- c -

• calcPropPercent() : LoopExtractor
• calcStatistics() : RankAnalyzer
• calculateAaComposition() : EnergyFeatures
• calculateBackboneHydrogenBonds() : EnergyFeatures
• calculateChainBreaks() : EnergyFeatures
• calculateClashes() : EnergyFeatures
• calculateDeviation() : LoopTableEntry
• calculateEnergy() : EffectiveSolvationPotential , PhiPsi , PhiPsiOmega , PhiPsiOmegaChi1 , PhiPsiOmegaChi1Chi2 , PhiPsiOmegaChi1Chi2PreAngle , PhiPsiOmegaChi1PreAngle , PhiPsiOmegaPreAngle , PhiPsiPreAngle , PolarSolvationPotential , RapdfPotential , SolvationPotential
• calculateEnergySmooth() : PhiPsi
• calculateFeatures() : EnergyFeatures
• calculateIdentity() : AlignmentBase
• calculateMatch() : AlignmentData , SecSequenceData , SequenceData
• calculateMaxEnergy() : TorsionPotential
• calculateMinEnergy() : TorsionPotential
• calculatePairwiseIdentity() : AlignmentBase
• calculateRot() : IntCoordConverter
• calculateSecondaryComposition() : EnergyFeatures
• calculateSolvation() : PolarSolvationPotential , SolvationPotential
• calculateTrans() : IntCoordConverter
• calcVdwPercent() : LoopExtractor
• checkAndSetChain() : PdbLoader
• checkModel() : PdbLoader
• checkSequence() : ScoringScheme
• clear() : AlignmentData , VectorTransformation
• clearAlignment() : Alignment , AlignmentBase
• clearTemplate() : Alignment , AlignmentBase
• clone() : AminoAcid , LigandSet , Nucleotide , Polymer , Protein , Spacer
• cluster() : LoopTable , RamachandranData
• code() : LoopTable
• collides() : Component
• compare() : Traceback
• concatenate() : LoopTable , LoopTableEntry
• connectIn() : AminoAcid
• connectOut() : AminoAcid
• constructSideChain() : AminoAcid
• copy() : AGPFunction , Align , Alignment , AlignmentBase , AlignmentData , AtchleyCorrelation , AtchleyDistance , CrossProduct , DotPFreq , DotPOdds , EDistance , FSAlign , GapFunction , HenikoffProfile , JensenShannon , LogAverage , NWAlign , NWAlignNoTermGaps , Panchenko , Pearson , Prof , Profile , ProfInput , PSICProfile , PssmInput , ScoringFunction , ScoringP2P , ScoringP2S , ScoringS2S , ScoringScheme , Sec , SecSequenceData , SeqDivergenceProfile , SequenceData , Ss2 , Ss2Input , Structure , SubMatrix , Substitution , SWAlign , Threading , ThreadingInput , ThreadingProf , ThreadingSs2 , Traceback , VGPFunction2 , VGPFunction , Zhou , AminoAcid , Atom , Bond , Component , Group , Ligand , Nucleotide , Polymer , SimpleBond , Spacer , LoopTable , LoopTableEntry , RamachandranData , RankAnalyzer , ranking_helper2 , ranking_helper , VectorTransformation
• CrossProduct() : CrossProduct
• cutTemplate() : Alignment , AlignmentBase