Rosetta 3.4
Namespaces | Classes | Typedefs | Enumerations | Functions | Variables
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::SizeResidueSelection
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< EnergyCArray_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_FAEmbednonconst_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)
MembraneEmbednonconst_MembraneEmbed_from_pose (pose::Pose &pose)
static basic::Tracer TR ("core.scoring.MembraneTopology")
MembraneTopology const & MembraneTopology_from_pose (pose::Pose const &pose)
MembraneTopologynonconst_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)
PoissonBoltzmannPotentialget_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_Inforetrieve_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 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 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< 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< 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< 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< 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< Weight > core::scoring::FArray5D_Weight
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

Enumeration Type Documentation

Enumerator:
ten_A_neighbor_graph 
twelve_A_neighbor_graph 
centroid_neighbor_graph 
num_context_graph_types 
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 
Enumerator:
etab_single_nblist 
cst_res_data 
hbond_res_data 
n_min_single_data 
Enumerator:
PHI 
PSI 
OMEGA 
CHI1 
CHI2 
CHI3 
CHI4 
protein_torsion_end 

enum for listing the variants

Enumerator:
hydrogen_interaction_cutoff 

enum for listing the variants

Enumerator:
loc_lj 
lk_sol 

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 
)
core::Real core::scoring::all_atom_rmsd ( const core::pose::Pose pose1,
const core::pose::Pose pose2,
std::list< Size residue_selection 
)
ObjexxFCL::FArray2D_int core::scoring::angles ( num_phi  ,
num_theta   
)
core::Real core::scoring::automorphic_rmsd ( core::conformation::Residue const &  rsd1,
core::conformation::Residue const &  rsd2,
bool  superimpose 
)
core::Real core::scoring::bb_rmsd ( const core::pose::Pose pose1,
const core::pose::Pose pose2 
)
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 
)
core::Real core::scoring::bb_rmsd_including_O ( const core::pose::Pose pose1,
const core::pose::Pose pose2 
)
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 
)
template<class T >
core::Real core::scoring::biggest_residue_deviation_no_super ( core::pose::Pose const &  pose1,
core::pose::Pose const &  pose2,
T *  predicate 
)
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 
)
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 
)
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 
)
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  
)
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 
)
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 
)
core::Real core::scoring::CA_rmsd_symmetric ( const core::pose::Pose native_pose,
const core::pose::Pose pose 
)
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 
)
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 
)
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 
)
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 
)
Real core::scoring::calpha_superimpose_pose ( pose::Pose mod_pose,
pose::Pose const &  ref_pose 
)
std::string const core::scoring::CENTROID_WTS ( "cen_std"  )
int core::scoring::compare_by_abs ( const void *  a,
const void *  b 
) [inline]
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)
Real core::scoring::compute_sc_radius ( conformation::Residue const &  res,
Vector const &  centroid 
)
void core::scoring::create_shuffle_map_recursive_rms ( std::vector< int sequence,
int const  N,
std::vector< std::vector< int > > &  map 
)
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 
)
std::string core::scoring::element_string ( std::string  atom)
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 
)
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 
)
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 
)
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 
)
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 
)
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 
)
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 
)
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 
)
void core::scoring::evaluaterdc ( const double *  par,
int  m_dat,
const void *  data,
double *  fvec,
int info 
)
void core::scoring::evaluaterdcDa ( const double *  par,
int  m_dat,
const void *  data,
double *  fvec,
int info 
)
void core::scoring::evaluaterdcDaR ( const double *  par,
int  m_dat,
const void *  data,
double *  fvec,
int info 
)
void core::scoring::evaluaterdcR ( const double *  par,
int  m_dat,
const void *  data,
double *  fvec,
int info 
)
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 
)
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 
)
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 
)
double core::scoring::frdcDa ( double  r0,
double  r1,
double  r2,
double  rdcconst,
double const  tensorDa,
const double *  par 
)
double core::scoring::frdcDaR ( double  r0,
double  r1,
double  r2,
double  rdcconst,
double const  tensorDa,
double const  tensorR,
const double *  par 
)
double core::scoring::frdcR ( double  r0,
double  r1,
double  r2,
double  rdcconst,
double const  tensorR,
const double *  par 
)
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 ( )
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]
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]
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]
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]
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]
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]
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]
void core::scoring::invert_exclude_residues ( Size  nres,
utility::vector1< int > const &  exclude_list,
ResidueSelection &  residue_selection 
)
ResidueSelection core::scoring::invert_exclude_residues ( core::Size  nres,
utility::vector1< int > const &  exclude_list 
)
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 
)
bool core::scoring::is_ligand_heavyatom ( core::pose::Pose const &  pose1,
core::pose::Pose const &  ,
core::Size  resno,
core::Size  atomno 
)
bool core::scoring::is_ligand_heavyatom_residues ( core::conformation::Residue const &  residue1,
core::conformation::Residue const &  ,
core::Size  atomno 
)
bool core::scoring::is_nbr_atom ( core::pose::Pose const &  pose1,
core::pose::Pose const &  ,
core::Size  resno,
core::Size  atomno 
)
bool core::scoring::is_polymer_heavyatom ( core::pose::Pose const &  pose1,
core::pose::Pose const &  ,
core::Size  resno,
core::Size  atomno 
)
bool core::scoring::is_protein_backbone ( core::pose::Pose const &  pose1,
core::pose::Pose const &  ,
core::Size  resno,
core::Size  atomno 
)
bool core::scoring::is_protein_backbone_including_O ( core::pose::Pose const &  pose1,
core::pose::Pose const &  ,
core::Size  resno,
core::Size  atomno 
)
bool core::scoring::is_protein_CA ( core::pose::Pose const &  pose1,
core::pose::Pose const &  ,
core::Size  resno,
core::Size  atomno 
)
bool core::scoring::is_protein_CA_or_CB ( core::pose::Pose const &  pose1,
core::pose::Pose const &  ,
core::Size  resno,
core::Size  atomno 
)
bool core::scoring::is_protein_sidechain_heavyatom ( core::pose::Pose const &  pose1,
core::pose::Pose const &  ,
core::Size  resno,
core::Size  atomno 
)
void core::scoring::jacobi ( Real  a[5][5],
Real  d[],
Real  v[5][5],
int nrot 
)
void core::scoring::jacobi3 ( Real  a[3][3],
Real  d[],
Real  v[3][3],
int nrot 
)
int core::scoring::m_inv_gen ( Tensor5  m,
int  n,
Tensor5  minv 
)
ObjexxFCL::FArray2D_ubyte core::scoring::masks ( num_bytes  ,
num_overlaps *  num_orientations 
)
std::string const core::scoring::MEMB_HIGHRES_WTS ( "membrane_highres"  )
Membrane_FAEmbed const & core::scoring::Membrane_FAEmbed_from_pose ( pose::Pose const &  pose)
MembraneEmbed const & core::scoring::MembraneEmbed_from_pose ( pose::Pose const &  pose)
MembraneTopology const & core::scoring::MembraneTopology_from_pose ( pose::Pose const &  pose)
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 
)
core::Real core::scoring::native_CA_rmsd ( const core::pose::Pose native_pose,
const core::pose::Pose pose 
)
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)
std::ostream& core::scoring::operator<< ( std::ostream &  out,
ScoreFunction const &  sf 
) [inline]
std::ostream& core::scoring::operator<< ( std::ostream &  out,
Hairpins const &  s 
)
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 
)
std::ostream & core::scoring::operator<< ( std::ostream &  out,
ResidualDipolarCoupling const &  rdc 
)
std::ostream& core::scoring::operator<< ( std::ostream &  out,
Helices const &  s 
)
std::ostream& core::scoring::operator<< ( std::ostream &  out,
Strands const &  s 
)
std::ostream& core::scoring::operator<< ( std::ostream &  out,
const Energies &  e 
)
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 
)
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 
)
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]
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)
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)
ResidualDipolarCouplingCOP core::scoring::retrieve_RDC_from_pose ( core::pose::Pose const &  pose)
ResidualDipolarCouplingOP core::scoring::retrieve_RDC_from_pose ( core::pose::Pose pose)
ResidualDipolarCoupling_RohlCOP core::scoring::retrieve_RDC_ROHL_from_pose ( core::pose::Pose const &  pose)
ResidualDipolarCoupling_RohlOP core::scoring::retrieve_RDC_ROHL_from_pose ( core::pose::Pose pose)
static numeric::random::RandomGenerator core::scoring::RG ( 280628  ) [static]
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 
)
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 
)
Real core::scoring::rms_at_corresponding_heavy_atoms ( pose::Pose const &  mod_pose,
pose::Pose const &  ref_pose 
)
template<class T >
core::Real core::scoring::rmsd_no_super ( core::conformation::ResidueCOPs const &  residues1,
core::conformation::ResidueCOPs const &  residues2,
T *  predicate 
)
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 
)
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 
)
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 
)
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 
)
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 
)
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]
static numeric::random::RandomGenerator core::scoring::ss_weights_RG ( 82645  ) [static]
std::string const core::scoring::STANDARD_WTS ( "standard"  )
void core::scoring::store_RDC_in_pose ( ResidualDipolarCouplingOP  rdc_info,
core::pose::Pose pose 
)
void core::scoring::store_RDC_ROHL_in_pose ( ResidualDipolarCoupling_RohlOP  rdc_info,
core::pose::Pose pose 
)
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 
)
basic::Tracer core::scoring::T ( "core.scoring.Ramachandran2B"  )
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]
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]
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 
)
int core::scoring::xyz_maxsub ( FArray2D< core::Real p1a,
FArray2D< core::Real p2a,
int  natoms 
)

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

Referenced by input_sasa_dats().

Referenced by input_sasa_dats().

std::string const core::scoring::RNA_HIRES_WTS
std::string const core::scoring::RNA_LORES_WTS
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_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
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