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| Packages that use IndexSet | |
|---|---|
| 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 IndexSet in jgromacs.analysis |
|---|
| Methods in jgromacs.analysis that return IndexSet | |
|---|---|
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 |
| Methods in jgromacs.analysis with parameters of type IndexSet | |
|---|---|
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,
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,
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 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 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 java.util.ArrayList<java.lang.Double> |
Distances.getDistanceTimeSeries(Trajectory t,
IndexSet indices1,
IndexSet indices2)
Returns the time series of the distance of two sets of atoms in a trajectory |
static java.util.ArrayList<java.lang.Double> |
Distances.getDistanceTimeSeries(Trajectory t,
int atomindex,
IndexSet referenceset)
Returns the time series of the distance of a single atom and a set of atoms in a trajectory |
static double |
Similarity.getDRMSD(Structure A,
IndexSet indicesA,
Structure B,
IndexSet indicesB)
Calculates dRMSD similarity between two groups of atoms |
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 jama.Matrix |
Dynamics.getFluctuationMatrix(Trajectory t,
IndexSet indices)
Calculates the F fluctuation matrix (variances of distances) for a group of atoms |
static double |
Dynamics.getFluctuationOfSubsets(Trajectory t,
IndexSet set1,
IndexSet set2)
Calculates the fluctuation between two subsets of atoms defined as the mean of entries of the selected submatrix of matrix F (fluctuation matrix) |
static jama.Matrix |
Distances.getMeanAtomicDistanceMatrix(Trajectory t,
IndexSet indices)
Calculates the mean distance matrix of atoms of given indices in a trajectory |
static double |
Similarity.getRMSD(Structure A,
IndexSet indicesA,
Structure B,
IndexSet indicesB)
Calculates RMSD similarity between two groups of atoms |
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.getRMSDiProfileNoSuperposition(Structure A,
IndexSet indicesA,
Structure B,
IndexSet indicesB)
Calculates the RMSDi profile between two groups of atoms 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 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 jama.Matrix |
Similarity.getSimilarityMatrixDRMSD(Trajectory t,
IndexSet indices)
Calculates the similarity matrix of all frames in a trajectory using the dRMSD measure taking into account only a subset of atoms |
static jama.Matrix |
Similarity.getSimilarityMatrixRMSD(Trajectory t,
IndexSet indices)
Calculates the similarity matrix of all frames in a trajectory using the RMSD measure taking into account only a subset of atoms |
static jama.Matrix |
Similarity.getSimilarityMatrixWDRMSD(Trajectory t,
IndexSet indices,
jama.Matrix W)
Calculates the similarity matrix of all frames in a trajectory using the wdRMSD (weighted dRMSD) measure taking into account only a subset of atoms |
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.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.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 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 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 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 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 |
| Uses of IndexSet in jgromacs.data |
|---|
| Methods in jgromacs.data that return IndexSet | |
|---|---|
IndexSet |
IndexSetList.fuseIntoOneIndexSet()
Returns the union of all index sets as a single index set |
IndexSet |
Structure.getAlphaCarbonIndexSet()
Returns the index set of alpha carbon atoms |
IndexSet |
Residue.getAtomIndices()
Returns the index set of all atoms |
IndexSet |
Residue.getBackBoneAtomIndices()
Returns the index set of backbone atoms |
IndexSet |
Structure.getBackboneIndexSet()
Returns the index set of backbone atoms |
IndexSet |
Residue.getHeavyAtomIndices()
Returns the index set of heavy atoms |
IndexSet |
Structure.getHeavyProteinIndexSet()
Returns the index set of protein atoms except of hydrogen atoms |
IndexSet |
Residue.getHydrogenAtomIndices()
Returns the index set of hydrogen atoms |
IndexSet |
IndexSetList.getIndexSet(int i)
Returns the index set of given index |
IndexSet |
IndexSetList.getIndexSet(java.lang.String name)
Returns the index set of given name |
IndexSet |
Structure.getIndexSetOfChainID(java.lang.String chainID)
Returns the index set of atoms of a given chain ID |
IndexSet |
Residue.getMainChainAtomIndices()
Returns the index set of main chain atoms |
IndexSet |
Structure.getMainChainIndexSet()
Returns the index set of main chain atoms |
IndexSet |
Residue.getMainChainPlusCbAtomIndices()
Returns the index set of main chain atoms and beta carbon atom |
IndexSet |
Structure.getMainChainPlusCbIndexSet()
Returns the index set of main chain plus beta carbon atoms |
IndexSet |
Residue.getMainChainPlusHAtomIndices()
Returns the index set of main chain atoms and hydrogen atoms |
IndexSet |
Structure.getMainChainPlusHIndexSet()
Returns the index set of main chain plus hydrogen atoms |
IndexSet |
Alignment.getMatchPositionIndices(int i)
Returns the set of position indices in sequence #i that are included in the match columns of alignment |
IndexSet |
Structure.getNonProteinIndexSet()
Returns the index set of non-protein atoms |
IndexSet |
Structure.getProteinIndexSet()
Returns the index set of protein atoms |
IndexSet |
Residue.getSideChainAtomIndices()
Returns the index set of side chain atoms |
IndexSet |
Structure.getSideChainIndexSet()
Returns the index set of side chain atoms |
IndexSet |
Residue.getSideChainMinusHAtomIndices()
Returns the index set of side chain atoms except of hydrogen atoms |
IndexSet |
Structure.getSideChainMinusHIndexSet()
Returns the index set of side chain atoms except of hydrogen atoms |
IndexSet |
Structure.getSystemIndexSet()
Returns the index set of all atoms in the system |
IndexSet |
Structure.getWaterIndexSet()
Returns the index set of water atoms |
IndexSet |
IndexSet.intersect(IndexSet other)
Returns the intersection of this index set and another |
IndexSet |
Structure.mapResidueIndicesToAtomIndices(java.util.ArrayList<java.lang.Integer> indices)
Maps residue indices to atomic indices (i.e. |
IndexSet |
IndexSet.subtract(IndexSet other)
Returns the subtraction of another index set from this index set |
IndexSet |
IndexSet.union(IndexSet other)
Returns the union of this index set and another |
| Methods in jgromacs.data that return types with arguments of type IndexSet | |
|---|---|
java.util.ArrayList<IndexSet> |
IndexSetList.getAsAnArrayList()
Returns index set list as an ArrayList object |
| Methods in jgromacs.data with parameters of type IndexSet | |
|---|---|
void |
IndexSetList.addIndexSet(IndexSet set)
Adds a new index set to the list |
void |
IndexSetList.addIndexSet(IndexSet set,
java.lang.String name)
Adds a new index set of given name to the list |
java.util.ArrayList<java.lang.Integer> |
Structure.convertIndicesToArrayListIndices(IndexSet indices)
Converts atomic indices into list indices |
Structure |
Structure.getSubStructure(IndexSet indices)
Returns the substructure defined by the given index set |
Trajectory |
Trajectory.getSubTrajectory(IndexSet indices)
Returns the subtrajectory defined by the given index set |
IndexSet |
IndexSet.intersect(IndexSet other)
Returns the intersection of this index set and another |
java.util.ArrayList<java.lang.Integer> |
Structure.mapAtomIndicesToResidueIndices(IndexSet indices)
Maps atomic indices to residue indices (i.e. |
void |
IndexSetList.removeIndexSet(IndexSet set)
Removes the given index set from the list |
void |
IndexSetList.setIndexSet(int i,
IndexSet set)
Replaces index set of given index with a new index set |
IndexSet |
IndexSet.subtract(IndexSet other)
Returns the subtraction of another index set from this index set |
IndexSet |
IndexSet.union(IndexSet other)
Returns the union of this index set and another |
| Constructors in jgromacs.data with parameters of type IndexSet | |
|---|---|
IndexSet(IndexSet set)
Constructs a new IndexSet object identical to a given IndexSet |
|
| Uses of IndexSet in jgromacs.io |
|---|
| Methods in jgromacs.io that return IndexSet | |
|---|---|
static IndexSet |
IOData.readIndexSetFromNDX(java.lang.String filename)
Reads an index set from the given NDX file |
| Methods in jgromacs.io with parameters of type IndexSet | |
|---|---|
static void |
IOData.writeIndexSetToNDX(java.lang.String filename,
IndexSet set)
Writes an index set to the given NDX file |
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