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Rosetta
2020.11
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All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
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Rosetta
2020.11
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#include <ScoringManager.hh>
Public Member Functions | |
| void | factory_register (methods::EnergyMethodCreatorOP creator) |
| The ScoringManager acts as an EnergyMethodFactory. All EnergyMethods must create a helper class, an EnergyMethodCreator class, that will respond to a call to its create_energy_method by returning a new instance of that EnergyMethod its helping. This Creator class must also register itself with the ScoringManager at load time and hand an instance of itself to the singleton ScoringManager instance. More... | |
| PairEPotential const & | get_PairEPotential () const |
| Get a const instance of the PairEPotential. More... | |
| GenBornPotential const & | get_GenBornPotential () const |
| Get a const instance of the GenBornPotential. More... | |
| HydroxylTorsionPotential const & | get_HydroxylTorsionPotential () const |
| Get a const instance of the HydroxylTorsionPotential. More... | |
| VdWTinkerPotential const & | get_VdWTinkerPotential () const |
| Get an instance of the VdWTinkerPotential scoring object. More... | |
| MultipoleElecPotential const & | get_MultipoleElecPotential (methods::EnergyMethodOptions const &options) const |
| Get an instance of the MultipoleElecPotential scoring object. More... | |
| SASAPotential const & | get_SASAPotential () const |
| Get an instance of the SASAPotential scoring object. More... | |
| FACTSPotential const & | get_FACTSPotential () const |
| Get an instance of the FACTSPotential scoring object, by const owning pointer. More... | |
| GenericBondedPotential const & | get_GenericBondedPotential () const |
| Get an instance of the GenericBondedPotential scoring object, by const owning pointer. More... | |
| dna::DNA_BasePotential const & | get_DNA_BasePotential () const |
| Get an instance of the DNA_BasePotential scoring object, by const owning pointer. More... | |
| RamachandranCOP | get_Ramachandran_ptr () const |
| Get an instance of the Ramachandran scoring object, by const owning pointer. More... | |
| Ramachandran const & | get_Ramachandran () const |
| Get a const instance of the Ramachandran scoring object. More... | |
| Ramachandran2BCOP | get_Ramachandran2B_ptr () const |
| Get an instance of the Ramachandran2B scoring object, by const owning pointer. More... | |
| Ramachandran2B const & | get_Ramachandran2B () const |
| Get an instance of the Ramachandran2B scoring object, by const instance. More... | |
| RamaPrePro const & | get_RamaPrePro () const |
| Get an instance of the RamaPrePro scoring object. More... | |
| P_AA_ABEGO3 const & | get_P_AA_ABEGO3 () const |
| Get an instance of the P_AA_ABEGO3 scoring object. More... | |
| dna::DNABFormPotential const & | get_DNABFormPotential () const |
| Get an instance of the DNABFormPotential scoring object. More... | |
| dna::DNATorsionPotential const & | get_DNATorsionPotential () const |
| Get an instance of the DNATorsionPotential scoring object. More... | |
| OmegaTether const & | get_OmegaTether () const |
| Get an instance of the OmegaTether scoring object. More... | |
| SmoothEnvPairPotential const & | get_SmoothEnvPairPotential () const |
| Get an instance of the SmoothEnvPairPotential scoring object. More... | |
| CenRotEnvPairPotential const & | get_CenRotEnvPairPotential () const |
| Get an instance of the CenRotEnvPairPotential scoring object. More... | |
| CenHBPotential const & | get_CenHBPotential () const |
| Get an instance of the CenHBPotential scoring object. More... | |
| EnvPairPotential const & | get_EnvPairPotential () const |
| Get an instance of the EnvPairPotential scoring object. More... | |
| dna::DNA_EnvPairPotential const & | get_DNA_EnvPairPotential () const |
| Get an instance of the DNA_EnvPairPotential scoring object. More... | |
| dna::DNA_DihedralPotential const & | get_DNA_DihedralPotential () const |
| Get an instance of the DNA_DihedralPotential scoring object. More... | |
| SecondaryStructurePotential const & | get_SecondaryStructurePotential () const |
| Get an instance of the SecondaryStructurePotential scoring object. More... | |
| AtomVDW const & | get_AtomVDW (std::string const &atom_type_set_name) const |
| Get an instance of the AtomVDW scoring object. More... | |
| rna::RNA_AtomVDW const & | get_RNA_AtomVDW () const |
| Get an instance of the RNA_AtomVDW scoring object. More... | |
| geometric_solvation::DatabaseOccSolEne const & | get_DatabaseOccSolEne (std::string const &atom_type_set_name, Real const &min_occ_energy) const |
| Get an instance of the DatabaseOccSolEne scoring object. More... | |
| carbon_hbonds::CarbonHBondPotential const & | get_CarbonHBondPotential () const |
| Get an instance of the CarbonHBondPotential scoring object. More... | |
| rna::RNA_SuitePotentialCOP | get_rna_suite_potential (bool const &calculate_suiteness_bonus, std::string const &suiteness_bonus) const |
| Get an instance of the RNA_SuitePotentialCOP scoring object, by const owning pointer. More... | |
| rna::TNA_SuitePotential const & | get_tna_suite_potential () const |
| Get an instance of the TNA_SuitePotentialCOP scoring object, by const owning pointer. More... | |
| loop_graph::evaluator::SixDTransRotPotentialCOP | get_LoopCloseSixDPotential (std::string const &database_file) const |
| Get an instance of the SixDTransRotPotential scoring object, by const owning pointer. More... | |
| rna::RNA_LowResolutionPotentialCOP | get_RNA_LowResolutionPotential (std::string const &database_file) const |
| Get an instance of the RNA_LowResolutionPotential scoring object. More... | |
| rna::RNP_LowResPotential const & | get_RNP_LowResPotential () const |
| Get an instance of the RNP_LowResPotential scoring object. More... | |
| rna::RNP_LowResPairDistPotential const & | get_RNP_LowResPairDistPotential () const |
| Get an instance of the RNP_LowResPairDistPotential scoring object. More... | |
| rna::RNP_LowResStackData const & | get_RNP_LowResStackData () const |
| Get an instance of the RNP_LowResStackData scoring object. More... | |
| rna::chemical_shift::RNA_ChemicalShiftPotential const & | get_RNA_ChemicalShiftPotential () const |
| Get an instance of the RNA_ChemicalShiftPotential scoring object. More... | |
| rna::data::RNA_DMS_Potential & | get_RNA_DMS_Potential () const |
| Get an instance of the RNA_DMS_Potential scoring object. More... | |
| rna::data::RNA_DMS_LowResolutionPotential & | get_RNA_DMS_LowResolutionPotential () const |
| Get an instance of the RNA_DMS_LowResolutionPotential scoring object. More... | |
| dna::DirectReadoutPotential const & | get_DirectReadoutPotential () const |
| Get an instance of the DirectReadoutPotential scoring object. More... | |
| mm::MMLJLibrary const & | get_MMLJLibrary () const |
| Get an instance of the MMLJLibrary scoring object. More... | |
| mm::MMLJEnergyTable const & | get_MMLJEnergyTable () const |
| Get an instance of the MMLJEnergyTable scoring object. More... | |
| mm::MMTorsionLibrary const & | get_MMTorsionLibrary () const |
| Get an instance of the MMTorsionLibrary scoring object. More... | |
| mm::MMBondAngleLibrary const & | get_MMBondAngleLibrary () const |
| Get an instance of the MMBondAngleLibrary scoring object. More... | |
| mm::MMBondLengthLibrary const & | get_MMBondLengthLibrary () const |
| Get an instance of the MMBondLengthLibrary scoring object. More... | |
| nv::NVlookup const & | get_NVLookupTable () const |
| Get an instance of the NVlookup scoring object. More... | |
| core::scoring::orbitals::OrbitalsLookup const & | get_OrbitalsLookupTable () const |
| Get an instance of the OrbitalsLookup scoring object. More... | |
| interface_::DDPlookup const & | get_DDPLookupTable () const |
| Get an instance of the DDPlookup scoring object. More... | |
| std::string const & | get_nmer_svm_list_file_contents (std::string const &filename) const |
| Get a string listing SVM files. More... | |
| utility::libsvm::Svm_rosettaCOP | get_nmer_svm (std::string const &filename) const |
| Get a const reference to an SVM object. More... | |
| std::string const & | get_nmer_svm_rank_list_file_contents (std::string const &filename) const |
| Get a string listing SVM rank files. More... | |
| utility::vector1< core::Real > const & | get_nmer_svm_rank (std::string const &filename) const |
| Get a const reference to a vector of floats corresponding to ranked SVM information. More... | |
| std::map< core::chemical::AA, utility::vector1< core::Real > > const & | get_nmer_pssm (std::string const &filename, core::Size nmer_length) const |
| Get a const reference to an NMerPSSM. More... | |
| std::map< char, utility::vector1< core::Real > > const & | get_nmer_svm_aa_matrix (std::string const &filename) const |
| Get the map of AA oneletter code->vector of floats used by the NMerSVMEnergy. More... | |
| P_AA const & | get_P_AA () const |
| Get an instance of the P_AA scoring object. More... | |
| P_AA_ss const & | get_P_AA_ss () const |
| Get an instance of the P_AA_ss scoring object. More... | |
| UnfoldedStatePotential const & | get_UnfoldedStatePotential (std::string const &type) const |
| Get an instance of the UnfoldedStatePotential scoring object. More... | |
| WaterAdductHBondPotential const & | get_WaterAdductHBondPotential () const |
| Get an instance of the WaterAdductHBondPotential scoring object. More... | |
| MembranePotential const & | get_MembranePotential () const |
| Get an instance of the MembranePotential scoring object. More... | |
| membrane::MembraneData const & | get_MembraneData () const |
| Get an instance of the MembraneData scoring object. More... | |
| Membrane_FAPotential const & | get_Membrane_FAPotential () const |
| Get an instance of the Membrane_FAPotential scoring object. More... | |
| ProQPotential const & | get_ProQPotential () const |
| Get an instance of the ProQPotential scoring object. More... | |
| PointWaterPotential const & | get_PointWaterPotential () const |
| Get an instance of PointWaterPotential scoring object. More... | |
| PoissonBoltzmannPotential const & | get_PoissonBoltzmannPotential () const |
| Get an instance of the PoissonBoltzmannPotential scoring object. More... | |
| SplitUnfoldedTwoBodyPotential const & | get_SplitUnfoldedTwoBodyPotential (std::string const &label_type, std::string const &value_type, std::string const &score_func_type) const |
| Get an instance of the SplitUnfoldedTwoBodyPotential scoring object. More... | |
| disulfides::FullatomDisulfidePotential const & | get_FullatomDisulfidePotential () const |
| Get an instance of the FullatomDisulfidePotential scoring object. More... | |
| disulfides::CentroidDisulfidePotential const & | get_CentroidDisulfidePotential () const |
| Get an instance of the CentroidDisulfidePotential scoring object. More... | |
| disulfides::DisulfideMatchingPotential const & | get_DisulfideMatchingPotential () const |
| Get an instance of the DisulfideMatchingPotential scoring object. More... | |
| carbohydrates::CHIEnergyFunction const & | get_CHIEnergyFunction () const |
| Get an instance of the CHIEnergyFunction scoring object. More... | |
| carbohydrates::OmegaPreferencesFunction const & | get_OmegaPreferencesFunction () const |
| Get an instance of the OmegaPreferencesFunction scoring object. More... | |
| bool | has_energy_method (ScoreType t) const |
| Test if there is an EnergyMethod class defined for a given score type. More... | |
| methods::EnergyMethodOP | energy_method (ScoreType const &t, methods::EnergyMethodOptions const &options) const |
| When a ScoreFunction the weight for a particular ScoreType set from 0 to some non-zero value, it will request an instance of the EnergyMethod class that is responsible for calculating that ScoreType. The ScoringManager responds to that request by asking the EnergyMethodCreator that has claimed responsibility for this ScoreType for a new instance. EnergyMethodCreators must first have registered themselves with the ScoringManager. This should have been done at load time, using a static-variable-initialization function call. See src/core/scoring/etable/EtableEnergy.cc for an example of how the EtableEnergyCreator class registers itself with the ScoringManager. More... | |
| etable::EtableOP | make_partially_soft_etable (std::string const &name, etable::EtableOptions etable_options) const |
| make etable for extra partially softies More... | |
| void | add_memb_etable (std::string const &name, etable::MembEtableOP etable) |
| Add a new membrane energy table to the membrane energy tables map. More... | |
| etable::MembEtableCAP | memb_etable (std::string const &table_id) const |
| Get a membrane energy table from the membrane energy tables map. More... | |
| etable::EtableCAP | etable (methods::EnergyMethodOptions const &options_in) const |
| Request an etable specifying an EnergyMethodOptions object; internally this will retrieve the EtableOptions object, and invoke the EtableOptions version of this function. More... | |
| etable::EtableCAP | etable (etable::EtableOptions const &options_in) const |
| Request an etable specifying an EtableOptions; internally this will query the ScoringManager's map from EtableOptions to Etables for the desired Etable, and construct a new one if needed. More... | |
| etable::EtableCAP | etable (std::string const &etable_id) const |
| Create and return an etable specified only by the etable_type of the etable::EtableOptions class. This, internally, will create an EtableOptions object, initialized from the command line, set the etable_type of this object, and then invoke the etable( EtableOptions ) method. More... | |
| core::scoring::elec::CPRepMapTypeCOP | get_cp_rep_map_byname () const |
| Get an owning pointer to data used by the FA_ElecEnergy in beta_nov15 mode. More... | |
| utility::vector1 < core::scoring::aa_composition_energy::AACompositionEnergySetupOP > | get_cloned_aa_comp_setup_helpers (core::scoring::methods::EnergyMethodOptions const &options) const |
| Get a vector of owning pointers to data used by the AACompositionEnergy score term. More... | |
| utility::vector1 < core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupOP > | get_cloned_mhc_epitope_setup_helpers (core::scoring::methods::EnergyMethodOptions const &options) const |
| Get a vector of owning pointers to data used by the MHCEpitopeEnergy score term. More... | |
| std::list< std::string > const & | get_mhc_matrix_contents (std::string const &filename) const |
| Get a const reference to a std::list containing the contents of a MHCEpitopePredictorMatrix matrix file. More... | |
| std::pair< std::map < std::string, core::Real > , core::Size > const & | get_mhc_map_from_db (std::string const &filename) const |
| Get a const reference to a std::pair containing the a map corresponding a sqlite MHC db and the peptide length. More... | |
| std::list< std::string > const & | get_mhc_csv_contents (std::string const &filename) const |
| Get a const reference to a std::list containing the contents of a MHCEpitopePredictorPreLoaded csv database file. More... | |
| utility::vector1 < core::scoring::netcharge_energy::NetChargeEnergySetupOP > | get_cloned_netcharge_setup_helpers (core::scoring::methods::EnergyMethodOptions const &options) const |
| Get a vector of owning pointers to data used by the NetChargeEnergy score term. More... | |
| core::chemical::mainchain_potential::MainchainScoreTableCOP | get_rama_prepro_mainchain_torsion_potential (core::chemical::ResidueTypeCOP restype, bool const use_polycubic_interpolation, bool const prepro_table) const |
| Get a particular MainchainScoreTable for the rama_prepro score term, for a particular residue type. More... | |
Static Public Member Functions | |
| static core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupOP | create_mhc_epitope_energy_setup_instance (std::string const &filename) |
| Create an instance of an MHCEpitopeEnergySetup object, by owning pointer. More... | |
Private Member Functions | |
| ScoringManager () | |
| ~ScoringManager () | |
Static Private Member Functions | |
| static PairEPotentialOP | create_pairE_potential_instance () |
| Create an instance of the PairEPotential object, by owning pointer. More... | |
| static GenBornPotentialOP | create_genborn_instance () |
| Create an instance of the GenBornPotential object, by owning pointer. More... | |
| static VdWTinkerPotentialOP | create_vdw_tinker_potential_instance () |
| Create an instance of the VdWTinkerPotential object, by owning pointer. More... | |
| static MultipoleElecPotentialOP | create_multipole_elec_instance (methods::EnergyMethodOptions const &options) |
| Create an instance of the HydroxylTorsionPotential object, by owning pointer. More... | |
| static SASAPotentialOP | create_sasa_potential_instance () |
| Create an instance of the SASAPotential object, by owning pointer. More... | |
| static HydroxylTorsionPotentialOP | create_hxl_potential_instance () |
| Create an instance of the HydroxylTorsionPotential object, by owning pointer. More... | |
| static FACTSPotentialOP | create_facts_potential_instance () |
| Create an instance of the FactsPotential object, by owning pointer. More... | |
| static GenericBondedPotentialOP | create_generic_bonded_potential_instance () |
| Create an instance of the GenericBondedPotential object, by owning pointer. More... | |
| static dna::DNA_BasePotentialOP | create_dnabase_potential_instance () |
| Create an instance of the FactsPotential object, by owning pointer. More... | |
| static RamachandranOP | create_rama_instance () |
| Create an instance of the Ramachandran object, by owning pointer. More... | |
| static Ramachandran2BOP | create_rama2b_instance () |
| Create an instance of the Ramachandran2B object, by owning pointer. More... | |
| static RamaPreProOP | create_ramapp_instance () |
| Create an instance of the RamaPrePro object, by owning pointer. More... | |
| static P_AA_ABEGO3_OP | create_p_aa_abego3_instance () |
| Create an instance of the P_AA_ABEGO3 object, by owning pointer. More... | |
| static utility::pointer::shared_ptr < std::string > | create_file_contents_instance (std::string const &filename) |
| Create an instance of the contents of a file. More... | |
| static utility::libsvm::Svm_rosettaOP | create_svm_rosetta (std::string const &filename) |
| Create an instance of an SVM, reading data from disk. More... | |
| static utility::pointer::shared_ptr < utility::vector1< core::Real > > | create_nmer_svm_rank (std::string const &filename) |
| Create an instance of an SVM rank cector, by reading data from disk. More... | |
| static utility::pointer::shared_ptr < std::map< core::chemical::AA, utility::vector1< core::Real > > > | create_nmer_pssm (std::string const &filename, core::Size nmer_length) |
| Create an instance of an NMerPSSM object, by reading data from disk. More... | |
| static utility::pointer::shared_ptr < std::map< char, utility::vector1< core::Real > > > | create_nmer_svm_aa_matrix (std::string const &filename) |
| static utility::pointer::shared_ptr < std::list< std::string > > | create_mhc_matrix_contents (std::string const &filename) |
| Create an instance of the file contents of a MHCEpitopePredictorMatrix matrix, by reading data from disk. More... | |
| static utility::pointer::shared_ptr < std::pair< std::map < std::string, core::Real > , core::Size > > | create_mhc_map_from_db (std::string const &filename) |
| Load the sqlite database from disk. Store peptides/scores as std::map, and length as core::Size. Return as a std::pair. More... | |
| static utility::pointer::shared_ptr < std::list< std::string > > | create_mhc_csv_contents (std::string const &filename) |
| Load the csv database file contents from disk and store as a std::list. More... | |
| static P_AAOP | create_p_aa_instance () |
| Create an instance of the P_AA object, by owning pointer. More... | |
| static P_AA_ssOP | create_p_aa_ss_instance () |
| Create an instance of the P_AA_ss object, by owning pointer. More... | |
| static dna::DNABFormPotentialOP | create_dna_bform_potential_instance () |
| Create an instance of the DNABFormPotential object, by owning pointer. More... | |
| static dna::DNATorsionPotentialOP | create_dna_torsion_potential_instance () |
| Create an instance of the DNATorsionPotential object, by owning pointer. More... | |
| static OmegaTetherOP | create_omegatether_instance () |
| Create an instance of the OmegaTether object, by owning pointer. More... | |
| static SmoothEnvPairPotentialOP | create_smoothenvpair_instance () |
| Create an instance of the SmoothEnvPairPotential object, by owning pointer. More... | |
| static CenRotEnvPairPotentialOP | create_cenrotenvpair_instance () |
| Create an instance of the CenRotEnvPairPotential object, by owning pointer. More... | |
| static CenHBPotentialOP | create_cenhbpotential_instance () |
| Create an instance of the CenHBPotential object, by owning pointer. More... | |
| static EnvPairPotentialOP | create_envpairpotential_instance () |
| Create an instance of the EnvPairPotential object, by owning pointer. More... | |
| static dna::DNA_EnvPairPotentialOP | create_dna_envpairpotential_instance () |
| Create an instance of the DNA_EnvPairPotential object, by owning pointer. More... | |
| static dna::DNA_DihedralPotentialOP | create_dna_dihedralpotential_instance () |
| Create an instance of the DNA_DihedralPotential object, by owning pointer. More... | |
| static SecondaryStructurePotentialOP | create_secondarystructurepotential_instance () |
| Create an instance of the SecondaryStructurePotential object, by owning pointer. More... | |
| static AtomVDWOP | create_atomvdw_instance (std::string const &atom_type_set_name) |
| Create an instance of the AtomVDW object, by owning pointer. More... | |
| static rna::RNA_AtomVDWOP | create_rna_atomvdw_instance () |
| Create an instance of the RNA_AtomVDW object, by owning pointer. More... | |
| static geometric_solvation::DatabaseOccSolEneOP | create_database_occsolene_instance (std::string const &atom_type_set_name, core::Real const &min_occ_energy) |
| Create an instance of the DatabaseOccSolEne object, by owning pointer. More... | |
| static carbon_hbonds::CarbonHBondPotentialOP | create_carbon_hbond_potential_instance () |
| Create an instance of the CarbonHBondPotential object, by owning pointer. More... | |
| static rna::RNA_SuitePotentialOP | create_rna_suitepotential_instance (bool const &calculate_suiteness_bonus, std::string const &suiteness_bonus) |
| Create an instance of the RNA_SuitePotential object, by owning pointer. More... | |
| static rna::TNA_SuitePotentialOP | create_tna_suitepotential_instance () |
| Create an instance of the TNA_SuitePotential object, by owning pointer. More... | |
| static loop_graph::evaluator::SixDTransRotPotentialOP | create_sixdtransrotpotential_instance (std::string const &database_file) |
| Create an instance of the SixDTransRotPotential object, by owning pointer. More... | |
| static rna::RNA_LowResolutionPotentialOP | create_rna_lowresolutionpotential_instance (std::string const &database_file) |
| Create an instance of the RNA_LowResolutionPotential object, by owning pointer. More... | |
| static rna::RNP_LowResPotentialOP | create_rnp_lowrespotential_instance () |
| Create an instance of the RNP_LowResPotential object, by owning pointer. More... | |
| static rna::RNP_LowResPairDistPotentialOP | create_rnp_lowrespairdistpotential_instance () |
| Create an instance of the RNP_LowResPairDistPotential object, by owning pointer. More... | |
| static rna::RNP_LowResStackDataOP | create_rnp_lowresstackdata_instance () |
| Create an instance of the RNP_LowResStackData object, by owning pointer. More... | |
| static rna::chemical_shift::RNA_ChemicalShiftPotentialOP | create_rna_chemshiftpotential_instance () |
| Create an instance of the RNA_ChemicalShiftPotential object, by owning pointer. More... | |
| static rna::data::RNA_DMS_PotentialOP | create_rna_dms_potential_instance () |
| Create an instance of the RNA_DMS_Potential object, by owning pointer. More... | |
| static rna::data::RNA_DMS_LowResolutionPotentialOP | create_rna_dms_lowrespotential_instance () |
| Create an instance of the RNA_DMS_LowResolutionPotential object, by owning pointer. More... | |
| static dna::DirectReadoutPotentialOP | create_dna_directreadoutpotential_instance () |
| Create an instance of the DirectReadoutPotential object, by owning pointer. More... | |
| static mm::MMLJLibraryOP | create_mm_lj_library_instance () |
| Create an instance of the MMLJLibrary object, by owning pointer. More... | |
| static mm::MMLJEnergyTableOP | create_mm_lj_energy_table_instance () |
| Create an instance of the MMLJEnergyTable object, by owning pointer. More... | |
| static mm::MMTorsionLibraryOP | create_mm_torsion_library_instance () |
| Create an instance of the MMTorsionLibrary object, by owning pointer. More... | |
| static mm::MMBondAngleLibraryOP | create_mm_bondangle_library_instance () |
| Create an instance of the MMBondAngleLibrary object, by owning pointer. More... | |
| static mm::MMBondLengthLibraryOP | create_mm_bondlength_library_instance () |
| Create an instance of the MMBondLengthLibrary object, by owning pointer. More... | |
| static carbohydrates::CHIEnergyFunctionOP | create_chi_energy_function_instance () |
| Create a (default) instance of the CHIEnergyFunction object, by owning pointer. More... | |
| static carbohydrates::OmegaPreferencesFunctionOP | create_omega_preferences_function_instance () |
| Create a (default) instance of the OmegaPreferencesFunction object, by owning pointer. More... | |
| static nv::NVlookupOP | create_nvlookup_instance () |
| Create an instance of the NVlookup object, by owning pointer. More... | |
| static orbitals::OrbitalsLookupOP | create_orbitals_lookup_instance () |
| Create an instance of the OrbitalsLookup object, by owning pointer. More... | |
| static interface_::DDPlookupOP | create_ddp_lookup_instance () |
| Create an instance of the DDPlookup object, by owning pointer. More... | |
| static UnfoldedStatePotentialOP | create_unfolded_state_potential_instance (std::string const &type) |
| Create an instance of the UnfoldedStatePotential object, by owning pointer. More... | |
| static WaterAdductHBondPotentialOP | create_water_adduct_hbond_potential_instance () |
| Create an instance of the WaterAdductHBondPotential object, by owning pointer. More... | |
| static MembranePotentialOP | create_membrane_potential_instance () |
| Create an instance of the MembranePotential object, by owning pointer. More... | |
| static membrane::MembraneDataOP | create_membrane_data_instance () |
| Create an instance of the MembraneData object, by owning pointer. More... | |
| static Membrane_FAPotentialOP | create_membrane_fa_potential_instance () |
| Create an instance of the Membrane_FAPotential object, by owning pointer. More... | |
| static ProQPotentialOP | create_proq_potential_instance () |
| Create an instance of the ProQPotential object, by owning pointer. More... | |
| static PointWaterPotentialOP | create_point_water_potential_instance () |
| Create an instance of the PointWaterPotential object by owning pointer. More... | |
| static PoissonBoltzmannPotentialOP | create_poisson_boltzmann_potential_instance () |
| Create an instance of the PoissonBoltzmannPotential object, by owning pointer. More... | |
| static SplitUnfoldedTwoBodyPotentialOP | create_split_unfolded_2body_potential_instance (std::string const &label_type, std::string const &value_type, std::string const &score_func_type) |
| Create an instance of the SplitUnfoldedTwoBodyPotential object, by owning pointer. More... | |
| static disulfides::FullatomDisulfidePotentialOP | create_fullatom_disulfide_potential_instance () |
| Create an instance of the FullatomDisulfidePotential object, by owning pointer. More... | |
| static disulfides::CentroidDisulfidePotentialOP | create_centroid_disulfide_potential_instance () |
| Create an instance of the CentroidDisulfidePotential object, by owning pointer. More... | |
| static disulfides::DisulfideMatchingPotentialOP | create_disulfide_matching_potential_instance () |
| Create an instance of the DisulfideMatchingPotential object, by owning pointer. More... | |
| static core::chemical::mainchain_potential::MainchainScoreTableOP | create_mainchain_scoretable_instance (core::chemical::mainchain_potential::MainchainScoreTableOP table_in) |
| Create an instance of a MainchainScoreTable, by owning pointer. More... | |
| static etable::MembEtableOP | create_memb_etable_instance_silly (etable::MembEtableOP table_in) |
| Create an instance of a MembEtable, by owning pointer. More... | |
| static etable::MembEtableOP | create_memb_etable_instance (std::string const &table_id) |
| Create an instance of a MembEtable, by owning pointer. More... | |
| static etable::EtableOP | create_etable_instance (etable::EtableOP table_in) |
| Create an instance of an Etable, by owning pointer. More... | |
| static core::scoring::aa_composition_energy::AACompositionEnergySetupOP | create_aa_composition_energy_setup_instance (std::string const &filename) |
| Create an instance of an AACompositionEnergySetup object, by owning pointer. More... | |
| static core::scoring::netcharge_energy::NetChargeEnergySetupOP | create_netcharge_energy_setup_instance (std::string const &filename) |
| Create an instance of an NetChargeEnergySetup object, by owning pointer. More... | |
Friends | |
| class | utility::SingletonBase< ScoringManager > |
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private |
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privatedefault |
| void core::scoring::ScoringManager::add_memb_etable | ( | std::string const & | name, |
| etable::MembEtableOP | etable | ||
| ) |
Add a new membrane energy table to the membrane energy tables map.
Made threadsafe on 25 July 2017.
References create_memb_etable_instance_silly(), and memb_etables_.
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staticprivate |
Create an instance of an AACompositionEnergySetup object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_cloned_aa_comp_setup_helpers().
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staticprivate |
Create an instance of the AtomVDW object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_AtomVDW().
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staticprivate |
Create an instance of the CarbonHBondPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_CarbonHBondPotential().
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staticprivate |
Create an instance of the CenHBPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_CenHBPotential().
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staticprivate |
Create an instance of the CenRotEnvPairPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_CenRotEnvPairPotential().
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staticprivate |
Create an instance of the CentroidDisulfidePotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_CentroidDisulfidePotential().
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staticprivate |
Create a (default) instance of the CHIEnergyFunction object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
References core::scoring::TR().
Referenced by get_CHIEnergyFunction().
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staticprivate |
Create an instance of the DatabaseOccSolEne object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_DatabaseOccSolEne().
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staticprivate |
Create an instance of the DDPlookup object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_DDPLookupTable().
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staticprivate |
Create an instance of the DisulfideMatchingPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_DisulfideMatchingPotential().
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staticprivate |
Create an instance of the DNABFormPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_DNABFormPotential().
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staticprivate |
Create an instance of the DNA_DihedralPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_DNA_DihedralPotential().
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staticprivate |
Create an instance of the DirectReadoutPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_DirectReadoutPotential().
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staticprivate |
Create an instance of the DNA_EnvPairPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_DNA_EnvPairPotential().
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staticprivate |
Create an instance of the DNATorsionPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_DNATorsionPotential().
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staticprivate |
Create an instance of the FactsPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_DNA_BasePotential().
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staticprivate |
Create an instance of the EnvPairPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_EnvPairPotential().
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staticprivate |
Create an instance of an Etable, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by etable().
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staticprivate |
Create an instance of the FactsPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_FACTSPotential().
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staticprivate |
Create an instance of the contents of a file.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
References core::scoring::TR().
Referenced by get_nmer_svm_list_file_contents(), and get_nmer_svm_rank_list_file_contents().
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staticprivate |
Create an instance of the FullatomDisulfidePotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_FullatomDisulfidePotential().
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staticprivate |
Create an instance of the GenBornPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_GenBornPotential().
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staticprivate |
Create an instance of the GenericBondedPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_GenericBondedPotential().
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staticprivate |
Create an instance of the HydroxylTorsionPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_HydroxylTorsionPotential().
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staticprivate |
Create an instance of a MainchainScoreTable, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_rama_prepro_mainchain_torsion_potential().
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staticprivate |
Create an instance of a MembEtable, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
References core::chemical::FA_STANDARD, and core::scoring::FA_STANDARD_DEFAULT.
Referenced by memb_etable().
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staticprivate |
Create an instance of a MembEtable, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by add_memb_etable().
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staticprivate |
Create an instance of the MembraneData object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_MembraneData().
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staticprivate |
Create an instance of the Membrane_FAPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_Membrane_FAPotential().
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staticprivate |
Create an instance of the MembranePotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_MembranePotential().
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staticprivate |
Load the csv database file contents from disk and store as a std::list.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
References core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::check_file_size(), protocols::abinitio::filename(), and core::scoring::TR().
Referenced by get_mhc_csv_contents().
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static |
Create an instance of an MHCEpitopeEnergySetup object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_cloned_mhc_epitope_setup_helpers().
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staticprivate |
Load the sqlite database from disk. Store peptides/scores as std::map, and length as core::Size. Return as a std::pair.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
References core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::check_file_size(), protocols::abinitio::filename(), core::scoring::pair, protocols::hybridization::score, core::scoring::TR(), and protocols::hybridization::val.
Referenced by get_mhc_map_from_db().
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staticprivate |
Create an instance of the file contents of a MHCEpitopePredictorMatrix matrix, by reading data from disk.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
References core::scoring::TR().
Referenced by get_mhc_matrix_contents().
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staticprivate |
Create an instance of the MMBondAngleLibrary object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
References core::chemical::FA_STANDARD.
Referenced by get_MMBondAngleLibrary().
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staticprivate |
Create an instance of the MMBondLengthLibrary object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
References core::chemical::FA_STANDARD.
Referenced by get_MMBondLengthLibrary().
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staticprivate |
Create an instance of the MMLJEnergyTable object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_MMLJEnergyTable().
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staticprivate |
Create an instance of the MMLJLibrary object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
References core::chemical::FA_STANDARD.
Referenced by get_MMLJLibrary().
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staticprivate |
Create an instance of the MMTorsionLibrary object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
References core::chemical::FA_STANDARD.
Referenced by get_MMTorsionLibrary().
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staticprivate |
Create an instance of the HydroxylTorsionPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_MultipoleElecPotential().
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staticprivate |
Create an instance of an NetChargeEnergySetup object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_cloned_netcharge_setup_helpers().
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staticprivate |
Create an instance of an NMerPSSM object, by reading data from disk.
Create an instance of an NMerPSSM std::map, by reading data from disk.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
References protocols::cluster::calibur::aa, core::chemical::aa_from_oneletter_code(), core::scoring::nmer_pssm, protocols::hybridization::score, core::id::to_string(), and core::scoring::TR().
Referenced by get_nmer_pssm().
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staticprivate |
Create an instance of an aa floats list used by the NMerSVMEnergy.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
References protocols::cluster::calibur::aa, core::scoring::TR(), and protocols::hybridization::val.
Referenced by get_nmer_svm_aa_matrix().
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staticprivate |
Create an instance of an SVM rank cector, by reading data from disk.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
References protocols::hybridization::score, protocols::sparta::split(), and core::scoring::TR().
Referenced by get_nmer_svm_rank().
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staticprivate |
Create an instance of the NVlookup object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_NVLookupTable().
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staticprivate |
Create a (default) instance of the OmegaPreferencesFunction object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
References core::scoring::TR().
Referenced by get_OmegaPreferencesFunction().
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staticprivate |
Create an instance of the OmegaTether object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_OmegaTether().
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staticprivate |
Create an instance of the OrbitalsLookup object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_OrbitalsLookupTable().
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staticprivate |
Create an instance of the P_AA_ABEGO3 object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_P_AA_ABEGO3().
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staticprivate |
Create an instance of the P_AA object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_P_AA().
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staticprivate |
Create an instance of the P_AA_ss object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_P_AA_ss().
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staticprivate |
Create an instance of the PairEPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_PairEPotential().
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staticprivate |
Create an instance of the PointWaterPotential object by owning pointer.
Create an instance of the ProQPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_PointWaterPotential().
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staticprivate |
Create an instance of the PoissonBoltzmannPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_PoissonBoltzmannPotential().
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staticprivate |
Create an instance of the ProQPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_ProQPotential().
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staticprivate |
Create an instance of the Ramachandran2B object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_Ramachandran2B_ptr().
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staticprivate |
Create an instance of the Ramachandran object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_Ramachandran_ptr().
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staticprivate |
Create an instance of the RamaPrePro object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_RamaPrePro().
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staticprivate |
Create an instance of the RNA_AtomVDW object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_RNA_AtomVDW().
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staticprivate |
Create an instance of the RNA_ChemicalShiftPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_RNA_ChemicalShiftPotential().
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staticprivate |
Create an instance of the RNA_DMS_LowResolutionPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_RNA_DMS_LowResolutionPotential().
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staticprivate |
Create an instance of the RNA_DMS_Potential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_RNA_DMS_Potential().
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staticprivate |
Create an instance of the RNA_LowResolutionPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
References core::scoring::TR().
Referenced by get_RNA_LowResolutionPotential().
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staticprivate |
Create an instance of the RNA_SuitePotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
References core::scoring::suiteness_bonus.
Referenced by get_rna_suite_potential().
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staticprivate |
Create an instance of the RNP_LowResPairDistPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_RNP_LowResPairDistPotential().
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staticprivate |
Create an instance of the RNP_LowResPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_RNP_LowResPotential().
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staticprivate |
Create an instance of the RNP_LowResStackData object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_RNP_LowResStackData().
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staticprivate |
Create an instance of the SASAPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_SASAPotential().
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staticprivate |
Create an instance of the SecondaryStructurePotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_SecondaryStructurePotential().
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staticprivate |
Create an instance of the SixDTransRotPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
References core::scoring::TR().
Referenced by get_LoopCloseSixDPotential().
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staticprivate |
Create an instance of the SmoothEnvPairPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_SmoothEnvPairPotential().
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staticprivate |
Create an instance of the SplitUnfoldedTwoBodyPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
References core::scoring::SPLIT_UNFOLDED_BOLTZ, core::scoring::SPLIT_UNFOLDED_ELE, core::scoring::SPLIT_UNFOLDED_MEAN, core::scoring::SPLIT_UNFOLDED_MEDIAN, core::scoring::SPLIT_UNFOLDED_MM, core::scoring::SPLIT_UNFOLDED_MODE, core::scoring::SPLIT_UNFOLDED_PDB, core::scoring::SPLIT_UNFOLDED_ROSETTA, core::scoring::SPLIT_UNFOLDED_UNIQUE, core::scoring::SPLIT_UNFOLDED_USER_DEFINED, core::scoring::TR(), core::scoring::UNFOLDED_SPLIT_MM_STD, and core::scoring::UNFOLDED_SPLIT_TALARIS2013.
Referenced by get_SplitUnfoldedTwoBodyPotential().
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staticprivate |
Create an instance of an SVM, reading data from disk.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
References core::scoring::TR().
Referenced by get_nmer_svm().
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staticprivate |
Create an instance of the TNA_SuitePotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_tna_suite_potential().
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staticprivate |
Create an instance of the UnfoldedStatePotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
References core::scoring::TR(), core::scoring::UNFOLDED_MM_STD, core::scoring::UNFOLDED_RNA, core::scoring::UNFOLDED_SCORE12, core::scoring::UNFOLDED_SPLIT_MM_STD, core::scoring::UNFOLDED_SPLIT_TALARIS2013, and core::scoring::UNFOLDED_SPLIT_USER_DEFINED.
Referenced by get_UnfoldedStatePotential().
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staticprivate |
Create an instance of the VdWTinkerPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_VdWTinkerPotential().
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staticprivate |
Create an instance of the WaterAdductHBondPotential object, by owning pointer.
Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!
Referenced by get_WaterAdductHBondPotential().
| methods::EnergyMethodOP core::scoring::ScoringManager::energy_method | ( | ScoreType const & | score_type, |
| methods::EnergyMethodOptions const & | options | ||
| ) | const |
When a ScoreFunction the weight for a particular ScoreType set from 0 to some non-zero value, it will request an instance of the EnergyMethod class that is responsible for calculating that ScoreType. The ScoringManager responds to that request by asking the EnergyMethodCreator that has claimed responsibility for this ScoreType for a new instance. EnergyMethodCreators must first have registered themselves with the ScoringManager. This should have been done at load time, using a static-variable-initialization function call. See src/core/scoring/etable/EtableEnergy.cc for an example of how the EtableEnergyCreator class registers itself with the ScoringManager.
I THINK that this is threadsafe (VKM, 20 July 2017).
References method_creator_map_, core::scoring::n_score_types, core::scoring::python, and core::id::to_string().
| etable::EtableCAP core::scoring::ScoringManager::etable | ( | methods::EnergyMethodOptions const & | options_in | ) | const |
Request an etable specifying an EnergyMethodOptions object; internally this will retrieve the EtableOptions object, and invoke the EtableOptions version of this function.
Threadsafe, since this calls the threadsafe etable( EtableOptions) function, below.
References core::scoring::methods::EnergyMethodOptions::etable_options().
Referenced by etable(), and make_partially_soft_etable().
| etable::EtableCAP core::scoring::ScoringManager::etable | ( | etable::EtableOptions const & | options_in | ) | const |
Request an etable specifying an EtableOptions; internally this will query the ScoringManager's map from EtableOptions to Etables for the desired Etable, and construct a new one if needed.
Made threadsafe on 25 July 2017.
References create_etable_instance(), etable(), core::scoring::etable::EtableOptions::etable_type, etables_by_options_, core::chemical::FA_STANDARD, core::scoring::FA_STANDARD_DEFAULT, core::scoring::FA_STANDARD_MULTIPOLE, core::scoring::FA_STANDARD_SOFT, and make_partially_soft_etable().
| etable::EtableCAP core::scoring::ScoringManager::etable | ( | std::string const & | etable_id | ) | const |
Create and return an etable specified only by the etable_type of the etable::EtableOptions class. This, internally, will create an EtableOptions object, initialized from the command line, set the etable_type of this object, and then invoke the etable( EtableOptions ) method.
Threadsafe, since this calls the threadsafe etable( EtableOptions ) function, above.
Threadsafe, since this calls the threadsafe etable( EtableOptions) function, above.
References etable(), and core::scoring::etable::EtableOptions::etable_type.
| void core::scoring::ScoringManager::factory_register | ( | methods::EnergyMethodCreatorOP | creator | ) |
The ScoringManager acts as an EnergyMethodFactory. All EnergyMethods must create a helper class, an EnergyMethodCreator class, that will respond to a call to its create_energy_method by returning a new instance of that EnergyMethod its helping. This Creator class must also register itself with the ScoringManager at load time and hand an instance of itself to the singleton ScoringManager instance.
I don't think that this function is threadsafe (VKM, 20 July 2017), but it probably doesn't matter. Factory registration presumably happens during Rosetta initialization, before any threads are spawned.
References method_creator_map_, and core::id::to_string().
| AtomVDW const & core::scoring::ScoringManager::get_AtomVDW | ( | std::string const & | atom_type_set_name | ) | const |
Get an instance of the AtomVDW scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References atom_vdw_, and create_atomvdw_instance().
| carbon_hbonds::CarbonHBondPotential const & core::scoring::ScoringManager::get_CarbonHBondPotential | ( | ) | const |
Get an instance of the CarbonHBondPotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References carbon_hbond_potential_, and create_carbon_hbond_potential_instance().
| CenHBPotential const & core::scoring::ScoringManager::get_CenHBPotential | ( | ) | const |
Get an instance of the CenHBPotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References cen_hb_potential_, and create_cenhbpotential_instance().
| CenRotEnvPairPotential const & core::scoring::ScoringManager::get_CenRotEnvPairPotential | ( | ) | const |
Get an instance of the CenRotEnvPairPotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References cen_rot_pair_potential_, and create_cenrotenvpair_instance().
| disulfides::CentroidDisulfidePotential const & core::scoring::ScoringManager::get_CentroidDisulfidePotential | ( | ) | const |
Get an instance of the CentroidDisulfidePotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References cen_disulfide_potential_, and create_centroid_disulfide_potential_instance().
| carbohydrates::CHIEnergyFunction const & core::scoring::ScoringManager::get_CHIEnergyFunction | ( | ) | const |
Get an instance of the CHIEnergyFunction scoring object.
Threadsafe and lazily loaded.
References CHI_energy_function_, and create_chi_energy_function_instance().
| utility::vector1< core::scoring::aa_composition_energy::AACompositionEnergySetupOP > core::scoring::ScoringManager::get_cloned_aa_comp_setup_helpers | ( | core::scoring::methods::EnergyMethodOptions const & | options | ) | const |
Get a vector of owning pointers to data used by the AACompositionEnergy score term.
If this vector has not yet been populated, this loads the data from disk (lazy loading).
References core::scoring::methods::EnergyMethodOptions::aa_composition_setup_file(), core::scoring::methods::EnergyMethodOptions::aa_composition_setup_file_count(), aa_composition_setup_helpers_, and create_aa_composition_energy_setup_instance().
| utility::vector1< core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupOP > core::scoring::ScoringManager::get_cloned_mhc_epitope_setup_helpers | ( | core::scoring::methods::EnergyMethodOptions const & | options | ) | const |
Get a vector of owning pointers to data used by the MHCEpitopeEnergy score term.
If this vector has not yet been populated, this loads the data from disk (lazy loading).
References create_mhc_epitope_energy_setup_instance(), core::scoring::methods::EnergyMethodOptions::mhc_epitope_setup_file(), core::scoring::methods::EnergyMethodOptions::mhc_epitope_setup_file_count(), and mhc_epitope_setup_helpers_.
| utility::vector1< core::scoring::netcharge_energy::NetChargeEnergySetupOP > core::scoring::ScoringManager::get_cloned_netcharge_setup_helpers | ( | core::scoring::methods::EnergyMethodOptions const & | options | ) | const |
Get a vector of owning pointers to data used by the NetChargeEnergy score term.
If this vector has not yet been populated, this loads the data from disk (lazy loading).
References create_netcharge_energy_setup_instance(), core::scoring::methods::EnergyMethodOptions::netcharge_setup_file(), core::scoring::methods::EnergyMethodOptions::netcharge_setup_file_count(), and netcharge_setup_helpers_.
| core::scoring::elec::CPRepMapTypeCOP core::scoring::ScoringManager::get_cp_rep_map_byname | ( | ) | const |
Get an owning pointer to data used by the FA_ElecEnergy in beta_nov15 mode.
If the data have not been loaded, this loads the data (lazy loading). Lazy loading is now threadsafe.
References cp_rep_map_byname_, and core::scoring::elec::read_cp_tables_from_db().
| geometric_solvation::DatabaseOccSolEne const & core::scoring::ScoringManager::get_DatabaseOccSolEne | ( | std::string const & | atom_type_set_name, |
| Real const & | min_occ_energy | ||
| ) | const |
Get an instance of the DatabaseOccSolEne scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_database_occsolene_instance(), and occ_hbond_sol_database_.
| interface_::DDPlookup const & core::scoring::ScoringManager::get_DDPLookupTable | ( | ) | const |
Get an instance of the DDPlookup scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_ddp_lookup_instance(), and DDP_lookup_table_.
| dna::DirectReadoutPotential const & core::scoring::ScoringManager::get_DirectReadoutPotential | ( | ) | const |
Get an instance of the DirectReadoutPotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_dna_directreadoutpotential_instance(), and dna_dr_potential_.
| disulfides::DisulfideMatchingPotential const & core::scoring::ScoringManager::get_DisulfideMatchingPotential | ( | ) | const |
Get an instance of the DisulfideMatchingPotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_disulfide_matching_potential_instance(), and disulfide_matching_potential_.
| dna::DNA_BasePotential const & core::scoring::ScoringManager::get_DNA_BasePotential | ( | ) | const |
Get an instance of the DNA_BasePotential scoring object, by const owning pointer.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_dnabase_potential_instance(), and DNA_base_potential_.
| dna::DNA_DihedralPotential const & core::scoring::ScoringManager::get_DNA_DihedralPotential | ( | ) | const |
Get an instance of the DNA_DihedralPotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_dna_dihedralpotential_instance(), and dna_dihedral_potential_.
| dna::DNA_EnvPairPotential const & core::scoring::ScoringManager::get_DNA_EnvPairPotential | ( | ) | const |
Get an instance of the DNA_EnvPairPotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_dna_envpairpotential_instance(), and dna_env_pair_potential_.
| dna::DNABFormPotential const & core::scoring::ScoringManager::get_DNABFormPotential | ( | ) | const |
Get an instance of the DNABFormPotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_dna_bform_potential_instance(), and dnabform_.
| dna::DNATorsionPotential const & core::scoring::ScoringManager::get_DNATorsionPotential | ( | ) | const |
Get an instance of the DNATorsionPotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_dna_torsion_potential_instance(), and dna_torsion_potential_.
| EnvPairPotential const & core::scoring::ScoringManager::get_EnvPairPotential | ( | ) | const |
Get an instance of the EnvPairPotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_envpairpotential_instance(), and env_pair_potential_.
| FACTSPotential const & core::scoring::ScoringManager::get_FACTSPotential | ( | ) | const |
Get an instance of the FACTSPotential scoring object, by const owning pointer.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_facts_potential_instance(), and facts_potential_.
| disulfides::FullatomDisulfidePotential const & core::scoring::ScoringManager::get_FullatomDisulfidePotential | ( | ) | const |
Get an instance of the FullatomDisulfidePotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_fullatom_disulfide_potential_instance(), and fa_disulfide_potential_.
| GenBornPotential const & core::scoring::ScoringManager::get_GenBornPotential | ( | ) | const |
Get a const instance of the GenBornPotential.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_genborn_instance(), and gen_born_potential_.
| GenericBondedPotential const & core::scoring::ScoringManager::get_GenericBondedPotential | ( | ) | const |
Get an instance of the GenericBondedPotential scoring object, by const owning pointer.
Threadsafe and lazily loaded.
References create_generic_bonded_potential_instance(), and generic_bonded_potential_.
| HydroxylTorsionPotential const & core::scoring::ScoringManager::get_HydroxylTorsionPotential | ( | ) | const |
Get a const instance of the HydroxylTorsionPotential.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_hxl_potential_instance(), and hxl_tors_potential_.
| loop_graph::evaluator::SixDTransRotPotentialCOP core::scoring::ScoringManager::get_LoopCloseSixDPotential | ( | std::string const & | database_file | ) | const |
Get an instance of the SixDTransRotPotential scoring object, by const owning pointer.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_sixdtransrotpotential_instance(), and loop_close_six_d_potential_.
| Membrane_FAPotential const & core::scoring::ScoringManager::get_Membrane_FAPotential | ( | ) | const |
Get an instance of the Membrane_FAPotential scoring object.
Threadsafe and lazily loaded.
References create_membrane_fa_potential_instance(), and membrane_fapotential_.
| membrane::MembraneData const & core::scoring::ScoringManager::get_MembraneData | ( | ) | const |
Get an instance of the MembraneData scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_membrane_data_instance(), and mp_base_potential_.
| MembranePotential const & core::scoring::ScoringManager::get_MembranePotential | ( | ) | const |
Get an instance of the MembranePotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_membrane_potential_instance(), and membrane_potential_.
| std::list< std::string > const & core::scoring::ScoringManager::get_mhc_csv_contents | ( | std::string const & | filename | ) | const |
Get a const reference to a std::list containing the contents of a MHCEpitopePredictorPreLoaded csv database file.
This is a PreLoaded csv containing, for example, NetMHCII data to be used by MHCEpitopePredictorPreLoaded.
The file will be loaded as a list and sent back to the Predictor to be parsed, to avoid doing the latter in the ScoringManager class.
This is a PreLoaded csv containing, for example, NetMHCII data to be used by MHCEpitopePredictorPreLoaded.
References create_mhc_csv_contents(), and mhc_csv_db_contents_map_.
| std::pair< std::map< std::string, core::Real >, core::Size > const & core::scoring::ScoringManager::get_mhc_map_from_db | ( | std::string const & | filename | ) | const |
Get a const reference to a std::pair containing the a map corresponding a sqlite MHC db and the peptide length.
This is a PreLoaded database containing, for example, NetMHCII data to be used by MHCEpitopePredictorPreLoaded.
References create_mhc_map_from_db(), and mhc_sqlite_db_contents_map_.
| std::list< std::string > const & core::scoring::ScoringManager::get_mhc_matrix_contents | ( | std::string const & | filename | ) | const |
Get a const reference to a std::list containing the contents of a MHCEpitopePredictorMatrix matrix file.
This is a matrix file containing, for example, Propred data to be used by MHCEpitopePredictorMatrix.
The file will be loaded as a list and sent back to the Predictor to be parsed, to avoid doing the latter in the ScoringManager class.
References create_mhc_matrix_contents(), and mhc_matrix_contents_map_.
| core::scoring::mm::MMBondAngleLibrary const & core::scoring::ScoringManager::get_MMBondAngleLibrary | ( | ) | const |
Get an instance of the MMBondAngleLibrary scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_mm_bondangle_library_instance(), and mm_bondangle_library_.
| core::scoring::mm::MMBondLengthLibrary const & core::scoring::ScoringManager::get_MMBondLengthLibrary | ( | ) | const |
Get an instance of the MMBondLengthLibrary scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_mm_bondlength_library_instance(), and mm_bondlength_library_.
| core::scoring::mm::MMLJEnergyTable const & core::scoring::ScoringManager::get_MMLJEnergyTable | ( | ) | const |
Get an instance of the MMLJEnergyTable scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_mm_lj_energy_table_instance(), and mm_lj_energy_table_.
| core::scoring::mm::MMLJLibrary const & core::scoring::ScoringManager::get_MMLJLibrary | ( | ) | const |
Get an instance of the MMLJLibrary scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_mm_lj_library_instance(), and mm_lj_library_.
| core::scoring::mm::MMTorsionLibrary const & core::scoring::ScoringManager::get_MMTorsionLibrary | ( | ) | const |
Get an instance of the MMTorsionLibrary scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_mm_torsion_library_instance(), and mm_torsion_library_.
| MultipoleElecPotential const & core::scoring::ScoringManager::get_MultipoleElecPotential | ( | methods::EnergyMethodOptions const & | options | ) | const |
Get an instance of the MultipoleElecPotential scoring object.
Threadsafe creation, lazily loaded.
Threadsafe and lazily loaded.
References create_multipole_elec_instance(), and multipole_elec_potential_.
| std::map< core::chemical::AA, utility::vector1< core::Real > > const & core::scoring::ScoringManager::get_nmer_pssm | ( | std::string const & | filename, |
| core::Size | nmer_length | ||
| ) | const |
Get a const reference to an NMerPSSM.
Get a const reference to an NMerPSSM std::map.
References create_nmer_pssm(), and nmer_pssm_map_.
| utility::libsvm::Svm_rosettaCOP core::scoring::ScoringManager::get_nmer_svm | ( | std::string const & | filename | ) | const |
Get a const reference to an SVM object.
Used by the NMerSVMEnergy. Loaded lazily in a threadsafe manner.
References create_svm_rosetta(), and nmer_svm_map_.
| std::map< char, utility::vector1< core::Real > > const & core::scoring::ScoringManager::get_nmer_svm_aa_matrix | ( | std::string const & | filename | ) | const |
Get the map of AA oneletter code->vector of floats used by the NMerSVMEnergy.
Loaded lazily in a threadsafe manner.
References create_nmer_svm_aa_matrix(), and nmer_svm_aa_matrix_map_.
| std::string const & core::scoring::ScoringManager::get_nmer_svm_list_file_contents | ( | std::string const & | filename | ) | const |
Get a string listing SVM files.
Used by the NMerSVMEnergy. Loaded lazily in a threadsafe manner.
References create_file_contents_instance(), and nmer_svm_list_file_contents_map_.
| utility::vector1< core::Real > const & core::scoring::ScoringManager::get_nmer_svm_rank | ( | std::string const & | filename | ) | const |
Get a const reference to a vector of floats corresponding to ranked SVM information.
Used by the NMerSVMEnergy. Loaded lazily in a threadsafe manner.
References create_nmer_svm_rank(), and nmer_svm_rank_map_.
| std::string const & core::scoring::ScoringManager::get_nmer_svm_rank_list_file_contents | ( | std::string const & | filename | ) | const |
Get a string listing SVM rank files.
Used by the NMerSVMEnergy. Loaded lazily in a threadsafe manner.
References create_file_contents_instance(), and nmer_svm_rank_list_file_contents_map_.
| nv::NVlookup const & core::scoring::ScoringManager::get_NVLookupTable | ( | ) | const |
Get an instance of the NVlookup scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_nvlookup_instance(), and NV_lookup_table_.
| carbohydrates::OmegaPreferencesFunction const & core::scoring::ScoringManager::get_OmegaPreferencesFunction | ( | ) | const |
Get an instance of the OmegaPreferencesFunction scoring object.
Threadsafe and lazily loaded.
References carbohydrate_omega_preferences_function_, and create_omega_preferences_function_instance().
| OmegaTether const & core::scoring::ScoringManager::get_OmegaTether | ( | ) | const |
Get an instance of the OmegaTether scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_omegatether_instance(), and omega_.
| orbitals::OrbitalsLookup const & core::scoring::ScoringManager::get_OrbitalsLookupTable | ( | ) | const |
Get an instance of the OrbitalsLookup scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_orbitals_lookup_instance(), and orbitals_lookup_table_.
| P_AA const & core::scoring::ScoringManager::get_P_AA | ( | ) | const |
Get an instance of the P_AA scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_p_aa_instance(), and p_aa_.
| P_AA_ABEGO3 const & core::scoring::ScoringManager::get_P_AA_ABEGO3 | ( | ) | const |
Get an instance of the P_AA_ABEGO3 scoring object.
Threadsafe and lazily loaded. Used by AbegoEnergy.
Threadsafe and lazily loaded. Used by AbegoEnergy.
References create_p_aa_abego3_instance(), and paa_abego3_.
| P_AA_ss const & core::scoring::ScoringManager::get_P_AA_ss | ( | ) | const |
Get an instance of the P_AA_ss scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_p_aa_ss_instance(), and p_aa_ss_.
| PairEPotential const & core::scoring::ScoringManager::get_PairEPotential | ( | ) | const |
Get a const instance of the PairEPotential.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_pairE_potential_instance(), and pairE_potential_.
| PointWaterPotential const & core::scoring::ScoringManager::get_PointWaterPotential | ( | ) | const |
Get an instance of PointWaterPotential scoring object.
References create_point_water_potential_instance(), and pwp_.
| PoissonBoltzmannPotential const & core::scoring::ScoringManager::get_PoissonBoltzmannPotential | ( | ) | const |
Get an instance of the PoissonBoltzmannPotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_poisson_boltzmann_potential_instance(), and PB_potential_.
| ProQPotential const & core::scoring::ScoringManager::get_ProQPotential | ( | ) | const |
Get an instance of the ProQPotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_proq_potential_instance(), and ProQ_potential_.
| core::chemical::mainchain_potential::MainchainScoreTableCOP core::scoring::ScoringManager::get_rama_prepro_mainchain_torsion_potential | ( | core::chemical::ResidueTypeCOP | restype, |
| bool const | use_polycubic_interpolation, | ||
| bool const | prepro_table | ||
| ) | const |
Get a particular MainchainScoreTable for the rama_prepro score term, for a particular residue type.
Get a particular MainchainScoreTable for the rama_prepro score term.
If this has not yet been populated, loads the data from disk (lazy loading) in a threadsafe manner.
References create_mainchain_scoretable_instance(), rama_prepro_mainchain_potentials_, rama_prepro_mainchain_potentials_beforeproline_, and core::chemical::mainchain_potential::read_rama_map_file_shapovalov().
Referenced by core::scoring::RamaPrePro::eval_rpp_rama_derivatives(), core::scoring::RamaPrePro::eval_rpp_rama_score(), core::scoring::RamaPrePro::get_mainchain_torsions_covered(), and core::scoring::RamaPrePro::read_canonical_rpp_tables().
| Ramachandran const & core::scoring::ScoringManager::get_Ramachandran | ( | ) | const |
Get a const instance of the Ramachandran scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References get_Ramachandran_ptr().
| Ramachandran2B const & core::scoring::ScoringManager::get_Ramachandran2B | ( | ) | const |
Get an instance of the Ramachandran2B scoring object, by const instance.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References get_Ramachandran2B_ptr().
| Ramachandran2BCOP core::scoring::ScoringManager::get_Ramachandran2B_ptr | ( | ) | const |
Get an instance of the Ramachandran2B scoring object, by const owning pointer.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_rama2b_instance(), and rama2b_.
Referenced by get_Ramachandran2B().
| RamachandranCOP core::scoring::ScoringManager::get_Ramachandran_ptr | ( | ) | const |
Get an instance of the Ramachandran scoring object, by const owning pointer.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_rama_instance(), and rama_.
Referenced by get_Ramachandran().
| RamaPrePro const & core::scoring::ScoringManager::get_RamaPrePro | ( | ) | const |
Get an instance of the RamaPrePro scoring object.
Threadsafe and lazily loaded.
References create_ramapp_instance(), and rama_pp_.
| rna::RNA_AtomVDW const & core::scoring::ScoringManager::get_RNA_AtomVDW | ( | ) | const |
Get an instance of the RNA_AtomVDW scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_rna_atomvdw_instance(), and rna_atom_vdw_.
| rna::chemical_shift::RNA_ChemicalShiftPotential const & core::scoring::ScoringManager::get_RNA_ChemicalShiftPotential | ( | ) | const |
Get an instance of the RNA_ChemicalShiftPotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_rna_chemshiftpotential_instance(), and rna_chemical_shift_potential_.
| rna::data::RNA_DMS_LowResolutionPotential & core::scoring::ScoringManager::get_RNA_DMS_LowResolutionPotential | ( | ) | const |
Get an instance of the RNA_DMS_LowResolutionPotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_rna_dms_lowrespotential_instance(), and rna_dms_low_resolution_potential_.
| rna::data::RNA_DMS_Potential & core::scoring::ScoringManager::get_RNA_DMS_Potential | ( | ) | const |
Get an instance of the RNA_DMS_Potential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_rna_dms_potential_instance(), and rna_dms_potential_.
| rna::RNA_LowResolutionPotentialCOP core::scoring::ScoringManager::get_RNA_LowResolutionPotential | ( | std::string const & | database_file | ) | const |
Get an instance of the RNA_LowResolutionPotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_rna_lowresolutionpotential_instance(), and rna_low_resolution_potential_.
| rna::RNA_SuitePotentialCOP core::scoring::ScoringManager::get_rna_suite_potential | ( | bool const & | calculate_suiteness_bonus, |
| std::string const & | suiteness_bonus | ||
| ) | const |
Get an instance of the RNA_SuitePotentialCOP scoring object, by const owning pointer.
Get an instance of the RNA_SuitePotential scoring object, by const owning pointer.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_rna_suitepotential_instance(), and rna_suite_potential_.
| rna::RNP_LowResPairDistPotential const & core::scoring::ScoringManager::get_RNP_LowResPairDistPotential | ( | ) | const |
Get an instance of the RNP_LowResPairDistPotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_rnp_lowrespairdistpotential_instance(), and rnp_low_res_pair_dist_potential_.
| rna::RNP_LowResPotential const & core::scoring::ScoringManager::get_RNP_LowResPotential | ( | ) | const |
Get an instance of the RNP_LowResPotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_rnp_lowrespotential_instance(), and rnp_low_res_potential_.
| rna::RNP_LowResStackData const & core::scoring::ScoringManager::get_RNP_LowResStackData | ( | ) | const |
Get an instance of the RNP_LowResStackData scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_rnp_lowresstackdata_instance(), and rnp_low_res_stack_data_.
| SASAPotential const & core::scoring::ScoringManager::get_SASAPotential | ( | ) | const |
Get an instance of the SASAPotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_sasa_potential_instance(), and sasa_potential_.
| SecondaryStructurePotential const & core::scoring::ScoringManager::get_SecondaryStructurePotential | ( | ) | const |
Get an instance of the SecondaryStructurePotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_secondarystructurepotential_instance(), and secondary_structure_potential_.
| SmoothEnvPairPotential const & core::scoring::ScoringManager::get_SmoothEnvPairPotential | ( | ) | const |
Get an instance of the SmoothEnvPairPotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_smoothenvpair_instance(), and smooth_env_pair_potential_.
| SplitUnfoldedTwoBodyPotential const & core::scoring::ScoringManager::get_SplitUnfoldedTwoBodyPotential | ( | std::string const & | label_type, |
| std::string const & | value_type, | ||
| std::string const & | score_func_type | ||
| ) | const |
Get an instance of the SplitUnfoldedTwoBodyPotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_split_unfolded_2body_potential_instance(), and sutbp_.
| rna::TNA_SuitePotential const & core::scoring::ScoringManager::get_tna_suite_potential | ( | ) | const |
Get an instance of the TNA_SuitePotentialCOP scoring object, by const owning pointer.
Get an instance of the TNA_SuitePotential scoring object, by const owning pointer.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_tna_suitepotential_instance(), and tna_suite_potential_.
| UnfoldedStatePotential const & core::scoring::ScoringManager::get_UnfoldedStatePotential | ( | std::string const & | type | ) | const |
Get an instance of the UnfoldedStatePotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_unfolded_state_potential_instance(), and unf_state_.
| VdWTinkerPotential const & core::scoring::ScoringManager::get_VdWTinkerPotential | ( | ) | const |
Get an instance of the VdWTinkerPotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_vdw_tinker_potential_instance(), and vdw_tinker_potential_.
| WaterAdductHBondPotential const & core::scoring::ScoringManager::get_WaterAdductHBondPotential | ( | ) | const |
Get an instance of the WaterAdductHBondPotential scoring object.
Threadsafe and lazily loaded.
Threadsafe and lazily loaded.
References create_water_adduct_hbond_potential_instance(), and water_adduct_hbond_potential_.
Test if there is an EnergyMethod class defined for a given score type.
I THINK that this is threadsafe (VKM, 20 July 2017).
References method_creator_map_, core::scoring::n_score_types, and core::scoring::python.
| etable::EtableOP core::scoring::ScoringManager::make_partially_soft_etable | ( | std::string const & | table_id, |
| etable::EtableOptions | etable_options | ||
| ) | const |
make etable for extra partially softies
Make etable for extra partial softies, pilot app r_play_with_etables does not really work anymore the etables it added will be somehow cleared or overwriten, so I do it here now
table_id: i.e. FA_STANDARD_SOFT40, the number in the end is a percentage, lj_radius are given for every 5% softie from 5% to 95% in database/chemical/atom_type_sets/fa_standard/extras/extra_soft_rep_params.txt FA_STANDARD_SOFT50 would be halfway between normal softrep and normal hardrep.
References etable(), core::chemical::FA_STANDARD, and core::scoring::etable::EtableOptions::lj_switch_dis2sigma.
Referenced by etable().
| etable::MembEtableCAP core::scoring::ScoringManager::memb_etable | ( | std::string const & | table_id | ) | const |
Get a membrane energy table from the membrane energy tables map.
Made threadsafe on 25 July 2017.
References create_memb_etable_instance(), and memb_etables_.
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friend |
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mutableprivate |
Cached data used by the AACompositionEnergy.
Accessor function has been made threadsafe (as of the wee hours of 26 July 2017).
Referenced by get_cloned_aa_comp_setup_helpers().
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mutableprivate |
Referenced by get_AtomVDW().
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mutableprivate |
Referenced by get_OmegaPreferencesFunction().
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mutableprivate |
Referenced by get_CarbonHBondPotential().
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mutableprivate |
Referenced by get_CentroidDisulfidePotential().
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mutableprivate |
Referenced by get_CenHBPotential().
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mutableprivate |
Referenced by get_CenRotEnvPairPotential().
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mutableprivate |
Referenced by get_CHIEnergyFunction().
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mutableprivate |
Cached data used by FA_ElecEnergy with beta_nov15.
Referenced by get_cp_rep_map_byname().
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mutableprivate |
Referenced by get_DDPLookupTable().
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mutableprivate |
Referenced by get_DisulfideMatchingPotential().
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mutableprivate |
Referenced by get_DNA_BasePotential().
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mutableprivate |
Referenced by get_DNA_DihedralPotential().
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mutableprivate |
Referenced by get_DirectReadoutPotential().
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mutableprivate |
Referenced by get_DNA_EnvPairPotential().
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mutableprivate |
Referenced by get_DNATorsionPotential().
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mutableprivate |
Referenced by get_DNABFormPotential().
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mutableprivate |
Referenced by get_EnvPairPotential().
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mutableprivate |
Referenced by etable().
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mutableprivate |
Referenced by get_FullatomDisulfidePotential().
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mutableprivate |
Referenced by get_FACTSPotential().
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mutableprivate |
Referenced by get_GenBornPotential().
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mutableprivate |
Referenced by get_GenericBondedPotential().
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mutableprivate |
Referenced by get_HydroxylTorsionPotential().
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mutableprivate |
Referenced by get_LoopCloseSixDPotential().
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mutableprivate |
Referenced by add_memb_etable(), and memb_etable().
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mutableprivate |
Referenced by get_Membrane_FAPotential().
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mutableprivate |
Referenced by get_MembranePotential().
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private |
The map of ( score type enum -> EnergyMethodCreatorOP ).
Actually a simple vector (since the key is a 1-based, continuous enum). Not threadsafe, but it doesn't really need to be, since it's initialized once by a single thread and never subsequently modified.
Referenced by energy_method(), factory_register(), and has_energy_method().
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mutableprivate |
Referenced by get_mhc_csv_contents().
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mutableprivate |
Cached data used by the MHCEpitopeEnergy.
Accessor function has been made threadsafe.
Referenced by get_cloned_mhc_epitope_setup_helpers().
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mutableprivate |
Referenced by get_mhc_matrix_contents().
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mutableprivate |
Referenced by get_mhc_map_from_db().
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mutableprivate |
Referenced by get_MMBondAngleLibrary().
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mutableprivate |
Referenced by get_MMBondLengthLibrary().
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mutableprivate |
Referenced by get_MMLJEnergyTable().
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mutableprivate |
Referenced by get_MMLJLibrary().
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mutableprivate |
Referenced by get_MMTorsionLibrary().
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mutableprivate |
Referenced by get_MembraneData().
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mutableprivate |
Referenced by get_MultipoleElecPotential().
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mutableprivate |
Cached data used by the NetChargeEnergy.
Accessor function has been made threadsafe.
Referenced by get_cloned_netcharge_setup_helpers().
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mutableprivate |
Referenced by get_nmer_pssm().
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mutableprivate |
Referenced by get_nmer_svm_aa_matrix().
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mutableprivate |
Referenced by get_nmer_svm_list_file_contents().
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mutableprivate |
Referenced by get_nmer_svm().
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mutableprivate |
Referenced by get_nmer_svm_rank_list_file_contents().
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mutableprivate |
Referenced by get_nmer_svm_rank().
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mutableprivate |
Referenced by get_NVLookupTable().
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mutableprivate |
Referenced by get_DatabaseOccSolEne().
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mutableprivate |
Referenced by get_OmegaTether().
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mutableprivate |
Referenced by get_OrbitalsLookupTable().
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mutableprivate |
Referenced by get_P_AA().
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mutableprivate |
Referenced by get_P_AA_ss().
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mutableprivate |
Referenced by get_P_AA_ABEGO3().
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mutableprivate |
Referenced by get_PairEPotential().
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mutableprivate |
Referenced by get_PoissonBoltzmannPotential().
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mutableprivate |
Referenced by get_ProQPotential().
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mutableprivate |
Referenced by get_PointWaterPotential().
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mutableprivate |
Referenced by get_Ramachandran2B_ptr().
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mutableprivate |
Referenced by get_Ramachandran_ptr().
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mutableprivate |
Referenced by get_RamaPrePro().
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mutableprivate |
Cached mainchain torsion potentials, used by rama_prepro.
This one is for potentials for residues NOT occurring before proline.
Referenced by get_rama_prepro_mainchain_torsion_potential().
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mutableprivate |
Cached mainchain torsion potentials, used by rama_prepro.
This one is for potentials for residues occurring before proline.
Referenced by get_rama_prepro_mainchain_torsion_potential().
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mutableprivate |
Referenced by get_RNA_AtomVDW().
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mutableprivate |
Referenced by get_RNA_ChemicalShiftPotential().
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mutableprivate |
Referenced by get_RNA_DMS_LowResolutionPotential().
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mutableprivate |
Referenced by get_RNA_DMS_Potential().
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mutableprivate |
Referenced by get_RNA_LowResolutionPotential().
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mutableprivate |
Referenced by get_rna_suite_potential().
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mutableprivate |
Referenced by get_RNP_LowResPairDistPotential().
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mutableprivate |
Referenced by get_RNP_LowResPotential().
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mutableprivate |
Referenced by get_RNP_LowResStackData().
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mutableprivate |
Referenced by get_SASAPotential().
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mutableprivate |
Referenced by get_SecondaryStructurePotential().
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mutableprivate |
Referenced by get_SmoothEnvPairPotential().
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mutableprivate |
Referenced by get_SplitUnfoldedTwoBodyPotential().
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mutableprivate |
Referenced by get_tna_suite_potential().
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mutableprivate |
Referenced by get_UnfoldedStatePotential().
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mutableprivate |
Referenced by get_VdWTinkerPotential().
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mutableprivate |
Referenced by get_WaterAdductHBondPotential().
1.8.7