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rna Directory Reference
Directory dependency graph for rna:
src/core/scoring/rna

Directories

directory  chemical_shift
 

Files

file  Gaussian_parameter.hh
 very simple class that records amplitude, center, and width of a Gaussian
 
file  RG_Energy_RNA.cc
 
file  RG_Energy_RNA.hh
 
file  RG_Energy_RNACreator.hh
 Declaration for the class that connects RG_Energy_RNA with the ScoringManager.
 
file  RNA_AtomVDW.cc
 
file  RNA_AtomVDW.fwd.hh
 
file  RNA_AtomVDW.hh
 Information on which atoms to use for computing clashes.
 
file  RNA_BaseBaseEnergy.cc
 Statistically derived rotamer pair potential class implementation.
 
file  RNA_BaseBaseEnergy.fwd.hh
 
file  RNA_BaseBaseEnergy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  RNA_BaseDoubletClasses.hh
 
file  RNA_BulgeEnergy.cc
 
file  RNA_BulgeEnergy.fwd.hh
 
file  RNA_BulgeEnergy.hh
 Score function class.
 
file  RNA_BulgeEnergyCreator.hh
 
file  RNA_CentroidInfo.cc
 
file  RNA_CentroidInfo.fwd.hh
 
file  RNA_CentroidInfo.hh
 
file  RNA_DataBackboneEnergy.cc
 Statistically derived rotamer pair potential class implementation.
 
file  RNA_DataBackboneEnergy.fwd.hh
 
file  RNA_DataBackboneEnergy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  RNA_DataBackboneEnergyCreator.hh
 Declaration for the class that connects RNA_DataBackboneEnergy with the ScoringManager.
 
file  RNA_DataInfo.cc
 
file  RNA_DataInfo.fwd.hh
 
file  RNA_DataInfo.hh
 
file  RNA_FA_Stack.hh
 
file  RNA_FilteredBaseBaseInfo.cc
 
file  RNA_FilteredBaseBaseInfo.fwd.hh
 
file  RNA_FilteredBaseBaseInfo.hh
 
file  RNA_FittedTorsionInfo.cc
 Statistically derived torsion information for RNA.
 
file  RNA_FittedTorsionInfo.hh
 Statistically derived torsion information for RNA.
 
file  RNA_FullAtomStackingEnergy.cc
 
file  RNA_FullAtomStackingEnergy.fwd.hh
 
file  RNA_FullAtomStackingEnergy.hh
 
file  RNA_FullAtomStackingEnergyCreator.hh
 Declaration for the class that connects RNA_FullAtomStackingEnergy with the ScoringManager.
 
file  RNA_FullAtomVDW_BasePhosphate.cc
 
file  RNA_FullAtomVDW_BasePhosphate.fwd.hh
 
file  RNA_FullAtomVDW_BasePhosphate.hh
 FullAtom VDW energy between the base and phosphate group in the same (intra) nucleotide.
 
file  RNA_FullAtomVDW_BasePhosphateCreator.fwd.hh
 
file  RNA_FullAtomVDW_BasePhosphateCreator.hh
 
file  RNA_LJ_BaseEnergy.cc
 
file  RNA_LJ_BaseEnergy.fwd.hh
 
file  RNA_LJ_BaseEnergy.hh
 van der waals over aromatics
 
file  RNA_LJ_BaseEnergyCreator.hh
 Declaration for the class that connects RNA_LJ_BaseEnergy with the ScoringManager.
 
file  RNA_LowResolutionPotential.cc
 
file  RNA_LowResolutionPotential.fwd.hh
 
file  RNA_LowResolutionPotential.hh
 
file  RNA_Mg_Energy.cc
 Statistically derived Mg(2+) binding potential for RNA.
 
file  RNA_Mg_Energy.hh
 Statistically derived Mg(2+) binding potential for RNA.
 
file  RNA_Mg_EnergyCreator.hh
 Declaration for the class that connects RNA_Mg_Energy with the ScoringManager.
 
file  RNA_Mg_KnowledgeBasedPotential.cc
 
file  RNA_Mg_KnowledgeBasedPotential.fwd.hh
 
file  RNA_Mg_KnowledgeBasedPotential.hh
 Information on which atoms to use for computing clashes.
 
file  RNA_PairwiseLowResolutionEnergy.cc
 Statistically derived rotamer pair potential class implementation.
 
file  RNA_PairwiseLowResolutionEnergy.fwd.hh
 
file  RNA_PairwiseLowResolutionEnergy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  RNA_PairwiseLowResolutionEnergyCreator.hh
 Declaration for the class that connects RNA_PairwiseLowResolutionEnergy with the ScoringManager.
 
file  RNA_RawBaseBaseInfo.cc
 
file  RNA_RawBaseBaseInfo.fwd.hh
 
file  RNA_RawBaseBaseInfo.hh
 
file  RNA_ScoringInfo.cc
 
file  RNA_ScoringInfo.fwd.hh
 
file  RNA_ScoringInfo.hh
 
file  RNA_SugarCloseEnergy.cc
 
file  RNA_SugarCloseEnergy.fwd.hh
 
file  RNA_SugarCloseEnergy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  RNA_SugarCloseEnergyCreator.hh
 
file  RNA_Torsion.fwd.hh
 
file  RNA_TorsionEnergy.cc
 
file  RNA_TorsionEnergy.fwd.hh
 
file  RNA_TorsionEnergy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  RNA_TorsionEnergyCreator.hh
 Declaration for the class that connects RNA_TorsionEnergy with the ScoringManager.
 
file  RNA_TorsionPotential.cc
 
file  RNA_TorsionPotential.fwd.hh
 
file  RNA_TorsionPotential.hh
 
file  RNA_Util.cc
 
file  RNA_Util.hh
 
file  RNA_VDW_Energy.cc
 Statistically derived clash check for RNA.
 
file  RNA_VDW_Energy.fwd.hh
 
file  RNA_VDW_Energy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  RNA_VDW_EnergyCreator.hh
 Declaration for the class that connects RNA_VDW_Energy with the ScoringManager.