SLIKMC  1.0
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Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
oCBFactorThe class BFactor is used to initialize and store B-factors database, evaluate the probability densities of conformations according to B-factors
oCBinarySearchAn auxiliary class performing binary search in a given sorted vector
oCChiDistributionAn auxiliary class for class Rotamer. This class is a data structure for storing a specific rotamer in one dihedral angle grid
oCCompareProtein_ScoreAn auxiliary class for class LoopTKSampler. This class is used as a comparator to compare two conformations according to their scores
oCDebug
oCLoopTKSamplerLoopTK Configuration Sampling technique. This sampler can be used to sample close-loop chain/subchain conformations
oCMHSamplerThe class MHSample is a sampler based on standard Metropolis-Hastings algorithm. This class can be used to generate free-end conformations
oCPriorInterface for user defined priors
oCProtein_ScoreAn auxiliary class for class LoopTKSampler. This class is a data structure for storing a chain conformation and its score
oCRamachandranPlotThe 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
oCRandomAn auxiliary class. The class is used for generating random values
oCRotamerThe 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
oCRotamerGridAn auxilliary class for class Rotamer. This class is a data structure for storing all rotamers in one dihedral angle grid
oCRotamerGridKeyAn auxilliary class for class Rotamer. This class used as a key to access one RotamerGrid in the map structure
oCRotamerGridKeyComparatorAn auxiliary class for class Rotamer. A Comparator to compare two RotamerGridKeys
oCRotamerGridSpecialAn 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}
oCSamplePrior
oCSidechainRotaterThe class SidechainRotater is used to rotate side-chain conformations for a given chain and evaluate a given chain according to its side-chain structure
oCSLIKMCSamplerSub-Loop Inverse Kinematic Markov Chain (SLIKMC) sampler. Support chain/subchain close-loop sampling, free-end sampling. Side-chain sampling is also supported
oCString
oCStringTokenizerAn auxiliary class. The class StringTokenzier is a java style utility class for retrieving tokens separated by delims
\CUtilityAn auxiliary class containing vector and matrix operations