- 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, PointList) - Static method in class jgromacs.analysis.Dynamics
-
Calculates the NxN atomic correlation matrix from a trajectory and a reference frame for superposition
- 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
- 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
- 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
- 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, 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
- 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
- getAtomInResidueOfIndex(int, String, int) - Method in class jgromacs.data.Structure
-
Returns atom #i of the residue of given index and chain ID
- getAtomInResidueOfIndex(int, int) - Method in class jgromacs.data.Structure
-
Returns atom #i of the residue of given index
- 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(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
- getContactMatrix() - Method in class jgromacs.analysis.GNM
-
Returns the contact matrix
- 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, PointList) - Static method in class jgromacs.analysis.Dynamics
-
Calculates the 3Nx3N coordinate correlation matrix from a trajectory and a reference frame for superposition
- 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
- 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
- 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
- getCoordinates() - Method in class jgromacs.data.Atom
-
Returns the coordinates of atom
- getCovarianceMatrixOverlap(Matrix, Matrix, int) - Static method in class jgromacs.analysis.Dynamics
-
Calculates the covariance overlap of two covariance matrices
- getCovarianceMatrixOverlap(Matrix, Matrix) - Static method in class jgromacs.analysis.Dynamics
-
Calculates the covariance overlap of two covariance matrices
- getCovarianceMatrixOverlap(Trajectory, Trajectory, int) - Static method in class jgromacs.analysis.Dynamics
-
Calculates the covariance overlap from two trajectories
- getCovarianceMatrixOverlap(Trajectory, Trajectory) - 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(Trajectory) - Static method in class jgromacs.analysis.Dynamics
-
Calculates the cumulative variance profile from a trajectory
- getCumulativeVariances(Matrix) - Static method in class jgromacs.analysis.Dynamics
-
Calculates the cumulative variance profile from a covariance matrix
- 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, Structure) - Static method in class jgromacs.analysis.Similarity
-
Calculates the atomic difference distance matrix between two structures
- 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
- 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, Structure) - Static method in class jgromacs.analysis.Similarity
-
Calculates dRMSD similarity between two structures
- getDRMSD(Structure, IndexSet, Structure, IndexSet) - Static method in class jgromacs.analysis.Similarity
-
Calculates dRMSD similarity between two groups of atoms
- 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, Structure) - Static method in class jgromacs.analysis.Similarity
-
Calculates the dRMSDi profile between two structures
- getDRMSDiProfile(Structure, IndexSet, Structure, IndexSet) - Static method in class jgromacs.analysis.Similarity
-
Calculates the dRMSDi profile between two groups of atoms
- 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 Br?schweiler, 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, String) - Method in class jgromacs.data.Structure
-
Returns the residue of given index and given chain ID
- getResidueByIndex(int) - Method in class jgromacs.data.Structure
-
Returns the residue of given index
- 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, Structure) - Static method in class jgromacs.analysis.Similarity
-
Calculates RMSD similarity between two structures
- getRMSD(Structure, IndexSet, Structure, IndexSet) - Static method in class jgromacs.analysis.Similarity
-
Calculates RMSD similarity between two groups of atoms
- getRMSDiProfile(PointList, PointList) - Static method in class jgromacs.analysis.Similarity
-
Calculates the RMSDi profile between two point lists
- getRMSDiProfile(Structure, Structure) - Static method in class jgromacs.analysis.Similarity
-
Calculates the RMSDi profile between two structures
- getRMSDiProfile(Structure, IndexSet, Structure, IndexSet) - Static method in class jgromacs.analysis.Similarity
-
Calculates the RMSDi profile between two groups of atoms
- getRMSDiProfileNoSuperposition(PointList, PointList) - Static method in class jgromacs.analysis.Similarity
-
Calculates the RMSDi profile between two point lists without superposition
- getRMSDiProfileNoSuperposition(Structure, Structure) - Static method in class jgromacs.analysis.Similarity
-
Calculates the RMSDi profile between two structures 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
- getRMSDnoSuperposition(PointList, PointList) - Static method in class jgromacs.analysis.Similarity
-
Calculates RMSD similarity between two point lists without doing superposition
- getRMSDnoSuperposition(Structure, Structure) - Static method in class jgromacs.analysis.Similarity
-
Calculates RMSD similarity between two structures 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
- 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, PointList) - Static method in class jgromacs.analysis.Dynamics
-
Calculates the RMSF profile from a trajectory and a reference frame for superposition
- 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, 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, 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, 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(int) - Method in class jgromacs.data.Alignment
-
Returns sequence #i of the alignment
- getSequence() - Method in class jgromacs.data.Structure
-
Returns the amino acid sequence of the structure
- 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, 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
- 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
- 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
- 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
- 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
- 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
- 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(IndexSet) - Method in class jgromacs.data.Trajectory
-
Returns the subtrajectory defined by the given index set
- getSubTrajectory(FrameIndexSet) - Method in class jgromacs.data.Trajectory
-
Returns the subtrajectory defined by the given frame list
- 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, Structure, Matrix) - Static method in class jgromacs.analysis.Similarity
-
Calculates the wdRMSD (weighted dRMSD) similarity of two structures
- getWDRMSD(Structure, IndexSet, Structure, IndexSet, Matrix) - Static method in class jgromacs.analysis.Similarity
-
Calculates wdRMSD (weighted dRMSD) similarity between two groups of atoms
- getWDRMSDiProfile(PointList, PointList, Matrix) - Static method in class jgromacs.analysis.Similarity
-
Calculates the wdRMSDi (weighted dRMSDi) profile between two point lists
- getWDRMSDiProfile(Structure, Structure, Matrix) - Static method in class jgromacs.analysis.Similarity
-
Calculates the wdRMSDi (weighted dRMSDi) profile between two structures
- getWDRMSDiProfile(Structure, IndexSet, Structure, IndexSet, Matrix) - Static method in class jgromacs.analysis.Similarity
-
Calculates the wdRMSDi (weighted dRMSDi) profile between two groups of atoms
- 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