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EliminatedRotamers(RotamerOptimization rO,
DistanceMatrix dM,
List<Residue> allResiduesList,
int maxRotCheckDepth,
double clashThreshold,
double pairClashThreshold,
double multiResClashThreshold,
double nucleicPruningFactor,
double nucleicPairsPruningFactor,
double multiResPairClashAddn,
boolean pruneClashes,
boolean prunePairClashes,
boolean print,
Residue[] residues)
EnergyExpansion(RotamerOptimization rO,
DistanceMatrix dM,
EliminatedRotamers eR,
MolecularAssembly molecularAssembly,
Potential potential,
AlgorithmListener algorithmListener,
List<Residue> allResiduesList,
int[][] resNeighbors,
boolean threeBodyTerm,
boolean decomposeOriginal,
boolean usingBoxOptimization,
boolean verbose,
boolean pruneClashes,
boolean prunePairClashes,
boolean master)
ThreeBodyEnergyRegion(RotamerOptimization rotamerOptimization,
DistanceMatrix dM,
EnergyExpansion eE,
EliminatedRotamers eR,
Residue[] residues,
List<Residue> allResiduesList,
BufferedWriter energyWriter,
Comm world,
int numProc,
double superpositionThreshold,
boolean master,
int rank,
boolean verbose,
boolean writeEnergyRestart,
boolean printFiles)
TwoBodyEnergyRegion(RotamerOptimization rotamerOptimization,
DistanceMatrix dM,
EnergyExpansion eE,
EliminatedRotamers eR,
Residue[] residues,
List<Residue> allResiduesList,
BufferedWriter energyWriter,
Comm world,
int numProc,
boolean prunePairClashes,
double superpositionThreshold,
boolean master,
int rank,
boolean verbose,
boolean writeEnergyRestart,
boolean printFiles)