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

F

findClosestAtom(Structure, IndexSet, IndexSet) - Static method in class jgromacs.analysis.Distances

Returns the atom from a given atom set that is closest to a reference set of atoms

findFrameWhereClosest(Trajectory, int, int) - Static method in class jgromacs.analysis.Distances

Returns the frame in which two atoms are closest to each other in a simulation

findFrameWhereMostDistant(Trajectory, int, int) - Static method in class jgromacs.analysis.Distances

Returns the frame in which two atoms are most distant from each other in a simulation

findSimilarFramesDRMSD(Trajectory, PointList, double) - Static method in class jgromacs.analysis.Similarity

Returns the list of frames in a trajectory that are more similar to a reference frame (based on the dRMSD similarity measure) than a cutoff value

findSimilarFramesDRMSD(Trajectory, Matrix, double) - Static method in class jgromacs.analysis.Similarity

Returns the list of frames in a trajectory that are more similar to a reference distance matrix (based on the dRMSD similarity measure) than a cutoff value

findSimilarFramesRMSD(Trajectory, PointList, double) - Static method in class jgromacs.analysis.Similarity

Returns the set of frames in a trajectory that are more similar to a reference frame (based on the RMSD similarity measure) than a cutoff value

FrameIndexSet - Class in jgromacs.data

Objects of this class represent a single frame index set

FrameIndexSet() - Constructor for class jgromacs.data.FrameIndexSet

Constructs a new FrameIndexSet object

FrameIndexSet(String) - Constructor for class jgromacs.data.FrameIndexSet

Constructs a new FrameIndexSet object of a given name

FrameIndexSet(ArrayList<Integer>) - Constructor for class jgromacs.data.FrameIndexSet

Constructs a new FrameIndexSet object and loads data from an ArrayList

FrameIndexSet(ArrayList<Integer>, String) - Constructor for class jgromacs.data.FrameIndexSet

Constructs a new FrameIndexSet object of a given name and loads data from an ArrayList

FrameIndexSet(TreeSet<Integer>) - Constructor for class jgromacs.data.FrameIndexSet

Constructs a new FrameIndexSet object and loads data from a TreeSet

FrameIndexSet(TreeSet<Integer>, String) - Constructor for class jgromacs.data.FrameIndexSet

Constructs a new FrameIndexSet object of a given name and loads data from a TreeSet

FrameIndexSet(FrameIndexSet) - Constructor for class jgromacs.data.FrameIndexSet

Constructs a new FrameIndexSet object identical to a given FrameIndexSet

fuseIntoOneIndexSet() - Method in class jgromacs.data.IndexSetList

Returns the union of all index sets as a single index set