Here are the classes, structs, unions and interfaces with brief descriptions:

BFactor	The class BFactor is used to initialize and store B-factors database, evaluate the probability densities of conformations according to B-factors
BinarySearch	An auxiliary class performing binary search in a given sorted vector
ChiDistribution	An auxiliary class for class Rotamer. This class is a data structure for storing a specific rotamer in one dihedral angle grid
CompareProtein_Score	An auxiliary class for class LoopTKSampler. This class is used as a comparator to compare two conformations according to their scores
Debug
LoopTKSampler	LoopTK Configuration Sampling technique. This sampler can be used to sample close-loop chain/subchain conformations
MHSampler	The class MHSample is a sampler based on standard Metropolis-Hastings algorithm. This class can be used to generate free-end conformations
Prior	Interface for user defined priors
Protein_Score	An auxiliary class for class LoopTKSampler. This class is a data structure for storing a chain conformation and its score
RamachandranPlot	The class RamachandranPlot is used to initialize and store database for Ramachandran plot, sample backbone dihedral angles according to residue type and evaluate the probability of one conformation according to backbone structure
Random	An auxiliary class. The class is used for generating random values
Rotamer	The class Rotamer is used to initialize side-chain database by parsing Dunbrack's Backbone Dependent Rotamer Library, sample one side-chain conformation for a given residue, evaluate the probability given one side-chain conformation
RotamerGrid	An auxilliary class for class Rotamer. This class is a data structure for storing all rotamers in one dihedral angle grid
RotamerGridKey	An auxilliary class for class Rotamer. This class used as a key to access one RotamerGrid in the map structure
RotamerGridKeyComparator	An auxiliary class for class Rotamer. A Comparator to compare two RotamerGridKeys
RotamerGridSpecial	An auxilliary class for class Rotamer. This class extends RotamerGrid and it adds additional structures for storing non-rotameric residues {ASN, ASP, PHE, TRP, HIS, TYR, GLN, GLU}
SamplePrior
SidechainRotater	The class SidechainRotater is used to rotate side-chain conformations for a given chain and evaluate a given chain according to its side-chain structure
SLIKMCSampler	Sub-Loop Inverse Kinematic Markov Chain (SLIKMC) sampler. Support chain/subchain close-loop sampling, free-end sampling. Side-chain sampling is also supported
String
StringTokenizer	An auxiliary class. The class StringTokenzier is a java style utility class for retrieving tokens separated by delims
Utility	An auxiliary class containing vector and matrix operations