All Classes

Class Summary

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