rna Directory Reference

Directory dependency graph for rna:

Directories
directory	chemical_shift
directory	data

Files
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_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_EnergyMethodOptions.cc
file	RNA_EnergyMethodOptions.fwd.hh
file	RNA_EnergyMethodOptions.hh
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_JR_SuiteEnergy.cc
file	RNA_JR_SuiteEnergy.fwd.hh
file	RNA_JR_SuiteEnergy.hh
file	RNA_JR_SuiteEnergyCreator.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_LowResolutionPotentialCreator.hh
	Declaration for the class that connects RNA_LowResolutionPotential with the ScoringManager.
file	RNA_Motif.cc
file	RNA_Motif.fwd.hh
file	RNA_Motif.hh
	find RNA motifs (u-turns, T-loops, etc.) in a pose
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_PartitionEnergy.cc
file	RNA_PartitionEnergy.hh
file	RNA_PartitionEnergyCreator.hh
	Declaration for the class that connects RNA_PartitionEnergy with the ScoringManager.
file	RNA_ScoringInfo.cc
file	RNA_ScoringInfo.fwd.hh
file	RNA_ScoringInfo.hh
file	RNA_ScoringUtil.cc
file	RNA_ScoringUtil.hh
file	RNA_StubCoordinateEnergy.cc
file	RNA_StubCoordinateEnergy.fwd.hh
file	RNA_StubCoordinateEnergy.hh
	Statistically derived rotamer pair potential class declaration.
file	RNA_StubCoordinateEnergyCreator.hh
	Declaration for the class that connects RNA_StubCoordinateEnergy with the ScoringManager.
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_SuiteEnergy.cc
file	RNA_SuiteEnergy.fwd.hh
file	RNA_SuiteEnergy.hh
file	RNA_SuiteEnergyCreator.hh
	Declaration for the class that connects RNA_ChemicalMappingEnergy with the ScoringManager.
file	RNA_SuitePotential.cc
file	RNA_SuitePotential.fwd.hh
file	RNA_SuitePotential.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_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.
file	RNP_LowResEnergy.cc
	Statistically derived rotamer pair potential class implementation.
file	RNP_LowResEnergy.fwd.hh
file	RNP_LowResEnergy.hh
	Statistically derived RNP potential.
file	RNP_LowResEnergyCreator.hh
	Energy method creator for the low resolution RNA/protein potential.
file	RNP_LowResPairDistEnergy.cc
	Statistically derived rotamer pair potential class implementation.
file	RNP_LowResPairDistEnergy.fwd.hh
file	RNP_LowResPairDistEnergy.hh
	Statistically derived RNP potential.
file	RNP_LowResPairDistEnergyCreator.hh
	Energy method creator for the low resolution RNA/protein potential.
file	RNP_LowResPairDistPotential.cc
	Statistically derived RNP low-res potential, simple distance-based.
file	RNP_LowResPairDistPotential.fwd.hh
file	RNP_LowResPairDistPotential.hh
file	RNP_LowResPotential.cc
	Statistically derived rotamer pair potential class implementation.
file	RNP_LowResPotential.fwd.hh
file	RNP_LowResPotential.hh
file	RNP_LowResStackData.cc
	Statistically derived rotamer pair potential class implementation.
file	RNP_LowResStackData.fwd.hh
file	RNP_LowResStackData.hh
file	RNP_LowResStackEnergy.cc
	Statistically derived rotamer pair potential class implementation.
file	RNP_LowResStackEnergy.fwd.hh
file	RNP_LowResStackEnergy.hh
	Statistically derived RNP potential.
file	RNP_LowResStackEnergyCreator.hh
	Energy method creator for the low resolution RNA/protein potential.
file	StackElecEnergy.cc
	FA_Elec, but just 'perpendicular' to bases... trying to separate from H-bonds & geom_sol.
file	StackElecEnergy.fwd.hh
file	StackElecEnergy.hh
file	StackElecEnergyCreator.hh
	Declaration for the class that connects StackElecEnergy with the ScoringManager.
file	TNA_SuiteEnergy.cc
file	TNA_SuiteEnergy.fwd.hh
file	TNA_SuiteEnergy.hh
file	TNA_SuiteEnergyCreator.hh
	Declaration for the class that connects TNA_SuiteEnergy with the ScoringManager.
file	TNA_SuitePotential.cc
file	TNA_SuitePotential.fwd.hh
file	TNA_SuitePotential.hh
file	util.cc
	Some useful nonmember functions.
file	util.hh
	Some useful nonmember functions.