.AtomType
  Constructs a new AtomType object of a given type
AtomType(String) - Constructor for class jgromacs.db.AtomType
  Constructs a new AtomType object of given code

## C

canRunWithoutArgument(boolean) - Method in class jgromacs.ui.Application
  Sets if the application can run without argument
centerPoints() - Method in class jgromacs.data.PointList
  Centers the points (around the origin)
clone() - Method in class jgromacs.data.Alignment
  Returns an identical Alignment object
clone() - Method in class jgromacs.data.Angle
  Returns an identical Angle object
clone() - Method in class jgromacs.data.Atom
  Returns an identical Atom object
clone() - Method in class jgromacs.data.FrameIndexSet
  Returns an identical FrameIndexSet object
clone() - Method in class jgromacs.data.IndexSet
  Returns an identical IndexSet object
clone() - Method in class jgromacs.data.IndexSetList
  Returns an identical IndexSetList object
clone() - Method in class jgromacs.data.Point3D
  Returns an identical Point3D object
clone() - Method in class jgromacs.data.PointList
  Returns an identical PointList object
clone() - Method in class jgromacs.data.Residue
  Returns an identical Residue object
clone() - Method in class jgromacs.data.Sequence
  Returns an identical Sequence object
clone() - Method in class jgromacs.data.SequencePosition
  Returns an identical SequencePosition object
clone() - Method in class jgromacs.data.Structure
  Returns an identical Structure object
clone() - Method in class jgromacs.data.Trajectory
  Returns an identical Trajectory object
clone() - Method in class jgromacs.db.AtomType
  Returns an identical AtomType object
clone() - Method in class jgromacs.db.ResidueType
  Returns an identical ResidueType object
CLOSEST - Static variable in class jgromacs.analysis.Distances
CLOSESTHEAVY - Static variable in class jgromacs.analysis.Distances
concat(Sequence) - Method in class jgromacs.data.Sequence
  Returns the given sequence concatenated to this sequence
containsSubSequence(Sequence) - Method in class jgromacs.data.Sequence
  Returns true if the given subsequence is contained in this sequence
convertFrameIndexToTime(int) - Method in class jgromacs.data.Trajectory
  Converts frame index to simulation time
convertIndicesToArrayListIndices(IndexSet) - Method in class jgromacs.data.Structure
  Converts atomic indices into list indices
convertTimeToFrameIndex(double) - Method in class jgromacs.data.Trajectory
  Converts simulation time to frame index
crossProduct(Point3D) - Method in class jgromacs.data.Point3D
  Returns the cross product of this vector and another vector

## D

distance(Atom) - Method in class jgromacs.data.Atom
  Returns the Euclidean distance between this atom and another atom
distance(Point3D) - Method in class jgromacs.data.Point3D
  Returns the Euclidean distance between this point and another point
distanceAlphaCarbons(Residue) - Method in class jgromacs.data.Residue
  Returns the Euclidean distance of alpha-carbon atoms of this amino acid an another
distanceClosest(Residue) - Method in class jgromacs.data.Residue
  Returns the Euclidean distance of the closest atoms of this amino acid and another
distanceClosestHeavy(Residue) - Method in class jgromacs.data.Residue
  Returns the Euclidean distance of the closest heavy atoms of this amino acid and another
Distances - Class in jgromacs.analysis
  Collection of methods for analysing distances
Distances() - Constructor for class jgromacs.analysis.Distances
Dynamics - Class in jgromacs.analysis
  Collection of methods for analysing molecular motions
Dynamics() - Constructor for class jgromacs.analysis.Dynamics

## E

equals(Object) - Method in class jgromacs.data.Alignment
  Returns true if the two alignments are identical
equals(Object) - Method in class jgromacs.data.Angle
  Returns true if the two angles are identical
equals(Object) - Method in class jgromacs.data.Atom
  Returns true if the two atoms are identical
equals(Object) - Method in class jgromacs.data.FrameIndexSet
  Returns true if this frame index set is identical to another
equals(Object) - Method in class jgromacs.data.IndexSet
  Returns true if this index sets is identical to another
equals(Object) - Method in class jgromacs.data.IndexSetList
  Returns true if the two index set lists are identical
equals(Object) - Method in class jgromacs.data.Point3D
  Returns true if the two 3D points are identical
equals(Object) - Method in class jgromacs.data.PointList
  Returns true if the two point lists are identical
equals(Object) - Method in class jgromacs.data.Residue
  Returns true if the two residues are identical
equals(Object) - Method in class jgromacs.data.Sequence
  Returns true if the two sequences are identical
equals(Object) - Method in class jgromacs.data.SequencePosition
  Returns true if the two sequence positions are identical
equals(Object) - Method in class jgromacs.data.Structure
  Returns true if the two structures are identical
equals(Object) - Method in class jgromacs.data.Trajectory
  Returns true if the two trajectories are identical
equals(Object) - Method in class jgromacs.db.AtomType
  Returns true if the two atom types are identical
equals(Object) - Method in class jgromacs.db.ResidueType
  Returns true if the two residue types are identical

## F

findClosestAtom(Structure, IndexSet, IndexSet) - Static method in class jgromacs.analysis.Distances
  Returns the atom from a given atom set that is closest to a reference set of atoms
findFrameWhereClosest(Trajectory, int, int) - Static method in class jgromacs.analysis.Distances
  Returns the frame in which two atoms are closest to each other in a simulation
findFrameWhereMostDistant(Trajectory, int, int) - Static method in class jgromacs.analysis.Distances
  Returns the frame in which two atoms are most distant from each other in a simulation
findSimilarFramesDRMSD(Trajectory, Matrix, double) - Static method in class jgromacs.analysis.Similarity
  Returns the list of frames in a trajectory that are more similar to a reference distance matrix (based on the dRMSD similarity measure) than a cutoff value
findSimilarFramesDRMSD(Trajectory, PointList, double) - Static method in class jgromacs.analysis.Similarity
  Returns the list of frames in a trajectory that are more similar to a reference frame (based on the dRMSD similarity measure) than a cutoff value
findSimilarFramesRMSD(Trajectory, PointList, double) - Static method in class jgromacs.analysis.Similarity
  Returns the set of frames in a trajectory that are more similar to a reference frame (based on the RMSD similarity measure) than a cutoff value
FrameIndexSet - Class in jgromacs.data
  Objects of this class represent a single frame index set
FrameIndexSet() - Constructor for class jgromacs.data.FrameIndexSet
  Constructs a new FrameIndexSet object
FrameIndexSet(String) - Constructor for class jgromacs.data.FrameIndexSet
  Constructs a new FrameIndexSet object of a given name
FrameIndexSet(ArrayList<Integer>) - Constructor for class jgromacs.data.FrameIndexSet
  Constructs a new FrameIndexSet object and loads data from an ArrayList
FrameIndexSet(ArrayList<Integer>, String) - Constructor for class jgromacs.data.FrameIndexSet
  Constructs a new FrameIndexSet object of a given name and loads data from an ArrayList
FrameIndexSet(TreeSet<Integer>) - Constructor for class jgromacs.data.FrameIndexSet
  Constructs a new FrameIndexSet object and loads data from a TreeSet
FrameIndexSet(TreeSet<Integer>, String) - Constructor for class jgromacs.data.FrameIndexSet
  Constructs a new FrameIndexSet object of a given name and loads data from a TreeSet
FrameIndexSet(FrameIndexSet) - Constructor for class jgromacs.data.FrameIndexSet
  Constructs a new FrameIndexSet object identical to a given FrameIndexSet
fuseIntoOneIndexSet() - Method in class jgromacs.data.IndexSetList
  Returns the union of all index sets as a single index set

## G

get1LetterCode() - Method in class jgromacs.data.Residue
  Returns the 1 letter code of residue type
get1LetterCode() - Method in class jgromacs.db.ResidueType
  Returns 1 letter code of residue type
get3LetterCode() - Method in class jgromacs.data.Residue
  Returns the 3 letter code of residue type
get3LetterCode() - Method in class jgromacs.db.ResidueType
  Returns 3 letter code of residue type
getAllAtomCoordinates() - Method in class jgromacs.data.Residue
  Returns the coordinates of all atoms
getAllAtomCoordinates() - Method in class jgromacs.data.Structure
  Returns the coordinates of all atoms
getAlphaCarbon() - Method in class jgromacs.data.Residue
  Returns the alpha carbon atom if any (otherwise returns null)
getAlphaCarbonCoordinates() - Method in class jgromacs.data.Residue
  Returns the position of alpha-carbon atom
getAlphaCarbonIndexSet() - Method in class jgromacs.data.Structure
  Returns the index set of alpha carbon atoms
getAngleBetweenPlanes(Point3D, Point3D, Point3D, Point3D) - Static method in class jgromacs.analysis.Angles
  Calculates the angle between two planes defined by points A, B, C and points B, C, D
getAngleBetweenVectors(Point3D, Point3D) - Static method in class jgromacs.analysis.Angles
  Calculates the angle between two vectors
getAnnotation() - Method in class jgromacs.data.SequencePosition
  Returns the annotation of sequence position
getAnnotationOfPosition(int) - Method in class jgromacs.data.Sequence
  Returns the annotation of sequence position #i
getAnnotationOfPositionOfIndex(int) - Method in class jgromacs.data.Sequence
  Returns the annotation of sequence position of given index
getArgumentValue(String) - Method in class jgromacs.ui.Application
  Returns the value defined by the given attribute flag
getAsAnArrayList() - Method in class jgromacs.data.IndexSetList
  Returns index set list as an ArrayList object
getAsArrayList() - Method in class jgromacs.data.FrameIndexSet
  Returns frame index set as an ArrayList
getAsArrayList() - Method in class jgromacs.data.IndexSet
  Returns index set as an ArrayList
getAsArrayList() - Method in class jgromacs.data.Sequence
  Returns sequence as an ArrayList object
getAsMatrix() - Method in class jgromacs.data.PointList
  Returns point coordinates in a 3xN matrix
getAsTreeSet() - Method in class jgromacs.data.FrameIndexSet
  Returns frame index set as a TreeSet
getAsTreeSet() - Method in class jgromacs.data.IndexSet
  Returns index set as a TreeSet
getAtom(int) - Method in class jgromacs.data.Residue
  Returns atom #i of the residue
getAtom(int) - Method in class jgromacs.data.Structure
  Returns atom #i of the structure
getAtomByIndex(int) - Method in class jgromacs.data.Residue
  Returns the atom of given index
getAtomByIndex(int) - Method in class jgromacs.data.Structure
  Returns the atom of given index
getAtomByName(String) - Method in class jgromacs.data.Residue
  Returns the atom of name
getAtomicCorrelationMatrix(Trajectory) - Static method in class jgromacs.analysis.Dynamics
  Calculates the NxN atomic correlation matrix from a trajectory using its first frame as the reference frame for superposition
getAtomicCorrelationMatrix(Trajectory, PointList) - Static method in class jgromacs.analysis.Dynamics
  Calculates the NxN atomic correlation matrix from a trajectory and a reference frame for superposition
getAtomicCovarianceMatrix(Trajectory) - Static method in class jgromacs.analysis.Dynamics
  Calculates the NxN atomic covariance matrix from a trajectory using its first frame as the reference frame for superposition
getAtomicCovarianceMatrix(Trajectory, PointList) - Static method in class jgromacs.analysis.Dynamics
  Calculates the NxN atomic covariance matrix from a trajectory and a reference frame for superposition
getAtomicDistanceMatrix(Structure) - Static method in class jgromacs.analysis.Distances
  Calculates the distance matrix of all atoms in a structure
getAtomicDistanceMatrix(Structure, IndexSet) - Static method in class jgromacs.analysis.Distances
  Calculates the distance matrix of atoms of given indices in a structure
getAtomicDistanceMatrix(Structure, IndexSet, IndexSet) - Static method in class jgromacs.analysis.Distances
  Calculates the distance matrix between two sets of atoms
getAtomIndices() - Method in class jgromacs.data.Residue
  Returns the index set of all atoms
getAtomIndicesInRadius(Structure, Atom, double) - Static method in class jgromacs.analysis.Distances
  Returns the index set of atoms in a structure that are closer to a reference atom than a given radius
getAtomIndicesInRadius(Structure, IndexSet, double) - Static method in class jgromacs.analysis.Distances
  Returns the index set of atoms in a structure that are closer to a reference set of atoms than a given radius
getAtomIndicesInRadius(Structure, IndexSet, IndexSet, double) - Static method in class jgromacs.analysis.Distances
  Returns the index set of atoms from a set of atoms that are closer to a reference set than a given radius
getAtomIndicesInRadius(Structure, Point3D, double) - Static method in class jgromacs.analysis.Distances
  Returns the index set of atoms in a structure that are closer to a reference point than a given radius
getAtomInResidueOfIndex(int, int) - Method in class jgromacs.data.Structure
  Returns atom #i of the residue of given index
getAtomInResidueOfIndex(int, String, int) - Method in class jgromacs.data.Structure
  Returns atom #i of the residue of given index and chain ID
getAtomsAsArrayList() - Method in class jgromacs.data.Residue
  Returns the list of atoms as an ArrayList object
getAtomType() - Method in class jgromacs.data.Atom
  Returns the type of atom
getBackBoneAtomIndices() - Method in class jgromacs.data.Residue
  Returns the index set of backbone atoms
getBackboneIndexSet() - Method in class jgromacs.data.Structure
  Returns the index set of backbone atoms
getBetaCarbon() - Method in class jgromacs.data.Residue
  Returns the beta carbon atom if any (otherwise returns null)
getBvalue() - Method in class jgromacs.data.Atom
  Returns the B-value of atom
getCarbonylOxygen() - Method in class jgromacs.data.Residue
  Returns the carbonyl oxygen atom of amino acid
getCentroid() - Method in class jgromacs.data.PointList
  Returns the centroid of points
getChainID() - Method in class jgromacs.data.Residue
  Returns the chain ID of residue
getChainIDs() - Method in class jgromacs.data.Structure
  Returns the list of chain IDs in the structure
getChains() - Method in class jgromacs.data.Structure
  Returns all chains in an array of Structure objects
getCode() - Method in class jgromacs.db.AtomType
  Returns the code of atom type
getCollapsedAlignment() - Method in class jgromacs.data.Alignment
  Returns the collapsed alignment in which only the match columns are included (i.e.
getCombinedCode() - Method in class jgromacs.data.Residue
  Returns residue index and the 3 letter code of residue type
getConsensusSequence() - Method in class jgromacs.data.Alignment
  Returns the (majority) consensus sequence of the alignment
getContactMatrix() - Method in class jgromacs.analysis.GNM
  Returns the contact matrix
getContactMatrix(PointList, double) - Static method in class jgromacs.analysis.Distances
  Calculates the contact matrix from a point list
getContactMatrix(Structure, int, double) - Static method in class jgromacs.analysis.Distances
  Calculates the contact matrix of residues in a structure by the given method
getContactOfMeanMatrix(Trajectory, int, double) - Static method in class jgromacs.analysis.Distances
  Calculates the contact matrix based on the mean residue distance matrix in a trajectory
getContactProbabilityMap(Trajectory, double) - Static method in class jgromacs.analysis.Dynamics
  Calculates the (residue) contact probability map for a trajectory as defined by Wei et al, 2009 (Residual Structure in Islet Amyloid Polypeptide Mediates Its Interactions with Soluble Insulin, Biochemistry)
getCoordinateCorrelationMatrix(Trajectory) - Static method in class jgromacs.analysis.Dynamics
  Calculates the 3Nx3N coordinate correlation matrix from a trajectory using its first frame as the reference frame for superposition
getCoordinateCorrelationMatrix(Trajectory, PointList) - Static method in class jgromacs.analysis.Dynamics
  Calculates the 3Nx3N coordinate correlation matrix from a trajectory and a reference frame for superposition
getCoordinateCovarianceMatrix(Trajectory) - Static method in class jgromacs.analysis.Dynamics
  Calculates the 3Nx3N coordinate covariance matrix from a trajectory using its first frame as the reference frame for superposition
getCoordinateCovarianceMatrix(Trajectory, PointList) - Static method in class jgromacs.analysis.Dynamics
  Calculates the 3Nx3N coordinate covariance matrix from a trajectory and a reference frame for superposition
getCoordinates() - Method in class jgromacs.data.Atom
  Returns the coordinates of atom
getCovarianceMatrixOverlap(Matrix, Matrix) - Static method in class jgromacs.analysis.Dynamics
  Calculates the covariance overlap of two covariance matrices
getCovarianceMatrixOverlap(Matrix, Matrix, int) - Static method in class jgromacs.analysis.Dynamics
  Calculates the covariance overlap of two covariance matrices
getCovarianceMatrixOverlap(Trajectory, Trajectory) - Static method in class jgromacs.analysis.Dynamics
  Calculates the covariance overlap from two trajectories
getCovarianceMatrixOverlap(Trajectory, Trajectory, int) - Static method in class jgromacs.analysis.Dynamics
  Calculates the covariance overlap from two trajectories
getCTerminalCarbon() - Method in class jgromacs.data.Residue
  Returns the C-terminal carbon atom of amino acid
getCumulativeVariances(Matrix) - Static method in class jgromacs.analysis.Dynamics
  Calculates the cumulative variance profile from a covariance matrix
getCumulativeVariances(Trajectory) - Static method in class jgromacs.analysis.Dynamics
  Calculates the cumulative variance profile from a trajectory
getDefaultIndexSetList() - Method in class jgromacs.data.Structure
  Returns the list of default index sets
getDeltaCarbon() - Method in class jgromacs.data.Residue
  Returns the delta carbon atom if any (otherwise returns null)
getDifferenceDistanceMatrix(PointList, PointList) - Static method in class jgromacs.analysis.Similarity
  Calculates the difference distance matrix between two point lists
getDifferenceDistanceMatrix(Structure, IndexSet, Structure, IndexSet) - Static method in class jgromacs.analysis.Similarity
  Calculates the atomic difference distance matrix between two sets of atoms defined by two index sets in two structures
getDifferenceDistanceMatrix(Structure, Structure) - Static method in class jgromacs.analysis.Similarity
  Calculates the atomic difference distance matrix between two structures
getDihedralChi1(Structure, int) - Static method in class jgromacs.analysis.Angles
  Calculates side chain dihedral angle Chi1 of residue #i of a structure The residue can be ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER,THR,TRP,TYR or VAL
getDihedralChi1TimeSeries(Trajectory, int) - Static method in class jgromacs.analysis.Angles
  Calculates the time series of dihedral angle Chi1 of residue #i over a trajectory The residue can be ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER,THR,TRP,TYR or VAL
getDihedralChi2(Structure, int) - Static method in class jgromacs.analysis.Angles
  Calculates side chain dihedral angle Chi2 of residue #i of a structure The residue can only be ARG,ASN,ASP,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,TRP or TYR
getDihedralChi2TimeSeries(Trajectory, int) - Static method in class jgromacs.analysis.Angles
  Calculates the time series of dihedral angle Chi2 of residue #i over a trajectory The residue can only be ARG,ASN,ASP,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,TRP or TYR
getDihedralChi3(Structure, int) - Static method in class jgromacs.analysis.Angles
  Calculates side chain dihedral angle Chi3 of residue #i of a structure The residue can only be ARG,GLN,GLU,LYS or MET
getDihedralChi3TimeSeries(Trajectory, int) - Static method in class jgromacs.analysis.Angles
  Calculates the time series of dihedral angle Chi3 of residue #i over a trajectory The residue can only be ARG,GLN,GLU,LYS or MET
getDihedralChi4(Structure, int) - Static method in class jgromacs.analysis.Angles
  Calculates side chain dihedral angle Chi4 of residue #i of a structure The residue can only be ARG or LYS
getDihedralChi4TimeSeries(Trajectory, int) - Static method in class jgromacs.analysis.Angles
  Calculates the time series of dihedral angle Chi4 of residue #i over a trajectory The residue can only be ARG or LYS
getDihedralChi5(Structure, int) - Static method in class jgromacs.analysis.Angles
  Calculates side chain dihedral angle Chi5 of residue #i of a structure The residue can only be ARG
getDihedralChi5TimeSeries(Trajectory, int) - Static method in class jgromacs.analysis.Angles
  Calculates the time series of dihedral angle Chi5 of residue #i over a trajectory The residue can only be ARG
getDihedralOmega(Structure, int) - Static method in class jgromacs.analysis.Angles
  Calculates dihedral angle Omega of residue #i of a structure
getDihedralOmegaTimeSeries(Trajectory, int) - Static method in class jgromacs.analysis.Angles
  Calculates the time series of dihedral angle Omega of residue #i over a trajectory
getDihedralPhi(Structure, int) - Static method in class jgromacs.analysis.Angles
  Calculates dihedral angle Phi of residue #i of a structure
getDihedralPhiTimeSeries(Trajectory, int) - Static method in class jgromacs.analysis.Angles
  Calculates the time series of dihedral angle Phi of residue #i over a trajectory
getDihedralPsi(Structure, int) - Static method in class jgromacs.analysis.Angles
  Calculates dihedral angle Psi of residue #i of a structure
getDihedralPsiTimeSeries(Trajectory, int) - Static method in class jgromacs.analysis.Angles
  Calculates the time series of dihedral angle Psi of residue #i over a trajectory
getDistanceMatrix(PointList) - Static method in class jgromacs.analysis.Distances
  Calculates the distance matrix from a point list
getDistanceOfAtomToAtomSet(Structure, int, IndexSet) - Static method in class jgromacs.analysis.Distances
  Calculates the distance of an atom to a reference set of atoms (i.e.
getDistanceOfTwoAtomSets(Structure, IndexSet, IndexSet) - Static method in class jgromacs.analysis.Distances
  Calculates the distance between two sets of atoms (i.e.
getDistanceRange(Trajectory, int, int) - Static method in class jgromacs.analysis.Distances
  Returns the range (max-min) of the distance of two atoms in a trajectory
getDistanceTimeSeries(Trajectory, int, int) - Static method in class jgromacs.analysis.Distances
  Returns the time series of the distance of two atoms in a trajectory
getDistanceTimeSeries(Trajectory, int, IndexSet) - Static method in class jgromacs.analysis.Distances
  Returns the time series of the distance of a single atom and a set of atoms in a trajectory
getDistanceTimeSeries(Trajectory, IndexSet, IndexSet) - Static method in class jgromacs.analysis.Distances
  Returns the time series of the distance of two sets of atoms in a trajectory
getDRMSD(Matrix, Matrix) - Static method in class jgromacs.analysis.Similarity
  Calculates dRMSD similarity between two distance matrices
getDRMSD(PointList, PointList) - Static method in class jgromacs.analysis.Similarity
  Calculates dRMSD similarity between two point lists
getDRMSD(Structure, IndexSet, Structure, IndexSet) - Static method in class jgromacs.analysis.Similarity
  Calculates dRMSD similarity between two groups of atoms
getDRMSD(Structure, Structure) - Static method in class jgromacs.analysis.Similarity
  Calculates dRMSD similarity between two structures
getDRMSDiProfile(Matrix, Matrix) - Static method in class jgromacs.analysis.Similarity
  Calculates the dRMSDi profile between two distance matrices
getDRMSDiProfile(PointList, PointList) - Static method in class jgromacs.analysis.Similarity
  Calculates the dRMSDi profile between two point lists
getDRMSDiProfile(Structure, IndexSet, Structure, IndexSet) - Static method in class jgromacs.analysis.Similarity
  Calculates the dRMSDi profile between two groups of atoms
getDRMSDiProfile(Structure, Structure) - Static method in class jgromacs.analysis.Similarity
  Calculates the dRMSDi profile between two structures
getDynamicalNetwork(Trajectory, double, double) - Static method in class jgromacs.analysis.Dynamics
  Calculates the dynamical network of a protein according to the definition of Sethi et al.
getEigenvectorMatrix() - Method in class jgromacs.analysis.GNM
  Returns the orthogonal matrix of eigenvectors (U)
getEnsembleAveragedRMSD(Trajectory, Trajectory) - Static method in class jgromacs.analysis.Dynamics
  Calculates the ensemble averaged RMSD between two conformational ensembles sampled in two trajectories as defined by Brüschweiler, 2002 (Efficient RMSD measures for the comparison of two molecular ensembles, Proteins: Structure, Function, and Bioinformatics)
getEpsilonCarbon() - Method in class jgromacs.data.Residue
  Returns the epsilon carbon atom if any (otherwise returns null)
getFirstFrameAsPointList() - Method in class jgromacs.data.Trajectory
  Returns the initial frame of trajectory as a PointList
getFirstFrameAsStructure() - Method in class jgromacs.data.Trajectory
  Returns the initial frame of trajectory as a Structure
getFluctuationMatrix(Trajectory) - Static method in class jgromacs.analysis.Dynamics
  Calculates the F fluctuation matrix (variances of distances) from a trajectory
getFluctuationMatrix(Trajectory, IndexSet) - Static method in class jgromacs.analysis.Dynamics
  Calculates the F fluctuation matrix (variances of distances) for a group of atoms
getFluctuationOfSubsets(Trajectory, IndexSet, IndexSet) - Static method in class jgromacs.analysis.Dynamics
  Calculates the fluctuation between two subsets of atoms defined as the mean of entries of the selected submatrix of matrix F (fluctuation matrix)
getFrameAsPointList(int) - Method in class jgromacs.data.Trajectory
  Returns frame #i of the trajectory as a PointList object
getFrameAsStructure(int) - Method in class jgromacs.data.Trajectory
  Returns frame #i of the trajectory as a Structure object
getFrames() - Method in class jgromacs.data.Trajectory
  Returns frames of the trajectory as an ArrayList object
getFramesWhereAtomIsCloseToPoint(Trajectory, int, Point3D, double) - Static method in class jgromacs.analysis.Distances
  Returns the list of frames in the trajectory where an atoms is closer to a reference point than a given cutoff
getFramesWhereAtomIsDistantFromPoint(Trajectory, int, Point3D, double) - Static method in class jgromacs.analysis.Distances
  Returns the list of frames in the trajectory where an atoms is more distant from a reference point than a given cutoff
getFramesWhereAtomsAreClose(Trajectory, int, int, double) - Static method in class jgromacs.analysis.Distances
  Returns the list of frames in a trajectory where two atoms are closer to each other than the given cutoff
getFramesWhereAtomsAreDistant(Trajectory, int, int, double) - Static method in class jgromacs.analysis.Distances
  Returns the list of frames in a trajectory where two atoms are more distant from each other than the given cutoff
getFrequencyContactMatrix(Trajectory, int, double, double) - Static method in class jgromacs.analysis.Distances
  Calculates the contact matrix of residues where two residues are said to be in contact if they are in contact in at least the given percentage of frames of the trajectory
getFullName() - Method in class jgromacs.db.AtomType
  Returns the full name of atom type
getFullName() - Method in class jgromacs.db.ResidueType
  Returns full name of residue type
getGammaCarbon() - Method in class jgromacs.data.Residue
  Returns the gamma carbon atom if any (otherwise returns null)
getHeavyAtomIndices() - Method in class jgromacs.data.Residue
  Returns the index set of heavy atoms
getHeavyProteinIndexSet() - Method in class jgromacs.data.Structure
  Returns the index set of protein atoms except of hydrogen atoms
getHydrogenAtomIndices() - Method in class jgromacs.data.Residue
  Returns the index set of hydrogen atoms
getInDegrees() - Method in class jgromacs.data.Angle
  Returns the value of angle in degrees
getIndex() - Method in class jgromacs.data.Atom
  Returns the index of atom
getIndex() - Method in class jgromacs.data.Residue
  Returns the index of residue
getIndex() - Method in class jgromacs.data.SequencePosition
  Returns the index of sequence position
getIndexOfPosition(int) - Method in class jgromacs.data.Sequence
  Returns the index of sequence position #i
getIndexSet(int) - Method in class jgromacs.data.IndexSetList
  Returns the index set of given index
getIndexSet(String) - Method in class jgromacs.data.IndexSetList
  Returns the index set of given name
getIndexSetOfChainID(String) - Method in class jgromacs.data.Structure
  Returns the index set of atoms of a given chain ID
getInRadians() - Method in class jgromacs.data.Angle
  Returns the value of angle in radians
getKirchhoffMatrix() - Method in class jgromacs.analysis.GNM
  Returns the Kirchhoff matrix
getLambdaMatrix() - Method in class jgromacs.analysis.GNM
  Returns the diagonal matrix of eigenvalues (Lambda)
getLastFrameAsPointList() - Method in class jgromacs.data.Trajectory
  Returns the last frame of trajectory as a PointList
getLastFrameAsStructure() - Method in class jgromacs.data.Trajectory
  Returns the last frame of trajectory as a Structure
getLogFileName() - Method in class jgromacs.ui.Application
  Returns the name of log file
getMainChainAtomIndices() - Method in class jgromacs.data.Residue
  Returns the index set of main chain atoms
getMainChainIndexSet() - Method in class jgromacs.data.Structure
  Returns the index set of main chain atoms
getMainChainPlusCbAtomIndices() - Method in class jgromacs.data.Residue
  Returns the index set of main chain atoms and beta carbon atom
getMainChainPlusCbIndexSet() - Method in class jgromacs.data.Structure
  Returns the index set of main chain plus beta carbon atoms
getMainChainPlusHAtomIndices() - Method in class jgromacs.data.Residue
  Returns the index set of main chain atoms and hydrogen atoms
getMainChainPlusHIndexSet() - Method in class jgromacs.data.Structure
  Returns the index set of main chain plus hydrogen atoms
getMatchPositionIndexSets() - Method in class jgromacs.data.Alignment
  Returns the list of match position index sets (i.e.
getMatchPositionIndices(int) - Method in class jgromacs.data.Alignment
  Returns the set of position indices in sequence #i that are included in the match columns of alignment
getMatchPositionIndicesAsArrayList(int) - Method in class jgromacs.data.Alignment
  Returns the list of match position indices in sequence #i as an ArrayList object
getMaximalDistance(Trajectory, int, int) - Static method in class jgromacs.analysis.Distances
  Returns the maximal distance of two atoms in a trajectory
getMaxSequenceLength() - Method in class jgromacs.data.Alignment
  Returns the length of the longest sequence in the alignment
getMeanAtomicDistanceMatrix(Trajectory) - Static method in class jgromacs.analysis.Distances
  Calculates the mean distance matrix of all atoms in a trajectory
getMeanAtomicDistanceMatrix(Trajectory, IndexSet) - Static method in class jgromacs.analysis.Distances
  Calculates the mean distance matrix of atoms of given indices in a trajectory
getMeanDistance(Trajectory, int, int) - Static method in class jgromacs.analysis.Distances
  Returns the mean of the distance of two atoms in a trajectory
getMeanFrame() - Method in class jgromacs.data.Trajectory
  Returns the mean frame of trajectory
getMeanResidueDistanceMatrix(Trajectory, int) - Static method in class jgromacs.analysis.Distances
  Calculates the mean distance matrix of residues in a trajectory by the given method
getMedoidDRMSD(Trajectory) - Static method in class jgromacs.analysis.Similarity
  Calculates the medoid frame of a trajectory using the dRMSD measure
getMedoidRMSD(Trajectory) - Static method in class jgromacs.analysis.Similarity
  Calculates the medoid frame of a trajectory using the RMSD measure
getMinimalDistance(Trajectory, int, int) - Static method in class jgromacs.analysis.Distances
  Returns the minimal distance of two atoms in a trajectory
getMinSequenceLength() - Method in class jgromacs.data.Alignment
  Returns the length of the shortest sequence in the alignment
getMostFrequentResidueType(int) - Method in class jgromacs.data.Alignment
  Returns the most frequent residue type in column #i of the alignment
getMSFProfile() - Method in class jgromacs.analysis.GNM
  Calculates the mean square fluctuation (MSF) profile
getName() - Method in class jgromacs.data.Atom
  Returns the name of atom
getName() - Method in class jgromacs.data.FrameIndexSet
  Returns the name of frame index set
getName() - Method in class jgromacs.data.IndexSet
  Returns the name of index set
getName() - Method in class jgromacs.data.Residue
  Returns the name of residue
getName() - Method in class jgromacs.data.Sequence
  Returns the name of sequence
getName() - Method in class jgromacs.data.Structure
  Returns the name of structure
getName() - Method in class jgromacs.data.Trajectory
  Returns the name of trajectory
getNonProteinIndexSet() - Method in class jgromacs.data.Structure
  Returns the index set of non-protein atoms
getNTerminalNitrogen() - Method in class jgromacs.data.Residue
  Returns the N-terminal nitrogen atom of amino acid
getNumberOfAtoms() - Method in class jgromacs.data.Residue
  Returns the number of atoms in the residue
getNumberOfAtoms() - Method in class jgromacs.data.Structure
  Returns the number of atoms in the structure
getNumberOfAtoms() - Method in class jgromacs.data.Trajectory
  Returns the number of atoms in the trajectory
getNumberOfAtomsInIndexSet(int) - Method in class jgromacs.data.IndexSetList
  Returns the number of atoms in the index set of given index
getNumberOfAtomsInIndexSet(String) - Method in class jgromacs.data.IndexSetList
  Returns the number of atoms in the index set of given name
getNumberOfChains() - Method in class jgromacs.data.Structure
  Returns the number of chains in the structure
getNumberOfFrames() - Method in class jgromacs.data.FrameIndexSet
  Returns the number of frames in this frame index set
getNumberOfFrames() - Method in class jgromacs.data.Trajectory
  Returns the number of frames in the trajectory
getNumberOfIndexSets() - Method in class jgromacs.data.IndexSetList
  Returns the number of index sets in the list
getNumberOfIndices() - Method in class jgromacs.data.IndexSet
  Returns the number of indices in this index set
getNumberOfPoints() - Method in class jgromacs.data.PointList
  Returns the number of points in the list
getNumberOfResidues() - Method in class jgromacs.data.Structure
  Returns the number of residues in the structure
getNumberOfResidues() - Method in class jgromacs.data.Trajectory
  Returns the number of residues in the trajectory
getNumberOfSequences() - Method in class jgromacs.data.Alignment
  Returns the number of sequences in the alignment
getOccupancy() - Method in class jgromacs.data.Atom
  Returns the occupancy of atom
getPCA(Matrix) - Static method in class jgromacs.analysis.Dynamics
  Calculates the principal components and the corresponding eigenvalues from a covariance matrix
getPCA(Trajectory) - Static method in class jgromacs.analysis.Dynamics
  Calculates the principal components and the corresponding eigenvalues from a trajectory
getPoint(int) - Method in class jgromacs.data.PointList
  Returns the point of index i
getPointsAsArrayList() - Method in class jgromacs.data.PointList
  Returns points in an ArrayList
getPosition(int) - Method in class jgromacs.data.Sequence
  Returns sequence position #i
getPositionByIndex(int) - Method in class jgromacs.data.Sequence
  Returns sequence position of given index
getProteinIndexSet() - Method in class jgromacs.data.Structure
  Returns the index set of protein atoms
getRamachandranPlot(Structure) - Static method in class jgromacs.analysis.Angles
  Calculates the Ramachandran Plot of a structure
getResidue(int) - Method in class jgromacs.data.Structure
  Returns residue #i of the structure
getResidueByIndex(int) - Method in class jgromacs.data.Structure
  Returns the residue of given index
getResidueByIndex(int, String) - Method in class jgromacs.data.Structure
  Returns the residue of given index and given chain ID
getResidueDistanceMatrix(Structure, int) - Static method in class jgromacs.analysis.Distances
  Calculates the distance matrix of residues in a structure by the given method
getResiduesAsArrayList() - Method in class jgromacs.data.Structure
  Returns residues as an ArrayList object
getResidueType() - Method in class jgromacs.data.Residue
  Returns the type of residue
getResidueType() - Method in class jgromacs.data.SequencePosition
  Returns the residue type of sequence position
getResidueTypeOfPosition(int) - Method in class jgromacs.data.Sequence
  Returns the residue type of sequence position #i
getResidueTypeOfPositionOfIndex(int) - Method in class jgromacs.data.Sequence
  Returns the residue type of sequence position of given index
getReverse() - Method in class jgromacs.data.Sequence
  Returns the reverse sequence
getRMSD(PointList, PointList) - Static method in class jgromacs.analysis.Similarity
  Calculates RMSD similarity between two point lists
getRMSD(Structure, IndexSet, Structure, IndexSet) - Static method in class jgromacs.analysis.Similarity
  Calculates RMSD similarity between two groups of atoms
getRMSD(Structure, Structure) - Static method in class jgromacs.analysis.Similarity
  Calculates RMSD similarity between two structures
getRMSDiProfile(PointList, PointList) - Static method in class jgromacs.analysis.Similarity
  Calculates the RMSDi profile between two point lists
getRMSDiProfile(Structure, IndexSet, Structure, IndexSet) - Static method in class jgromacs.analysis.Similarity
  Calculates the RMSDi profile between two groups of atoms
getRMSDiProfile(Structure, Structure) - Static method in class jgromacs.analysis.Similarity
  Calculates the RMSDi profile between two structures
getRMSDiProfileNoSuperposition(PointList, PointList) - Static method in class jgromacs.analysis.Similarity
  Calculates the RMSDi profile between two point lists without superposition
getRMSDiProfileNoSuperposition(Structure, IndexSet, Structure, IndexSet) - Static method in class jgromacs.analysis.Similarity
  Calculates the RMSDi profile between two groups of atoms without superposition
getRMSDiProfileNoSuperposition(Structure, Structure) - Static method in class jgromacs.analysis.Similarity
  Calculates the RMSDi profile between two structures without superposition
getRMSDnoSuperposition(PointList, PointList) - Static method in class jgromacs.analysis.Similarity
  Calculates RMSD similarity between two point lists without doing superposition
getRMSDnoSuperposition(Structure, IndexSet, Structure, IndexSet) - Static method in class jgromacs.analysis.Similarity
  Calculates RMSD similarity between two groups of atoms without superposition
getRMSDnoSuperposition(Structure, Structure) - Static method in class jgromacs.analysis.Similarity
  Calculates RMSD similarity between two structures without doing superposition
getRMSFaroundTheMeanProfile(Trajectory, PointList) - Static method in class jgromacs.analysis.Dynamics
  Calculates the RMSF profile from a trajectory by superposing all frames to a reference frame R and calculating the RMSDi deviations with regards to the mean structure
getRMSFaroundTheMeanProfile(Trajectory, Structure) - Static method in class jgromacs.analysis.Dynamics
  Calculates the RMSF profile from a trajectory by superposing all frames to a reference frame R and calculating the RMSDi deviations with regards to the mean structure
getRMSFprofile(Trajectory, IndexSet, Structure, IndexSet) - Static method in class jgromacs.analysis.Dynamics
  Calculates the RMSF profile of a group of atoms from a trajectory and a reference frame for superposition
getRMSFprofile(Trajectory, PointList) - Static method in class jgromacs.analysis.Dynamics
  Calculates the RMSF profile from a trajectory and a reference frame for superposition
getRMSFprofile(Trajectory, PointList, PointList) - Static method in class jgromacs.analysis.Dynamics
  Calculates the RMSF profile from a trajectory by superposing all frames to a reference frame R and calculating the RMSDi deviations with regards to a reference frame Q
getRMSFprofile(Trajectory, Structure) - Static method in class jgromacs.analysis.Dynamics
  Calculates the RMSF profile from a trajectory and a reference frame for superposition
getRMSFprofile(Trajectory, Structure, Structure) - Static method in class jgromacs.analysis.Dynamics
  Calculates the RMSF profile from a trajectory by superposing all frames to a reference frame R and calculating the RMSDi deviations with regards to a reference frame Q
getRootMeanSquareInnerProduct(Matrix, Matrix, int, int) - Static method in class jgromacs.analysis.Dynamics
  Calculates the root mean square inner product (RMSIP) from two covariance matrices
getRootMeanSquareInnerProduct(Trajectory, Trajectory, int, int) - Static method in class jgromacs.analysis.Dynamics
  Calculates the root mean square inner product (RMSIP) from two trajectories
getSequence() - Method in class jgromacs.data.Structure
  Returns the amino acid sequence of the structure
getSequence(int) - Method in class jgromacs.data.Alignment
  Returns sequence #i of the alignment
getSequenceLength() - Method in class jgromacs.data.Sequence
  Returns the length of sequence (gaps excluded)
getSequenceLengthWithGaps() - Method in class jgromacs.data.Sequence
  Returns the length of sequence (gaps included)
getSequencesAsArrayList() - Method in class jgromacs.data.Alignment
  Returns sequences of the alignment as an ArrayList object
getSideChainAtomIndices() - Method in class jgromacs.data.Residue
  Returns the index set of side chain atoms
getSideChainIndexSet() - Method in class jgromacs.data.Structure
  Returns the index set of side chain atoms
getSideChainMinusHAtomIndices() - Method in class jgromacs.data.Residue
  Returns the index set of side chain atoms except of hydrogen atoms
getSideChainMinusHIndexSet() - Method in class jgromacs.data.Structure
  Returns the index set of side chain atoms except of hydrogen atoms
getSimilarityMatrixDRMSD(Trajectory) - Static method in class jgromacs.analysis.Similarity
  Calculates the similarity matrix of all frames in a trajectory using the dRMSD measure
getSimilarityMatrixDRMSD(Trajectory, IndexSet) - Static method in class jgromacs.analysis.Similarity
  Calculates the similarity matrix of all frames in a trajectory using the dRMSD measure taking into account only a subset of atoms
getSimilarityMatrixRMSD(Trajectory) - Static method in class jgromacs.analysis.Similarity
  Calculates the similarity matrix of all frames in a trajectory using the RMSD measure
getSimilarityMatrixRMSD(Trajectory, IndexSet) - Static method in class jgromacs.analysis.Similarity
  Calculates the similarity matrix of all frames in a trajectory using the RMSD measure taking into account only a subset of atoms
getSimilarityMatrixWDRMSD(Trajectory, Matrix) - Static method in class jgromacs.analysis.Similarity
  Calculates the similarity matrix of all frames in a trajectory using the wdRMSD (weighted dRMSD) measure
getSimilarityMatrixWDRMSD(Trajectory, IndexSet, Matrix) - Static method in class jgromacs.analysis.Similarity
  Calculates the similarity matrix of all frames in a trajectory using the wdRMSD (weighted dRMSD) measure taking into account only a subset of atoms
getSimilarityTimeSeriesDRMSD(Trajectory, IndexSet, Structure, IndexSet) - Static method in class jgromacs.analysis.Similarity
  Returns the time series of dRMSD in a trajectory with regards to a reference structure taking into account only a subset of atoms
getSimilarityTimeSeriesDRMSD(Trajectory, PointList) - Static method in class jgromacs.analysis.Similarity
  Returns the time series of dRMSD in a trajectory with regards to a reference point list
getSimilarityTimeSeriesDRMSD(Trajectory, Structure) - Static method in class jgromacs.analysis.Similarity
  Returns the time series of dRMSD in a trajectory with regards to a reference structure
getSimilarityTimeSeriesRMSD(Trajectory, IndexSet, Structure, IndexSet) - Static method in class jgromacs.analysis.Similarity
  Returns the time series of RMSD in a trajectory with regards to a reference structure taking into account only a subset of atoms
getSimilarityTimeSeriesRMSD(Trajectory, PointList) - Static method in class jgromacs.analysis.Similarity
  Returns the time series of RMSD in a trajectory with regards to a reference point list
getSimilarityTimeSeriesRMSD(Trajectory, Structure) - Static method in class jgromacs.analysis.Similarity
  Returns the time series of RMSD in a trajectory with regards to a reference structure
getSimilarityTimeSeriesWDRMSD(Trajectory, IndexSet, Structure, IndexSet, Matrix) - Static method in class jgromacs.analysis.Similarity
  Returns the time series of wdRMSD (weighted dRMSD) in a trajectory with regards to a reference structure taking into account only a subset of atoms
getSimilarityTimeSeriesWDRMSD(Trajectory, PointList, Matrix) - Static method in class jgromacs.analysis.Similarity
  Returns the time series of wdRMSD (weighted dRMSD) in a trajectory with regards to a reference point list
getSimilarityTimeSeriesWDRMSD(Trajectory, Structure, Matrix) - Static method in class jgromacs.analysis.Similarity
  Returns the time series of wdRMSD (weighted dRMSD) in a trajectory with regards to a reference structure
getStartTime() - Method in class jgromacs.data.Trajectory
  Returns the start time of trajectory
getStructuralRadius(Trajectory) - Static method in class jgromacs.analysis.Dynamics
  Calculates the structural radius of the conformational ensemble sampled in the trajectory as defined by Kuzmanic and Zagrovic, 2010 (Determination of Ensemble-Average Pairwise Root Mean-Square Deviation from Experimental B-Factors, Biophysical Journal)
getSubList(ArrayList<Integer>) - Method in class jgromacs.data.PointList
  Returns a subset of points defined by an ArrayList of indices
getSubSequence(int, int) - Method in class jgromacs.data.Sequence
  Returns subsequence beginning at sequence position #begin and ending at sequence position #end
getSubSequenceFrom(int) - Method in class jgromacs.data.Sequence
  Returns subsequence beginning at sequence position #begin
getSubSequenceTo(int) - Method in class jgromacs.data.Sequence
  Returns subsequence ending at sequence position #end
getSubStructure(IndexSet) - Method in class jgromacs.data.Structure
  Returns the substructure defined by the given index set
getSubTrajectory(int, int) - Method in class jgromacs.data.Trajectory
  Returns the subtrajectory between the given start and end frames
getSubTrajectory(int, int, int) - Method in class jgromacs.data.Trajectory
  Returns the subtrajectory between the given start and end frames using the given sampling frequency
getSubTrajectory(FrameIndexSet) - Method in class jgromacs.data.Trajectory
  Returns the subtrajectory defined by the given frame list
getSubTrajectory(IndexSet) - Method in class jgromacs.data.Trajectory
  Returns the subtrajectory defined by the given index set
getSystemIndexSet() - Method in class jgromacs.data.Structure
  Returns the index set of all atoms in the system
getTimeStep() - Method in class jgromacs.data.Trajectory
  Returns the time step of trajectory
getTorsionAngleTimeSeries(Trajectory, int, int, int, int) - Static method in class jgromacs.analysis.Angles
  Calculates the time series of torsion angle over a trajectory defined by four atoms
getTrajectoryOfAtom(Trajectory, int) - Static method in class jgromacs.analysis.Dynamics
  Returns the trajectory of a single atom in the course of the simulation
getVarianceOfDistance(Trajectory, int, int) - Static method in class jgromacs.analysis.Distances
  Returns the variance of the distance of two atoms in a trajectory
getWaterIndexSet() - Method in class jgromacs.data.Structure
  Returns the index set of water atoms
getWDRMSD(PointList, PointList, Matrix) - Static method in class jgromacs.analysis.Similarity
  Calculates the wdRMSD (weighted dRMSD) similarity of two point lists
getWDRMSD(Structure, IndexSet, Structure, IndexSet, Matrix) - Static method in class jgromacs.analysis.Similarity
  Calculates wdRMSD (weighted dRMSD) similarity between two groups of atoms
getWDRMSD(Structure, Structure, Matrix) - Static method in class jgromacs.analysis.Similarity
  Calculates the wdRMSD (weighted dRMSD) similarity of two structures
getWDRMSDiProfile(PointList, PointList, Matrix) - Static method in class jgromacs.analysis.Similarity
  Calculates the wdRMSDi (weighted dRMSDi) profile between two point lists
getWDRMSDiProfile(Structure, IndexSet, Structure, IndexSet, Matrix) - Static method in class jgromacs.analysis.Similarity
  Calculates the wdRMSDi (weighted dRMSDi) profile between two groups of atoms
getWDRMSDiProfile(Structure, Structure, Matrix) - Static method in class jgromacs.analysis.Similarity
  Calculates the wdRMSDi (weighted dRMSDi) profile between two structures
getX() - Method in class jgromacs.data.Point3D
  Returns the X coordinate of point
getXCoordinate() - Method in class jgromacs.data.Atom
  Returns the X coordinate of atom
getY() - Method in class jgromacs.data.Point3D
  Returns the Y coordinate of point
getYCoordinate() - Method in class jgromacs.data.Atom
  Returns the Y coordinate of atom
getZ() - Method in class jgromacs.data.Point3D
  Returns the Z coordinate of point
getZCoordinate() - Method in class jgromacs.data.Atom
  Returns the Z coordinate of atom
getZetaCarbon() - Method in class jgromacs.data.Residue
  Returns the zeta carbon atom if any (otherwise returns null)
GNM - Class in jgromacs.analysis
  Objects of this class represent a Gaussian Network Model (GNM) of a protein
GNM(Structure, double, int) - Constructor for class jgromacs.analysis.GNM
  Constructs a new Gaussian Network Model

## H

hashCode() - Method in class jgromacs.data.Alignment
  Returns hash code
hashCode() - Method in class jgromacs.data.Angle
  Returns hash code
hashCode() - Method in class jgromacs.data.Atom
  Returns hash code
hashCode() - Method in class jgromacs.data.FrameIndexSet
  Returns hash code
hashCode() - Method in class jgromacs.data.IndexSet
  Returns hash code
hashCode() - Method in class jgromacs.data.IndexSetList
  Returns hash code
hashCode() - Method in class jgromacs.data.Point3D
  Returns hash code
hashCode() - Method in class jgromacs.data.PointList
  Returns hash code
hashCode() - Method in class jgromacs.data.Residue
  Returns hash code
hashCode() - Method in class jgromacs.data.Sequence
  Returns hash code
hashCode() - Method in class jgromacs.data.SequencePosition
  Returns hash code
hashCode() - Method in class jgromacs.data.Structure
  Returns hash code
hashCode() - Method in class jgromacs.data.Trajectory
  Returns hash code
hashCode() - Method in class jgromacs.db.AtomType
  Returns hash code
hashCode() - Method in class jgromacs.db.ResidueType
  Returns hash code
howManyModelsInPDB(String) - Static method in class jgromacs.io.IOData
  Returns the number of models in the given PDB file

## I

IndexSet - Class in jgromacs.data
  Objects of this class represent a single index set
IndexSet() - Constructor for class jgromacs.data.IndexSet
  Constructs a new IndexSet object
IndexSet(String) - Constructor for class jgromacs.data.IndexSet
  Constructs a new IndexSet object of a given name
IndexSet(ArrayList<Integer>) - Constructor for class jgromacs.data.IndexSet
  Constructs a new IndexSet object and loads data from an ArrayList
IndexSet(ArrayList<Integer>, String) - Constructor for class jgromacs.data.IndexSet
  Constructs a new IndexSet object of a given name and loads data from an ArrayList
IndexSet(TreeSet<Integer>) - Constructor for class jgromacs.data.IndexSet
  Constructs a new IndexSet object and loads data from a TreeSet
IndexSet(TreeSet<Integer>, String) - Constructor for class jgromacs.data.IndexSet
  Constructs a new IndexSet object of a given name and loads data from a TreeSet
IndexSet(IndexSet) - Constructor for class jgromacs.data.IndexSet
  Constructs a new IndexSet object identical to a given IndexSet
IndexSetList - Class in jgromacs.data
  Objects of this class represent a list of index sets
IndexSetList() - Constructor for class jgromacs.data.IndexSetList
  Constructs a new IndexSetList object
innerProduct(Point3D) - Method in class jgromacs.data.Point3D
  Returns the inner product of this vector and another vector
insertGap(int) - Method in class jgromacs.data.Sequence
  Inserts a new gap to position #i
insertPosition(int, int, ResidueType) - Method in class jgromacs.data.Sequence
  Inserts sequence position of given index and residue type to position #i Note that you may have to re-index sequence positions after using this method
insertPosition(int, int, ResidueType, String) - Method in class jgromacs.data.Sequence
  Inserts sequence position of given index, residue type and annotation to position #i Note that you may have to re-index sequence positions after using this method
insertPosition(int, SequencePosition) - Method in class jgromacs.data.Sequence
  Inserts the given sequence position to position #i Note that you may have to re-index sequence positions after using this method
insertPosition(int, ResidueType, String) - Method in class jgromacs.data.Sequence
  Inserts sequence position of given residue type and annotation to position #i Note that you may have to re-index sequence positions after using this method
intersect(FrameIndexSet) - Method in class jgromacs.data.FrameIndexSet
  Returns the intersection of this frame index set and another
intersect(IndexSet) - Method in class jgromacs.data.IndexSet
  Returns the intersection of this index set and another
IOData - Class in jgromacs.io
  This class contains static methods for IO of data objects
IOData() - Constructor for class jgromacs.io.IOData
IOMath - Class in jgromacs.io
  This class contains static methods for IO of ArrayList and Matrix objects
IOMath() - Constructor for class jgromacs.io.IOMath
isAlphaCarbon() - Method in class jgromacs.data.Atom
  Returns true if it is an alpha carbon atom
isAminoAcid() - Method in class jgromacs.data.Residue
  Returns true if it is an amino acid
isAminoAcid() - Method in class jgromacs.db.ResidueType
  Returns true if it is an amino acid (not water or else)
isArgumentGiven(String) - Method in class jgromacs.ui.Application
  Returns true if the attribute defined by the given flag was called by the user
isAtomIn(Atom) - Method in class jgromacs.data.Residue
  Returns true if the given atom is in the residue
isBackboneAtom() - Method in class jgromacs.data.Atom
  Returns true if it is a backbone atom
isBetaCarbon() - Method in class jgromacs.data.Atom
  Returns true if it is a beta carbon atom
isCarbonylOxygen() - Method in class jgromacs.data.Atom
  Returns true if it is a carbonyl oxygen atom
isCTerminalCarbon() - Method in class jgromacs.data.Atom
  Returns true if it is a C-terminal carbon atom
isDeltaCarbon() - Method in class jgromacs.data.Atom
  Returns true if it is a delta carbon atom
isEpsilonCarbon() - Method in class jgromacs.data.Atom
  Returns true if it is an epsilon carbon atom
isFrameIn(int) - Method in class jgromacs.data.FrameIndexSet
  Returns true if the frame index set contains a given frame index
isGammaCarbon() - Method in class jgromacs.data.Atom
  Returns true if it is a gamma carbon atom
isHeavyAtom() - Method in class jgromacs.data.Atom
  Returns true if it is a heavy atom (not hydrogen)
isHydrogenAtom() - Method in class jgromacs.data.Atom
  Returns true if the atom is a Hydrogen
isIndexIn(int) - Method in class jgromacs.data.IndexSet
  Returns true if the index set contains a given index
isMainChainAtom() - Method in class jgromacs.data.Atom
  Returns true if it is a main chain atom
isMainChainHydrogenAtom() - Method in class jgromacs.data.Atom
  Returns true if it is a main chain hydrogen atom
isMainChainPlusCbAtom() - Method in class jgromacs.data.Atom
  Returns true if it is a main chain or beta carbon atom
isMainChainPlusHAtom() - Method in class jgromacs.data.Atom
  Returns true if it is a main chain or hydrogen atom
isMatchColumn(int) - Method in class jgromacs.data.Alignment
  Returns true if column #i is a match column (i.e.
isNTerminalNitrogen() - Method in class jgromacs.data.Atom
  Returns true if it is an N-terminal nitrogen atom
isOther() - Method in class jgromacs.data.Residue
  Returns true if it is not an amino acid neither a water molecule
isOther() - Method in class jgromacs.db.ResidueType
  Returns true if it is not an amino acid nor water
isPositionAGap(int) - Method in class jgromacs.data.Sequence
  Returns true if sequence position #i is a gap
isSideChainAtom() - Method in class jgromacs.data.Atom
  Returns true if it is a side chain atom
isSideChainMinusHAtom() - Method in class jgromacs.data.Atom
  Returns true if it is a side chain atom but not hydrogen
isTerminalOxygen() - Method in class jgromacs.data.Atom
  Returns true if it is a terminal oxygen atom
isWater() - Method in class jgromacs.data.Residue
  Returns true if it is a water molecule
isWater() - Method in class jgromacs.db.ResidueType
  Returns true if it is water (not amino acid or else)
isZetaCarbon() - Method in class jgromacs.data.Atom
  Returns true if it is a zeta carbon atom

## J

jgromacs.analysis - package jgromacs.analysis
  jgromacs.analysis is a collection of classes providing static methods for various analysis tasks
jgromacs.data - package jgromacs.data
  jgromacs.data is a collection of classes representing multiple levels of structural data
jgromacs.db - package jgromacs.db
  jgromacs.db contains two classes defining atom and residue types
jgromacs.io - package jgromacs.io
  jgromacs.io provides parsers for reading and methods for writing GROMACS files
jgromacs.ui - package jgromacs.ui
  jgromacs.ui helps to create JGromacs applications with user-friendly UIs

## L

length() - Method in class jgromacs.data.Point3D
  Returns the length of the vector
loadFromMatrix(Matrix) - Method in class jgromacs.data.PointList
  Loads point coordinates from a 3xN matrix

## M

main(String[]) - Static method in class jgromacs.ui.TemplateApplication
mapAtomIndicesToResidueIndices(IndexSet) - Method in class jgromacs.data.Structure
  Maps atomic indices to residue indices (i.e.
mapResidueIndicesToAtomIndices(ArrayList<Integer>) - Method in class jgromacs.data.Structure
  Maps residue indices to atomic indices (i.e.
minus(Point3D) - Method in class jgromacs.data.Point3D
  Subtracts another vector from this vector
multiplyByScalar(double) - Method in class jgromacs.data.Point3D
  Returns this vector multiplied by a scalar

## P

plus(Point3D) - Method in class jgromacs.data.Point3D
  Adds another vector to this vector
Point3D - Class in jgromacs.data
  Objects of this class represent a single 3D point
Point3D() - Constructor for class jgromacs.data.Point3D
  Constructs a new Point3D object
Point3D(double, double, double) - Constructor for class jgromacs.data.Point3D
  Constructs a new Point3D object with the given coordinates
PointList - Class in jgromacs.data
  Objects of this class represent a list of 3D points
PointList() - Constructor for class jgromacs.data.PointList
  Constructs a new PointList object

## R

readAlignmentFromFASTA(String) - Static method in class jgromacs.io.IOData
  Reads an alignment from the given FASTA file
readArrayListFromFile(String) - Static method in class jgromacs.io.IOMath
  Reads ArrayList from the given file
readDumpedTrajectory(Structure, String) - Static method in class jgromacs.io.IOData
  Reads a trajectory from the given dumped XTC or TRR file
readFromFile(String) - Static method in class jgromacs.io.IOData
  Reads a JGromacs object (Structure, IndexSetList, Trajectory or Sequence) from a file automatically identifying the type of the file
readIndexSetFromNDX(String) - Static method in class jgromacs.io.IOData
  Reads an index set from the given NDX file
readIndexSetListFromNDX(String) - Static method in class jgromacs.io.IOData
  Reads an index set list from the given NDX file
readMatrixFromFile(String) - Static method in class jgromacs.io.IOMath
  Reads Matrix from the given file
readSequenceFromFASTA(String) - Static method in class jgromacs.io.IOData
  Reads a sequence from the given FASTA file
readStructureFromGRO(String) - Static method in class jgromacs.io.IOData
  Reads structure from the given GRO file
readStructureFromPDB(String) - Static method in class jgromacs.io.IOData
  Reads structure from the given PDB file
readStructureFromPDB(String, int) - Static method in class jgromacs.io.IOData
  Reads the given model from the given PDB file
readStructuresFromPDB(String) - Static method in class jgromacs.io.IOData
  Reads an ensemble of structures from the given PDB file
readStructuresFromPDBsInDirectory(String) - Static method in class jgromacs.io.IOData
  Reads an ensemble of structures from PDB files in the given directory
readTrajectory(Structure, String) - Static method in class jgromacs.io.IOData
  Reads a trajectory from the given XTC or TRR file
reIndexPositions() - Method in class jgromacs.data.Sequence
  Reindexes all positions in the sequence starting from 1
reIndexPositions(int) - Method in class jgromacs.data.Sequence
  Reindexes all positions in the sequence starting from a given index
removeAtom(int) - Method in class jgromacs.data.Residue
  Removes atom #i from the residue
removeAtom(int) - Method in class jgromacs.data.Structure
  Removes atom #i from the structure
removeAtom(Atom) - Method in class jgromacs.data.Residue
  Removes the given atom from the residue
removeAtom(Atom) - Method in class jgromacs.data.Structure
  Removes the given atom from the structure
removeAtomByIndex(int) - Method in class jgromacs.data.Residue
  Removes atom of given index from the residue
removeAtomByIndex(int) - Method in class jgromacs.data.Structure
  Removes the atom of given index from the structure
removeColumn(int) - Method in class jgromacs.data.Alignment
  Removes column #i from the alignment
removeFrame(int) - Method in class jgromacs.data.FrameIndexSet
  Removes a frame from the frame index set
removeFrame(int) - Method in class jgromacs.data.Trajectory
  Removes frame #i from the trajectory
removeGaps() - Method in class jgromacs.data.Sequence
  Removes all gaps from the sequence
removeIndex(int) - Method in class jgromacs.data.IndexSet
  Removes an index from the index set
removeIndexSet(int) - Method in class jgromacs.data.IndexSetList
  Removes index set of given index from the list
removeIndexSet(IndexSet) - Method in class jgromacs.data.IndexSetList
  Removes the given index set from the list
removePoint(int) - Method in class jgromacs.data.PointList
  Removes the point of index i from the point list
removePoint(Point3D) - Method in class jgromacs.data.PointList
  Removes the given point from the point list
removePosition(int) - Method in class jgromacs.data.Sequence
  Removes sequence position #i
removePosition(SequencePosition) - Method in class jgromacs.data.Sequence
  Removes the given sequence position
removePositionByIndex(int) - Method in class jgromacs.data.Sequence
  Removes the sequence position of given index
removeResidue(int) - Method in class jgromacs.data.Structure
  Removes residue #i from the structure
removeResidue(Residue) - Method in class jgromacs.data.Structure
  Removes a residue from the structure
removeSequence(int) - Method in class jgromacs.data.Alignment
  Removes sequence #i from the alignment
removeSequence(Sequence) - Method in class jgromacs.data.Alignment
  Removes the given sequence from the alignment
Residue - Class in jgromacs.data
  Objects of this class represent a single residue
Residue() - Constructor for class jgromacs.data.Residue
  Constructs a new Residue object
Residue(int, String, String, ResidueType) - Constructor for class jgromacs.data.Residue
  Constructs a new Residue object of given index, name, chainID and residue type
Residue(int, String, ResidueType) - Constructor for class jgromacs.data.Residue
  Constructs a new Residue object of given index, name and residue type
Residue(String) - Constructor for class jgromacs.data.Residue
  Constructs a new Residue object of given name
ResidueType - Class in jgromacs.db
  Objects of this class represent a residue type
ResidueType() - Constructor for class jgromacs.db.ResidueType
  Constructs a new ResidueType object
ResidueType(int) - Constructor for class jgromacs.db.ResidueType
  Constructs a new ResidueType object of a given type
ResidueType(String) - Constructor for class jgromacs.db.ResidueType
  Constructs a new ResidueType object of given code
rotate(Matrix) - Method in class jgromacs.data.PointList
  Rotates the points by a given 3x3 rotation matrix
run(String[]) - Method in class jgromacs.ui.Application
  Don't override this method!
runCore() - Method in class jgromacs.ui.Application
  You can override this method to include your own code.
runCore() - Method in class jgromacs.ui.TemplateApplication
runGromacsCommand(String, String[]) - Static method in class jgromacs.io.IOData
  Executes Gromacs commands from within the Java code and reads the listed output files back into JGromacs objects.

## S

Sequence - Class in jgromacs.data
  Objects of this class represent a single amino acid sequence
Sequence() - Constructor for class jgromacs.data.Sequence
  Constructs a new Sequence object
Sequence(String) - Constructor for class jgromacs.data.Sequence
  Constructs a new Sequence object of given name
SequencePosition - Class in jgromacs.data
  Objects of this class represent a single sequence position
SequencePosition() - Constructor for class jgromacs.data.SequencePosition
  Constructs a new SequencePosition object
SequencePosition(int, String) - Constructor for class jgromacs.data.SequencePosition
  Constructs a new SequencePosition object of given index and annotation
SequencePosition(int, ResidueType) - Constructor for class jgromacs.data.SequencePosition
  Constructs a new SequencePosition object of given index and residue type
SequencePosition(int, ResidueType, String) - Constructor for class jgromacs.data.SequencePosition
  Constructs a new SequencePosition object of given index, residue type and annotation
SequencePosition(ResidueType, String) - Constructor for class jgromacs.data.SequencePosition
  Constructs a new SequencePosition object of residue type and annotation
setAllAtomCoordinates(PointList) - Method in class jgromacs.data.Residue
  Sets the coordinates of all atoms
setAllAtomCoordinates(PointList) - Method in class jgromacs.data.Structure
  Sets the coordinates of all atoms
setAnnotation(String) - Method in class jgromacs.data.SequencePosition
  Sets the annotation of sequence position
setAtom(int, Atom) - Method in class jgromacs.data.Residue
  Replaces atom #i of the residue with the given atom
setAtomCoordinates(int, Point3D) - Method in class jgromacs.data.Residue
  Sets the coordinates of atom #i
setAtomCoordinates(int, Point3D) - Method in class jgromacs.data.Structure
  Sets the coordinates of atom #i
setAtomInResidue(int, int, Atom) - Method in class jgromacs.data.Structure
  Replaces atom #j of residue #i with a new atom
setAtomInResidueOfIndex(int, int, Atom) - Method in class jgromacs.data.Structure
  Replaces atom #i of the residue of given index with a new atom
setAtomOfIndexCoordinates(int, Point3D) - Method in class jgromacs.data.Residue
  Sets the coordinates of atom of given index
setAtomOfIndexCoordinates(int, Point3D) - Method in class jgromacs.data.Structure
  Sets the coordinates of atom of given index
setAtomType(AtomType) - Method in class jgromacs.data.Atom
  Sets the type of atom
setBvalue(double) - Method in class jgromacs.data.Atom
  Sets the B-value of atom
setChainID(String) - Method in class jgromacs.data.Residue
  Sets the chain ID of residue
setCoordinates(Point3D) - Method in class jgromacs.data.Atom
  Sets the coordinates of atom
setFrame(int, PointList) - Method in class jgromacs.data.Trajectory
  Replaces frame #i with a new frame
setInDegrees(double) - Method in class jgromacs.data.Angle
  Sets the value of angle in degrees
setIndex(int) - Method in class jgromacs.data.Atom
  Sets the index of atom
setIndex(int) - Method in class jgromacs.data.Residue
  Sets the index of residue
setIndex(int) - Method in class jgromacs.data.SequencePosition
  Sets the index of sequence position
setIndexSet(int, IndexSet) - Method in class jgromacs.data.IndexSetList
  Replaces index set of given index with a new index set
setInRadians(double) - Method in class jgromacs.data.Angle
  Sets the value of angle in radians
setLogFileName(String) - Method in class jgromacs.ui.Application
  Sets the name of log file
setName(String) - Method in class jgromacs.data.Atom
  Sets the name of atom
setName(String) - Method in class jgromacs.data.FrameIndexSet
  Sets the name of frame index set
setName(String) - Method in class jgromacs.data.IndexSet
  Sets the name of index set
setName(String) - Method in class jgromacs.data.Residue
  Sets the name of residue
setName(String) - Method in class jgromacs.data.Sequence
  Sets the name of sequence
setName(String) - Method in class jgromacs.data.Structure
  Sets the name of structure
setName(String) - Method in class jgromacs.data.Trajectory
  Sets the name of trajectory
setOccupancy(double) - Method in class jgromacs.data.Atom
  Sets the occupancy of atom
setPoint(int, Point3D) - Method in class jgromacs.data.PointList
  Replaces the point of index i with a given point
setPointFromArrayList(ArrayList<Point3D>) - Method in class jgromacs.data.PointList
  Loads points from an ArrayList
setPosition(int, int, ResidueType) - Method in class jgromacs.data.Sequence
  Replaces position #i with the a sequence position of given index and residue type
setPosition(int, int, ResidueType, String) - Method in class jgromacs.data.Sequence
  Replaces position #i with the a sequence position of given index, residue type and annotation
setPosition(int, SequencePosition) - Method in class jgromacs.data.Sequence
  Replaces position #i with the given sequence position
setPosition(int, ResidueType, String) - Method in class jgromacs.data.Sequence
  Replaces position #i with the a sequence position of given residue type and annotation
setPositionByIndex(int, ResidueType) - Method in class jgromacs.data.Sequence
  Replaces the position of given index with the a sequence position of given residue type
setPositionByIndex(int, ResidueType, String) - Method in class jgromacs.data.Sequence
  Replaces the position of given index with the a sequence position of given residue type and annotation
setResidue(int, Residue) - Method in class jgromacs.data.Structure
  Replaces residue #i with a new residue
setResidueType(ResidueType) - Method in class jgromacs.data.Residue
  Sets the type of residue
setResidueType(ResidueType) - Method in class jgromacs.data.SequencePosition
  Sets the residue type of sequence position
setSequence(int, Sequence) - Method in class jgromacs.data.Alignment
  Replaces sequence #i of the alignment with a new sequence
setStartTime(double) - Method in class jgromacs.data.Trajectory
  Sets the start time of trajectory
setStructure(Structure) - Method in class jgromacs.data.Trajectory
  Sets the structure described by the trajectory
setTimeStep(double) - Method in class jgromacs.data.Trajectory
  Sets the time step of trajectory
setWritingToLogFile(boolean) - Method in class jgromacs.ui.Application
  Sets if the application writes log file
setX(double) - Method in class jgromacs.data.Point3D
  Sets the X coordinate of point
setXCoordinate(double) - Method in class jgromacs.data.Atom
  Sets the X coordinate of atom
setY(double) - Method in class jgromacs.data.Point3D
  Sets the Y coordinate of point
setYCoordinate(double) - Method in class jgromacs.data.Atom
  Sets the Y coordinate of atom
setZ(double) - Method in class jgromacs.data.Point3D
  Sets the Z coordinate of point
setZCoordinate(double) - Method in class jgromacs.data.Atom
  Sets the Z coordinate of atom
Similarity - Class in jgromacs.analysis
  Collection of methods for measuring structural similarity
Similarity() - Constructor for class jgromacs.analysis.Similarity
Structure - Class in jgromacs.data
  Objects of this class represent a single structure
Structure() - Constructor for class jgromacs.data.Structure
  Constructs a new Structure object
Structure(String) - Constructor for class jgromacs.data.Structure
  Constructs a new Structure object of given name
subtract(FrameIndexSet) - Method in class jgromacs.data.FrameIndexSet
  Returns the subtraction of another frame index set from this frame index set
subtract(IndexSet) - Method in class jgromacs.data.IndexSet
  Returns the subtraction of another index set from this index set
superposeTo(PointList, PointList) - Static method in class jgromacs.analysis.Superposition
  Calculates the superposition of a point list to another
superposeTo(Structure, IndexSet, Structure, IndexSet) - Static method in class jgromacs.analysis.Superposition
  Calculates the superposition of a structure to another using a subset of atoms for fitting
superposeTo(Structure, Structure) - Static method in class jgromacs.analysis.Superposition
  Calculates the superposition of a structure to another
superposeTo(Trajectory, PointList) - Static method in class jgromacs.analysis.Superposition
  Calculates the superposition of each frame of a trajectory to a common reference frame
superposeTo(Trajectory, Structure) - Static method in class jgromacs.analysis.Superposition
  Calculates the superposition of each frame of a trajectory to a common reference frame
superposeTo(Trajectory, Structure, IndexSet) - Static method in class jgromacs.analysis.Superposition
  Calculates the superposition of each frame of a trajectory to a common reference frame using a subset of atoms for fitting
Superposition - Class in jgromacs.analysis
  Collection of methods for superposing structures
Superposition() - Constructor for class jgromacs.analysis.Superposition

## T

TemplateApplication - Class in jgromacs.ui
  Template JGromacs application
TemplateApplication() - Constructor for class jgromacs.ui.TemplateApplication
toString() - Method in class jgromacs.data.Alignment
  Returns the String representation of alignment
toString() - Method in class jgromacs.data.Angle
  Returns the String representation of angle
toString() - Method in class jgromacs.data.Atom
  Returns the String representation of atom
toString() - Method in class jgromacs.data.FrameIndexSet
  Returns the String representation of frame index set
toString() - Method in class jgromacs.data.IndexSet
  Returns the String representation of index set
toString() - Method in class jgromacs.data.IndexSetList
  Returns the String representation of index set list
toString() - Method in class jgromacs.data.Point3D
  Returns the String representation of point
toString() - Method in class jgromacs.data.PointList
  Returns the String representation of point list
toString() - Method in class jgromacs.data.Residue
  Returns the String representation of residue
toString() - Method in class jgromacs.data.Sequence
  Returns the String representation of sequence
toString() - Method in class jgromacs.data.SequencePosition
  Returns the String representation of sequence position
toString() - Method in class jgromacs.data.Structure
  Returns the String representation of structure
toString() - Method in class jgromacs.data.Trajectory
  Returns the String representation of trajectory
toString() - Method in class jgromacs.db.AtomType
  Returns the String representation of atom type
toString() - Method in class jgromacs.db.ResidueType
  Returns the String representation of residue type
toString1Letter() - Method in class jgromacs.data.Sequence
  Returns a String representation in which each residue is represented by its 1 letter code
toString1Letter(int) - Method in class jgromacs.data.Sequence
  Returns a String representation in which each residue is represented by its 1 letter code and the string is split to lines of the given length
toString3Letter() - Method in class jgromacs.data.Sequence
  Returns a String representation in which each residue is represented by its 3 letter code
toString3Letter(int) - Method in class jgromacs.data.Sequence
  Returns a String representation in which each residue is represented by its 3 letter code and the string is split to lines of the given length
toStringAsGRO() - Method in class jgromacs.data.Structure
  Returns the String representation of structure in GRO format
toStringAsPDB() - Method in class jgromacs.data.Structure
  Returns the String representation of structure in PDB format
toStringInfo() - Method in class jgromacs.data.Alignment
  Returns summary information about the alignment
toStringInfo() - Method in class jgromacs.data.FrameIndexSet
  Returns summary information about the frame index set
toStringInfo() - Method in class jgromacs.data.IndexSet
  Returns summary information about the index set
toStringInfo() - Method in class jgromacs.data.IndexSetList
  Returns summary information about the index set list
toStringInfo() - Method in class jgromacs.data.PointList
  Returns summary information about the point list
toStringInfo() - Method in class jgromacs.data.Residue
  Returns summary information about the residue
toStringInfo() - Method in class jgromacs.data.Sequence
  Returns summary information about the sequence
toStringInfo() - Method in class jgromacs.data.Structure
  Returns summary information about the structure
Trajectory - Class in jgromacs.data
  Objects of this class represent a single trajectory
Trajectory() - Constructor for class jgromacs.data.Trajectory
  Constructs a new Trajectory object
Trajectory(String) - Constructor for class jgromacs.data.Trajectory
  Constructs a new Trajectory object of given name
Trajectory(Structure) - Constructor for class jgromacs.data.Trajectory
  Constructs a new Trajectory object of given structure
Trajectory(Structure[]) - Constructor for class jgromacs.data.Trajectory
  Constructs a new Trajectory object made from an ensemble of structures
transformByMatrix(Matrix) - Method in class jgromacs.data.Point3D
  Returns the resulting vector of a matrix transformation
translate(Point3D) - Method in class jgromacs.data.PointList
  Translates the points by a given vector

## U

union(FrameIndexSet) - Method in class jgromacs.data.FrameIndexSet
  Returns the union of this frame index set and another
union(IndexSet) - Method in class jgromacs.data.IndexSet
  Returns the union of this index set and another

## W

weightedSuperposeTo(PointList, PointList, ArrayList<Double>) - Static method in class jgromacs.analysis.Superposition
  Calculates the weighted superposition of a point list to another
weightedSuperposeTo(Structure, Structure, ArrayList<Double>) - Static method in class jgromacs.analysis.Superposition
  Calculates the weighted superposition of a structure to another
weightedSuperposeTo(Trajectory, PointList, ArrayList<Double>) - Static method in class jgromacs.analysis.Superposition
  Calculates the weighted superposition of each frame of a trajectory to a common reference frame
weightedSuperposeTo(Trajectory, Structure, ArrayList<Double>) - Static method in class jgromacs.analysis.Superposition
  Calculates the weighted superposition of each frame of a trajectory to a common reference frame
writeAlignmentToFASTA(String, Alignment) - Static method in class jgromacs.io.IOData
  Writes an alignment to the given FASTA file
writeArrayListToFile(ArrayList<Double>, String) - Static method in class jgromacs.io.IOMath
  Writes an ArrayList to the given file
writeIndexSetListToNDX(String, IndexSetList) - Static method in class jgromacs.io.IOData
  Writes an index set list to the given NDX file
writeIndexSetToNDX(String, IndexSet) - Static method in class jgromacs.io.IOData
  Writes an index set to the given NDX file
writeMatrixToFile(Matrix, String) - Static method in class jgromacs.io.IOMath
  Writes a Matrix to the given file
writeScalarToFile(double, String) - Static method in class jgromacs.io.IOMath
  Writes a scalar to the given file
writeSequenceToFASTA(String, Sequence) - Static method in class jgromacs.io.IOData
  Writes a sequence to the given FASTA file
writeStructureToGRO(String, Structure) - Static method in class jgromacs.io.IOData
  Writes a structure to the given GRO file
writeStructureToPDB(String, Structure) - Static method in class jgromacs.io.IOData
  Writes a structure to the given PDB file
writeToLogFile(String) - Method in class jgromacs.ui.Application
  Sets if the application writes log file

## X

XMLFileName - Variable in class jgromacs.ui.Application
  XML configuration file name

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