A C D E F G H I J L M P R S T U W

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

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 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

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