rna Directory Reference

Directory dependency graph for rna:

Directories
directory	chemical_shift
directory	data

Files
file	RG_Energy_RNA.cc
	Radius of gyration energy function definition.
file	RG_Energy_RNA.hh
	Radius of gyration score for RNA, to match Rosetta++.
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
	Statistically derived rotamer pair potential class declaration.
file	RNA_AtomVDW.hh
	Information on which atoms to use for computing clashes.
file	RNA_BulgeEnergy.cc
	RNA_Bulge energy method implementation.
file	RNA_BulgeEnergy.fwd.hh
	RNA_Bulge energy method forward declaration.
file	RNA_BulgeEnergy.hh
	Score function class.
file	RNA_BulgeEnergyCreator.hh
	Declaration for the class that connects RNA_BulgeEnergy with the ScoringManager.
file	RNA_CentroidInfo.cc
	Statistically derived rotamer pair potential class implementation.
file	RNA_CentroidInfo.fwd.hh
	Statistically derived rotamer pair potential class implementation.
file	RNA_CentroidInfo.hh
	Statistically derived rotamer pair potential class implementation.
file	RNA_EnergyMethodOptions.cc
file	RNA_EnergyMethodOptions.fwd.hh
file	RNA_EnergyMethodOptions.hh
file	RNA_FilteredBaseBaseInfo.cc
	Statistically derived RNA potential.
file	RNA_FilteredBaseBaseInfo.fwd.hh
	Statistically derived rotamer pair potential class implementation.
file	RNA_FilteredBaseBaseInfo.hh
	Statistically derived RNA potential.
file	RNA_FullAtomStackingEnergy.cc
	Statistically derived rotamer pair potential class implementation.
file	RNA_FullAtomStackingEnergy.fwd.hh
	Statistically derived rotamer pair potential class declaration.
file	RNA_FullAtomStackingEnergy.hh
	Statistically derived rotamer pair potential class declaration.
file	RNA_FullAtomStackingEnergyCreator.hh
	Declaration for the class that connects RNA_FullAtomStackingEnergy with the ScoringManager.
file	RNA_FullAtomVDW_BasePhosphate.cc
	RNA_FullAtomVDW_BasePhosphate energy method class implementation.
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
	Declaration for the class that connects RNA_FullAtomVDW_BasePhosphate with the ScoringManager.
file	RNA_JR_SuiteEnergy.cc
	Jane Richardson style RNA Suite Energy.
file	RNA_JR_SuiteEnergy.fwd.hh
	Jane Richardson style RNA Suite Energy.
file	RNA_JR_SuiteEnergy.hh
	Jane Richardson style RNA Suite Energy.
file	RNA_JR_SuiteEnergyCreator.hh
	Declaration for the class that connects RNA_JR_SuiteEnergy with the ScoringManager.
file	RNA_LJ_BaseEnergy.cc
file	RNA_LJ_BaseEnergy.fwd.hh
	LJ Aromatic Energy.
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
	Statistically derived rotamer pair potential class implementation.
file	RNA_LowResolutionPotential.fwd.hh
	Statistically derived rotamer pair potential class implementation.
file	RNA_LowResolutionPotential.hh
	Statistically derived rotamer pair potential class implementation.
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
	Statistically derived rotamer pair potential class declaration.
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
	Statistically derived rotamer pair potential class declaration.
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
	Statistically derived rotamer pair potential class implementation.
file	RNA_RawBaseBaseInfo.fwd.hh
	Statistically derived rotamer pair potential class implementation.
file	RNA_RawBaseBaseInfo.hh
	Statistically derived rotamer pair potential class implementation.
file	RNA_ScoringInfo.cc
	Statistically derived rotamer pair potential class implementation.
file	RNA_ScoringInfo.fwd.hh
	Statistically derived rotamer pair potential class implementation.
file	RNA_ScoringInfo.hh
	Statistically derived rotamer pair potential class implementation.
file	RNA_ScoringUtil.cc
file	RNA_ScoringUtil.hh
file	RNA_SugarCloseEnergy.cc
	RNA_SugarClose energy method class implementation.
file	RNA_SugarCloseEnergy.fwd.hh
	OmegaTether energy method class forward declaration.
file	RNA_SugarCloseEnergy.hh
	Statistically derived rotamer pair potential class declaration.
file	RNA_SugarCloseEnergyCreator.hh
	Declaration for the class that connects RNA_SugarCloseEnergy with the ScoringManager.
file	RNA_SuiteEnergy.cc
	RNA Suite Energy.
file	RNA_SuiteEnergy.fwd.hh
	RNA Suite Energy.
file	RNA_SuiteEnergy.hh
	RNA Suite Energy.
file	RNA_SuiteEnergyCreator.hh
	Declaration for the class that connects RNA_SuiteEnergy with the ScoringManager.
file	RNA_SuitePotential.cc
	RNA_SuitePotential potential class implementation.
file	RNA_SuitePotential.fwd.hh
	RNA_SuitePotential potential class forward delcaration.
file	RNA_SuitePotential.hh
	RNA_SuitePotential potential class delcaration.
file	RNA_TorsionEnergy.cc
	RNA_Torsion energy method class implementation.
file	RNA_TorsionEnergy.fwd.hh
	OmegaTether energy method class forward declaration.
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
	RNA_TorsionPotential potential class implementation.
file	RNA_TorsionPotential.fwd.hh
	RNA_TorsionPotential potential class forward delcaration.
file	RNA_TorsionPotential.hh
	RNA_TorsionPotential potential class delcaration.
file	RNA_VDW_Energy.cc
	Statistically derived clash check for RNA.
file	RNA_VDW_Energy.fwd.hh
	Statistically derived rotamer pair potential class declaration.
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.
file	StackElecEnergy.cc
	FA_Elec, but just 'perpendicular' to bases... trying to separate from H-bonds & geom_sol.
file	StackElecEnergy.fwd.hh
	Statistically derived rotamer pair potential class declaration.
file	StackElecEnergy.hh
	FA_Elec, but just 'perpendicular' to bases... trying to separate from H-bonds & geom_sol.
file	StackElecEnergyCreator.hh
	Declaration for the class that connects StackElecEnergy with the ScoringManager.