Here is a list of all documented class members with links to the class documentation for each member:

- a -

• addCustomPrior() : SLIKMCSampler

- b -

• BFactor() : BFactor

- c -

• construct() : RamachandranPlot

- d -

• disableBFactors() : LoopTKSampler
• disableBfactors() : MHSampler , SLIKMCSampler
• disableCollisionChecking() : SLIKMCSampler
• disableCustomPriors() : SLIKMCSampler
• disableFreeEnd() : SLIKMCSampler
• disableLog() : SLIKMCSampler
• disableRamachandran() : SLIKMCSampler
• disableSidechain() : SLIKMCSampler
• dispSettings() : SLIKMCSampler

- e -

• enableBFactors() : LoopTKSampler
• enableBfactors() : MHSampler , SLIKMCSampler
• enableCollisionChecking() : SLIKMCSampler
• enableCustomPriors() : SLIKMCSampler
• enableFreeEnd() : SLIKMCSampler
• enableLog() : SLIKMCSampler
• enableRamachandran() : SLIKMCSampler
• enableSidechain() : SLIKMCSampler
• evalAtomPositions() : BFactor
• evalSidechain() : SidechainRotater
• evalSidechain_log() : Rotamer
• evaluate() : Prior , SamplePrior
• evaluate_log() : LoopTKSampler

- g -

• getAllTokens() : StringTokenizer
• getMetricTensor_log() : SLIKMCSampler
• getP_log() : SLIKMCSampler , MHSampler
• getProbDensity_log() : BFactor
• getQ_log() : SLIKMCSampler
• getRandomDihedralAngle() : RamachandranPlot
• getResidueAngleProbability() : RamachandranPlot
• getSidechainAngles() : SidechainRotater

- h -

• hasMoreTokens() : StringTokenizer

- i -

• initSidechainDatabase() : Rotamer
• isSpecial() : Rotamer

- l -

• LoopTKSampler() : LoopTKSampler

- m -

• matrix_multiply_trash() : Utility
• MAX_COLLISION_DETECT : SLIKMCSampler
• MAX_IK_SAMPLE : SLIKMCSampler
• MAX_METROPOLIS_REJECT : SLIKMCSampler
• MHSampler() : MHSampler
• MHStep() : MHSampler , SLIKMCSampler

- n -

• nextDouble() : Random
• nextInt() : Random
• nextNormal() : Random
• nextToken() : StringTokenizer

- o -

• operator==() : RotamerGridKey
• output() : Rotamer , BFactor

- p -

• perturb() : LoopTKSampler
• print() : RotamerGridKey
• protein : SLIKMCSampler

- r -

• RamachandranPlot() : RamachandranPlot
• read() : Rotamer
• read_common() : Rotamer
• read_special() : Rotamer
• Rotamer() : Rotamer
• RotamerGridKey() : RotamerGridKey
• rotateSidechain() : SidechainRotater

- s -

• sample() : LoopTKSampler , MHSampler , SLIKMCSampler , Rotamer
• sample_common() : Rotamer
• sample_Special() : Rotamer
• search() : BinarySearch
• SidechainRotater() : SidechainRotater
• SLIKMCSampler() : SLIKMCSampler
• StringTokenizer() : StringTokenizer
• subchains : SLIKMCSampler

- t -

• toString() : RotamerGridKey
• type() : Rotamer

- ~ -

• ~LoopTKSampler() : LoopTKSampler
• ~MHSampler() : MHSampler
• ~RamachandranPlot() : RamachandranPlot
• ~SidechainRotater() : SidechainRotater
• ~SLIKMCSampler() : SLIKMCSampler