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Rosetta 3.5
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All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
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Rosetta 3.5
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Classes | |
| class | APBSWrapper |
| class | PQR |
| class | APBSResult |
| class | APBSConfig |
| class | AtomVDW |
| class | CenHBPotential |
| class | ChemicalShiftAnisotropy |
| ChemicalShiftAnisotropys are mainly handled by this class related classed: CSA — a single line in an CSA file - representing a single csa coupling ChemicalShiftAnisotropyEnergy – an energy method which triggers computations handled by this class. More... | |
| class | CSA |
| 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 | DipolarCoupling |
| DipolarCouplings are mainly handled by this class related classed: DC — a single line in an DC file - representing a single dc coupling DipolarCouplingEnergy – an energy method which triggers computations handled by this class. More... | |
| class | DC |
| 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 |
| struct | SelfNeighInfo |
| class | FACTSResidueInfo |
| class | FACTSPoseInfo |
| class | FACTSRotamerSetInfo |
| class | FACTSPotential |
| 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 | MinScoreScoreFunction |
| 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 |
Functions | |
| static basic::Tracer | TR ("core.scoring.AtomVDW") |
| void | store_CSA_in_pose (ChemicalShiftAnisotropyOP csa_info, core::pose::Pose &pose) |
| ChemicalShiftAnisotropyCOP | retrieve_CSA_from_pose (core::pose::Pose const &pose) |
| ChemicalShiftAnisotropyOP | retrieve_CSA_from_pose (core::pose::Pose &pose) |
| std::ostream & | operator<< (std::ostream &out, CSA const &csa) |
| std::ostream & | operator<< (std::ostream &out, ChemicalShiftAnisotropy const &csa) |
| static Real const | BOGUS_ENERGY (99999.99) |
| void | store_DC_in_pose (DipolarCouplingOP dc_info, core::pose::Pose &pose) |
| DipolarCouplingCOP | retrieve_DC_from_pose (core::pose::Pose const &pose) |
| DipolarCouplingOP | retrieve_DC_from_pose (core::pose::Pose &pose) |
| std::ostream & | operator<< (std::ostream &out, DC const &dc) |
| std::ostream & | operator<< (std::ostream &out, DipolarCoupling const &dc) |
| std::string | element_string_dc (std::string atom) |
| std::ostream & | operator<< (std::ostream &out, const Energies &e) |
| std::ostream & | operator<< (std::ostream &ost, EMapVector const &emap) |
| output operator (index;value) More... | |
| 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 More... | |
| 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 More... | |
| 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 More... | |
| template<class T , class T_Etable > | |
| void | inline_residue_atom_pair_energy (conformation::Residue const &res1, conformation::Residue const &res2, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap) |
| template<class T , class T_Etable > | |
| void | inline_residue_atom_pair_energy_sidechain_backbone (conformation::Residue const &res1, conformation::Residue const &res2, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap) |
| template<class T , class T_Etable > | |
| void | inline_residue_atom_pair_energy_sidechain_whole (conformation::Residue const &res1, conformation::Residue const &res2, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap) |
| template<class T , class T_Etable > | |
| void | inline_residue_atom_pair_energy_backbone_backbone (conformation::Residue const &res1, conformation::Residue const &res2, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap) |
| template<class T , class T_Etable > | |
| void | inline_residue_atom_pair_energy_sidechain_sidechain (conformation::Residue const &res1, conformation::Residue const &res2, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap) |
| void | interpolate_value_and_deriv (ObjexxFCL::FArray1D< Real > const &potential, Real const &bin_width, Real const &r, Real &value, Real &deriv) |
| Membrane_FAEmbed const & | Membrane_FAEmbed_from_pose (pose::Pose const &pose) |
| Membrane_FAEmbed & | nonconst_Membrane_FAEmbed_from_pose (pose::Pose &pose) |
| static numeric::random::RandomGenerator | RG (280628) |
| static basic::Tracer | TR ("core.scoring.MembranePotential") |
| MembraneEmbed const & | MembraneEmbed_from_pose (pose::Pose const &pose) |
| MembraneEmbed & | nonconst_MembraneEmbed_from_pose (pose::Pose &pose) |
| static basic::Tracer | TR ("core.scoring.MembraneTopology") |
| MembraneTopology const & | MembraneTopology_from_pose (pose::Pose const &pose) |
| MembraneTopology & | nonconst_MembraneTopology_from_pose (pose::Pose &pose) |
| void | eval_atom_derivatives_for_minnode (MinimizationNode const &min_node, conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap const &res_weights, utility::vector1< DerivVectorPair > &atom_derivs) |
| Evaluate the derivatives for all atoms on the input residue for the terms that apply to this residue (which are stored on the input minimization node). More... | |
| 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. More... | |
| 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. More... | |
| 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") |
| 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 *) |
| void | evaluaterdcDa (const double *par, int m_dat, const void *data, double *fvec, int *) |
| void | evaluaterdcR (const double *par, int m_dat, const void *data, double *fvec, int *) |
| void | evaluaterdcDaR (const double *par, int m_dat, const void *data, double *fvec, int *) |
| 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") |
| core::Real | gdtsc (const core::pose::Pose &ref, const core::pose::Pose &model, const std::map< core::Size, core::Size > &residues) |
| Returns a single, Global Distance Test-like value that measures the extent to which the functional ends of a model's sidechains agree with their counterparts in a given reference structure. More... | |
| core::Real | gdtha (const core::pose::Pose &ref, const core::pose::Pose &model, const std::map< core::Size, core::Size > &residues) |
| Returns the average fraction of residues superimposable under a series of distance thresholds– 0.5, 1.0, 2.0, and 4.0 Angstroms. More... | |
| 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. More... | |
| 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, Size, utility::vector1< Size > const &) |
| 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, Size, utility::vector1< Size > const &) |
| 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. More... | |
| 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. More... | |
| 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. More... | |
| 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. More... | |
| 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. More... | |
| 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. More... | |
| 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. More... | |
| Real | superimpose_pose (pose::Pose &mod_pose, pose::MiniPose 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. More... | |
| 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.". More... | |
| 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 More... | |
| 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. More... | |
| 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. More... | |
| 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. More... | |
| 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. More... | |
| 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. More... | |
| 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, More... | |
| 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, More... | |
| 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);. More... | |
| 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. More... | |
| void | get_overlap (Real const radius_a, Real const radius_b, Real const distance_ijxyz, int °ree_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) More... | |
| 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) More... | |
| Real | calc_total_sasa (pose::Pose const &pose, Real const probe_radius) |
| returns total sasa More... | |
| 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 More... | |
| 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, bool const include_probe_radius_in_atom_radii=true, bool const use_lj_radii=false) |
| returns total sasa More... | |
| 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) More... | |
| 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) More... | |
| 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) More... | |
| 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) More... | |
| void | show_detail (std::ostream &out, EnergyMap &energies, EnergyMap weights) |
| template<class T > | |
| void | vector1_remove (utility::vector1< T > &v, T const &t) |
| private – handles setting the derived data More... | |
| 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. More... | |
| 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. More... | |
| std::string | getScoreFunctionName (bool const is_fullatom=true) |
| use the logic of getScoreFunction to get the name. The name format is <weights_tag>[_<patch_tag> ... ] More... | |
| 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 More... | |
| std::istream & | operator>> (std::istream &is, ScoreType &score_type) |
| input operator for ScoreType enum type More... | |
| std::ostream & | operator<< (std::ostream &os, ScoreType const &score_type) |
| output operator for ScoreType enum type More... | |
| std::ostream & | operator<< (std::ostream &os, ScoreTypes const &score_types) |
| output operator for ScoreTypes list type More... | |
| std::string | name_from_score_type (ScoreType score_type) |
| Returns the name of the ScoreType <score_type> More... | |
| 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 More... | |
| 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") |
| std::string const | UNFOLDED_RNA ("UNFOLDED_RNA") |
| SS_Info const & | retrieve_const_ss_info_from_pose (pose::Pose const &pose) |
| helper function More... | |
| SS_Info & | retrieve_nonconst_ss_info_from_pose (pose::Pose &pose) |
| helper function More... | |
| void | fill_bb_pos (pose::Pose const &pose, BB_Pos &bb_pos) |
| helper function More... | |
| 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. More... | |
| 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. More... | |
| 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. More... | |
| Vector | compute_bb_centroid (conformation::Residue const &r1) |
| Compute the average coordinate of the backbone heavy atoms (aka center of mass). More... | |
| 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. More... | |
| 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. More... | |
| 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. More... | |
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 |
| std::string const | UNFOLDED_RNA |
Definition at line 31 of file APBSWrapper.fwd.hh.
| typedef utility::pointer::access_ptr< APBSConfig const > core::scoring::APBSConfigCAP |
Definition at line 32 of file APBSWrapper.fwd.hh.
| typedef utility::pointer::owning_ptr< APBSConfig const > core::scoring::APBSConfigCOP |
Definition at line 30 of file APBSWrapper.fwd.hh.
Definition at line 28 of file APBSWrapper.fwd.hh.
Definition at line 37 of file APBSWrapper.fwd.hh.
| typedef utility::pointer::access_ptr< APBSResult const > core::scoring::APBSResultCAP |
Definition at line 38 of file APBSWrapper.fwd.hh.
| typedef utility::pointer::owning_ptr< APBSResult const > core::scoring::APBSResultCOP |
Definition at line 36 of file APBSWrapper.fwd.hh.
Definition at line 34 of file APBSWrapper.fwd.hh.
Definition at line 25 of file APBSWrapper.fwd.hh.
| typedef utility::pointer::access_ptr< APBSWrapper const > core::scoring::APBSWrapperCAP |
Definition at line 26 of file APBSWrapper.fwd.hh.
| typedef utility::pointer::owning_ptr< APBSWrapper const > core::scoring::APBSWrapperCOP |
Definition at line 24 of file APBSWrapper.fwd.hh.
Definition at line 22 of file APBSWrapper.fwd.hh.
Definition at line 173 of file NeighborList.hh.
| typedef ObjexxFCL::FArray2D< CArrayP_TableEnergy > core::scoring::AtomPairEnergyTable |
| typedef utility::pointer::owning_ptr< AtomVDW const > core::scoring::AtomVDWCOP |
Definition at line 27 of file AtomVDW.fwd.hh.
Definition at line 24 of file AtomVDW.fwd.hh.
| typedef ObjexxFCL::CArray< Energy > core::scoring::CArray_Energy |
| typedef ObjexxFCL::CArray< TableEnergy > core::scoring::CArray_TableEnergy |
| typedef ObjexxFCL::CArrayP< Energy > core::scoring::CArrayP_Energy |
| typedef ObjexxFCL::CArrayP< TableEnergy > core::scoring::CArrayP_TableEnergy |
| typedef utility::pointer::owning_ptr< CenHBPotential const > core::scoring::CenHBPotentialCOP |
Definition at line 28 of file CenHBPotential.fwd.hh.
Definition at line 25 of file CenHBPotential.fwd.hh.
Definition at line 24 of file EnvPairPotential.fwd.hh.
| typedef utility::pointer::owning_ptr< ChemicalShiftAnisotropy const > core::scoring::ChemicalShiftAnisotropyCOP |
Definition at line 27 of file ChemicalShiftAnisotropy.fwd.hh.
| typedef utility::pointer::owning_ptr< ChemicalShiftAnisotropy > core::scoring::ChemicalShiftAnisotropyOP |
Definition at line 25 of file ChemicalShiftAnisotropy.fwd.hh.
| typedef utility::pointer::owning_ptr< ContextGraph const > core::scoring::ContextGraphCOP |
Definition at line 26 of file ContextGraph.fwd.hh.
Definition at line 23 of file ContextGraph.fwd.hh.
Definition at line 34 of file DenseEnergyContainer.fwd.hh.
| typedef utility::pointer::owning_ptr< DenseNeighborIterator > core::scoring::DenseNeighborIteratorOP |
Definition at line 30 of file DenseEnergyContainer.fwd.hh.
Definition at line 370 of file SecondaryStructurePotential.cc.
| typedef utility::pointer::owning_ptr< DipolarCoupling const > core::scoring::DipolarCouplingCOP |
Definition at line 27 of file DipolarCoupling.fwd.hh.
Definition at line 25 of file DipolarCoupling.fwd.hh.
| typedef utility::pointer::owning_ptr< Energies const > core::scoring::EnergiesCOP |
Definition at line 28 of file Energies.fwd.hh.
Definition at line 26 of file Energies.fwd.hh.
Definition at line 26 of file EnergyGraph.fwd.hh.
| typedef EMapVector core::scoring::EnergyMap |
Definition at line 21 of file EnergyMap.fwd.hh.
Definition at line 30 of file EnvPairPotential.fwd.hh.
Definition at line 27 of file EnvPairPotential.fwd.hh.
Definition at line 28 of file FACTSPotential.fwd.hh.
| typedef utility::pointer::owning_ptr< FACTSPotential const > core::scoring::FACTSPotentialCOP |
Definition at line 39 of file FACTSPotential.fwd.hh.
Definition at line 36 of file FACTSPotential.fwd.hh.
Definition at line 23 of file FACTSPotential.fwd.hh.
Definition at line 32 of file FACTSPotential.fwd.hh.
| typedef ObjexxFCL::FArray1D< Energy > core::scoring::FArray1D_Energy |
| typedef ObjexxFCL::FArray1D< Length > core::scoring::FArray1D_Length |
| typedef ObjexxFCL::FArray1D< Probability > core::scoring::FArray1D_Probability |
| typedef ObjexxFCL::FArray1D< TableEnergy > core::scoring::FArray1D_TableEnergy |
| typedef ObjexxFCL::FArray1D< TableProbability > core::scoring::FArray1D_TableProbability |
| typedef ObjexxFCL::FArray1D< Weight > core::scoring::FArray1D_Weight |
| typedef ObjexxFCL::FArray2D< Energy > core::scoring::FArray2D_Energy |
| typedef ObjexxFCL::FArray2D< Length > core::scoring::FArray2D_Length |
| typedef ObjexxFCL::FArray2D< Probability > core::scoring::FArray2D_Probability |
| typedef ObjexxFCL::FArray2D< TableEnergy > core::scoring::FArray2D_TableEnergy |
| typedef ObjexxFCL::FArray2D< TableProbability > core::scoring::FArray2D_TableProbability |
| typedef ObjexxFCL::FArray2D< Weight > core::scoring::FArray2D_Weight |
| typedef ObjexxFCL::FArray3D< Energy > core::scoring::FArray3D_Energy |
| typedef ObjexxFCL::FArray3D< Length > core::scoring::FArray3D_Length |
| typedef ObjexxFCL::FArray3D< Probability > core::scoring::FArray3D_Probability |
| typedef ObjexxFCL::FArray3D< TableEnergy > core::scoring::FArray3D_TableEnergy |
| typedef ObjexxFCL::FArray3D< TableProbability > core::scoring::FArray3D_TableProbability |
| typedef ObjexxFCL::FArray3D< Weight > core::scoring::FArray3D_Weight |
| typedef ObjexxFCL::FArray4D< Energy > core::scoring::FArray4D_Energy |
| typedef ObjexxFCL::FArray4D< Length > core::scoring::FArray4D_Length |
| typedef ObjexxFCL::FArray4D< Probability > core::scoring::FArray4D_Probability |
| typedef ObjexxFCL::FArray4D< TableEnergy > core::scoring::FArray4D_TableEnergy |
| typedef ObjexxFCL::FArray4D< TableProbability > core::scoring::FArray4D_TableProbability |
| typedef ObjexxFCL::FArray4D< Weight > core::scoring::FArray4D_Weight |
| typedef ObjexxFCL::FArray5D< Energy > core::scoring::FArray5D_Energy |
| typedef ObjexxFCL::FArray5D< Length > core::scoring::FArray5D_Length |
| typedef ObjexxFCL::FArray5D< Probability > core::scoring::FArray5D_Probability |
| typedef ObjexxFCL::FArray5D< TableEnergy > core::scoring::FArray5D_TableEnergy |
| typedef ObjexxFCL::FArray5D< TableProbability > core::scoring::FArray5D_TableProbability |
| typedef ObjexxFCL::FArray5D< Weight > core::scoring::FArray5D_Weight |
Definition at line 28 of file GenBornPotential.fwd.hh.
Definition at line 39 of file GenBornPotential.fwd.hh.
Definition at line 36 of file GenBornPotential.fwd.hh.
Definition at line 24 of file GenBornPotential.fwd.hh.
| typedef utility::pointer::owning_ptr< GenBornRotamerSetInfo > core::scoring::GenBornRotamerSetInfoOP |
Definition at line 32 of file GenBornPotential.fwd.hh.
| typedef utility::pointer::owning_ptr< InterfaceInfo > core::scoring::InterfaceInfoOP |
Definition at line 38 of file InterchainPotential.fwd.hh.
| 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 |
Definition at line 34 of file LREnergyContainer.fwd.hh.
Definition at line 32 of file LREnergyContainer.fwd.hh.
| typedef core::Real core::scoring::matrix[3][3] |
Definition at line 360 of file ResidualDipolarCoupling.cc.
Definition at line 28 of file Membrane_FAPotential.fwd.hh.
| typedef utility::pointer::owning_ptr< Membrane_FAPotential const > core::scoring::Membrane_FAPotentialCOP |
Definition at line 33 of file Membrane_FAPotential.fwd.hh.
Definition at line 31 of file Membrane_FAPotential.fwd.hh.
Definition at line 35 of file MembranePotential.fwd.hh.
Definition at line 39 of file MembranePotential.fwd.hh.
Definition at line 34 of file MembraneTopology.fwd.hh.
Definition at line 28 of file MinimizationGraph.fwd.hh.
Definition at line 25 of file MinimizationGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< NeighborList const > core::scoring::NeighborListCOP |
Definition at line 25 of file NeighborList.fwd.hh.
Definition at line 23 of file NeighborList.fwd.hh.
| typedef utility::pointer::owning_ptr< OmegaTether const > core::scoring::OmegaTetherCOP |
Definition at line 25 of file OmegaTether.fwd.hh.
Definition at line 22 of file OmegaTether.fwd.hh.
| typedef utility::pointer::owning_ptr< OneToAllEnergyContainer > core::scoring::OneToAllEnergyContainerOP |
Definition at line 34 of file OneToAllEnergyContainer.fwd.hh.
| typedef utility::pointer::owning_ptr< OneToAllNeighborIterator > core::scoring::OneToAllNeighborIteratorOP |
Definition at line 30 of file OneToAllEnergyContainer.fwd.hh.
| typedef utility::pointer::owning_ptr< P_AA const > core::scoring::P_AACOP |
Definition at line 26 of file P_AA.fwd.hh.
Definition at line 23 of file P_AA.fwd.hh.
| typedef utility::pointer::owning_ptr< PairEPotential const > core::scoring::PairEPotentialCOP |
Definition at line 25 of file PairEPotential.fwd.hh.
Definition at line 22 of file PairEPotential.fwd.hh.
Definition at line 70 of file PoissonBoltzmannPotential.cc.
| typedef utility::pointer::owning_ptr< PeptideBondedEnergyContainer > core::scoring::PeptideBondedEnergyContainerOP |
Definition at line 28 of file PeptideBondedEnergyContainer.fwd.hh.
| typedef utility::pointer::owning_ptr< PeptideBondedNeighborIterator > core::scoring::PeptideBondedNeighborIteratorOP |
Definition at line 24 of file PeptideBondedEnergyContainer.fwd.hh.
| typedef utility::pointer::access_ptr< PoissonBoltzmannPotential > core::scoring::PoissonBoltzmannPotentialAP |
Definition at line 27 of file PoissonBoltzmannPotential.fwd.hh.
| typedef utility::pointer::access_ptr< PoissonBoltzmannPotential const > core::scoring::PoissonBoltzmannPotentialCAP |
Definition at line 28 of file PoissonBoltzmannPotential.fwd.hh.
| typedef utility::pointer::owning_ptr< PoissonBoltzmannPotential const > core::scoring::PoissonBoltzmannPotentialCOP |
Definition at line 25 of file DFIRE_Potential.fwd.hh.
| typedef utility::pointer::owning_ptr< PoissonBoltzmannPotential > core::scoring::PoissonBoltzmannPotentialOP |
Definition at line 22 of file DFIRE_Potential.fwd.hh.
| typedef utility::pointer::access_ptr< PQR > core::scoring::PQRAP |
Definition at line 43 of file APBSWrapper.fwd.hh.
| typedef utility::pointer::access_ptr< PQR const > core::scoring::PQRCAP |
Definition at line 44 of file APBSWrapper.fwd.hh.
| typedef utility::pointer::owning_ptr< PQR const > core::scoring::PQRCOP |
Definition at line 42 of file APBSWrapper.fwd.hh.
| typedef utility::pointer::owning_ptr< PQR > core::scoring::PQROP |
Definition at line 40 of file APBSWrapper.fwd.hh.
| typedef utility::pointer::owning_ptr< Predicate const > core::scoring::PredicateCOP |
Definition at line 214 of file rms_util.hh.
Definition at line 213 of file rms_util.hh.
| typedef core::Real core::scoring::Probability |
| typedef Ramachandran core::scoring::R |
Definition at line 67 of file Ramachandran.cc.
| typedef utility::pointer::owning_ptr< Ramachandran2B const > core::scoring::Ramachandran2BCOP |
Definition at line 25 of file Ramachandran2B.fwd.hh.
Definition at line 22 of file Ramachandran2B.fwd.hh.
| typedef utility::pointer::owning_ptr<Ramachandran const > core::scoring::RamachandranCOP |
Definition at line 24 of file Ramachandran.fwd.hh.
Definition at line 22 of file Ramachandran.fwd.hh.
| typedef utility::pointer::owning_ptr< ResidualDipolarCoupling_Rohl const > core::scoring::ResidualDipolarCoupling_RohlCOP |
Definition at line 26 of file ResidualDipolarCoupling_Rohl.fwd.hh.
| typedef utility::pointer::owning_ptr< ResidualDipolarCoupling_Rohl > core::scoring::ResidualDipolarCoupling_RohlOP |
Definition at line 24 of file ResidualDipolarCoupling_Rohl.fwd.hh.
| typedef utility::pointer::owning_ptr< ResidualDipolarCoupling const > core::scoring::ResidualDipolarCouplingCOP |
Definition at line 27 of file ResidualDipolarCoupling.fwd.hh.
| typedef utility::pointer::owning_ptr< ResidualDipolarCoupling > core::scoring::ResidualDipolarCouplingOP |
Definition at line 25 of file ResidualDipolarCoupling.fwd.hh.
Definition at line 26 of file ResidueNeighborList.fwd.hh.
Definition at line 24 of file ResidueNeighborList.fwd.hh.
| typedef utility::pointer::owning_ptr< ResidueNeighborConstIterator const > core::scoring::ResidueNeighborConstIteratorCOP |
Definition at line 29 of file LREnergyContainer.fwd.hh.
| typedef utility::pointer::owning_ptr< ResidueNeighborConstIterator > core::scoring::ResidueNeighborConstIteratorOP |
Definition at line 27 of file LREnergyContainer.fwd.hh.
| typedef utility::pointer::owning_ptr< ResidueNeighborIterator const > core::scoring::ResidueNeighborIteratorCOP |
Definition at line 25 of file LREnergyContainer.fwd.hh.
| typedef utility::pointer::owning_ptr< ResidueNeighborIterator > core::scoring::ResidueNeighborIteratorOP |
Definition at line 23 of file LREnergyContainer.fwd.hh.
| typedef utility::pointer::owning_ptr< ResiduePairNeighborList const > core::scoring::ResiduePairNeighborListCOP |
Definition at line 31 of file ResidueNeighborList.fwd.hh.
| typedef utility::pointer::owning_ptr< ResiduePairNeighborList > core::scoring::ResiduePairNeighborListOP |
Definition at line 28 of file ResidueNeighborList.fwd.hh.
| typedef std::list< core::Size > core::scoring::ResidueSelection |
Definition at line 50 of file rms_util.hh.
Definition at line 51 of file rms_util.hh.
| typedef utility::pointer::owning_ptr< ResPairMinimizationData const > core::scoring::ResPairMinimizationDataCOP |
Definition at line 31 of file MinimizationData.fwd.hh.
| typedef utility::pointer::owning_ptr< ResPairMinimizationData > core::scoring::ResPairMinimizationDataOP |
Definition at line 30 of file MinimizationData.fwd.hh.
| typedef utility::pointer::owning_ptr< ResSingleMinimizationData const > core::scoring::ResSingleMinimizationDataCOP |
Definition at line 28 of file MinimizationData.fwd.hh.
| typedef utility::pointer::owning_ptr< ResSingleMinimizationData > core::scoring::ResSingleMinimizationDataOP |
Definition at line 25 of file MinimizationData.fwd.hh.
| typedef core::Real core::scoring::rvec |
Definition at line 351 of file ResidualDipolarCoupling.cc.
| typedef core::Real core::scoring::rvec5[5] |
Definition at line 362 of file ResidualDipolarCoupling.cc.
| typedef Real core::scoring::Score |
| typedef utility::pointer::owning_ptr< ScoreFunction const > core::scoring::ScoreFunctionCOP |
Definition at line 30 of file ScoreFunction.fwd.hh.
Definition at line 27 of file ScoreFunctionInfo.fwd.hh.
Definition at line 24 of file ScoreFunctionInfo.fwd.hh.
Definition at line 27 of file ScoreFunction.fwd.hh.
| typedef boost::shared_ptr< ScoreFunction > core::scoring::ScoreFunctionSP |
Definition at line 31 of file ScoreFunction.fwd.hh.
| typedef utility::vector1< ScoreType > core::scoring::ScoreTypes |
Definition at line 441 of file ScoreType.hh.
| typedef utility::pointer::owning_ptr< SecondaryStructurePotential const > core::scoring::SecondaryStructurePotentialCOP |
Definition at line 26 of file SecondaryStructurePotential.fwd.hh.
| typedef utility::pointer::owning_ptr< SecondaryStructurePotential > core::scoring::SecondaryStructurePotentialOP |
Definition at line 23 of file SecondaryStructurePotential.fwd.hh.
| typedef utility::pointer::access_ptr< SetupPoissonBoltzmannPotential > core::scoring::SetupPoissonBoltzmannPotentialAP |
Definition at line 25 of file SetupPoissonBoltzmannPotential.fwd.hh.
| typedef utility::pointer::access_ptr< SetupPoissonBoltzmannPotential const > core::scoring::SetupPoissonBoltzmannPotentialCAP |
Definition at line 26 of file SetupPoissonBoltzmannPotential.fwd.hh.
| typedef utility::pointer::owning_ptr< SetupPoissonBoltzmannPotential const > core::scoring::SetupPoissonBoltzmannPotentialCOP |
Definition at line 24 of file SetupPoissonBoltzmannPotential.fwd.hh.
| typedef utility::pointer::owning_ptr< SetupPoissonBoltzmannPotential > core::scoring::SetupPoissonBoltzmannPotentialOP |
Definition at line 22 of file SetupPoissonBoltzmannPotential.fwd.hh.
| typedef utility::pointer::owning_ptr< SigmoidWeightedCenList<Real> > core::scoring::SigmoidWeightedCenListRealOP |
Definition at line 25 of file SmoothEnvPairPotential.fwd.hh.
| typedef utility::pointer::owning_ptr< SigmoidWeightedCenList<numeric::xyzVector<Real> > > core::scoring::SigmoidWeightedCenListVectorOP |
Definition at line 30 of file SmoothEnvPairPotential.fwd.hh.
| typedef utility::pointer::owning_ptr< SmoothEnvPairPotential const > core::scoring::SmoothEnvPairPotentialCOP |
Definition at line 35 of file SmoothEnvPairPotential.fwd.hh.
| typedef utility::pointer::owning_ptr< SmoothEnvPairPotential > core::scoring::SmoothEnvPairPotentialOP |
Definition at line 32 of file SmoothEnvPairPotential.fwd.hh.
| typedef utility::pointer::owning_ptr< SS_Info const > core::scoring::SS_InfoCOP |
Definition at line 30 of file SS_Info.fwd.hh.
Definition at line 27 of file SS_Info.fwd.hh.
| typedef utility::pointer::owning_ptr< SS_Killhairpins_Info const > core::scoring::SS_Killhairpins_InfoCOP |
Definition at line 28 of file SS_Killhairpins_Info.fwd.hh.
Definition at line 25 of file SS_Killhairpins_Info.fwd.hh.
| typedef float core::scoring::TableEnergy |
| typedef float core::scoring::TableProbability |
Definition at line 28 of file TenANeighborGraph.fwd.hh.
Definition at line 25 of file TenANeighborGraph.fwd.hh.
| typedef core::Real core::scoring::Tensor[3][3] |
Definition at line 349 of file ResidualDipolarCoupling.cc.
| typedef core::Real core::scoring::Tensor5[5][5] |
Definition at line 350 of file ResidualDipolarCoupling.cc.
| typedef utility::pointer::owning_ptr< TwelveANeighborGraph const > core::scoring::TwelveANeighborGraphCOP |
Definition at line 28 of file TwelveANeighborGraph.fwd.hh.
Definition at line 25 of file TwelveANeighborGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< UnfoldedStatePotential > core::scoring::UnfoldedStatePotentialOP |
Definition at line 22 of file UnfoldedStatePotential.fwd.hh.
| typedef utility::pointer::owning_ptr< WaterAdductHBondPotential const > core::scoring::WaterAdductHBondPotentialCOP |
Definition at line 27 of file WaterAdductHBondPotential.fwd.hh.
| typedef utility::pointer::owning_ptr< WaterAdductHBondPotential > core::scoring::WaterAdductHBondPotentialOP |
Definition at line 24 of file WaterAdductHBondPotential.fwd.hh.
| typedef Real core::scoring::Weight |
| Enumerator | |
|---|---|
| ten_A_neighbor_graph | |
| twelve_A_neighbor_graph | |
| centroid_neighbor_graph | |
| num_context_graph_types | |
Definition at line 20 of file ContextGraphTypes.hh.
| 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 | |
Definition at line 41 of file MinimizationData.hh.
| Enumerator | |
|---|---|
| etab_single_nblist | |
| cst_res_data | |
| hbond_res_data | |
| n_min_single_data | |
Definition at line 34 of file MinimizationData.hh.
| Enumerator | |
|---|---|
| PHI | |
| PSI | |
| OMEGA | |
| CHI1 | |
| CHI2 | |
| CHI3 | |
| CHI4 | |
| protein_torsion_end | |
Definition at line 21 of file ProteinTorsion.hh.
enum for listing the variants
| Enumerator | |
|---|---|
| hydrogen_interaction_cutoff | |
Definition at line 23 of file ScoreFunctionParameter.hh.
enum for listing the variants
| Enumerator | |
|---|---|
| loc_lj | |
| lk_sol | |
Definition at line 23 of file ScoreFunctionVariant.hh.
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 | |
| gauss | |
| 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_mg | |
| rna_mg_rep | |
| rna_mg_indirect | |
| mg_chem_pot | |
| rna_torsion | |
| rna_sugar_close | |
| fa_stack | |
| fa_stack_aro | |
| dna_bb_torsion | |
| dna_sugar_close | |
| dna_base_distance | |
| 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 | |
| metalhash_constraint | |
| rna_bond_geometry | |
| rama | |
| omega | |
| fa_dun | |
| fa_dun_dev | |
| fa_dun_rot | |
| fa_dun_semi | |
| dna_chi | |
| p_aa_pp | |
| yhh_planarity | |
| h2o_intra | |
| ref | |
| ref_nc | |
| seqdep_ref | |
| nmer_ref | |
| nmer_pssm | |
| envsmooth | |
| e_pH | |
| rna_bulge | |
| mg_ref | |
| 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 | |
| csa | |
| dc | |
| rdc | |
| rdc_segments | |
| rdc_rohl | |
| holes | |
| holes_decoy | |
| holes_resl | |
| holes_min | |
| holes_min_mean | |
| rna_chem_shift | |
| 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. |
Definition at line 35 of file ScoreType.hh.
| core::Real core::scoring::all_atom_rmsd | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2 | ||
| ) |
Definition at line 732 of file rms_util.cc.
References is_heavyatom(), rms, and rmsd_with_super().
Referenced by protocols::rna::RNA_DeNovoProtocol::apply(), protocols::simple_moves::ScoreMover::apply(), protocols::simple_filters::SelectRmsdEvaluator::apply(), protocols::idealize::IdealizeMover::apply(), protocols::idealize::basic_idealize(), protocols::rna::RNA_DeNovoProtocol::calc_rmsds(), protocols::swa::rna::StepWiseRNA_Clusterer::check_for_closeness_without_job_parameters(), protocols::rna::RNA_Relaxer::find_fragment_by_simple_rmsd_cutoff(), protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::rna::RNA_Relaxer::lores_monte_carlo(), protocols::coarse_rna::CoarseRNA_DeNovoProtocol::output_to_silent_file(), protocols::features::ProteinRMSDFeatures::report_features(), and protocols::swa::RigidBodySampler::save_silent_struct().
| core::Real core::scoring::all_atom_rmsd | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2, | ||
| std::list< Size > | residue_selection | ||
| ) |
Definition at line 743 of file rms_util.cc.
References is_heavyatom(), rms, and rmsd_with_super().
| 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 | ||
| ) |
RMSD between residues, accounting for automorphisms (symmetries). Does NOT include H atoms – they add lots of extra symmetries.
Just iterates over all automorphisms for this residue type and chooses the minimum RMS.
Definition at line 284 of file rms_util.cc.
References core::conformation::Residue::atom_type(), core::chemical::AtomType::is_hydrogen(), core::chemical::ResidueType::name3(), core::chemical::ResidueType::natoms(), core::chemical::AutomorphismIterator::next(), core::conformation::Residue::nheavyatoms(), core::chemical::tr(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().
Referenced by protocols::ligand_docking::append_automorphic_rmsd(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::ligand_docking::check_RMSD(), protocols::simple_filters::SidechainRmsdFilter::compute(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), and protocols::ligand_docking::LigandDockProtocol::optimize_orientation3().
| core::Real core::scoring::bb_rmsd | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2 | ||
| ) |
Definition at line 657 of file rms_util.cc.
References core::sequence::end, protocols::loops::start, and core::pose::Pose::total_residue().
| core::Real core::scoring::bb_rmsd | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2, | ||
| Size | , | ||
| Size | , | ||
| utility::vector1< Size > const & | |||
| ) |
Definition at line 670 of file rms_util.cc.
References is_protein_backbone(), rms, and rmsd_with_super().
| core::Real core::scoring::bb_rmsd_including_O | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2 | ||
| ) |
Definition at line 683 of file rms_util.cc.
References core::sequence::end, protocols::loops::start, and core::pose::Pose::total_residue().
Referenced by protocols::grafting::GraftMoverBase::perturb_backbone_for_test().
| core::Real core::scoring::bb_rmsd_including_O | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2, | ||
| Size | , | ||
| Size | , | ||
| utility::vector1< Size > const & | |||
| ) |
Definition at line 696 of file rms_util.cc.
References is_protein_backbone_including_O(), rms, and rmsd_with_super().
| core::Real core::scoring::biggest_residue_deviation_no_super | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | pose2, | ||
| T * | predicate | ||
| ) |
function to return the biggest deviation between an atom in a pair of poses,
Definition at line 668 of file rms_util.tmpl.hh.
References is_heavyatom(), is_ligand_heavyatom(), is_polymer_heavyatom(), core::conformation::Residue::natoms(), core::pose::num_atoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().
Referenced by protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf().
| 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
Definition at line 709 of file rms_util.tmpl.hh.
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 |
| core::Real core::scoring::CA_gdtmm | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2, | ||
| const std::map< core::Size, core::Size > & | residues | ||
| ) |
Computes the gdtmm between zero or more CA residues in pose1 and pose2, whose correspondence is specified in the map parameter.
Definition at line 607 of file rms_util.cc.
References retrieve_coordinates(), and xyz_gdtmm().
Referenced by protocols::simple_filters::StructuralSimilarityEvaluator::apply(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::simple_filters::RmsdEvaluator::apply(), protocols::simple_moves::ScoreMover::apply(), protocols::simple_filters::SelectGdtEvaluator::apply(), CA_gdtmm(), protocols::cluster::GatherPosesMover::get_distance_measure(), native_CA_gdtmm(), and protocols::jobdist::not_universal_main().
| core::Real core::scoring::CA_gdtmm | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | pose2, | ||
| std::list< Size > | residue_selection, | ||
| core::Real & | m_1_1, | ||
| core::Real & | m_2_2, | ||
| core::Real & | m_3_3, | ||
| core::Real & | m_4_3, | ||
| core::Real & | m_7_4 | ||
| ) |
Definition at line 851 of file rms_util.cc.
References fill_rmsd_coordinates(), core::pose::Pose::total_residue(), core::chemical::tr(), and xyz_gdtmm().
| core::Real core::scoring::CA_gdtmm | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | pose2, | ||
| core::Real & | m_1_1, | ||
| core::Real & | m_2_2, | ||
| core::Real & | m_3_3, | ||
| core::Real & | m_4_3, | ||
| core::Real & | m_7_4 | ||
| ) |
Calculate gdtmm score based on the C-alpha positions in pose1 and pose2. Also returns the five components of the gdtmm score.
Definition at line 875 of file rms_util.cc.
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 | ||
| ) |
Calculate gdtmm score based on the C-alpha positions in pose1 and pose2.
Definition at line 953 of file rms_util.cc.
References CA_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.
Definition at line 962 of file rms_util.cc.
References CA_gdtmm().
| 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.
Definition at line 768 of file rms_util.cc.
References fill_rmsd_coordinates(), is_protein_CA(), and core::pose::Pose::total_residue().
Referenced by protocols::simple_filters::RmsdEvaluator::apply(), protocols::simple_moves::ScoreMover::apply(), protocols::simple_filters::SelectMaxsubEvaluator::apply(), and protocols::jobdist::not_universal_main().
| int core::scoring::CA_maxsub | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2, | ||
| std::list< Size > | residue_selection, | ||
| Real | rms | ||
| ) |
Definition at line 791 of file rms_util.cc.
References fill_rmsd_coordinates(), and core::chemical::tr().
| int core::scoring::CA_maxsub_by_subset | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2, | ||
| utility::vector1< bool > | |||
| ) |
Definition at line 828 of file rms_util.cc.
References fill_rmsd_coordinates(), is_protein_CA(), and core::pose::Pose::total_residue().
| core::Real core::scoring::CA_rmsd | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2 | ||
| ) |
Definition at line 526 of file rms_util.cc.
References core::sequence::end, protocols::loops::start, and core::pose::Pose::total_residue().
Referenced by protocols::simple_moves::symmetry::DetectSymmetry::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::simple_filters::RmsdEvaluator::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::simple_filters::SelectRmsdEvaluator::apply(), protocols::relax::ClassicRelax::apply(), protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::idealize::IdealizeMover::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()(), protocols::hybridization::hConvergenceCheck::operator()(), OPT_1GRP_KEY(), protocols::frag_picker::FragmentCandidate::output_silent(), 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(), protocols::optimize_weights::IterativeOptEDriver::single_structure_data_for_pose(), 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 | ||
| ) |
Definition at line 537 of file rms_util.cc.
References fill_rmsd_coordinates(), rms, and core::chemical::tr().
| core::Real core::scoring::CA_rmsd | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2, | ||
| const std::map< core::Size, core::Size > & | residues | ||
| ) |
Computes the root mean squared deviation between zero or more CA residues in pose1 and pose2, whose correspondence is specified in the map parameter.
Definition at line 583 of file rms_util.cc.
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 | ||
| ) |
Definition at line 633 of file rms_util.cc.
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 | ||
| ) |
Definition at line 709 of file rms_util.cc.
References fill_rmsd_coordinates(), and core::chemical::tr().
| core::Real core::scoring::CA_rmsd_symmetric | ( | const core::pose::Pose & | native_pose, |
| const core::pose::Pose & | pose | ||
| ) |
Definition at line 1097 of file rms_util.cc.
References core::pose::Pose::conformation(), create_shuffle_map_recursive_rms(), fill_rmsd_coordinates(), is_protein_CA(), core::pose::symmetry::is_symmetric(), protocols::forge::build::SegmentInsertConnectionScheme::N, rms, and core::chemical::tr().
Referenced by protocols::relax::FastRelax::apply(), protocols::simple_filters::SymmetricRmsdEvaluator::apply(), protocols::relax::FastRelax::batch_apply(), protocols::symmetric_docking::SymDockProtocol::calc_rms(), protocols::relax::FastRelax::cmd_accept_to_best(), and protocols::cluster::GatherPosesMover::get_distance_measure().
| void core::scoring::calc_atom_masks | ( | core::conformation::Residue const & | irsd, |
| core::conformation::Residue const & | jrsd, | ||
| Real const | probe_radius, | ||
| Real const | cutoff_distance, | ||
| utility::vector1< Real > const & | radii, | ||
| id::AtomID_Map< bool > const & | atom_subset, | ||
| core::id::AtomID_Map< utility::vector1< ObjexxFCL::ubyte > > & | atom_masks | ||
| ) |
Definition at line 675 of file sasa.cc.
References core::scoring::packstat::old::angles, core::conformation::Residue::atom(), core::conformation::Residue::atom_type(), core::scoring::packstat::old::get_orientation(), core::scoring::packstat::old::get_overlap(), core::chemical::AtomType::is_h2o(), core::scoring::packstat::old::masks, core::conformation::Residue::natoms(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_radius(), num_bytes, core::conformation::Residue::seqpos(), and protocols::kinmatch::xyz().
Referenced by calc_per_atom_sasa().
| Real core::scoring::calc_per_atom_sasa | ( | pose::Pose const & | pose, |
| id::AtomID_Map< Real > & | atom_sasa, | ||
| utility::vector1< Real > & | rsd_sasa, | ||
| Real const | probe_radius, | ||
| bool const | use_big_polar_H | ||
| ) |
returns total sasa
Definition at line 472 of file sasa.cc.
References core::id::AtomID_Map< T >::clear(), and core::pose::initialize_atomid_map().
Referenced by protocols::toolbox::task_operations::SelectBySASAOperation::apply(), protocols::fldsgn::topology::calc_delta_sasa(), calc_per_res_hydrophobic_sasa(), protocols::toolbox::SelectResiduesByLayer::calc_rsd_sasa(), protocols::toolbox::task_operations::LayerOperations::calc_rsd_sasa(), protocols::fldsgn::topology::Sheet::calc_sasa_bothsides(), calc_total_sasa(), protocols::fldsgn::filters::CoreDunbrackFilter::compute(), protocols::sasa_scores::compute_residue_sasas_for_sasa_scores(), protocols::simple_moves::ConsensusDesignMover::create_consensus_design_task(), protocols::hotspot_hashing::HotspotStubSet::prepare_hashing_packer_task_(), core::pose::metrics::simple_calculators::SasaCalculator::recompute(), core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator::recompute(), protocols::features::ResidueBurialFeatures::report_features(), and protocols::features::HBondFeatures::report_features().
| 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, | ||
| bool const | include_probe_radius_in_atom_radii, | ||
| bool const | use_lj_radii | ||
| ) |
returns total sasa
Definition at line 484 of file sasa.cc.
References core::io::serialization::at(), core::conformation::Residue::atom_type_set(), core::scoring::packstat::old::bit_count, calc_atom_masks(), core::id::AtomID_Map< T >::clear(), core::chemical::AtomType::element(), core::chemical::AtomTypeSet::extra_parameter_index(), core::pose::initialize_atomid_map(), core::scoring::packstat::old::input_sasa_dats(), core::chemical::AtomType::is_polar_hydrogen(), core::scoring::packstat::old::maskbits, core::chemical::AtomTypeSet::n_atomtypes(), core::chemical::AtomType::name(), num_bytes, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and TR().
| Real core::scoring::calc_per_res_hydrophobic_sasa | ( | pose::Pose const & | pose, |
| utility::vector1< Real > & | rsd_sasa, | ||
| utility::vector1< Real > & | rsd_hydrophobic_sasa, | ||
| Real const | probe_radius, | ||
| bool | use_naccess_sasa_radii | ||
| ) |
Uses the method above to calculate total SASA and then only looks at the hydrophobic contribution. Returns the total hydrophobic SASA for the passed in pose. This method is being used for a protein surface score being developed by ronj. Note: Uses an atom id mask that ignores H's in the pose - only sees and computes the SASA for heavy atoms in the pose. This is done to keep things fast. Only computes the amount of hSASA per residue, not per atom. Doesn't make sense to calculate a per-atom hSASA. (ronj)
sasa.cc::calc_per_atom_hydrophobic_sasa
Definition at line 879 of file sasa.cc.
References core::io::serialization::at(), 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::chemical::ResidueType::nheavyatoms(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::id::AtomID_Map< T >::resize(), core::pose::Pose::total_residue(), and TR().
Referenced by protocols::analysis::InterfaceAnalyzerMover::compute_separated_sasa().
| Real core::scoring::calc_total_sasa | ( | pose::Pose const & | pose, |
| Real const | probe_radius | ||
| ) |
returns total sasa
Definition at line 462 of file sasa.cc.
References calc_per_atom_sasa().
Referenced by protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), and core::scoring::methods::SA_Energy::finalize_total_energy().
| Real core::scoring::calpha_superimpose_pose | ( | pose::Pose & | mod_pose, |
| pose::Pose const & | ref_pose | ||
| ) |
Superimpose two poses by their calpha coordinates. Ignores residues that do not have atoms named "CA.".
both poses must have the same length.
Definition at line 1075 of file rms_util.cc.
References core::conformation::Residue::atom_index(), core::id::BOGUS_ATOM_ID, core::conformation::Residue::has(), core::pose::initialize_atomid_map(), core::pose::Pose::residue(), superimpose_pose(), and core::pose::Pose::total_residue().
Referenced by protocols::protein_interface_design::filters::RmsdFilter::compute(), and protocols::star::Extender::extend_unaligned().
| std::string const core::scoring::CENTROID_WTS | ( | "cen_std" | ) |
|
inline |
Definition at line 373 of file ResidualDipolarCoupling.cc.
Referenced by core::scoring::ResidualDipolarCoupling::compute_tensor_stats().
| Vector core::scoring::compute_bb_centroid | ( | conformation::Residue const & | res) |
Compute the average coordinate of the backbone heavy atoms (aka center of mass).
returns the origin if there are no backbone atoms
Definition at line 145 of file util.cc.
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(), core::pack::interaction_graph::SymmOnTheFlyNode::set_rotamers(), 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.
Definition at line 160 of file util.cc.
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(), core::pack::interaction_graph::SymmOnTheFlyNode::set_rotamers(), 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)
Definition at line 1489 of file rms_util.cc.
References CA_rmsd(), core::pose::Pose::fold_tree(), and core::pose::Pose::total_residue().
Referenced by protocols::nonlocal::StarTreeBuilder::do_compute_jump_rmsd().
| Vector core::scoring::compute_sc_centroid | ( | conformation::Residue const & | res) |
Compute the average coordiante of the sidechain atoms, (aka center of mass) or, if there are no side chain heavy atoms, compute the center of mass of the backbone.
Definition at line 174 of file util.cc.
References compute_bb_centroid(), core::chemical::ResidueType::first_sidechain_atom(), core::chemical::ResidueType::nheavyatoms(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().
Referenced by core::pack::interaction_graph::SimpleNode::set_alternate(), core::pack::interaction_graph::SimpleNode::set_current(), core::pack::interaction_graph::SymmOnTheFlyNode::set_rotamers(), and core::pack::interaction_graph::OnTheFlyNode::set_rotamers().
| Real core::scoring::compute_sc_radius | ( | conformation::Residue const & | res, |
| Vector const & | centroid | ||
| ) |
Given a representative point for the center of the sidechain, compute the largest distance of all sidechain heavy atoms to that point.
Definition at line 193 of file util.cc.
References core::chemical::ResidueType::first_sidechain_atom(), core::chemical::ResidueType::nheavyatoms(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().
Referenced by core::pack::interaction_graph::SimpleNode::set_alternate(), core::pack::interaction_graph::SimpleNode::set_current(), core::pack::interaction_graph::SymmOnTheFlyNode::set_rotamers(), and core::pack::interaction_graph::OnTheFlyNode::set_rotamers().
| void core::scoring::create_shuffle_map_recursive_rms | ( | std::vector< int > | sequence, |
| int const | N, | ||
| std::vector< std::vector< int > > & | map | ||
| ) |
Definition at line 1153 of file rms_util.cc.
References protocols::forge::build::SegmentInsertConnectionScheme::N.
Referenced by CA_rmsd_symmetric(), and sym_rmsd_with_super_subset().
| bool core::scoring::dimer_pairing_pointer_sorter | ( | DimerPairingOP const & | a, |
| DimerPairingOP const & | b | ||
| ) |
Definition at line 373 of file SecondaryStructurePotential.cc.
Referenced by core::scoring::SecondaryStructurePotential::sspair().
| 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" | ) |
| std::string core::scoring::element_string | ( | std::string | atom) |
Definition at line 316 of file ResidualDipolarCoupling.cc.
Referenced by core::scoring::RDC::get_RDC_data_type().
| std::string core::scoring::element_string_dc | ( | std::string | atom) |
Definition at line 168 of file DipolarCoupling.cc.
Referenced by core::scoring::DC::get_DC_data_type().
| void core::scoring::eval_atom_derivatives_for_minedge | ( | MinimizationEdge const & | min_edge, |
| conformation::Residue const & | res1, | ||
| conformation::Residue const & | res2, | ||
| ResSingleMinimizationData const & | res1_min_data, | ||
| ResSingleMinimizationData const & | res2_min_data, | ||
| pose::Pose const & | pose, | ||
| EnergyMap const & | respair_weights, | ||
| utility::vector1< DerivVectorPair > & | r1atom_derivs, | ||
| utility::vector1< DerivVectorPair > & | r2atom_derivs | ||
| ) |
Definition at line 999 of file MinimizationGraph.cc.
References core::scoring::MinimizationEdge::active_2benmeths_begin(), core::scoring::MinimizationEdge::active_2benmeths_end(), and core::scoring::MinimizationEdge::res_pair_min_data().
Referenced by core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::optimization::atom_tree_get_atompairE_deriv(), core::optimization::cartesian_collect_atompairE_deriv(), core::pack::scmin::CartSCMinMultifunc::dfunc(), and core::pack::scmin::SCMinMultifunc::dfunc().
| void core::scoring::eval_atom_derivatives_for_minnode | ( | MinimizationNode const & | min_node, |
| conformation::Residue const & | rsd, | ||
| pose::Pose const & | pose, | ||
| EnergyMap const & | res_weights, | ||
| utility::vector1< DerivVectorPair > & | atom_derivs | ||
| ) |
Evaluate the derivatives for all atoms on the input residue for the terms that apply to this residue (which are stored on the input minimization node).
Definition at line 904 of file MinimizationGraph.cc.
References core::scoring::MinimizationNode::active_1benmeths_begin(), core::scoring::MinimizationNode::active_1benmeths_end(), core::scoring::MinimizationNode::active_intrares2benmeths_begin(), core::scoring::MinimizationNode::active_intrares2benmeths_end(), and core::scoring::MinimizationNode::res_min_data().
Referenced by core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::optimization::atom_tree_get_atompairE_deriv(), core::optimization::cartesian_collect_atompairE_deriv(), core::pack::scmin::CartSCMinMultifunc::dfunc(), and core::pack::scmin::SCMinMultifunc::dfunc().
| void core::scoring::eval_bbbb_sr2b_energies | ( | conformation::Residue const & | r1, |
| conformation::Residue const & | r2, | ||
| Vector const & | r1bb_centroid, | ||
| Vector const & | r2bb_centroid, | ||
| Real const & | r1bb_radius, | ||
| Real const & | r2bb_radius, | ||
| pose::Pose const & | pose, | ||
| ScoreFunction const & | sfxn, | ||
| EnergyMap & | emap | ||
| ) |
With two bounding spheres for a pair of backbones, evaluate all the backbone/sidechain energies. This will avoid a call to EnergyMethod E's backbone_backbone_energiy method if either a) E's atomic_interaction_cutoff + r1bb_radius + r2bb_radius < dist( r1bb_centroid, r2sc_centroid ) or b) E returns "false" in a call to its divides_backbone_and_- sidechain_energetics() method. The reason the call is avoided if "false" is returned is that, the entirety of a residue-pair-energy evaluation should be returned in the sidechain_sidechain_energy evaluation, if E does not implement its own versions of the bb/bb, bb/sc and sc/sc energy evaluation methods. Both context-dependent and context-independent 2-body energies are evaluated in this function.
Definition at line 107 of file util.cc.
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.
Definition at line 70 of file util.cc.
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 | ||
| ) |
Definition at line 1078 of file MinimizationGraph.cc.
References core::scoring::MinimizationNode::dof_deriv_1benmeths_begin(), core::scoring::MinimizationNode::dof_deriv_1benmeths_end(), core::scoring::MinimizationNode::dof_deriv_2benmeths_begin(), core::scoring::MinimizationNode::dof_deriv_2benmeths_end(), and core::scoring::MinimizationNode::res_min_data().
Referenced by core::pack::scmin::CartSCMinMultifunc::dfunc(), core::pack::scmin::SCMinMultifunc::dfunc(), and core::scoring::ScoreFunction::eval_dof_derivative().
| void core::scoring::eval_res_onebody_energies_for_minnode | ( | MinimizationNode const & | min_node, |
| conformation::Residue const & | rsd, | ||
| pose::Pose const & | pose, | ||
| ScoreFunction const & | sfxn, | ||
| EnergyMap & | emap | ||
| ) |
Deprecated.
Definition at line 962 of file MinimizationGraph.cc.
References core::scoring::MinimizationNode::active_1benmeths_ext_begin(), core::scoring::MinimizationNode::active_1benmeths_ext_end(), core::scoring::MinimizationNode::active_1benmeths_std_begin(), core::scoring::MinimizationNode::active_1benmeths_std_end(), core::scoring::MinimizationNode::active_intrares2benmeths_ext_begin(), core::scoring::MinimizationNode::active_intrares2benmeths_ext_end(), core::scoring::MinimizationNode::active_intrares2benmeths_std_begin(), core::scoring::MinimizationNode::active_intrares2benmeths_std_end(), and core::scoring::MinimizationNode::res_min_data().
Referenced by core::pack::compare_mingraph_and_energy_graph(), core::scoring::ScoreFunction::eval_onebody_energies(), core::pack::scmin::CartSCMinMultifunc::operator()(), and core::pack::scmin::SCMinMultifunc::operator()().
| void core::scoring::eval_res_pair_energy_for_minedge | ( | MinimizationEdge const & | min_edge, |
| conformation::Residue const & | res1, | ||
| conformation::Residue const & | res2, | ||
| pose::Pose const & | pose, | ||
| ScoreFunction const & | sfxn, | ||
| EnergyMap & | emap | ||
| ) |
Deprecated.
Definition at line 1052 of file MinimizationGraph.cc.
References core::scoring::MinimizationEdge::active_2benmeths_ext_begin(), core::scoring::MinimizationEdge::active_2benmeths_ext_end(), core::scoring::MinimizationEdge::active_2benmeths_std_begin(), core::scoring::MinimizationEdge::active_2benmeths_std_end(), and core::scoring::MinimizationEdge::res_pair_min_data().
Referenced by core::pack::compare_mingraph_and_energy_graph(), core::scoring::ScoreFunction::eval_twobody_neighbor_energies(), core::pack::scmin::CartSCMinMultifunc::operator()(), and core::pack::scmin::SCMinMultifunc::operator()().
| void core::scoring::eval_scsc_sr2b_energies | ( | conformation::Residue const & | r1, |
| conformation::Residue const & | r2, | ||
| Vector const & | r1sc_centroid, | ||
| Vector const & | r2sc_centroid, | ||
| Real const & | r1sc_radius, | ||
| Real const & | r2sc_radius, | ||
| pose::Pose const & | pose, | ||
| ScoreFunction const & | sfxn, | ||
| EnergyMap & | emap | ||
| ) |
With two bounding spheres for a pair of sidechains, evaluate all the sidechain/sidechain energies. This will avoid a call to EnergyMethod E's sidechain_sidechain_energiy method if a) E's atomic_interaction_cutoff + r1sc_radius + r2sc_radius < dist( r1sc_centroid, r2sc_centroid ) and b) E returns "true" in a call to its divides_backbone_and_- sidechain_energetics() method. Both context-dependent and context-independent 2-body energies are evaluated in this function.
Definition at line 37 of file util.cc.
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(), core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), and core::pack::interaction_graph::SymmOnTheFlyNode::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 | ||
| ) |
Definition at line 1256 of file MinimizationGraph.cc.
References core::scoring::MinimizationNode::dof_deriv_1benmeths_begin(), core::scoring::MinimizationNode::dof_deriv_1benmeths_end(), core::scoring::MinimizationNode::dof_deriv_2benmeths_begin(), core::scoring::MinimizationNode::dof_deriv_2benmeths_end(), core::scoring::MinimizationNode::res_min_data(), and core::scoring::MinimizationNode::weight().
Referenced by core::scoring::symmetry::SymmetricScoreFunction::eval_dof_derivative().
| void core::scoring::eval_weighted_res_onebody_energies_for_minnode | ( | MinimizationNode const & | min_node, |
| conformation::Residue const & | rsd, | ||
| pose::Pose const & | pose, | ||
| ScoreFunction const & | sfxn, | ||
| EnergyMap & | emap, | ||
| EnergyMap & | scratch_emap | ||
| ) |
Definition at line 1144 of file MinimizationGraph.cc.
References core::scoring::EMapVector::accumulate(), core::scoring::MinimizationNode::active_1benmeths_ext_begin(), core::scoring::MinimizationNode::active_1benmeths_ext_end(), core::scoring::MinimizationNode::active_1benmeths_std_begin(), core::scoring::MinimizationNode::active_1benmeths_std_end(), core::scoring::MinimizationNode::active_intrares2benmeths_ext_begin(), core::scoring::MinimizationNode::active_intrares2benmeths_ext_end(), core::scoring::MinimizationNode::active_intrares2benmeths_std_begin(), core::scoring::MinimizationNode::active_intrares2benmeths_std_end(), core::scoring::MinimizationNode::res_min_data(), core::scoring::MinimizationNode::weight(), and core::scoring::EMapVector::zero().
Referenced by core::scoring::symmetry::SymmetricScoreFunction::eval_onebody_energies().
| void core::scoring::eval_weighted_res_pair_energy_for_minedge | ( | MinimizationEdge const & | min_edge, |
| conformation::Residue const & | res1, | ||
| conformation::Residue const & | res2, | ||
| pose::Pose const & | pose, | ||
| ScoreFunction const & | sfxn, | ||
| EnergyMap & | emap, | ||
| EnergyMap & | scratch_emap | ||
| ) |
evaluates the atom derivative for this edge, and applies the edge weight into the f1 and f2 vectors before accumulating into the F1 and F2 vectors
Definition at line 1225 of file MinimizationGraph.cc.
References core::scoring::EMapVector::accumulate(), core::scoring::MinimizationEdge::active_2benmeths_ext_begin(), core::scoring::MinimizationEdge::active_2benmeths_ext_end(), core::scoring::MinimizationEdge::active_2benmeths_std_begin(), core::scoring::MinimizationEdge::active_2benmeths_std_end(), core::scoring::MinimizationEdge::res_pair_min_data(), core::scoring::MinimizationEdge::weight(), and core::scoring::EMapVector::zero().
Referenced by core::scoring::symmetry::SymmetricScoreFunction::eval_twobody_neighbor_energies().
| void core::scoring::evaluaterdc | ( | const double * | par, |
| int | m_dat, | ||
| const void * | data, | ||
| double * | fvec, | ||
| int * | |||
| ) |
Definition at line 846 of file ResidualDipolarCoupling.cc.
References core::scoring::data_struct::frdc, core::scoring::data_struct::r0, core::scoring::data_struct::r1, core::scoring::data_struct::r2, core::scoring::data_struct::rdc, core::scoring::data_struct::rdcconst, and core::scoring::data_struct::rdcweight.
Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore_nls().
| void core::scoring::evaluaterdcDa | ( | const double * | par, |
| int | m_dat, | ||
| const void * | data, | ||
| double * | fvec, | ||
| int * | |||
| ) |
Definition at line 855 of file ResidualDipolarCoupling.cc.
References core::scoring::data_structDa::frdcDa, core::scoring::data_structDa::r0, core::scoring::data_structDa::r1, core::scoring::data_structDa::r2, core::scoring::data_structDa::rdc, core::scoring::data_structDa::rdcconst, core::scoring::data_structDa::rdcweight, and core::scoring::data_structDa::tensorDa.
Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDa().
| void core::scoring::evaluaterdcDaR | ( | const double * | par, |
| int | m_dat, | ||
| const void * | data, | ||
| double * | fvec, | ||
| int * | |||
| ) |
Definition at line 873 of file ResidualDipolarCoupling.cc.
References core::scoring::data_structDaR::frdcDaR, core::scoring::data_structDaR::r0, core::scoring::data_structDaR::r1, core::scoring::data_structDaR::r2, core::scoring::data_structDaR::rdc, core::scoring::data_structDaR::rdcconst, core::scoring::data_structDaR::rdcweight, core::scoring::data_structDaR::tensorDa, and core::scoring::data_structDaR::tensorR.
Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDaR().
| void core::scoring::evaluaterdcR | ( | const double * | par, |
| int | m_dat, | ||
| const void * | data, | ||
| double * | fvec, | ||
| int * | |||
| ) |
Definition at line 864 of file ResidualDipolarCoupling.cc.
References core::scoring::data_structR::frdcR, core::scoring::data_structR::r0, core::scoring::data_structR::r1, core::scoring::data_structR::r2, core::scoring::data_structR::rdc, core::scoring::data_structR::rdcconst, core::scoring::data_structR::rdcweight, and core::scoring::data_structR::tensorR.
Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsR().
| std::string const core::scoring::FA_STANDARD_DEFAULT | ( | "FA_STANDARD_DEFAULT" | ) |
global etable_id
| std::string const core::scoring::FA_STANDARD_SOFT | ( | "FA_STANDARD_SOFT" | ) |
| void core::scoring::fill_bb_pos | ( | pose::Pose const & | pose, |
| BB_Pos & | bb_pos | ||
| ) |
helper function
Definition at line 115 of file SecondaryStructurePotential.cc.
References core::scoring::BB_Pos::take_coordinates_from_pose().
Referenced by core::scoring::SecondaryStructurePotential::setup_for_scoring().
| 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 | ||
| ) |
Definition at line 749 of file rms_util.tmpl.hh.
References core::conformation::Residue::is_virtual_residue(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().
Referenced by CA_gdtmm(), CA_maxsub(), CA_maxsub_by_subset(), CA_rmsd(), and CA_rmsd_symmetric().
| void core::scoring::fill_score_range | ( | std::map< std::string, ScoreType > & | M, |
| std::string | prefix, | ||
| int | first, | ||
| int | last | ||
| ) |
Definition at line 40 of file ScoreTypeManager.cc.
Referenced by core::scoring::ScoreTypeManager::setup_score_type_names().
| 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.
Definition at line 2945 of file ScoreFunction.cc.
References core::scoring::ScoreFunction::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 | ||
| ) |
Definition at line 744 of file ResidualDipolarCoupling.cc.
References protocols::match::upstream::b, and core::pack::dunbrack::c.
Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore_nls().
| double core::scoring::frdcDa | ( | double | r0, |
| double | r1, | ||
| double | r2, | ||
| double | rdcconst, | ||
| double const | tensorDa, | ||
| const double * | par | ||
| ) |
Definition at line 760 of file ResidualDipolarCoupling.cc.
References protocols::match::upstream::b, and core::pack::dunbrack::c.
Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDa().
| double core::scoring::frdcDaR | ( | double | r0, |
| double | r1, | ||
| double | r2, | ||
| double | rdcconst, | ||
| double const | tensorDa, | ||
| double const | tensorR, | ||
| const double * | par | ||
| ) |
Definition at line 792 of file ResidualDipolarCoupling.cc.
References protocols::match::upstream::b, and core::pack::dunbrack::c.
Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDaR().
| double core::scoring::frdcR | ( | double | r0, |
| double | r1, | ||
| double | r2, | ||
| double | rdcconst, | ||
| double const | tensorR, | ||
| const double * | par | ||
| ) |
Definition at line 776 of file ResidualDipolarCoupling.cc.
References protocols::match::upstream::b, and core::pack::dunbrack::c.
Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsR().
| core::Real core::scoring::gdtha | ( | const core::pose::Pose & | ref, |
| const core::pose::Pose & | mod, | ||
| const std::map< core::Size, core::Size > & | residues | ||
| ) |
Returns the average fraction of residues superimposable under a series of distance thresholds– 0.5, 1.0, 2.0, and 4.0 Angstroms.
Definition at line 167 of file rms_util.cc.
References core::conformation::Residue::name1(), core::pose::Pose::residue(), core::chemical::tr(), and core::pose::Pose::xyz().
Referenced by protocols::comparative_modeling::Align_RmsdEvaluator::apply().
| core::Real core::scoring::gdtsc | ( | const core::pose::Pose & | ref, |
| const core::pose::Pose & | model, | ||
| const std::map< core::Size, core::Size > & | residues | ||
| ) |
Returns a single, Global Distance Test-like value that measures the extent to which the functional ends of a model's sidechains agree with their counterparts in a given reference structure.
Instead of comparing residue positions on the basis of CAs, gdtsc uses a characteristic atom near the end of each sidechain type for the evaluation of residue-residue distance deviations.
The traditional GDT score is a weighted sum of the fraction of residues superimposed within limits of 1, 2, 4, and 8Å. For gdtsc, the backbone superposition is used to calculate fractions of corresponding model-ref sidechain atom pairs that fit under 10 distance-limit values from 0.5A to 5A. Ambiguity in Asp or Glu terminal oxygen naming is not currently considered.
Reference: Keedy, DA. The other 90% of the protein. Proteins. 2009; 77 Suppl 9:29-49.
Definition at line 76 of file rms_util.cc.
References core::pose::Pose::is_fullatom(), core::conformation::Residue::name1(), core::pose::Pose::residue(), core::chemical::tr(), and core::pose::Pose::xyz().
Referenced by protocols::comparative_modeling::Align_RmsdEvaluator::apply().
| 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
Definition at line 354 of file sasa.cc.
References num_phi, and num_theta.
Referenced by core::pack::interaction_graph::RotamerDots::get_atom_atom_coverage(), core::pack::interaction_graph::InvRotamerDots::overlap_exposed(), 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
Definition at line 851 of file sasa.cc.
References core::scoring::packstat::old::angles, and core::scoring::packstat::old::input_sasa_dats().
Referenced by core::pack::interaction_graph::RotamerDots::initialize_sasa_arrays().
| 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
Definition at line 863 of file sasa.cc.
References core::scoring::packstat::old::input_sasa_dats(), and core::scoring::packstat::old::masks.
Referenced by core::pack::interaction_graph::RotamerDots::initialize_sasa_arrays().
| int core::scoring::get_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
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.
Definition at line 263 of file sasa.cc.
References 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
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
Definition at line 172 of file sasa.cc.
Referenced by core::scoring::packstat::compute_cav_ball_volumes(), core::scoring::packstat::compute_sasa(), core::pack::interaction_graph::RotamerDots::get_atom_atom_coverage(), core::pack::interaction_graph::HPatchNode< V, E, G >::initialize_atom_atom_overlap_cache(), core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::initialize_atom_atom_overlaps(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::initialize_bg_bg_atom_atom_overlaps(), core::pack::interaction_graph::InvRotamerDots::overlap_exposed(), core::scoring::packstat::prune_1pass(), core::scoring::packstat::prune_hidden_cavity_balls(), and core::pack::interaction_graph::InvRotamerDots::write_circle_intersection_mask_to_kinemage().
| 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.
Definition at line 258 of file ScoreFunctionFactory.cc.
References CENTROID_WTS, core::scoring::ScoreFunctionFactory::create_score_function(), and T().
Referenced by protocols::simple_moves::ProlineFixMover::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::simple_filters::SAXSScoreFilter::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::simple_moves::ConsensusDesignMover::apply(), protocols::simple_moves::symmetry::SymMinMover::apply(), protocols::simple_filters::TruncatedScoreEvaluator::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::topology_broker::TopologyBroker::apply(), protocols::simple_moves::MinMover::apply(), protocols::rbsegment_relax::AutoRBMover::AutoRBMover(), protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE(), protocols::canonical_sampling::canonical_sampling_main(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::noesy_assign::FragsToAtomDist::compute_average_distances(), protocols::electron_density::dockPoseIntoMap(), protocols::enzdes::EnzdesBaseProtocol::EnzdesBaseProtocol(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::fascore(), protocols::swa::protein::StepWiseProteinFilterer::filter(), protocols::swa::StepWiseFilterer::filter(), protocols::floppy_tail::FloppyTailMover::FloppyTailMover(), protocols::flxbb::FlxbbDesign_main(), protocols::swa::protein::generate_beta_database_test(), protocols::jd2::DockDesignParser::generate_mover_from_pose(), protocols::relax::generate_relax_from_cmd(), protocols::abinitio::AbrelaxApplication::generate_scorefxn(), protocols::features::get_current_model_score(), protocols::loops::get_fa_scorefxn(), protocols::features::helixAssembly::HelixBundleFeatures::HelixBundleFeatures(), protocols::hybridization::HybridizeProtocol::init(), protocols::swa::protein::StepWiseProteinPoseMinimizer::initialize_parameters(), 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::loophash::LoopHashRelaxProtocol::manual_call(), protocols::simple_moves::PeptideStapleMover::minimize_(), protocols::jobdist::not_universal_main(), protocols::dna::PDBOutput::output_pdb(), protocols::frag_picker::FragmentCandidate::output_silent(), 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(), protocols::flexpep_docking::FlexPepDockingProtocol::set_default(), protocols::grafting::GraftMoverBase::set_default_fa_scorefunction(), protocols::relax::CentroidRelax::set_defaults(), protocols::simple_moves::SaneMinMover::set_defaults_(), and protocols::anchored_design::AnchorMoversData::set_unset_scorefunctions().
| std::string core::scoring::getScoreFunctionName | ( | bool const | is_fullatom) |
use the logic of getScoreFunction to get the name. The name format is <weights_tag>[_<patch_tag> ... ]
Definition at line 325 of file ScoreFunctionFactory.cc.
References CENTROID_WTS, SCORE12_PATCH, and STANDARD_WTS.
|
inline |
intraresidue atom pair energy evaluations
Definition at line 222 of file atom_pair_energy_inline.hh.
References core::conformation::Residue::atom(), core::conformation::Residue::atom_type(), core::conformation::Residue::attached_H_begin(), core::conformation::Residue::attached_H_end(), core::chemical::AtomType::is_virtual(), core::conformation::Residue::nheavyatoms(), and residue_fast_pair_energy_attached_H().
Referenced by core::scoring::etable::count_pair::CountPairIntraResC3::residue_atom_pair_energy(), core::scoring::etable::count_pair::CountPairIntraResC4::residue_atom_pair_energy(), and core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior >::residue_atom_pair_energy().
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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
Definition at line 144 of file atom_pair_energy_inline.hh.
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(), and residue_fast_pair_energy_attached_H().
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::CountPairAll::residue_atom_pair_energy(), core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >::residue_atom_pair_energy(), and core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy().
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inline |
Definition at line 293 of file atom_pair_energy_inline.hh.
References inline_residue_atom_pair_energy(), and core::conformation::Residue::nheavyatoms().
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inline |
Definition at line 341 of file atom_pair_energy_inline.hh.
References inline_residue_atom_pair_energy(), and core::conformation::Residue::last_backbone_atom().
Referenced by core::scoring::etable::count_pair::CountPairAll::residue_atom_pair_energy_backbone_backbone(), core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >::residue_atom_pair_energy_backbone_backbone(), and core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_backbone_backbone().
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inline |
Definition at line 309 of file atom_pair_energy_inline.hh.
References core::conformation::Residue::first_sidechain_atom(), inline_residue_atom_pair_energy(), core::conformation::Residue::last_backbone_atom(), and core::conformation::Residue::nheavyatoms().
Referenced by core::scoring::etable::count_pair::CountPairAll::residue_atom_pair_energy_sidechain_backbone(), core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >::residue_atom_pair_energy_sidechain_backbone(), and core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_sidechain_backbone().
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Definition at line 357 of file atom_pair_energy_inline.hh.
References core::conformation::Residue::first_sidechain_atom(), inline_residue_atom_pair_energy(), and core::conformation::Residue::nheavyatoms().
Referenced by core::scoring::etable::count_pair::CountPairAll::residue_atom_pair_energy_sidechain_sidechain(), core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >::residue_atom_pair_energy_sidechain_sidechain(), and core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_sidechain_sidechain().
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Definition at line 325 of file atom_pair_energy_inline.hh.
References core::conformation::Residue::first_sidechain_atom(), inline_residue_atom_pair_energy(), and core::conformation::Residue::nheavyatoms().
Referenced by core::scoring::etable::count_pair::CountPairAll::residue_atom_pair_energy_sidechain_whole(), core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >::residue_atom_pair_energy_sidechain_whole(), and core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_sidechain_whole().
| void core::scoring::input_sasa_dats | ( | ) |
Reads in the SASA database files sampling/SASA-angles.dat and sampling/SASA-masks.dat into FArrays above.
sasa.cc::input_sasa_dats
Definition at line 108 of file sasa.cc.
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().
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Definition at line 31 of file interpolation_util.hh.
Referenced by core::scoring::carbon_hbonds::CarbonHBondPotential::get_potential(), core::scoring::rna::RNA_LowResolutionPotential::get_rna_axis_score(), core::scoring::rna::RNA_LowResolutionPotential::get_rna_backbone_backbone_score(), and core::scoring::rna::RNA_LowResolutionPotential::get_rna_stagger_score().
| void core::scoring::invert_exclude_residues | ( | Size | nres, |
| utility::vector1< int > const & | exclude_list, | ||
| ResidueSelection & | residue_selection | ||
| ) |
Definition at line 230 of file rms_util.cc.
Referenced by protocols::simple_filters::NativeEvaluatorCreator::add_evaluators(), protocols::cluster::GatherPosesMover::get_distance_measure(), invert_exclude_residues(), native_CA_gdtmm(), and native_CA_rmsd().
| ResidueSelection core::scoring::invert_exclude_residues | ( | core::Size | nres, |
| utility::vector1< int > const & | exclude_list | ||
| ) |
Definition at line 248 of file rms_util.cc.
References invert_exclude_residues().
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inline |
Definition at line 363 of file ResidualDipolarCoupling.cc.
| bool core::scoring::is_heavyatom | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | , | ||
| core::Size | resno, | ||
| core::Size | atomno | ||
| ) |
Definition at line 469 of file rms_util.cc.
References core::conformation::Residue::atom_is_hydrogen(), and core::pose::Pose::residue().
Referenced by all_atom_rmsd(), biggest_residue_deviation_no_super(), biggest_residue_deviation_no_super_subset(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_atoms_kA_to_native(), protocols::features::ProteinRMSDFeatures::report_features(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), rmsd_no_super(), rmsd_no_super_subset(), rmsd_with_super(), rmsd_with_super_subset(), core::chemical::ResidueType::setup_atom_ordering(), and sym_rmsd_with_super_subset().
| bool core::scoring::is_ligand_heavyatom | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | , | ||
| core::Size | resno, | ||
| core::Size | atomno | ||
| ) |
Definition at line 436 of file rms_util.cc.
References core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::is_polymer(), and core::pose::Pose::residue().
Referenced by protocols::ligand_docking::append_multi_residue_ligand_RMSD(), biggest_residue_deviation_no_super(), biggest_residue_deviation_no_super_subset(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_atoms_kA_to_native(), rmsd_no_super(), rmsd_no_super_subset(), rmsd_with_super(), rmsd_with_super_subset(), and sym_rmsd_with_super_subset().
| bool core::scoring::is_ligand_heavyatom_residues | ( | core::conformation::Residue const & | residue1, |
| core::conformation::Residue const & | , | ||
| core::Size | atomno | ||
| ) |
Definition at line 448 of file rms_util.cc.
References core::conformation::Residue::atom_is_hydrogen(), and core::conformation::Residue::is_polymer().
Referenced by protocols::ligand_docking::check_RMSD(), and rmsd_no_super().
| bool core::scoring::is_nbr_atom | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | , | ||
| core::Size | resno, | ||
| core::Size | atomno | ||
| ) |
Definition at line 481 of file rms_util.cc.
References core::conformation::Residue::nbr_atom(), and core::pose::Pose::residue().
Referenced by nbr_atom_rmsd(), and protocols::features::ProteinRMSDFeatures::report_features().
| bool core::scoring::is_polymer_heavyatom | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | , | ||
| core::Size | resno, | ||
| core::Size | atomno | ||
| ) |
Definition at line 457 of file rms_util.cc.
References core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::is_polymer(), and core::pose::Pose::residue().
Referenced by biggest_residue_deviation_no_super(), biggest_residue_deviation_no_super_subset(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_atoms_kA_to_native(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), rmsd_no_super(), rmsd_no_super_subset(), rmsd_with_super(), rmsd_with_super_subset(), protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics(), and sym_rmsd_with_super_subset().
| bool core::scoring::is_protein_backbone | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | , | ||
| core::Size | resno, | ||
| core::Size | atomno | ||
| ) |
Definition at line 395 of file rms_util.cc.
References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), and core::pose::Pose::residue().
Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::addLowResStatistics(), bb_rmsd(), protocols::docking::calc_Irmsd(), protocols::docking::calc_Lrmsd(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf(), protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::features::ProteinRMSDFeatures::report_features(), and protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().
| bool core::scoring::is_protein_backbone_including_O | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | , | ||
| core::Size | resno, | ||
| core::Size | atomno | ||
| ) |
Definition at line 409 of file rms_util.cc.
References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), and core::pose::Pose::residue().
Referenced by bb_rmsd_including_O(), protocols::swa::StepWiseScreener::filter_and_output(), protocols::swa::protein::StepWiseProteinScreener::filter_and_output(), protocols::antibody2::global_loop_rmsd(), and protocols::features::ProteinRMSDFeatures::report_features().
| bool core::scoring::is_protein_CA | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | , | ||
| core::Size | resno, | ||
| core::Size | atomno | ||
| ) |
Definition at line 371 of file rms_util.cc.
References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), and core::pose::Pose::residue().
Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::addLowResStatistics(), protocols::simple_moves::symmetry::SymmetricRMSMover::apply(), CA_gdtmm(), CA_maxsub(), CA_maxsub_by_subset(), CA_rmsd_symmetric(), protocols::ub_e2c::ubi_e2c_modeler::calc_Lrmsd(), protocols::symmetric_docking::SymDockProtocol::calc_rms(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), protocols::protein_interface_design::filters::RmsdFilter::compute(), protocols::antibody::AntibodyModeler::global_loop_rmsd(), protocols::ub_e2c::ubi_e2c_modeler::monoub_calc_Lrmsd(), core::scoring::IsProteinCAPredicate::operator()(), protocols::features::ProteinRMSDFeatures::report_features(), and protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().
| bool core::scoring::is_protein_CA_or_CB | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | , | ||
| core::Size | resno, | ||
| core::Size | atomno | ||
| ) |
Definition at line 383 of file rms_util.cc.
References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), and core::pose::Pose::residue().
Referenced by protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf(), and protocols::features::ProteinRMSDFeatures::report_features().
| bool core::scoring::is_protein_sidechain_heavyatom | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | , | ||
| core::Size | resno, | ||
| core::Size | atomno | ||
| ) |
Definition at line 424 of file rms_util.cc.
References core::chemical::ResidueType::atom_is_hydrogen(), core::chemical::ResidueType::first_sidechain_atom(), core::chemical::ResidueType::is_protein(), and core::pose::Pose::residue_type().
Referenced by protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::enzdes::RepackWithoutLigandFilter::compute(), and protocols::features::ProteinRMSDFeatures::report_features().
Definition at line 2449 of file ResidualDipolarCoupling.cc.
References protocols::match::upstream::b, core::pack::dunbrack::c, ROTATE, and core::scoring::hbonds::t().
Referenced by protocols::evaluation::PCA::calc_fit_R(), and m_inv_gen().
Definition at line 2530 of file ResidualDipolarCoupling.cc.
References protocols::match::upstream::b, core::pack::dunbrack::c, ROTATE, and core::scoring::hbonds::t().
Referenced by core::scoring::ResidualDipolarCoupling::compute_tensor_stats().
Definition at line 2394 of file ResidualDipolarCoupling.cc.
References jacobi().
Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore().
| 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) |
Definition at line 210 of file Membrane_FAPotential.cc.
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_FAEMBED.
Referenced by core::scoring::Membrane_FAPotential::compute_fa_projection(), core::scoring::hbonds::get_membrane_depth_dependent_weight(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), and core::scoring::hbonds::HBondEnergy::setup_for_scoring().
| MembraneEmbed const & core::scoring::MembraneEmbed_from_pose | ( | pose::Pose const & | pose) |
Pose must already contain a cenlist object or this method will fail.
Definition at line 1135 of file MembranePotential.cc.
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_EMBED.
Referenced by protocols::rigid::MovePoseToMembraneCenterMover::apply(), protocols::rigid::MembraneCenterPerturbationMover::apply(), protocols::rigid::MembraneNormalPerturbationMover::apply(), core::scoring::methods::MembraneEnvSmoothEnergy::calc_energy(), core::scoring::Membrane_FAPotential::compute_fa_projection(), core::scoring::MembranePotential::evaluate_env(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::hbonds::get_membrane_depth_dependent_weight(), core::scoring::etable::BaseEtableEnergy< Derived >::memb_atom_pair_energy_(), core::scoring::etable::BaseEtableEnergy< Derived >::memb_eval_dE_dR_over_r_(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), core::scoring::hbonds::HBondEnergy::setup_for_scoring(), core::scoring::MembranePotential::termini_penalty(), and core::scoring::MembranePotential::tm_projection_penalty().
| MembraneTopology const & core::scoring::MembraneTopology_from_pose | ( | pose::Pose const & | pose) |
Definition at line 292 of file MembraneTopology.cc.
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY.
Referenced by protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), core::scoring::MembranePotential::check_spanning(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::MembranePotential::evaluate_cbeta(), core::scoring::MembranePotential::init_membrane_center_normal(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::scoring::MembranePotential::score_normal_center(), core::scoring::MembranePotential::termini_penalty(), and core::scoring::MembranePotential::tm_projection_penalty().
| std::string const core::scoring::MM_STD_WTS | ( | "mm_std" | ) |
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inline |
Definition at line 366 of file ResidualDipolarCoupling.cc.
| 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
Definition at line 112 of file ScoreType.cc.
References core::scoring::ScoreTypeManager::name_from_score_type().
Referenced by protocols::ligand_docking::InterfaceScoreCalculator::add_scores_to_job(), protocols::ligand_docking::append_interface_deltas(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::simple_filters::EnergyPerResidueFilter::apply(), protocols::hybridization::FoldTreeHybridize::apply(), core::scoring::ScoreFunction::check_methods(), protocols::optimize_weights::IterativeOptEDriver::converged(), 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::initialize_free_and_fixed(), protocols::optimize_weights::IterativeOptEDriver::IterativeOptEDriver(), core::import_pose::atom_tree_diffs::map_of_weighted_scores(), core::scoring::methods::EnergyMethodOptions::method_weights(), operator<<(), protocols::optimize_weights::IterativeOptEDriver::optimize_weights(), protocols::simple_filters::ScoreCutoffFilter::output_residue_pair_energies(), protocols::optimize_weights::IterativeOptEDriver::output_weighted_unfolded_energies(), core::scoring::ScoreFunction::perturb_weights(), core::scoring::EMapVector::print(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::process_score(), protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::process_score(), protocols::simple_filters::EnergyPerResidueFilter::report(), protocols::jd2::ScoreMap::score_map_from_scored_pose(), protocols::moves::PyMolMover::send_energy(), protocols::abinitio::FragmentSampler::set_score_weight(), protocols::abinitio::ClassicAbinitio::set_score_weight(), protocols::abinitio::MembraneAbinitio::set_score_weight(), core::scoring::Energies::show(), protocols::optimize_weights::WrapperOptEMultifunc::WrapperOptEMultifunc(), protocols::optimize_weights::IterativeOptEDriver::write_new_scorefile(), protocols::optimize_weights::IterativeOptEDriver::write_parameters_to_std_out(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::write_to_file(), and protocols::optimize_weights::OptEData::write_to_file().
| core::Real core::scoring::native_CA_gdtmm | ( | const core::pose::Pose & | native_pose, |
| const core::pose::Pose & | pose | ||
| ) |
Definition at line 268 of file rms_util.cc.
References CA_gdtmm(), invert_exclude_residues(), and core::pose::Pose::total_residue().
Referenced by protocols::relax::FastRelax::batch_apply().
| core::Real core::scoring::native_CA_rmsd | ( | const core::pose::Pose & | native_pose, |
| const core::pose::Pose & | pose | ||
| ) |
Definition at line 254 of file rms_util.cc.
References CA_rmsd(), invert_exclude_residues(), and core::pose::Pose::total_residue().
Referenced by protocols::simple_moves::ScoreMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::relax::FastRelax::apply(), protocols::relax::FastRelax::batch_apply(), protocols::relax::FastRelax::cmd_accept_to_best(), protocols::jobdist::main_plain_pdb_mover(), and protocols::jobdist::universal_main().
| core::Real core::scoring::nbr_atom_rmsd | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2 | ||
| ) |
Definition at line 755 of file rms_util.cc.
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.
Definition at line 220 of file Membrane_FAPotential.cc.
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_FAEMBED.
Referenced by core::scoring::Membrane_FAPotential::compute_fa_projection(), core::scoring::Membrane_FAPotential::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.
Definition at line 1146 of file MembranePotential.cc.
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_EMBED.
Referenced by core::scoring::ChemicalShiftAnisotropy::compute_csascore(), core::scoring::DipolarCoupling::compute_dcscore(), core::scoring::Membrane_FAPotential::compute_fa_projection(), core::scoring::MembranePotential::compute_membrane_embedding(), core::scoring::MembranePotential::finalize(), and core::scoring::Membrane_FAPotential::finalize().
| MembraneTopology & core::scoring::nonconst_MembraneTopology_from_pose | ( | pose::Pose & | pose) |
Either returns a non-const reference to the cenlist object already stored in the pose, or creates a new cenist object, places it in the pose, and returns a non-const reference to it.
Definition at line 304 of file MembraneTopology.cc.
References core::pose::Pose::data(), core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY, and core::scoring::MembraneTopology::MembraneTopology().
Referenced by core::scoring::MembranePotential::compute_membrane_embedding().
| 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;
Definition at line 82 of file ScoreType.cc.
References core::scoring::ScoreTypeManager::name_from_score_type().
| std::ostream& core::scoring::operator<< | ( | std::ostream & | out, |
| Hairpin const & | s | ||
| ) |
Definition at line 91 of file SS_Killhairpins_Info.cc.
References core::scoring::Hairpin::s1_end(), core::scoring::Hairpin::s1_start(), core::scoring::Hairpin::s2_end(), and core::scoring::Hairpin::s2_start().
| std::ostream & core::scoring::operator<< | ( | std::ostream & | os, |
| ScoreTypes const & | score_types | ||
| ) |
output operator for ScoreTypes list type
output operator for ScoreTypes list
Definition at line 94 of file ScoreType.cc.
| std::ostream & core::scoring::operator<< | ( | std::ostream & | out, |
| CSA const & | csa | ||
| ) |
Definition at line 103 of file ChemicalShiftAnisotropy.cc.
References core::scoring::CSA::show().
| std::ostream & core::scoring::operator<< | ( | std::ostream & | out, |
| DC const & | dc | ||
| ) |
Definition at line 104 of file DipolarCoupling.cc.
References core::scoring::DC::show().
| std::ostream & core::scoring::operator<< | ( | std::ostream & | out, |
| ChemicalShiftAnisotropy const & | csa | ||
| ) |
Definition at line 108 of file ChemicalShiftAnisotropy.cc.
References core::scoring::ChemicalShiftAnisotropy::show().
| std::ostream & core::scoring::operator<< | ( | std::ostream & | out, |
| DipolarCoupling const & | dc | ||
| ) |
Definition at line 109 of file DipolarCoupling.cc.
References core::scoring::DipolarCoupling::show().
| std::ostream & core::scoring::operator<< | ( | std::ostream & | out, |
| RDC const & | rdc | ||
| ) |
Definition at line 115 of file ResidualDipolarCoupling.cc.
References core::scoring::RDC::show().
| std::ostream & core::scoring::operator<< | ( | std::ostream & | out, |
| ResidualDipolarCoupling const & | rdc | ||
| ) |
Definition at line 120 of file ResidualDipolarCoupling.cc.
References core::scoring::ResidualDipolarCoupling::show().
| std::ostream& core::scoring::operator<< | ( | std::ostream & | out, |
| Hairpins const & | s | ||
| ) |
Definition at line 152 of file SS_Killhairpins_Info.cc.
References core::scoring::Hairpins::list().
| std::ostream& core::scoring::operator<< | ( | std::ostream & | out, |
| Strands const & | s | ||
| ) |
Definition at line 213 of file SS_Info.cc.
References core::scoring::Strands::SS_dimer, core::scoring::Strands::SS_resnum, core::scoring::Strands::SS_strand, core::scoring::Strands::SS_strand_end, core::scoring::Strands::total_SS_dimer, and core::scoring::Strands::total_strands.
| std::ostream& core::scoring::operator<< | ( | std::ostream & | out, |
| Helices const & | s | ||
| ) |
Definition at line 269 of file SS_Info.cc.
References core::scoring::Helices::HH_helix_end, core::scoring::Helices::HH_resnum, and core::scoring::Helices::total_HH_dimer.
|
inline |
output operator (index;value)
Definition at line 402 of file EnergyMap.hh.
References n_score_types.
| std::ostream& core::scoring::operator<< | ( | std::ostream & | out, |
| const Energies & | e | ||
| ) |
Definition at line 685 of file Energies.cc.
References protocols::comparative_modeling::features::A, core::scoring::EMapVector::begin(), core::scoring::EMapVector::end(), core::scoring::Energies::get_scorefxn_info(), name_from_score_type(), core::scoring::Energies::residue_total_energies(), core::scoring::ScoreFunctionInfo::scores_present(), core::scoring::Energies::size(), and core::scoring::Energies::total_energies().
|
inline |
Definition at line 1081 of file ScoreFunction.hh.
References core::scoring::ScoreFunction::show().
| bool core::scoring::operator== | ( | ScoreFunctionInfo const & | a, |
| ScoreFunctionInfo const & | b | ||
| ) |
Definition at line 99 of file ScoreFunctionInfo.cc.
References core::scoring::ScoreFunctionInfo::context_graphs_required_, core::scoring::ScoreFunctionInfo::energy_method_options_, core::scoring::ScoreFunctionInfo::max_atomic_interaction_distance_, core::scoring::ScoreFunctionInfo::max_context_neighbor_cutoff_, n_score_types, num_context_graph_types, and core::scoring::ScoreFunctionInfo::scores_present_.
| 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.
Definition at line 59 of file ScoreType.cc.
References core::scoring::ScoreTypeManager::is_score_type(), core::scoring::ScoreTypeManager::score_type_from_name(), and total_score.
|
inline |
class T must define
Definition at line 63 of file atom_pair_energy_inline.hh.
References core::conformation::Residue::atom().
Referenced by inline_intraresidue_atom_pair_energy(), and inline_residue_atom_pair_energy().
| core::Real core::scoring::residue_sc_rmsd_no_super | ( | core::conformation::ResidueCOP | res1, |
| core::conformation::ResidueCOP | res2, | ||
| bool const | fxnal_group_only | ||
| ) |
utility function to calculate per-residue sidechain rmsd without superposition
Iterates over all non-hydrogen sidechain atoms of two residues and returns their rmsd without superposition.
Definition at line 1331 of file rms_util.cc.
References core::pose::num_atoms().
Referenced by protocols::cluster::GatherPosesMover::get_distance_measure(), and protocols::hotspot_hashing::residue_sc_rmsd_no_super().
| SS_Info const& core::scoring::retrieve_const_ss_info_from_pose | ( | pose::Pose const & | pose) |
helper function
Definition at line 90 of file SecondaryStructurePotential.cc.
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::SS_INFO.
Referenced by core::scoring::SecondaryStructurePotential::hspair(), core::scoring::SecondaryStructurePotential::sheets_from_dimers(), and core::scoring::SecondaryStructurePotential::sspair().
| 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>
Definition at line 563 of file rms_util.cc.
References protocols::kinmatch::xyz(), and core::pose::Pose::xyz().
Referenced by CA_gdtmm(), and CA_rmsd().
| ChemicalShiftAnisotropyCOP core::scoring::retrieve_CSA_from_pose | ( | core::pose::Pose const & | pose) |
Definition at line 74 of file ChemicalShiftAnisotropy.cc.
References core::pose::datacache::CacheableDataType::CHEMICAL_SHIFT_ANISOTROPY_DATA, and core::pose::Pose::data().
Referenced by core::scoring::methods::ChemicalShiftAnisotropyEnergy::csa_from_pose(), core::scoring::methods::ChemicalShiftAnisotropyEnergy::eval_atom_derivative(), and core::scoring::methods::ChemicalShiftAnisotropyEnergy::setup_for_minimizing().
| ChemicalShiftAnisotropyOP core::scoring::retrieve_CSA_from_pose | ( | core::pose::Pose & | pose) |
Definition at line 82 of file ChemicalShiftAnisotropy.cc.
References core::pose::datacache::CacheableDataType::CHEMICAL_SHIFT_ANISOTROPY_DATA, and core::pose::Pose::data().
| DipolarCouplingCOP core::scoring::retrieve_DC_from_pose | ( | core::pose::Pose const & | pose) |
Definition at line 75 of file DipolarCoupling.cc.
References core::pose::datacache::CacheableDataType::CHEMICAL_SHIFT_ANISOTROPY_DATA, and core::pose::Pose::data().
Referenced by core::scoring::methods::DipolarCouplingEnergy::dc_from_pose(), core::scoring::methods::DipolarCouplingEnergy::eval_atom_derivative(), and core::scoring::methods::DipolarCouplingEnergy::setup_for_minimizing().
| DipolarCouplingOP core::scoring::retrieve_DC_from_pose | ( | core::pose::Pose & | pose) |
Definition at line 83 of file DipolarCoupling.cc.
References core::pose::datacache::CacheableDataType::CHEMICAL_SHIFT_ANISOTROPY_DATA, and core::pose::Pose::data().
| SS_Info& core::scoring::retrieve_nonconst_ss_info_from_pose | ( | pose::Pose & | pose) |
helper function
Definition at line 100 of file SecondaryStructurePotential.cc.
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::SS_INFO.
Referenced by core::scoring::SecondaryStructurePotential::setup_for_scoring().
| ResidualDipolarCouplingCOP core::scoring::retrieve_RDC_from_pose | ( | core::pose::Pose const & | pose) |
Definition at line 82 of file ResidualDipolarCoupling.cc.
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::RESIDUAL_DIPOLAR_COUPLING_DATA.
Referenced by core::scoring::methods::ResidualDipolarCouplingEnergy::eval_atom_derivative(), core::scoring::methods::ResidualDipolarCouplingEnergy::rdc_from_pose(), and core::scoring::methods::ResidualDipolarCouplingEnergy::setup_for_minimizing().
| ResidualDipolarCouplingOP core::scoring::retrieve_RDC_from_pose | ( | core::pose::Pose & | pose) |
Definition at line 92 of file ResidualDipolarCoupling.cc.
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::RESIDUAL_DIPOLAR_COUPLING_DATA.
| ResidualDipolarCoupling_RohlCOP core::scoring::retrieve_RDC_ROHL_from_pose | ( | core::pose::Pose const & | pose) |
Definition at line 54 of file ResidualDipolarCoupling_Rohl.cc.
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::RESIDUAL_DIPOLAR_COUPLING_DATA_ROHL.
Referenced by core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl::rdc_from_pose().
| ResidualDipolarCoupling_RohlOP core::scoring::retrieve_RDC_ROHL_from_pose | ( | core::pose::Pose & | pose) |
Definition at line 62 of file ResidualDipolarCoupling_Rohl.cc.
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::RESIDUAL_DIPOLAR_COUPLING_DATA_ROHL.
|
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.
Definition at line 1226 of file rms_util.cc.
References core::pose::Pose::residue(), and core::pose::Pose::xyz().
Referenced by protocols::fldsgn::MatchResidues::compute_comb().
| 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.
Definition at line 1180 of file rms_util.cc.
References core::pose::Pose::total_residue().
Referenced by protocols::swa::StepWiseClusterer::check_for_closeness(), 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.
Definition at line 1195 of file rms_util.cc.
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 | ||
| ) |
Definition at line 1249 of file rms_util.cc.
References core::pose::Pose::total_residue().
Referenced by protocols::swa::StepWiseClusterer::check_for_closeness(), protocols::swa::protein::output_silent_struct(), and protocols::swa::PoseFilter_RMSD_Screen::passes_filter().
| Real core::scoring::rms_at_corresponding_atoms_no_super | ( | pose::Pose const & | mod_pose, |
| pose::Pose const & | ref_pose, | ||
| std::map< core::id::AtomID, core::id::AtomID > | atom_id_map, | ||
| utility::vector1< Size > const & | calc_rms_res | ||
| ) |
Definition at line 1261 of file rms_util.cc.
References core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::pose::Pose::xyz().
| Real core::scoring::rms_at_corresponding_heavy_atoms | ( | pose::Pose const & | mod_pose, |
| pose::Pose const & | ref_pose | ||
| ) |
Definition at line 1292 of file rms_util.cc.
References rms_at_corresponding_atoms(), and setup_matching_heavy_atoms().
Referenced by protocols::coarse_rna::CoarseRNA_DeNovoProtocol::apply(), protocols::swa::rna::Output_data(), protocols::swa::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file(), and protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::Update_pose_data_list().
| 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);
Definition at line 547 of file rms_util.tmpl.hh.
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().
| core::Real core::scoring::rmsd_no_super | ( | core::conformation::ResidueCOPs const & | residues1, |
| core::conformation::ResidueCOPs const & | residues2, | ||
| T * | predicate | ||
| ) |
Definition at line 581 of file rms_util.tmpl.hh.
References is_ligand_heavyatom_residues(), and core::pose::num_atoms().
| 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);
Definition at line 630 of file rms_util.tmpl.hh.
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::flexpep_docking::FlexPepDockingProtocol::addLowResStatistics(), 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::antibody::AntibodyModeler::global_loop_rmsd(), protocols::antibody2::global_loop_rmsd(), protocols::ub_e2c::ubi_e2c_modeler::monoub_calc_Lrmsd(), and protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().
| 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 | ||
| ) |
Definition at line 394 of file rms_util.tmpl.hh.
References is_heavyatom(), is_ligand_heavyatom(), is_polymer_heavyatom(), core::conformation::Residue::natoms(), core::pose::num_atoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().
Referenced by all_atom_rmsd(), protocols::ligand_docking::append_multi_residue_ligand_RMSD(), bb_rmsd(), bb_rmsd_including_O(), protocols::swa::StepWiseScreener::filter_and_output(), protocols::swa::protein::StepWiseProteinScreener::filter_and_output(), protocols::cluster::GatherPosesMover::get_distance_measure(), nbr_atom_rmsd(), protocols::features::ProteinRMSDFeatures::report_features(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), and rmsd_with_super().
| 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);
Definition at line 455 of file rms_util.tmpl.hh.
References rmsd_with_super(), and core::pose::Pose::total_residue().
| 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);
Definition at line 485 of file rms_util.tmpl.hh.
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
Definition at line 44 of file ScoreType.cc.
References core::scoring::ScoreTypeManager::score_type_from_name().
Referenced by protocols::relax::FastRelax::apply(), core::scoring::ScoreFunctionFactory::apply_user_defined_reweighting_(), protocols::relax::FastRelax::batch_apply(), protocols::enzdes::EnzdesScorefileFilter::compute_metrics_for_residue_subset(), core::pose::energy_from_pose(), protocols::enzdes::EnzdesScorefileFilter::examine_pose(), protocols::ddg::ddGMover::get_scorefunction_header(), protocols::jd2::parser::ScoreFunctionLoader::load_data(), protocols::simple_filters::ScoreTypeFilter::parse_def(), protocols::simple_filters::EnergyPerResidueFilter::parse_my_tag(), protocols::simple_filters::ResidueIEFilter::parse_my_tag(), protocols::simple_filters::ScoreTypeFilter::parse_my_tag(), protocols::simple_filters::ResidueSetChainEnergyFilter::parse_my_tag(), protocols::enzdes::EnzScoreFilter::parse_my_tag(), protocols::optimize_weights::OptEData::read_from_file(), protocols::simple_moves::symmetry::SymShakeStructureMover::reduce_fa_rep(), protocols::simple_moves::ShakeStructureMover::reduce_fa_rep(), protocols::simple_moves::symmetry::SymShakeStructureMover::setup_for_run(), protocols::simple_moves::ShakeStructureMover::setup_for_run(), and protocols::ddg::ddGMover::store_energies().
| 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 | ||
| ) |
Definition at line 1450 of file rms_util.cc.
References core::conformation::Residue::atom_index(), core::chemical::ResidueType::has_atom_name(), core::conformation::Residue::is_virtual(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().
Referenced by setup_matching_CA_atoms(), and setup_matching_protein_backbone_heavy_atoms().
| void core::scoring::setup_matching_CA_atoms | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | pose2, | ||
| std::map< core::id::AtomID, core::id::AtomID > & | atom_id_map | ||
| ) |
Definition at line 1427 of file rms_util.cc.
References setup_matching_atoms_with_given_names().
Referenced by protocols::swa::protein::output_silent_struct().
| void core::scoring::setup_matching_heavy_atoms | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | pose2, | ||
| std::map< core::id::AtomID, core::id::AtomID > & | atom_id_map | ||
| ) |
Definition at line 1303 of file rms_util.cc.
References core::conformation::Residue::atom_index(), core::conformation::Residue::atom_name(), core::conformation::Residue::has(), core::conformation::Residue::is_virtual(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::sequence(), and core::pose::Pose::total_residue().
Referenced by protocols::swa::PoseFilter_RMSD_Screen::initialize_corresponding_atom_id_map(), protocols::swa::StepWiseClusterer::initialize_corresponding_atom_id_map(), protocols::swa::protein::output_silent_struct(), and rms_at_corresponding_heavy_atoms().
| void core::scoring::setup_matching_protein_backbone_heavy_atoms | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | pose2, | ||
| std::map< core::id::AtomID, core::id::AtomID > & | atom_id_map | ||
| ) |
Definition at line 1437 of file rms_util.cc.
References setup_matching_atoms_with_given_names().
Referenced by protocols::swa::PoseFilter_RMSD_Screen::initialize_corresponding_atom_id_map(), protocols::swa::StepWiseClusterer::initialize_corresponding_atom_id_map(), and protocols::swa::protein::output_silent_struct().
| void core::scoring::show_detail | ( | std::ostream & | out, |
| EnergyMap & | energies, | ||
| EnergyMap | weights | ||
| ) |
Definition at line 518 of file ScoreFunction.cc.
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" | ) |
Definition at line 70 of file ResidualDipolarCoupling.cc.
Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDa(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDaR(), and core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsR().
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| std::string const core::scoring::STANDARD_WTS | ( | "standard" | ) |
| void core::scoring::store_CSA_in_pose | ( | ChemicalShiftAnisotropyOP | csa_info, |
| core::pose::Pose & | pose | ||
| ) |
Definition at line 70 of file ChemicalShiftAnisotropy.cc.
References core::pose::datacache::CacheableDataType::CHEMICAL_SHIFT_ANISOTROPY_DATA, and core::pose::Pose::data().
Referenced by core::scoring::methods::ChemicalShiftAnisotropyEnergy::csa_from_pose().
| void core::scoring::store_DC_in_pose | ( | DipolarCouplingOP | dc_info, |
| core::pose::Pose & | pose | ||
| ) |
Definition at line 71 of file DipolarCoupling.cc.
References core::pose::datacache::CacheableDataType::CHEMICAL_SHIFT_ANISOTROPY_DATA, and core::pose::Pose::data().
Referenced by core::scoring::methods::DipolarCouplingEnergy::dc_from_pose().
| void core::scoring::store_RDC_in_pose | ( | ResidualDipolarCouplingOP | rdc_info, |
| core::pose::Pose & | pose | ||
| ) |
Definition at line 76 of file ResidualDipolarCoupling.cc.
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::RESIDUAL_DIPOLAR_COUPLING_DATA.
Referenced by core::scoring::methods::ResidualDipolarCouplingEnergy::rdc_from_pose(), protocols::frag_picker::scores::RDCScore::score(), and protocols::abinitio::IterativeBase::score().
| void core::scoring::store_RDC_ROHL_in_pose | ( | ResidualDipolarCoupling_RohlOP | rdc_info, |
| core::pose::Pose & | pose | ||
| ) |
Definition at line 49 of file ResidualDipolarCoupling_Rohl.cc.
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::RESIDUAL_DIPOLAR_COUPLING_DATA_ROHL.
Referenced by core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl::rdc_from_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.
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 );
Definition at line 990 of file rms_util.cc.
Referenced by protocols::loops::addScoresForLoopParts(), protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::align_all_pose(), protocols::rna::RNA_DeNovoProtocol::align_and_output_to_silent_file(), protocols::swa::StepWisePoseSetup::align_pose(), protocols::swa::StepWisePoseSetup::align_poses(), protocols::swa::rna::align_poses(), protocols::rna::RNA_ChunkLibrary::align_to_chunk(), protocols::antibody::Antibody::align_to_native(), protocols::antibody2::align_to_native(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::align_VDW_rep_screen_pose(), protocols::antibody2::GraftOneCDRLoop::apply(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::comparative_modeling::LoopRelaxMover::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::simple_moves::SuperimposeMover::superimpose(), protocols::fldsgn::MatchResidues::superimpose_comb(), protocols::grafting::GraftMoverBase::superimpose_overhangs_heavy(), protocols::fibril::superimpose_pose_on_subset_bb(), protocols::toolbox::pose_manipulation::superimpose_pose_on_subset_CA(), protocols::hybridization::FoldTreeHybridize::superimpose_strand_pairings_to_templates(), and protocols::docking::ConformerSwitchMover::switch_conformer().
| Real core::scoring::superimpose_pose | ( | pose::Pose & | mod_pose, |
| pose::MiniPose 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.
Definition at line 1001 of file rms_util.cc.
References core::conformation::Residue::natoms(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), rms, core::pose::Pose::set_xyz(), core::pose::Pose::total_residue(), core::pose::MiniPose::xyz(), and core::conformation::Residue::xyz().
| core::Real core::scoring::sym_rmsd_with_super_subset | ( | core::pose::Pose const & | native_pose, |
| core::pose::Pose const & | pose2, | ||
| ObjexxFCL::FArray1D_bool const & | subset, | ||
| T * | predicate | ||
| ) |
Select a subset atoms for Symmetric RMS via a predicate function/functor. Example of use, to calculate C-alpha RMSD: rmsd_with_super(pose1, pose2, is_protein_CA, subset);.
Definition at line 793 of file rms_util.tmpl.hh.
References core::pose::Pose::conformation(), create_shuffle_map_recursive_rms(), is_heavyatom(), is_ligand_heavyatom(), is_polymer_heavyatom(), protocols::forge::build::SegmentInsertConnectionScheme::N, core::conformation::Residue::natoms(), core::pose::num_atoms(), core::pose::Pose::residue(), rms, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().
Referenced by protocols::protein_interface_design::filters::RmsdFilter::compute().
| basic::Tracer core::scoring::T | ( | "core.scoring.Ramachandran2B" | ) |
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Referenced by core::scoring::ScoreFunctionFactory::apply_user_defined_reweighting_(), core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking(), core::scoring::ChemicalShiftAnisotropy::compute_csascore(), core::scoring::DipolarCoupling::compute_dcscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDa(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDaR(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsR(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::rna::RNA_TorsionPotential::get_f1_f2(), core::scoring::ResidualDipolarCoupling::iterate_tensor_weights(), core::scoring::DockingScoreFunction::operator()(), core::scoring::MinScoreScoreFunction::operator()(), core::scoring::rna::RNA_TorsionPotential::print_torsion_info(), core::scoring::ChemicalShiftAnisotropy::read_CSA_file(), core::scoring::DipolarCoupling::read_DC_file(), core::scoring::ResidualDipolarCoupling_Rohl::read_RDC_file(), core::scoring::ResidualDipolarCoupling::read_RDC_file(), core::scoring::ResidualDipolarCoupling::reserve_buffers(), core::scoring::rna::RNA_Mg_Energy::residue_pair_energy_one_way(), core::scoring::rna::rna_residue_name_to_num(), core::scoring::rna::RNA_AtomVDW::vdw_atom_list(), and core::scoring::NeighborList::~NeighborList().
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Referenced by core::scoring::sc::MolecularSurfaceCalculator::add_atom(), protocols::protein_interface_design::movers::add_coordinate_constraints(), core::scoring::geometric_solvation::add_to_individual_sol_energies(), core::scoring::APBSWrapper::APBSWrapper(), protocols::simple_moves::MembraneTopology::apply(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::apply(), core::scoring::sc::ShapeComplementarityCalculator::AssignAttentionNumbers(), core::scoring::sc::ShapeComplementarityCalculator::Calc(), core::scoring::sc::MolecularSurfaceCalculator::Calc(), core::scoring::sc::ShapeComplementarityCalculator::CalcNeighborDistance(), 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::geometric_solvation::ExactOccludedHbondSolEnergy::ExactOccludedHbondSolEnergy(), core::scoring::FACTSPotential::FACTSPotential(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::final_cleanup(), protocols::protein_interface_design::movers::generate_taskfactory_and_add_task_awareness(), core::scoring::sc::MolecularSurfaceCalculator::GenerateMolecularSurfaces(), 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::rna::chemical_shift::RNA_ChemicalShiftPotential::import_exp_chemical_shift_data(), core::scoring::MembraneTopology::initialize(), core::scoring::etable::MembEtable::input_etable(), core::scoring::etable::Etable::input_etable(), core::scoring::PoissonBoltzmannPotential::load_APBS_potential(), core::scoring::etable::MembEtable::make_pairenergy_table(), core::scoring::etable::Etable::make_pairenergy_table(), core::scoring::etable::MembEtable::MembEtable(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_no_bb(), core::scoring::etable::MembEtable::modify_pot(), core::scoring::etable::Etable::modify_pot_one_pair(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), protocols::simple_moves::MembraneTopology::parse_my_tag(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::parse_my_tag(), protocols::protein_interface_design::movers::parse_stub_sets(), core::scoring::MembraneTopology::print(), protocols::print_ddgs(), core::scoring::etable::Etable::read_alternate_parameter_set(), protocols::read_in_mutations(), core::scoring::sc::MolecularSurfaceCalculator::ReadScRadii(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::refresh_coordinate_constraints(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::RNA_ChemicalShiftPotential(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::setup_for_derivatives(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::setup_for_minimizing(), core::scoring::etable::MembEtable::smooth_etables(), core::scoring::etable::Etable::smooth_etables_one_pair(), core::scoring::PoissonBoltzmannPotential::solve_pb(), core::scoring::geometric_solvation::WaterWeightGridSet::WaterWeightGridSet(), core::scoring::PoissonBoltzmannPotential::write_config(), and core::scoring::PoissonBoltzmannPotential::write_pqr().
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| std::string const core::scoring::UNFOLDED_MM_STD | ( | "UNFOLDED_MM_STD" | ) |
| std::string const core::scoring::UNFOLDED_RNA | ( | "UNFOLDED_RNA" | ) |
| std::string const core::scoring::UNFOLDED_SCORE12 | ( | "UNFOLDED_SCORE12" | ) |
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private – handles setting the derived data
Definition at line 2784 of file ScoreFunction.cc.
References core::scoring::hbonds::t().
Referenced by core::scoring::ScoreFunction::remove_method().
| core::Real core::scoring::xyz_gdtmm | ( | FArray2D< core::Real > | p1a, |
| FArray2D< core::Real > | p2a | ||
| ) |
Calculate gdtmm based on the given sets of xyz coordinates in p1a and p2a.
Definition at line 894 of file rms_util.cc.
Referenced by protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), protocols::comparative_modeling::Align_RmsdEvaluator::apply(), CA_gdtmm(), and protocols::hybridization::get_gdtmm().
| 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.
Definition at line 904 of file rms_util.cc.
References core::chemical::tr().
| int core::scoring::xyz_maxsub | ( | FArray2D< core::Real > | p1a, |
| FArray2D< core::Real > | p2a, | ||
| int | natoms | ||
| ) |
Definition at line 816 of file rms_util.cc.
Referenced by protocols::comparative_modeling::Align_RmsdEvaluator::apply().
| short const core::scoring::bit_count[] |
Definition at line 70 of file sasa.cc.
Referenced by core::scoring::packstat::compute_cav_ball_volumes(), core::scoring::packstat::compute_sasa(), core::scoring::packstat::prune_1pass(), and core::scoring::packstat::prune_hidden_cavity_balls().
| std::string const core::scoring::CENTROID_WTS |
Referenced by protocols::docking::DockingSlideIntoContact::DockingSlideIntoContact(), getScoreFunction(), getScoreFunctionName(), protocols::flexpep_docking::FlexPepDockingProtocol::set_default(), protocols::simple_moves::symmetry::SymmetrySlider::setup(), protocols::surface_docking::SlideIntoSurface::SlideIntoSurface(), protocols::simple_moves::symmetry::SymDockingSlideIntoContact::SymDockingSlideIntoContact(), and protocols::simple_moves::symmetry::SymmetrySlider::SymmetrySlider().
| std::string const core::scoring::DNA_INT_WTS |
| std::string const core::scoring::DNA_INT_WTS_GB |
| std::string const core::scoring::DOCK_LOW_PATCH |
Referenced by protocols::docking::DockingSlideIntoContact::DockingSlideIntoContact(), protocols::simple_moves::symmetry::SymmetrySlider::setup(), protocols::surface_docking::SlideIntoSurface::SlideIntoSurface(), protocols::simple_moves::symmetry::SymDockingSlideIntoContact::SymDockingSlideIntoContact(), and protocols::simple_moves::symmetry::SymmetrySlider::SymmetrySlider().
| std::string const core::scoring::DOCK_PATCH |
| std::string const core::scoring::FA_STANDARD_DEFAULT |
| std::string const core::scoring::FA_STANDARD_SOFT |
| int const core::scoring::maskbits = 162 |
Definition at line 87 of file sasa.cc.
Referenced by core::scoring::packstat::compute_cav_ball_volumes(), core::scoring::packstat::compute_sasa(), and core::scoring::packstat::prune_hidden_cavity_balls().
| std::string const core::scoring::MEMB_HIGHRES_WTS |
| std::string const core::scoring::MM_STD_WTS |
| int const core::scoring::num_bytes = 21 |
Definition at line 82 of file sasa.cc.
Referenced by calc_atom_masks(), calc_per_atom_sasa(), get_num_bytes(), and input_sasa_dats().
| int const core::scoring::num_orientations = 162 |
Definition at line 86 of file sasa.cc.
Referenced by input_sasa_dats().
| int const core::scoring::num_overlaps = 100 |
Definition at line 85 of file sasa.cc.
Referenced by input_sasa_dats().
| int const core::scoring::num_phi = 64 |
Definition at line 83 of file sasa.cc.
Referenced by get_2way_orientation(), get_orientation(), and input_sasa_dats().
| int const core::scoring::num_theta = 64 |
Definition at line 84 of file sasa.cc.
Referenced by get_2way_orientation(), get_orientation(), and input_sasa_dats().
| std::string const core::scoring::RNA_HIRES_WTS |
Referenced by protocols::rna::RNA_Relaxer::apply(), and protocols::rna::RNA_Minimizer::RNA_Minimizer().
| std::string const core::scoring::RNA_LORES_PLUS_HIRES_WTS |
| std::string const core::scoring::RNA_LORES_WTS |
| std::string const core::scoring::SCORE12_PATCH |
Referenced by protocols::protein_interface_design::movers::BuildAlaPose::apply(), protocols::protein_interface_design::movers::InterfaceRecapitulationMover::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::protein_interface_design::movers::BestHotspotCstMover::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::forge::remodel::RemodelAccumulator::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::fldsgn::potentials::SetSecStructEnergies::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::jumping::ResiduePairJump::build_sidechain_rotamers(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::forge::components::BDR::centroid_build(), protocols::forge::remodel::RemodelMover::centroid_build(), protocols::optimize_weights::IterativeOptEDriver::collect_decoy_discrimination_data(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::compute(), protocols::simple_filters::ResiduesInInterfaceFilter::compute(), protocols::protein_interface_design::filters::HbondsToResidueFilter::compute(), protocols::fldsgn::filters::CoreDunbrackFilter::compute(), protocols::protein_interface_design::movers::MapHotspot::create_rotamer_set(), core::scoring::ScoreFunctionFactory::create_score_function(), protocols::forge::components::BDR::design_refine(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::forge::remodel::RemodelMover::design_refine_seq_relax(), protocols::protein_interface_design::find_lowest_constraint_energy_residue(), protocols::jd2::DockDesignParser::generate_mover_from_pose(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), getScoreFunctionName(), hbonded(), 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(), and protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize().
| std::string const core::scoring::SCORE13 |
| std::string const core::scoring::SOFT_REP_DESIGN_WTS |
| std::string const core::scoring::SOFT_REP_WTS |
| std::string const core::scoring::STANDARD_WTS |
Referenced by protocols::protein_interface_design::movers::BuildAlaPose::apply(), protocols::protein_interface_design::movers::InterfaceRecapitulationMover::apply(), protocols::simple_moves::SetReturningPackRotamersMover::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::protein_interface_design::movers::BestHotspotCstMover::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::simple_moves::MinPackMover::apply(), protocols::forge::remodel::RemodelAccumulator::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::antibody::GraftMover::apply(), protocols::fldsgn::potentials::SetSecStructEnergies::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::jumping::ResiduePairJump::build_sidechain_rotamers(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::forge::components::BDR::centroid_build(), protocols::forge::remodel::RemodelMover::centroid_build(), protocols::optimize_weights::IterativeOptEDriver::collect_decoy_discrimination_data(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::compute(), protocols::simple_filters::ResiduesInInterfaceFilter::compute(), protocols::protein_interface_design::filters::HbondsToResidueFilter::compute(), protocols::fldsgn::filters::CoreDunbrackFilter::compute(), protocols::protein_interface_design::movers::MapHotspot::create_rotamer_set(), core::scoring::ScoreFunctionFactory::create_score_function(), protocols::forge::components::BDR::design_refine(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::forge::remodel::RemodelMover::design_refine_seq_relax(), protocols::protein_interface_design::find_lowest_constraint_energy_residue(), protocols::jd2::DockDesignParser::generate_mover_from_pose(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), getScoreFunctionName(), hbonded(), 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::symmetry::SymPackRotamersMover::setup(), protocols::simple_moves::PackRotamersMover::setup(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), and protocols::symmetric_docking::SymDockBaseProtocol::SymDockBaseProtocol().
| std::string const core::scoring::UNFOLDED_MM_STD |
Referenced by core::scoring::ScoringManager::get_UnfoldedStatePotential().
| std::string const core::scoring::UNFOLDED_RNA |
Referenced by core::scoring::ScoringManager::get_UnfoldedStatePotential().
| std::string const core::scoring::UNFOLDED_SCORE12 |
Referenced by protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), protocols::optimize_weights::IterativeOptEDriver::configure_new_scorefunction(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), core::scoring::ScoringManager::get_UnfoldedStatePotential(), and protocols::optimize_weights::IterativeOptEDriver::output_weighted_unfolded_energies().
1.8.4