Uses of Class
jgromacs.data.Structure

Packages that use Structure

jgromacs.analysis	jgromacs.analysis is a collection of classes providing static methods for various analysis tasks
jgromacs.data	jgromacs.data is a collection of classes representing multiple levels of structural data
jgromacs.io	jgromacs.io provides parsers for reading and methods for writing GROMACS files

Uses of Structure in jgromacs.analysis

Methods in jgromacs.analysis that return Structure

static Structure	Superposition.superposeTo(Structure toBeSuperposed, IndexSet indices1, Structure reference, IndexSet indices2) Calculates the superposition of a structure to another using a subset of atoms for fitting
static Structure	Superposition.superposeTo(Structure toBeSuperposed, Structure reference) Calculates the superposition of a structure to another
static Structure	Superposition.weightedSuperposeTo(Structure toBeSuperposed, Structure reference, java.util.ArrayList<java.lang.Double> weights) Calculates the weighted superposition of a structure to another

Methods in jgromacs.analysis with parameters of type Structure

static Atom	Distances.findClosestAtom(Structure s, IndexSet atomset, IndexSet referenceset) Returns the atom from a given atom set that is closest to a reference set of atoms
static jama.Matrix	Distances.getAtomicDistanceMatrix(Structure s) Calculates the distance matrix of all atoms in a structure
static jama.Matrix	Distances.getAtomicDistanceMatrix(Structure s, IndexSet indices) Calculates the distance matrix of atoms of given indices in a structure
static jama.Matrix	Distances.getAtomicDistanceMatrix(Structure s, IndexSet indices1, IndexSet indices2) Calculates the distance matrix between two sets of atoms
static IndexSet	Distances.getAtomIndicesInRadius(Structure s, Atom atom, double radius) Returns the index set of atoms in a structure that are closer to a reference atom than a given radius
static IndexSet	Distances.getAtomIndicesInRadius(Structure s, IndexSet referenceindices, double radius) Returns the index set of atoms in a structure that are closer to a reference set of atoms than a given radius
static IndexSet	Distances.getAtomIndicesInRadius(Structure s, IndexSet atomIndices, IndexSet referenceIndices, double radius) Returns the index set of atoms from a set of atoms that are closer to a reference set than a given radius
static IndexSet	Distances.getAtomIndicesInRadius(Structure s, Point3D point, double radius) Returns the index set of atoms in a structure that are closer to a reference point than a given radius
static jama.Matrix	Distances.getContactMatrix(Structure s, int distanceBetween, double cutoff) Calculates the contact matrix of residues in a structure by the given method
static jama.Matrix	Similarity.getDifferenceDistanceMatrix(Structure s1, IndexSet indices1, Structure s2, IndexSet indices2) Calculates the atomic difference distance matrix between two sets of atoms defined by two index sets in two structures
static jama.Matrix	Similarity.getDifferenceDistanceMatrix(Structure s1, Structure s2) Calculates the atomic difference distance matrix between two structures
static Angle	Angles.getDihedralChi1(Structure s, int i) 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
static Angle	Angles.getDihedralChi2(Structure s, int i) 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
static Angle	Angles.getDihedralChi3(Structure s, int i) Calculates side chain dihedral angle Chi3 of residue #i of a structure The residue can only be ARG,GLN,GLU,LYS or MET
static Angle	Angles.getDihedralChi4(Structure s, int i) Calculates side chain dihedral angle Chi4 of residue #i of a structure The residue can only be ARG or LYS
static Angle	Angles.getDihedralChi5(Structure s, int i) Calculates side chain dihedral angle Chi5 of residue #i of a structure The residue can only be ARG
static Angle	Angles.getDihedralOmega(Structure s, int i) Calculates dihedral angle Omega of residue #i of a structure
static Angle	Angles.getDihedralPhi(Structure s, int i) Calculates dihedral angle Phi of residue #i of a structure
static Angle	Angles.getDihedralPsi(Structure s, int i) Calculates dihedral angle Psi of residue #i of a structure
static double	Distances.getDistanceOfAtomToAtomSet(Structure s, int atomindex, IndexSet referenceset) Calculates the distance of an atom to a reference set of atoms (i.e.
static double	Distances.getDistanceOfTwoAtomSets(Structure s, IndexSet indices1, IndexSet indices2) Calculates the distance between two sets of atoms (i.e.
static double	Similarity.getDRMSD(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB) Calculates dRMSD similarity between two groups of atoms
static double	Similarity.getDRMSD(Structure A, Structure B) Calculates dRMSD similarity between two structures
static java.util.ArrayList<java.lang.Double>	Similarity.getDRMSDiProfile(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB) Calculates the dRMSDi profile between two groups of atoms
static java.util.ArrayList<java.lang.Double>	Similarity.getDRMSDiProfile(Structure A, Structure B) Calculates the dRMSDi profile between two structures
static jama.Matrix	Angles.getRamachandranPlot(Structure s) Calculates the Ramachandran Plot of a structure
static jama.Matrix	Distances.getResidueDistanceMatrix(Structure s, int distanceBetween) Calculates the distance matrix of residues in a structure by the given method
static double	Similarity.getRMSD(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB) Calculates RMSD similarity between two groups of atoms
static double	Similarity.getRMSD(Structure A, Structure B) Calculates RMSD similarity between two structures
static java.util.ArrayList<java.lang.Double>	Similarity.getRMSDiProfile(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB) Calculates the RMSDi profile between two groups of atoms
static java.util.ArrayList<java.lang.Double>	Similarity.getRMSDiProfile(Structure A, Structure B) Calculates the RMSDi profile between two structures
static java.util.ArrayList<java.lang.Double>	Similarity.getRMSDiProfileNoSuperposition(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB) Calculates the RMSDi profile between two groups of atoms without superposition
static java.util.ArrayList<java.lang.Double>	Similarity.getRMSDiProfileNoSuperposition(Structure A, Structure B) Calculates the RMSDi profile between two structures without superposition
static double	Similarity.getRMSDnoSuperposition(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB) Calculates RMSD similarity between two groups of atoms without superposition
static double	Similarity.getRMSDnoSuperposition(Structure A, Structure B) Calculates RMSD similarity between two structures without doing superposition
static java.util.ArrayList<java.lang.Double>	Dynamics.getRMSFaroundTheMeanProfile(Trajectory t, Structure R) 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
static java.util.ArrayList<java.lang.Double>	Dynamics.getRMSFprofile(Trajectory t, IndexSet indicesT, Structure R, IndexSet indicesR) Calculates the RMSF profile of a group of atoms from a trajectory and a reference frame for superposition
static java.util.ArrayList<java.lang.Double>	Dynamics.getRMSFprofile(Trajectory t, Structure R) Calculates the RMSF profile from a trajectory and a reference frame for superposition
static java.util.ArrayList<java.lang.Double>	Dynamics.getRMSFprofile(Trajectory t, Structure R, Structure Q) 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
static java.util.ArrayList<java.lang.Double>	Similarity.getSimilarityTimeSeriesDRMSD(Trajectory t, IndexSet indicesT, Structure R, IndexSet indicesR) Returns the time series of dRMSD in a trajectory with regards to a reference structure taking into account only a subset of atoms
static java.util.ArrayList<java.lang.Double>	Similarity.getSimilarityTimeSeriesDRMSD(Trajectory t, Structure R) Returns the time series of dRMSD in a trajectory with regards to a reference structure
static java.util.ArrayList<java.lang.Double>	Similarity.getSimilarityTimeSeriesRMSD(Trajectory t, IndexSet indicesT, Structure R, IndexSet indicesR) Returns the time series of RMSD in a trajectory with regards to a reference structure taking into account only a subset of atoms
static java.util.ArrayList<java.lang.Double>	Similarity.getSimilarityTimeSeriesRMSD(Trajectory t, Structure R) Returns the time series of RMSD in a trajectory with regards to a reference structure
static java.util.ArrayList<java.lang.Double>	Similarity.getSimilarityTimeSeriesWDRMSD(Trajectory t, IndexSet indicesT, Structure R, IndexSet indicesR, jama.Matrix W) 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
static java.util.ArrayList<java.lang.Double>	Similarity.getSimilarityTimeSeriesWDRMSD(Trajectory t, Structure R, jama.Matrix W) Returns the time series of wdRMSD (weighted dRMSD) in a trajectory with regards to a reference structure
static double	Similarity.getWDRMSD(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB, jama.Matrix W) Calculates wdRMSD (weighted dRMSD) similarity between two groups of atoms
static double	Similarity.getWDRMSD(Structure A, Structure B, jama.Matrix W) Calculates the wdRMSD (weighted dRMSD) similarity of two structures
static java.util.ArrayList<java.lang.Double>	Similarity.getWDRMSDiProfile(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB, jama.Matrix W) Calculates the wdRMSDi (weighted dRMSDi) profile between two groups of atoms
static java.util.ArrayList<java.lang.Double>	Similarity.getWDRMSDiProfile(Structure A, Structure B, jama.Matrix W) Calculates the wdRMSDi (weighted dRMSDi) profile between two structures
static Structure	Superposition.superposeTo(Structure toBeSuperposed, IndexSet indices1, Structure reference, IndexSet indices2) Calculates the superposition of a structure to another using a subset of atoms for fitting
static Structure	Superposition.superposeTo(Structure toBeSuperposed, Structure reference) Calculates the superposition of a structure to another
static Trajectory	Superposition.superposeTo(Trajectory t, Structure reference) Calculates the superposition of each frame of a trajectory to a common reference frame
static Trajectory	Superposition.superposeTo(Trajectory t, Structure reference, IndexSet indices) Calculates the superposition of each frame of a trajectory to a common reference frame using a subset of atoms for fitting
static Structure	Superposition.weightedSuperposeTo(Structure toBeSuperposed, Structure reference, java.util.ArrayList<java.lang.Double> weights) Calculates the weighted superposition of a structure to another
static Trajectory	Superposition.weightedSuperposeTo(Trajectory t, Structure reference, java.util.ArrayList<java.lang.Double> weights) Calculates the weighted superposition of each frame of a trajectory to a common reference frame

Constructors in jgromacs.analysis with parameters of type Structure

GNM(Structure s, double cutoff, int distanceBetween)
Constructs a new Gaussian Network Model

Uses of Structure in jgromacs.data

Methods in jgromacs.data that return Structure

Structure[]	Structure.getChains() Returns all chains in an array of Structure objects
Structure	Trajectory.getFirstFrameAsStructure() Returns the initial frame of trajectory as a Structure
Structure	Trajectory.getFrameAsStructure(int i) Returns frame #i of the trajectory as a Structure object
Structure	Trajectory.getLastFrameAsStructure() Returns the last frame of trajectory as a Structure
Structure	Structure.getSubStructure(IndexSet indices) Returns the substructure defined by the given index set

Methods in jgromacs.data with parameters of type Structure

void	Trajectory.setStructure(Structure structure) Sets the structure described by the trajectory

Constructors in jgromacs.data with parameters of type Structure

Trajectory(Structure structure)
Constructs a new Trajectory object of given structure

Trajectory(Structure[] ensemble)
Constructs a new Trajectory object made from an ensemble of structures

Uses of Structure in jgromacs.io

Methods in jgromacs.io that return Structure

static Structure	IOData.readStructureFromGRO(java.lang.String filename) Reads structure from the given GRO file
static Structure	IOData.readStructureFromPDB(java.lang.String filename) Reads structure from the given PDB file
static Structure	IOData.readStructureFromPDB(java.lang.String filename, int model) Reads the given model from the given PDB file
static Structure[]	IOData.readStructuresFromPDB(java.lang.String filename) Reads an ensemble of structures from the given PDB file
static Structure[]	IOData.readStructuresFromPDBsInDirectory(java.lang.String path) Reads an ensemble of structures from PDB files in the given directory

Methods in jgromacs.io with parameters of type Structure

static Trajectory	IOData.readDumpedTrajectory(Structure structure, java.lang.String filename) Reads a trajectory from the given dumped XTC or TRR file
static Trajectory	IOData.readTrajectory(Structure structure, java.lang.String filename) Reads a trajectory from the given XTC or TRR file
static void	IOData.writeStructureToGRO(java.lang.String filename, Structure structure) Writes a structure to the given GRO file
static void	IOData.writeStructureToPDB(java.lang.String filename, Structure structure) Writes a structure to the given PDB file