Namespaces
	carbohydrates

	dfire

Classes
class	AspartimidePenaltyEnergy

class	AspartimidePenaltyEnergyCreator

class	BBDepCartBondedParameters

class	BBIndepCartBondedParameters

class	Burial_v2Energy

class	Burial_v2EnergyCreator

class	BurialEnergy

class	BurialEnergyCreator

class	CartBondedParameters

class	CartesianBondedEnergy

class	CartesianBondedEnergyCreator

class	CenHBEnergy

class	CenHBEnergyCreator

class	CenPairEnergy

class	CenPairEnergyCreator

class	CenPairMotifDegreeEnergy

class	CenPairMotifDegreeEnergyCreator

class	CenPairMotifEnergy

class	CenPairMotifEnergyCreator

class	CenRotEnvEnergy

class	CenRotEnvEnergyCreator

class	CenRotPairEnergy

class	CenRotPairEnergyCreator

class	ChainbreakEnergy
	ChainbreakEnergy class iterates across all residues in finalize() and determines a penalty between residues i and i+1 across a cutpoint by how much their virtual atoms do not align. More...

class	ChainbreakEnergyCreator

class	ChemicalShiftAnisotropyEnergy

class	ChemicalShiftAnisotropyEnergyCreator

class	ContactOrderEnergy

class	ContactOrderEnergyCreator

class	ContextDependentLRTwoBodyEnergy

class	ContextDependentOneBodyEnergy

class	ContextDependentTwoBodyEnergy

class	ContextIndependentLRTwoBodyEnergy

class	ContextIndependentOneBodyEnergy

class	ContextIndependentTwoBodyEnergy

class	CustomAtomPairEnergy

class	CustomAtomPairEnergyCreator

class	D2H_SA_Energy

class	D2H_SA_EnergyCreator

class	DipolarCouplingEnergy

class	DipolarCouplingEnergyCreator

class	DirectReadoutEnergy
	Implementation of Kono and Sarai's knowledge-based protein-DNA interaction energy. More...

class	DirectReadoutEnergyCreator

class	DistanceChainbreakEnergy
	DistanceChainbreakEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by how far apart their N and C atom are. More...

class	DistanceChainbreakEnergyCreator

class	DNA_BaseEnergy

class	DNA_BaseEnergyCreator

class	DNA_DihedralEnergy

class	DNA_DihedralEnergyCreator

class	DNA_EnvPairEnergy
	Implementation of env and pair terms for protein-DNA interactions. More...

class	DNA_EnvPairEnergyCreator

class	DNA_ReferenceEnergy

class	DNA_ReferenceEnergyCreator

class	EnergyMethod
	base class for the energy method hierarchy More...

class	EnergyMethodCreator
	The EnergyMethodCreator class's responsibilities are to create on demand a new EnergyMethod class, and to tell the ScoringManager singleton which ScoreTypes the EnergyMethod it creates is responsible for. The EnergyMethodCreator must register itself with the ScoringManager at load time (before main() begins) so that the ScoringManager is ready to start creating EnergyMethods by the time the first ScoreFunction requests one. More...

class	EnergyMethodOptions

class	EnergyMethodRegistrator
	This templated class will register an instance of an EnergyMethodCreator (class T) with the ScoringManager. It will ensure that no energy method creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...

class	EnvEnergy

class	EnvEnergyCreator

class	EnvSmoothEnergy

class	EnvSmoothEnergyCreator

class	Fa_MbenvEnergy

class	Fa_MbenvEnergyCreator

class	Fa_MbsolvEnergy

class	Fa_MbsolvEnergyCreator

class	FACTSEnergy

class	FACTSEnergyCreator

class	FreeDOF_Energy

class	FreeDOF_EnergyCreator

class	FreeDOF_Options

class	GaussianOverlapEnergy

class	GaussianOverlapEnergyCreator

class	GenBornEnergy

class	GenBornEnergyCreator

class	GoapEnergy

class	GoapEnergyCreator

class	GoapRsdType

class	HybridVDW_Energy

class	HybridVDW_EnergyCreator

class	HydroxylTorsionEnergy

class	HydroxylTorsionEnergyCreator

class	IdealParametersDatabase

class	IntermolEnergy

class	IntermolEnergyCreator

class	LinearChainbreakEnergy
	LinearChainbreakEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by how much their psueduo atoms do not align. More...

class	LinearChainbreakEnergyCreator

class	LK_hack

class	LK_hackCreator

class	LK_PolarNonPolarEnergy

class	LK_PolarNonPolarEnergyCreator

class	LK_SigmoidalFunc

class	LongRangeTwoBodyEnergy

class	MembraneCbetaEnergy

class	MembraneCbetaEnergyCreator

class	MembraneCenPairEnergy

class	MembraneCenPairEnergyCreator

class	MembraneEnvEnergy

class	MembraneEnvEnergyCreator

class	MembraneEnvPenalties

class	MembraneEnvPenaltiesCreator

class	MembraneEnvSmoothEnergy

class	MembraneEnvSmoothEnergyCreator

class	MembraneLipo

class	MembraneLipoCreator

class	MissingEnergy

class	MissingEnergyCreator

class	MMBondAngleEnergy

class	MMBondAngleEnergyCreator

class	MMBondLengthEnergy

class	MMBondLengthEnergyCreator

class	MMLJEnergyInter

class	MMLJEnergyInterCreator

class	MMLJEnergyIntra

class	MMLJEnergyIntraCreator

class	MMTorsionEnergy

class	MMTorsionEnergyCreator

class	MultipoleElecEnergy

class	MultipoleElecEnergyCreator

class	MultipoleElecResPairMinData

class	NeighborListData

class	NMerPSSMEnergy

class	NMerPSSMEnergyCreator

class	NMerRefEnergy

class	NMerRefEnergyCreator

class	NMerSVMEnergy

class	NMerSVMEnergyCreator

class	OmegaTetherEnergy

class	OmegaTetherEnergyCreator

class	OneBodyEnergy

class	OtherPoseEnergy

class	OtherPoseEnergyCreator

class	P_AA_Energy

class	P_AA_EnergyCreator

class	P_AA_pp_Energy

class	P_AA_pp_EnergyCreator

class	P_AA_ss_Energy

class	P_AA_ss_EnergyCreator

class	PackStatEnergy

class	PackStatEnergyCreator

class	PairEnergy

class	PairEnergyCreator

class	PBLifetimeCache

class	PeptideBondEnergy
	PeptideBondEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by the distance the C-N bond. Evantually I'd also like to add bond angle constraints as well, but that's handled by OmegaTether at the moment. More...

class	PeptideBondEnergyCreator

class	pHEnergy

class	pHEnergyCreator

class	PoissonBoltzmannEnergy

class	PoissonBoltzmannEnergyCreator

class	ProClosureEnergy

class	ProClosureEnergyCreator

class	ProQ_Energy

class	ProQ_EnergyCreator

class	PyEnergyMethodRegistrator
	This class will register an instance of an EnergyMethodCreator (class T) with the ScoringManager. It will ensure that no energy method creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...

class	RamachandranEnergy

class	RamachandranEnergy2B

class	RamachandranEnergy2BCreator

class	RamachandranEnergyCreator

class	RamaPreProEnergy

class	RamaPreProEnergyCreator

class	ReferenceEnergy

class	ReferenceEnergyCreator

class	ReferenceEnergyNoncanonical

class	ReferenceEnergyNoncanonicalCreator

class	ResidualDipolarCouplingEnergy

class	ResidualDipolarCouplingEnergy_Rohl

class	ResidualDipolarCouplingEnergy_RohlCreator

class	ResidualDipolarCouplingEnergyCreator

class	ResidueCartBondedParameters

class	RG_Energy_Fast

class	RG_Energy_FastCreator

class	RG_Local_MinData

class	RG_LocalEnergy

class	RG_LocalEnergyCreator

class	RG_MinData

class	RingClosureEnergy

class	RingClosureEnergyCreator

class	RMS_Energy

class	RMS_EnergyCreator

class	SA_Energy

class	SA_EnergyCreator

class	SASAEnergy

class	SASAEnergyCreator

class	SecondaryStructureEnergy

class	SecondaryStructureEnergyCreator

class	SequenceDependentRefEnergy

class	SequenceDependentRefEnergyCreator

class	ShortRangeTwoBodyEnergy

class	SmoothCenPairEnergy

class	SmoothCenPairEnergyCreator

class	SmoothEnvEnergy

class	SmoothEnvEnergyCreator

class	SplitUnfoldedTwoBodyEnergy

class	SplitUnfoldedTwoBodyEnergyCreator

class	SSElementMotifContactEnergy

class	SSElementMotifContactEnergyCreator

class	SuckerEnergy

class	SuckerEnergyCreator

class	SymmetricLigandEnergy

class	SymmetricLigandEnergyCreator

class	TwoBodyEnergy

class	UnfoldedStateEnergy

class	UnfoldedStateEnergyCreator

class	VdWTinkerEnergy

class	VdWTinkerEnergyCreator

class	VdWTinkerResPairMinData

class	WaterAdductHBondEnergy

class	WaterAdductHBondEnergyCreator

class	WaterAdductIntraEnergy

class	WaterAdductIntraEnergyCreator

class	WholeStructureEnergy
	Base class for EnergyMethods which are meaningful only on entire structures, for example, the Radius of Gyration. These EnergyMethods do all of their work in the "finalize_total_energy" section of score function evaluation. More...

class	YHHPlanarityEnergy

class	YHHPlanarityEnergyCreator

Typedefs
typedef utility::pointer::weak_ptr < AspartimidePenaltyEnergy >	AspartimidePenaltyEnergyAP

typedef utility::pointer::weak_ptr < AspartimidePenaltyEnergy const >	AspartimidePenaltyEnergyCAP

typedef utility::pointer::shared_ptr < AspartimidePenaltyEnergy >	AspartimidePenaltyEnergyOP

typedef utility::pointer::shared_ptr < AspartimidePenaltyEnergy const >	AspartimidePenaltyEnergyCOP

typedef utility::pointer::weak_ptr < CartBondedParameters >	CartBondedParametersAP

typedef utility::pointer::weak_ptr < CartBondedParameters const >	CartBondedParametersCAP

typedef utility::pointer::shared_ptr < CartBondedParameters >	CartBondedParametersOP

typedef utility::pointer::shared_ptr < CartBondedParameters const >	CartBondedParametersCOP

typedef utility::pointer::weak_ptr < ResidueCartBondedParameters >	ResidueCartBondedParametersAP

typedef utility::pointer::weak_ptr < ResidueCartBondedParameters const >	ResidueCartBondedParametersCAP

typedef utility::pointer::shared_ptr < ResidueCartBondedParameters >	ResidueCartBondedParametersOP

typedef utility::pointer::shared_ptr < ResidueCartBondedParameters const >	ResidueCartBondedParametersCOP

typedef utility::pointer::weak_ptr < IdealParametersDatabase >	IdealParametersDatabaseAP

typedef utility::pointer::weak_ptr < IdealParametersDatabase const >	IdealParametersDatabaseCAP

typedef utility::pointer::shared_ptr < IdealParametersDatabase >	IdealParametersDatabaseOP

typedef utility::pointer::shared_ptr < IdealParametersDatabase const >	IdealParametersDatabaseCOP

typedef utility::pointer::weak_ptr < CartesianBondedEnergy >	CartesianBondedEnergyAP

typedef utility::pointer::weak_ptr < CartesianBondedEnergy const >	CartesianBondedEnergyCAP

typedef utility::pointer::shared_ptr < CartesianBondedEnergy >	CartesianBondedEnergyOP

typedef utility::pointer::shared_ptr < CartesianBondedEnergy const >	CartesianBondedEnergyCOP

typedef utility::vector1 < std::pair< atm_name_quad, CartBondedParametersCOP > >	torsionparam_vector

typedef utility::pointer::shared_ptr < ChemicalShiftAnisotropyEnergy >	ChemicalShiftAnisotropyEnergyOP

typedef utility::pointer::shared_ptr < ContextDependentLRTwoBodyEnergy >	ContextDependentLRTwoBodyEnergyOP

typedef utility::pointer::shared_ptr < ContextDependentLRTwoBodyEnergy const >	ContextDependentLRTwoBodyEnergyCOP

typedef utility::pointer::shared_ptr < ContextDependentOneBodyEnergy >	ContextDependentOneBodyEnergyOP

typedef utility::pointer::shared_ptr < ContextDependentTwoBodyEnergy >	ContextDependentTwoBodyEnergyOP

typedef utility::pointer::shared_ptr < ContextDependentTwoBodyEnergy const >	ContextDependentTwoBodyEnergyCOP

typedef utility::pointer::shared_ptr < ContextIndependentLRTwoBodyEnergy >	ContextIndependentLRTwoBodyEnergyOP

typedef utility::pointer::shared_ptr < ContextIndependentLRTwoBodyEnergy const >	ContextIndependentLRTwoBodyEnergyCOP

typedef utility::pointer::shared_ptr < ContextIndependentOneBodyEnergy >	ContextIndependentOneBodyEnergyOP

typedef utility::pointer::shared_ptr < ContextIndependentOneBodyEnergy const >	ContextIndependentOneBodyEnergyCOP

typedef utility::pointer::shared_ptr < ContextIndependentTwoBodyEnergy >	ContextIndependentTwoBodyEnergyOP

typedef utility::pointer::shared_ptr < ContextIndependentTwoBodyEnergy const >	ContextIndependentTwoBodyEnergyCOP

typedef utility::pointer::shared_ptr < PoissonBoltzmannEnergy >	PoissonBoltzmannEnergyOP

typedef utility::pointer::shared_ptr < PoissonBoltzmannEnergy const >	PoissonBoltzmannEnergyCOP

typedef utility::pointer::shared_ptr < DipolarCouplingEnergy >	DipolarCouplingEnergyOP

typedef utility::pointer::shared_ptr < EnergyMethod >	EnergyMethodOP

typedef utility::pointer::shared_ptr < EnergyMethod const >	EnergyMethodCOP

typedef utility::pointer::shared_ptr < EnergyMethodCreator >	EnergyMethodCreatorOP

typedef utility::pointer::shared_ptr < EnergyMethodCreator const >	EnergyMethodCreatorCOP

typedef utility::pointer::shared_ptr < EnergyMethodOptions >	EnergyMethodOptionsOP

typedef utility::pointer::shared_ptr < EnergyMethodOptions const >	EnergyMethodOptionsCOP

typedef utility::pointer::shared_ptr < Fa_MbenvEnergy >	Fa_MbenvEnergyOP

typedef utility::pointer::shared_ptr < FreeDOF_Options >	FreeDOF_OptionsOP

typedef utility::pointer::shared_ptr < FreeDOF_Options const >	FreeDOF_OptionsCOP

typedef utility::pointer::shared_ptr < GoapRsdType >	GoapRsdTypeOP

typedef utility::pointer::shared_ptr < GoapRsdType const >	GoapRsdTypeCOP

typedef utility::pointer::shared_ptr < GoapEnergy >	GoapEnergyOP

typedef std::map< std::string, GoapRsdTypeOP >	GoapRsdTypeMap

typedef utility::pointer::shared_ptr < HydroxylTorsionEnergy >	HydroxylTorsionEnergyOP

typedef utility::pointer::shared_ptr < LongRangeTwoBodyEnergy >	LongRangeTwoBodyEnergyOP

typedef utility::pointer::shared_ptr < LongRangeTwoBodyEnergy const >	LongRangeTwoBodyEnergyCOP

typedef utility::pointer::weak_ptr < MMBondAngleEnergy >	MMBondAngleEnergyAP

typedef utility::pointer::weak_ptr < MMBondAngleEnergy const >	MMBondAngleEnergyCAP

typedef utility::pointer::shared_ptr < MMBondAngleEnergy >	MMBondAngleEnergyOP

typedef utility::pointer::shared_ptr < MMBondAngleEnergy const >	MMBondAngleEnergyCOP

typedef utility::pointer::weak_ptr < MMBondLengthEnergy >	MMBondLengthEnergyAP

typedef utility::pointer::weak_ptr < MMBondLengthEnergy const >	MMBondLengthEnergyCAP

typedef utility::pointer::shared_ptr < MMBondLengthEnergy >	MMBondLengthEnergyOP

typedef utility::pointer::shared_ptr < MMBondLengthEnergy const >	MMBondLengthEnergyCOP

typedef utility::pointer::weak_ptr < MMLJEnergyInter >	MMLJEnergyInterAP

typedef utility::pointer::weak_ptr < MMLJEnergyInter const >	MMLJEnergyInterCAP

typedef utility::pointer::shared_ptr < MMLJEnergyInter >	MMLJEnergyInterOP

typedef utility::pointer::shared_ptr < MMLJEnergyInter const >	MMLJEnergyInterCOP

typedef utility::pointer::weak_ptr < MMLJEnergyIntra >	MMLJEnergyIntraAP

typedef utility::pointer::weak_ptr < MMLJEnergyIntra const >	MMLJEnergyIntraCAP

typedef utility::pointer::shared_ptr < MMLJEnergyIntra >	MMLJEnergyIntraOP

typedef utility::pointer::shared_ptr < MMLJEnergyIntra const >	MMLJEnergyIntraCOP

typedef utility::pointer::shared_ptr < NeighborListData >	NeighborListDataOP

typedef utility::pointer::shared_ptr < NeighborListData const >	NeighborListDataCOP

typedef std::pair < mm::mm_torsion_atom_quad, core::Real >	mm_torsion_atom_quad_angle_pair

typedef utility::vector1 < mm_torsion_atom_quad_angle_pair > ::const_iterator	mmtaqap_iter

typedef utility::pointer::weak_ptr < MMTorsionEnergy >	MMTorsionEnergyAP

typedef utility::pointer::weak_ptr < MMTorsionEnergy const >	MMTorsionEnergyCAP

typedef utility::pointer::shared_ptr < MMTorsionEnergy >	MMTorsionEnergyOP

typedef utility::pointer::shared_ptr < MMTorsionEnergy const >	MMTorsionEnergyCOP

typedef utility::pointer::shared_ptr < MultipoleElecResPairMinData >	MultipoleElecResPairMinDataOP

typedef utility::pointer::shared_ptr < MultipoleElecResPairMinData const >	MultipoleElecResPairMinDataCOP

typedef utility::pointer::shared_ptr < NMerPSSMEnergy >	NMerPSSMEnergyOP

typedef utility::pointer::shared_ptr < NMerPSSMEnergy const >	NMerPSSMEnergyCOP

typedef utility::pointer::shared_ptr < NMerRefEnergy >	NMerRefEnergyOP

typedef utility::pointer::shared_ptr < NMerRefEnergy const >	NMerRefEnergyCOP

typedef utility::pointer::shared_ptr < NMerSVMEnergy >	NMerSVMEnergyOP

typedef utility::pointer::shared_ptr < NMerSVMEnergy const >	NMerSVMEnergyCOP

typedef utility::pointer::shared_ptr < OmegaTetherEnergy >	OmegaTetherEnergyOP

typedef utility::pointer::shared_ptr < OmegaTetherEnergy const >	OmegaTetherEnergyCOP

typedef utility::pointer::shared_ptr < OneBodyEnergy >	OneBodyEnergyOP

typedef utility::pointer::shared_ptr < OneBodyEnergy const >	OneBodyEnergyCOP

typedef utility::pointer::shared_ptr < OtherPoseEnergy >	OtherPoseEnergyOP

typedef utility::pointer::shared_ptr < OtherPoseEnergy const >	OtherPoseEnergyCOP

typedef utility::pointer::shared_ptr < P_AA_Energy >	P_AA_EnergyOP

typedef utility::pointer::shared_ptr < P_AA_pp_Energy >	P_AA_pp_EnergyOP

typedef utility::pointer::shared_ptr < P_AA_ss_Energy >	P_AA_ss_EnergyOP

typedef utility::pointer::shared_ptr < pHEnergy >	pHEnergyOP

typedef utility::pointer::weak_ptr < PoissonBoltzmannEnergy >	PoissonBoltzmannEnergyAP

typedef utility::pointer::weak_ptr < PoissonBoltzmannEnergy const >	PoissonBoltzmannEnergyCAP

typedef utility::pointer::shared_ptr < PBLifetimeCache >	PBLifetimeCacheOP

typedef utility::pointer::shared_ptr < PBLifetimeCache const >	PBLifetimeCacheCOP

typedef utility::pointer::weak_ptr < PBLifetimeCache >	PBLifetimeCacheAP

typedef utility::pointer::weak_ptr < PBLifetimeCache const >	PBLifetimeCacheCAP

typedef utility::pointer::shared_ptr < ProClosureEnergy >	ProClosureEnergyOP

typedef utility::pointer::shared_ptr < ProClosureEnergy const >	ProClosureEnergyCOP

typedef utility::pointer::shared_ptr < RamachandranEnergy >	RamachandranEnergyOP

typedef utility::pointer::shared_ptr < RamachandranEnergy const >	RamachandranEnergyCOP

typedef utility::pointer::shared_ptr < RamachandranEnergy2B >	RamachandranEnergy2BOP

typedef utility::pointer::shared_ptr < RamachandranEnergy2B const >	RamachandranEnergy2BCOP

typedef utility::pointer::weak_ptr < RamaPreProEnergy >	RamaPreProEnergyAP

typedef utility::pointer::weak_ptr < RamaPreProEnergy const >	RamaPreProEnergyCAP

typedef utility::pointer::shared_ptr < RamaPreProEnergy >	RamaPreProEnergyOP

typedef utility::pointer::shared_ptr < RamaPreProEnergy const >	RamaPreProEnergyCOP

typedef utility::pointer::shared_ptr < ReferenceEnergy >	ReferenceEnergyOP

typedef utility::pointer::shared_ptr < ReferenceEnergy const >	ReferenceEnergyCOP

typedef utility::pointer::shared_ptr < ReferenceEnergyNoncanonical >	ReferenceEnergyNoncanonicalOP

typedef utility::pointer::shared_ptr < ReferenceEnergyNoncanonical const >	ReferenceEnergyNoncanonicalCOP

typedef utility::pointer::shared_ptr < ResidualDipolarCouplingEnergy >	ResidualDipolarCouplingEnergyOP

typedef utility::pointer::shared_ptr < RG_MinData >	RG_MinDataOP

typedef utility::pointer::shared_ptr < RG_Local_MinData >	RG_Local_MinDataOP

typedef utility::pointer::shared_ptr < RingClosureEnergy >	RingClosureEnergyOP

typedef utility::pointer::shared_ptr < RingClosureEnergy const >	RingClosureEnergyCOP

typedef utility::pointer::shared_ptr < SequenceDependentRefEnergy >	SequenceDependentRefEnergyOP

typedef utility::pointer::shared_ptr < SequenceDependentRefEnergy const >	SequenceDependentRefEnergyCOP

typedef utility::pointer::shared_ptr < ShortRangeTwoBodyEnergy >	ShortRangeTwoBodyEnergyOP

typedef utility::pointer::shared_ptr < ShortRangeTwoBodyEnergy const >	ShortRangeTwoBodyEnergyCOP

typedef utility::pointer::shared_ptr < SplitUnfoldedTwoBodyEnergy >	SplitUnfoldedTwoBodyEnergyOP

typedef utility::pointer::shared_ptr < TwoBodyEnergy >	TwoBodyEnergyOP

typedef utility::pointer::shared_ptr < TwoBodyEnergy const >	TwoBodyEnergyCOP

typedef utility::pointer::shared_ptr < UnfoldedStateEnergy >	UnfoldedStateEnergyOP

typedef utility::pointer::shared_ptr < VdWTinkerResPairMinData >	VdWTinkerResPairMinDataOP

typedef utility::pointer::shared_ptr < VdWTinkerResPairMinData const >	VdWTinkerResPairMinDataCOP

typedef utility::pointer::shared_ptr < WaterAdductIntraEnergy >	WaterAdductIntraEnergyOP

typedef utility::pointer::shared_ptr < WholeStructureEnergy >	WholeStructureEnergyOP

typedef utility::pointer::shared_ptr < YHHPlanarityEnergy >	YHHPlanarityEnergyOP

Enumerations
enum	EnergyMethodType { ci_2b = 1, cd_2b, ci_lr_2b, cd_lr_2b, ci_1b, cd_1b, ws, n_energy_method_types = ws }

enum	EnergyMethods { etable_method = 1, dunbrack_method, hbond_method, elec_method, lkball_method, mm_lj_energy_inter_method, pair_e_method, reference_e_method, vdw_method, ramachandran_method, n_energy_methods = ramachandran_method }

enum	LongRangeEnergyType { constraints_lr = 1, gen_born_lr, multipole_elec_lr, vdw_tinker_lr, sasa_lr, PB_elec_lr, cart_bonded_lr, rama2b_lr, ramaprepro_lr, aspartimide_penalty_lr, rna_suite_lr, rna_stub_coord_lr, DFIRE, sym_bonus_lr, elec_dens_energy, elec_dens_fast_energy, elec_dens_cen_energy, elec_dens_allatom_cen_energy, elec_dens_atomwise_energy, patterson_corr_energy, fa_disulfide_energy, disulfide_matching_energy, centroid_disulfide_energy, n_long_range_types = centroid_disulfide_energy }

Functions
static THREAD_LOCAL basic::Tracer	TR ("core.scoring.AspartimidePenaltyEnergy")

static THREAD_LOCAL basic::Tracer	TR ("core.scoring.CartesianBondedEnergy")

static THREAD_LOCAL basic::Tracer	GEOMETRIES ("core.scoring.CartesianBondedEnergy.GEOMETRIES")

std::string	get_restag (core::chemical::ResidueType const &restype)
	helper function More...

static THREAD_LOCAL basic::Tracer	TR ("core.scoring.CenPairMotifDegreeEnergy")

static THREAD_LOCAL basic::Tracer	TR ("core.scoring.CenPairMotifEnergy")

bool	is_lower_cutpoint (core::Size residue, core::pose::Pose const &pose)

bool	is_upper_cutpoint (core::Size residue, core::pose::Pose const &pose)

void	find_cutpoint_variants (core::pose::Pose const &pose, core::kinematics::FoldTree const &, utility::vector1< int > &cutpoints)

bool	lower_upper_connected_across_cutpoint (core::conformation::Residue const &lower_rsd, core::conformation::Residue const &upper_rsd)
	helper function for looking at residue connections to get lower/upper partners More...

Size	get_upper_cutpoint_partner_for_lower (pose::Pose const &pose, Size const lower_res)

Size	get_lower_cutpoint_partner_for_upper (pose::Pose const &pose, Size const upper_res)

core::Size	get_upper_cutpoint_partner_for_lower (core::pose::Pose const &pose, core::Size const lower_res)
	Instead of assuming cutpoint partner is simply cutpoint+1, find which residue connects via lower/upper. More...

core::Size	get_lower_cutpoint_partner_for_upper (core::pose::Pose const &pose, core::Size const upper_res)
	Instead of assuming cutpoint partner is simply res-1, find which residue connects via lower/upper. More...

static THREAD_LOCAL basic::Tracer	tr ("core.scoring.methods.Chainbreak", basic::t_info)

static THREAD_LOCAL basic::Tracer	tr ("core.scoring.methods.CustomAtomPairEnergy")

void	swap_seqpos (core::Size &seqpos1, core::Size &seqpos2)

static THREAD_LOCAL basic::Tracer	TR ("core.scoring.methods.D2H_SA_Energy.cc")

std::string const	dna_deriv_atom (" C5 ")
	the atom through which the knowledge based potential applies a force More...

bool	count_pair_bs (Size const pos1, Size const pos2, BasePartner const &partner)
	ordered!!!! requires pos1<pos2 More...

BasePartner const &	retrieve_base_partner_from_pose_inline (pose::Pose const &pose)
	same as dna::retrieve_base_partner_from_pose More...

static basic::Tracer	TR ("core.scoring.methods.DNA_DihedralEnergy")

static basic::Tracer	TR ("core.scoring.methods.DNA_ReferenceEnergy")

bool	operator== (EnergyMethodOptions const &a, EnergyMethodOptions const &b)
	used inside ScoreFunctionInfo::operator== More...

bool	operator!= (EnergyMethodOptions const &a, EnergyMethodOptions const &b)
	used inside ScoreFunctionInfo::operator== More...

std::ostream &	operator<< (std::ostream &out, EnergyMethodOptions const &options)

Real	sqr (Real x)

bool	operator== (FreeDOF_Options const &a, FreeDOF_Options const &b)

std::ostream &	operator<< (std::ostream &out, const FreeDOF_Options &options)

bool	count_atom (int const &atype)

static THREAD_LOCAL basic::Tracer	TR ("core.scoring.GoapEnergy")

Real const	vdw_scale_factor (0.8)

static THREAD_LOCAL basic::Tracer	TR ("core.scoring.HydroxylTorsionEnergy")

static THREAD_LOCAL basic::Tracer	tr ("core.scoring.methods.LinearChainbreak", basic::t_info)

static THREAD_LOCAL basic::Tracer	TR ("core.mm.MMBondAngleEnergy")

static THREAD_LOCAL basic::Tracer	TR ("core.mm.MMBondLengthEnergy")

static THREAD_LOCAL basic::Tracer	TR ("core.scoring.methods.MMTorsionEnergy")

MultipoleElecResidueInfo const &	retrieve_mp_residue_info (pose::Pose const &pose, Size const seqpos)

MultipoleElecResidueInfo &	retrieve_nonconst_mp_residue_info (pose::Pose &pose, Size const seqpos)

MultipoleElecResPairMinData &	retrieve_nonconst_mp_pairdata (ResPairMinimizationData &pairdata)

MultipoleElecResPairMinData const &	retrieve_mp_pairdata (ResPairMinimizationData const &pairdata)

MultipoleElecResidueInfo &	retrieve_nonconst_mp_resdata (ResSingleMinimizationData &resdata)

MultipoleElecResidueInfo const &	retrieve_mp_resdata (ResSingleMinimizationData const &resdata)

MultipoleElecResidueInfoCOP	retrieve_mp_resdata_ptr (ResSingleMinimizationData const &resdata)

static THREAD_LOCAL basic::Tracer	TR ("core.scoring.methods.ProQ_Energy.cc")

static THREAD_LOCAL basic::Tracer	TR ("core.scoring.RamaPreProEnergy")

static THREAD_LOCAL basic::Tracer	TR ("core.scoring.SSElementMotifContactEnergy")

static THREAD_LOCAL basic::Tracer	TR ("core.scoring.methods.TwoBodyEnergy")

static THREAD_LOCAL basic::Tracer	tr ("core.scoring.methods")

core::Real	get_residue_weight_by_ss (const char ss)

bool	residues_interact (conformation::Residue const &rsd1, conformation::Residue const &rsd2, core::Real const interaction_cutoff)

bool	atoms_interact (conformation::Residue const &rsd1, conformation::Residue const &rsd2, core::id::AtomID const &id1, core::id::AtomID const &id2, core::Real const interaction_cutoff)

void	determine_lo_and_hi_residues (core::pose::Pose const &pose, core::Size const rsd1, core::Size const rsd2, bool &res1_is_lo, bool &res2_is_lo)
	Given two residues that may or may not be connected, determine which of the two, if any, is the lower one and which is the upper. More...

void	create_long_range_energy_container (core::pose::Pose &pose, core::scoring::ScoreType const scoretype, core::scoring::methods::LongRangeEnergyType const lr_type)
	Determines whether a long-range energies container exists in the pose energies object. If not, creates a new one and appends the score type to it, if necessary. More...

VdWTinkerResidueInfo const &	retrieve_vdw_residue_info (pose::Pose const &pose, Size const seqpos)

VdWTinkerResidueInfo &	retrieve_nonconst_vdw_residue_info (pose::Pose &pose, Size const seqpos)

VdWTinkerResPairMinData &	retrieve_nonconst_vdw_pairdata (ResPairMinimizationData &pairdata)

VdWTinkerResPairMinData const &	retrieve_vdw_pairdata (ResPairMinimizationData const &pairdata)

VdWTinkerResidueInfo &	retrieve_nonconst_vdw_resdata (ResSingleMinimizationData &resdata)

VdWTinkerResidueInfo const &	retrieve_vdw_resdata (ResSingleMinimizationData const &resdata)

VdWTinkerResidueInfoCOP	retrieve_vdw_resdata_ptr (ResSingleMinimizationData const &resdata)

Variables
static const Real	K_LENGTH =300.0

static const Real	K_ANGLE =80.0

static const Real	K_TORSION =20.0

static const Real	K_TORSION_PROTON =10.0

static const Real	K_TORSION_IMPROPER =40.0

Distance const	start_sig = 9.8

Distance const	end_sig = 10.2

DistanceSquared const	start_sig2 = start_sig*start_sig

DistanceSquared const	end_sig2 = end_sig*end_sig

Typedef Documentation

typedef utility::pointer::weak_ptr< AspartimidePenaltyEnergy > core::scoring::methods::AspartimidePenaltyEnergyAP

typedef utility::pointer::weak_ptr< AspartimidePenaltyEnergy const > core::scoring::methods::AspartimidePenaltyEnergyCAP

typedef utility::pointer::shared_ptr< AspartimidePenaltyEnergy const > core::scoring::methods::AspartimidePenaltyEnergyCOP

typedef utility::pointer::shared_ptr< AspartimidePenaltyEnergy > core::scoring::methods::AspartimidePenaltyEnergyOP

typedef utility::pointer::weak_ptr< CartBondedParameters > core::scoring::methods::CartBondedParametersAP

typedef utility::pointer::weak_ptr< CartBondedParameters const > core::scoring::methods::CartBondedParametersCAP

typedef utility::pointer::shared_ptr< CartBondedParameters const > core::scoring::methods::CartBondedParametersCOP

typedef utility::pointer::shared_ptr< CartBondedParameters > core::scoring::methods::CartBondedParametersOP

typedef utility::pointer::weak_ptr< CartesianBondedEnergy > core::scoring::methods::CartesianBondedEnergyAP

typedef utility::pointer::weak_ptr< CartesianBondedEnergy const > core::scoring::methods::CartesianBondedEnergyCAP

typedef utility::pointer::shared_ptr< CartesianBondedEnergy const > core::scoring::methods::CartesianBondedEnergyCOP

typedef utility::pointer::shared_ptr< CartesianBondedEnergy > core::scoring::methods::CartesianBondedEnergyOP

typedef utility::pointer::shared_ptr< ChemicalShiftAnisotropyEnergy > core::scoring::methods::ChemicalShiftAnisotropyEnergyOP

typedef utility::pointer::shared_ptr< ContextDependentLRTwoBodyEnergy const > core::scoring::methods::ContextDependentLRTwoBodyEnergyCOP

typedef utility::pointer::shared_ptr< ContextDependentLRTwoBodyEnergy > core::scoring::methods::ContextDependentLRTwoBodyEnergyOP

typedef utility::pointer::shared_ptr< ContextDependentOneBodyEnergy > core::scoring::methods::ContextDependentOneBodyEnergyOP

typedef utility::pointer::shared_ptr< ContextDependentTwoBodyEnergy const > core::scoring::methods::ContextDependentTwoBodyEnergyCOP

typedef utility::pointer::shared_ptr< ContextDependentTwoBodyEnergy > core::scoring::methods::ContextDependentTwoBodyEnergyOP

typedef utility::pointer::shared_ptr< ContextIndependentLRTwoBodyEnergy const > core::scoring::methods::ContextIndependentLRTwoBodyEnergyCOP

typedef utility::pointer::shared_ptr< ContextIndependentLRTwoBodyEnergy > core::scoring::methods::ContextIndependentLRTwoBodyEnergyOP

typedef utility::pointer::shared_ptr< ContextIndependentOneBodyEnergy const > core::scoring::methods::ContextIndependentOneBodyEnergyCOP

typedef utility::pointer::shared_ptr< ContextIndependentOneBodyEnergy > core::scoring::methods::ContextIndependentOneBodyEnergyOP

typedef utility::pointer::shared_ptr< ContextIndependentTwoBodyEnergy const > core::scoring::methods::ContextIndependentTwoBodyEnergyCOP

typedef utility::pointer::shared_ptr< ContextIndependentTwoBodyEnergy > core::scoring::methods::ContextIndependentTwoBodyEnergyOP

typedef utility::pointer::shared_ptr< DipolarCouplingEnergy > core::scoring::methods::DipolarCouplingEnergyOP

typedef utility::pointer::shared_ptr< EnergyMethod const > core::scoring::methods::EnergyMethodCOP

typedef utility::pointer::shared_ptr< EnergyMethodCreator const > core::scoring::methods::EnergyMethodCreatorCOP

typedef utility::pointer::shared_ptr< EnergyMethodCreator > core::scoring::methods::EnergyMethodCreatorOP

typedef utility::pointer::shared_ptr< EnergyMethod > core::scoring::methods::EnergyMethodOP

typedef utility::pointer::shared_ptr< EnergyMethodOptions const > core::scoring::methods::EnergyMethodOptionsCOP

typedef utility::pointer::shared_ptr< EnergyMethodOptions > core::scoring::methods::EnergyMethodOptionsOP

typedef utility::pointer::shared_ptr< Fa_MbenvEnergy > core::scoring::methods::Fa_MbenvEnergyOP

typedef utility::pointer::shared_ptr< FreeDOF_Options const > core::scoring::methods::FreeDOF_OptionsCOP

typedef utility::pointer::shared_ptr< FreeDOF_Options > core::scoring::methods::FreeDOF_OptionsOP

typedef utility::pointer::shared_ptr< GoapEnergy > core::scoring::methods::GoapEnergyOP

typedef utility::pointer::shared_ptr< GoapRsdType const > core::scoring::methods::GoapRsdTypeCOP

typedef std::map< std::string, GoapRsdTypeOP > core::scoring::methods::GoapRsdTypeMap

typedef utility::pointer::shared_ptr< GoapRsdType > core::scoring::methods::GoapRsdTypeOP

typedef utility::pointer::shared_ptr< HydroxylTorsionEnergy > core::scoring::methods::HydroxylTorsionEnergyOP

typedef utility::pointer::weak_ptr< IdealParametersDatabase > core::scoring::methods::IdealParametersDatabaseAP

typedef utility::pointer::weak_ptr< IdealParametersDatabase const > core::scoring::methods::IdealParametersDatabaseCAP

typedef utility::pointer::shared_ptr< IdealParametersDatabase const > core::scoring::methods::IdealParametersDatabaseCOP

typedef utility::pointer::shared_ptr< IdealParametersDatabase > core::scoring::methods::IdealParametersDatabaseOP

typedef utility::pointer::shared_ptr< LongRangeTwoBodyEnergy const > core::scoring::methods::LongRangeTwoBodyEnergyCOP

typedef utility::pointer::shared_ptr< LongRangeTwoBodyEnergy > core::scoring::methods::LongRangeTwoBodyEnergyOP

typedef std::pair< mm::mm_torsion_atom_quad, core::Real > core::scoring::methods::mm_torsion_atom_quad_angle_pair

typedef utility::pointer::weak_ptr< MMBondAngleEnergy > core::scoring::methods::MMBondAngleEnergyAP

typedef utility::pointer::weak_ptr< MMBondAngleEnergy const > core::scoring::methods::MMBondAngleEnergyCAP

typedef utility::pointer::shared_ptr< MMBondAngleEnergy const > core::scoring::methods::MMBondAngleEnergyCOP

typedef utility::pointer::shared_ptr< MMBondAngleEnergy > core::scoring::methods::MMBondAngleEnergyOP

typedef utility::pointer::weak_ptr< MMBondLengthEnergy > core::scoring::methods::MMBondLengthEnergyAP

typedef utility::pointer::weak_ptr< MMBondLengthEnergy const > core::scoring::methods::MMBondLengthEnergyCAP

typedef utility::pointer::shared_ptr< MMBondLengthEnergy const > core::scoring::methods::MMBondLengthEnergyCOP

typedef utility::pointer::shared_ptr< MMBondLengthEnergy > core::scoring::methods::MMBondLengthEnergyOP

typedef utility::pointer::weak_ptr< MMLJEnergyInter > core::scoring::methods::MMLJEnergyInterAP

typedef utility::pointer::weak_ptr< MMLJEnergyInter const > core::scoring::methods::MMLJEnergyInterCAP

typedef utility::pointer::shared_ptr< MMLJEnergyInter const > core::scoring::methods::MMLJEnergyInterCOP

typedef utility::pointer::shared_ptr< MMLJEnergyInter > core::scoring::methods::MMLJEnergyInterOP

typedef utility::pointer::weak_ptr< MMLJEnergyIntra > core::scoring::methods::MMLJEnergyIntraAP

typedef utility::pointer::weak_ptr< MMLJEnergyIntra const > core::scoring::methods::MMLJEnergyIntraCAP

typedef utility::pointer::shared_ptr< MMLJEnergyIntra const > core::scoring::methods::MMLJEnergyIntraCOP

typedef utility::pointer::shared_ptr< MMLJEnergyIntra > core::scoring::methods::MMLJEnergyIntraOP

typedef utility::vector1< mm_torsion_atom_quad_angle_pair >::const_iterator core::scoring::methods::mmtaqap_iter

typedef utility::pointer::weak_ptr< MMTorsionEnergy > core::scoring::methods::MMTorsionEnergyAP

typedef utility::pointer::weak_ptr< MMTorsionEnergy const > core::scoring::methods::MMTorsionEnergyCAP

typedef utility::pointer::shared_ptr< MMTorsionEnergy const > core::scoring::methods::MMTorsionEnergyCOP

typedef utility::pointer::shared_ptr< MMTorsionEnergy > core::scoring::methods::MMTorsionEnergyOP

typedef utility::pointer::shared_ptr< MultipoleElecResPairMinData const > core::scoring::methods::MultipoleElecResPairMinDataCOP

typedef utility::pointer::shared_ptr< MultipoleElecResPairMinData > core::scoring::methods::MultipoleElecResPairMinDataOP

typedef utility::pointer::shared_ptr< NeighborListData const > core::scoring::methods::NeighborListDataCOP

typedef utility::pointer::shared_ptr< NeighborListData > core::scoring::methods::NeighborListDataOP

typedef utility::pointer::shared_ptr< NMerPSSMEnergy const > core::scoring::methods::NMerPSSMEnergyCOP

typedef utility::pointer::shared_ptr< NMerPSSMEnergy > core::scoring::methods::NMerPSSMEnergyOP

typedef utility::pointer::shared_ptr< NMerRefEnergy const > core::scoring::methods::NMerRefEnergyCOP

typedef utility::pointer::shared_ptr< NMerRefEnergy > core::scoring::methods::NMerRefEnergyOP

typedef utility::pointer::shared_ptr< NMerSVMEnergy const > core::scoring::methods::NMerSVMEnergyCOP

typedef utility::pointer::shared_ptr< NMerSVMEnergy > core::scoring::methods::NMerSVMEnergyOP

typedef utility::pointer::shared_ptr< OmegaTetherEnergy const > core::scoring::methods::OmegaTetherEnergyCOP

typedef utility::pointer::shared_ptr< OmegaTetherEnergy > core::scoring::methods::OmegaTetherEnergyOP

typedef utility::pointer::shared_ptr< OneBodyEnergy const > core::scoring::methods::OneBodyEnergyCOP

typedef utility::pointer::shared_ptr< OneBodyEnergy > core::scoring::methods::OneBodyEnergyOP

typedef utility::pointer::shared_ptr< OtherPoseEnergy const > core::scoring::methods::OtherPoseEnergyCOP

typedef utility::pointer::shared_ptr< OtherPoseEnergy > core::scoring::methods::OtherPoseEnergyOP

typedef utility::pointer::shared_ptr< P_AA_Energy > core::scoring::methods::P_AA_EnergyOP

typedef utility::pointer::shared_ptr< P_AA_pp_Energy > core::scoring::methods::P_AA_pp_EnergyOP

typedef utility::pointer::shared_ptr< P_AA_ss_Energy > core::scoring::methods::P_AA_ss_EnergyOP

typedef utility::pointer::weak_ptr< PBLifetimeCache > core::scoring::methods::PBLifetimeCacheAP

typedef utility::pointer::weak_ptr< PBLifetimeCache const > core::scoring::methods::PBLifetimeCacheCAP

typedef utility::pointer::shared_ptr< PBLifetimeCache const > core::scoring::methods::PBLifetimeCacheCOP

typedef utility::pointer::shared_ptr< PBLifetimeCache > core::scoring::methods::PBLifetimeCacheOP

typedef utility::pointer::shared_ptr< pHEnergy > core::scoring::methods::pHEnergyOP

typedef utility::pointer::weak_ptr< PoissonBoltzmannEnergy > core::scoring::methods::PoissonBoltzmannEnergyAP

typedef utility::pointer::weak_ptr< PoissonBoltzmannEnergy const > core::scoring::methods::PoissonBoltzmannEnergyCAP

typedef utility::pointer::shared_ptr< PoissonBoltzmannEnergy const > core::scoring::methods::PoissonBoltzmannEnergyCOP

typedef utility::pointer::shared_ptr< PoissonBoltzmannEnergy > core::scoring::methods::PoissonBoltzmannEnergyOP

typedef utility::pointer::shared_ptr< ProClosureEnergy const > core::scoring::methods::ProClosureEnergyCOP

typedef utility::pointer::shared_ptr< ProClosureEnergy > core::scoring::methods::ProClosureEnergyOP

typedef utility::pointer::shared_ptr< RamachandranEnergy2B const > core::scoring::methods::RamachandranEnergy2BCOP

typedef utility::pointer::shared_ptr< RamachandranEnergy2B > core::scoring::methods::RamachandranEnergy2BOP

typedef utility::pointer::shared_ptr< RamachandranEnergy const > core::scoring::methods::RamachandranEnergyCOP

typedef utility::pointer::shared_ptr< RamachandranEnergy > core::scoring::methods::RamachandranEnergyOP

typedef utility::pointer::weak_ptr< RamaPreProEnergy > core::scoring::methods::RamaPreProEnergyAP

typedef utility::pointer::weak_ptr< RamaPreProEnergy const > core::scoring::methods::RamaPreProEnergyCAP

typedef utility::pointer::shared_ptr< RamaPreProEnergy const > core::scoring::methods::RamaPreProEnergyCOP

typedef utility::pointer::shared_ptr< RamaPreProEnergy > core::scoring::methods::RamaPreProEnergyOP

typedef utility::pointer::shared_ptr< ReferenceEnergy const > core::scoring::methods::ReferenceEnergyCOP

typedef utility::pointer::shared_ptr< ReferenceEnergyNoncanonical const > core::scoring::methods::ReferenceEnergyNoncanonicalCOP

typedef utility::pointer::shared_ptr< ReferenceEnergyNoncanonical > core::scoring::methods::ReferenceEnergyNoncanonicalOP

typedef utility::pointer::shared_ptr< ReferenceEnergy > core::scoring::methods::ReferenceEnergyOP

typedef utility::pointer::shared_ptr< ResidualDipolarCouplingEnergy > core::scoring::methods::ResidualDipolarCouplingEnergyOP

typedef utility::pointer::weak_ptr< ResidueCartBondedParameters > core::scoring::methods::ResidueCartBondedParametersAP

typedef utility::pointer::weak_ptr< ResidueCartBondedParameters const > core::scoring::methods::ResidueCartBondedParametersCAP

typedef utility::pointer::shared_ptr< ResidueCartBondedParameters const > core::scoring::methods::ResidueCartBondedParametersCOP

typedef utility::pointer::shared_ptr< ResidueCartBondedParameters > core::scoring::methods::ResidueCartBondedParametersOP

typedef utility::pointer::shared_ptr< RG_Local_MinData > core::scoring::methods::RG_Local_MinDataOP

typedef utility::pointer::shared_ptr< RG_MinData > core::scoring::methods::RG_MinDataOP

typedef utility::pointer::shared_ptr< RingClosureEnergy const > core::scoring::methods::RingClosureEnergyCOP

typedef utility::pointer::shared_ptr< RingClosureEnergy > core::scoring::methods::RingClosureEnergyOP

typedef utility::pointer::shared_ptr< SequenceDependentRefEnergy const > core::scoring::methods::SequenceDependentRefEnergyCOP

typedef utility::pointer::shared_ptr< SequenceDependentRefEnergy > core::scoring::methods::SequenceDependentRefEnergyOP

typedef utility::pointer::shared_ptr< ShortRangeTwoBodyEnergy const > core::scoring::methods::ShortRangeTwoBodyEnergyCOP

typedef utility::pointer::shared_ptr< ShortRangeTwoBodyEnergy > core::scoring::methods::ShortRangeTwoBodyEnergyOP

typedef utility::pointer::shared_ptr<SplitUnfoldedTwoBodyEnergy> core::scoring::methods::SplitUnfoldedTwoBodyEnergyOP

typedef utility::vector1< std::pair< atm_name_quad, CartBondedParametersCOP > > core::scoring::methods::torsionparam_vector

typedef utility::pointer::shared_ptr< TwoBodyEnergy const > core::scoring::methods::TwoBodyEnergyCOP

typedef utility::pointer::shared_ptr< TwoBodyEnergy > core::scoring::methods::TwoBodyEnergyOP

typedef utility::pointer::shared_ptr< UnfoldedStateEnergy > core::scoring::methods::UnfoldedStateEnergyOP

typedef utility::pointer::shared_ptr< VdWTinkerResPairMinData const > core::scoring::methods::VdWTinkerResPairMinDataCOP

typedef utility::pointer::shared_ptr< VdWTinkerResPairMinData > core::scoring::methods::VdWTinkerResPairMinDataOP

typedef utility::pointer::shared_ptr< WaterAdductIntraEnergy > core::scoring::methods::WaterAdductIntraEnergyOP

typedef utility::pointer::shared_ptr< WholeStructureEnergy > core::scoring::methods::WholeStructureEnergyOP

typedef utility::pointer::shared_ptr< YHHPlanarityEnergy > core::scoring::methods::YHHPlanarityEnergyOP

Enumeration Type Documentation

enum core::scoring::methods::EnergyMethods

Enumerator
etable_method
dunbrack_method
hbond_method
elec_method
lkball_method
mm_lj_energy_inter_method
pair_e_method
reference_e_method
vdw_method
ramachandran_method
n_energy_methods

enum core::scoring::methods::EnergyMethodType

Enumerator
ci_2b
cd_2b
ci_lr_2b
cd_lr_2b
ci_1b
cd_1b
ws
n_energy_method_types

enum core::scoring::methods::LongRangeEnergyType

Enumerator
constraints_lr
gen_born_lr
multipole_elec_lr
vdw_tinker_lr
sasa_lr
PB_elec_lr
cart_bonded_lr
rama2b_lr
ramaprepro_lr
aspartimide_penalty_lr
rna_suite_lr
rna_stub_coord_lr
DFIRE
sym_bonus_lr
elec_dens_energy
elec_dens_fast_energy
elec_dens_cen_energy
elec_dens_allatom_cen_energy
elec_dens_atomwise_energy
patterson_corr_energy
fa_disulfide_energy
disulfide_matching_energy
centroid_disulfide_energy
n_long_range_types

Function Documentation

bool core::scoring::methods::atoms_interact	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		core::id::AtomID const &	id1,
		core::id::AtomID const &	id2,
		core::Real const	interaction_cutoff
	)

References core::id::AtomID::atomno(), core::kinematics::distance(), core::id::AtomID::rsd(), core::conformation::Residue::seqpos(), and core::conformation::Residue::xyz().

bool core::scoring::methods::count_atom ( int const & atype )

inline

Referenced by core::scoring::methods::SuckerEnergy::eval_atom_derivative(), and core::scoring::methods::SuckerEnergy::residue_pair_energy().

bool core::scoring::methods::count_pair_bs	(	Size const	pos1,
		Size const	pos2,
		BasePartner const &	partner
	)

inline

ordered!!!! requires pos1<pos2

Referenced by core::scoring::methods::DNA_BaseEnergy::eval_atom_derivative(), and core::scoring::methods::DNA_BaseEnergy::residue_pair_energy().

void core::scoring::methods::create_long_range_energy_container	(	core::pose::Pose &	pose,
		core::scoring::ScoreType const	scoretype,
		core::scoring::methods::LongRangeEnergyType const	lr_type
	)

Determines whether a long-range energies container exists in the pose energies object. If not, creates a new one and appends the score type to it, if necessary.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References core::pose::Pose::energies().

Referenced by core::scoring::methods::RamaPreProEnergy::setup_for_scoring(), and core::scoring::methods::AspartimidePenaltyEnergy::setup_for_scoring().

void core::scoring::methods::determine_lo_and_hi_residues	(	core::pose::Pose const &	pose,
		core::Size const	rsd1,
		core::Size const	rsd2,
		bool &	res1_is_lo,
		bool &	res2_is_lo
	)

Given two residues that may or may not be connected, determine which of the two, if any, is the lower one and which is the upper.

Inputs are rsd1 and rsd2; outputs are rsd1_is_lo and rsd2_is_lo. Both will be false if the residues aren't conventionally connected (i.e. the C of one connected to the N of the other).

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), core::chemical::ResidueConnection::index(), core::conformation::Residue::lower_connect(), core::pose::Pose::residue(), core::conformation::Residue::residue_connection_partner(), and core::conformation::Residue::upper_connect().

Referenced by core::scoring::methods::RamaPreProEnergy::defines_residue_pair_energy(), core::scoring::methods::AspartimidePenaltyEnergy::defines_residue_pair_energy(), core::scoring::methods::RamaPreProEnergy::residue_pair_energy(), and core::scoring::methods::AspartimidePenaltyEnergy::residue_pair_energy().

std::string const core::scoring::methods::dna_deriv_atom ( " C5 " )

the atom through which the knowledge based potential applies a force

Referenced by core::scoring::methods::DNA_BaseEnergy::eval_atom_derivative().

void core::scoring::methods::find_cutpoint_variants	(	core::pose::Pose const &	pose,
		core::kinematics::FoldTree const &	,
		utility::vector1< int > &	cutpoints
	)

References is_lower_cutpoint(), and core::pose::Pose::size().

Referenced by core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), and core::scoring::methods::LinearChainbreakEnergy::finalize_total_energy().

static THREAD_LOCAL basic::Tracer core::scoring::methods::GEOMETRIES ( "core.scoring.CartesianBondedEnergy.GEOMETRIES" )

static

core::Size core::scoring::methods::get_lower_cutpoint_partner_for_upper	(	core::pose::Pose const &	pose,
		core::Size const	upper_res
	)

Instead of assuming cutpoint partner is simply res-1, find which residue connects via lower/upper.

Size core::scoring::methods::get_lower_cutpoint_partner_for_upper	(	pose::Pose const &	pose,
		Size const	upper_res
	)

References core::chemical::CUTPOINT_LOWER, core::chemical::ResidueType::has_variant_type(), lower_upper_connected_across_cutpoint(), core::pose::Pose::residue(), and core::pose::Pose::residue_type().

Referenced by core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::methods::LinearChainbreakEnergy::eval_atom_derivative(), core::pose::rna::is_cutpoint_closed_torsion(), and protocols::toolbox::AtomID_Mapper::renumber_after_variant_changes().

core::Real core::scoring::methods::get_residue_weight_by_ss ( const char ss )

References tr().

Referenced by core::scoring::methods::EnvEnergy::residue_energy(), and core::scoring::methods::CenPairEnergy::residue_pair_energy().

std::string core::scoring::methods::get_restag ( core::chemical::ResidueType const & restype )

helper function

References core::chemical::ResidueType::aa(), core::chemical::get_L_equivalent(), core::chemical::is_canonical_D_aa(), core::chemical::ResidueType::is_NA(), core::chemical::ResidueType::is_protein(), core::chemical::ResidueType::name(), core::chemical::ResidueType::name3(), core::chemical::name_from_aa(), and core::chemical::PATCH_LINKER.

core::Size core::scoring::methods::get_upper_cutpoint_partner_for_lower	(	core::pose::Pose const &	pose,
		core::Size const	lower_res
	)

Instead of assuming cutpoint partner is simply cutpoint+1, find which residue connects via lower/upper.

Size core::scoring::methods::get_upper_cutpoint_partner_for_lower	(	pose::Pose const &	pose,
		Size const	lower_res
	)

Instead of assuming cutpoint partner is simply cutpoint+1, find which residue connects via lower/upper. Important in handling cyclized nucleotides.

References core::chemical::CUTPOINT_UPPER, core::chemical::ResidueType::has_variant_type(), lower_upper_connected_across_cutpoint(), core::pose::Pose::residue(), and core::pose::Pose::residue_type().

Referenced by protocols::stepwise::modeler::declare_chemical_bonds_at_cutpoints(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::methods::LinearChainbreakEnergy::eval_atom_derivative(), protocols::stepwise::modeler::figure_out_moving_chain_break_res(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), core::scoring::methods::LinearChainbreakEnergy::finalize_total_energy(), protocols::farna::movers::RNA_LoopCloser::get_chainbreak_xyz(), protocols::farna::movers::RNA_LoopCloser::get_cutpoints_closed(), protocols::stepwise::modeler::is_cutpoint_closed(), core::pose::rna::is_cutpoint_closed_torsion(), protocols::toolbox::AtomID_Mapper::renumber_after_variant_changes(), and protocols::farna::movers::RNA_LoopCloser::rna_ccd_close().

bool core::scoring::methods::is_lower_cutpoint	(	core::Size	residue,
		core::pose::Pose const &	pose
	)

References core::chemical::CUTPOINT_LOWER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), and core::pose::Pose::residue().

Referenced by core::scoring::methods::LinearChainbreakEnergy::eval_atom_derivative(), and find_cutpoint_variants().

bool core::scoring::methods::is_upper_cutpoint	(	core::Size	residue,
		core::pose::Pose const &	pose
	)

References core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), and core::pose::Pose::residue().

Referenced by core::scoring::methods::LinearChainbreakEnergy::eval_atom_derivative().

bool core::scoring::methods::lower_upper_connected_across_cutpoint	(	core::conformation::Residue const &	lower_rsd,
		core::conformation::Residue const &	upper_rsd
	)

helper function for looking at residue connections to get lower/upper partners

References core::conformation::Residue::connect_map_size(), core::conformation::Residue::connected_residue_at_resconn(), core::conformation::Residue::lower_connect_atom(), core::conformation::Residue::residue_connect_atom_index(), core::conformation::Residue::residue_connection_conn_id(), core::conformation::Residue::seqpos(), and core::conformation::Residue::upper_connect_atom().

Referenced by get_lower_cutpoint_partner_for_upper(), and get_upper_cutpoint_partner_for_lower().

bool core::scoring::methods::operator!=	(	EnergyMethodOptions const &	a,
		EnergyMethodOptions const &	b
	)

used inside ScoreFunctionInfo::operator==

References protocols::match::upstream::b.

std::ostream& core::scoring::methods::operator<<	(	std::ostream &	out,
		const FreeDOF_Options &	options
	)

References core::scoring::methods::FreeDOF_Options::show().

std::ostream & core::scoring::methods::operator<<	(	std::ostream &	out,
		EnergyMethodOptions const &	options
	)

References core::scoring::methods::EnergyMethodOptions::show().

bool core::scoring::methods::operator==	(	FreeDOF_Options const &	a,
		FreeDOF_Options const &	b
	)

References core::scoring::methods::FreeDOF_Options::free_2HOprime_bonus_, core::scoring::methods::FreeDOF_Options::free_side_chain_bonus_, core::scoring::methods::FreeDOF_Options::free_sugar_bonus_, core::scoring::methods::FreeDOF_Options::free_suite_bonus_, and core::scoring::methods::FreeDOF_Options::pack_phosphate_penalty_.

bool core::scoring::methods::operator==	(	EnergyMethodOptions const &	a,
		EnergyMethodOptions const &	b
	)

used inside ScoreFunctionInfo::operator==

bool core::scoring::methods::residues_interact	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		core::Real const	interaction_cutoff
	)

References core::kinematics::tree::distance_squared(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_radius(), and core::conformation::Residue::xyz().

BasePartner const & core::scoring::methods::retrieve_base_partner_from_pose_inline ( pose::Pose const & pose )

inline

same as dna::retrieve_base_partner_from_pose

References core::pose::datacache::CacheableDataType::BASE_PARTNER, and core::pose::Pose::data().

Referenced by core::scoring::methods::DNA_BaseEnergy::eval_atom_derivative(), core::scoring::methods::DNA_BaseEnergy::residue_pair_energy(), and core::scoring::methods::DNA_ReferenceEnergy::residue_pair_energy().

MultipoleElecResPairMinData const& core::scoring::methods::retrieve_mp_pairdata ( ResPairMinimizationData const & pairdata )

inline

References core::scoring::ResPairMinimizationData::get_data(), core::scoring::ResPairMinimizationData::get_data_ref(), and core::scoring::mp_respair_data.

MultipoleElecResidueInfo const& core::scoring::methods::retrieve_mp_resdata ( ResSingleMinimizationData const & resdata )

inline

References core::scoring::ResSingleMinimizationData::get_data_ref(), and core::scoring::mp_res_data.

Referenced by core::scoring::methods::MultipoleElecEnergy::eval_intrares_derivatives(), and core::scoring::methods::MultipoleElecEnergy::eval_intrares_energy_ext().

MultipoleElecResidueInfoCOP core::scoring::methods::retrieve_mp_resdata_ptr ( ResSingleMinimizationData const & resdata )

inline

References core::scoring::ResSingleMinimizationData::get_data(), and core::scoring::mp_res_data.

Referenced by core::scoring::methods::MultipoleElecEnergy::setup_for_minimizing_for_residue_pair().

MultipoleElecResidueInfo const& core::scoring::methods::retrieve_mp_residue_info	(	pose::Pose const &	pose,
		Size const	seqpos
	)

inline

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO.

Referenced by core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::MultipoleElecEnergy::residue_pair_energy(), and core::scoring::methods::MultipoleElecEnergy::residue_pair_energy_ext().

MultipoleElecResPairMinData& core::scoring::methods::retrieve_nonconst_mp_pairdata ( ResPairMinimizationData & pairdata )

inline

References core::scoring::ResPairMinimizationData::get_data(), core::scoring::mp_respair_data, and core::scoring::ResPairMinimizationData::set_data().

Referenced by core::scoring::methods::MultipoleElecEnergy::setup_for_minimizing_for_residue_pair().

MultipoleElecResidueInfo& core::scoring::methods::retrieve_nonconst_mp_resdata ( ResSingleMinimizationData & resdata )

inline

References core::scoring::ResSingleMinimizationData::get_data(), core::scoring::mp_res_data, and core::scoring::ResSingleMinimizationData::set_data().

Referenced by core::scoring::methods::MultipoleElecEnergy::setup_for_scoring_for_residue().

MultipoleElecResidueInfo& core::scoring::methods::retrieve_nonconst_mp_residue_info	(	pose::Pose &	pose,
		Size const	seqpos
	)

inline

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO.

VdWTinkerResPairMinData& core::scoring::methods::retrieve_nonconst_vdw_pairdata ( ResPairMinimizationData & pairdata )

inline

References core::scoring::ResPairMinimizationData::get_data(), core::scoring::ResPairMinimizationData::set_data(), and core::scoring::vdw_respair_data.

Referenced by core::scoring::methods::VdWTinkerEnergy::setup_for_minimizing_for_residue_pair().

VdWTinkerResidueInfo& core::scoring::methods::retrieve_nonconst_vdw_resdata ( ResSingleMinimizationData & resdata )

inline

References core::scoring::ResSingleMinimizationData::get_data(), core::scoring::ResSingleMinimizationData::set_data(), and core::scoring::vdw_res_data.

Referenced by core::scoring::methods::VdWTinkerEnergy::setup_for_scoring_for_residue().

VdWTinkerResidueInfo& core::scoring::methods::retrieve_nonconst_vdw_residue_info	(	pose::Pose &	pose,
		Size const	seqpos
	)

inline

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::VDWTINKER_POSE_INFO.

VdWTinkerResPairMinData const& core::scoring::methods::retrieve_vdw_pairdata ( ResPairMinimizationData const & pairdata )

inline

References core::scoring::ResPairMinimizationData::get_data(), core::scoring::ResPairMinimizationData::get_data_ref(), and core::scoring::vdw_respair_data.

VdWTinkerResidueInfo const& core::scoring::methods::retrieve_vdw_resdata ( ResSingleMinimizationData const & resdata )

inline

References core::scoring::ResSingleMinimizationData::get_data_ref(), and core::scoring::vdw_res_data.

Referenced by core::scoring::methods::VdWTinkerEnergy::eval_intrares_derivatives(), core::scoring::methods::VdWTinkerEnergy::eval_intrares_energy_ext(), and core::scoring::methods::VdWTinkerEnergy::eval_residue_pair_derivatives().

VdWTinkerResidueInfoCOP core::scoring::methods::retrieve_vdw_resdata_ptr ( ResSingleMinimizationData const & resdata )

inline

References core::scoring::ResSingleMinimizationData::get_data(), and core::scoring::vdw_res_data.

Referenced by core::scoring::methods::VdWTinkerEnergy::setup_for_minimizing_for_residue_pair().

VdWTinkerResidueInfo const& core::scoring::methods::retrieve_vdw_residue_info	(	pose::Pose const &	pose,
		Size const	seqpos
	)

inline

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::VDWTINKER_POSE_INFO.

Referenced by core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::VdWTinkerEnergy::residue_pair_energy(), and core::scoring::methods::VdWTinkerEnergy::residue_pair_energy_ext().

Real core::scoring::methods::sqr ( Real x )

inline

Referenced by core::scoring::methods::MembraneEnvSmoothEnergy::sigmoidish_neighbor(), and core::scoring::methods::EnvSmoothEnergy::sigmoidish_neighbor().

void core::scoring::methods::swap_seqpos	(	core::Size &	seqpos1,
		core::Size &	seqpos2
	)

static THREAD_LOCAL basic::Tracer core::scoring::methods::TR ( "core.scoring.HydroxylTorsionEnergy" )

static

static THREAD_LOCAL basic::Tracer core::scoring::methods::TR ( "core.scoring.methods.TwoBodyEnergy" )

static

static THREAD_LOCAL basic::Tracer core::scoring::methods::tr	(	"core.scoring.methods.Chainbreak"	,
		basic::t_info
	)

static

Referenced by core::scoring::methods::LinearChainbreakEnergy::do_score_ovp(), core::scoring::methods::ResidualDipolarCouplingEnergy::eval_dipolar(), core::scoring::methods::DistanceChainbreakEnergy::finalize_total_energy(), core::scoring::methods::LinearChainbreakEnergy::finalize_total_energy(), get_residue_weight_by_ss(), core::scoring::methods::ResidualDipolarCouplingEnergy::setup_for_minimizing(), and core::scoring::methods::CustomAtomPairEnergy::setup_for_scoring().

static THREAD_LOCAL basic::Tracer core::scoring::methods::tr ( "core.scoring.methods" )

static

static basic::Tracer core::scoring::methods::TR ( "core.scoring.methods.DNA_ReferenceEnergy" )

static

static THREAD_LOCAL basic::Tracer core::scoring::methods::tr	(	"core.scoring.methods.LinearChainbreak"	,
		basic::t_info
	)

static

static THREAD_LOCAL basic::Tracer core::scoring::methods::TR ( "core.scoring.methods.D2H_SA_Energy.cc" )

static

static THREAD_LOCAL basic::Tracer core::scoring::methods::TR ( "core.scoring.CenPairMotifEnergy" )

static

static THREAD_LOCAL basic::Tracer core::scoring::methods::TR ( "core.scoring.CenPairMotifDegreeEnergy" )

static

static THREAD_LOCAL basic::Tracer core::scoring::methods::tr ( "core.scoring.methods.CustomAtomPairEnergy" )

static

static THREAD_LOCAL basic::Tracer core::scoring::methods::TR ( "core.scoring.GoapEnergy" )

static

static THREAD_LOCAL basic::Tracer core::scoring::methods::TR ( "core.scoring.SSElementMotifContactEnergy" )

static

static basic::Tracer core::scoring::methods::TR ( "core.scoring.methods.DNA_DihedralEnergy" )

static

static THREAD_LOCAL basic::Tracer core::scoring::methods::TR ( "core.scoring.methods.MMTorsionEnergy" )

static

static THREAD_LOCAL basic::Tracer core::scoring::methods::TR ( "core.mm.MMBondLengthEnergy" )

static

static THREAD_LOCAL basic::Tracer core::scoring::methods::TR ( "core.scoring.methods.ProQ_Energy.cc" )

static

static THREAD_LOCAL basic::Tracer core::scoring::methods::TR ( "core.mm.MMBondAngleEnergy" )

static

static THREAD_LOCAL basic::Tracer core::scoring::methods::TR ( "core.scoring.AspartimidePenaltyEnergy" )

static

static THREAD_LOCAL basic::Tracer core::scoring::methods::TR ( "core.scoring.RamaPreProEnergy" )

static

static THREAD_LOCAL basic::Tracer core::scoring::methods::TR ( "core.scoring.CartesianBondedEnergy" )

static

Real const core::scoring::methods::vdw_scale_factor ( 0. 8 )

Referenced by core::scoring::methods::HybridVDW_Energy::eval_atom_derivative(), and core::scoring::methods::HybridVDW_Energy::residue_pair_energy().

Variable Documentation

Distance const core::scoring::methods::end_sig = 10.2

Referenced by core::scoring::methods::MembraneEnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::scoring::methods::EnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::scoring::methods::MembraneEnvSmoothEnergy::sigmoidish_neighbor(), and core::scoring::methods::EnvSmoothEnergy::sigmoidish_neighbor().

DistanceSquared const core::scoring::methods::end_sig2 = end_sig*end_sig

Referenced by core::scoring::methods::MembraneEnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::scoring::methods::EnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::scoring::methods::MembraneEnvSmoothEnergy::sigmoidish_neighbor(), and core::scoring::methods::EnvSmoothEnergy::sigmoidish_neighbor().

const Real core::scoring::methods::K_ANGLE =80.0

static

Referenced by core::scoring::methods::IdealParametersDatabase::IdealParametersDatabase().

const Real core::scoring::methods::K_LENGTH =300.0

static

Referenced by core::scoring::methods::IdealParametersDatabase::IdealParametersDatabase().

const Real core::scoring::methods::K_TORSION =20.0

static

Referenced by core::scoring::methods::IdealParametersDatabase::IdealParametersDatabase().

const Real core::scoring::methods::K_TORSION_IMPROPER =40.0

static

Referenced by core::scoring::methods::IdealParametersDatabase::IdealParametersDatabase().

const Real core::scoring::methods::K_TORSION_PROTON =10.0

static

Referenced by core::scoring::methods::IdealParametersDatabase::IdealParametersDatabase().

Distance const core::scoring::methods::start_sig = 9.8

Referenced by core::scoring::methods::MembraneEnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::scoring::methods::EnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::scoring::methods::MembraneEnvSmoothEnergy::sigmoidish_neighbor(), and core::scoring::methods::EnvSmoothEnergy::sigmoidish_neighbor().

DistanceSquared const core::scoring::methods::start_sig2 = start_sig*start_sig

Referenced by core::scoring::methods::MembraneEnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::scoring::methods::EnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::scoring::methods::MembraneEnvSmoothEnergy::sigmoidish_neighbor(), and core::scoring::methods::EnvSmoothEnergy::sigmoidish_neighbor().

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation