## Uses of Classjgromacs.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