core::scoring Namespace Reference

Namespaces
namespace	carbon_hbonds
namespace	constraints
namespace	custom_pair_distance
namespace	disulfides
namespace	dna
namespace	dssp
namespace	electron_density
namespace	electron_density_atomwise
namespace	EnergiesCacheableDataType
namespace	etable
namespace	geometric_solvation
namespace	hackaro
namespace	hackelec
namespace	hbonds
namespace	interface
namespace	methods
namespace	mm
namespace	nv
namespace	orbitals
namespace	packing
namespace	packstat
namespace	rna
namespace	saxs
namespace	sc
namespace	solid_surface
namespace	sym_e
namespace	symmetry
namespace	trie
Classes
class	AtomVDW
class	CenHBPotential
class	ContextGraph
class	ContextGraphFactory
class	DenseNeighborIterator
class	DenseNeighborConstIterator
class	DenseEnergyContainer
class	DerivVectorPair
	A glorified struct for holding f1/f2 vectors used to represent the derivatives in our internal-geometry based minimization algorithms. More...
class	DockingScoreFunction
class	Energies
	A cached energies object. More...
class	EnergyNode
class	EnergyEdge
class	EnergyGraph
	Class to hold the component energies between pairs of residues. Each node represents a residue in its corresponding structure. Each edge in the graph holds a two-body energy map representing the unweighted components of the energy function for those terms with non-zero weight. The EnergyGraph may be accessed from the pose's Energies object, but at a price of an extra score evaluation. This second score evaluation may be avoided if you use the ScoreFunction::score_components( pose ) method. More...
class	EMapVector
	A vector for storing energy data, initially all values are 0. More...
class	CenListInfo
	Keep track of the cenlist information. More...
class	EnvPairPotential
class	GenBornResidueInfo
class	GenBornPoseInfo
class	GenBornRotamerSetInfo
class	GenBornPotential
class	ResidueNeighborIterator
class	ResidueNeighborConstIterator
class	LREnergyContainer
class	Membrane_FAEmbed
class	Membrane_FAPotential
class	MembraneEmbed
class	MembranePotential
class	MembraneTopology
class	ResSingleMinimizationData
class	ResPairMinimizationData
class	MinimizationNode
class	MinimizationEdge
class	MinimizationGraph
	Class to hold all the minimization-specific data that's required to efficiently evaluate the score function and its derivatives on a structure of fixed sequence and chemical identity. More...
class	AtomNeighbor
	an atom-atom neighborlist object More...
class	NeighborList
class	OmegaTether
class	OneToAllNeighborIterator
class	OneToAllNeighborConstIterator
class	OneToAllEnergyContainer
class	P_AA
class	PairEPotential
class	PeptideBondedNeighborIterator
class	PeptideBondedNeighborConstIterator
class	PeptideBondedEnergyContainer
class	PoissonBoltzmannPotential
class	Ramachandran
class	Ramachandran2B
struct	data_struct
struct	data_structDa
struct	data_structR
struct	data_structDaR
class	ResidualDipolarCoupling
	ResidualDipolarCouplings are mainly handled by this class related classed: RDC --- a single line in an RDC file - representing a single dipolar coupling ResidualDipolarCouplingEnergy -- an energy method which triggers computations handled by this class. More...
class	RDC
class	ResidualDipolarCoupling_Rohl
class	RDC_Rohl
class	SmallAtNb
class	ResidueNblistData
class	ResiduePairNeighborList
class	Predicate
class	IsProteinCAPredicate
class	ResRangePredicate
class	SelectedResPredicate
class	ExcludedResPredicate
class	ScoreFunction
	This object defines a ScoreFunction, it contains methods for calculating the various scoring components (called ScoreType's) used in Rosetta. It also contains weights that are applied to each of those components. Only scoring components with non-zero weights are calculated. More...
class	ScoreFunctionFactory
	a collection of functions making a single score_function More...
class	ScoreFunctionInfo
	Info on the scorefunction settings. More...
class	ScoreTypeManager
class	ScoringManager
class	DimerPairing
class	SecondaryStructurePotential
	secondary structure scoring cut from classic rosetta structure.h/structure.cc More...
class	SecondaryStructureWeights
	Holds weights and flags for configuring a SecondaryStructureEnergy evaluation. More...
class	SigmoidWeightedCenList
	Keep track of the cenlist information stores both centroid counts (T = Real) as well as d_centroid_counts (T = Vector) More...
class	SmoothScoreTermCoeffs
class	SmoothEnvPairPotential
class	BB_Pos
struct	Strands
struct	Helices
class	SS_Info
struct	Hairpin
struct	Hairpins
class	SS_Killhairpins_Info
class	TenANeighborNode
class	TenANeighborEdge
class	TenANeighborGraph
class	TwelveANeighborNode
class	TwelveANeighborEdge
class	TwelveANeighborGraph
class	UnfoldedStatePotential
class	WaterAdductHBondPotential
Typedefs
typedef utility::pointer::owning_ptr < ContextGraph >	ContextGraphOP
typedef utility::pointer::owning_ptr < ContextGraph const >	ContextGraphCOP
typedef utility::pointer::owning_ptr < DenseNeighborIterator >	DenseNeighborIteratorOP
typedef utility::pointer::owning_ptr < DenseEnergyContainer >	DenseEnergyContainerOP
typedef utility::pointer::owning_ptr < Energies >	EnergiesOP
typedef utility::pointer::owning_ptr < Energies const >	EnergiesCOP
typedef utility::pointer::owning_ptr < EnergyGraph >	EnergyGraphOP
typedef EMapVector	EnergyMap
typedef utility::pointer::owning_ptr < CenListInfo >	CenListInfoOP
typedef utility::pointer::owning_ptr < GenBornResidueInfo >	GenBornResidueInfoOP
typedef utility::pointer::owning_ptr < GenBornPoseInfo >	GenBornPoseInfoOP
typedef utility::pointer::owning_ptr < GenBornRotamerSetInfo >	GenBornRotamerSetInfoOP
typedef utility::pointer::owning_ptr < ResidueNeighborIterator >	ResidueNeighborIteratorOP
typedef utility::pointer::owning_ptr < ResidueNeighborIterator const >	ResidueNeighborIteratorCOP
typedef utility::pointer::owning_ptr < ResidueNeighborConstIterator >	ResidueNeighborConstIteratorOP
typedef utility::pointer::owning_ptr < ResidueNeighborConstIterator const >	ResidueNeighborConstIteratorCOP
typedef utility::pointer::owning_ptr < LREnergyContainer >	LREnergyContainerOP
typedef utility::pointer::owning_ptr < LREnergyContainer const >	LREnergyContainerCOP
typedef utility::pointer::owning_ptr < Membrane_FAEmbed >	Membrane_FAEmbedOP
typedef utility::pointer::owning_ptr < MembraneEmbed >	MembraneEmbedOP
typedef utility::pointer::owning_ptr < MembranePotential >	MembranePotentialOP
typedef utility::pointer::owning_ptr < MembraneTopology >	MembraneTopologyOP
typedef utility::pointer::owning_ptr < ResSingleMinimizationData >	ResSingleMinimizationDataOP
typedef utility::pointer::owning_ptr < ResSingleMinimizationData const >	ResSingleMinimizationDataCOP
typedef utility::pointer::owning_ptr < ResPairMinimizationData >	ResPairMinimizationDataOP
typedef utility::pointer::owning_ptr < ResPairMinimizationData const >	ResPairMinimizationDataCOP
typedef utility::pointer::owning_ptr < MinimizationGraph >	MinimizationGraphOP
typedef utility::pointer::owning_ptr < MinimizationGraph const >	MinimizationGraphCOP
typedef utility::pointer::owning_ptr < NeighborList >	NeighborListOP
typedef utility::pointer::owning_ptr < NeighborList const >	NeighborListCOP
typedef utility::vector1 < AtomNeighbor >	AtomNeighbors
typedef utility::pointer::owning_ptr < OneToAllNeighborIterator >	OneToAllNeighborIteratorOP
typedef utility::pointer::owning_ptr < OneToAllEnergyContainer >	OneToAllEnergyContainerOP
typedef utility::pointer::owning_ptr < PeptideBondedNeighborIterator >	PeptideBondedNeighborIteratorOP
typedef utility::pointer::owning_ptr < PeptideBondedEnergyContainer >	PeptideBondedEnergyContainerOP
typedef PoissonBoltzmannPotential	PB
typedef Ramachandran	R
typedef core::Real	Tensor [3][3]
typedef core::Real	Tensor5 [5][5]
typedef core::Real	rvec [3]
typedef core::Real	matrix [3][3]
typedef core::Real	rvec5 [5]
typedef utility::pointer::owning_ptr < ResidualDipolarCoupling >	ResidualDipolarCouplingOP
typedef utility::pointer::owning_ptr < ResidualDipolarCoupling const >	ResidualDipolarCouplingCOP
typedef utility::pointer::owning_ptr < ResidualDipolarCoupling_Rohl >	ResidualDipolarCoupling_RohlOP
typedef utility::pointer::owning_ptr < ResidualDipolarCoupling_Rohl const >	ResidualDipolarCoupling_RohlCOP
typedef utility::pointer::owning_ptr < ResidueNblistData >	ResidueNblistDataOP
typedef utility::pointer::owning_ptr < ResidueNblistData const >	ResidueNblistDataCOP
typedef utility::pointer::owning_ptr < ResiduePairNeighborList >	ResiduePairNeighborListOP
typedef utility::pointer::owning_ptr < ResiduePairNeighborList const >	ResiduePairNeighborListCOP
typedef std::list< core::Size >	ResidueSelection
typedef utility::vector1 < core::Size >	ResidueSelectionVector
typedef utility::pointer::owning_ptr < Predicate >	PredicateOP
typedef utility::pointer::owning_ptr < Predicate const >	PredicateCOP
typedef utility::pointer::owning_ptr < ScoreFunction >	ScoreFunctionOP
typedef utility::pointer::owning_ptr < ScoreFunction const >	ScoreFunctionCOP
typedef utility::pointer::owning_ptr < ScoreFunctionInfo >	ScoreFunctionInfoOP
typedef utility::pointer::owning_ptr < ScoreFunctionInfo const >	ScoreFunctionInfoCOP
typedef utility::vector1 < ScoreType >	ScoreTypes
typedef utility::pointer::owning_ptr < DimerPairing >	DimerPairingOP
typedef utility::pointer::owning_ptr < SigmoidWeightedCenList< Real > >	SigmoidWeightedCenListRealOP
typedef utility::pointer::owning_ptr < SigmoidWeightedCenList < numeric::xyzVector< Real > > >	SigmoidWeightedCenListVectorOP
typedef utility::pointer::owning_ptr < SS_Info >	SS_InfoOP
typedef utility::pointer::owning_ptr < SS_Info const >	SS_InfoCOP
typedef utility::pointer::owning_ptr < SS_Killhairpins_Info >	SS_Killhairpins_InfoOP
typedef utility::pointer::owning_ptr < SS_Killhairpins_Info const >	SS_Killhairpins_InfoCOP
typedef utility::pointer::owning_ptr < TenANeighborGraph >	TenANeighborGraphOP
typedef utility::pointer::owning_ptr < TenANeighborGraph const >	TenANeighborGraphCOP
typedef utility::pointer::owning_ptr < TwelveANeighborGraph >	TwelveANeighborGraphOP
typedef utility::pointer::owning_ptr < TwelveANeighborGraph const >	TwelveANeighborGraphCOP
typedef core::Real	Probability
typedef Real	Weight
typedef Real	Score
typedef float	TableEnergy
typedef float	TableProbability
typedef ObjexxFCL::CArray< Energy >	CArray_Energy
typedef ObjexxFCL::CArrayP < Energy >	CArrayP_Energy
typedef ObjexxFCL::CArray < TableEnergy >	CArray_TableEnergy
typedef ObjexxFCL::CArrayP < TableEnergy >	CArrayP_TableEnergy
typedef ObjexxFCL::FArray1D < Length >	FArray1D_Length
typedef ObjexxFCL::FArray2D < Length >	FArray2D_Length
typedef ObjexxFCL::FArray3D < Length >	FArray3D_Length
typedef ObjexxFCL::FArray4D < Length >	FArray4D_Length
typedef ObjexxFCL::FArray5D < Length >	FArray5D_Length
typedef ObjexxFCL::FArray1D < Weight >	FArray1D_Weight
typedef ObjexxFCL::FArray2D < Weight >	FArray2D_Weight
typedef ObjexxFCL::FArray3D < Weight >	FArray3D_Weight
typedef ObjexxFCL::FArray4D < Weight >	FArray4D_Weight
typedef ObjexxFCL::FArray5D < Weight >	FArray5D_Weight
typedef ObjexxFCL::FArray1D < Energy >	FArray1D_Energy
typedef ObjexxFCL::FArray2D < Energy >	FArray2D_Energy
typedef ObjexxFCL::FArray3D < Energy >	FArray3D_Energy
typedef ObjexxFCL::FArray4D < Energy >	FArray4D_Energy
typedef ObjexxFCL::FArray5D < Energy >	FArray5D_Energy
typedef ObjexxFCL::FArray1D < TableEnergy >	FArray1D_TableEnergy
typedef ObjexxFCL::FArray2D < TableEnergy >	FArray2D_TableEnergy
typedef ObjexxFCL::FArray3D < TableEnergy >	FArray3D_TableEnergy
typedef ObjexxFCL::FArray4D < TableEnergy >	FArray4D_TableEnergy
typedef ObjexxFCL::FArray5D < TableEnergy >	FArray5D_TableEnergy
typedef ObjexxFCL::FArray2D < CArrayP_TableEnergy >	AtomPairEnergyTable
typedef ObjexxFCL::FArray1D < Probability >	FArray1D_Probability
typedef ObjexxFCL::FArray2D < Probability >	FArray2D_Probability
typedef ObjexxFCL::FArray3D < Probability >	FArray3D_Probability
typedef ObjexxFCL::FArray4D < Probability >	FArray4D_Probability
typedef ObjexxFCL::FArray5D < Probability >	FArray5D_Probability
typedef ObjexxFCL::FArray1D < TableProbability >	FArray1D_TableProbability
typedef ObjexxFCL::FArray2D < TableProbability >	FArray2D_TableProbability
typedef ObjexxFCL::FArray3D < TableProbability >	FArray3D_TableProbability
typedef ObjexxFCL::FArray4D < TableProbability >	FArray4D_TableProbability
typedef ObjexxFCL::FArray5D < TableProbability >	FArray5D_TableProbability
typedef ObjexxFCL::KeyFArray1D < Real >	KeyFArray1D_Real
typedef ObjexxFCL::KeyFArray2D < Real >	KeyFArray2D_Real
typedef ObjexxFCL::KeyFArray3D < Real >	KeyFArray3D_Real
typedef ObjexxFCL::KeyFArray1D < Weight >	KeyFArray1D_Weight
typedef ObjexxFCL::KeyFArray2D < Weight >	KeyFArray2D_Weight
typedef ObjexxFCL::KeyFArray3D < Weight >	KeyFArray3D_Weight
typedef ObjexxFCL::KeyFArray1D < Energy >	KeyFArray1D_Energy
typedef ObjexxFCL::KeyFArray2D < Energy >	KeyFArray2D_Energy
typedef ObjexxFCL::KeyFArray3D < Energy >	KeyFArray3D_Energy
typedef ObjexxFCL::KeyFArray1D < Probability >	KeyFArray1D_Probability
typedef ObjexxFCL::KeyFArray2D < Probability >	KeyFArray2D_Probability
typedef ObjexxFCL::KeyFArray3D < Probability >	KeyFArray3D_Probability
typedef utility::pointer::owning_ptr < UnfoldedStatePotential >	UnfoldedStatePotentialOP
typedef utility::pointer::owning_ptr < InterfaceInfo >	InterfaceInfoOP
Enumerations
enum	ContextGraphType { ten_A_neighbor_graph = 1, twelve_A_neighbor_graph, centroid_neighbor_graph, num_context_graph_types = centroid_neighbor_graph }
enum	min_single_data { etab_single_nblist = 1, cst_res_data, hbond_res_data, n_min_single_data = hbond_res_data }
enum	min_pair_data {   etab_pair_nblist = 1, cst_respair_data, hackelec_pair_nblist, fa_dslf_respair_data,   fa_custom_pair_dist_data, hbond_respair_data, n_min_pair_data = hbond_respair_data }
enum	ProteinTorsion {   PHI = 1, PSI, OMEGA, CHI1,   CHI2, CHI3, CHI4, protein_torsion_end }
enum	ScoreFunctionParameter { hydrogen_interaction_cutoff = 1 }
	enum for listing the variants More...
enum	ScoreFunctionVariant { loc_lj, lk_sol }
	enum for listing the variants More...
enum	ScoreType {   fa_atr = 1, fa_rep, fa_sol, fa_intra_atr,   fa_intra_rep, fa_intra_sol, fa_intra_RNA_base_phos_atr, fa_intra_RNA_base_phos_rep,   fa_intra_RNA_base_phos_sol, lk_hack, lk_ball, lk_ball_iso,   coarse_fa_atr, coarse_fa_rep, coarse_fa_sol, coarse_beadlj,   mm_lj_intra_rep, mm_lj_intra_atr, mm_lj_inter_rep, mm_lj_inter_atr,   mm_twist, mm_bend, mm_stretch, lk_costheta,   lk_polar, lk_nonpolar, lk_polar_intra_RNA, lk_nonpolar_intra_RNA,   hack_elec, hack_elec_bb_bb, hack_elec_bb_sc, hack_elec_sc_sc,   h2o_hbond, dna_dr, dna_bp, dna_bs,   peptide_bond, pcs, pcs2, fastsaxs,   saxs_score, saxs_cen_score, saxs_fa_score, pddf_score,   fa_mbenv, fa_mbsolv, hack_elec_rna_phos_phos, hack_elec_rna_phos_sugr,   hack_elec_rna_phos_base, hack_elec_rna_sugr_sugr, hack_elec_rna_sugr_base, hack_elec_rna_base_base,   hack_elec_aro_aro, hack_elec_aro_all, hack_aro, rna_fa_atr_base,   rna_fa_rep_base, rna_data_backbone, ch_bond, ch_bond_bb_bb,   ch_bond_sc_sc, ch_bond_bb_sc, pro_close, rama2b,   vdw, cenpack, cenpack_smooth, cen_hb,   hybrid_vdw, rna_vdw, rna_base_backbone, rna_backbone_backbone,   rna_repulsive, rna_base_pair_pairwise, rna_base_axis_pairwise, rna_base_stagger_pairwise,   rna_base_stack_pairwise, rna_base_stack_axis_pairwise, rna_data_base, rna_base_pair,   rna_base_axis, rna_base_stagger, rna_base_stack, rna_base_stack_axis,   rna_torsion, rna_sugar_close, fa_stack, fa_stack_aro,   CI_geom_sol, CI_geom_sol_intra_RNA, fa_cust_pair_dist, custom_atom_pair,   orbitals_hpol, orbitals_haro, orbitals_orbitals, orbitals_hpol_bb,   PyRosettaTwoBodyContextIndepenedentEnergy_first, PyRosettaTwoBodyContextIndepenedentEnergy_last = PyRosettaTwoBodyContextIndepenedentEnergy_first + 10, python, n_ci_2b_score_types = python,   fa_pair, fa_pair_aro_aro, fa_pair_aro_pol, fa_pair_pol_pol,   fa_plane, hbond_sr_bb, hbond_lr_bb, hbond_bb_sc,   hbond_sr_bb_sc, hbond_lr_bb_sc, hbond_sc, hbond_intra,   PyRosettaTwoBodyContextDependentEnergy_first, PyRosettaTwoBodyContextDependentEnergy_last = PyRosettaTwoBodyContextDependentEnergy_first + 10, interface_dd_pair, geom_sol,   geom_sol_intra_RNA, occ_sol_fitted, occ_sol_fitted_onebody, occ_sol_exact,   pair, cen_pair_smooth, Mpair, suck,   rna_rg, interchain_pair, interchain_vdw, n_shortranged_2b_score_types = interchain_vdw,   gb_elec, dslf_ss_dst, dslf_cs_ang, dslf_ss_dih,   dslf_ca_dih, dslf_cbs_ds, dslfc_cen_dst, dslfc_cb_dst,   dslfc_ang, dslfc_cb_dih, dslfc_bb_dih, dslfc_rot,   dslfc_trans, dslfc_RT, atom_pair_constraint, constant_constraint,   coordinate_constraint, angle_constraint, dihedral_constraint, big_bin_constraint,   dunbrack_constraint, site_constraint, rna_bond_geometry, rama,   omega, fa_dun, p_aa_pp, yhh_planarity,   h2o_intra, ref, seqdep_ref, envsmooth,   e_pH, rna_bulge, special_rot, PB_elec,   cen_env_smooth, cbeta_smooth, env, cbeta,   DFIRE, Menv, Mcbeta, Menv_non_helix,   Menv_termini, Menv_tm_proj, Mlipo, rg,   co, hs_pair, ss_pair, rsigma,   sheet, burial, abego, natbias_ss,   natbias_hs, natbias_hh, natbias_stwist, aa_cmp,   dock_ens_conf, rdc, rdc_segments, rdc_rohl,   holes, holes_decoy, holes_resl, holes_min,   holes_min_mean, dab_sasa, dab_sev, sa,   interchain_env, interchain_contact, chainbreak, linear_chainbreak,   overlap_chainbreak, distance_chainbreak, dof_constraint, cart_bonded,   cart_bonded_angle, cart_bonded_length, cart_bonded_torsion, neigh_vect,   neigh_count, neigh_vect_raw, symE_bonus, sym_lig,   pack_stat, rms, res_type_constraint, res_type_linking_constraint,   pocket_constraint, backbone_stub_constraint, surface, p_aa,   unfolded, elec_dens_fast, elec_dens_window, elec_dens_whole_structure_ca,   elec_dens_whole_structure_allatom, elec_dens_atomwise, patterson_cc, hpatch,   Menv_smooth, PyRosettaEnergy_first, PyRosettaEnergy_last = PyRosettaEnergy_first + 10, total_score,   n_score_types = total_score, end_of_score_type_enumeration = total_score }
	Type for looking up cached energies I guess we could get rid of the fa_ prefix, except maybe for fa_pair, to distinguish from std::pair and the centroid pair score... More...
Functions
static basic::Tracer	TR ("core.scoring.AtomVDW")
static Real const	BOGUS_ENERGY (99999.99)
std::ostream &	operator<< (std::ostream &out, const Energies &e)
std::ostream &	operator<< (std::ostream &ost, EMapVector const &emap)
	output operator (index;value)
template<class T , class T_Etable >
void	residue_fast_pair_energy_attached_H (conformation::Residue const &res1, int const atomno1, conformation::Residue const &res2, Size const atomno2, Size const at1hbegin, Size const at1hend, Size const at2hbegin, Size const at2hend, T const &count_pair, T_Etable const &etable_energy, EnergyMap &emap)
	class T must define
template<class T , class T_Etable >
void	inline_residue_atom_pair_energy (conformation::Residue const &res1, conformation::Residue const &res2, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap, int res1_start, int res1_end, int res2_start, int res2_end)
	templated atom pair energy calculations
template<class T , class T_Etable >
void	inline_intraresidue_atom_pair_energy (conformation::Residue const &res, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap)
	intraresidue atom pair energy evaluations
template<class T , class T_Etable >
void	inline_residue_atom_pair_energy (conformation::Residue const &res1, conformation::Residue const &res2, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap)
template<class T , class T_Etable >
void	inline_residue_atom_pair_energy_sidechain_backbone (conformation::Residue const &res1, conformation::Residue const &res2, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap)
template<class T , class T_Etable >
void	inline_residue_atom_pair_energy_sidechain_whole (conformation::Residue const &res1, conformation::Residue const &res2, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap)
template<class T , class T_Etable >
void	inline_residue_atom_pair_energy_backbone_backbone (conformation::Residue const &res1, conformation::Residue const &res2, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap)
template<class T , class T_Etable >
void	inline_residue_atom_pair_energy_sidechain_sidechain (conformation::Residue const &res1, conformation::Residue const &res2, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap)
void	interpolate_value_and_deriv (ObjexxFCL::FArray1D< Real > const &potential, Real const &bin_width, Real const &r, Real &value, Real &deriv)
Membrane_FAEmbed const &	Membrane_FAEmbed_from_pose (pose::Pose const &pose)
Membrane_FAEmbed &	nonconst_Membrane_FAEmbed_from_pose (pose::Pose &pose)
static numeric::random::RandomGenerator	RG (280628)
static basic::Tracer	TR ("core.scoring.MembranePotential")
MembraneEmbed const &	MembraneEmbed_from_pose (pose::Pose const &pose)
MembraneEmbed &	nonconst_MembraneEmbed_from_pose (pose::Pose &pose)
static basic::Tracer	TR ("core.scoring.MembraneTopology")
MembraneTopology const &	MembraneTopology_from_pose (pose::Pose const &pose)
MembraneTopology &	nonconst_MembraneTopology_from_pose (pose::Pose &pose)
void	eval_atom_derivatives_for_minnode (MinimizationNode const &min_node, conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap const &res_weights, utility::vector1< DerivVectorPair > &atom_derivs)
	Evaluate the derivatives for all atoms on the input residue for the terms that apply to this residue (which are stored on the input minimization node).
void	eval_res_onebody_energies_for_minnode (MinimizationNode const &min_node, conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap)
	Deprecated.
void	eval_atom_derivatives_for_minedge (MinimizationEdge const &min_edge, conformation::Residue const &res1, conformation::Residue const &res2, ResSingleMinimizationData const &res1_min_data, ResSingleMinimizationData const &res2_min_data, pose::Pose const &pose, EnergyMap const &respair_weights, utility::vector1< DerivVectorPair > &r1atom_derivs, utility::vector1< DerivVectorPair > &r2atom_derivs)
void	eval_res_pair_energy_for_minedge (MinimizationEdge const &min_edge, conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap)
	Deprecated.
Real	eval_dof_deriv_for_minnode (MinimizationNode const &min_node, conformation::Residue const &rsd, pose::Pose const &pose, id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, ScoreFunction const &sfxn, EnergyMap const &weights)
void	eval_weighted_res_onebody_energies_for_minnode (MinimizationNode const &min_node, conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap, EnergyMap &scratch_emap)
void	eval_weighted_res_pair_energy_for_minedge (MinimizationEdge const &min_edge, conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap, EnergyMap &scratch_emap)
Real	eval_weighted_dof_deriv_for_minnode (MinimizationNode const &min_node, conformation::Residue const &rsd, pose::Pose const &pose, id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, ScoreFunction const &sfxn, EnergyMap const &weights)
static basic::Tracer	tr ("core.scoring.NeighborList")
void	dump_pqr (core::pose::Pose const &pose, std::ostream &out, std::string const &tag, utility::vector1< Size > const &zero_charge_chains)
PoissonBoltzmannPotential &	get_PB_potential ()
basic::Tracer	T ("core.scoring.Ramachandran2B")
Real	sqr (Real x)
void	store_RDC_in_pose (ResidualDipolarCouplingOP rdc_info, core::pose::Pose &pose)
ResidualDipolarCouplingCOP	retrieve_RDC_from_pose (core::pose::Pose const &pose)
ResidualDipolarCouplingOP	retrieve_RDC_from_pose (core::pose::Pose &pose)
std::ostream &	operator<< (std::ostream &out, RDC const &rdc)
std::ostream &	operator<< (std::ostream &out, ResidualDipolarCoupling const &rdc)
std::string	element_string (std::string atom)
int	m_inv_gen (Tensor5 m, int n, Tensor5 minv)
void	jacobi (Real a[5][5], Real d[], Real v[5][5], int *nrot)
void	jacobi3 (Real a[3][3], Real d[], Real v[3][3], int *nrot)
Real	iprod (const rvec a, const rvec b)
void	mvmul (matrix a, const rvec src, rvec dest)
int	compare_by_abs (const void *a, const void *b)
double	frdc (double r0, double r1, double r2, double rdcconst, const double *par)
double	frdcDa (double r0, double r1, double r2, double rdcconst, double const tensorDa, const double *par)
double	frdcR (double r0, double r1, double r2, double rdcconst, double const tensorR, const double *par)
double	frdcDaR (double r0, double r1, double r2, double rdcconst, double const tensorDa, double const tensorR, const double *par)
void	evaluaterdc (const double *par, int m_dat, const void *data, double *fvec, int *info)
void	evaluaterdcDa (const double *par, int m_dat, const void *data, double *fvec, int *info)
void	evaluaterdcR (const double *par, int m_dat, const void *data, double *fvec, int *info)
void	evaluaterdcDaR (const double *par, int m_dat, const void *data, double *fvec, int *info)
void	store_RDC_ROHL_in_pose (ResidualDipolarCoupling_RohlOP rdc_info, core::pose::Pose &pose)
ResidualDipolarCoupling_RohlCOP	retrieve_RDC_ROHL_from_pose (core::pose::Pose const &pose)
ResidualDipolarCoupling_RohlOP	retrieve_RDC_ROHL_from_pose (core::pose::Pose &pose)
static basic::Tracer	tr ("core.scoring.rms_util")
void	invert_exclude_residues (Size nres, utility::vector1< int > const &exclude_list, ResidueSelection &residue_selection)
ResidueSelection	invert_exclude_residues (core::Size nres, utility::vector1< int > const &exclude_list)
Real	native_CA_rmsd (const core::pose::Pose &native_pose, const core::pose::Pose &pose)
Real	native_CA_gdtmm (const core::pose::Pose &native_pose, const core::pose::Pose &pose)
core::Real	automorphic_rmsd (core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2, bool superimpose)
	RMSD between residues, accounting for automorphisms (symmetries). Does NOT include H atoms -- they add lots of extra symmetries.
bool	is_protein_CA (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno)
bool	is_protein_CA_or_CB (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno)
bool	is_protein_backbone (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno)
bool	is_protein_backbone_including_O (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno)
bool	is_protein_sidechain_heavyatom (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno)
bool	is_ligand_heavyatom (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno)
bool	is_ligand_heavyatom_residues (core::conformation::Residue const &residue1, core::conformation::Residue const &, core::Size atomno)
bool	is_polymer_heavyatom (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno)
bool	is_heavyatom (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno)
bool	is_nbr_atom (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno)
core::Real	CA_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2)
core::Real	CA_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2, Size start, Size end)
void	retrieve_coordinates (const core::pose::Pose &pose, const utility::vector1< core::Size > &residues, FArray2D< core::Real > *coords)
core::Real	CA_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2, const std::map< core::Size, core::Size > &residues)
core::Real	CA_gdtmm (const core::pose::Pose &pose1, const core::pose::Pose &pose2, const std::map< core::Size, core::Size > &residues)
core::Real	CA_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2, Size start, Size end, utility::vector1< Size > const &exclude)
core::Real	bb_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2)
core::Real	bb_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2, Size start, Size end, utility::vector1< Size > const &exclude)
core::Real	bb_rmsd_including_O (const core::pose::Pose &pose1, const core::pose::Pose &pose2)
core::Real	bb_rmsd_including_O (const core::pose::Pose &pose1, const core::pose::Pose &pose2, Size start, Size end, utility::vector1< Size > const &exclude)
core::Real	CA_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2, std::list< Size > residue_selection)
core::Real	all_atom_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2)
core::Real	all_atom_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2, std::list< Size > residue_selection)
core::Real	nbr_atom_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2)
int	CA_maxsub (const core::pose::Pose &pose1, const core::pose::Pose &pose2, Real rms=4.0)
	Calculates a C-alpha maxsub-based superposition between pose1 and pose2, returns the number of residues superimposed past a certain threshold. See maxsub.hh and maxsub.cc for more information.
int	CA_maxsub (const core::pose::Pose &pose1, const core::pose::Pose &pose2, std::list< Size > residue_selection, Real rms)
int	xyz_maxsub (FArray2D< core::Real > p1a, FArray2D< core::Real > p2a, int natoms)
int	CA_maxsub_by_subset (const core::pose::Pose &pose1, const core::pose::Pose &pose2, utility::vector1< bool >)
core::Real	CA_gdtmm (core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::list< Size > residue_selection, core::Real &m_1_1, core::Real &m_2_2, core::Real &m_3_3, core::Real &m_4_3, core::Real &m_7_4)
core::Real	CA_gdtmm (core::pose::Pose const &pose1, core::pose::Pose const &pose2, core::Real &m_1_1, core::Real &m_2_2, core::Real &m_3_3, core::Real &m_4_3, core::Real &m_7_4)
	Calculate gdtmm score based on the C-alpha positions in pose1 and pose2. Also returns the five components of the gdtmm score.
core::Real	xyz_gdtmm (FArray2D< core::Real > p1a, FArray2D< core::Real > p2a)
	Calculate gdtmm based on the given sets of xyz coordinates in p1a and p2a.
core::Real	xyz_gdtmm (FArray2D< core::Real > p1a, FArray2D< core::Real > p2a, core::Real &m_1_1, core::Real &m_2_2, core::Real &m_3_3, core::Real &m_4_3, core::Real &m_7_4)
	Calculate gdtmm based on the given sets of xyz coordinates in p1a and p2a.
core::Real	CA_gdtmm (core::pose::Pose const &pose1, core::pose::Pose const &pose2)
	Calculate gdtmm score based on the C-alpha positions in pose1 and pose2.
core::Real	CA_gdtmm (core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::list< Size > residue_selection)
	Calculate gdtmm score based on the C-alpha positions in pose1 and pose2.
Real	superimpose_pose (pose::Pose &mod_pose, pose::Pose const &ref_pose, id::AtomID_Map< id::AtomID > const &atom_map)
	Superimpose mod_pose onto ref_pose using the mapping of atoms from mod_pose to ref_pose given by atom_map.
Real	calpha_superimpose_pose (pose::Pose &mod_pose, pose::Pose const &ref_pose)
	Superimpose two poses by their calpha coordinates. Ignores residues that do not have atoms named "CA.".
core::Real	CA_rmsd_symmetric (const core::pose::Pose &native_pose, const core::pose::Pose &pose)
void	create_shuffle_map_recursive_rms (std::vector< int > sequence, int const N, std::vector< std::vector< int > > &map)
Real	rms_at_corresponding_atoms (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::id::AtomID, core::id::AtomID > atom_id_map)
Real	rms_at_corresponding_atoms (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::id::AtomID, core::id::AtomID > atom_id_map, utility::vector1< Size > const &calc_rms_res)
Real	rms_at_all_corresponding_atoms (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::id::AtomID, core::id::AtomID > atom_id_map)
Real	rms_at_corresponding_atoms_no_super (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::id::AtomID, core::id::AtomID > atom_id_map)
Real	rms_at_corresponding_atoms_no_super (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::id::AtomID, core::id::AtomID > atom_id_map, utility::vector1< Size > const &calc_rms_res)
Real	rms_at_corresponding_heavy_atoms (pose::Pose const &mod_pose, pose::Pose const &ref_pose)
void	setup_matching_heavy_atoms (core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::map< core::id::AtomID, core::id::AtomID > &atom_id_map)
core::Real	residue_sc_rmsd_no_super (core::conformation::ResidueCOP res1, core::conformation::ResidueCOP res2, bool const fxnal_group_only=false)
	utility function to calculate per-residue sidechain rmsd without superposition
void	setup_matching_CA_atoms (core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::map< core::id::AtomID, core::id::AtomID > &atom_id_map)
void	setup_matching_protein_backbone_heavy_atoms (core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::map< core::id::AtomID, core::id::AtomID > &atom_id_map)
void	setup_matching_atoms_with_given_names (core::pose::Pose const &pose1, core::pose::Pose const &pose2, utility::vector1< std::string > const &atom_names_to_find, std::map< core::id::AtomID, core::id::AtomID > &atom_id_map)
void	compute_jump_rmsd (const core::pose::Pose &reference, const core::pose::Pose &model, boost::unordered_map< core::Size, core::Real > *rmsds)
	Computes the RMSD of the jump residues between <model> and <native>, storing the results in a map keyed by jump_id.
template<class T >
core::Real	rmsd_with_super (core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::list< core::Size > const &subset_residues, T *predicate)
template<class T >
core::Real	rmsd_with_super (core::pose::Pose const &pose1, core::pose::Pose const &pose2, T *predicate)
	Select atoms for RMS via a predicate function/functor.
template<class T >
core::Real	rmsd_with_super_subset (core::pose::Pose const &pose1, core::pose::Pose const &pose2, ObjexxFCL::FArray1D_bool const &subset, T *predicate)
	Select a subset atoms for RMS via a predicate function/functor.
template<class T >
core::Real	rmsd_no_super (core::pose::Pose const &pose1, core::pose::Pose const &pose2, T *predicate)
	Select atoms for RMS via a predicate function/functor.
template<class T >
core::Real	rmsd_no_super (core::conformation::ResidueCOPs const &residues1, core::conformation::ResidueCOPs const &residues2, T *predicate)
template<class T >
core::Real	rmsd_no_super_subset (core::pose::Pose const &pose1, core::pose::Pose const &pose2, ObjexxFCL::FArray1D_bool const &subset, T *predicate)
	Select atoms for RMS via a predicate function/functor.
template<class T >
core::Real	biggest_residue_deviation_no_super (core::pose::Pose const &pose1, core::pose::Pose const &pose2, T *predicate)
	function to return the biggest deviation between an atom in a pair of poses,
template<class T >
core::Real	biggest_residue_deviation_no_super_subset (core::pose::Pose const &pose1, core::pose::Pose const &pose2, ObjexxFCL::FArray1D_bool const &subset, T *predicate)
	function to return the biggest deviation between an atom in a pair of poses,
template<class T >
void	fill_rmsd_coordinates (int &natoms, ObjexxFCL::FArray2D< core::Real > &p1a, ObjexxFCL::FArray2D< core::Real > &p2a, core::pose::Pose const &pose1, core::pose::Pose const &pose2, T *predicate)
template<class T >
core::Real	sym_rmsd_with_super_subset (core::pose::Pose const &native_pose, core::pose::Pose const &pose2, ObjexxFCL::FArray1D_bool const &subset, T *predicate)
	Select a subset atoms for Symmetric RMS via a predicate function/functor. Example of use, to calculate C-alpha RMSD: rmsd_with_super(pose1, pose2, is_protein_CA, subset);.
ObjexxFCL::FArray2D_int	angles (num_phi, num_theta)
ObjexxFCL::FArray2D_ubyte	masks (num_bytes, num_overlaps *num_orientations)
void	input_sasa_dats ()
	Reads in the SASA database files sampling/SASA-angles.dat and sampling/SASA-masks.dat into FArrays above.
void	get_overlap (Real const radius_a, Real const radius_b, Real const distance_ijxyz, int &degree_of_overlap)
void	get_orientation (Vector const &a_xyz, Vector const &b_xyz, int &phi_index, int &theta_index, Real distance_ijxyz)
	Gets the orientation of a to b (i to j, see below). Does this by calculating two angles, aphi and theta. (j)
void	get_2way_orientation (Vector const &a_xyz, Vector const &b_xyz, int &phi_a2b_index, int &theta_a2b_index, int &phi_b2a_index, int &theta_b2a_index, Real distance_ijxyz)
	Gets the orientation of a to b (i to j, see below). Does this by calculating two angles, aphi and theta. (j)
Real	calc_total_sasa (pose::Pose const &pose, Real const probe_radius)
	returns total sasa
Real	calc_per_atom_sasa (pose::Pose const &pose, id::AtomID_Map< Real > &atom_sasa, utility::vector1< Real > &rsd_sasa, Real const probe_radius, bool const use_big_polar_H=false)
	returns total sasa
Real	calc_per_atom_sasa (pose::Pose const &pose, id::AtomID_Map< Real > &atom_sasa, utility::vector1< Real > &rsd_sasa, Real const probe_radius, bool const use_big_polar_H, id::AtomID_Map< bool > &atom_subset, bool const use_naccess_sasa_radii=false, bool const expand_polar_radii=false, Real const polar_expansion_radius=1.0)
	returns total sasa
void	calc_atom_masks (core::conformation::Residue const &irsd, core::conformation::Residue const &jrsd, Real const probe_radius, Real const cutoff_distance, utility::vector1< Real > const &radii, id::AtomID_Map< bool > const &atom_subset, core::id::AtomID_Map< utility::vector1< ObjexxFCL::ubyte > > &atom_masks)
int	get_num_bytes ()
	Returns the number of bytes the overlap arrays use for tracking SASA. Adding this in so that the values in the SASA database files can be used in SASA-based scores. (ronj)
ObjexxFCL::FArray2D_int const &	get_angles ()
	Returns const access to the angles FArray, which contains the information in the SASA database file sampling/SASA-angles.dat. Adding this in so that the values in the SASA database files can be used in SASA-based scores. (ronj)
ObjexxFCL::FArray2D_ubyte const &	get_masks ()
	Returns const access to the masks FArray, which contains the information in the SASA database file sampling/SASA-masks.dat. Adding this in so that the values in the SASA database files can be used in SASA-based scores. (ronj)
Real	calc_per_res_hydrophobic_sasa (pose::Pose const &pose, utility::vector1< Real > &rsd_sasa, utility::vector1< Real > &rsd_hydrophobic_sasa, Real const probe_radius, bool use_naccess_sasa_radii)
	Uses the method above to calculate total SASA and then only looks at the hydrophobic contribution. Returns the total hydrophobic SASA for the passed in pose. This method is being used for a protein surface score being developed by ronj. Note: Uses an atom id mask that ignores H's in the pose - only sees and computes the SASA for heavy atoms in the pose. This is done to keep things fast. Only computes the amount of hSASA per residue, not per atom. Doesn't make sense to calculate a per-atom hSASA. (ronj)
void	print_dot_bit_string (utility::vector1< ObjexxFCL::ubyte > &values)
	helper method I was using to try to confirm that the dots are being overlapped and bits are being set correctly (ronj).
void	show_detail (std::ostream &out, EnergyMap &energies, EnergyMap weights)
template<class T >
void	vector1_remove (utility::vector1< T > &v, T const &t)
std::string	find_weights_file (std::string name, std::string extension)
	Utility function to locate a weights or patch file, either with a fully qualified path, in the local directory, or in the database. Names may be passed either with or without the optional extension.
std::ostream &	operator<< (std::ostream &out, ScoreFunction const &sf)
std::string const	STANDARD_WTS ("standard")
std::string const	CENTROID_WTS ("cen_std")
std::string const	SOFT_REP_WTS ("soft_rep")
std::string const	SOFT_REP_DESIGN_WTS ("soft_rep_design")
std::string const	DNA_INT_WTS ("dna_no_gb")
std::string const	DNA_INT_WTS_GB ("dna")
std::string const	MM_STD_WTS ("mm_std")
std::string const	RNA_LORES_WTS ("rna_lores")
std::string const	RNA_HIRES_WTS ("rna_hires")
std::string const	RNA_LORES_PLUS_HIRES_WTS ("rna_lores_plus_hires")
std::string const	MEMB_HIGHRES_WTS ("membrane_highres")
std::string const	SCORE12_PATCH ("score12")
std::string const	SCORE13 ("score13")
std::string const	DOCK_PATCH ("docking")
std::string const	DOCK_LOW_PATCH ("docking_cen")
core::scoring::ScoreFunctionOP	getScoreFunction (bool const is_fullatom=true)
	A helper function which returns a scoring function owning pointer according to the user's command line parameters -score:weights and -score:patch By default it returns weights=standard and patch=score12 for fullatom, and weights=cen_std and patch="" for centroid.
bool	operator== (ScoreFunctionInfo const &a, ScoreFunctionInfo const &b)
ScoreType	score_type_from_name (std::string const &name)
	give a ScoreType string name and return its enum type
std::istream &	operator>> (std::istream &is, ScoreType &score_type)
	input operator for ScoreType enum type
std::ostream &	operator<< (std::ostream &os, ScoreType const &score_type)
	output operator for ScoreType enum type
std::ostream &	operator<< (std::ostream &os, ScoreTypes const &score_types)
	output operator for ScoreTypes list type
std::string	name_from_score_type (ScoreType score_type)
	Returns the name of the ScoreType <score_type>
void	fill_score_range (std::map< std::string, ScoreType > &M, std::string prefix, int first, int last)
std::string const	FA_STANDARD_DEFAULT ("FA_STANDARD_DEFAULT")
	global etable_id
std::string const	FA_STANDARD_SOFT ("FA_STANDARD_SOFT")
std::string const	UNFOLDED_SCORE12 ("UNFOLDED_SCORE12")
std::string const	UNFOLDED_MM_STD ("UNFOLDED_MM_STD")
SS_Info const &	retrieve_const_ss_info_from_pose (pose::Pose const &pose)
	helper function
SS_Info &	retrieve_nonconst_ss_info_from_pose (pose::Pose &pose)
	helper function
void	fill_bb_pos (pose::Pose const &pose, BB_Pos &bb_pos)
	helper function
bool	dimer_pairing_pointer_sorter (DimerPairingOP const &a, DimerPairingOP const &b)
static numeric::random::RandomGenerator	ss_weights_RG (82645)
std::ostream &	operator<< (std::ostream &out, Strands const &s)
std::ostream &	operator<< (std::ostream &out, Helices const &s)
static basic::Tracer	trKillHairpinsIO ("core.score.SS_Killhairpins_Info")
std::ostream &	operator<< (std::ostream &out, Hairpin const &s)
std::ostream &	operator<< (std::ostream &out, Hairpins const &s)
void	eval_scsc_sr2b_energies (conformation::Residue const &r1, conformation::Residue const &r2, Vector const &r1sc_centroid, Vector const &r2sc_centroid, Real const &r1sc_radius, Real const &r2sc_radius, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap)
	With two bounding spheres for a pair of sidechains, evaluate all the sidechain/sidechain energies. This will avoid a call to EnergyMethod E's sidechain_sidechain_energiy method if a) E's atomic_interaction_cutoff + r1sc_radius + r2sc_radius < dist( r1sc_centroid, r2sc_centroid ) and b) E returns "true" in a call to its divides_backbone_and_- sidechain_energetics() method. Both context-dependent and context-independent 2-body energies are evaluated in this function.
void	eval_bbsc_sr2b_energies (conformation::Residue const &r1, conformation::Residue const &r2, Vector const &r1bb_centroid, Vector const &r2sc_centroid, Real const &r1bb_radius, Real const &r2sc_radius, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap)
	With two bounding spheres for a backbone and a sidechain, evaluate all the backbone/sidechain energies. This will avoid a call to EnergyMethod E's backbone_sidechain_energiy method if either a) E's atomic_interaction_cutoff + r1bb_radius + r2sc_radius < dist( r1bb_centroid, r2sc_centroid ) or b) E returns "false" in a call to its divides_backbone_and_- sidechain_energetics() method. The reason the call is avoided if "false" is returned is that, the entirety of a residue-pair-energy evaluation should be returned in the sidechain_sidechain_energy evaluation, if E does not implement its own versions of the bb/bb, bb/sc and sc/sc energy evaluation methods. Both context-dependent and context-independent 2-body energies are evaluated in this function.
void	eval_bbbb_sr2b_energies (conformation::Residue const &r1, conformation::Residue const &r2, Vector const &r1bb_centroid, Vector const &r2bb_centroid, Real const &r1bb_radius, Real const &r2bb_radius, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap)
	With two bounding spheres for a pair of backbones, evaluate all the backbone/sidechain energies. This will avoid a call to EnergyMethod E's backbone_backbone_energiy method if either a) E's atomic_interaction_cutoff + r1bb_radius + r2bb_radius < dist( r1bb_centroid, r2sc_centroid ) or b) E returns "false" in a call to its divides_backbone_and_- sidechain_energetics() method. The reason the call is avoided if "false" is returned is that, the entirety of a residue-pair-energy evaluation should be returned in the sidechain_sidechain_energy evaluation, if E does not implement its own versions of the bb/bb, bb/sc and sc/sc energy evaluation methods. Both context-dependent and context-independent 2-body energies are evaluated in this function.
Vector	compute_bb_centroid (conformation::Residue const &r1)
	Compute the average coordinate of the backbone heavy atoms (aka center of mass).
Real	compute_bb_radius (conformation::Residue const &r1, Vector const &r1bb_centroid)
	Given a representative point for the center of the backbone, compute the largest distance of all backbone heavy atoms to that point.
Vector	compute_sc_centroid (conformation::Residue const &r1)
	Compute the average coordiante of the sidechain atoms, (aka center of mass) or, if there are no side chain heavy atoms, compute the center of mass of the backbone.
Real	compute_sc_radius (conformation::Residue const &r1, Vector const &r1sc_centroid)
	Given a representative point for the center of the sidechain, compute the largest distance of all sidechain heavy atoms to that point.
Variables
short const	bit_count []
int const	num_bytes = 21
int const	num_phi = 64
int const	num_theta = 64
int const	num_overlaps = 100
int const	num_orientations = 162
int const	maskbits = 162
std::string const	STANDARD_WTS
std::string const	SCORE13
std::string const	CENTROID_WTS
std::string const	SOFT_REP_WTS
std::string const	SOFT_REP_DESIGN_WTS
std::string const	DNA_INT_WTS
std::string const	DNA_INT_WTS_GB
std::string const	MM_STD_WTS
std::string const	RNA_LORES_WTS
std::string const	RNA_HIRES_WTS
std::string const	RNA_LORES_PLUS_HIRES_WTS
std::string const	MEMB_HIGHRES_WTS
std::string const	SCORE12_PATCH
std::string const	DOCK_PATCH
std::string const	DOCK_LOW_PATCH
std::string const	FA_STANDARD_DEFAULT
std::string const	FA_STANDARD_SOFT
std::string const	UNFOLDED_SCORE12
std::string const	UNFOLDED_MM_STD

---

Typedef Documentation

typedef utility::vector1< AtomNeighbor > core::scoring::AtomNeighbors

typedef ObjexxFCL::FArray2D< CArrayP_TableEnergy > core::scoring::AtomPairEnergyTable

typedef ObjexxFCL::CArray< Energy > core::scoring::CArray_Energy

typedef ObjexxFCL::CArray< TableEnergy > core::scoring::CArray_TableEnergy

typedef ObjexxFCL::CArrayP< Energy > core::scoring::CArrayP_Energy

typedef ObjexxFCL::CArrayP< TableEnergy > core::scoring::CArrayP_TableEnergy

typedef utility::pointer::owning_ptr< CenListInfo > core::scoring::CenListInfoOP

typedef utility::pointer::owning_ptr< ContextGraph const > core::scoring::ContextGraphCOP

typedef utility::pointer::owning_ptr< ContextGraph > core::scoring::ContextGraphOP

typedef utility::pointer::owning_ptr< DenseEnergyContainer > core::scoring::DenseEnergyContainerOP

typedef utility::pointer::owning_ptr< DenseNeighborIterator > core::scoring::DenseNeighborIteratorOP

typedef utility::pointer::owning_ptr< DimerPairing > core::scoring::DimerPairingOP

typedef utility::pointer::owning_ptr< Energies const > core::scoring::EnergiesCOP

typedef utility::pointer::owning_ptr< Energies > core::scoring::EnergiesOP

typedef utility::pointer::owning_ptr< EnergyGraph > core::scoring::EnergyGraphOP

typedef EMapVector core::scoring::EnergyMap

typedef ObjexxFCL::FArray1D< Energy > core::scoring::FArray1D_Energy

typedef ObjexxFCL::FArray1D< Length > core::scoring::FArray1D_Length

typedef ObjexxFCL::FArray1D< Probability > core::scoring::FArray1D_Probability

typedef ObjexxFCL::FArray1D< TableEnergy > core::scoring::FArray1D_TableEnergy

typedef ObjexxFCL::FArray1D< TableProbability > core::scoring::FArray1D_TableProbability

typedef ObjexxFCL::FArray1D< Weight > core::scoring::FArray1D_Weight

typedef ObjexxFCL::FArray2D< Energy > core::scoring::FArray2D_Energy

typedef ObjexxFCL::FArray2D< Length > core::scoring::FArray2D_Length

typedef ObjexxFCL::FArray2D< Probability > core::scoring::FArray2D_Probability

typedef ObjexxFCL::FArray2D< TableEnergy > core::scoring::FArray2D_TableEnergy

typedef ObjexxFCL::FArray2D< TableProbability > core::scoring::FArray2D_TableProbability

typedef ObjexxFCL::FArray2D< Weight > core::scoring::FArray2D_Weight

typedef ObjexxFCL::FArray3D< Energy > core::scoring::FArray3D_Energy

typedef ObjexxFCL::FArray3D< Length > core::scoring::FArray3D_Length

typedef ObjexxFCL::FArray3D< Probability > core::scoring::FArray3D_Probability

typedef ObjexxFCL::FArray3D< TableEnergy > core::scoring::FArray3D_TableEnergy

typedef ObjexxFCL::FArray3D< TableProbability > core::scoring::FArray3D_TableProbability

typedef ObjexxFCL::FArray3D< Weight > core::scoring::FArray3D_Weight

typedef ObjexxFCL::FArray4D< Energy > core::scoring::FArray4D_Energy

typedef ObjexxFCL::FArray4D< Length > core::scoring::FArray4D_Length

typedef ObjexxFCL::FArray4D< Probability > core::scoring::FArray4D_Probability

typedef ObjexxFCL::FArray4D< TableEnergy > core::scoring::FArray4D_TableEnergy

typedef ObjexxFCL::FArray4D< TableProbability > core::scoring::FArray4D_TableProbability

typedef ObjexxFCL::FArray4D< Weight > core::scoring::FArray4D_Weight

typedef ObjexxFCL::FArray5D< Energy > core::scoring::FArray5D_Energy

typedef ObjexxFCL::FArray5D< Length > core::scoring::FArray5D_Length

typedef ObjexxFCL::FArray5D< Probability > core::scoring::FArray5D_Probability

typedef ObjexxFCL::FArray5D< TableEnergy > core::scoring::FArray5D_TableEnergy

typedef ObjexxFCL::FArray5D< TableProbability > core::scoring::FArray5D_TableProbability

typedef ObjexxFCL::FArray5D< Weight > core::scoring::FArray5D_Weight

typedef utility::pointer::owning_ptr< GenBornPoseInfo > core::scoring::GenBornPoseInfoOP

typedef utility::pointer::owning_ptr< GenBornResidueInfo > core::scoring::GenBornResidueInfoOP

typedef utility::pointer::owning_ptr< GenBornRotamerSetInfo > core::scoring::GenBornRotamerSetInfoOP

typedef utility::pointer::owning_ptr< InterfaceInfo > core::scoring::InterfaceInfoOP

typedef ObjexxFCL::KeyFArray1D< Energy > core::scoring::KeyFArray1D_Energy

typedef ObjexxFCL::KeyFArray1D< Probability > core::scoring::KeyFArray1D_Probability

typedef ObjexxFCL::KeyFArray1D< Real > core::scoring::KeyFArray1D_Real

typedef ObjexxFCL::KeyFArray1D< Weight > core::scoring::KeyFArray1D_Weight

typedef ObjexxFCL::KeyFArray2D< Energy > core::scoring::KeyFArray2D_Energy

typedef ObjexxFCL::KeyFArray2D< Probability > core::scoring::KeyFArray2D_Probability

typedef ObjexxFCL::KeyFArray2D< Real > core::scoring::KeyFArray2D_Real

typedef ObjexxFCL::KeyFArray2D< Weight > core::scoring::KeyFArray2D_Weight

typedef ObjexxFCL::KeyFArray3D< Energy > core::scoring::KeyFArray3D_Energy

typedef ObjexxFCL::KeyFArray3D< Probability > core::scoring::KeyFArray3D_Probability

typedef ObjexxFCL::KeyFArray3D< Real > core::scoring::KeyFArray3D_Real

typedef ObjexxFCL::KeyFArray3D< Weight > core::scoring::KeyFArray3D_Weight

typedef utility::pointer::owning_ptr< LREnergyContainer const > core::scoring::LREnergyContainerCOP

typedef utility::pointer::owning_ptr< LREnergyContainer > core::scoring::LREnergyContainerOP

typedef core::Real core::scoring::matrix[3][3]

typedef utility::pointer::owning_ptr< Membrane_FAEmbed > core::scoring::Membrane_FAEmbedOP

typedef utility::pointer::owning_ptr< MembraneEmbed > core::scoring::MembraneEmbedOP

typedef utility::pointer::owning_ptr< MembranePotential > core::scoring::MembranePotentialOP

typedef utility::pointer::owning_ptr< MembraneTopology > core::scoring::MembraneTopologyOP

typedef utility::pointer::owning_ptr< MinimizationGraph const > core::scoring::MinimizationGraphCOP

typedef utility::pointer::owning_ptr< MinimizationGraph > core::scoring::MinimizationGraphOP

typedef utility::pointer::owning_ptr< NeighborList const > core::scoring::NeighborListCOP

typedef utility::pointer::owning_ptr< NeighborList > core::scoring::NeighborListOP

typedef utility::pointer::owning_ptr< OneToAllEnergyContainer > core::scoring::OneToAllEnergyContainerOP

typedef utility::pointer::owning_ptr< OneToAllNeighborIterator > core::scoring::OneToAllNeighborIteratorOP

typedef PoissonBoltzmannPotential core::scoring::PB

typedef utility::pointer::owning_ptr< PeptideBondedEnergyContainer > core::scoring::PeptideBondedEnergyContainerOP

typedef utility::pointer::owning_ptr< PeptideBondedNeighborIterator > core::scoring::PeptideBondedNeighborIteratorOP

typedef utility::pointer::owning_ptr< Predicate const > core::scoring::PredicateCOP

typedef utility::pointer::owning_ptr< Predicate > core::scoring::PredicateOP

typedef core::Real core::scoring::Probability

typedef Ramachandran core::scoring::R

typedef utility::pointer::owning_ptr< ResidualDipolarCoupling_Rohl const > core::scoring::ResidualDipolarCoupling_RohlCOP

typedef utility::pointer::owning_ptr< ResidualDipolarCoupling_Rohl > core::scoring::ResidualDipolarCoupling_RohlOP

typedef utility::pointer::owning_ptr< ResidualDipolarCoupling const > core::scoring::ResidualDipolarCouplingCOP

typedef utility::pointer::owning_ptr< ResidualDipolarCoupling > core::scoring::ResidualDipolarCouplingOP

typedef utility::pointer::owning_ptr< ResidueNblistData const > core::scoring::ResidueNblistDataCOP

typedef utility::pointer::owning_ptr< ResidueNblistData > core::scoring::ResidueNblistDataOP

typedef utility::pointer::owning_ptr< ResidueNeighborConstIterator const > core::scoring::ResidueNeighborConstIteratorCOP

typedef utility::pointer::owning_ptr< ResidueNeighborConstIterator > core::scoring::ResidueNeighborConstIteratorOP

typedef utility::pointer::owning_ptr< ResidueNeighborIterator const > core::scoring::ResidueNeighborIteratorCOP

typedef utility::pointer::owning_ptr< ResidueNeighborIterator > core::scoring::ResidueNeighborIteratorOP

typedef utility::pointer::owning_ptr< ResiduePairNeighborList const > core::scoring::ResiduePairNeighborListCOP

typedef utility::pointer::owning_ptr< ResiduePairNeighborList > core::scoring::ResiduePairNeighborListOP

typedef std::list< core::Size > core::scoring::ResidueSelection

typedef utility::vector1< core::Size > core::scoring::ResidueSelectionVector

typedef utility::pointer::owning_ptr< ResPairMinimizationData const > core::scoring::ResPairMinimizationDataCOP

typedef utility::pointer::owning_ptr< ResPairMinimizationData > core::scoring::ResPairMinimizationDataOP

typedef utility::pointer::owning_ptr< ResSingleMinimizationData const > core::scoring::ResSingleMinimizationDataCOP

typedef utility::pointer::owning_ptr< ResSingleMinimizationData > core::scoring::ResSingleMinimizationDataOP

typedef core::Real core::scoring::rvec

typedef core::Real core::scoring::rvec5[5]

typedef Real core::scoring::Score

typedef utility::pointer::owning_ptr< ScoreFunction const > core::scoring::ScoreFunctionCOP

typedef utility::pointer::owning_ptr< ScoreFunctionInfo const > core::scoring::ScoreFunctionInfoCOP

typedef utility::pointer::owning_ptr< ScoreFunctionInfo > core::scoring::ScoreFunctionInfoOP

typedef utility::pointer::owning_ptr< ScoreFunction > core::scoring::ScoreFunctionOP

typedef utility::vector1< ScoreType > core::scoring::ScoreTypes

typedef utility::pointer::owning_ptr< SigmoidWeightedCenList<Real> > core::scoring::SigmoidWeightedCenListRealOP

typedef utility::pointer::owning_ptr< SigmoidWeightedCenList<numeric::xyzVector<Real> > > core::scoring::SigmoidWeightedCenListVectorOP

typedef utility::pointer::owning_ptr< SS_Info const > core::scoring::SS_InfoCOP

typedef utility::pointer::owning_ptr< SS_Info > core::scoring::SS_InfoOP

typedef utility::pointer::owning_ptr< SS_Killhairpins_Info const > core::scoring::SS_Killhairpins_InfoCOP

typedef utility::pointer::owning_ptr< SS_Killhairpins_Info > core::scoring::SS_Killhairpins_InfoOP

typedef float core::scoring::TableEnergy

typedef float core::scoring::TableProbability

typedef utility::pointer::owning_ptr< TenANeighborGraph const > core::scoring::TenANeighborGraphCOP

typedef utility::pointer::owning_ptr< TenANeighborGraph > core::scoring::TenANeighborGraphOP

typedef core::Real core::scoring::Tensor[3][3]

typedef core::Real core::scoring::Tensor5[5][5]

typedef utility::pointer::owning_ptr< TwelveANeighborGraph const > core::scoring::TwelveANeighborGraphCOP

typedef utility::pointer::owning_ptr< TwelveANeighborGraph > core::scoring::TwelveANeighborGraphOP

typedef utility::pointer::owning_ptr< UnfoldedStatePotential > core::scoring::UnfoldedStatePotentialOP

typedef Real core::scoring::Weight

---

Enumeration Type Documentation

enum core::scoring::ContextGraphType

Enumerator:

ten_A_neighbor_graph
twelve_A_neighbor_graph
centroid_neighbor_graph
num_context_graph_types

enum core::scoring::min_pair_data

Enumerator:

etab_pair_nblist
cst_respair_data
hackelec_pair_nblist
fa_dslf_respair_data
fa_custom_pair_dist_data
hbond_respair_data
n_min_pair_data

enum core::scoring::min_single_data

Enumerator:

etab_single_nblist
cst_res_data
hbond_res_data
n_min_single_data

enum core::scoring::ProteinTorsion

Enumerator:

PHI
PSI
OMEGA
CHI1
CHI2
CHI3
CHI4
protein_torsion_end

enum core::scoring::ScoreFunctionParameter

enum for listing the variants

Enumerator:

hydrogen_interaction_cutoff

enum core::scoring::ScoreFunctionVariant

enum for listing the variants

Enumerator:

loc_lj
lk_sol

enum core::scoring::ScoreType

Type for looking up cached energies I guess we could get rid of the fa_ prefix, except maybe for fa_pair, to distinguish from std::pair and the centroid pair score...

Enumerator:

fa_atr	begin short ranged ci2b scores -- these guys are cached in the energy graph -- when appropriate -- they are reused between rounds of scoring.
fa_rep
fa_sol
fa_intra_atr
fa_intra_rep
fa_intra_sol
fa_intra_RNA_base_phos_atr
fa_intra_RNA_base_phos_rep
fa_intra_RNA_base_phos_sol
lk_hack
lk_ball
lk_ball_iso
coarse_fa_atr
coarse_fa_rep
coarse_fa_sol
coarse_beadlj
mm_lj_intra_rep
mm_lj_intra_atr
mm_lj_inter_rep
mm_lj_inter_atr
mm_twist
mm_bend
mm_stretch
lk_costheta
lk_polar
lk_nonpolar
lk_polar_intra_RNA
lk_nonpolar_intra_RNA
hack_elec
hack_elec_bb_bb
hack_elec_bb_sc
hack_elec_sc_sc
h2o_hbond
dna_dr
dna_bp
dna_bs
peptide_bond
pcs
pcs2
fastsaxs
saxs_score
saxs_cen_score
saxs_fa_score
pddf_score
fa_mbenv
fa_mbsolv
hack_elec_rna_phos_phos
hack_elec_rna_phos_sugr
hack_elec_rna_phos_base
hack_elec_rna_sugr_sugr
hack_elec_rna_sugr_base
hack_elec_rna_base_base
hack_elec_aro_aro
hack_elec_aro_all
hack_aro
rna_fa_atr_base
rna_fa_rep_base
rna_data_backbone
ch_bond
ch_bond_bb_bb
ch_bond_sc_sc
ch_bond_bb_sc
pro_close	proline closure energy
rama2b
vdw
cenpack
cenpack_smooth
cen_hb
hybrid_vdw
rna_vdw
rna_base_backbone
rna_backbone_backbone
rna_repulsive
rna_base_pair_pairwise
rna_base_axis_pairwise
rna_base_stagger_pairwise
rna_base_stack_pairwise
rna_base_stack_axis_pairwise
rna_data_base
rna_base_pair
rna_base_axis
rna_base_stagger
rna_base_stack
rna_base_stack_axis
rna_torsion
rna_sugar_close
fa_stack
fa_stack_aro
CI_geom_sol
CI_geom_sol_intra_RNA
fa_cust_pair_dist
custom_atom_pair
orbitals_hpol
orbitals_haro
orbitals_orbitals
orbitals_hpol_bb
PyRosettaTwoBodyContextIndepenedentEnergy_first
PyRosettaTwoBodyContextIndepenedentEnergy_last
python
n_ci_2b_score_types
fa_pair	keep this guy at the end of the ci2b scores
fa_pair_aro_aro	== fa_pair_pol_pol
fa_pair_aro_pol
fa_pair_pol_pol
fa_plane
hbond_sr_bb
hbond_lr_bb
hbond_bb_sc
hbond_sr_bb_sc
hbond_lr_bb_sc
hbond_sc
hbond_intra
PyRosettaTwoBodyContextDependentEnergy_first
PyRosettaTwoBodyContextDependentEnergy_last
interface_dd_pair
geom_sol
geom_sol_intra_RNA
occ_sol_fitted
occ_sol_fitted_onebody
occ_sol_exact
pair
cen_pair_smooth
Mpair
suck
rna_rg
interchain_pair
interchain_vdw
n_shortranged_2b_score_types
gb_elec
dslf_ss_dst
dslf_cs_ang
dslf_ss_dih
dslf_ca_dih
dslf_cbs_ds
dslfc_cen_dst
dslfc_cb_dst
dslfc_ang
dslfc_cb_dih
dslfc_bb_dih
dslfc_rot
dslfc_trans
dslfc_RT
atom_pair_constraint
constant_constraint
coordinate_constraint
angle_constraint
dihedral_constraint
big_bin_constraint
dunbrack_constraint
site_constraint
rna_bond_geometry
rama
omega
fa_dun
p_aa_pp
yhh_planarity
h2o_intra
ref
seqdep_ref
envsmooth
e_pH
rna_bulge
special_rot
PB_elec
cen_env_smooth	Whole structure energies centroid whole structure energies
cbeta_smooth
env
cbeta
DFIRE
Menv
Mcbeta
Menv_non_helix
Menv_termini
Menv_tm_proj
Mlipo
rg
co
hs_pair
ss_pair
rsigma
sheet
burial
abego
natbias_ss	Whole structure energies, centroid score.
natbias_hs
natbias_hh
natbias_stwist
aa_cmp	amino acid composition score
dock_ens_conf
rdc
rdc_segments
rdc_rohl
holes
holes_decoy
holes_resl
holes_min
holes_min_mean
dab_sasa
dab_sev
sa
interchain_env
interchain_contact
chainbreak
linear_chainbreak
overlap_chainbreak
distance_chainbreak
dof_constraint
cart_bonded
cart_bonded_angle
cart_bonded_length
cart_bonded_torsion
neigh_vect
neigh_count
neigh_vect_raw
symE_bonus
sym_lig
pack_stat
rms
res_type_constraint
res_type_linking_constraint
pocket_constraint
backbone_stub_constraint
surface
p_aa
unfolded
elec_dens_fast
elec_dens_window
elec_dens_whole_structure_ca
elec_dens_whole_structure_allatom
elec_dens_atomwise
patterson_cc
hpatch
Menv_smooth
PyRosettaEnergy_first
PyRosettaEnergy_last
total_score
n_score_types	This element marks the end of the active score types. Elements in the enumeration up to this point will have space allocated for them in the EnergyMap object. Elements past this point are considered inactive and will not have space allocated for them. If you wish to use an inactive score type, you must move that score type into its appropriate position in the ScoreType enumeration (described above) and then recompile. Inactive score types must still have their names included in the ScoreTypeManager's string-to-score-type map.
end_of_score_type_enumeration	This element marks the very end of the score type enumeration. Elements between the n_score_types element and this element are considered inactive. They may not be used by any EnergyMethod or they will result in an out-of-bounds write and unexpected behavior. To use an inactived score type, the score type must be moved to an earlier position in this enumeration, and the program must be recompiled. Keep this guy last.

---

Function Documentation

core::Real core::scoring::all_atom_rmsd	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2
	)

References is_heavyatom(), rms, and rmsd_with_super().

Referenced by protocols::simple_moves::ScoreMover::apply(), protocols::simple_filters::SelectRmsdEvaluator::apply(), protocols::rna::RNA_DeNovoProtocol::apply(), protocols::idealize::IdealizeMover::apply(), protocols::idealize::basic_idealize(), protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::coarse_rna::CoarseRNA_DeNovoProtocol::output_to_silent_file(), and protocols::swa::RigidBodySampler::save_silent_struct().

core::Real core::scoring::all_atom_rmsd	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		std::list< Size >	residue_selection
	)

References is_heavyatom(), rms, and rmsd_with_super().

ObjexxFCL::FArray2D_int core::scoring::angles	(	num_phi	,
		num_theta
	)

Referenced by core::scoring::packstat::compute_cav_ball_volumes(), core::scoring::packstat::compute_sasa(), core::scoring::packstat::prune_1pass(), and core::scoring::packstat::prune_hidden_cavity_balls().

core::Real core::scoring::automorphic_rmsd	(	core::conformation::Residue const &	rsd1,
		core::conformation::Residue const &	rsd2,
		bool	superimpose
	)

RMSD between residues, accounting for automorphisms (symmetries). Does NOT include H atoms -- they add lots of extra symmetries.

Just iterates over all automorphisms for this residue type and chooses the minimum RMS.

References core::conformation::Residue::atom_type(), core::chemical::AtomType::is_hydrogen(), core::chemical::ResidueType::name3(), core::chemical::ResidueType::natoms(), core::chemical::AutomorphismIterator::next(), core::conformation::Residue::nheavyatoms(), core::chemical::tr(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by protocols::ligand_docking::append_automorphic_rmsd(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::ligand_docking::check_RMSD(), and protocols::motifs::MotifSearch::incorporate_motifs().

core::Real core::scoring::bb_rmsd	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2
	)

References core::sequence::end, and core::pose::Pose::total_residue().

core::Real core::scoring::bb_rmsd	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		Size	start,
		Size	end,
		utility::vector1< Size > const &	exclude
	)

References is_protein_backbone(), rms, and rmsd_with_super().

core::Real core::scoring::bb_rmsd_including_O	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2
	)

References core::sequence::end, and core::pose::Pose::total_residue().

core::Real core::scoring::bb_rmsd_including_O	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		Size	start,
		Size	end,
		utility::vector1< Size > const &	exclude
	)

References is_protein_backbone_including_O(), rms, and rmsd_with_super().

template<class T >

core::Real core::scoring::biggest_residue_deviation_no_super	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		T *	predicate
	)

function to return the biggest deviation between an atom in a pair of poses,

References is_heavyatom(), is_ligand_heavyatom(), is_polymer_heavyatom(), core::conformation::Residue::natoms(), core::pose::num_atoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf().

template<class T >

core::Real core::scoring::biggest_residue_deviation_no_super_subset	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		ObjexxFCL::FArray1D_bool const &	subset,
		T *	predicate
	)

function to return the biggest deviation between an atom in a pair of poses,

as specified by the predicate and the subset

References is_heavyatom(), is_ligand_heavyatom(), is_polymer_heavyatom(), core::conformation::Residue::natoms(), core::pose::num_atoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

static Real const core::scoring::BOGUS_ENERGY

(

99999.

99

)

[static]

core::Real core::scoring::CA_gdtmm	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		const std::map< core::Size, core::Size > &	residues
	)

Computes the gdtmm between zero or more CA residues in pose1 and pose2, whose correspondence is specified in the map parameter.

References retrieve_coordinates(), and xyz_gdtmm().

Referenced by protocols::simple_moves::ScoreMover::apply(), protocols::simple_filters::StructuralSimilarityEvaluator::apply(), protocols::simple_filters::SelectGdtEvaluator::apply(), protocols::simple_filters::RmsdEvaluator::apply(), protocols::loophash::Mover_LoopHashRefine::apply(), CA_gdtmm(), protocols::cluster::GatherPosesMover::get_distance_measure(), native_CA_gdtmm(), and protocols::jobdist::not_universal_main().

core::Real core::scoring::CA_gdtmm	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		std::list< Size >	residue_selection,
		core::Real &	m_1_1,
		core::Real &	m_2_2,
		core::Real &	m_3_3,
		core::Real &	m_4_3,
		core::Real &	m_7_4
	)

References fill_rmsd_coordinates(), core::pose::Pose::total_residue(), core::chemical::tr(), and xyz_gdtmm().

core::Real core::scoring::CA_gdtmm	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		core::Real &	m_1_1,
		core::Real &	m_2_2,
		core::Real &	m_3_3,
		core::Real &	m_4_3,
		core::Real &	m_7_4
	)

Calculate gdtmm score based on the C-alpha positions in pose1 and pose2. Also returns the five components of the gdtmm score.

References fill_rmsd_coordinates(), is_protein_CA(), core::pose::Pose::total_residue(), and xyz_gdtmm().

core::Real core::scoring::CA_gdtmm	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		std::list< Size >	residue_selection
	)

Calculate gdtmm score based on the C-alpha positions in pose1 and pose2.

References CA_gdtmm().

core::Real core::scoring::CA_gdtmm	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2
	)

Calculate gdtmm score based on the C-alpha positions in pose1 and pose2.

References CA_gdtmm().

int core::scoring::CA_maxsub	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		std::list< Size >	residue_selection,
		Real	rms
	)

References fill_rmsd_coordinates(), and core::chemical::tr().

int core::scoring::CA_maxsub	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		Real	rms
	)

Calculates a C-alpha maxsub-based superposition between pose1 and pose2, returns the number of residues superimposed past a certain threshold. See maxsub.hh and maxsub.cc for more information.

References fill_rmsd_coordinates(), is_protein_CA(), and core::pose::Pose::total_residue().

Referenced by protocols::simple_moves::ScoreMover::apply(), protocols::simple_filters::SelectMaxsubEvaluator::apply(), protocols::simple_filters::RmsdEvaluator::apply(), and protocols::jobdist::not_universal_main().

int core::scoring::CA_maxsub_by_subset	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		utility::vector1< bool >
	)

References fill_rmsd_coordinates(), is_protein_CA(), and core::pose::Pose::total_residue().

core::Real core::scoring::CA_rmsd	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2
	)

References core::sequence::end, and core::pose::Pose::total_residue().

Referenced by protocols::simple_moves::SuperimposeMover::apply(), protocols::simple_filters::SelectRmsdEvaluator::apply(), protocols::simple_filters::RmsdEvaluator::apply(), protocols::relax::ClassicRelax::apply(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::idealize::IdealizeMover::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), compute_jump_rmsd(), core::scoring::methods::RMS_Energy::finalize_total_energy(), protocols::relax::fix_worst_bad_ramas(), protocols::loophash::LoopHashLibrary::get_all(), protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::loophash::LoopHashLibrary::graft_loop(), protocols::jobdist::main_plain_pdb_mover(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_close_gaps(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_include_cut(), native_CA_rmsd(), protocols::loops::native_loop_core_CA_rmsd(), protocols::jobdist::not_universal_main(), protocols::abinitio::hConvergenceCheck::operator()(), OPT_1GRP_KEY(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::process_fragments(), protocols::toolbox::pose_metric_calculators::FragQualCalculator::recompute(), core::fragment::FragmentRmsd::rmsd(), protocols::simple_moves::ShakeStructureMover::set_temp_based_on_ens_diversity(), and protocols::jobdist::universal_main().

core::Real core::scoring::CA_rmsd	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		Size	start,
		Size	end
	)

References fill_rmsd_coordinates(), rms, and core::chemical::tr().

core::Real core::scoring::CA_rmsd	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		const std::map< core::Size, core::Size > &	residues
	)

Computes the root mean squared deviation between zero or more CA residues in pose1 and pose2, whose correspondence is specified in the map parameter.

References retrieve_coordinates().

core::Real core::scoring::CA_rmsd	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		Size	start,
		Size	end,
		utility::vector1< Size > const &	exclude
	)

References fill_rmsd_coordinates(), and rms.

core::Real core::scoring::CA_rmsd	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		std::list< Size >	residue_selection
	)

References fill_rmsd_coordinates(), and core::chemical::tr().

core::Real core::scoring::CA_rmsd_symmetric	(	const core::pose::Pose &	native_pose,
		const core::pose::Pose &	pose
	)

References make_table_of_pilot_apps::begin, core::pose::Pose::conformation(), create_shuffle_map_recursive_rms(), fill_rmsd_coordinates(), is_protein_CA(), core::pose::symmetry::is_symmetric(), protocols::forge::build::SegmentInsertConnectionScheme::N, rms, and core::chemical::tr().

Referenced by protocols::simple_filters::SymmetricRmsdEvaluator::apply(), protocols::relax::FastRelax::apply(), protocols::relax::FastRelax::batch_apply(), protocols::symmetric_docking::SymDockProtocol::calc_rms(), protocols::relax::FastRelax::cmd_accept_to_best(), and protocols::cluster::GatherPosesMover::get_distance_measure().

void core::scoring::calc_atom_masks	(	core::conformation::Residue const &	irsd,
		core::conformation::Residue const &	jrsd,
		Real const	probe_radius,
		Real const	cutoff_distance,
		utility::vector1< Real > const &	radii,
		id::AtomID_Map< bool > const &	atom_subset,
		core::id::AtomID_Map< utility::vector1< ObjexxFCL::ubyte > > &	atom_masks
	)

References core::scoring::packstat::old::angles, core::conformation::Residue::atom(), core::conformation::Residue::atom_type(), core::scoring::packstat::old::get_orientation(), core::scoring::packstat::old::get_overlap(), core::chemical::AtomType::is_h2o(), core::scoring::packstat::old::masks, core::conformation::Residue::natoms(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_radius(), num_bytes, core::conformation::Residue::seqpos(), and protocols::kinmatch::xyz().

Referenced by calc_per_atom_sasa().

Real core::scoring::calc_per_atom_sasa	(	pose::Pose const &	pose,
		id::AtomID_Map< Real > &	atom_sasa,
		utility::vector1< Real > &	rsd_sasa,
		Real const	probe_radius,
		bool const	use_big_polar_H
	)

returns total sasa

References core::id::AtomID_Map< T >::clear(), and core::pose::initialize_atomid_map().

Referenced by protocols::fldsgn::topology::calc_delta_sasa(), calc_per_res_hydrophobic_sasa(), protocols::fldsgn::topology::Sheet::calc_sasa_bothsides(), calc_total_sasa(), protocols::fldsgn::filters::CoreDunbrackFilter::compute(), protocols::simple_moves::ConsensusDesignMover::create_consensus_design_task(), protocols::hotspot_hashing::HotspotStubSet::prepare_hashing_packer_task_(), core::pose::metrics::simple_calculators::SasaCalculator::recompute(), and core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator::recompute().

Real core::scoring::calc_per_atom_sasa	(	pose::Pose const &	pose,
		id::AtomID_Map< Real > &	atom_sasa,
		utility::vector1< Real > &	rsd_sasa,
		Real const	probe_radius,
		bool const	use_big_polar_H,
		id::AtomID_Map< bool > &	atom_subset,
		bool const	use_naccess_sasa_radii,
		bool const	expand_polar_radii,
		Real const	polar_expansion_radius
	)

returns total sasa

References core::conformation::Residue::atom_type_set(), core::scoring::packstat::old::bit_count, calc_atom_masks(), core::id::AtomID_Map< T >::clear(), core::chemical::AtomType::element(), core::chemical::AtomTypeSet::extra_parameter_index(), core::pose::initialize_atomid_map(), core::scoring::packstat::old::input_sasa_dats(), core::chemical::AtomType::is_polar_hydrogen(), core::scoring::packstat::old::maskbits, core::chemical::AtomTypeSet::n_atomtypes(), core::chemical::AtomType::name(), num_bytes, core::pose::Pose::pdb_info(), print_dot_bit_string(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and TR().

Real core::scoring::calc_per_res_hydrophobic_sasa	(	pose::Pose const &	pose,
		utility::vector1< Real > &	rsd_sasa,
		utility::vector1< Real > &	rsd_hydrophobic_sasa,
		Real const	probe_radius,
		bool	use_naccess_sasa_radii
	)

Uses the method above to calculate total SASA and then only looks at the hydrophobic contribution. Returns the total hydrophobic SASA for the passed in pose. This method is being used for a protein surface score being developed by ronj. Note: Uses an atom id mask that ignores H's in the pose - only sees and computes the SASA for heavy atoms in the pose. This is done to keep things fast. Only computes the amount of hSASA per residue, not per atom. Doesn't make sense to calculate a per-atom hSASA. (ronj)

sasa.cc::calc_per_atom_hydrophobic_sasa

References core::conformation::Residue::atom_type(), calc_per_atom_sasa(), core::id::AtomID_Map< T >::clear(), core::chemical::AtomType::element(), core::pose::initialize_atomid_map(), core::chemical::AtomType::is_hydrogen(), core::pose::Pose::n_residue(), core::conformation::Residue::name3(), core::conformation::Residue::natoms(), core::chemical::ResidueType::natoms(), core::conformation::Residue::nheavyatoms(), core::chemical::ResidueType::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::id::AtomID_Map< T >::resize(), core::pose::Pose::total_residue(), and TR().

Referenced by protocols::analysis::InterfaceAnalyzerMover::compute_separated_sasa().

Real core::scoring::calc_total_sasa	(	pose::Pose const &	pose,
		Real const	probe_radius
	)

returns total sasa

References calc_per_atom_sasa().

Referenced by protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), and core::scoring::methods::SA_Energy::finalize_total_energy().

Real core::scoring::calpha_superimpose_pose	(	pose::Pose &	mod_pose,
		pose::Pose const &	ref_pose
	)

Superimpose two poses by their calpha coordinates. Ignores residues that do not have atoms named "CA.".

both poses must have the same length.

References core::conformation::Residue::atom_index(), core::id::BOGUS_ATOM_ID, core::conformation::Residue::has(), core::pose::initialize_atomid_map(), core::pose::Pose::residue(), superimpose_pose(), and core::pose::Pose::total_residue().

Referenced by protocols::simple_moves::SuperimposeMover::apply(), protocols::protein_interface_design::filters::RmsdFilter::compute(), protocols::star::Extender::extend_unaligned(), and protocols::relax::RelaxProtocolBase::set_up_constraints().

std::string const core::scoring::CENTROID_WTS

(

"cen_std"

)

int core::scoring::compare_by_abs	(	const void *	a,
		const void *	b
	)		[inline]

Referenced by core::scoring::ResidualDipolarCoupling::compute_tensor_stats().

Vector core::scoring::compute_bb_centroid

(

conformation::Residue const &

res

)

Compute the average coordinate of the backbone heavy atoms (aka center of mass).

returns the origin if there are no backbone atoms

References core::chemical::ResidueType::first_sidechain_atom(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by compute_sc_centroid(), core::pack::interaction_graph::SimpleNode::set_current(), and core::pack::interaction_graph::OnTheFlyNode::set_rotamers().

Real core::scoring::compute_bb_radius	(	conformation::Residue const &	res,
		Vector const &	bb_centroid
	)

Given a representative point for the center of the backbone, compute the largest distance of all backbone heavy atoms to that point.

References core::chemical::ResidueType::first_sidechain_atom(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by core::pack::interaction_graph::SimpleNode::set_current(), and core::pack::interaction_graph::OnTheFlyNode::set_rotamers().

void core::scoring::compute_jump_rmsd	(	const core::pose::Pose &	reference,
		const core::pose::Pose &	model,
		boost::unordered_map< core::Size, core::Real > *	rmsds
	)

Computes the RMSD of the jump residues between <model> and <native>, storing the results in a map keyed by jump_id.

Computes the RMSD of the jump residues (jump point +/- 1 residue) of <model> and <reference>. Jump residues are identified by scanning <reference>'s FoldTree. Results are stored in the output parameter <rmsds>, keyed by the index of the jump point. For example,

Jump 100 => 10 rmsds[10] = rmsd(residues 9-11 in reference, residues 9-11 in model)

References CA_rmsd(), core::pose::Pose::fold_tree(), and core::pose::Pose::total_residue().

Referenced by protocols::nonlocal::StarTreeBuilder::do_compute_jump_rmsd().

Vector core::scoring::compute_sc_centroid

(

conformation::Residue const &

res

)

Compute the average coordiante of the sidechain atoms, (aka center of mass) or, if there are no side chain heavy atoms, compute the center of mass of the backbone.

References compute_bb_centroid(), core::chemical::ResidueType::first_sidechain_atom(), core::chemical::ResidueType::nheavyatoms(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by core::pack::interaction_graph::SimpleNode::set_alternate(), core::pack::interaction_graph::SimpleNode::set_current(), and core::pack::interaction_graph::OnTheFlyNode::set_rotamers().

Real core::scoring::compute_sc_radius	(	conformation::Residue const &	res,
		Vector const &	centroid
	)

Given a representative point for the center of the sidechain, compute the largest distance of all sidechain heavy atoms to that point.

References core::chemical::ResidueType::first_sidechain_atom(), core::chemical::ResidueType::nheavyatoms(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by core::pack::interaction_graph::SimpleNode::set_alternate(), core::pack::interaction_graph::SimpleNode::set_current(), and core::pack::interaction_graph::OnTheFlyNode::set_rotamers().

void core::scoring::create_shuffle_map_recursive_rms	(	std::vector< int >	sequence,
		int const	N,
		std::vector< std::vector< int > > &	map
	)

References protocols::forge::build::SegmentInsertConnectionScheme::N.

Referenced by CA_rmsd_symmetric(), and sym_rmsd_with_super_subset().

bool core::scoring::dimer_pairing_pointer_sorter	(	DimerPairingOP const &	a,
		DimerPairingOP const &	b
	)

std::string const core::scoring::DNA_INT_WTS

(

"dna_no_gb"

)

std::string const core::scoring::DNA_INT_WTS_GB

(

"dna"

)

std::string const core::scoring::DOCK_LOW_PATCH

(

"docking_cen"

)

std::string const core::scoring::DOCK_PATCH

(

"docking"

)

void core::scoring::dump_pqr	(	core::pose::Pose const &	pose,
		std::ostream &	out,
		std::string const &	tag,
		utility::vector1< Size > const &	zero_charge_chains
	)

References core::chemical::ResidueType::atomic_charge(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

std::string core::scoring::element_string

(

std::string

atom

)

Referenced by core::scoring::RDC::get_RDC_data_type().

void core::scoring::eval_atom_derivatives_for_minedge	(	MinimizationEdge const &	min_edge,
		conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		ResSingleMinimizationData const &	res1_min_data,
		ResSingleMinimizationData const &	res2_min_data,
		pose::Pose const &	pose,
		EnergyMap const &	respair_weights,
		utility::vector1< DerivVectorPair > &	r1atom_derivs,
		utility::vector1< DerivVectorPair > &	r2atom_derivs
	)

References core::scoring::MinimizationEdge::active_2benmeths_begin(), core::scoring::MinimizationEdge::active_2benmeths_end(), and core::scoring::MinimizationEdge::res_pair_min_data().

Referenced by core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::optimization::atom_tree_get_atompairE_deriv(), core::optimization::cartesian_collect_atompairE_deriv(), and core::pack::scmin::SCMinMultifunc::dfunc().

void core::scoring::eval_atom_derivatives_for_minnode	(	MinimizationNode const &	min_node,
		conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		EnergyMap const &	res_weights,
		utility::vector1< DerivVectorPair > &	atom_derivs
	)

Evaluate the derivatives for all atoms on the input residue for the terms that apply to this residue (which are stored on the input minimization node).

References core::scoring::MinimizationNode::active_1benmeths_begin(), core::scoring::MinimizationNode::active_1benmeths_end(), core::scoring::MinimizationNode::active_intrares2benmeths_begin(), core::scoring::MinimizationNode::active_intrares2benmeths_end(), and core::scoring::MinimizationNode::res_min_data().

Referenced by core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::optimization::atom_tree_get_atompairE_deriv(), core::optimization::cartesian_collect_atompairE_deriv(), and core::pack::scmin::SCMinMultifunc::dfunc().

void core::scoring::eval_bbbb_sr2b_energies	(	conformation::Residue const &	r1,
		conformation::Residue const &	r2,
		Vector const &	r1bb_centroid,
		Vector const &	r2bb_centroid,
		Real const &	r1bb_radius,
		Real const &	r2bb_radius,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap
	)

With two bounding spheres for a pair of backbones, evaluate all the backbone/sidechain energies. This will avoid a call to EnergyMethod E's backbone_backbone_energiy method if either a) E's atomic_interaction_cutoff + r1bb_radius + r2bb_radius < dist( r1bb_centroid, r2sc_centroid ) or b) E returns "false" in a call to its divides_backbone_and_- sidechain_energetics() method. The reason the call is avoided if "false" is returned is that, the entirety of a residue-pair-energy evaluation should be returned in the sidechain_sidechain_energy evaluation, if E does not implement its own versions of the bb/bb, bb/sc and sc/sc energy evaluation methods. Both context-dependent and context-independent 2-body energies are evaluated in this function.

References core::scoring::ScoreFunction::cd_2b_begin(), core::scoring::ScoreFunction::cd_2b_end(), core::scoring::ScoreFunction::ci_2b_begin(), and core::scoring::ScoreFunction::ci_2b_end().

void core::scoring::eval_bbsc_sr2b_energies	(	conformation::Residue const &	r1,
		conformation::Residue const &	r2,
		Vector const &	r1bb_centroid,
		Vector const &	r2sc_centroid,
		Real const &	r1bb_radius,
		Real const &	r2sc_radius,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap
	)

With two bounding spheres for a backbone and a sidechain, evaluate all the backbone/sidechain energies. This will avoid a call to EnergyMethod E's backbone_sidechain_energiy method if either a) E's atomic_interaction_cutoff + r1bb_radius + r2sc_radius < dist( r1bb_centroid, r2sc_centroid ) or b) E returns "false" in a call to its divides_backbone_and_- sidechain_energetics() method. The reason the call is avoided if "false" is returned is that, the entirety of a residue-pair-energy evaluation should be returned in the sidechain_sidechain_energy evaluation, if E does not implement its own versions of the bb/bb, bb/sc and sc/sc energy evaluation methods. Both context-dependent and context-independent 2-body energies are evaluated in this function.

References core::scoring::ScoreFunction::cd_2b_begin(), core::scoring::ScoreFunction::cd_2b_end(), core::scoring::ScoreFunction::ci_2b_begin(), and core::scoring::ScoreFunction::ci_2b_end().

Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy().

Real core::scoring::eval_dof_deriv_for_minnode	(	MinimizationNode const &	min_node,
		conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		id::DOF_ID const &	dof_id,
		id::TorsionID const &	torsion_id,
		ScoreFunction const &	sfxn,
		EnergyMap const &	weights
	)

References core::scoring::MinimizationNode::dof_deriv_1benmeths_begin(), core::scoring::MinimizationNode::dof_deriv_1benmeths_end(), core::scoring::MinimizationNode::dof_deriv_2benmeths_begin(), core::scoring::MinimizationNode::dof_deriv_2benmeths_end(), and core::scoring::MinimizationNode::res_min_data().

Referenced by core::pack::scmin::SCMinMultifunc::dfunc(), and core::scoring::ScoreFunction::eval_dof_derivative().

void core::scoring::eval_res_onebody_energies_for_minnode	(	MinimizationNode const &	min_node,
		conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap
	)

Deprecated.

References core::scoring::MinimizationNode::active_1benmeths_ext_begin(), core::scoring::MinimizationNode::active_1benmeths_ext_end(), core::scoring::MinimizationNode::active_1benmeths_std_begin(), core::scoring::MinimizationNode::active_1benmeths_std_end(), core::scoring::MinimizationNode::active_intrares2benmeths_ext_begin(), core::scoring::MinimizationNode::active_intrares2benmeths_ext_end(), core::scoring::MinimizationNode::active_intrares2benmeths_std_begin(), core::scoring::MinimizationNode::active_intrares2benmeths_std_end(), and core::scoring::MinimizationNode::res_min_data().

Referenced by core::pack::compare_mingraph_and_energy_graph(), core::scoring::ScoreFunction::eval_onebody_energies(), and core::pack::scmin::SCMinMultifunc::operator()().

void core::scoring::eval_res_pair_energy_for_minedge	(	MinimizationEdge const &	min_edge,
		conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap
	)

Deprecated.

References core::scoring::MinimizationEdge::active_2benmeths_ext_begin(), core::scoring::MinimizationEdge::active_2benmeths_ext_end(), core::scoring::MinimizationEdge::active_2benmeths_std_begin(), core::scoring::MinimizationEdge::active_2benmeths_std_end(), and core::scoring::MinimizationEdge::res_pair_min_data().

Referenced by core::pack::compare_mingraph_and_energy_graph(), core::scoring::ScoreFunction::eval_twobody_neighbor_energies(), and core::pack::scmin::SCMinMultifunc::operator()().

void core::scoring::eval_scsc_sr2b_energies	(	conformation::Residue const &	r1,
		conformation::Residue const &	r2,
		Vector const &	r1sc_centroid,
		Vector const &	r2sc_centroid,
		Real const &	r1sc_radius,
		Real const &	r2sc_radius,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap
	)

With two bounding spheres for a pair of sidechains, evaluate all the sidechain/sidechain energies. This will avoid a call to EnergyMethod E's sidechain_sidechain_energiy method if a) E's atomic_interaction_cutoff + r1sc_radius + r2sc_radius < dist( r1sc_centroid, r2sc_centroid ) and b) E returns "true" in a call to its divides_backbone_and_- sidechain_energetics() method. Both context-dependent and context-independent 2-body energies are evaluated in this function.

References core::scoring::ScoreFunction::cd_2b_begin(), core::scoring::ScoreFunction::cd_2b_end(), core::scoring::ScoreFunction::ci_2b_begin(), and core::scoring::ScoreFunction::ci_2b_end().

Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy(), and core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy().

Real core::scoring::eval_weighted_dof_deriv_for_minnode	(	MinimizationNode const &	min_node,
		conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		id::DOF_ID const &	dof_id,
		id::TorsionID const &	torsion_id,
		ScoreFunction const &	sfxn,
		EnergyMap const &	weights
	)

References core::scoring::MinimizationNode::dof_deriv_1benmeths_begin(), core::scoring::MinimizationNode::dof_deriv_1benmeths_end(), core::scoring::MinimizationNode::dof_deriv_2benmeths_begin(), core::scoring::MinimizationNode::dof_deriv_2benmeths_end(), core::scoring::MinimizationNode::res_min_data(), and core::scoring::MinimizationNode::weight().

Referenced by core::scoring::symmetry::SymmetricScoreFunction::eval_dof_derivative().

void core::scoring::eval_weighted_res_onebody_energies_for_minnode	(	MinimizationNode const &	min_node,
		conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap,
		EnergyMap &	scratch_emap
	)

References core::scoring::EMapVector::accumulate(), core::scoring::MinimizationNode::active_1benmeths_ext_begin(), core::scoring::MinimizationNode::active_1benmeths_ext_end(), core::scoring::MinimizationNode::active_1benmeths_std_begin(), core::scoring::MinimizationNode::active_1benmeths_std_end(), core::scoring::MinimizationNode::active_intrares2benmeths_ext_begin(), core::scoring::MinimizationNode::active_intrares2benmeths_ext_end(), core::scoring::MinimizationNode::active_intrares2benmeths_std_begin(), core::scoring::MinimizationNode::active_intrares2benmeths_std_end(), core::scoring::MinimizationNode::res_min_data(), core::scoring::MinimizationNode::weight(), and core::scoring::EMapVector::zero().

Referenced by core::scoring::symmetry::SymmetricScoreFunction::eval_onebody_energies().

void core::scoring::eval_weighted_res_pair_energy_for_minedge	(	MinimizationEdge const &	min_edge,
		conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap,
		EnergyMap &	scratch_emap
	)

evaluates the atom derivative for this edge, and applies the edge weight into the f1 and f2 vectors before accumulating into the F1 and F2 vectors

References core::scoring::EMapVector::accumulate(), core::scoring::MinimizationEdge::active_2benmeths_ext_begin(), core::scoring::MinimizationEdge::active_2benmeths_ext_end(), core::scoring::MinimizationEdge::active_2benmeths_std_begin(), core::scoring::MinimizationEdge::active_2benmeths_std_end(), core::scoring::MinimizationEdge::res_pair_min_data(), core::scoring::MinimizationEdge::weight(), and core::scoring::EMapVector::zero().

Referenced by core::scoring::symmetry::SymmetricScoreFunction::eval_twobody_neighbor_energies().

void core::scoring::evaluaterdc	(	const double *	par,
		int	m_dat,
		const void *	data,
		double *	fvec,
		int *	info
	)

References core::scoring::data_struct::frdc, core::scoring::data_struct::r0, core::scoring::data_struct::r1, core::scoring::data_struct::r2, core::scoring::data_struct::rdc, and core::scoring::data_struct::rdcconst.

Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore_nls().

void core::scoring::evaluaterdcDa	(	const double *	par,
		int	m_dat,
		const void *	data,
		double *	fvec,
		int *	info
	)

References core::scoring::data_structDa::frdcDa, core::scoring::data_structDa::r0, core::scoring::data_structDa::r1, core::scoring::data_structDa::r2, core::scoring::data_structDa::rdc, core::scoring::data_structDa::rdcconst, and core::scoring::data_structDa::tensorDa.

Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDa().

void core::scoring::evaluaterdcDaR	(	const double *	par,
		int	m_dat,
		const void *	data,
		double *	fvec,
		int *	info
	)

References core::scoring::data_structDaR::frdcDaR, core::scoring::data_structDaR::r0, core::scoring::data_structDaR::r1, core::scoring::data_structDaR::r2, core::scoring::data_structDaR::rdc, core::scoring::data_structDaR::rdcconst, core::scoring::data_structDaR::tensorDa, and core::scoring::data_structDaR::tensorR.

Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDaR().

void core::scoring::evaluaterdcR	(	const double *	par,
		int	m_dat,
		const void *	data,
		double *	fvec,
		int *	info
	)

References core::scoring::data_structR::frdcR, core::scoring::data_structR::r0, core::scoring::data_structR::r1, core::scoring::data_structR::r2, core::scoring::data_structR::rdc, core::scoring::data_structR::rdcconst, and core::scoring::data_structR::tensorR.

Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsR().

std::string const core::scoring::FA_STANDARD_DEFAULT

(

"FA_STANDARD_DEFAULT"

)

global etable_id

std::string const core::scoring::FA_STANDARD_SOFT

(

"FA_STANDARD_SOFT"

)

void core::scoring::fill_bb_pos	(	pose::Pose const &	pose,
		BB_Pos &	bb_pos
	)

helper function

References core::scoring::BB_Pos::take_coordinates_from_pose().

Referenced by core::scoring::SecondaryStructurePotential::setup_for_scoring().

template<class T >

void core::scoring::fill_rmsd_coordinates	(	int &	natoms,
		ObjexxFCL::FArray2D< core::Real > &	p1a,
		ObjexxFCL::FArray2D< core::Real > &	p2a,
		core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		T *	predicate
	)

References core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by CA_gdtmm(), CA_maxsub(), CA_maxsub_by_subset(), CA_rmsd(), and CA_rmsd_symmetric().

void core::scoring::fill_score_range	(	std::map< std::string, ScoreType > &	M,
		std::string	prefix,
		int	first,
		int	last
	)

std::string core::scoring::find_weights_file	(	std::string	name,
		std::string	extension
	)

Utility function to locate a weights or patch file, either with a fully qualified path, in the local directory, or in the database. Names may be passed either with or without the optional extension.

Utility function to locate a weights or patch file, either with a fully qualified path, in the local directory, or in the database. Names may be passes either with or without the optional extension.

References make_table_of_pilot_apps::name.

Referenced by core::scoring::ScoreFunction::add_weights_from_file(), and core::scoring::ScoreFunction::apply_patch_from_file().

double core::scoring::frdc	(	double	r0,
		double	r1,
		double	r2,
		double	rdcconst,
		const double *	par
	)

References protocols::match::upstream::b, and core::pack::dunbrack::c.

Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore_nls().

double core::scoring::frdcDa	(	double	r0,
		double	r1,
		double	r2,
		double	rdcconst,
		double const	tensorDa,
		const double *	par
	)

References protocols::match::upstream::b, and core::pack::dunbrack::c.

Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDa().

double core::scoring::frdcDaR	(	double	r0,
		double	r1,
		double	r2,
		double	rdcconst,
		double const	tensorDa,
		double const	tensorR,
		const double *	par
	)

References protocols::match::upstream::b, and core::pack::dunbrack::c.

Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDaR().

double core::scoring::frdcR	(	double	r0,
		double	r1,
		double	r2,
		double	rdcconst,
		double const	tensorR,
		const double *	par
	)

References protocols::match::upstream::b, and core::pack::dunbrack::c.

Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsR().

void core::scoring::get_2way_orientation	(	Vector const &	a_xyz,
		Vector const &	b_xyz,
		int &	phi_a2b_index,
		int &	theta_a2b_index,
		int &	phi_b2a_index,
		int &	theta_b2a_index,
		Real	distance_ijxyz
	)

Gets the orientation of a to b (i to j, see below). Does this by calculating two angles, aphi and theta. (j)

sasa.cc::get_2way_orientation

Detailed:

ronj This function is the same as the function above but get the orientation of a to b simultaneously with the ronj orientation of b to a. The same result could be achieved by making two separate get_2way_orientation() calls ronj but this method does it more efficiently by avoiding an atan2 and acos call. Instead, once you compute the ronj phi and theta for a on b, you can add/subtrate pi factors to get the phi and theta for b on a. ronj Still not sure how this method returns the correct values, though.

References make_table_of_pilot_apps::d, make_table_of_pilot_apps::f, num_phi, and num_theta.

Referenced by core::pack::interaction_graph::RotamerDots::get_atom_atom_coverage(), and core::pack::interaction_graph::InvRotamerDots::write_circle_intersection_mask_to_kinemage().

ObjexxFCL::FArray2D_int const & core::scoring::get_angles

(

)

Returns const access to the angles FArray, which contains the information in the SASA database file sampling/SASA-angles.dat. Adding this in so that the values in the SASA database files can be used in SASA-based scores. (ronj)

get_angles

References core::scoring::packstat::old::angles, and core::scoring::packstat::old::input_sasa_dats().

ObjexxFCL::FArray2D_ubyte const & core::scoring::get_masks

(

)

Returns const access to the masks FArray, which contains the information in the SASA database file sampling/SASA-masks.dat. Adding this in so that the values in the SASA database files can be used in SASA-based scores. (ronj)

get_masks

References core::scoring::packstat::old::input_sasa_dats(), and core::scoring::packstat::old::masks.

int core::scoring::get_num_bytes

(

)

Returns the number of bytes the overlap arrays use for tracking SASA. Adding this in so that the values in the SASA database files can be used in SASA-based scores. (ronj)

get_angles

References num_bytes.

void core::scoring::get_orientation	(	Vector const &	a_xyz,
		Vector const &	b_xyz,
		int &	phi_index,
		int &	theta_index,
		Real	distance_ijxyz
	)

Gets the orientation of a to b (i to j, see below). Does this by calculating two angles, aphi and theta. (j)

sasa.cc::get_orientation

Detailed:

ronj This function is used to get two indexes (phi and theta) which are used to get the index of a dot on the ronj surface of the 'a' sphere. When calculating how much surface area sphere b covers on a, we can get the degree ronj of overlap from the function above, but it's not necessarily the case that the vector that connects the center ronj of atom 'a' and atom 'b' goes through one of the predetermined dot locations on the surface of 'a'. In fact, ronj it's very unlikely that the vector goes through a predetermined dot. Instead, what is done is the actual point ronj of intersection (the outermost point of a on the line from the center of 'a' to center of 'b') is converted ronj to spherical polar coordinates. Then, the values are used to find the location of the closest predetermined ronj point on the surface of 'a' using a lookup table. So what this function needs to do is convert the ronj cartesian coordinate of the actual point of intersection into polar coordinates. ronj ronj To get the spherical, polar coordinates of a cartesian point x,y,z, use these equations: ronj r = sqrt( x^2 + y^2 + z^2 ) ronj theta = arccos( z / r ) ronj phi = arctan( y / x )

ronj Then, once we have the true phi and theta, we need to translate this into an index (or offset) for the correct ronj value in the database file. There are 64 phi angle bin and 64 theta bins in the database file sampling/SASA-angles.dat. ronj We need to convert the phi and theta into indexes for this file by multiplying them by num_phi / 2*pi. ronj Note: I think phi and theta have been reversed in the function below. The code below uses the following: ronj phi = arccos( z ) ronj theta = arctan( y / x )

ronj After a couple of weeks trying to write tests for this function, I have been unsuccessful in figuring out why ronj it's doing what it does. Despite using the wrong equations, it seems to work. Comparing the total residue ronj SASA values calculated by calc_per_atom_sasa() below results in a correlation of 0.98 against what the program ronj NACCESS finds for the same residues. This test was done on a small 110aa protein. I also looked at the per-atom ronj total SASA and the correlation for all atoms (mini v. NACCESS) was approximately 0.94. I'm using exactly the same ronj van der Waals radii for both programs so I feel like the correlations should be 1.0. Explanations for the ronj differences can be 1) this method is doing something wrong in calculating the closest surface point, 2) this ronj method is correct but the masks that are in the database are not aligned to the surface points correctly, 3) the ronj differences are solely due to the different way that the two program calculate surface area.

References make_table_of_pilot_apps::d, num_phi, num_theta, and protocols::swa::phi().

Referenced by core::scoring::packstat::compute_cav_ball_volumes(), core::scoring::packstat::compute_sasa(), core::scoring::packstat::prune_1pass(), and core::scoring::packstat::prune_hidden_cavity_balls().

void core::scoring::get_overlap	(	Real const	radius_a,
		Real const	radius_b,
		Real const	distance_ijxyz,
		int &	degree_of_overlap
	)

sasa.cc::get_overlap

Detailed:

getting overlap from a to b (or i to j, as the atoms are referred to in calc_per_atom_sasa below). this returns the degree of overlap between two atoms adapted from erics code in area.c GetD2 and returns value from 1 to 100. This calculation is based on the law of cosines. See LeGrand and Merz, Journal of Computational Chemistry 14(3):349-52 (1993). Note that equation (4) is wrong, the denominator should be 2*ri*riq instead of 2*ri*rq (j)

The function gets passed in the sasa radius of atom i (plus the probe radius), the sasa radius of atom j (plus the probe radius), the distance between the atom centers, and a reference to the degree of overlap (represented as an int). The degree of overlap that's returned can be thought of as how much of atom a is covered by atom b. A value of 100 means that atom a is completely covered up by atom b. A value of 1 means that not much of the surface of 'a' is covered up by 'b'. The law of cosines relates the cosine of one angle of a triangle to the lengths of its sides. More specifically, c^2 = a^2 + b^2 - 2*a*b*cos theta, where theta is the angle between sides a and b. For the function we want to compute the angle of the cone of intersection between spheres 'a' and 'b'. Let the radius of atom a be ri, and the radius of atom b be rq, and the distance between atom centers be riq. Let the angle between ri and riq be theta_iq. The cosine of theta_iq will be equivalent to ( ri^2 + riq^2 - rq^2 ) / 2 * ri * riq

Referenced by core::scoring::packstat::compute_cav_ball_volumes(), core::scoring::packstat::compute_sasa(), core::scoring::packstat::prune_1pass(), and core::scoring::packstat::prune_hidden_cavity_balls().

PoissonBoltzmannPotential & core::scoring::get_PB_potential

(

)

References core::scoring::PoissonBoltzmannPotential::isLoaded(), core::scoring::PoissonBoltzmannPotential::read_APBS_potential(), and TR().

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

core::scoring::ScoreFunctionOP core::scoring::getScoreFunction

(

bool const

is_fullatom

)

A helper function which returns a scoring function owning pointer according to the user's command line parameters -score:weights and -score:patch By default it returns weights=standard and patch=score12 for fullatom, and weights=cen_std and patch="" for centroid.

References CENTROID_WTS, core::scoring::ScoreFunctionFactory::create_score_function(), and T().

Referenced by protocols::topology_broker::TopologyBroker::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::simple_moves::symmetry::SymMinMover::apply(), protocols::simple_moves::ProlineFixMover::apply(), protocols::simple_moves::MinMover::apply(), protocols::simple_moves::ConsensusDesignMover::apply(), protocols::simple_filters::TruncatedScoreEvaluator::apply(), protocols::simple_filters::SAXSScoreFilter::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::abinitio::ResolutionSwitcher::apply(), JDtestmover::apply(), protocols::rbsegment_relax::AutoRBMover::AutoRBMover(), protocols::canonical_sampling::canonical_sampling_main(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::protein_interface_design::BuriedUnsatHbondFilter::compute(), protocols::electron_density::dockPoseIntoMap(), protocols::enzdes::EnzdesBaseProtocol::EnzdesBaseProtocol(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::fascore(), protocols::swa::StepWiseFilterer::filter(), protocols::swa::protein::StepWiseProteinFilterer::filter(), protocols::flxbb::FlxbbDesign_main(), protocols::swa::protein::generate_beta_database_test(), protocols::relax::generate_relax_from_cmd(), protocols::features::get_current_model_score(), protocols::loops::get_fa_scorefxn(), protocols::jd2::JobDistributor::go_main(), protocols::comparative_modeling::hybridize::HybridizeProtocol::init(), JDtestmover::JDtestmover(), protocols::ligand_docking::LigandBaseProtocol::LigandBaseProtocol(), protocols::loophash::MPI_LoopHashRefine::load_structures_from_cmdline_into_library(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::LoopMover_Refine_Backrub(), protocols::analysis::InterfaceAnalyzerMover::make_separated_pose(), protocols::jobdist::not_universal_main(), protocols::simple_moves::RotamerTrialsMinMover::parse_my_tag(), core::util::rebuild_disulfide(), protocols::relax::WorkUnit_BatchRelax::run(), protocols::abinitio::run_boinc_debug(), protocols::rotamer_recovery::RotamerRecoveryMover::score_function(), and protocols::flexpep_docking::FlexPepDockingProtocol::set_default().

template<class T , class T_Etable >

void core::scoring::inline_intraresidue_atom_pair_energy	(	conformation::Residue const &	res,
		T_Etable const &	etable_energy,
		T const &	count_pair,
		EnergyMap &	emap
	)		[inline]

intraresidue atom pair energy evaluations

References core::conformation::Residue::atom(), core::conformation::Residue::atom_type(), core::conformation::Residue::attached_H_begin(), core::conformation::Residue::attached_H_end(), core::chemical::AtomType::is_virtual(), core::conformation::Residue::nheavyatoms(), residue_fast_pair_energy_attached_H(), and core::conformation::Atom::xyz().

Referenced by core::scoring::etable::count_pair::CountPairIntraResC4::residue_atom_pair_energy(), core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior >::residue_atom_pair_energy(), and core::scoring::etable::count_pair::CountPairIntraResC3::residue_atom_pair_energy().

template<class T , class T_Etable >

void core::scoring::inline_residue_atom_pair_energy	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		T_Etable const &	etable_energy,
		T const &	count_pair,
		EnergyMap &	emap
	)		[inline]

References inline_residue_atom_pair_energy(), and core::conformation::Residue::nheavyatoms().

template<class T , class T_Etable >

void core::scoring::inline_residue_atom_pair_energy	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		T_Etable const &	etable_energy,
		T const &	count_pair,
		EnergyMap &	emap,
		int	res1_start,
		int	res1_end,
		int	res2_start,
		int	res2_end
	)		[inline]

templated atom pair energy calculations

loops over the heavy atoms of residue1 and the heavy atoms of residue2, evaluates their energies, and if a pair of heavy atoms is close enough, descendes into the attached hydrogen atoms for each.

Templates are for count_pair type resolution and etable type resolution: there are no polymorphic lookups within these functions

class T must define class T_Etable must define atom_pair_energy( Atom const &, Atom const &, Real, EnergyMap &, Distance ) and

References core::conformation::Residue::atom(), core::conformation::Residue::atom_type(), core::conformation::Residue::attached_H_begin(), core::conformation::Residue::attached_H_end(), core::chemical::AtomType::is_virtual(), residue_fast_pair_energy_attached_H(), and core::conformation::Atom::xyz().

Referenced by inline_residue_atom_pair_energy(), inline_residue_atom_pair_energy_backbone_backbone(), inline_residue_atom_pair_energy_sidechain_backbone(), inline_residue_atom_pair_energy_sidechain_sidechain(), inline_residue_atom_pair_energy_sidechain_whole(), core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy(), core::scoring::etable::count_pair::CountPairAll::residue_atom_pair_energy(), and core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >::residue_atom_pair_energy().

template<class T , class T_Etable >

void core::scoring::inline_residue_atom_pair_energy_backbone_backbone	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		T_Etable const &	etable_energy,
		T const &	count_pair,
		EnergyMap &	emap
	)		[inline]

References inline_residue_atom_pair_energy(), and core::conformation::Residue::last_backbone_atom().

Referenced by core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_backbone_backbone(), core::scoring::etable::count_pair::CountPairAll::residue_atom_pair_energy_backbone_backbone(), and core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >::residue_atom_pair_energy_backbone_backbone().

template<class T , class T_Etable >

void core::scoring::inline_residue_atom_pair_energy_sidechain_backbone	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		T_Etable const &	etable_energy,
		T const &	count_pair,
		EnergyMap &	emap
	)		[inline]

References core::conformation::Residue::first_sidechain_atom(), inline_residue_atom_pair_energy(), core::conformation::Residue::last_backbone_atom(), and core::conformation::Residue::nheavyatoms().

Referenced by core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_sidechain_backbone(), core::scoring::etable::count_pair::CountPairAll::residue_atom_pair_energy_sidechain_backbone(), and core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >::residue_atom_pair_energy_sidechain_backbone().

template<class T , class T_Etable >

void core::scoring::inline_residue_atom_pair_energy_sidechain_sidechain	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		T_Etable const &	etable_energy,
		T const &	count_pair,
		EnergyMap &	emap
	)		[inline]

References core::conformation::Residue::first_sidechain_atom(), inline_residue_atom_pair_energy(), and core::conformation::Residue::nheavyatoms().

Referenced by core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_sidechain_sidechain(), core::scoring::etable::count_pair::CountPairAll::residue_atom_pair_energy_sidechain_sidechain(), and core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >::residue_atom_pair_energy_sidechain_sidechain().

template<class T , class T_Etable >

void core::scoring::inline_residue_atom_pair_energy_sidechain_whole	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		T_Etable const &	etable_energy,
		T const &	count_pair,
		EnergyMap &	emap
	)		[inline]

References core::conformation::Residue::first_sidechain_atom(), inline_residue_atom_pair_energy(), and core::conformation::Residue::nheavyatoms().

Referenced by core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_sidechain_whole(), core::scoring::etable::count_pair::CountPairAll::residue_atom_pair_energy_sidechain_whole(), and core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >::residue_atom_pair_energy_sidechain_whole().

void core::scoring::input_sasa_dats

(

)

Reads in the SASA database files sampling/SASA-angles.dat and sampling/SASA-masks.dat into FArrays above.

sasa.cc::input_sasa_dats

References core::scoring::packstat::old::angles, core::init(), core::scoring::packstat::old::masks, num_bytes, num_orientations, num_overlaps, num_phi, and num_theta.

Referenced by core::scoring::packstat::compute_sasa().

void core::scoring::interpolate_value_and_deriv	(	ObjexxFCL::FArray1D< Real > const &	potential,
		Real const &	bin_width,
		Real const &	r,
		Real &	value,
		Real &	deriv
	)		[inline]

Referenced by core::scoring::carbon_hbonds::CarbonHBondPotential::get_potential().

void core::scoring::invert_exclude_residues	(	Size	nres,
		utility::vector1< int > const &	exclude_list,
		ResidueSelection &	residue_selection
	)

Referenced by protocols::simple_filters::NativeEvaluatorCreator::add_evaluators(), protocols::cluster::GatherPosesMover::get_distance_measure(), invert_exclude_residues(), native_CA_gdtmm(), and native_CA_rmsd().

ResidueSelection core::scoring::invert_exclude_residues	(	core::Size	nres,
		utility::vector1< int > const &	exclude_list
	)

References invert_exclude_residues().

Real core::scoring::iprod	(	const rvec	a,
		const rvec	b
	)		[inline]

References XX, YY, and ZZ.

bool core::scoring::is_heavyatom	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	,
		core::Size	resno,
		core::Size	atomno
	)

References core::conformation::Residue::atom_is_hydrogen(), and core::pose::Pose::residue().

Referenced by all_atom_rmsd(), biggest_residue_deviation_no_super(), biggest_residue_deviation_no_super_subset(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_atoms_kA_to_native(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), rmsd_no_super(), rmsd_no_super_subset(), rmsd_with_super(), rmsd_with_super_subset(), and sym_rmsd_with_super_subset().

bool core::scoring::is_ligand_heavyatom	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	,
		core::Size	resno,
		core::Size	atomno
	)

References core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::is_polymer(), and core::pose::Pose::residue().

Referenced by protocols::ligand_docking::append_multi_residue_ligand_RMSD(), biggest_residue_deviation_no_super(), biggest_residue_deviation_no_super_subset(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_atoms_kA_to_native(), rmsd_no_super(), rmsd_no_super_subset(), rmsd_with_super(), rmsd_with_super_subset(), and sym_rmsd_with_super_subset().

bool core::scoring::is_ligand_heavyatom_residues	(	core::conformation::Residue const &	residue1,
		core::conformation::Residue const &	,
		core::Size	atomno
	)

References core::conformation::Residue::atom_is_hydrogen(), and core::conformation::Residue::is_polymer().

Referenced by protocols::ligand_docking::check_RMSD(), and rmsd_no_super().

bool core::scoring::is_nbr_atom	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	,
		core::Size	resno,
		core::Size	atomno
	)

References core::conformation::Residue::nbr_atom(), and core::pose::Pose::residue().

Referenced by nbr_atom_rmsd().

bool core::scoring::is_polymer_heavyatom	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	,
		core::Size	resno,
		core::Size	atomno
	)

References core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::is_polymer(), and core::pose::Pose::residue().

Referenced by biggest_residue_deviation_no_super(), biggest_residue_deviation_no_super_subset(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_atoms_kA_to_native(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), rmsd_no_super(), rmsd_no_super_subset(), rmsd_with_super(), rmsd_with_super_subset(), and sym_rmsd_with_super_subset().

bool core::scoring::is_protein_backbone	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	,
		core::Size	resno,
		core::Size	atomno
	)

References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), and core::pose::Pose::residue().

Referenced by bb_rmsd(), protocols::docking::calc_Irmsd(), protocols::docking::calc_Lrmsd(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf(), and protocols::cluster::GatherPosesMover::get_distance_measure().

bool core::scoring::is_protein_backbone_including_O	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	,
		core::Size	resno,
		core::Size	atomno
	)

References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), and core::pose::Pose::residue().

Referenced by bb_rmsd_including_O().

bool core::scoring::is_protein_CA	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	,
		core::Size	resno,
		core::Size	atomno
	)

References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), and core::pose::Pose::residue().

Referenced by protocols::simple_moves::symmetry::SymmetricRMSMover::apply(), CA_gdtmm(), CA_maxsub(), CA_maxsub_by_subset(), CA_rmsd_symmetric(), protocols::ub_e2c::ubi_e2c_modeler::calc_Lrmsd(), protocols::symmetric_docking::SymDockProtocol::calc_rms(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), protocols::protein_interface_design::filters::RmsdFilter::compute(), protocols::antibody2::Ab_ModelCDRH3::global_loop_rmsd(), protocols::antibody::AntibodyModeler::global_loop_rmsd(), and core::scoring::IsProteinCAPredicate::operator()().

bool core::scoring::is_protein_CA_or_CB	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	,
		core::Size	resno,
		core::Size	atomno
	)

References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), and core::pose::Pose::residue().

Referenced by protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf().

bool core::scoring::is_protein_sidechain_heavyatom	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	,
		core::Size	resno,
		core::Size	atomno
	)

References core::chemical::ResidueType::atom_is_hydrogen(), core::chemical::ResidueType::first_sidechain_atom(), core::chemical::ResidueType::is_protein(), and core::pose::Pose::residue_type().

Referenced by protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), and protocols::enzdes::RepackWithoutLigandFilter::compute().

void core::scoring::jacobi	(	Real	a[5][5],
		Real	d[],
		Real	v[5][5],
		int *	nrot
	)

References protocols::match::upstream::b, core::pack::dunbrack::c, ROTATE, and core::scoring::hbonds::t().

Referenced by m_inv_gen().

void core::scoring::jacobi3	(	Real	a[3][3],
		Real	d[],
		Real	v[3][3],
		int *	nrot
	)

References protocols::match::upstream::b, core::pack::dunbrack::c, ROTATE, and core::scoring::hbonds::t().

Referenced by core::scoring::ResidualDipolarCoupling::compute_tensor_stats().

int core::scoring::m_inv_gen	(	Tensor5	m,
		int	n,
		Tensor5	minv
	)

References jacobi().

Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore().

ObjexxFCL::FArray2D_ubyte core::scoring::masks	(	num_bytes	,
		num_overlaps *	num_orientations
	)

Referenced by core::scoring::packstat::compute_cav_ball_volumes(), core::scoring::packstat::compute_sasa(), core::scoring::packstat::prune_1pass(), and core::scoring::packstat::prune_hidden_cavity_balls().

std::string const core::scoring::MEMB_HIGHRES_WTS

(

"membrane_highres"

)

Membrane_FAEmbed const & core::scoring::Membrane_FAEmbed_from_pose

(

pose::Pose const &

pose

)

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

Referenced by core::scoring::Membrane_FAPotential::compute_fa_projection(), core::scoring::hbonds::get_membrane_depth_dependent_weight(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), and core::scoring::hbonds::HBondEnergy::setup_for_scoring().

MembraneEmbed const & core::scoring::MembraneEmbed_from_pose

(

pose::Pose const &

pose

)

Pose must already contain a cenlist object or this method will fail.

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

Referenced by protocols::rigid::MembraneNormalPerturbationMover::apply(), protocols::rigid::MembraneCenterPerturbationMover::apply(), protocols::rigid::MovePoseToMembraneCenterMover::apply(), core::scoring::Membrane_FAPotential::compute_fa_projection(), core::scoring::MembranePotential::evaluate_env(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::hbonds::get_membrane_depth_dependent_weight(), core::scoring::etable::BaseEtableEnergy< Derived >::memb_atom_pair_energy_(), core::scoring::etable::BaseEtableEnergy< Derived >::memb_eval_dE_dR_over_r_(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), core::scoring::hbonds::HBondEnergy::setup_for_scoring(), core::scoring::MembranePotential::termini_penalty(), and core::scoring::MembranePotential::tm_projection_penalty().

MembraneTopology const & core::scoring::MembraneTopology_from_pose

(

pose::Pose const &

pose

)

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

Referenced by protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::abinitio::MembraneAbinitio::apply(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::MembranePotential::evaluate_cbeta(), core::scoring::MembranePotential::init_membrane_center_normal(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), protocols::abinitio::MembraneAbinitio::print_debug(), core::scoring::MembranePotential::termini_penalty(), and core::scoring::MembranePotential::tm_projection_penalty().

std::string const core::scoring::MM_STD_WTS

(

"mm_std"

)

void core::scoring::mvmul	(	matrix	a,
		const rvec	src,
		rvec	dest
	)		[inline]

References XX, YY, and ZZ.

std::string core::scoring::name_from_score_type

(

ScoreType

score_type

)

Returns the name of the ScoreType <score_type>

example(s): name_from_score_type(fa_sol) See also: ScoreFunction ScoreType Energies Energies.residue_total_energies score_type_from_name

References core::scoring::ScoreTypeManager::name_from_score_type().

Referenced by protocols::ligand_docking::append_interface_deltas(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::simple_filters::ScoreTypeFilter::apply(), protocols::simple_filters::EnergyPerResidueFilter::apply(), protocols::protein_interface_design::EnergyPerResidueFilter::apply(), protocols::protein_interface_design::ScoreTypeFilter::apply(), protocols::jobdist::PlainPdbJobDistributor::dump_scores(), core::io::silent::SilentStruct::energies_from_pose(), core::io::pdb::extract_scores(), protocols::ddg::ddGMover::get_scorefunction_header(), protocols::optimize_weights::IterativeOptEDriver::IterativeOptEDriver(), core::import_pose::atom_tree_diffs::map_of_weighted_scores(), core::scoring::methods::EnergyMethodOptions::method_weights(), operator<<(), protocols::simple_filters::ScoreCutoffFilter::output_residue_pair_energies(), core::scoring::ScoreFunction::perturb_weights(), core::scoring::EMapVector::print(), protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::process_score(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::process_score(), protocols::simple_filters::ScoreTypeFilter::report(), protocols::simple_filters::EnergyPerResidueFilter::report(), protocols::protein_interface_design::EnergyPerResidueFilter::report(), protocols::protein_interface_design::ScoreTypeFilter::report(), protocols::jd2::ScoreMap::score_map_from_scored_pose(), protocols::moves::PyMolMover::send_energy(), protocols::abinitio::MembraneAbinitio::set_score_weight(), protocols::abinitio::FragmentSampler::set_score_weight(), protocols::abinitio::ClassicAbinitio::set_score_weight(), core::scoring::Energies::show(), protocols::optimize_weights::WrapperOptEMultifunc::WrapperOptEMultifunc(), protocols::optimize_weights::OptEData::write_to_file(), and protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::write_to_file().

core::Real core::scoring::native_CA_gdtmm	(	const core::pose::Pose &	native_pose,
		const core::pose::Pose &	pose
	)

References CA_gdtmm(), invert_exclude_residues(), and core::pose::Pose::total_residue().

Referenced by protocols::relax::FastRelax::batch_apply().

core::Real core::scoring::native_CA_rmsd	(	const core::pose::Pose &	native_pose,
		const core::pose::Pose &	pose
	)

References CA_rmsd(), invert_exclude_residues(), and core::pose::Pose::total_residue().

Referenced by protocols::simple_moves::ScoreMover::apply(), protocols::relax::FastRelax::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::relax::FastRelax::batch_apply(), protocols::relax::FastRelax::cmd_accept_to_best(), protocols::jobdist::main_plain_pdb_mover(), and protocols::jobdist::universal_main().

core::Real core::scoring::nbr_atom_rmsd	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2
	)

References is_nbr_atom(), rms, and rmsd_with_super().

Membrane_FAEmbed & core::scoring::nonconst_Membrane_FAEmbed_from_pose

(

pose::Pose &

pose

)

Either returns a non-const reference to the cenlist object already stored in the pose, or creates a new cenist object, places it in the pose, and returns a non-const reference to it.

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

Referenced by core::scoring::Membrane_FAPotential::compute_fa_projection(), and core::scoring::Membrane_FAPotential::finalize().

MembraneEmbed & core::scoring::nonconst_MembraneEmbed_from_pose

(

pose::Pose &

pose

)

Either returns a non-const reference to the cenlist object already stored in the pose, or creates a new cenist object, places it in the pose, and returns a non-const reference to it.

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

Referenced by core::scoring::Membrane_FAPotential::compute_fa_projection(), core::scoring::MembranePotential::compute_membrane_embedding(), core::scoring::MembranePotential::finalize(), and core::scoring::Membrane_FAPotential::finalize().

MembraneTopology & core::scoring::nonconst_MembraneTopology_from_pose

(

pose::Pose &

pose

)

Either returns a non-const reference to the cenlist object already stored in the pose, or creates a new cenist object, places it in the pose, and returns a non-const reference to it.

References core::pose::Pose::data(), core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY, and core::scoring::MembraneTopology::MembraneTopology().

Referenced by protocols::abinitio::MembraneAbinitio::add_spanning_region(), protocols::abinitio::MembraneAbinitio::apply(), core::scoring::MembranePotential::compute_membrane_embedding(), and protocols::abinitio::MembraneAbinitio::move_all_inserted().

std::ostream& core::scoring::operator<<	(	std::ostream &	out,
		ScoreFunction const &	sf
	)		[inline]

References core::scoring::ScoreFunction::show().

std::ostream& core::scoring::operator<<	(	std::ostream &	out,
		Hairpins const &	s
	)

References core::scoring::Hairpins::list().

std::ostream& core::scoring::operator<<	(	std::ostream &	ost,
		EMapVector const &	emap
	)		[inline]

output operator (index;value)

References n_score_types.

std::ostream & core::scoring::operator<<	(	std::ostream &	out,
		RDC const &	rdc
	)

References core::scoring::RDC::show().

std::ostream & core::scoring::operator<<	(	std::ostream &	out,
		ResidualDipolarCoupling const &	rdc
	)

References core::scoring::ResidualDipolarCoupling::show().

std::ostream& core::scoring::operator<<	(	std::ostream &	out,
		Helices const &	s
	)

References core::scoring::Helices::HH_helix_end, core::scoring::Helices::HH_resnum, and core::scoring::Helices::total_HH_dimer.

std::ostream& core::scoring::operator<<	(	std::ostream &	out,
		Strands const &	s
	)

References core::scoring::Strands::SS_dimer, core::scoring::Strands::SS_resnum, core::scoring::Strands::SS_strand, core::scoring::Strands::SS_strand_end, core::scoring::Strands::total_SS_dimer, and core::scoring::Strands::total_strands.

std::ostream& core::scoring::operator<<	(	std::ostream &	out,
		const Energies &	e
	)

References protocols::comparative_modeling::features::A, core::scoring::EMapVector::begin(), core::scoring::EMapVector::end(), core::scoring::Energies::get_scorefxn_info(), name_from_score_type(), core::scoring::Energies::residue_total_energies(), core::scoring::ScoreFunctionInfo::scores_present(), core::scoring::Energies::size(), and core::scoring::Energies::total_energies().

std::ostream & core::scoring::operator<<	(	std::ostream &	os,
		ScoreTypes const &	score_types
	)

output operator for ScoreTypes list type

output operator for ScoreTypes list

std::ostream& core::scoring::operator<<	(	std::ostream &	out,
		Hairpin const &	s
	)

References core::scoring::Hairpin::s1_end(), core::scoring::Hairpin::s1_start(), core::scoring::Hairpin::s2_end(), and core::scoring::Hairpin::s2_start().

std::ostream & core::scoring::operator<<	(	std::ostream &	os,
		ScoreType const &	score_type
	)

output operator for ScoreType enum type

example usage: std::cout << score_type_gly << std::endl;

References core::scoring::ScoreTypeManager::name_from_score_type().

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

References n_score_types, and num_context_graph_types.

std::istream & core::scoring::operator>>	(	std::istream &	is,
		ScoreType &	score_type
	)

input operator for ScoreType enum type

read in a string name from a file or std::cin and directly convert it to an ScoreType enum type, for example, std::cin >> ScoreType. This will first check if the lookup map has been set up already. If the string name cannot be converted properly, it will flag the input stream as failure (e.g., istream.fail() is true) and set ScoreType enum type to total_score.

References core::scoring::ScoreTypeManager::is_score_type(), make_table_of_pilot_apps::name, core::scoring::ScoreTypeManager::score_type_from_name(), and total_score.

void core::scoring::print_dot_bit_string

(

utility::vector1< ObjexxFCL::ubyte > &

values

)

helper method I was using to try to confirm that the dots are being overlapped and bits are being set correctly (ronj).

sasa.cc::print_dot_bit_string

References num_bytes.

Referenced by calc_per_atom_sasa().

template<class T , class T_Etable >

void core::scoring::residue_fast_pair_energy_attached_H	(	conformation::Residue const &	res1,
		int const	atomno1,
		conformation::Residue const &	res2,
		Size const	atomno2,
		Size const	at1hbegin,
		Size const	at1hend,
		Size const	at2hbegin,
		Size const	at2hend,
		T const &	count_pair,
		T_Etable const &	etable_energy,
		EnergyMap &	emap
	)		[inline]

class T must define

References core::conformation::Residue::atom().

Referenced by inline_intraresidue_atom_pair_energy(), and inline_residue_atom_pair_energy().

core::Real core::scoring::residue_sc_rmsd_no_super	(	core::conformation::ResidueCOP	res1,
		core::conformation::ResidueCOP	res2,
		bool const	fxnal_group_only
	)

utility function to calculate per-residue sidechain rmsd without superposition

Iterates over all non-hydrogen sidechain atoms of two residues and returns their rmsd without superposition.

References core::pose::num_atoms().

Referenced by protocols::cluster::GatherPosesMover::get_distance_measure().

SS_Info const& core::scoring::retrieve_const_ss_info_from_pose

(

pose::Pose const &

pose

)

helper function

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

void core::scoring::retrieve_coordinates	(	const core::pose::Pose &	pose,
		const utility::vector1< core::Size > &	residues,
		FArray2D< core::Real > *	coords
	)

Populates the output parameter with the xyz coordinates of a subset of <pose>'s CA atoms, which are specified in <residues>

References core::pose::Pose::xyz(), and protocols::kinmatch::xyz().

Referenced by CA_gdtmm(), and CA_rmsd().

SS_Info& core::scoring::retrieve_nonconst_ss_info_from_pose

(

pose::Pose &

pose

)

helper function

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

Referenced by core::scoring::SecondaryStructurePotential::setup_for_scoring().

ResidualDipolarCouplingCOP core::scoring::retrieve_RDC_from_pose

(

core::pose::Pose const &

pose

)

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

Referenced by core::scoring::methods::ResidualDipolarCouplingEnergy::eval_atom_derivative(), and core::scoring::methods::ResidualDipolarCouplingEnergy::setup_for_minimizing().

ResidualDipolarCouplingOP core::scoring::retrieve_RDC_from_pose

(

core::pose::Pose &

pose

)

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

ResidualDipolarCoupling_RohlCOP core::scoring::retrieve_RDC_ROHL_from_pose

(

core::pose::Pose const &

pose

)

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

ResidualDipolarCoupling_RohlOP core::scoring::retrieve_RDC_ROHL_from_pose

(

core::pose::Pose &

pose

)

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

static numeric::random::RandomGenerator core::scoring::RG

(

280628

)

[static]

Referenced by core::scoring::MembranePotential::compute_membrane_embedding().

Real core::scoring::rms_at_all_corresponding_atoms	(	pose::Pose const &	mod_pose,
		pose::Pose const &	ref_pose,
		std::map< core::id::AtomID, core::id::AtomID >	atom_id_map
	)

Calculates RMSD of all atoms in AtomID map, no need for the poses to be the same length.

References core::pose::Pose::residue(), and core::pose::Pose::xyz().

Real core::scoring::rms_at_corresponding_atoms	(	pose::Pose const &	mod_pose,
		pose::Pose const &	ref_pose,
		std::map< core::id::AtomID, core::id::AtomID >	atom_id_map
	)

Should be more robust to crazy variant type mismatches. Both poses must have the same length.

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

Referenced by protocols::swa::protein::output_silent_struct(), protocols::swa::PoseFilter_RMSD_Screen::passes_filter(), and rms_at_corresponding_heavy_atoms().

Real core::scoring::rms_at_corresponding_atoms	(	pose::Pose const &	mod_pose,
		pose::Pose const &	ref_pose,
		std::map< core::id::AtomID, core::id::AtomID >	atom_id_map,
		utility::vector1< Size > const &	calc_rms_res
	)

Should be more robust to crazy variant type mismatches. Both poses must have the same length.

References core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

Real core::scoring::rms_at_corresponding_atoms_no_super	(	pose::Pose const &	mod_pose,
		pose::Pose const &	ref_pose,
		std::map< core::id::AtomID, core::id::AtomID >	atom_id_map
	)

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

Referenced by protocols::swa::protein::output_silent_struct(), and protocols::swa::PoseFilter_RMSD_Screen::passes_filter().

Real core::scoring::rms_at_corresponding_atoms_no_super	(	pose::Pose const &	mod_pose,
		pose::Pose const &	ref_pose,
		std::map< core::id::AtomID, core::id::AtomID >	atom_id_map,
		utility::vector1< Size > const &	calc_rms_res
	)

References core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

Real core::scoring::rms_at_corresponding_heavy_atoms	(	pose::Pose const &	mod_pose,
		pose::Pose const &	ref_pose
	)

References rms_at_corresponding_atoms(), and setup_matching_heavy_atoms().

Referenced by protocols::coarse_rna::CoarseRNA_DeNovoProtocol::apply(), protocols::swa::rna::Output_data(), and protocols::swa::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file().

template<class T >

core::Real core::scoring::rmsd_no_super	(	core::conformation::ResidueCOPs const &	residues1,
		core::conformation::ResidueCOPs const &	residues2,
		T *	predicate
	)

References is_ligand_heavyatom_residues(), and core::pose::num_atoms().

template<class T >

core::Real core::scoring::rmsd_no_super	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		T *	predicate
	)

Select atoms for RMS via a predicate function/functor.

Calculates minimal rms, NOT allowing rotation/translation -- uses current coordinates as-is. Parameter "predicate" should be a function pointer [ or class that defines operator() ] with the following signature:

bool my_pred_func(Pose const & pose1, Pose const & pose2, Size resno, Size atomno);

It should return true if the atom should be included and false otherwise.

Example of use, to calculate C-alpha RMSD: rmsd_no_super(pose1, pose2, is_protein_CA);

References is_heavyatom(), is_ligand_heavyatom(), is_polymer_heavyatom(), core::conformation::Residue::natoms(), core::pose::num_atoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by protocols::ligand_docking::append_multi_residue_ligand_RMSD(), protocols::ligand_docking::check_RMSD(), protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf(), and core::import_pose::atom_tree_diffs::rms_error_with_noise().

template<class T >

core::Real core::scoring::rmsd_no_super_subset	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		ObjexxFCL::FArray1D_bool const &	subset,
		T *	predicate
	)

Select atoms for RMS via a predicate function/functor.

Calculates minimal rms over a subset of residues, NOT allowing rotation/translation -- uses current coordinates as-is. Parameter "predicate" should be a function pointer [ or class that defines operator() ] with the following signature:

bool my_pred_func(Pose const & pose1, Pose const & pose2, Size resno, Size atomno); the subset is a vector of all the residues, with true for those over which to calculate the rms

It should return true if the atom should be included and false otherwise.

Example of use, to calculate C-alpha RMSD: rmsd_no_super_subset(pose1, pose2, subset, is_protein_CA);

References is_heavyatom(), is_ligand_heavyatom(), is_polymer_heavyatom(), core::conformation::Residue::natoms(), core::pose::num_atoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::best_Kmer_rms(), protocols::docking::calc_Lrmsd(), protocols::ub_e2c::ubi_e2c_modeler::calc_Lrmsd(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), protocols::protein_interface_design::filters::RmsdFilter::compute(), protocols::enzdes::RepackWithoutLigandFilter::compute(), protocols::antibody2::Ab_ModelCDRH3::global_loop_rmsd(), and protocols::antibody::AntibodyModeler::global_loop_rmsd().

template<class T >

core::Real core::scoring::rmsd_with_super	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		std::list< core::Size > const &	subset_residues,
		T *	predicate
	)

References is_heavyatom(), is_ligand_heavyatom(), is_polymer_heavyatom(), core::conformation::Residue::natoms(), core::pose::num_atoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by all_atom_rmsd(), protocols::ligand_docking::append_multi_residue_ligand_RMSD(), bb_rmsd(), bb_rmsd_including_O(), protocols::cluster::GatherPosesMover::get_distance_measure(), nbr_atom_rmsd(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), and rmsd_with_super().

template<class T >

core::Real core::scoring::rmsd_with_super	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		T *	predicate
	)

Select atoms for RMS via a predicate function/functor.

Calculates minimal rms, allowing rotation/translation for best fit. Parameter "predicate" should be a function pointer [ or class that defines operator() ] with the following signature:

bool my_pred_func(Pose const & pose1, Pose const & pose2, Size resno, Size atomno);

It should return true if the atom should be included and false otherwise.

Example of use, to calculate C-alpha RMSD: rmsd_with_super(pose1, pose2, is_protein_CA);

References rmsd_with_super(), and core::pose::Pose::total_residue().

template<class T >

core::Real core::scoring::rmsd_with_super_subset	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		ObjexxFCL::FArray1D_bool const &	subset,
		T *	predicate
	)

Select a subset atoms for RMS via a predicate function/functor.

Calculates minimal rms, allowing rotation/translation for best fit. Same as above function, but allows a subset of residues over which to superposition to be passed in Parameter "predicate" should be a function pointer [ or class that defines operator() ] with the following signature:

bool my_pred_func(Pose const & pose1, Pose const & pose2, Size resno, Size atomno);

It should return true if the atom should be included and false otherwise.

Example of use, to calculate C-alpha RMSD: rmsd_with_super(pose1, pose2, is_protein_CA, subset);

References is_heavyatom(), is_ligand_heavyatom(), is_polymer_heavyatom(), core::conformation::Residue::natoms(), core::pose::num_atoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by protocols::simple_moves::symmetry::SymmetricRMSMover::apply(), protocols::docking::calc_Irmsd(), protocols::symmetric_docking::SymDockProtocol::calc_rms(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), and protocols::protein_interface_design::filters::RmsdFilter::compute().

std::string const core::scoring::RNA_HIRES_WTS

(

"rna_hires"

)

std::string const core::scoring::RNA_LORES_PLUS_HIRES_WTS

(

"rna_lores_plus_hires"

)

std::string const core::scoring::RNA_LORES_WTS

(

"rna_lores"

)

std::string const core::scoring::SCORE12_PATCH

(

"score12"

)

std::string const core::scoring::SCORE13

(

"score13"

)

ScoreType core::scoring::score_type_from_name

(

std::string const &

name

)

give a ScoreType string name and return its enum type

Returns the ScoreType titled <name>

example(s): score_type_from_name("fa_sol") See also: ScoreFunction ScoreType Energies Energies.residue_total_energies name_from_score_type

References core::scoring::ScoreTypeManager::score_type_from_name().

Referenced by protocols::relax::FastRelax::apply(), protocols::relax::FastRelax::batch_apply(), protocols::enzdes::EnzdesScorefileFilter::examine_pose(), protocols::ddg::ddGMover::get_scorefunction_header(), protocols::optimize_weights::ConstraintedOptimizationWeightFunc::initialize_constraints_from_file(), protocols::jd2::parser::ScoreFunctionLoader::load_data(), protocols::simple_filters::ScoreTypeFilter::parse_my_tag(), protocols::simple_filters::EnergyPerResidueFilter::parse_my_tag(), protocols::protein_interface_design::EnergyPerResidueFilter::parse_my_tag(), protocols::protein_interface_design::ScoreTypeFilter::parse_my_tag(), protocols::moves::RampingMover::parse_my_tag(), protocols::enzdes::EnzScoreFilter::parse_my_tag(), protocols::optimize_weights::OptEData::read_from_file(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::read_from_file(), protocols::simple_moves::symmetry::SymShakeStructureMover::reduce_fa_rep(), protocols::simple_moves::ShakeStructureMover::reduce_fa_rep(), protocols::optimize_weights::WrapperOptEMultifunc::register_variable_expression(), protocols::match::downstream::ScoringSecMatchRPE::ScoringSecMatchRPE(), protocols::simple_moves::symmetry::SymShakeStructureMover::setup_for_run(), and protocols::simple_moves::ShakeStructureMover::setup_for_run().

void core::scoring::setup_matching_atoms_with_given_names	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		utility::vector1< std::string > const &	atom_names_to_find,
		std::map< core::id::AtomID, core::id::AtomID > &	atom_id_map
	)

References core::conformation::Residue::atom_index(), core::chemical::ResidueType::has_atom_name(), core::conformation::Residue::is_virtual(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by setup_matching_CA_atoms(), and setup_matching_protein_backbone_heavy_atoms().

void core::scoring::setup_matching_CA_atoms	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		std::map< core::id::AtomID, core::id::AtomID > &	atom_id_map
	)

References setup_matching_atoms_with_given_names().

Referenced by protocols::swa::protein::output_silent_struct().

void core::scoring::setup_matching_heavy_atoms	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		std::map< core::id::AtomID, core::id::AtomID > &	atom_id_map
	)

References core::conformation::Residue::atom_index(), core::conformation::Residue::atom_name(), core::conformation::Residue::has(), core::conformation::Residue::is_virtual(), make_table_of_pilot_apps::name, core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::sequence(), and core::pose::Pose::total_residue().

Referenced by protocols::swa::protein::output_silent_struct(), and rms_at_corresponding_heavy_atoms().

void core::scoring::setup_matching_protein_backbone_heavy_atoms	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		std::map< core::id::AtomID, core::id::AtomID > &	atom_id_map
	)

References setup_matching_atoms_with_given_names().

Referenced by protocols::swa::protein::output_silent_struct().

void core::scoring::show_detail	(	std::ostream &	out,
		EnergyMap &	energies,
		EnergyMap	weights
	)

References n_score_types.

std::string const core::scoring::SOFT_REP_DESIGN_WTS

(

"soft_rep_design"

)

std::string const core::scoring::SOFT_REP_WTS

(

"soft_rep"

)

Real core::scoring::sqr

(

Real

x

)

[inline]

Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDa(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDaR(), and core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsR().

static numeric::random::RandomGenerator core::scoring::ss_weights_RG

(

82645

)

[static]

Referenced by core::scoring::SecondaryStructureWeights::setup_parallel_antiparallel_weights().

std::string const core::scoring::STANDARD_WTS

(

"standard"

)

void core::scoring::store_RDC_in_pose	(	ResidualDipolarCouplingOP	rdc_info,
		core::pose::Pose &	pose
	)

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

Referenced by protocols::simple_filters::SelectRDC_Evaluator::apply(), and protocols::frag_picker::scores::RDCScore::score().

void core::scoring::store_RDC_ROHL_in_pose	(	ResidualDipolarCoupling_RohlOP	rdc_info,
		core::pose::Pose &	pose
	)

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

Real core::scoring::superimpose_pose	(	pose::Pose &	mod_pose,
		pose::Pose const &	ref_pose,
		id::AtomID_Map< id::AtomID > const &	atom_map
	)

Superimpose mod_pose onto ref_pose using the mapping of atoms from mod_pose to ref_pose given by atom_map.

Superimpose mod_pose onto ref_pose using the AtomID mapping, which maps atoms in mod_pose onto atoms in ref_pose. Returns rmsd over alignment.

Note:

Atoms in mod_pose whose ids map to bogus atom ids will not be used in the fitting

Usage example: superimpose pose1 onto pose2 by mapping C-alphas of residue 10-30 onto residues 20-40

id::AtomID_Map< id::AtomID > atom_map; id::initialize( atom_map, pose1, id::BOGUS_ATOM_ID ); // maps every atomid to bogus atom

for ( Size i=10; i<=30; ++i ) { id::AtomID const id1( pose1.residue(i).atom_index("CA"), i ); id::AtomID const id2( pose2.residue(i+10).atom_index("CA"), i+10 ); atom_map[ id1 ] = id2; } superimpose_pose( pose1, pose2, atom_map );

References core::chemical::ResidueType::natoms(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), rms, core::pose::Pose::set_xyz(), core::pose::Pose::total_residue(), core::conformation::Residue::xyz(), and core::pose::Pose::xyz().

Referenced by protocols::loops::addScoresForLoopParts(), protocols::rna::RNA_DeNovoProtocol::align_and_output_to_silent_file(), protocols::swa::StepWisePoseSetup::align_pose(), protocols::swa::rna::align_poses(), protocols::antibody2::Ab_Info::align_to_native(), protocols::antibody::Antibody::align_to_native(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::antibody2::Ab_GraftOneCDR_Mover::apply(), protocols::antibody::GraftOneMover::apply(), calpha_superimpose_pose(), core::sequence::calpha_superimpose_with_mapping(), protocols::swa::InputStreamWithResidueInfo::copy_next_pose_segment(), protocols::loops::loop_rmsd_with_superimpose_core(), protocols::fibril::superimpose_pose_on_subset_bb(), protocols::toolbox::pose_manipulation::superimpose_pose_on_subset_CA(), and protocols::docking::ConformerSwitchMover::switch_conformer().

template<class T >

core::Real core::scoring::sym_rmsd_with_super_subset	(	core::pose::Pose const &	native_pose,
		core::pose::Pose const &	pose2,
		ObjexxFCL::FArray1D_bool const &	subset,
		T *	predicate
	)

Select a subset atoms for Symmetric RMS via a predicate function/functor. Example of use, to calculate C-alpha RMSD: rmsd_with_super(pose1, pose2, is_protein_CA, subset);.

References make_table_of_pilot_apps::begin, core::pose::Pose::conformation(), create_shuffle_map_recursive_rms(), is_heavyatom(), is_ligand_heavyatom(), is_polymer_heavyatom(), protocols::forge::build::SegmentInsertConnectionScheme::N, core::conformation::Residue::natoms(), core::pose::num_atoms(), core::pose::Pose::residue(), rms, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by protocols::protein_interface_design::filters::RmsdFilter::compute().

basic::Tracer core::scoring::T

(

"core.scoring.Ramachandran2B"

)

Referenced by core::scoring::etable::EtableOptions::EtableOptions(), core::scoring::Ramachandran2B::eval_rama_score_all(), core::scoring::dna::get_base_pair_params_old(), core::scoring::dna::get_base_pair_stub(), core::scoring::dna::get_base_step_params(), core::scoring::dna::get_base_stub(), core::scoring::dna::get_stub_stub_params(), getScoreFunction(), core::init(), and core::init_random_generators().

static basic::Tracer core::scoring::TR

(

"core.scoring.MembraneTopology"

)

[static]

static basic::Tracer core::scoring::tr

(

"core.scoring.rms_util"

)

[static]

static basic::Tracer core::scoring::TR

(

"core.scoring.MembranePotential"

)

[static]

static basic::Tracer core::scoring::tr

(

"core.scoring.NeighborList"

)

[static]

Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDa(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDaR(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsR(), core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::ResidualDipolarCoupling::iterate_tensor_weights(), core::scoring::DockingScoreFunction::operator()(), core::scoring::ResidualDipolarCoupling_Rohl::read_RDC_file(), core::scoring::ResidualDipolarCoupling::read_RDC_file(), core::scoring::ResidualDipolarCoupling::reserve_buffers(), and core::scoring::NeighborList::~NeighborList().

static basic::Tracer core::scoring::TR

(

"core.scoring.AtomVDW"

)

[static]

Referenced by protocols::protein_interface_design::movers::add_coordinate_constraints(), core::scoring::geometric_solvation::add_to_individual_sol_energies(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::apply(), protocols::evaluation::SingleValuePoseEvaluator< core::Size >::apply(), core::scoring::geometric_solvation::compute_exact_geosol(), core::scoring::MembranePotential::compute_membrane_embedding(), protocols::ddG_main(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::design(), core::scoring::etable::Etable::Etable(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::ExactOccludedHbondSolEnergy(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::final_cleanup(), protocols::protein_interface_design::movers::generate_taskfactory_and_add_task_awareness(), get_PB_potential(), core::scoring::packstat::SimplePDB::get_spheres(), core::scoring::geometric_solvation::WaterWeightGridSet::get_sum_water_weight_grid(), core::scoring::geometric_solvation::WaterWeightGridSet::get_water_weight_grid(), core::scoring::MembraneTopology::initialize(), core::scoring::etable::MembEtable::MembEtable(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_no_bb(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::parse_my_tag(), protocols::protein_interface_design::movers::parse_stub_sets(), core::scoring::MembraneTopology::print(), protocols::print_ddgs(), protocols::read_in_mutations(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::refresh_coordinate_constraints(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::setup_for_derivatives(), and core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::setup_for_minimizing().

static basic::Tracer core::scoring::trKillHairpinsIO

(

"core.score.SS_Killhairpins_Info"

)

[static]

Referenced by core::scoring::SS_Killhairpins_Info::setup_from_kill_hairpins_file(), and core::scoring::SS_Killhairpins_Info::setup_from_psipred().

std::string const core::scoring::UNFOLDED_MM_STD

(

"UNFOLDED_MM_STD"

)

std::string const core::scoring::UNFOLDED_SCORE12

(

"UNFOLDED_SCORE12"

)

template<class T >

void core::scoring::vector1_remove	(	utility::vector1< T > &	v,
		T const &	t
	)		[inline]

private -- handles setting the derived data

References core::scoring::hbonds::t().

core::Real core::scoring::xyz_gdtmm	(	FArray2D< core::Real >	p1a,
		FArray2D< core::Real >	p2a,
		core::Real &	m_1_1,
		core::Real &	m_2_2,
		core::Real &	m_3_3,
		core::Real &	m_4_3,
		core::Real &	m_7_4
	)

Calculate gdtmm based on the given sets of xyz coordinates in p1a and p2a.

References core::chemical::tr().

core::Real core::scoring::xyz_gdtmm	(	FArray2D< core::Real >	p1a,
		FArray2D< core::Real >	p2a
	)

Calculate gdtmm based on the given sets of xyz coordinates in p1a and p2a.

Referenced by protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), protocols::comparative_modeling::Align_RmsdEvaluator::apply(), CA_gdtmm(), and protocols::comparative_modeling::hybridize::HybridizeProtocol::get_gdtmm().

int core::scoring::xyz_maxsub	(	FArray2D< core::Real >	p1a,
		FArray2D< core::Real >	p2a,
		int	natoms
	)

Referenced by protocols::comparative_modeling::Align_RmsdEvaluator::apply().

---

Variable Documentation

short const core::scoring::bit_count[]

Initial value:

 { 
  0,1,1,2,1,2,2,3, 1,2,2,3,2,3,3,4,   1,2,2,3,2,3,3,4, 2,3,3,4,3,4,4,5,  
  1,2,2,3,2,3,3,4, 2,3,3,4,3,4,4,5,   2,3,3,4,3,4,4,5, 3,4,4,5,4,5,5,6,  
  1,2,2,3,2,3,3,4, 2,3,3,4,3,4,4,5,   2,3,3,4,3,4,4,5, 3,4,4,5,4,5,5,6,  
  2,3,3,4,3,4,4,5, 3,4,4,5,4,5,5,6,   3,4,4,5,4,5,5,6, 4,5,5,6,5,6,6,7,  
  1,2,2,3,2,3,3,4, 2,3,3,4,3,4,4,5,   2,3,3,4,3,4,4,5, 3,4,4,5,4,5,5,6,  
  2,3,3,4,3,4,4,5, 3,4,4,5,4,5,5,6,   3,4,4,5,4,5,5,6, 4,5,5,6,5,6,6,7,  
  2,3,3,4,3,4,4,5, 3,4,4,5,4,5,5,6,   3,4,4,5,4,5,5,6, 4,5,5,6,5,6,6,7,  
  3,4,4,5,4,5,5,6, 4,5,5,6,5,6,6,7,   4,5,5,6,5,6,6,7, 5,6,6,7,6,7,7,8,  
}

Referenced by core::scoring::packstat::compute_cav_ball_volumes(), core::scoring::packstat::compute_sasa(), core::scoring::packstat::prune_1pass(), and core::scoring::packstat::prune_hidden_cavity_balls().

std::string const core::scoring::CENTROID_WTS

Referenced by protocols::docking::DockingSlideIntoContact::DockingSlideIntoContact(), getScoreFunction(), protocols::flexpep_docking::FlexPepDockingProtocol::set_default(), protocols::simple_moves::symmetry::SymmetrySlider::setup(), protocols::surface_docking::SlideIntoSurface::SlideIntoSurface(), protocols::simple_moves::symmetry::SymDockingSlideIntoContact::SymDockingSlideIntoContact(), and protocols::simple_moves::symmetry::SymmetrySlider::SymmetrySlider().

std::string const core::scoring::DNA_INT_WTS

std::string const core::scoring::DNA_INT_WTS_GB

std::string const core::scoring::DOCK_LOW_PATCH

Referenced by protocols::docking::DockingSlideIntoContact::DockingSlideIntoContact(), protocols::simple_moves::symmetry::SymmetrySlider::setup(), protocols::surface_docking::SlideIntoSurface::SlideIntoSurface(), protocols::simple_moves::symmetry::SymDockingSlideIntoContact::SymDockingSlideIntoContact(), and protocols::simple_moves::symmetry::SymmetrySlider::SymmetrySlider().

std::string const core::scoring::DOCK_PATCH

Referenced by protocols::jd2::DockDesignParser::generate_mover_from_pose(), and protocols::symmetric_docking::SymDockBaseProtocol::SymDockBaseProtocol().

std::string const core::scoring::FA_STANDARD_DEFAULT

Referenced by core::scoring::geometric_solvation::DatabaseOccSolEne::DatabaseOccSolEne(), core::scoring::ScoringManager::etable(), and core::scoring::ScoringManager::memb_etable().

std::string const core::scoring::FA_STANDARD_SOFT

Referenced by core::scoring::ScoringManager::etable().

int const core::scoring::maskbits = 162

Referenced by core::scoring::packstat::compute_cav_ball_volumes(), core::scoring::packstat::compute_sasa(), and core::scoring::packstat::prune_hidden_cavity_balls().

std::string const core::scoring::MEMB_HIGHRES_WTS

std::string const core::scoring::MM_STD_WTS

int const core::scoring::num_bytes = 21

Referenced by calc_atom_masks(), calc_per_atom_sasa(), get_num_bytes(), input_sasa_dats(), and print_dot_bit_string().

int const core::scoring::num_orientations = 162

Referenced by input_sasa_dats().

int const core::scoring::num_overlaps = 100

Referenced by input_sasa_dats().

int const core::scoring::num_phi = 64

Referenced by get_2way_orientation(), get_orientation(), and input_sasa_dats().

int const core::scoring::num_theta = 64

Referenced by get_2way_orientation(), get_orientation(), and input_sasa_dats().

std::string const core::scoring::RNA_HIRES_WTS

Referenced by protocols::rna::RNA_Relaxer::apply(), protocols::rna::classify_base_pairs(), and protocols::rna::RNA_Minimizer::RNA_Minimizer().

std::string const core::scoring::RNA_LORES_PLUS_HIRES_WTS

std::string const core::scoring::RNA_LORES_WTS

Referenced by protocols::rna::check_base_pair(), and protocols::rna::get_number_base_stacks().

std::string const core::scoring::SCORE12_PATCH

Referenced by protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::InterfaceRecapitulationMover::apply(), protocols::protein_interface_design::movers::BuildAlaPose::apply(), protocols::protein_interface_design::movers::BestHotspotCstMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::remodel::RemodelAccumulator::apply(), protocols::fldsgn::potentials::SetSecStructEnergies::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::jumping::ResiduePairJump::build_sidechain_rotamers(), protocols::simple_filters::ResiduesInInterfaceFilter::compute(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::compute(), protocols::protein_interface_design::filters::HbondsToResidueFilter::compute(), protocols::protein_interface_design::HbondsToResidueFilter::compute(), protocols::protein_interface_design::ResiduesInInterfaceFilter::compute(), protocols::fldsgn::filters::CoreDunbrackFilter::compute(), protocols::protein_interface_design::movers::MapHotspot::create_rotamer_set(), core::scoring::ScoreFunctionFactory::create_score_function(), protocols::protein_interface_design::find_lowest_constraint_energy_residue(), protocols::jd2::DockDesignParser::generate_mover_from_pose(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), hbonded(), main(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all(), core::pack::optimize_H_and_notify(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::parse_my_tag(), protocols::protein_interface_design::movers::parse_stub_sets(), protocols::forge::remodel::RemodelAccumulator::recover_checkpoint(), protocols::forge::remodel::RemodelEnzdesCstModule::RemodelEnzdesCstModule(), and protocols::forge::methods::restore_residues().

std::string const core::scoring::SCORE13

std::string const core::scoring::SOFT_REP_DESIGN_WTS

Referenced by protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::jd2::DockDesignParser::generate_mover_from_pose(), and protocols::forge::remodel::RemodelMover::RemodelMover().

std::string const core::scoring::SOFT_REP_WTS

std::string const core::scoring::STANDARD_WTS

Referenced by protocols::simple_moves::SetReturningPackRotamersMover::apply(), protocols::simple_moves::MinPackMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::InterfaceRecapitulationMover::apply(), protocols::protein_interface_design::movers::BuildAlaPose::apply(), protocols::protein_interface_design::movers::BestHotspotCstMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::remodel::RemodelAccumulator::apply(), protocols::fldsgn::potentials::SetSecStructEnergies::apply(), protocols::antibody::GraftMover::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::jumping::ResiduePairJump::build_sidechain_rotamers(), protocols::simple_filters::ResiduesInInterfaceFilter::compute(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::compute(), protocols::protein_interface_design::filters::HbondsToResidueFilter::compute(), protocols::protein_interface_design::HbondsToResidueFilter::compute(), protocols::protein_interface_design::ResiduesInInterfaceFilter::compute(), protocols::fldsgn::filters::CoreDunbrackFilter::compute(), protocols::protein_interface_design::movers::MapHotspot::create_rotamer_set(), core::scoring::ScoreFunctionFactory::create_score_function(), protocols::protein_interface_design::find_lowest_constraint_energy_residue(), protocols::jd2::DockDesignParser::generate_mover_from_pose(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), hbonded(), main(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all(), core::pack::optimize_H_and_notify(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::parse_my_tag(), protocols::protein_interface_design::movers::parse_stub_sets(), protocols::forge::remodel::RemodelAccumulator::recover_checkpoint(), protocols::forge::remodel::RemodelEnzdesCstModule::RemodelEnzdesCstModule(), protocols::forge::methods::restore_residues(), protocols::simple_moves::PackRotamersMover::setup(), and protocols::symmetric_docking::SymDockBaseProtocol::SymDockBaseProtocol().

std::string const core::scoring::UNFOLDED_MM_STD

Referenced by core::scoring::ScoringManager::get_UnfoldedStatePotential().

std::string const core::scoring::UNFOLDED_SCORE12

Referenced by core::scoring::ScoringManager::get_UnfoldedStatePotential().