A C D E F G H I J L M P R S T U W X
All Classes All Packages
All Classes All Packages
All Classes All Packages
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
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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
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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
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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
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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
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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
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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
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Template JGromacs application
- TemplateApplication() - Constructor for class jgromacs.ui.TemplateApplication
- toString() - Method in class jgromacs.data.Alignment
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Returns the String representation of alignment
- toString() - Method in class jgromacs.data.Angle
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Returns the String representation of angle
- toString() - Method in class jgromacs.data.Atom
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Returns the String representation of atom
- toString() - Method in class jgromacs.data.FrameIndexSet
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Returns the String representation of frame index set
- toString() - Method in class jgromacs.data.IndexSet
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Returns the String representation of index set
- toString() - Method in class jgromacs.data.IndexSetList
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Returns the String representation of index set list
- toString() - Method in class jgromacs.data.Point3D
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Returns the String representation of point
- toString() - Method in class jgromacs.data.PointList
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Returns the String representation of point list
- toString() - Method in class jgromacs.data.Residue
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Returns the String representation of residue
- toString() - Method in class jgromacs.data.Sequence
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Returns the String representation of sequence
- toString() - Method in class jgromacs.data.SequencePosition
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Returns the String representation of sequence position
- toString() - Method in class jgromacs.data.Structure
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Returns the String representation of structure
- toString() - Method in class jgromacs.data.Trajectory
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Returns the String representation of trajectory
- toString() - Method in class jgromacs.db.AtomType
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Returns the String representation of atom type
- toString() - Method in class jgromacs.db.ResidueType
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Returns the String representation of residue type
- toString1Letter() - Method in class jgromacs.data.Sequence
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Returns a String representation in which each residue is represented by its 1 letter code
- toString1Letter(int) - Method in class jgromacs.data.Sequence
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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
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Returns a String representation in which each residue is represented by its 3 letter code
- toString3Letter(int) - Method in class jgromacs.data.Sequence
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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
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Returns the String representation of structure in GRO format
- toStringAsPDB() - Method in class jgromacs.data.Structure
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Returns the String representation of structure in PDB format
- toStringInfo() - Method in class jgromacs.data.Alignment
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Returns summary information about the alignment
- toStringInfo() - Method in class jgromacs.data.FrameIndexSet
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Returns summary information about the frame index set
- toStringInfo() - Method in class jgromacs.data.IndexSet
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Returns summary information about the index set
- toStringInfo() - Method in class jgromacs.data.IndexSetList
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Returns summary information about the index set list
- toStringInfo() - Method in class jgromacs.data.PointList
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Returns summary information about the point list
- toStringInfo() - Method in class jgromacs.data.Residue
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Returns summary information about the residue
- toStringInfo() - Method in class jgromacs.data.Sequence
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Returns summary information about the sequence
- toStringInfo() - Method in class jgromacs.data.Structure
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Returns summary information about the structure
- Trajectory - Class in jgromacs.data
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Objects of this class represent a single trajectory
- Trajectory() - Constructor for class jgromacs.data.Trajectory
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Constructs a new Trajectory object
- Trajectory(String) - Constructor for class jgromacs.data.Trajectory
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Constructs a new Trajectory object of given name
- Trajectory(Structure) - Constructor for class jgromacs.data.Trajectory
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Constructs a new Trajectory object of given structure
- Trajectory(Structure[]) - Constructor for class jgromacs.data.Trajectory
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Constructs a new Trajectory object made from an ensemble of structures
- transformByMatrix(Matrix) - Method in class jgromacs.data.Point3D
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Returns the resulting vector of a matrix transformation
- translate(Point3D) - Method in class jgromacs.data.PointList
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Translates the points by a given vector
U
- union(FrameIndexSet) - Method in class jgromacs.data.FrameIndexSet
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Returns the union of this frame index set and another
- union(IndexSet) - Method in class jgromacs.data.IndexSet
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Returns the union of this index set and another
W
- weightedSuperposeTo(PointList, PointList, ArrayList<Double>) - Static method in class jgromacs.analysis.Superposition
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Calculates the weighted superposition of a point list to another
- weightedSuperposeTo(Structure, Structure, ArrayList<Double>) - Static method in class jgromacs.analysis.Superposition
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Calculates the weighted superposition of a structure to another
- weightedSuperposeTo(Trajectory, PointList, ArrayList<Double>) - Static method in class jgromacs.analysis.Superposition
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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
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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
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Writes an alignment to the given FASTA file
- writeArrayListToFile(ArrayList<Double>, String) - Static method in class jgromacs.io.IOMath
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Writes an ArrayList to the given file
- writeIndexSetListToNDX(String, IndexSetList) - Static method in class jgromacs.io.IOData
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Writes an index set list to the given NDX file
- writeIndexSetToNDX(String, IndexSet) - Static method in class jgromacs.io.IOData
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Writes an index set to the given NDX file
- writeMatrixToFile(Matrix, String) - Static method in class jgromacs.io.IOMath
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Writes a Matrix to the given file
- writeScalarToFile(double, String) - Static method in class jgromacs.io.IOMath
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Writes a scalar to the given file
- writeSequenceToFASTA(String, Sequence) - Static method in class jgromacs.io.IOData
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Writes a sequence to the given FASTA file
- writeStructureToGRO(String, Structure) - Static method in class jgromacs.io.IOData
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Writes a structure to the given GRO file
- writeStructureToPDB(String, Structure) - Static method in class jgromacs.io.IOData
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Writes a structure to the given PDB file
- writeToLogFile(String) - Method in class jgromacs.ui.Application
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Sets if the application writes log file
X
- XMLFileName - Variable in class jgromacs.ui.Application
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XML configuration file name
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