scoring Directory Reference

Directory dependency graph for scoring:

Directories
directory	aa_composition_energy
directory	aa_repeat_energy
directory	annealing
directory	bin_transitions
directory	carbohydrates
directory	carbon_hbonds
directory	constraints
directory	cryst
directory	custom_pair_distance
directory	disulfides
directory	dna
directory	dssp
directory	elec
directory	electron_density
directory	electron_density_atomwise
directory	etable
directory	facts
directory	fiber_diffraction
directory	func
directory	geometric_solvation
directory	hackaro
directory	hbonds
directory	interface_
directory	lkball
directory	loop_graph
directory	magnesium
directory	memb_etable
directory	membrane
directory	methods
directory	mm
directory	motif
directory	nv
directory	orbitals
directory	packing
directory	packstat
directory	power_diagram
directory	rna
directory	sasa
directory	saxs
directory	sc
directory	solid_surface
directory	sym_e
directory	symmetry
directory	trie
directory	vdwaals

Files
file	APBSWrapper.cc
file	APBSWrapper.fwd.hh
file	APBSWrapper.hh
file	AtomVDW.cc
file	AtomVDW.fwd.hh
file	AtomVDW.hh
file	CenHBPotential.cc
file	CenHBPotential.fwd.hh
file	CenHBPotential.hh
file	CenRotEnvPairPotential.cc
file	CenRotEnvPairPotential.fwd.hh
file	CenRotEnvPairPotential.hh
file	ChemicalShiftAnisotropy.cc
	Uses NMR CSA for scoring (Bertram R et al J of Magn Reson 147, 9-16)
file	ChemicalShiftAnisotropy.fwd.hh
file	ChemicalShiftAnisotropy.hh
	Uses NMR CSA for scoring.
file	constants.hh
	core::scoring package constants
file	ContextGraph.cc
	Context graph class.
file	ContextGraph.fwd.hh
	Context graph class forward declaration.
file	ContextGraph.hh
	Context graph class declaration.
file	ContextGraphFactory.cc
	Context graph class factory implementation.
file	ContextGraphFactory.fwd.hh
	Context graph class factory forward declaration.
file	ContextGraphFactory.hh
	Context graph factory class declaration.
file	ContextGraphTypes.hh
file	DenseEnergyContainer.cc
	A container for storing all-against-all energies as the upper triangle of a matrix.
file	DenseEnergyContainer.fwd.hh
file	DenseEnergyContainer.hh
	A container for storing all-against-all energies as the upper triangle of a matrix.
file	DerivVectorPair.cc
file	DerivVectorPair.fwd.hh
	Class for storing a pair of derivative vectors, f1 and f2, used in our internal-geometry minimization algorithm.
file	DerivVectorPair.hh
	Serialization routines for the DerivVectorPair class.
file	DipolarCoupling.cc
	Uses NMR DC for scoring (Bertram R et al J of Magn Reson 147, 9-16)
file	DipolarCoupling.fwd.hh
file	DipolarCoupling.hh
	Uses NMR DC for scoring.
file	DockingScoreFunction.cc
file	DockingScoreFunction.fwd.hh
	core::scoring::DockingScoreFunction forward declarations
file	DockingScoreFunction.hh
file	Energies.cc
	Energies class to store cached energies and track the residue neighbor relationships.
file	Energies.fwd.hh
	Energies forward declarations header.
file	Energies.hh
	Energies class.
file	EnergiesCacheableDataType.hh
	enum for the DataCache within the Energies class
file	EnergyGraph.cc
	Energy graph class implementation.
file	EnergyGraph.fwd.hh
	Energy graph class forward declaration.
file	EnergyGraph.hh
	Energy graph class declaration.
file	EnergyMap.cc
	Vector of scores implementation.
file	EnergyMap.fwd.hh
	Vector of scores forward declaration.
file	EnergyMap.hh
	Vector of scores declaration.
file	EnvPairPotential.cc
file	EnvPairPotential.fwd.hh
file	EnvPairPotential.hh
file	GenBornPotential.cc
file	GenBornPotential.fwd.hh
file	GenBornPotential.hh
file	interpolation_util.hh
file	LREnergyContainer.cc
file	LREnergyContainer.fwd.hh
file	LREnergyContainer.hh
file	Membrane_FAPotential.cc
	Membrane FA Potential - Class for Fullatom Membrane Scoring Methods.
file	Membrane_FAPotential.fwd.hh
file	Membrane_FAPotential.hh
file	MembranePotential.cc
	Membrane Potential - Base Scoring Methods for LowRes Energy Function.
file	MembranePotential.fwd.hh
	Membrane Potential - Base Scoring Methods for LowRes Energy Function.
file	MembranePotential.hh
	Membrane Potential - Base Scoring Methods for LowRes Energy Function.
file	MembraneTopology.cc
file	MembraneTopology.fwd.hh
file	MembraneTopology.hh
file	MinimizationData.cc
	A container class for use by certain EnergyMethods during derivative and.
file	MinimizationData.fwd.hh
	Forward declaration of the container class for use by certain EnergyMethods.
file	MinimizationData.hh
	A container class for use by certain EnergyMethods during derivative and.
file	MinimizationGraph.cc
	Minimization graph class implementation.
file	MinimizationGraph.fwd.hh
	Minimization graph class forward declaration.
file	MinimizationGraph.hh
	Minimization graph class declaration.
file	MinScoreScoreFunction.cc
file	MinScoreScoreFunction.fwd.hh
	core::scoring::MinScoreScoreFunction forward declarations
file	MinScoreScoreFunction.hh
file	MultipoleElecPotential.cc
file	MultipoleElecPotential.fwd.hh
file	MultipoleElecPotential.hh
file	NeighborList.cc
file	NeighborList.fwd.hh
	Foward declaration of NeighborList class and owning pointer typedefs.
file	NeighborList.hh
file	NeighborList.tmpl.hh
file	OmegaTether.cc
	OmegaTether potential class implementation.
file	OmegaTether.fwd.hh
	Omega Tether potential class forward delcaration.
file	OmegaTether.hh
	OmegaTether potential class delcaration.
file	OneToAllEnergyContainer.cc
	A container interface for storing and scoring long range energies.
file	OneToAllEnergyContainer.fwd.hh
file	OneToAllEnergyContainer.hh
	A container interface for storing and scoring long range energies.
file	P_AA.cc
	Amino acid probability arrays and functions.
file	P_AA.fwd.hh
file	P_AA.hh
	Amino acid probability arrays and functions.
file	P_AA_ss.cc
	Amino acid probability arrays and functions.
file	P_AA_ss.fwd.hh
file	P_AA_ss.hh
file	PairEPotential.cc
	pairE knowledge-based potential class
file	PairEPotential.fwd.hh
	pairE knowledge-based potential class forward delcaration
file	PairEPotential.hh
file	PoissonBoltzmannPotential.cc
	PoissonBoltzmann potential class implementation.
file	PoissonBoltzmannPotential.fwd.hh
	PoissonBoltzmann potential class forward delcaration.
file	PoissonBoltzmannPotential.hh
	Poisson Boltzmann potential class delcaration.
file	PolymerBondedEnergyContainer.cc
	A container interface long range energies for polymer-bonded residue interactions only.
file	PolymerBondedEnergyContainer.fwd.hh
file	PolymerBondedEnergyContainer.hh
	A container interface long range energies for polymer-bonded residue interactions only.
file	ProQPotential.cc
file	ProQPotential.fwd.hh
	Membrane Potential.
file	ProQPotential.hh
file	ProteinTorsion.hh
	Ramachandran potential class delcaration.
file	Ramachandran.cc
	Ramachandran potential class implementation.
file	Ramachandran.fwd.hh
	Ramachandran potential class forward declaration.
file	Ramachandran.hh
	Ramachandran potential class delcaration.
file	Ramachandran2B.cc
	Neighbor-dependent Ramachandran potential class implementation.
file	Ramachandran2B.fwd.hh
file	Ramachandran2B.hh
	Neighbor-dependent Ramachandran potential class delcaration.
file	RamaPrePro.cc
file	RamaPrePro.fwd.hh
file	RamaPrePro.hh
	RamaPrePro potential class delcaration.
file	ResidualDipolarCoupling.cc
	Uses NMR RDC for scoring.
file	ResidualDipolarCoupling.fwd.hh
file	ResidualDipolarCoupling.hh
	Uses NMR RDC for scoring.
file	ResidualDipolarCoupling_Rohl.cc
	Uses NMR RDC for scoring.
file	ResidualDipolarCoupling_Rohl.fwd.hh
file	ResidualDipolarCoupling_Rohl.hh
file	ResidueNeighborList.cc
file	ResidueNeighborList.fwd.hh
	Forward declaration of a container class for use by the Etable and FA_Elec classes for storing residue-pair level atom-neighbor information.
file	ResidueNeighborList.hh
	A container class for use by the Etable and FA_Elec classes for storing lists of atom neighbors.
file	rms_util.cc
	RMS stuff from rosetta++.
file	rms_util.hh
file	rms_util.tmpl.hh
file	sasa.cc
	routines which calculate solvent accessible surface area
file	sasa.hh
	routines which calculate solvent accessible surface area
file	SASAPotential.cc
file	SASAPotential.fwd.hh
file	SASAPotential.hh
file	ScoreFunction.cc
	ScoreFunction class definition.
file	ScoreFunction.fwd.hh
	core::scoring::ScoreFunction forward declarations
file	ScoreFunction.hh
	Score function class.
file	ScoreFunctionFactory.cc
file	ScoreFunctionFactory.hh
file	ScoreFunctionInfo.cc
	Score function class descriptor.
file	ScoreFunctionInfo.fwd.hh
file	ScoreFunctionInfo.hh
file	ScoreType.cc
file	ScoreType.hh
	Score type enumeration.
file	ScoreTypeManager.cc
	Method definitions for ScoreTypeManager.
file	ScoreTypeManager.hh
	Score type enumeration.
file	ScoringManager.cc
	Scoring manager class.
file	ScoringManager.fwd.hh
file	ScoringManager.hh
	Scoring manager class header.
file	SecondaryStructurePotential.cc
	Scoring manager class header.
file	SecondaryStructurePotential.fwd.hh
file	SecondaryStructurePotential.hh
file	SecondaryStructureWeights.cc
file	SecondaryStructureWeights.hh
file	SmoothEnvPairPotential.cc
file	SmoothEnvPairPotential.fwd.hh
file	SmoothEnvPairPotential.hh
file	SplitUnfoldedTwoBodyPotential.cc
	Reads in and stores the two body energies for each residue type for the split unfolded energy.
file	SplitUnfoldedTwoBodyPotential.fwd.hh
file	SplitUnfoldedTwoBodyPotential.hh
	Reads in and stores the two body energies for each residue type for the split unfolded energy.
file	SS_Info.cc
file	SS_Info.fwd.hh
	Data cache forward declarations for the secondary-structure based scores.
file	SS_Info.hh
file	SS_Killhairpins_Info.cc
file	SS_Killhairpins_Info.fwd.hh
file	SS_Killhairpins_Info.hh
	Scoring manager class header.
file	TenANeighborGraph.cc
	Neighbor graph to represent for each residue the number of other residues within 10 Angstroms.
file	TenANeighborGraph.fwd.hh
	Ten Angstrom Neighbor graph class forward declaration.
file	TenANeighborGraph.hh
	Ten Angstrom Neighbor Graph class declaration.
file	TMscore.cc
file	TMscore.hh
	reimplementation of TMscore sequence-based structure superposition
file	TwelveANeighborGraph.cc
	Neighbor graph to represent for each residue the number of other residues within 12 Angstroms.
file	TwelveANeighborGraph.fwd.hh
	Twelve Angstrom Neighbor graph class forward declaration.
file	TwelveANeighborGraph.hh
	Twelve Angstrom Neighbor Graph class declaration.
file	types.hh
	core::scoring package type declarations
file	UnfoldedStatePotential.cc
	Unfolded state energies based on energies of residues in fragments, definition file.
file	UnfoldedStatePotential.fwd.hh
	Unfolded state energies based on energies of residues in fragments, forward declaration.
file	UnfoldedStatePotential.hh
	Unfolded state energies based on energies of residues in fragments, declaration (header) file.
file	util.cc
	Nonmember functions for evaluating some or all energy methods on residues or residue pairs.
file	util.hh
	Nonmember functions for evaluating some or all energy methods on residues or residue pairs.
file	VdWTinkerPotential.cc
file	VdWTinkerPotential.fwd.hh
file	VdWTinkerPotential.hh
file	WaterAdductHBondPotential.cc
file	WaterAdductHBondPotential.fwd.hh
file	WaterAdductHBondPotential.hh