# All Classes and Interfaces

Classes
Class
Description
Alignment
Objects of this class represent a sequence alignment
Angle
Objects of this class represent an angle
Angles
Collection of methods for analysing angles
Application
Parent class of JGromacs applications.
Atom
Objects of this class represent a single atom
AtomType
Objects of this class represent an atom type
Distances
Collection of methods for analysing distances
Dynamics
Collection of methods for analysing molecular motions
FrameIndexSet
Objects of this class represent a single frame index set
GNM
Objects of this class represent a Gaussian Network Model (GNM) of a protein
IndexSet
Objects of this class represent a single index set
IndexSetList
Objects of this class represent a list of index sets
IOData
This class contains static methods for IO of data objects
IOMath
This class contains static methods for IO of ArrayList and Matrix objects
Point3D
Objects of this class represent a single 3D point
PointList
Objects of this class represent a list of 3D points
Residue
Objects of this class represent a single residue
ResidueType
Objects of this class represent a residue type
Sequence
Objects of this class represent a single amino acid sequence
SequencePosition
Objects of this class represent a single sequence position
Similarity
Collection of methods for measuring structural similarity
Structure
Objects of this class represent a single structure
Superposition
Collection of methods for superposing structures
TemplateApplication
Template JGromacs application
Trajectory
Objects of this class represent a single trajectory